notebook_GMOS_03_12amp_process_science_data.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "#%matplotlib inline\n",
    "import os, sys\n",
    "#sys.path.append('/Users/hhsieh/anaconda3/envs/astroconda/lib/python3.6/site-packages')\n",
    "#sys.path.append('/opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages')\n",
    "from astropy.io import fits\n",
    "from astropy.io.fits import getheader\n",
    "from astropy.modeling import models\n",
    "from astropy import nddata\n",
    "from astropy import units as u\n",
    "import ccdproc as cp\n",
    "from ccdproc import CCDData, ImageFileCollection\n",
    "import numpy as np\n",
    "import math, glob, os, bz2, subprocess, sys\n",
    "import cosmics_py3\n",
    "#import sqlite3\n",
    "#from sqlite3 import Error\n",
    "import scipy.signal as signal\n",
    "import scipy.ndimage as ndimage\n",
    "import datetime\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Done.\n"
     ]
    }
   ],
   "source": [
    "def create_directory(path):\n",
    "    if not os.path.exists(path):\n",
    "        os.mkdir(path)\n",
    "        print('Directory {:s} successfully created.'.format(path))\n",
    "    else:\n",
    "        print('Directory {:s} already exists.'.format(path))\n",
    "    return None\n",
    "\n",
    "def decompress_file_bzip2(filename):\n",
    "    cmd = ['bzip2','-d',filename]\n",
    "    process = subprocess.call(cmd)\n",
    "    return None\n",
    "\n",
    "def compress_file_fpack(filename):\n",
    "    fpack_command  = '/Users/hhsieh/Astro/tools/cfitsio/fpack'\n",
    "    delete_command = '/bin/rm'\n",
    "    fpack_cmd = [fpack_command,filename]\n",
    "    process = subprocess.call(fpack_cmd)\n",
    "    if process == 0:\n",
    "        delete_cmd = [delete_command,filename]\n",
    "        process = subprocess.call(delete_cmd)\n",
    "    else:\n",
    "        print('fpack command failed.')\n",
    "    return None\n",
    "\n",
    "def decompress_file_fpack(filename):\n",
    "    funpack_command = '/Users/hhsieh/Astro/tools/cfitsio/funpack'\n",
    "    delete_command  = '/bin/rm'\n",
    "    funpack_cmd = [funpack_command,filename]\n",
    "    process = subprocess.call(funpack_cmd)\n",
    "    if process == 0:\n",
    "        delete_cmd = [delete_command,filename]\n",
    "        process = subprocess.call(delete_cmd)\n",
    "    else:\n",
    "        print('funpack command failed.')\n",
    "    return None\n",
    "\n",
    "def decompress_directory_bzip2(file_path):\n",
    "    print('>>> Starting decompression of bz2 files in {:s}...'.format(file_path))\n",
    "    os.chdir(file_path)\n",
    "    for bz2_file in sorted(glob.glob('*.bz2')):\n",
    "        decompress_file_bzip2(bz2_file)\n",
    "    print('>>> Decompression of bz2 files complete.')\n",
    "    return None\n",
    "\n",
    "def compress_directory_fpack(file_path):\n",
    "    print('>>> Starting fpack compression of FITS files in {:s}...'.format(file_path))\n",
    "    os.chdir(file_path)\n",
    "    for fits_file in sorted(glob.glob('*.fits')):\n",
    "        compress_file_fpack(fits_file)\n",
    "    print('>>> fpack compression of FITS files complete.')\n",
    "    return None\n",
    "    \n",
    "def decompress_directory_fpack(file_path):\n",
    "    print('>>> Starting decompression of fz files in {:s}...'.format(file_path))\n",
    "    os.chdir(file_path)\n",
    "    for fz_file in sorted(glob.glob('*.fz')):\n",
    "        decompress_file_fpack(fz_file)\n",
    "    print('>>> Decompression of fz files complete.')\n",
    "    return None\n",
    "\n",
    "\n",
    "#def get_date_id():\n",
    "#    # obtain YYYYMMDD date from filename of GMOS FITS files being processed\n",
    "#    # return: YYYYMMDD date id\n",
    "#    for raw_mef_file in sorted(glob.glob('*.fits')):\n",
    "#        fits_date = raw_mef_file[1:9]\n",
    "#    return fits_date\n",
    "\n",
    "def get_date_id():\n",
    "    # obtain YYYYMMDD date from filename of GMOS FITS files being processed (regardless of current compression state)\n",
    "    # return: YYYYMMDD date id\n",
    "    fits_date = ''\n",
    "    if len(glob.glob('*.fits')) > 0:\n",
    "        for raw_mef_file in sorted(glob.glob('*.fits')):\n",
    "            fits_date = raw_mef_file[1:9]\n",
    "    elif len(glob.glob('*.fits.fz')) > 0:\n",
    "        for raw_mef_file in sorted(glob.glob('*.fits.fz')):\n",
    "            fits_date = raw_mef_file[1:9]\n",
    "    elif len(glob.glob('*.fits.bz2')) > 0:\n",
    "        for raw_mef_file in sorted(glob.glob('*.fits.bz2')):\n",
    "            fits_date = raw_mef_file[1:9]\n",
    "    return fits_date\n",
    "\n",
    "def create_stats_files(fits_date,imgtype):\n",
    "    for extid in range(2,10):\n",
    "        ext_stats = 'n{:s}.{:s}.{:02d}.stats'.format(fits_date,imgtype,extid+1)\n",
    "        outputfile = open(ext_stats,'w')\n",
    "        outputfile.write('# Extension {:02d}              NPIX        MEAN     STDDEV         MIN         MAX\\n'.format(extid+1))\n",
    "        outputfile.close()\n",
    "    return None\n",
    "        \n",
    "def compile_stats_files(fits_date,imgtype):\n",
    "    print('Starting image statistics output...')\n",
    "    output_stats_filename = 'n{:s}.{:s}.stats'.format(fits_date,imgtype)\n",
    "    output_stats_file = open(output_stats_filename,'w')\n",
    "    cmd1 = '/bin/rm'\n",
    "    for stats_filename in glob.glob('*.??.stats'):\n",
    "        stats_file = open(stats_filename,'r')\n",
    "        for line in stats_file:\n",
    "            output_stats_file.write(line)\n",
    "        stats_file.close()\n",
    "        cmd = [cmd1,stats_filename]\n",
    "        process = subprocess.call(cmd)\n",
    "    output_stats_file.close()\n",
    "    print('>>> Image statistics output complete.')\n",
    "    return None\n",
    "\n",
    "def split_extensions(imgtype):\n",
    "    # split 12-element GMOS multi-extension FITS files into individual elements\n",
    "    # return: dimensions of extensions; also writes individual extension files to working directory\n",
    "    for raw_mef_file in glob.glob('*.fits'):\n",
    "        hdulist = fits.open(raw_mef_file)\n",
    "        print('Splitting {:s}...'.format(raw_mef_file))\n",
    "        fits_date = raw_mef_file[1:9]\n",
    "        fits_id   = raw_mef_file[11:14]\n",
    "        hdr1 = getheader(raw_mef_file,0)\n",
    "        for extid in range(2,10):\n",
    "            extension = hdulist[extid+1].data\n",
    "            hdr2 = hdulist[extid+1].header\n",
    "            radecsys = hdr2['RADECSYS']\n",
    "            hdr2['RADESYSA'] = radecsys\n",
    "            del hdr2['RADECSYS']\n",
    "            imstat_npix = extension.size\n",
    "            imstat_min = np.min(extension)\n",
    "            imstat_max = np.max(extension)\n",
    "            imstat_mean = np.mean(extension)\n",
    "            imstat_stdev = np.std(extension)\n",
    "            ext_filename = 'n' + fits_date + '.' + fits_id + '.{:02d}.fits'.format(extid+1)\n",
    "            outputfilename = 'n{:s}.{:s}.{:02d}.stats'.format(fits_date,imgtype,extid+1)\n",
    "            outputfile = open(outputfilename,'a')\n",
    "            outputfile.write('{:s}   {:>8d}    {:>8.2f}    {:>7.2f}    {:>8.2f}    {:>8.2f}\\n'.format(ext_filename,imstat_npix,imstat_mean,imstat_stdev,imstat_min,imstat_max))\n",
    "            outputfile.close()\n",
    "            dimensions = extension.shape\n",
    "            dimension1 = dimensions[0]\n",
    "            dimension2 = dimensions[1]\n",
    "            hdr = hdr1 + hdr2\n",
    "            fits.writeto(ext_filename,extension,hdr)\n",
    "        hdulist.close()\n",
    "    return dimension1, dimension2\n",
    "    print('>>> Multi-extension fits file splitting complete.')\n",
    "    return None\n",
    "    \n",
    "def remove_wrong_dimensions(dimension1,dimension2):\n",
    "    # identify bias files with correct binning and remove others\n",
    "    # return: none; retains bias files with correct binning and removes others\n",
    "    for raw_mef_file in glob.glob('*.fits'):\n",
    "        hdulist = fits.open(raw_mef_file)\n",
    "        extension01 = hdulist[1].data\n",
    "        bias_dimensions = extension01.shape\n",
    "        bias_dimension1 = bias_dimensions[0]\n",
    "        bias_dimension2 = bias_dimensions[1]\n",
    "        hdulist.close()\n",
    "        delete_file = '/bin/rm'\n",
    "        if (bias_dimension1 != dimension1) or (bias_dimension2 != dimension2):\n",
    "            delete_cmd = [delete_file,raw_mef_file]\n",
    "            process = subprocess.call(delete_cmd)\n",
    "    print('>>> Bias frame selection complete.')\n",
    "    return None\n",
    "\n",
    "\n",
    "def add_fits_header_line(fits_file,param_name,param_value,param_comment):\n",
    "    # Add line to FITS header\n",
    "    hdulist = fits.open(fits_file)\n",
    "    data = hdulist[0].data\n",
    "    hdr = hdulist[0].header\n",
    "    hdr[param_name] = (param_value,param_comment)\n",
    "    fits.writeto(fits_file,data,hdr,overwrite=True)\n",
    "    return None\n",
    "\n",
    "def overscan_and_trim():\n",
    "    # Do overscan correction and trim images in current directory\n",
    "    print('Starting overscan correction and trimming...')\n",
    "    for fits_file in sorted(glob.glob('*.???.??.fits')):\n",
    "        ot_fits_file = fits_file[0:16] + '.ot.fits'\n",
    "        fits_data = CCDData.read(fits_file,unit=u.adu)\n",
    "        file_ext = fits_file[14:16]\n",
    "        # Overscan correction\n",
    "        if ((file_ext == '03') or (file_ext=='05') or (file_ext=='07') or (file_ext=='09')):\n",
    "            o_fits_data  = cp.subtract_overscan(fits_data, fits_section='[257:288,1:2112]', overscan_axis=1, add_keyword={'oscansub': True, 'calstat': 'O'}, model=models.Polynomial1D(1))\n",
    "        else:\n",
    "            o_fits_data  = cp.subtract_overscan(fits_data, fits_section='[1:32,1:2112]', overscan_axis=1, add_keyword={'oscansub': True, 'calstat': 'O'}, model=models.Polynomial1D(1))\n",
    "        # Image trimming\n",
    "        if ((file_ext == '03') or (file_ext=='07')):\n",
    "            ot_fits_data = cp.trim_image(o_fits_data,fits_section='[1:256,65:2110]',add_keyword={'trimmed': True, 'calstat': 'OT'})\n",
    "        elif ((file_ext == '04') or (file_ext == '08')):\n",
    "            ot_fits_data = cp.trim_image(o_fits_data,fits_section='[33:282,65:2110]',add_keyword={'trimmed': True, 'calstat': 'OT'})\n",
    "        elif ((file_ext == '05') or (file_ext =='09')):\n",
    "            ot_fits_data = cp.trim_image(o_fits_data,fits_section='[7:256,65:2110]',add_keyword={'trimmed': True, 'calstat': 'OT'})\n",
    "        else: # file_ext == '02' or file_ext == '10'\n",
    "            ot_fits_data = cp.trim_image(o_fits_data,fits_section='[33:288,65:2110]',add_keyword={'trimmed': True, 'calstat': 'OT'})\n",
    "        ot_fits_data.write(ot_fits_file)\n",
    "        delete_file = '/bin/rm'\n",
    "        delete_cmd = [delete_file,fits_file]\n",
    "        process = subprocess.call(delete_cmd)\n",
    "    print('>>> Overscan correction and trimming complete.')\n",
    "    return None\n",
    "\n",
    "def bias_median_combine(dateid):\n",
    "    print('Starting median combination of bias frames...')\n",
    "    for extid in range(2,10):\n",
    "        bias_list = []\n",
    "        ext_file_format = '*.{:02d}.ot.fits'.format(extid+1)\n",
    "        output_filename = 'n' + dateid + '.bias.{:02d}.fits'.format(extid+1)\n",
    "        for fits_file in sorted(glob.glob(ext_file_format)):\n",
    "            fits_data = CCDData.read(fits_file)\n",
    "            bias_list.append(fits_data)\n",
    "            delete_file = '/bin/rm'\n",
    "            delete_cmd = [delete_file,fits_file]\n",
    "            process = subprocess.call(delete_cmd)\n",
    "        master_bias = cp.combine(bias_list,method='median')\n",
    "        master_bias.write(output_filename)\n",
    "    print('>>> Median combination of bias frames complete.')\n",
    "    return None\n",
    "\n",
    "def bias_correct(dateid,cwd_raw_bias):\n",
    "    print('Starting bias subtraction...')\n",
    "    delete_cmd = '/bin/rm'\n",
    "    for extid in range(2,10):\n",
    "        bias_filename = cwd_raw_bias + 'n' + dateid + '.bias.{:02d}.fits'.format(extid+1)\n",
    "        ext_file_format = '*.{:02d}.ot.fits'.format(extid+1)\n",
    "        for fits_file in sorted(glob.glob(ext_file_format)):\n",
    "            fits_data = CCDData.read(fits_file)\n",
    "            bias_data = CCDData.read(bias_filename)\n",
    "            fits_date_imageid = fits_file[0:13]\n",
    "            output_filename = fits_date_imageid + '.{:02d}.otz.fits'.format(extid+1)\n",
    "            bias_corrected_data = cp.subtract_bias(fits_data,bias_data,add_keyword={'zerocorr':True,'calstat':'OTZ'})\n",
    "            bias_corrected_data.write(output_filename)\n",
    "            delete_file = [delete_cmd,fits_file]\n",
    "            process = subprocess.call(delete_file)\n",
    "    print('>>> Bias subtraction complete.')\n",
    "    return None\n",
    "\n",
    "def concatenate_gmos_amps():\n",
    "    print('>>> Starting adjacent amp area concatenation...')\n",
    "    delete_cmd = '/bin/rm'\n",
    "    for fits_file in sorted(glob.glob('*.03.otz.fits')):\n",
    "        file_prefix = fits_file[0:13]\n",
    "        ext1_filename = file_prefix + '.03.otz.fits'\n",
    "        ext2_filename = file_prefix + '.04.otz.fits'\n",
    "        hdr = getheader(ext1_filename,0)\n",
    "        hdulist1 = fits.open(ext1_filename)\n",
    "        ext1_data = hdulist1[0].data\n",
    "        hdulist2 = fits.open(ext2_filename)\n",
    "        ext2_data = hdulist2[0].data\n",
    "        hdulist1.close()\n",
    "        hdulist2.close()\n",
    "        chip1_data = np.hstack((ext1_data,ext2_data))\n",
    "        output_filename = file_prefix + '.chip1.otz.fits'\n",
    "        fits.writeto(output_filename,chip1_data,hdr)\n",
    "        delete_file = [delete_cmd,ext1_filename]\n",
    "        process = subprocess.call(delete_file)\n",
    "        delete_file = [delete_cmd,ext2_filename]\n",
    "        process = subprocess.call(delete_file)\n",
    "\n",
    "        ext1_filename = file_prefix + '.05.otz.fits'\n",
    "        ext2_filename = file_prefix + '.06.otz.fits'\n",
    "        ext3_filename = file_prefix + '.07.otz.fits'\n",
    "        ext4_filename = file_prefix + '.08.otz.fits'\n",
    "        hdr = getheader(ext1_filename,0)\n",
    "        hdulist1 = fits.open(ext1_filename)\n",
    "        ext1_data = hdulist1[0].data\n",
    "        hdulist2 = fits.open(ext2_filename)\n",
    "        ext2_data = hdulist2[0].data\n",
    "        hdulist3 = fits.open(ext3_filename)\n",
    "        ext3_data = hdulist3[0].data\n",
    "        hdulist4 = fits.open(ext4_filename)\n",
    "        ext4_data = hdulist4[0].data\n",
    "        hdulist1.close()\n",
    "        hdulist2.close()\n",
    "        hdulist3.close()\n",
    "        hdulist4.close()\n",
    "        chip1_data = np.hstack((ext1_data,ext2_data,ext3_data,ext4_data))\n",
    "        output_filename = file_prefix + '.chip2.otz.fits'\n",
    "        fits.writeto(output_filename,chip1_data,hdr)\n",
    "        delete_file = [delete_cmd,ext1_filename]\n",
    "        process = subprocess.call(delete_file)\n",
    "        delete_file = [delete_cmd,ext2_filename]\n",
    "        process = subprocess.call(delete_file)\n",
    "        delete_file = [delete_cmd,ext3_filename]\n",
    "        process = subprocess.call(delete_file)\n",
    "        delete_file = [delete_cmd,ext4_filename]\n",
    "        process = subprocess.call(delete_file)\n",
    "\n",
    "        ext1_filename = file_prefix + '.09.otz.fits'\n",
    "        ext2_filename = file_prefix + '.10.otz.fits'\n",
    "        hdr = getheader(ext1_filename,0)\n",
    "        hdulist1 = fits.open(ext1_filename)\n",
    "        ext1_data = hdulist1[0].data\n",
    "        hdulist2 = fits.open(ext2_filename)\n",
    "        ext2_data = hdulist2[0].data\n",
    "        hdulist1.close()\n",
    "        hdulist2.close()\n",
    "        chip1_data = np.hstack((ext1_data,ext2_data))\n",
    "        output_filename = file_prefix + '.chip3.otz.fits'\n",
    "        fits.writeto(output_filename,chip1_data,hdr)\n",
    "        delete_file = [delete_cmd,ext1_filename]\n",
    "        process = subprocess.call(delete_file)\n",
    "        delete_file = [delete_cmd,ext2_filename]\n",
    "        process = subprocess.call(delete_file)\n",
    "    print('>>> Adjacent amp area concatenation complete.')\n",
    "    return None\n",
    "\n",
    "def flatfield_correction(base_dir,data_dir,flatfield_chip1_file,flatfield_chip2_file,flatfield_chip3_file):\n",
    "    print('Starting flatfield correction...')\n",
    "    for fits_file in sorted(glob.glob('*.chip1.otz.fits')):\n",
    "        fits_data = CCDData.read(fits_file)\n",
    "        flat_data = CCDData.read(base_dir+data_dir+'/'+flatfield_chip1_file,unit=u.adu)\n",
    "        fits_date_imageid = fits_file[0:13]\n",
    "        output_filename = fits_date_imageid + '.chip1.otzf.fits'\n",
    "        flat_corrected_data = cp.flat_correct(fits_data,flat_data,add_keyword={'flatcorr': True, 'calstat': 'OTZF'})\n",
    "        flat_corrected_data.write(output_filename)\n",
    "        add_fits_header_line(output_filename,'BIAS_1',fits_date_imageid+'.bias.03.fits','1st bias frame used')\n",
    "        add_fits_header_line(output_filename,'BIAS_2',fits_date_imageid+'.bias.04.fits','2nd bias frame used')\n",
    "        add_fits_header_line(output_filename,'BIAS_3','n/a','3rd bias frame used')\n",
    "        add_fits_header_line(output_filename,'BIAS_4','n/a','4th bias frame used')\n",
    "        add_fits_header_line(output_filename,'FLATUSED',flatfield_chip1_file,'Flatfield frame used')\n",
    "        delete_file = '/bin/rm'\n",
    "        delete_cmd = [delete_file,fits_file]\n",
    "        process = subprocess.call(delete_cmd)\n",
    "\n",
    "    for fits_file in sorted(glob.glob('*.chip2.otz.fits')):\n",
    "        fits_data = CCDData.read(fits_file)\n",
    "        flat_data = CCDData.read(base_dir+data_dir+'/'+flatfield_chip2_file,unit=u.adu)\n",
    "        fits_date_imageid = fits_file[0:13]\n",
    "        output_filename = fits_date_imageid + '.chip2.otzf.fits'\n",
    "        flat_corrected_data = cp.flat_correct(fits_data,flat_data,add_keyword={'flatcorr': True, 'calstat': 'OTZF'})\n",
    "        flat_corrected_data.write(output_filename)\n",
    "        add_fits_header_line(output_filename,'BIAS_1',fits_date_imageid+'.bias.05.fits','1st bias frame used')\n",
    "        add_fits_header_line(output_filename,'BIAS_2',fits_date_imageid+'.bias.06.fits','2nd bias frame used')\n",
    "        add_fits_header_line(output_filename,'BIAS_3',fits_date_imageid+'.bias.07.fits','3rd bias frame used')\n",
    "        add_fits_header_line(output_filename,'BIAS_4',fits_date_imageid+'.bias.08.fits','4th bias frame used')\n",
    "        add_fits_header_line(output_filename,'FLATUSED',flatfield_chip2_file,'Flatfield frame used')\n",
    "        delete_file = '/bin/rm'\n",
    "        delete_cmd = [delete_file,fits_file]\n",
    "        process = subprocess.call(delete_cmd)\n",
    "\n",
    "    for fits_file in sorted(glob.glob('*.chip3.otz.fits')):\n",
    "        fits_data = CCDData.read(fits_file)\n",
    "        flat_data = CCDData.read(base_dir+data_dir+'/'+flatfield_chip3_file,unit=u.adu)\n",
    "        fits_date_imageid = fits_file[0:13]\n",
    "        output_filename = fits_date_imageid + '.chip3.otzf.fits'\n",
    "        flat_corrected_data = cp.flat_correct(fits_data,flat_data,add_keyword={'flatcorr': True, 'calstat': 'OTZF'})\n",
    "        flat_corrected_data.write(output_filename)\n",
    "        add_fits_header_line(output_filename,'BIAS_1',fits_date_imageid+'.bias.09.fits','1st bias frame used')\n",
    "        add_fits_header_line(output_filename,'BIAS_2',fits_date_imageid+'.bias.10.fits','2nd bias frame used')\n",
    "        add_fits_header_line(output_filename,'BIAS_3','n/a','3rd bias frame used')\n",
    "        add_fits_header_line(output_filename,'BIAS_4','n/a','4th bias frame used')\n",
    "        add_fits_header_line(output_filename,'FLATUSED',flatfield_chip3_file,'Flatfield frame used')\n",
    "        delete_file = '/bin/rm'\n",
    "        delete_cmd = [delete_file,fits_file]\n",
    "        process = subprocess.call(delete_cmd)\n",
    "\n",
    "    print('>>> Flatfield correction complete.')\n",
    "    return None\n",
    "\n",
    "def cosmicray_cleaning():\n",
    "    print('Starting cosmic ray correction...')\n",
    "    for fits_file in sorted(glob.glob('*.chip1.otzf.fits')):\n",
    "        print('Cosmic ray cleaning for {:s}'.format(fits_file))\n",
    "        file_prefix = fits_file[0:19]\n",
    "        hdr = getheader(fits_file,0)\n",
    "        fits_gain = hdr['gain']\n",
    "        fits_readnoise = hdr['rdnoise']\n",
    "        array,header = cosmics_py3.fromfits(fits_file,verbose=False)\n",
    "        c = cosmics_py3.cosmicsimage(array,gain=fits_gain,readnoise=fits_readnoise,sigclip=5.0,sigfrac=0.3,objlim=5.0,verbose=False)\n",
    "        c.run(maxiter=4)\n",
    "        output_file = file_prefix + '.otzfc.fits'\n",
    "        cosmics_py3.tofits(output_file,c.cleanarray,header,verbose=False)\n",
    "        add_fits_header_line(output_file,'CRCORR',True,'Cosmic ray removal performed? (T/F)')\n",
    "        add_fits_header_line(output_file,'CALSTAT','OTZFC','Image calibration status')\n",
    "        add_fits_header_line(output_file,'CRR_GAIN',fits_gain,'CR removal parameter: gain')\n",
    "        add_fits_header_line(output_file,'CRR_NOIS',fits_readnoise,'CR removal parameter: read noise')\n",
    "        add_fits_header_line(output_file,'CRR_SIGC',5.0,'CR removal parameter: sigclip')\n",
    "        add_fits_header_line(output_file,'CRR_SIGF',0.3,'CR removal parameter: sigfrac')\n",
    "        add_fits_header_line(output_file,'CRR_OBJL',5.0,'CR removal parameter: objlim')\n",
    "        delete_file = '/bin/rm'\n",
    "        delete_cmd = [delete_file,fits_file]\n",
    "        process = subprocess.call(delete_cmd)\n",
    "\n",
    "    for fits_file in sorted(glob.glob('*.chip2.otzf.fits')):\n",
    "        print('Cosmic ray cleaning for {:s}'.format(fits_file))\n",
    "        file_prefix = fits_file[0:19]\n",
    "        hdr = getheader(fits_file,0)\n",
    "        fits_gain = hdr['gain']\n",
    "        fits_readnoise = hdr['rdnoise']\n",
    "        array,header = cosmics_py3.fromfits(fits_file,verbose=False)\n",
    "        c = cosmics_py3.cosmicsimage(array,gain=fits_gain,readnoise=fits_readnoise,sigclip=5.0,sigfrac=0.3,objlim=5.0,verbose=False)\n",
    "        c.run(maxiter=4)\n",
    "        output_file = file_prefix + '.otzfc.fits'\n",
    "        cosmics_py3.tofits(output_file,c.cleanarray,header,verbose=False)\n",
    "        add_fits_header_line(output_file,'CRCORR',True,'Cosmic ray removal performed? (T/F)')\n",
    "        add_fits_header_line(output_file,'CALSTAT','OTZFC','Image calibration status')\n",
    "        add_fits_header_line(output_file,'CRR_GAIN',fits_gain,'CR removal parameter: gain')\n",
    "        add_fits_header_line(output_file,'CRR_NOIS',fits_readnoise,'CR removal parameter: read noise')\n",
    "        add_fits_header_line(output_file,'CRR_SIGC',5.0,'CR removal parameter: sigclip')\n",
    "        add_fits_header_line(output_file,'CRR_SIGF',0.3,'CR removal parameter: sigfrac')\n",
    "        add_fits_header_line(output_file,'CRR_OBJL',5.0,'CR removal parameter: objlim')\n",
    "        delete_file = '/bin/rm'\n",
    "        delete_cmd = [delete_file,fits_file]\n",
    "        process = subprocess.call(delete_cmd)\n",
    "\n",
    "    for fits_file in sorted(glob.glob('*.chip3.otzf.fits')):\n",
    "        print('Cosmic ray cleaning for {:s}'.format(fits_file))\n",
    "        file_prefix = fits_file[0:19]\n",
    "        hdr = getheader(fits_file,0)\n",
    "        fits_gain = hdr['gain']\n",
    "        fits_readnoise = hdr['rdnoise']\n",
    "        array,header = cosmics_py3.fromfits(fits_file,verbose=False)\n",
    "        c = cosmics_py3.cosmicsimage(array,gain=fits_gain,readnoise=fits_readnoise,sigclip=5.0,sigfrac=0.3,objlim=5.0,verbose=False)\n",
    "        c.run(maxiter=4)\n",
    "        output_file = file_prefix + '.otzfc.fits'\n",
    "        cosmics_py3.tofits(output_file,c.cleanarray,header,verbose=False)\n",
    "        add_fits_header_line(output_file,'CRCORR',True,'Cosmic ray removal performed? (T/F)')\n",
    "        add_fits_header_line(output_file,'CALSTAT','OTZFC','Image calibration status')\n",
    "        add_fits_header_line(output_file,'CRR_GAIN',fits_gain,'CR removal parameter: gain')\n",
    "        add_fits_header_line(output_file,'CRR_NOIS',fits_readnoise,'CR removal parameter: read noise')\n",
    "        add_fits_header_line(output_file,'CRR_SIGC',5.0,'CR removal parameter: sigclip')\n",
    "        add_fits_header_line(output_file,'CRR_SIGF',0.3,'CR removal parameter: sigfrac')\n",
    "        add_fits_header_line(output_file,'CRR_OBJL',5.0,'CR removal parameter: objlim')\n",
    "        delete_file = '/bin/rm'\n",
    "        delete_cmd = [delete_file,fits_file]\n",
    "        process = subprocess.call(delete_cmd)\n",
    "        \n",
    "    print('>>> Cosmic ray correction complete.')\n",
    "    return None\n",
    "\n",
    "def move_reduced_data(rawfitsdir,rawbiasdir,flatdir,path_stats):\n",
    "    move_file = 'mv'\n",
    "    os.chdir(rawfitsdir)\n",
    "    for fits_file in sorted(glob.glob('*.otzfc.fits')):\n",
    "        move_cmd = [move_file,fits_file,flatdir]\n",
    "        process = subprocess.call(move_cmd)\n",
    "    for stats_file in sorted(glob.glob('*.stats')):\n",
    "        move_cmd = [move_file,stats_file,path_stats]\n",
    "        process = subprocess.call(move_cmd)\n",
    "    os.chdir(rawbiasdir)\n",
    "    for fits_file in sorted(glob.glob('*.bias.??.fits')):\n",
    "        move_cmd = [move_file,fits_file,flatdir]\n",
    "        process = subprocess.call(move_cmd)\n",
    "    for stats_file in sorted(glob.glob('*.stats')):\n",
    "        move_cmd = [move_file,stats_file,path_stats]\n",
    "        process = subprocess.call(move_cmd)\n",
    "    print('>>> Processed data moved to output directory.')\n",
    "    return None\n",
    "\n",
    "def move_reduced_science_data(rawfitsdir,flatdir,path_stats):\n",
    "    move_file = 'mv'\n",
    "    os.chdir(rawfitsdir)\n",
    "    for fits_file in sorted(glob.glob('*.otzfc.fits')):\n",
    "        move_cmd = [move_file,fits_file,flatdir]\n",
    "        process = subprocess.call(move_cmd)\n",
    "    for stats_file in sorted(glob.glob('*.stats')):\n",
    "        move_cmd = [move_file,stats_file,path_stats]\n",
    "        process = subprocess.call(move_cmd)\n",
    "    #os.chdir(rawbiasdir)\n",
    "    #for fits_file in sorted(glob.glob('*.bias.??.fits')):\n",
    "    #    move_cmd = [move_file,fits_file,flatdir]\n",
    "    #    process = subprocess.call(move_cmd)\n",
    "    #for stats_file in sorted(glob.glob('*.stats')):\n",
    "    #    move_cmd = [move_file,stats_file,path_stats]\n",
    "    #    process = subprocess.call(move_cmd)\n",
    "    print('>>> Processed data moved to output directory.')\n",
    "    return None\n",
    "\n",
    "def move_reduced_bias_data(rawbiasdir,flatdir,path_stats):\n",
    "    move_file = 'mv'\n",
    "    #os.chdir(rawfitsdir)\n",
    "    #for fits_file in sorted(glob.glob('*.otzfc.fits')):\n",
    "    #    move_cmd = [move_file,fits_file,flatdir]\n",
    "    #    process = subprocess.call(move_cmd)\n",
    "    #for stats_file in sorted(glob.glob('*.stats')):\n",
    "    #    move_cmd = [move_file,stats_file,path_stats]\n",
    "    #    process = subprocess.call(move_cmd)\n",
    "    os.chdir(rawbiasdir)\n",
    "    if os.path.exists(flatdir):\n",
    "        for fits_file in sorted(glob.glob('*.bias.??.fits')):\n",
    "            move_cmd = [move_file,fits_file,flatdir]\n",
    "            process = subprocess.call(move_cmd)\n",
    "    for stats_file in sorted(glob.glob('*.stats')):\n",
    "        move_cmd = [move_file,stats_file,path_stats]\n",
    "        process = subprocess.call(move_cmd)\n",
    "    print('>>> Processed bias data moved to output directory.')\n",
    "    return None\n",
    "\n",
    "def move_flatfield_images(base_dir,data_dir,path_procfits,flatfield_chip1,flatfield_chip2,flatfield_chip3):\n",
    "    move_file = 'mv'\n",
    "    os.chdir(base_dir + data_dir)\n",
    "    move_cmd = [move_file,flatfield_chip1,path_procfits]\n",
    "    process = subprocess.call(move_cmd)\n",
    "    move_cmd = [move_file,flatfield_chip2,path_procfits]\n",
    "    process = subprocess.call(move_cmd)\n",
    "    move_cmd = [move_file,flatfield_chip3,path_procfits]\n",
    "    process = subprocess.call(move_cmd)\n",
    "    return None\n",
    "\n",
    "    \n",
    "print('Done.')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Done.\n"
     ]
    }
   ],
   "source": [
    "def fix_gain_rdnoise_gmosn_hamamatsu():\n",
    "    # Fix gain and read noise values in FITS headers\n",
    "    for fits_file in sorted(glob.glob('*.???.??.fits')):\n",
    "        with fits.open(fits_file) as hdulist:\n",
    "            data = hdulist[0].data\n",
    "            hdr = hdulist[0].header\n",
    "        hdr['GAIN'] = 1.63\n",
    "        hdr['RDNOISE'] = 4.14\n",
    "        fits.writeto(fits_file,data,hdr,overwrite=True)\n",
    "    print('>>> Gain and read noise updated in image headers.')\n",
    "    return None\n",
    "\n",
    "def fix_gain_rdnoise_gmoss_hamamatsu():\n",
    "    # Fix gain and read noise values in FITS headers\n",
    "    for fits_file in sorted(glob.glob('*.???.??.fits')):\n",
    "        with fits.open(fits_file) as hdulist:\n",
    "            data = hdulist[0].data\n",
    "            hdr = hdulist[0].header\n",
    "        hdr['GAIN'] = 1.83\n",
    "        hdr['RDNOISE'] = 3.98\n",
    "        fits.writeto(fits_file,data,hdr,overwrite=True)\n",
    "    print('>>> Gain and read noise updated in image headers.')\n",
    "    return None\n",
    "\n",
    "def convert_to_long_target_desig(short_desig):\n",
    "    long_desig = short_desig\n",
    "    if short_desig == '133P': long_desig = '133P/1996 N2 (Elst-Pizarro 1)'\n",
    "    if short_desig == '176P': long_desig = '176P/1999 RE70 (LINEAR 52)'\n",
    "    if short_desig == '238P': long_desig = '238P/2005 U1 (Read 3)'\n",
    "    if short_desig == '259P': long_desig = '259P/2008 R1 (Garradd 4)'\n",
    "    if short_desig == '288P': long_desig = '288P/2006 VW139 (300163)'\n",
    "    if short_desig == '2006 VW139': long_desig = '288P/2006 VW139 (300163)'\n",
    "    if short_desig == '313P': long_desig = '313P/2014 S4 (Gibbs 16)'\n",
    "    if short_desig == '324P': long_desig = '324P/2010 R2 (La Sagra 4)'\n",
    "    if short_desig == '358P': long_desig = '358P/2012 T1 (PanSTARRS 11)'\n",
    "    return long_desig\n",
    "\n",
    "def fix_gmos_header_info(instr_id,filter_id):\n",
    "    # Fix header information for PDS submission\n",
    "    for fits_file in sorted(glob.glob('*.otzfc.fits')):\n",
    "        with fits.open(fits_file) as hdulist:\n",
    "            #hdulist = fits.open(fits_file)\n",
    "            data = hdulist[0].data\n",
    "            hdr = hdulist[0].header\n",
    "\n",
    "        # Change keywords for CDi_j parameters (conflict with other WCS keywords)\n",
    "        cd1_1,cd1_1_comment = hdr['CD1_1'],hdr.comments['CD1_1']\n",
    "        cd1_2,cd1_2_comment = hdr['CD1_2'],hdr.comments['CD1_2']\n",
    "        cd2_1,cd2_1_comment = hdr['CD2_1'],hdr.comments['CD2_1']\n",
    "        cd2_2,cd2_2_comment = hdr['CD2_2'],hdr.comments['CD2_2']\n",
    "        hdr['x_CD1_1'] = (cd1_1,cd1_1_comment)\n",
    "        hdr['x_CD1_2'] = (cd1_2,cd1_2_comment)\n",
    "        hdr['x_CD2_1'] = (cd2_1,cd2_1_comment)\n",
    "        hdr['x_CD2_2'] = (cd2_2,cd2_2_comment)\n",
    "        del hdr['CD1_1']\n",
    "        del hdr['CD1_2']\n",
    "        del hdr['CD2_1']\n",
    "        del hdr['CD2_2']\n",
    "        \n",
    "        # Change keyword for EPOCH parameter\n",
    "        target_epoch,target_epoch_comment = hdr['EPOCH'],hdr.comments['EPOCH']\n",
    "        hdr['TRGEPOCH'] = (target_epoch,target_epoch_comment)\n",
    "        del hdr['EPOCH']\n",
    "        \n",
    "        # Remove RADVEL parameter (not correctly populated)\n",
    "        del hdr['RADVEL']\n",
    "        \n",
    "        # Change EXPTIME value to integer format\n",
    "        exptime = int(round(hdr['EXPTIME']))\n",
    "        hdr['EXPTIME'] = exptime\n",
    "        \n",
    "        # Add keyword for full object designation\n",
    "        object_name = hdr['OBJECT']\n",
    "        object_desig = convert_to_long_target_desig(object_name)\n",
    "        hdr['OBJDESIG'] = object_desig\n",
    "\n",
    "        # Add central filter wavelength keyword\n",
    "        if instr_id == 'gmosn':\n",
    "            if filter_id == 'g':   hdr['CENTWAVE'] = 475\n",
    "            elif filter_id == 'r': hdr['CENTWAVE'] = 630\n",
    "            elif filter_id == 'i': hdr['CENTWAVE'] = 780\n",
    "        elif instr_id == 'gmoss':\n",
    "            if filter_id == 'g':   hdr['CENTWAVE'] = 475\n",
    "            elif filter_id == 'r': hdr['CENTWAVE'] = 630\n",
    "            elif filter_id == 'i': hdr['CENTWAVE'] = 780\n",
    "        \n",
    "        # Remove checksums\n",
    "        if 'CHECKSUM' in hdr: del hdr['CHECKSUM']\n",
    "        if 'DATASUM'  in hdr: del hdr['DATASUM']\n",
    "        \n",
    "        fits.writeto(fits_file,data,hdr,overwrite=True,checksum=True)\n",
    "        \n",
    "    print('>>> Header information fixed for PDS submission.')\n",
    "\n",
    "    return None\n",
    "\n",
    "def find_flatfield_files(base_dir,data_dir,instr_id,filter_id):\n",
    "    ff_chip1_filename,ff_chip2_filename,ff_chip3_filename = 'none','none','none'\n",
    "    os.chdir(base_dir + data_dir)\n",
    "    decompress_directory_fpack(base_dir + data_dir)\n",
    "    flatfield_filename_pattern = 'n*.' + instr_id + '.twiskyflat.' + filter_id + '*.fits'\n",
    "    if len(glob.glob(flatfield_filename_pattern)) != 3:\n",
    "        print('Incorrect number of flatfield files found.')\n",
    "    else:\n",
    "        for flatfield_file in sorted(glob.glob(flatfield_filename_pattern)):\n",
    "            if flatfield_file[-10:-5] == 'chip1': ff_chip1_filename = flatfield_file\n",
    "            if flatfield_file[-10:-5] == 'chip2': ff_chip2_filename = flatfield_file\n",
    "            if flatfield_file[-10:-5] == 'chip3': ff_chip3_filename = flatfield_file\n",
    "    return ff_chip1_filename,ff_chip2_filename,ff_chip3_filename\n",
    "                \n",
    "def trim_gmoss_data_with_bad_amp(data_path):\n",
    "    # Trim GMOS-S data with bad amp 5 in current directory\n",
    "    print('Trimming GMOS-S data with bad amp #5...')\n",
    "    os.chdir(data_path)\n",
    "    for fits_file_fz in sorted(glob.glob('n*.???.chip2.otzfc.fits.fz')):\n",
    "        decompress_file_fpack(fits_file_fz)\n",
    "        fits_file = fits_file_fz[:-3]\n",
    "        new_fits_file = fits_file[0:13] + '.chip2a.otzfc.fits'        \n",
    "        fits_data = CCDData.read(fits_file,unit=u.adu)\n",
    "        trimmed_fits_data = cp.trim_image(fits_data,fits_section='[251:1012,1:2046]')        \n",
    "        trimmed_fits_data.write(new_fits_file)\n",
    "        compress_file_fpack(fits_file)\n",
    "        compress_file_fpack(new_fits_file)\n",
    "    print('>>> Trimming GMOS-S data with bad amp #5 complete.')\n",
    "    return None\n",
    "\n",
    "print('Done.')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Done.\n"
     ]
    }
   ],
   "source": [
    "def process_bias_data(path_rawbias,instr_id,date_id,reduction_log):\n",
    "    print('\\n{:s} - Processing bias-frame data in {:s}...'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),path_rawbias))\n",
    "    reduction_log.write('\\n{:s} - Processing bias-frame science data in {:s}...\\n'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),path_rawbias))\n",
    "    \n",
    "    # decompress raw bias fits files\n",
    "    print('\\n{:s} - Decompressing, filtering, and splitting bias files...'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S')))\n",
    "    reduction_log.write('{:s} - Decompressing, filtering, and splitting bias files...\\n'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S')))\n",
    "    os.chdir(path_rawbias)\n",
    "    decompress_directory_bzip2(path_rawbias)       # decompress downloaded GMOS files\n",
    "    decompress_directory_fpack(path_rawbias)       # decompress previously fpacked GMOS files\n",
    "    #remove_wrong_dimensions(dim1,dim2)       # find and retain bias frames matching data file binning\n",
    "    #date_id = get_date_id()\n",
    "    create_stats_files(date_id,'bias')       # create files to record image statistics\n",
    "    split_extensions('bias')                 # split bias MEFs into individual FITS files\n",
    "    if instr_id == 'gmosn':\n",
    "        fix_gain_rdnoise_gmosn_hamamatsu()\n",
    "    elif instr_id == 'gmoss':\n",
    "        fix_gain_rdnoise_gmoss_hamamatsu()\n",
    "    compile_stats_files(date_id,'bias')      # collect image stats of bias files together and delete individual files\n",
    "    \n",
    "    # perform overscan corrections and trim data for bias frames\n",
    "    os.chdir(path_rawbias)\n",
    "    overscan_and_trim()\n",
    "    bias_median_combine(date_id)\n",
    "    \n",
    "    print('\\n{:s} - Processing bias-frame data in {:s} complete.'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),path_rawbias))\n",
    "    reduction_log.write('\\n{:s} - Processing bias-frame science data in {:s} complete.\\n'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),path_rawbias))\n",
    "    return reduction_log\n",
    "\n",
    "\n",
    "def process_science_data(base_dir,data_dir,path_rawfits,path_rawbias,path_procfits,path_stats,instr_id,filter_id,reduction_log):\n",
    "    print('\\n{:s} - Processing {:s}-band science data in {:s}...'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),filter_id,data_dir))\n",
    "    reduction_log.write('\\n{:s} - Processing {:s}-band science data in {:s}...\\n'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),filter_id,data_dir))\n",
    "    \n",
    "    flatfield_chip1_filename,flatfield_chip2_filename,flatfield_chip3_filename = find_flatfield_files(base_dir,data_dir,instr_id,filter_id)\n",
    "    \n",
    "    if flatfield_chip1_filename != 'none' and flatfield_chip2_filename != 'none' and flatfield_chip3_filename != 'none':\n",
    "        if not os.path.isdir(path_procfits): os.mkdir(path_procfits)\n",
    "        if not os.path.isdir(path_stats):    os.mkdir(path_stats)\n",
    "        # Process raw science fits files\n",
    "        print('\\n{:s} - Decompressing and splitting data files...'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S')))\n",
    "        reduction_log.write('{:s} - Decompressing and splitting data files...\\n'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S')))\n",
    "        os.chdir(path_rawfits)\n",
    "        decompress_directory_bzip2(path_rawfits)       # decompress downloaded GMOS files\n",
    "        decompress_directory_fpack(path_rawfits)       # decompress previously fpacked GMOS files\n",
    "        date_id = get_date_id()\n",
    "        create_stats_files(date_id,'scidata.{:s}'.format(filter_id))    # create files to record image statistics\n",
    "        dim1, dim2 = split_extensions('scidata') # split science MEFs into individual FITS files\n",
    "        if instr_id == 'gmosn':\n",
    "            fix_gain_rdnoise_gmosn_hamamatsu()\n",
    "        elif instr_id == 'gmoss':\n",
    "            fix_gain_rdnoise_gmoss_hamamatsu()\n",
    "        compile_stats_files(date_id,'scidata.{:s}'.format(filter_id))   # collect image stats of science files together and delete individual files\n",
    "            \n",
    "        # Process science frames\n",
    "        os.chdir(path_rawfits)\n",
    "        overscan_and_trim()                                                    # Perform overscan correction and trim data\n",
    "        bias_correct(date_id,path_rawbias)                                      # Perform bias correction\n",
    "        concatenate_gmos_amps()                                                # Join science frames\n",
    "        flatfield_correction(base_dir,data_dir,flatfield_chip1_filename,flatfield_chip2_filename,flatfield_chip3_filename)  # Do flatfield corrections\n",
    "        cosmicray_cleaning()                                                   # Do cosmic ray cleaning\n",
    "        #fix_gmos_header_info(instr_id,filter_id)\n",
    "    \n",
    "        ## Clean up data\n",
    "        #move_reduced_data(path_rawfits,path_rawbias,path_procfits,path_stats)\n",
    "        ##move_flatfield_images(base_dir,data_dir,path_procfits,flatfield_chip1_filename,flatfield_chip2_filename,flatfield_chip3_filename)\n",
    "        #compress_directory_fpack(base_dir+data_dir)\n",
    "        #compress_directory_fpack(path_rawfits)\n",
    "        #compress_directory_fpack(path_rawbias)\n",
    "        #compress_directory_fpack(path_procfits)\n",
    "        print('{:s} - Processing science data in {:s} complete.'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),data_dir))\n",
    "        reduction_log.write('{:s} - Processing science data in {:s} complete.\\n'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),data_dir))\n",
    "            \n",
    "    else:\n",
    "        print('{:s} - Appropriate flatfield images for {:s} not found.'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),path_rawfits))        \n",
    "        reduction_log.write('{:s} - Appropriate flatfield images for {:s} not found.\\n'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),path_rawfits))        \n",
    "            \n",
    "    return reduction_log\n",
    "\n",
    "\n",
    "def clean_up_science_data(path_rawfits,path_procfits,path_stats):\n",
    "    # Clean up data\n",
    "    move_reduced_science_data(path_rawfits,path_procfits,path_stats)\n",
    "    compress_directory_fpack(path_rawfits)\n",
    "    return None\n",
    "\n",
    "def clean_up_common_data(base_dir,data_dir,path_rawbias,path_procfits,path_stats):\n",
    "    # Clean up data\n",
    "    move_reduced_bias_data(path_rawbias,path_procfits,path_stats)\n",
    "    compress_directory_fpack(base_dir+data_dir)\n",
    "    compress_directory_fpack(path_rawbias)\n",
    "    if os.path.exists(path_procfits): compress_directory_fpack(path_procfits)\n",
    "    return None\n",
    "\n",
    "\n",
    "def process_images(base_dir,data_dir,path_rawfits,path_rawbias,path_procfits,path_stats,instr_id,filter_id,reduction_log):\n",
    "    print('\\n{:s} - Processing {:s}-band science data in {:s}...'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),filter_id,data_dir))\n",
    "    reduction_log.write('\\n{:s} - Processing {:s}-band science data in {:s}...\\n'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),filter_id,data_dir))\n",
    "\n",
    "    flatfield_chip1_filename,flatfield_chip2_filename,flatfield_chip3_filename = find_flatfield_files(base_dir,data_dir,instr_id,filter_id)\n",
    "\n",
    "    if flatfield_chip1_filename != 'none' and flatfield_chip2_filename != 'none' and flatfield_chip3_filename != 'none':\n",
    "        if not os.path.isdir(path_procfits): os.mkdir(path_procfits)\n",
    "        if not os.path.isdir(path_stats):    os.mkdir(path_stats)\n",
    "        # Process raw science fits files\n",
    "        print('\\n{:s} - Decompressing and splitting data files...'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S')))\n",
    "        reduction_log.write('{:s} - Decompressing and splitting data files...\\n')\n",
    "        os.chdir(path_rawfits)\n",
    "        decompress_directory_bzip2(path_rawfits)       # decompress downloaded GMOS files\n",
    "        decompress_directory_fpack(path_rawfits)       # decompress previously fpacked GMOS files\n",
    "        date_id = get_date_id()\n",
    "        create_stats_files(date_id,'scidata')    # create files to record image statistics\n",
    "        dim1, dim2 = split_extensions('scidata') # split science MEFs into individual FITS files\n",
    "        if instr_id == 'gmosn':\n",
    "            fix_gain_rdnoise_gmosn_hamamatsu()\n",
    "        elif instr_id == 'gmoss':\n",
    "            fix_gain_rdnoise_gmoss_hamamatsu()\n",
    "        compile_stats_files(date_id,'scidata')   # collect image stats of science files together and delete individual files\n",
    "\n",
    "        # decompress raw bias fits files\n",
    "        print('\\n{:s} - Decompressing, filtering, and splitting bias files...'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S')))\n",
    "        reduction_log.write('{:s} - Decompressing, filtering, and splitting bias files...\\n'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S')))\n",
    "        os.chdir(path_rawbias)\n",
    "        decompress_directory_bzip2(path_rawbias)       # decompress downloaded GMOS files\n",
    "        decompress_directory_fpack(path_rawbias)       # decompress previously fpacked GMOS files\n",
    "        remove_wrong_dimensions(dim1,dim2)       # find and retain bias frames matching data file binning\n",
    "        create_stats_files(date_id,'bias')       # create files to record image statistics\n",
    "        split_extensions('bias')                 # split bias MEFs into individual FITS files\n",
    "        if instr_id == 'gmosn':\n",
    "            fix_gain_rdnoise_gmosn_hamamatsu()\n",
    "        elif instr_id == 'gmoss':\n",
    "            fix_gain_rdnoise_gmoss_hamamatsu()\n",
    "        compile_stats_files(date_id,'bias')      # collect image stats of bias files together and delete individual files\n",
    "    \n",
    "        # perform overscan corrections and trim data for bias frames\n",
    "        os.chdir(path_rawbias)\n",
    "        overscan_and_trim()\n",
    "        bias_median_combine(date_id)\n",
    "\n",
    "        # Process science frames\n",
    "        os.chdir(path_rawfits)\n",
    "        overscan_and_trim()                                                    # Perform overscan correction and trim data\n",
    "        bias_correct(date_id,path_rawbias)                                      # Perform bias correction\n",
    "        concatenate_gmos_amps()                                                # Join science frames\n",
    "        flatfield_correction(base_dir,data_dir,flatfield_chip1_filename,flatfield_chip2_filename,flatfield_chip3_filename)  # Do flatfield corrections\n",
    "        cosmicray_cleaning()                                                   # Do cosmic ray cleaning\n",
    "        #fix_gmos_header_info(instr_id,filter_id)\n",
    "    \n",
    "        # Clean up data\n",
    "        move_reduced_data(path_rawfits,path_rawbias,path_procfits,path_stats)\n",
    "        #move_flatfield_images(base_dir,data_dir,path_procfits,flatfield_chip1_filename,flatfield_chip2_filename,flatfield_chip3_filename)\n",
    "        compress_directory_fpack(base_dir+data_dir)\n",
    "        compress_directory_fpack(path_rawfits)\n",
    "        compress_directory_fpack(path_rawbias)\n",
    "        compress_directory_fpack(path_procfits)\n",
    "        if instr_id == 'gmoss':\n",
    "            trim_gmoss_data_with_bad_amp(path_procfits)\n",
    "        print('{:s} - Processing science data in {:s} complete.'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),data_dir))\n",
    "        reduction_log.write('{:s} - Processing science data in {:s} complete.\\n'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),data_dir))\n",
    "        \n",
    "    else:\n",
    "        print('{:s} - Appropriate flatfield images for {:s} not found.'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),path_rawfits))        \n",
    "        reduction_log.write('{:s} - Appropriate flatfield images for {:s} not found.\\n'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),path_rawfits))        \n",
    "\n",
    "    return None\n",
    "\n",
    "\n",
    "print('Done.')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "def process_gemini_science_data(base_dir):\n",
    "    os.chdir(base_dir)\n",
    "    for data_dir in sorted(glob.glob('ut*_gemini?/')):\n",
    "    \n",
    "        if data_dir[-2:-1] == 'N':   instr_id = 'gmosn'\n",
    "        elif data_dir[-2:-1] == 'S': instr_id = 'gmoss'\n",
    "        else: instr_id = 'not recognized'\n",
    "\n",
    "        if instr_id == 'gmosn' or instr_id == 'gmoss':\n",
    "            os.chdir(base_dir + data_dir)\n",
    "            reduction_logfile = base_dir + data_dir + 'log_reduction_{:s}_{:s}_{:s}.txt'.format(data_dir[2:10],instr_id,datetime.datetime.today().strftime('%Y%m%d_%H%M%S'))\n",
    "            path_rawbias  = base_dir + data_dir + 'rawfits_bias/'\n",
    "            path_procfits = base_dir + data_dir + 'flatfits_pyt/'\n",
    "            path_stats    = base_dir + data_dir + 'stats/'\n",
    "            if not os.path.exists(path_procfits):\n",
    "                with open(reduction_logfile,'w') as reduction_log:\n",
    "                    if os.path.exists(path_rawbias):\n",
    "                        if len(os.listdir(path_rawbias)) > 0:\n",
    "                            if len(glob.glob('rawfits_?/')) > 0:\n",
    "                                print('\\n{:s} - Starting processing of data in {:s}...'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),data_dir))\n",
    "                                reduction_log.write('\\n{:s} - Starting processing of data in {:s}...\\n'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),data_dir))\n",
    "                                os.chdir(base_dir + data_dir)\n",
    "                                for dir_rawfits in sorted(glob.glob('rawfits_?/')):\n",
    "                                    os.chdir(base_dir + data_dir + dir_rawfits)\n",
    "                                    date_id = get_date_id()\n",
    "                                reduction_log = process_bias_data(path_rawbias,instr_id,date_id,reduction_log)\n",
    "                                os.chdir(base_dir + data_dir)\n",
    "                                for dir_rawfits in sorted(glob.glob('rawfits_?/')):\n",
    "                                    filter_id = dir_rawfits[-2:-1]\n",
    "                                    path_rawfits  = base_dir + data_dir + dir_rawfits\n",
    "                                    reduction_log = process_science_data(base_dir,data_dir,path_rawfits,path_rawbias,path_procfits,path_stats,instr_id,filter_id,reduction_log)\n",
    "                                    clean_up_science_data(path_rawfits,path_procfits,path_stats)\n",
    "                                clean_up_common_data(base_dir,data_dir,path_rawbias,path_procfits,path_stats)\n",
    "                                print('\\n{:s} - Processing of data in {:s} complete.'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),data_dir))\n",
    "                                reduction_log.write('{:s} - Processing of data in {:s} complete.\\n'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),data_dir))\n",
    "                            else:\n",
    "                                print('{:s} - Raw science data in {:s} not found.'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),data_dir))\n",
    "                                reduction_log.write('{:s} - Raw science data in {:s} not found.\\n'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),data_dir))\n",
    "                        else:\n",
    "                            print('{:s} - Bias directory in {:s} is empty.'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),data_dir))\n",
    "                            reduction_log.write('{:s} - Bias directory in {:s} is empty.\\n'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),data_dir))\n",
    "                    else:\n",
    "                        print('{:s} - Bias directory in {:s} not found.'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),data_dir))\n",
    "                        reduction_log.write('{:s} - Bias directory in {:s} not found.\\n'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),data_dir))\n",
    "            else:\n",
    "                print('{:s} - Science data in {:s} already processed.'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),data_dir))\n",
    "        else:\n",
    "            print('{:s} - Directory name format not recognized for {:s}.'.format(datetime.datetime.today().strftime('%Y-%m-%d %H:%M:%S'),data_dir))\n",
    "    return None\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2023-02-26 08:53:37 - Science data in ut20200813_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20200814_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20200822_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20200922_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20190404_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20190424_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20190803_geminiS/ already processed.\n",
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      "2023-02-26 08:53:37 - Science data in ut20190805_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20190806_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20190831_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20190920_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20190929_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20191006_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20191027_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20191115_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20191120_geminiS/ already processed.\n",
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      "2023-02-26 08:53:37 - Science data in ut20191217_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20200220_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20200223_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20200220_geminiS/ already processed.\n",
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      "2023-02-26 08:53:37 - Science data in ut20200801_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20200813_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20200817_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20200908_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20200910_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20201014_geminiN/ already processed.\n",
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      "2023-02-26 08:53:37 - Science data in ut20210103_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20210129_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20201027_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20201111_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20201112_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20201119_geminiS/ already processed.\n",
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      "2023-02-26 08:53:37 - Science data in ut20201212_geminiS/ already processed.\n",
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      "2023-02-26 08:53:37 - Science data in ut20210517_geminiN/ already processed.\n",
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      "2023-02-26 08:53:37 - Science data in ut20210613_geminiS/ already processed.\n",
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      "2023-02-26 08:53:37 - Science data in ut20220326_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220329_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220330_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220331_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220401_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220423_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220501_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220504_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220505_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220526_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220527_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220528_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220607_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220707_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220827_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220804_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220810_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220821_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220822_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220826_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220831_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220903_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220904_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220907_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220908_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220918_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220922_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220925_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220928_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221001_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221002_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221007_geminiN/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220826_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220827_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220828_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220923_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221022_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221023_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221027_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221118_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221119_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221122_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221217_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221218_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221219_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221224_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20230118_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20230125_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20230126_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20230127_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220828_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220905_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20220922_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221022_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221023_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221024_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221027_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221030_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221118_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221119_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221121_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221123_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221124_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221217_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20221218_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20230113_geminiS/ already processed.\n",
      "2023-02-26 08:53:37 - Science data in ut20230122_geminiS/ already processed.\n",
      "\n",
      "2023-02-26 08:53:37 - Starting processing of data in ut20230213_geminiS/...\n",
      "\n",
      "2023-02-26 08:53:37 - Processing bias-frame data in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230213_geminiS/rawfits_bias/...\n",
      "\n",
      "2023-02-26 08:53:37 - Decompressing, filtering, and splitting bias files...\n",
      ">>> Starting decompression of bz2 files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230213_geminiS/rawfits_bias/...\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">>> Decompression of bz2 files complete.\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230213_geminiS/rawfits_bias/...\n",
      ">>> Decompression of fz files complete.\n",
      "Splitting S20230113S0261.fits...\n",
      "Splitting S20230113S0262.fits...\n",
      "Splitting S20230113S0263.fits...\n",
      "Splitting S20230113S0264.fits...\n",
      "Splitting S20230113S0265.fits...\n",
      ">>> Gain and read noise updated in image headers.\n",
      "Starting image statistics output...\n",
      ">>> Image statistics output complete.\n",
      "Starting overscan correction and trimming...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">>> Overscan correction and trimming complete.\n",
      "Starting median combination of bias frames...\n",
      ">>> Median combination of bias frames complete.\n",
      "\n",
      "2023-02-26 08:54:08 - Processing bias-frame data in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230213_geminiS/rawfits_bias/ complete.\n",
      "\n",
      "2023-02-26 08:54:08 - Processing r-band science data in ut20230213_geminiS/...\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230213_geminiS/...\n",
      ">>> Decompression of fz files complete.\n",
      "\n",
      "2023-02-26 08:54:11 - Decompressing and splitting data files...\n",
      ">>> Starting decompression of bz2 files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230213_geminiS/rawfits_r/...\n",
      ">>> Decompression of bz2 files complete.\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230213_geminiS/rawfits_r/...\n",
      ">>> Decompression of fz files complete.\n",
      "Splitting S20230213S0218.fits...\n",
      "Splitting S20230213S0219.fits...\n",
      "Splitting S20230213S0220.fits...\n",
      "Splitting S20230213S0221.fits...\n",
      "Splitting S20230213S0222.fits...\n",
      "Splitting S20230213S0223.fits...\n",
      "Splitting S20230213S0224.fits...\n",
      "Splitting S20230213S0225.fits...\n",
      "Splitting S20230213S0226.fits...\n",
      "Splitting S20230213S0227.fits...\n",
      ">>> Gain and read noise updated in image headers.\n",
      "Starting image statistics output...\n",
      ">>> Image statistics output complete.\n",
      "Starting overscan correction and trimming...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">>> Overscan correction and trimming complete.\n",
      "Starting bias subtraction...\n",
      ">>> Bias subtraction complete.\n",
      ">>> Starting adjacent amp area concatenation...\n",
      ">>> Adjacent amp area concatenation complete.\n",
      "Starting flatfield correction...\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      ">>> Flatfield correction complete.\n",
      "Starting cosmic ray correction...\n",
      "Cosmic ray cleaning for n20230213.218.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 7 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4727 cosmic pixels (4727 new)\n",
      "Iteration 2\n",
      "855 cosmic pixels (750 new)\n",
      "Iteration 3\n",
      "285 cosmic pixels (234 new)\n",
      "Iteration 4\n",
      "113 cosmic pixels (68 new)\n",
      "Cosmic ray cleaning for n20230213.219.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 7 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4756 cosmic pixels (4756 new)\n",
      "Iteration 2\n",
      "903 cosmic pixels (797 new)\n",
      "Iteration 3\n",
      "209 cosmic pixels (148 new)\n",
      "Iteration 4\n",
      "94 cosmic pixels (43 new)\n",
      "Cosmic ray cleaning for n20230213.220.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 9 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4567 cosmic pixels (4567 new)\n",
      "Iteration 2\n",
      "841 cosmic pixels (759 new)\n",
      "Iteration 3\n",
      "238 cosmic pixels (186 new)\n",
      "Iteration 4\n",
      "124 cosmic pixels (84 new)\n",
      "Cosmic ray cleaning for n20230213.221.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 12 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4525 cosmic pixels (4525 new)\n",
      "Iteration 2\n",
      "829 cosmic pixels (742 new)\n",
      "Iteration 3\n",
      "180 cosmic pixels (142 new)\n",
      "Iteration 4\n",
      "73 cosmic pixels (46 new)\n",
      "Cosmic ray cleaning for n20230213.222.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 12 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4547 cosmic pixels (4547 new)\n",
      "Iteration 2\n",
      "927 cosmic pixels (798 new)\n",
      "Iteration 3\n",
      "218 cosmic pixels (167 new)\n",
      "Iteration 4\n",
      "112 cosmic pixels (62 new)\n",
      "Cosmic ray cleaning for n20230213.223.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 11 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4814 cosmic pixels (4814 new)\n",
      "Iteration 2\n",
      "932 cosmic pixels (802 new)\n",
      "Iteration 3\n",
      "250 cosmic pixels (178 new)\n",
      "Iteration 4\n",
      "117 cosmic pixels (58 new)\n",
      "Cosmic ray cleaning for n20230213.224.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 15 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4358 cosmic pixels (4358 new)\n",
      "Iteration 2\n",
      "843 cosmic pixels (718 new)\n",
      "Iteration 3\n",
      "241 cosmic pixels (174 new)\n",
      "Iteration 4\n",
      "118 cosmic pixels (66 new)\n",
      "Cosmic ray cleaning for n20230213.225.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 26 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4613 cosmic pixels (4613 new)\n",
      "Iteration 2\n",
      "1208 cosmic pixels (916 new)\n",
      "Iteration 3\n",
      "475 cosmic pixels (271 new)\n",
      "Iteration 4\n",
      "267 cosmic pixels (111 new)\n",
      "Cosmic ray cleaning for n20230213.226.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 26 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4333 cosmic pixels (4333 new)\n",
      "Iteration 2\n",
      "826 cosmic pixels (728 new)\n",
      "Iteration 3\n",
      "207 cosmic pixels (159 new)\n",
      "Iteration 4\n",
      "91 cosmic pixels (57 new)\n",
      "Cosmic ray cleaning for n20230213.227.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 23 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4413 cosmic pixels (4413 new)\n",
      "Iteration 2\n",
      "738 cosmic pixels (651 new)\n",
      "Iteration 3\n",
      "188 cosmic pixels (138 new)\n",
      "Iteration 4\n",
      "103 cosmic pixels (70 new)\n",
      "Cosmic ray cleaning for n20230213.218.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 17 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "23643 cosmic pixels (23643 new)\n",
      "Iteration 2\n",
      "4891 cosmic pixels (2400 new)\n",
      "Iteration 3\n",
      "2952 cosmic pixels (532 new)\n",
      "Iteration 4\n",
      "2628 cosmic pixels (181 new)\n",
      "Cosmic ray cleaning for n20230213.219.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 17 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "21715 cosmic pixels (21715 new)\n",
      "Iteration 2\n",
      "4291 cosmic pixels (1836 new)\n",
      "Iteration 3\n",
      "2807 cosmic pixels (401 new)\n",
      "Iteration 4\n",
      "2589 cosmic pixels (137 new)\n",
      "Cosmic ray cleaning for n20230213.220.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 15 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "21205 cosmic pixels (21205 new)\n",
      "Iteration 2\n",
      "4188 cosmic pixels (1735 new)\n",
      "Iteration 3\n",
      "2742 cosmic pixels (314 new)\n",
      "Iteration 4\n",
      "2578 cosmic pixels (124 new)\n",
      "Cosmic ray cleaning for n20230213.221.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 18 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "20639 cosmic pixels (20639 new)\n",
      "Iteration 2\n",
      "4068 cosmic pixels (1611 new)\n",
      "Iteration 3\n",
      "2791 cosmic pixels (373 new)\n",
      "Iteration 4\n",
      "2620 cosmic pixels (148 new)\n",
      "Cosmic ray cleaning for n20230213.222.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 28 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "23514 cosmic pixels (23514 new)\n",
      "Iteration 2\n",
      "4624 cosmic pixels (2143 new)\n",
      "Iteration 3\n",
      "2831 cosmic pixels (424 new)\n",
      "Iteration 4\n",
      "2570 cosmic pixels (136 new)\n",
      "Cosmic ray cleaning for n20230213.223.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 30 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "23613 cosmic pixels (23613 new)\n",
      "Iteration 2\n",
      "4502 cosmic pixels (2058 new)\n",
      "Iteration 3\n",
      "2855 cosmic pixels (447 new)\n",
      "Iteration 4\n",
      "2578 cosmic pixels (134 new)\n",
      "Cosmic ray cleaning for n20230213.224.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 34 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "23010 cosmic pixels (23010 new)\n",
      "Iteration 2\n",
      "4342 cosmic pixels (1895 new)\n",
      "Iteration 3\n",
      "2832 cosmic pixels (434 new)\n",
      "Iteration 4\n",
      "2576 cosmic pixels (148 new)\n",
      "Cosmic ray cleaning for n20230213.225.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 46 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "28227 cosmic pixels (28227 new)\n",
      "Iteration 2\n",
      "5479 cosmic pixels (2786 new)\n",
      "Iteration 3\n",
      "3237 cosmic pixels (625 new)\n",
      "Iteration 4\n",
      "2822 cosmic pixels (214 new)\n",
      "Cosmic ray cleaning for n20230213.226.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 54 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "28792 cosmic pixels (28792 new)\n",
      "Iteration 2\n",
      "5690 cosmic pixels (2924 new)\n",
      "Iteration 3\n",
      "3394 cosmic pixels (691 new)\n",
      "Iteration 4\n",
      "2963 cosmic pixels (256 new)\n",
      "Cosmic ray cleaning for n20230213.227.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 48 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "28614 cosmic pixels (28614 new)\n",
      "Iteration 2\n",
      "5591 cosmic pixels (2872 new)\n",
      "Iteration 3\n",
      "3239 cosmic pixels (621 new)\n",
      "Iteration 4\n",
      "2848 cosmic pixels (209 new)\n",
      "Cosmic ray cleaning for n20230213.218.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 3 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4327 cosmic pixels (4327 new)\n",
      "Iteration 2\n",
      "795 cosmic pixels (711 new)\n",
      "Iteration 3\n",
      "206 cosmic pixels (139 new)\n",
      "Iteration 4\n",
      "132 cosmic pixels (66 new)\n",
      "Cosmic ray cleaning for n20230213.219.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 3 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4210 cosmic pixels (4210 new)\n",
      "Iteration 2\n",
      "710 cosmic pixels (620 new)\n",
      "Iteration 3\n",
      "215 cosmic pixels (143 new)\n",
      "Iteration 4\n",
      "131 cosmic pixels (55 new)\n",
      "Cosmic ray cleaning for n20230213.220.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 6 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4306 cosmic pixels (4306 new)\n",
      "Iteration 2\n",
      "792 cosmic pixels (706 new)\n",
      "Iteration 3\n",
      "170 cosmic pixels (122 new)\n",
      "Iteration 4\n",
      "84 cosmic pixels (37 new)\n",
      "Cosmic ray cleaning for n20230213.221.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 4 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4256 cosmic pixels (4256 new)\n",
      "Iteration 2\n",
      "753 cosmic pixels (659 new)\n",
      "Iteration 3\n",
      "188 cosmic pixels (130 new)\n",
      "Iteration 4\n",
      "138 cosmic pixels (70 new)\n",
      "Cosmic ray cleaning for n20230213.222.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 13 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4668 cosmic pixels (4668 new)\n",
      "Iteration 2\n",
      "763 cosmic pixels (673 new)\n",
      "Iteration 3\n",
      "183 cosmic pixels (140 new)\n",
      "Iteration 4\n",
      "70 cosmic pixels (35 new)\n",
      "Cosmic ray cleaning for n20230213.223.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 10 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4174 cosmic pixels (4174 new)\n",
      "Iteration 2\n",
      "737 cosmic pixels (629 new)\n",
      "Iteration 3\n",
      "192 cosmic pixels (134 new)\n",
      "Iteration 4\n",
      "71 cosmic pixels (29 new)\n",
      "Cosmic ray cleaning for n20230213.224.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 13 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4271 cosmic pixels (4271 new)\n",
      "Iteration 2\n",
      "749 cosmic pixels (668 new)\n",
      "Iteration 3\n",
      "155 cosmic pixels (110 new)\n",
      "Iteration 4\n",
      "76 cosmic pixels (32 new)\n",
      "Cosmic ray cleaning for n20230213.225.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 21 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4129 cosmic pixels (4129 new)\n",
      "Iteration 2\n",
      "742 cosmic pixels (657 new)\n",
      "Iteration 3\n",
      "168 cosmic pixels (116 new)\n",
      "Iteration 4\n",
      "86 cosmic pixels (29 new)\n",
      "Cosmic ray cleaning for n20230213.226.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 27 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "6409 cosmic pixels (6409 new)\n",
      "Iteration 2\n",
      "3937 cosmic pixels (2072 new)\n",
      "Iteration 3\n",
      "3421 cosmic pixels (909 new)\n",
      "Iteration 4\n",
      "3363 cosmic pixels (433 new)\n",
      "Cosmic ray cleaning for n20230213.227.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 23 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4189 cosmic pixels (4189 new)\n",
      "Iteration 2\n",
      "714 cosmic pixels (650 new)\n",
      "Iteration 3\n",
      "167 cosmic pixels (125 new)\n",
      "Iteration 4\n",
      "70 cosmic pixels (36 new)\n",
      ">>> Cosmic ray correction complete.\n",
      "2023-02-26 09:05:31 - Processing science data in ut20230213_geminiS/ complete.\n",
      ">>> Processed data moved to output directory.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230213_geminiS/rawfits_r/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Processed bias data moved to output directory.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230213_geminiS/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230213_geminiS/rawfits_bias/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230213_geminiS/flatfits_pyt/...\n",
      ">>> fpack compression of FITS files complete.\n",
      "\n",
      "2023-02-26 09:05:59 - Processing of data in ut20230213_geminiS/ complete.\n",
      "\n",
      "2023-02-26 09:05:59 - Starting processing of data in ut20230215_geminiS/...\n",
      "\n",
      "2023-02-26 09:05:59 - Processing bias-frame data in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230215_geminiS/rawfits_bias/...\n",
      "\n",
      "2023-02-26 09:05:59 - Decompressing, filtering, and splitting bias files...\n",
      ">>> Starting decompression of bz2 files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230215_geminiS/rawfits_bias/...\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">>> Decompression of bz2 files complete.\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230215_geminiS/rawfits_bias/...\n",
      ">>> Decompression of fz files complete.\n",
      "Splitting S20230215S0126.fits...\n",
      "Splitting S20230215S0127.fits...\n",
      "Splitting S20230215S0128.fits...\n",
      "Splitting S20230215S0129.fits...\n",
      "Splitting S20230215S0130.fits...\n",
      ">>> Gain and read noise updated in image headers.\n",
      "Starting image statistics output...\n",
      ">>> Image statistics output complete.\n",
      "Starting overscan correction and trimming...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">>> Overscan correction and trimming complete.\n",
      "Starting median combination of bias frames...\n",
      ">>> Median combination of bias frames complete.\n",
      "\n",
      "2023-02-26 09:06:27 - Processing bias-frame data in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230215_geminiS/rawfits_bias/ complete.\n",
      "\n",
      "2023-02-26 09:06:27 - Processing r-band science data in ut20230215_geminiS/...\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230215_geminiS/...\n",
      ">>> Decompression of fz files complete.\n",
      "\n",
      "2023-02-26 09:06:30 - Decompressing and splitting data files...\n",
      ">>> Starting decompression of bz2 files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230215_geminiS/rawfits_r/...\n",
      ">>> Decompression of bz2 files complete.\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230215_geminiS/rawfits_r/...\n",
      ">>> Decompression of fz files complete.\n",
      "Splitting S20230215S0099.fits...\n",
      "Splitting S20230215S0100.fits...\n",
      "Splitting S20230215S0101.fits...\n",
      ">>> Gain and read noise updated in image headers.\n",
      "Starting image statistics output...\n",
      ">>> Image statistics output complete.\n",
      "Starting overscan correction and trimming...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">>> Overscan correction and trimming complete.\n",
      "Starting bias subtraction...\n",
      ">>> Bias subtraction complete.\n",
      ">>> Starting adjacent amp area concatenation...\n",
      ">>> Adjacent amp area concatenation complete.\n",
      "Starting flatfield correction...\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      ">>> Flatfield correction complete.\n",
      "Starting cosmic ray correction...\n",
      "Cosmic ray cleaning for n20230215.099.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 4 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4477 cosmic pixels (4477 new)\n",
      "Iteration 2\n",
      "827 cosmic pixels (709 new)\n",
      "Iteration 3\n",
      "246 cosmic pixels (180 new)\n",
      "Iteration 4\n",
      "113 cosmic pixels (56 new)\n",
      "Cosmic ray cleaning for n20230215.100.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 6 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4364 cosmic pixels (4364 new)\n",
      "Iteration 2\n",
      "826 cosmic pixels (740 new)\n",
      "Iteration 3\n",
      "227 cosmic pixels (180 new)\n",
      "Iteration 4\n",
      "84 cosmic pixels (52 new)\n",
      "Cosmic ray cleaning for n20230215.101.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 3 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4557 cosmic pixels (4557 new)\n",
      "Iteration 2\n",
      "787 cosmic pixels (696 new)\n",
      "Iteration 3\n",
      "220 cosmic pixels (169 new)\n",
      "Iteration 4\n",
      "94 cosmic pixels (61 new)\n",
      "Cosmic ray cleaning for n20230215.099.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 16 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "15375 cosmic pixels (15375 new)\n",
      "Iteration 2\n",
      "11956 cosmic pixels (5538 new)\n",
      "Iteration 3\n",
      "10720 cosmic pixels (2617 new)\n",
      "Iteration 4\n",
      "9833 cosmic pixels (1152 new)\n",
      "Cosmic ray cleaning for n20230215.100.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 15 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "15474 cosmic pixels (15474 new)\n",
      "Iteration 2\n",
      "13113 cosmic pixels (5303 new)\n",
      "Iteration 3\n",
      "11675 cosmic pixels (2542 new)\n",
      "Iteration 4\n",
      "10905 cosmic pixels (1242 new)\n",
      "Cosmic ray cleaning for n20230215.101.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 14 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "11391 cosmic pixels (11391 new)\n",
      "Iteration 2\n",
      "8916 cosmic pixels (4182 new)\n",
      "Iteration 3\n",
      "7923 cosmic pixels (1880 new)\n",
      "Iteration 4\n",
      "7387 cosmic pixels (906 new)\n",
      "Cosmic ray cleaning for n20230215.099.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 3 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4609 cosmic pixels (4609 new)\n",
      "Iteration 2\n",
      "735 cosmic pixels (663 new)\n",
      "Iteration 3\n",
      "178 cosmic pixels (133 new)\n",
      "Iteration 4\n",
      "76 cosmic pixels (38 new)\n",
      "Cosmic ray cleaning for n20230215.100.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 2 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4112 cosmic pixels (4112 new)\n",
      "Iteration 2\n",
      "651 cosmic pixels (588 new)\n",
      "Iteration 3\n",
      "177 cosmic pixels (119 new)\n",
      "Iteration 4\n",
      "88 cosmic pixels (34 new)\n",
      "Cosmic ray cleaning for n20230215.101.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 3 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4411 cosmic pixels (4411 new)\n",
      "Iteration 2\n",
      "755 cosmic pixels (677 new)\n",
      "Iteration 3\n",
      "184 cosmic pixels (123 new)\n",
      "Iteration 4\n",
      "92 cosmic pixels (34 new)\n",
      ">>> Cosmic ray correction complete.\n",
      "2023-02-26 09:09:27 - Processing science data in ut20230215_geminiS/ complete.\n",
      ">>> Processed data moved to output directory.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230215_geminiS/rawfits_r/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Processed bias data moved to output directory.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230215_geminiS/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230215_geminiS/rawfits_bias/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230215_geminiS/flatfits_pyt/...\n",
      ">>> fpack compression of FITS files complete.\n",
      "\n",
      "2023-02-26 09:09:40 - Processing of data in ut20230215_geminiS/ complete.\n",
      "\n",
      "2023-02-26 09:09:40 - Starting processing of data in ut20230216_geminiS/...\n",
      "\n",
      "2023-02-26 09:09:40 - Processing bias-frame data in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230216_geminiS/rawfits_bias/...\n",
      "\n",
      "2023-02-26 09:09:40 - Decompressing, filtering, and splitting bias files...\n",
      ">>> Starting decompression of bz2 files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230216_geminiS/rawfits_bias/...\n",
      ">>> Decompression of bz2 files complete.\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230216_geminiS/rawfits_bias/...\n",
      ">>> Decompression of fz files complete.\n",
      "Splitting S20230216S0074.fits...\n",
      "Splitting S20230216S0075.fits...\n",
      "Splitting S20230216S0076.fits...\n",
      "Splitting S20230216S0077.fits...\n",
      "Splitting S20230216S0078.fits...\n",
      ">>> Gain and read noise updated in image headers.\n",
      "Starting image statistics output...\n",
      ">>> Image statistics output complete.\n",
      "Starting overscan correction and trimming...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">>> Overscan correction and trimming complete.\n",
      "Starting median combination of bias frames...\n",
      ">>> Median combination of bias frames complete.\n",
      "\n",
      "2023-02-26 09:10:11 - Processing bias-frame data in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230216_geminiS/rawfits_bias/ complete.\n",
      "\n",
      "2023-02-26 09:10:11 - Processing r-band science data in ut20230216_geminiS/...\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230216_geminiS/...\n",
      ">>> Decompression of fz files complete.\n",
      "\n",
      "2023-02-26 09:10:13 - Decompressing and splitting data files...\n",
      ">>> Starting decompression of bz2 files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230216_geminiS/rawfits_r/...\n",
      ">>> Decompression of bz2 files complete.\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230216_geminiS/rawfits_r/...\n",
      ">>> Decompression of fz files complete.\n",
      "Splitting S20230216S0012.fits...\n",
      "Splitting S20230216S0013.fits...\n",
      "Splitting S20230216S0014.fits...\n",
      "Splitting S20230216S0015.fits...\n",
      "Splitting S20230216S0016.fits...\n",
      "Splitting S20230216S0017.fits...\n",
      "Splitting S20230216S0018.fits...\n",
      ">>> Gain and read noise updated in image headers.\n",
      "Starting image statistics output...\n",
      ">>> Image statistics output complete.\n",
      "Starting overscan correction and trimming...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">>> Overscan correction and trimming complete.\n",
      "Starting bias subtraction...\n",
      ">>> Bias subtraction complete.\n",
      ">>> Starting adjacent amp area concatenation...\n",
      ">>> Adjacent amp area concatenation complete.\n",
      "Starting flatfield correction...\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      ">>> Flatfield correction complete.\n",
      "Starting cosmic ray correction...\n",
      "Cosmic ray cleaning for n20230216.012.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 7 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4490 cosmic pixels (4490 new)\n",
      "Iteration 2\n",
      "878 cosmic pixels (773 new)\n",
      "Iteration 3\n",
      "244 cosmic pixels (173 new)\n",
      "Iteration 4\n",
      "123 cosmic pixels (74 new)\n",
      "Cosmic ray cleaning for n20230216.013.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 5 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4616 cosmic pixels (4616 new)\n",
      "Iteration 2\n",
      "887 cosmic pixels (764 new)\n",
      "Iteration 3\n",
      "221 cosmic pixels (165 new)\n",
      "Iteration 4\n",
      "87 cosmic pixels (49 new)\n",
      "Cosmic ray cleaning for n20230216.014.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 6 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4562 cosmic pixels (4562 new)\n",
      "Iteration 2\n",
      "846 cosmic pixels (746 new)\n",
      "Iteration 3\n",
      "196 cosmic pixels (141 new)\n",
      "Iteration 4\n",
      "66 cosmic pixels (38 new)\n",
      "Cosmic ray cleaning for n20230216.015.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 4 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4179 cosmic pixels (4179 new)\n",
      "Iteration 2\n",
      "801 cosmic pixels (637 new)\n",
      "Iteration 3\n",
      "287 cosmic pixels (183 new)\n",
      "Iteration 4\n",
      "160 cosmic pixels (73 new)\n",
      "Cosmic ray cleaning for n20230216.016.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 4 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4681 cosmic pixels (4681 new)\n",
      "Iteration 2\n",
      "772 cosmic pixels (639 new)\n",
      "Iteration 3\n",
      "195 cosmic pixels (122 new)\n",
      "Iteration 4\n",
      "98 cosmic pixels (33 new)\n",
      "Cosmic ray cleaning for n20230216.017.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 4 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4262 cosmic pixels (4262 new)\n",
      "Iteration 2\n",
      "852 cosmic pixels (708 new)\n",
      "Iteration 3\n",
      "242 cosmic pixels (171 new)\n",
      "Iteration 4\n",
      "140 cosmic pixels (70 new)\n",
      "Cosmic ray cleaning for n20230216.018.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 4 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4410 cosmic pixels (4410 new)\n",
      "Iteration 2\n",
      "848 cosmic pixels (691 new)\n",
      "Iteration 3\n",
      "311 cosmic pixels (200 new)\n",
      "Iteration 4\n",
      "141 cosmic pixels (73 new)\n",
      "Cosmic ray cleaning for n20230216.012.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 17 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "18984 cosmic pixels (18984 new)\n",
      "Iteration 2\n",
      "16570 cosmic pixels (6209 new)\n",
      "Iteration 3\n",
      "15173 cosmic pixels (3069 new)\n",
      "Iteration 4\n",
      "14232 cosmic pixels (1521 new)\n",
      "Cosmic ray cleaning for n20230216.013.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 18 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "13674 cosmic pixels (13674 new)\n",
      "Iteration 2\n",
      "11014 cosmic pixels (4818 new)\n",
      "Iteration 3\n",
      "9993 cosmic pixels (2280 new)\n",
      "Iteration 4\n",
      "9305 cosmic pixels (1053 new)\n",
      "Cosmic ray cleaning for n20230216.014.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 18 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "14754 cosmic pixels (14754 new)\n",
      "Iteration 2\n",
      "11935 cosmic pixels (5211 new)\n",
      "Iteration 3\n",
      "10724 cosmic pixels (2467 new)\n",
      "Iteration 4\n",
      "10051 cosmic pixels (1184 new)\n",
      "Cosmic ray cleaning for n20230216.015.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 16 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "14919 cosmic pixels (14919 new)\n",
      "Iteration 2\n",
      "12371 cosmic pixels (5284 new)\n",
      "Iteration 3\n",
      "11446 cosmic pixels (2562 new)\n",
      "Iteration 4\n",
      "10677 cosmic pixels (1239 new)\n",
      "Cosmic ray cleaning for n20230216.016.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 13 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "18547 cosmic pixels (18547 new)\n",
      "Iteration 2\n",
      "16173 cosmic pixels (6308 new)\n",
      "Iteration 3\n",
      "15207 cosmic pixels (3112 new)\n",
      "Iteration 4\n",
      "14269 cosmic pixels (1576 new)\n",
      "Cosmic ray cleaning for n20230216.017.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 17 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "17110 cosmic pixels (17110 new)\n",
      "Iteration 2\n",
      "14068 cosmic pixels (5946 new)\n",
      "Iteration 3\n",
      "13001 cosmic pixels (2894 new)\n",
      "Iteration 4\n",
      "12136 cosmic pixels (1456 new)\n",
      "Cosmic ray cleaning for n20230216.018.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 16 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "14706 cosmic pixels (14706 new)\n",
      "Iteration 2\n",
      "12451 cosmic pixels (5105 new)\n",
      "Iteration 3\n",
      "11584 cosmic pixels (2606 new)\n",
      "Iteration 4\n",
      "10810 cosmic pixels (1278 new)\n",
      "Cosmic ray cleaning for n20230216.012.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Building mask of saturated stars ...\n",
      "We have 2 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4340 cosmic pixels (4340 new)\n",
      "Iteration 2\n",
      "796 cosmic pixels (706 new)\n",
      "Iteration 3\n",
      "231 cosmic pixels (148 new)\n",
      "Iteration 4\n",
      "98 cosmic pixels (38 new)\n",
      "Cosmic ray cleaning for n20230216.013.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 1 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4626 cosmic pixels (4626 new)\n",
      "Iteration 2\n",
      "855 cosmic pixels (754 new)\n",
      "Iteration 3\n",
      "204 cosmic pixels (143 new)\n",
      "Iteration 4\n",
      "93 cosmic pixels (44 new)\n",
      "Cosmic ray cleaning for n20230216.014.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 1 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4572 cosmic pixels (4572 new)\n",
      "Iteration 2\n",
      "844 cosmic pixels (751 new)\n",
      "Iteration 3\n",
      "178 cosmic pixels (117 new)\n",
      "Iteration 4\n",
      "69 cosmic pixels (25 new)\n",
      "Cosmic ray cleaning for n20230216.015.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 1 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "3959 cosmic pixels (3959 new)\n",
      "Iteration 2\n",
      "694 cosmic pixels (588 new)\n",
      "Iteration 3\n",
      "177 cosmic pixels (121 new)\n",
      "Iteration 4\n",
      "79 cosmic pixels (39 new)\n",
      "Cosmic ray cleaning for n20230216.016.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 2 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4217 cosmic pixels (4217 new)\n",
      "Iteration 2\n",
      "814 cosmic pixels (727 new)\n",
      "Iteration 3\n",
      "183 cosmic pixels (133 new)\n",
      "Iteration 4\n",
      "65 cosmic pixels (30 new)\n",
      "Cosmic ray cleaning for n20230216.017.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 1 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "3954 cosmic pixels (3954 new)\n",
      "Iteration 2\n",
      "650 cosmic pixels (581 new)\n",
      "Iteration 3\n",
      "135 cosmic pixels (92 new)\n",
      "Iteration 4\n",
      "49 cosmic pixels (23 new)\n",
      "Cosmic ray cleaning for n20230216.018.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 2 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4229 cosmic pixels (4229 new)\n",
      "Iteration 2\n",
      "712 cosmic pixels (601 new)\n",
      "Iteration 3\n",
      "190 cosmic pixels (135 new)\n",
      "Iteration 4\n",
      "73 cosmic pixels (30 new)\n",
      ">>> Cosmic ray correction complete.\n",
      "2023-02-26 09:17:09 - Processing science data in ut20230216_geminiS/ complete.\n",
      ">>> Processed data moved to output directory.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230216_geminiS/rawfits_r/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Processed bias data moved to output directory.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230216_geminiS/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230216_geminiS/rawfits_bias/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230216_geminiS/flatfits_pyt/...\n",
      ">>> fpack compression of FITS files complete.\n",
      "\n",
      "2023-02-26 09:17:31 - Processing of data in ut20230216_geminiS/ complete.\n",
      "\n",
      "2023-02-26 09:17:31 - Starting processing of data in ut20230217_geminiS/...\n",
      "\n",
      "2023-02-26 09:17:31 - Processing bias-frame data in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230217_geminiS/rawfits_bias/...\n",
      "\n",
      "2023-02-26 09:17:31 - Decompressing, filtering, and splitting bias files...\n",
      ">>> Starting decompression of bz2 files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230217_geminiS/rawfits_bias/...\n",
      ">>> Decompression of bz2 files complete.\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230217_geminiS/rawfits_bias/...\n",
      ">>> Decompression of fz files complete.\n",
      "Splitting S20230217S0130.fits...\n",
      "Splitting S20230217S0131.fits...\n",
      "Splitting S20230217S0132.fits...\n",
      "Splitting S20230217S0133.fits...\n",
      "Splitting S20230217S0134.fits...\n",
      ">>> Gain and read noise updated in image headers.\n",
      "Starting image statistics output...\n",
      ">>> Image statistics output complete.\n",
      "Starting overscan correction and trimming...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">>> Overscan correction and trimming complete.\n",
      "Starting median combination of bias frames...\n",
      ">>> Median combination of bias frames complete.\n",
      "\n",
      "2023-02-26 09:17:57 - Processing bias-frame data in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230217_geminiS/rawfits_bias/ complete.\n",
      "\n",
      "2023-02-26 09:17:57 - Processing r-band science data in ut20230217_geminiS/...\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230217_geminiS/...\n",
      ">>> Decompression of fz files complete.\n",
      "\n",
      "2023-02-26 09:17:59 - Decompressing and splitting data files...\n",
      ">>> Starting decompression of bz2 files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230217_geminiS/rawfits_r/...\n",
      ">>> Decompression of bz2 files complete.\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230217_geminiS/rawfits_r/...\n",
      ">>> Decompression of fz files complete.\n",
      "Splitting S20230217S0040.fits...\n",
      "Splitting S20230217S0041.fits...\n",
      "Splitting S20230217S0042.fits...\n",
      "Splitting S20230217S0043.fits...\n",
      "Splitting S20230217S0044.fits...\n",
      "Splitting S20230217S0045.fits...\n",
      "Splitting S20230217S0046.fits...\n",
      "Splitting S20230217S0047.fits...\n",
      "Splitting S20230217S0048.fits...\n",
      "Splitting S20230217S0049.fits...\n",
      ">>> Gain and read noise updated in image headers.\n",
      "Starting image statistics output...\n",
      ">>> Image statistics output complete.\n",
      "Starting overscan correction and trimming...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">>> Overscan correction and trimming complete.\n",
      "Starting bias subtraction...\n",
      ">>> Bias subtraction complete.\n",
      ">>> Starting adjacent amp area concatenation...\n",
      ">>> Adjacent amp area concatenation complete.\n",
      "Starting flatfield correction...\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      ">>> Flatfield correction complete.\n",
      "Starting cosmic ray correction...\n",
      "Cosmic ray cleaning for n20230217.040.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 7 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4681 cosmic pixels (4681 new)\n",
      "Iteration 2\n",
      "884 cosmic pixels (773 new)\n",
      "Iteration 3\n",
      "278 cosmic pixels (208 new)\n",
      "Iteration 4\n",
      "97 cosmic pixels (50 new)\n",
      "Cosmic ray cleaning for n20230217.041.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 7 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4491 cosmic pixels (4491 new)\n",
      "Iteration 2\n",
      "778 cosmic pixels (664 new)\n",
      "Iteration 3\n",
      "208 cosmic pixels (141 new)\n",
      "Iteration 4\n",
      "97 cosmic pixels (46 new)\n",
      "Cosmic ray cleaning for n20230217.042.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 5 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4467 cosmic pixels (4467 new)\n",
      "Iteration 2\n",
      "822 cosmic pixels (713 new)\n",
      "Iteration 3\n",
      "240 cosmic pixels (178 new)\n",
      "Iteration 4\n",
      "94 cosmic pixels (59 new)\n",
      "Cosmic ray cleaning for n20230217.043.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 4 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4392 cosmic pixels (4392 new)\n",
      "Iteration 2\n",
      "929 cosmic pixels (769 new)\n",
      "Iteration 3\n",
      "265 cosmic pixels (175 new)\n",
      "Iteration 4\n",
      "122 cosmic pixels (50 new)\n",
      "Cosmic ray cleaning for n20230217.044.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 3 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4350 cosmic pixels (4350 new)\n",
      "Iteration 2\n",
      "872 cosmic pixels (729 new)\n",
      "Iteration 3\n",
      "269 cosmic pixels (160 new)\n",
      "Iteration 4\n",
      "141 cosmic pixels (67 new)\n",
      "Cosmic ray cleaning for n20230217.045.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 4 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4705 cosmic pixels (4705 new)\n",
      "Iteration 2\n",
      "920 cosmic pixels (777 new)\n",
      "Iteration 3\n",
      "321 cosmic pixels (224 new)\n",
      "Iteration 4\n",
      "138 cosmic pixels (67 new)\n",
      "Cosmic ray cleaning for n20230217.046.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 3 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4644 cosmic pixels (4644 new)\n",
      "Iteration 2\n",
      "1011 cosmic pixels (834 new)\n",
      "Iteration 3\n",
      "326 cosmic pixels (213 new)\n",
      "Iteration 4\n",
      "133 cosmic pixels (53 new)\n",
      "Cosmic ray cleaning for n20230217.047.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 6 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4712 cosmic pixels (4712 new)\n",
      "Iteration 2\n",
      "830 cosmic pixels (713 new)\n",
      "Iteration 3\n",
      "187 cosmic pixels (129 new)\n",
      "Iteration 4\n",
      "87 cosmic pixels (45 new)\n",
      "Cosmic ray cleaning for n20230217.048.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 5 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4423 cosmic pixels (4423 new)\n",
      "Iteration 2\n",
      "869 cosmic pixels (771 new)\n",
      "Iteration 3\n",
      "207 cosmic pixels (158 new)\n",
      "Iteration 4\n",
      "73 cosmic pixels (39 new)\n",
      "Cosmic ray cleaning for n20230217.049.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 8 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4727 cosmic pixels (4727 new)\n",
      "Iteration 2\n",
      "846 cosmic pixels (749 new)\n",
      "Iteration 3\n",
      "208 cosmic pixels (154 new)\n",
      "Iteration 4\n",
      "98 cosmic pixels (51 new)\n",
      "Cosmic ray cleaning for n20230217.040.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 18 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "15485 cosmic pixels (15485 new)\n",
      "Iteration 2\n",
      "12943 cosmic pixels (5206 new)\n",
      "Iteration 3\n",
      "12024 cosmic pixels (2688 new)\n",
      "Iteration 4\n",
      "11144 cosmic pixels (1271 new)\n",
      "Cosmic ray cleaning for n20230217.041.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 15 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "13608 cosmic pixels (13608 new)\n",
      "Iteration 2\n",
      "11009 cosmic pixels (4598 new)\n",
      "Iteration 3\n",
      "10218 cosmic pixels (2343 new)\n",
      "Iteration 4\n",
      "9539 cosmic pixels (1140 new)\n",
      "Cosmic ray cleaning for n20230217.042.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 19 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "15190 cosmic pixels (15190 new)\n",
      "Iteration 2\n",
      "12200 cosmic pixels (5156 new)\n",
      "Iteration 3\n",
      "11040 cosmic pixels (2518 new)\n",
      "Iteration 4\n",
      "10280 cosmic pixels (1196 new)\n",
      "Cosmic ray cleaning for n20230217.043.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 12 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "14784 cosmic pixels (14784 new)\n",
      "Iteration 2\n",
      "12541 cosmic pixels (5039 new)\n",
      "Iteration 3\n",
      "11669 cosmic pixels (2594 new)\n",
      "Iteration 4\n",
      "10945 cosmic pixels (1347 new)\n",
      "Cosmic ray cleaning for n20230217.044.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 10 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "18082 cosmic pixels (18082 new)\n",
      "Iteration 2\n",
      "15570 cosmic pixels (5942 new)\n",
      "Iteration 3\n",
      "14634 cosmic pixels (3090 new)\n",
      "Iteration 4\n",
      "13811 cosmic pixels (1635 new)\n",
      "Cosmic ray cleaning for n20230217.045.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 13 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "17563 cosmic pixels (17563 new)\n",
      "Iteration 2\n",
      "14861 cosmic pixels (5748 new)\n",
      "Iteration 3\n",
      "13861 cosmic pixels (2996 new)\n",
      "Iteration 4\n",
      "12932 cosmic pixels (1547 new)\n",
      "Cosmic ray cleaning for n20230217.046.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 11 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "15632 cosmic pixels (15632 new)\n",
      "Iteration 2\n",
      "13112 cosmic pixels (5263 new)\n",
      "Iteration 3\n",
      "12233 cosmic pixels (2738 new)\n",
      "Iteration 4\n",
      "11291 cosmic pixels (1352 new)\n",
      "Cosmic ray cleaning for n20230217.047.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 18 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "15918 cosmic pixels (15918 new)\n",
      "Iteration 2\n",
      "13005 cosmic pixels (5250 new)\n",
      "Iteration 3\n",
      "12034 cosmic pixels (2737 new)\n",
      "Iteration 4\n",
      "11086 cosmic pixels (1237 new)\n",
      "Cosmic ray cleaning for n20230217.048.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 19 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "14280 cosmic pixels (14280 new)\n",
      "Iteration 2\n",
      "11400 cosmic pixels (4865 new)\n",
      "Iteration 3\n",
      "10495 cosmic pixels (2406 new)\n",
      "Iteration 4\n",
      "9698 cosmic pixels (1106 new)\n",
      "Cosmic ray cleaning for n20230217.049.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 17 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "13542 cosmic pixels (13542 new)\n",
      "Iteration 2\n",
      "11057 cosmic pixels (4659 new)\n",
      "Iteration 3\n",
      "10161 cosmic pixels (2316 new)\n",
      "Iteration 4\n",
      "9422 cosmic pixels (1069 new)\n",
      "Cosmic ray cleaning for n20230217.040.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 4 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4432 cosmic pixels (4432 new)\n",
      "Iteration 2\n",
      "783 cosmic pixels (701 new)\n",
      "Iteration 3\n",
      "205 cosmic pixels (163 new)\n",
      "Iteration 4\n",
      "88 cosmic pixels (51 new)\n",
      "Cosmic ray cleaning for n20230217.041.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 5 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4600 cosmic pixels (4600 new)\n",
      "Iteration 2\n",
      "757 cosmic pixels (667 new)\n",
      "Iteration 3\n",
      "180 cosmic pixels (131 new)\n",
      "Iteration 4\n",
      "65 cosmic pixels (29 new)\n",
      "Cosmic ray cleaning for n20230217.042.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 5 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4610 cosmic pixels (4610 new)\n",
      "Iteration 2\n",
      "805 cosmic pixels (695 new)\n",
      "Iteration 3\n",
      "176 cosmic pixels (130 new)\n",
      "Iteration 4\n",
      "46 cosmic pixels (12 new)\n",
      "Cosmic ray cleaning for n20230217.043.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 1 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4361 cosmic pixels (4361 new)\n",
      "Iteration 2\n",
      "755 cosmic pixels (658 new)\n",
      "Iteration 3\n",
      "186 cosmic pixels (139 new)\n",
      "Iteration 4\n",
      "57 cosmic pixels (21 new)\n",
      "Cosmic ray cleaning for n20230217.044.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 0 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4121 cosmic pixels (4121 new)\n",
      "Iteration 2\n",
      "709 cosmic pixels (587 new)\n",
      "Iteration 3\n",
      "224 cosmic pixels (158 new)\n",
      "Iteration 4\n",
      "125 cosmic pixels (55 new)\n",
      "Cosmic ray cleaning for n20230217.045.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 1 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4219 cosmic pixels (4219 new)\n",
      "Iteration 2\n",
      "711 cosmic pixels (605 new)\n",
      "Iteration 3\n",
      "189 cosmic pixels (120 new)\n",
      "Iteration 4\n",
      "65 cosmic pixels (20 new)\n",
      "Cosmic ray cleaning for n20230217.046.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 1 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4212 cosmic pixels (4212 new)\n",
      "Iteration 2\n",
      "761 cosmic pixels (659 new)\n",
      "Iteration 3\n",
      "192 cosmic pixels (144 new)\n",
      "Iteration 4\n",
      "81 cosmic pixels (51 new)\n",
      "Cosmic ray cleaning for n20230217.047.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 3 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4328 cosmic pixels (4328 new)\n",
      "Iteration 2\n",
      "672 cosmic pixels (584 new)\n",
      "Iteration 3\n",
      "169 cosmic pixels (118 new)\n",
      "Iteration 4\n",
      "95 cosmic pixels (39 new)\n",
      "Cosmic ray cleaning for n20230217.048.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 2 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4147 cosmic pixels (4147 new)\n",
      "Iteration 2\n",
      "722 cosmic pixels (610 new)\n",
      "Iteration 3\n",
      "164 cosmic pixels (108 new)\n",
      "Iteration 4\n",
      "72 cosmic pixels (29 new)\n",
      "Cosmic ray cleaning for n20230217.049.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 5 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4270 cosmic pixels (4270 new)\n",
      "Iteration 2\n",
      "700 cosmic pixels (611 new)\n",
      "Iteration 3\n",
      "196 cosmic pixels (141 new)\n",
      "Iteration 4\n",
      "74 cosmic pixels (32 new)\n",
      ">>> Cosmic ray correction complete.\n",
      "2023-02-26 09:28:25 - Processing science data in ut20230217_geminiS/ complete.\n",
      ">>> Processed data moved to output directory.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230217_geminiS/rawfits_r/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Processed bias data moved to output directory.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230217_geminiS/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230217_geminiS/rawfits_bias/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230217_geminiS/flatfits_pyt/...\n",
      ">>> fpack compression of FITS files complete.\n",
      "\n",
      "2023-02-26 09:28:51 - Processing of data in ut20230217_geminiS/ complete.\n",
      "\n",
      "2023-02-26 09:28:51 - Starting processing of data in ut20230219_geminiS/...\n",
      "\n",
      "2023-02-26 09:28:51 - Processing bias-frame data in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230219_geminiS/rawfits_bias/...\n",
      "\n",
      "2023-02-26 09:28:51 - Decompressing, filtering, and splitting bias files...\n",
      ">>> Starting decompression of bz2 files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230219_geminiS/rawfits_bias/...\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">>> Decompression of bz2 files complete.\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230219_geminiS/rawfits_bias/...\n",
      ">>> Decompression of fz files complete.\n",
      "Splitting S20230219S0065.fits...\n",
      "Splitting S20230219S0066.fits...\n",
      "Splitting S20230219S0067.fits...\n",
      "Splitting S20230219S0068.fits...\n",
      "Splitting S20230219S0069.fits...\n",
      ">>> Gain and read noise updated in image headers.\n",
      "Starting image statistics output...\n",
      ">>> Image statistics output complete.\n",
      "Starting overscan correction and trimming...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">>> Overscan correction and trimming complete.\n",
      "Starting median combination of bias frames...\n",
      ">>> Median combination of bias frames complete.\n",
      "\n",
      "2023-02-26 09:29:17 - Processing bias-frame data in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230219_geminiS/rawfits_bias/ complete.\n",
      "\n",
      "2023-02-26 09:29:17 - Processing r-band science data in ut20230219_geminiS/...\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230219_geminiS/...\n",
      ">>> Decompression of fz files complete.\n",
      "\n",
      "2023-02-26 09:29:20 - Decompressing and splitting data files...\n",
      ">>> Starting decompression of bz2 files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230219_geminiS/rawfits_r/...\n",
      ">>> Decompression of bz2 files complete.\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230219_geminiS/rawfits_r/...\n",
      ">>> Decompression of fz files complete.\n",
      "Splitting S20230219S0008.fits...\n",
      "Splitting S20230219S0009.fits...\n",
      "Splitting S20230219S0010.fits...\n",
      "Splitting S20230219S0018.fits...\n",
      "Splitting S20230219S0019.fits...\n",
      "Splitting S20230219S0020.fits...\n",
      ">>> Gain and read noise updated in image headers.\n",
      "Starting image statistics output...\n",
      ">>> Image statistics output complete.\n",
      "Starting overscan correction and trimming...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">>> Overscan correction and trimming complete.\n",
      "Starting bias subtraction...\n",
      ">>> Bias subtraction complete.\n",
      ">>> Starting adjacent amp area concatenation...\n",
      ">>> Adjacent amp area concatenation complete.\n",
      "Starting flatfield correction...\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      ">>> Flatfield correction complete.\n",
      "Starting cosmic ray correction...\n",
      "Cosmic ray cleaning for n20230219.008.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 3 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4234 cosmic pixels (4234 new)\n",
      "Iteration 2\n",
      "764 cosmic pixels (659 new)\n",
      "Iteration 3\n",
      "197 cosmic pixels (129 new)\n",
      "Iteration 4\n",
      "90 cosmic pixels (48 new)\n",
      "Cosmic ray cleaning for n20230219.009.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 5 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4369 cosmic pixels (4369 new)\n",
      "Iteration 2\n",
      "782 cosmic pixels (668 new)\n",
      "Iteration 3\n",
      "248 cosmic pixels (180 new)\n",
      "Iteration 4\n",
      "121 cosmic pixels (65 new)\n",
      "Cosmic ray cleaning for n20230219.010.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 7 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4732 cosmic pixels (4732 new)\n",
      "Iteration 2\n",
      "801 cosmic pixels (714 new)\n",
      "Iteration 3\n",
      "169 cosmic pixels (126 new)\n",
      "Iteration 4\n",
      "56 cosmic pixels (30 new)\n",
      "Cosmic ray cleaning for n20230219.018.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 9 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4861 cosmic pixels (4861 new)\n",
      "Iteration 2\n",
      "911 cosmic pixels (795 new)\n",
      "Iteration 3\n",
      "231 cosmic pixels (175 new)\n",
      "Iteration 4\n",
      "99 cosmic pixels (58 new)\n",
      "Cosmic ray cleaning for n20230219.019.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 7 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4565 cosmic pixels (4565 new)\n",
      "Iteration 2\n",
      "812 cosmic pixels (704 new)\n",
      "Iteration 3\n",
      "188 cosmic pixels (141 new)\n",
      "Iteration 4\n",
      "74 cosmic pixels (42 new)\n",
      "Cosmic ray cleaning for n20230219.020.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 8 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4496 cosmic pixels (4496 new)\n",
      "Iteration 2\n",
      "790 cosmic pixels (671 new)\n",
      "Iteration 3\n",
      "239 cosmic pixels (178 new)\n",
      "Iteration 4\n",
      "101 cosmic pixels (48 new)\n",
      "Cosmic ray cleaning for n20230219.008.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 14 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "12366 cosmic pixels (12366 new)\n",
      "Iteration 2\n",
      "10721 cosmic pixels (4088 new)\n",
      "Iteration 3\n",
      "9397 cosmic pixels (1996 new)\n",
      "Iteration 4\n",
      "8717 cosmic pixels (966 new)\n",
      "Cosmic ray cleaning for n20230219.009.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 16 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "12402 cosmic pixels (12402 new)\n",
      "Iteration 2\n",
      "10461 cosmic pixels (3992 new)\n",
      "Iteration 3\n",
      "9119 cosmic pixels (1945 new)\n",
      "Iteration 4\n",
      "8449 cosmic pixels (921 new)\n",
      "Cosmic ray cleaning for n20230219.010.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 16 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "12005 cosmic pixels (12005 new)\n",
      "Iteration 2\n",
      "10069 cosmic pixels (3913 new)\n",
      "Iteration 3\n",
      "8738 cosmic pixels (1900 new)\n",
      "Iteration 4\n",
      "8087 cosmic pixels (882 new)\n",
      "Cosmic ray cleaning for n20230219.018.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 16 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "17163 cosmic pixels (17163 new)\n",
      "Iteration 2\n",
      "14650 cosmic pixels (5525 new)\n",
      "Iteration 3\n",
      "12895 cosmic pixels (2642 new)\n",
      "Iteration 4\n",
      "11940 cosmic pixels (1226 new)\n",
      "Cosmic ray cleaning for n20230219.019.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 16 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "14837 cosmic pixels (14837 new)\n",
      "Iteration 2\n",
      "12495 cosmic pixels (4711 new)\n",
      "Iteration 3\n",
      "11040 cosmic pixels (2348 new)\n",
      "Iteration 4\n",
      "10319 cosmic pixels (1122 new)\n",
      "Cosmic ray cleaning for n20230219.020.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 16 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "17143 cosmic pixels (17143 new)\n",
      "Iteration 2\n",
      "14607 cosmic pixels (5563 new)\n",
      "Iteration 3\n",
      "12682 cosmic pixels (2613 new)\n",
      "Iteration 4\n",
      "11808 cosmic pixels (1241 new)\n",
      "Cosmic ray cleaning for n20230219.008.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 4 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "7406 cosmic pixels (7406 new)\n",
      "Iteration 2\n",
      "4581 cosmic pixels (2475 new)\n",
      "Iteration 3\n",
      "4092 cosmic pixels (1119 new)\n",
      "Iteration 4\n",
      "4003 cosmic pixels (543 new)\n",
      "Cosmic ray cleaning for n20230219.009.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 5 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4103 cosmic pixels (4103 new)\n",
      "Iteration 2\n",
      "737 cosmic pixels (642 new)\n",
      "Iteration 3\n",
      "124 cosmic pixels (80 new)\n",
      "Iteration 4\n",
      "33 cosmic pixels (11 new)\n",
      "Cosmic ray cleaning for n20230219.010.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 4 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "6165 cosmic pixels (6165 new)\n",
      "Iteration 2\n",
      "2496 cosmic pixels (1574 new)\n",
      "Iteration 3\n",
      "1821 cosmic pixels (624 new)\n",
      "Iteration 4\n",
      "1584 cosmic pixels (269 new)\n",
      "Cosmic ray cleaning for n20230219.018.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Building mask of saturated stars ...\n",
      "We have 3 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4504 cosmic pixels (4504 new)\n",
      "Iteration 2\n",
      "720 cosmic pixels (649 new)\n",
      "Iteration 3\n",
      "160 cosmic pixels (113 new)\n",
      "Iteration 4\n",
      "52 cosmic pixels (14 new)\n",
      "Cosmic ray cleaning for n20230219.019.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 2 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4590 cosmic pixels (4590 new)\n",
      "Iteration 2\n",
      "737 cosmic pixels (672 new)\n",
      "Iteration 3\n",
      "131 cosmic pixels (109 new)\n",
      "Iteration 4\n",
      "44 cosmic pixels (32 new)\n",
      "Cosmic ray cleaning for n20230219.020.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 3 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4378 cosmic pixels (4378 new)\n",
      "Iteration 2\n",
      "763 cosmic pixels (693 new)\n",
      "Iteration 3\n",
      "140 cosmic pixels (107 new)\n",
      "Iteration 4\n",
      "37 cosmic pixels (19 new)\n",
      ">>> Cosmic ray correction complete.\n",
      "2023-02-26 09:35:25 - Processing science data in ut20230219_geminiS/ complete.\n",
      ">>> Processed data moved to output directory.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230219_geminiS/rawfits_r/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Processed bias data moved to output directory.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230219_geminiS/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230219_geminiS/rawfits_bias/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230219_geminiS/flatfits_pyt/...\n",
      ">>> fpack compression of FITS files complete.\n",
      "\n",
      "2023-02-26 09:35:44 - Processing of data in ut20230219_geminiS/ complete.\n",
      "\n",
      "2023-02-26 09:35:44 - Starting processing of data in ut20230226_geminiS/...\n",
      "\n",
      "2023-02-26 09:35:44 - Processing bias-frame data in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230226_geminiS/rawfits_bias/...\n",
      "\n",
      "2023-02-26 09:35:44 - Decompressing, filtering, and splitting bias files...\n",
      ">>> Starting decompression of bz2 files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230226_geminiS/rawfits_bias/...\n",
      ">>> Decompression of bz2 files complete.\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230226_geminiS/rawfits_bias/...\n",
      ">>> Decompression of fz files complete.\n",
      "Splitting S20230226S0131.fits...\n",
      "Splitting S20230226S0132.fits...\n",
      "Splitting S20230226S0133.fits...\n",
      "Splitting S20230226S0134.fits...\n",
      "Splitting S20230226S0135.fits...\n",
      "Splitting S20230226S0221.fits...\n",
      "Splitting S20230226S0222.fits...\n",
      "Splitting S20230226S0223.fits...\n",
      "Splitting S20230226S0224.fits...\n",
      "Splitting S20230226S0225.fits...\n",
      ">>> Gain and read noise updated in image headers.\n",
      "Starting image statistics output...\n",
      ">>> Image statistics output complete.\n",
      "Starting overscan correction and trimming...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">>> Overscan correction and trimming complete.\n",
      "Starting median combination of bias frames...\n",
      ">>> Median combination of bias frames complete.\n",
      "\n",
      "2023-02-26 09:36:43 - Processing bias-frame data in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230226_geminiS/rawfits_bias/ complete.\n",
      "\n",
      "2023-02-26 09:36:43 - Processing r-band science data in ut20230226_geminiS/...\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230226_geminiS/...\n",
      ">>> Decompression of fz files complete.\n",
      "\n",
      "2023-02-26 09:36:45 - Decompressing and splitting data files...\n",
      ">>> Starting decompression of bz2 files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230226_geminiS/rawfits_r/...\n",
      ">>> Decompression of bz2 files complete.\n",
      ">>> Starting decompression of fz files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230226_geminiS/rawfits_r/...\n",
      ">>> Decompression of fz files complete.\n",
      "Splitting S20230226S0073.fits...\n",
      "Splitting S20230226S0074.fits...\n",
      "Splitting S20230226S0075.fits...\n",
      ">>> Gain and read noise updated in image headers.\n",
      "Starting image statistics output...\n",
      ">>> Image statistics output complete.\n",
      "Starting overscan correction and trimming...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n",
      "WARNING: FITSFixedWarning: 'datfix' made the change 'Invalid parameter values: MJD-OBS and DATE-OBS are inconsistent'. [astropy.wcs.wcs]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">>> Overscan correction and trimming complete.\n",
      "Starting bias subtraction...\n",
      ">>> Bias subtraction complete.\n",
      ">>> Starting adjacent amp area concatenation...\n",
      ">>> Adjacent amp area concatenation complete.\n",
      "Starting flatfield correction...\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      ">>> Flatfield correction complete.\n",
      "Starting cosmic ray correction...\n",
      "Cosmic ray cleaning for n20230226.073.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 42 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4261 cosmic pixels (4261 new)\n",
      "Iteration 2\n",
      "746 cosmic pixels (634 new)\n",
      "Iteration 3\n",
      "262 cosmic pixels (192 new)\n",
      "Iteration 4\n",
      "148 cosmic pixels (87 new)\n",
      "Cosmic ray cleaning for n20230226.074.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 34 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "3942 cosmic pixels (3942 new)\n",
      "Iteration 2\n",
      "652 cosmic pixels (575 new)\n",
      "Iteration 3\n",
      "186 cosmic pixels (142 new)\n",
      "Iteration 4\n",
      "82 cosmic pixels (46 new)\n",
      "Cosmic ray cleaning for n20230226.075.chip1.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 38 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4209 cosmic pixels (4209 new)\n",
      "Iteration 2\n",
      "767 cosmic pixels (660 new)\n",
      "Iteration 3\n",
      "243 cosmic pixels (175 new)\n",
      "Iteration 4\n",
      "111 cosmic pixels (66 new)\n",
      "Cosmic ray cleaning for n20230226.073.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 103 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "1404 cosmic pixels (1404 new)\n",
      "Iteration 2\n",
      "285 cosmic pixels (266 new)\n",
      "Iteration 3\n",
      "60 cosmic pixels (40 new)\n",
      "Iteration 4\n",
      "53 cosmic pixels (32 new)\n",
      "Cosmic ray cleaning for n20230226.074.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 100 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "1609 cosmic pixels (1609 new)\n",
      "Iteration 2\n",
      "254 cosmic pixels (225 new)\n",
      "Iteration 3\n",
      "81 cosmic pixels (56 new)\n",
      "Iteration 4\n",
      "61 cosmic pixels (34 new)\n",
      "Cosmic ray cleaning for n20230226.075.chip2.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 97 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "1795 cosmic pixels (1795 new)\n",
      "Iteration 2\n",
      "378 cosmic pixels (315 new)\n",
      "Iteration 3\n",
      "169 cosmic pixels (70 new)\n",
      "Iteration 4\n",
      "162 cosmic pixels (49 new)\n",
      "Cosmic ray cleaning for n20230226.073.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 51 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "3930 cosmic pixels (3930 new)\n",
      "Iteration 2\n",
      "830 cosmic pixels (666 new)\n",
      "Iteration 3\n",
      "395 cosmic pixels (217 new)\n",
      "Iteration 4\n",
      "311 cosmic pixels (97 new)\n",
      "Cosmic ray cleaning for n20230226.074.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 48 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4717 cosmic pixels (4717 new)\n",
      "Iteration 2\n",
      "966 cosmic pixels (793 new)\n",
      "Iteration 3\n",
      "470 cosmic pixels (255 new)\n",
      "Iteration 4\n",
      "353 cosmic pixels (123 new)\n",
      "Cosmic ray cleaning for n20230226.075.chip3.otzf.fits\n",
      "Detecting saturated stars ...\n",
      "Building mask of saturated stars ...\n",
      "We have 48 saturated stars.\n",
      "Mask of saturated stars done\n",
      "Starting 4 L.A.Cosmic iterations ...\n",
      "Iteration 1\n",
      "4107 cosmic pixels (4107 new)\n",
      "Iteration 2\n",
      "857 cosmic pixels (694 new)\n",
      "Iteration 3\n",
      "397 cosmic pixels (234 new)\n",
      "Iteration 4\n",
      "284 cosmic pixels (95 new)\n",
      ">>> Cosmic ray correction complete.\n",
      "2023-02-26 09:39:32 - Processing science data in ut20230226_geminiS/ complete.\n",
      ">>> Processed data moved to output directory.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230226_geminiS/rawfits_r/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Processed bias data moved to output directory.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230226_geminiS/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230226_geminiS/rawfits_bias/...\n",
      ">>> fpack compression of FITS files complete.\n",
      ">>> Starting fpack compression of FITS files in /volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230226_geminiS/flatfits_pyt/...\n",
      ">>> fpack compression of FITS files complete.\n",
      "\n",
      "2023-02-26 09:39:43 - Processing of data in ut20230226_geminiS/ complete.\n",
      "Done.\n"
     ]
    }
   ],
   "source": [
    "process_gemini_science_data('/volumes/Fantom12a/BackupData/TargetedObjects/MBCs/P2020O1/')\n",
    "process_gemini_science_data('/volumes/Fantom12a/BackupData/TargetedObjects/MBCs/P2019A4/')\n",
    "process_gemini_science_data('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2019B-LP-104/')\n",
    "process_gemini_science_data('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2020A-LP-104/')\n",
    "process_gemini_science_data('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2020A-LP-104/')\n",
    "process_gemini_science_data('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GN-2020B-LP-104/')\n",
    "process_gemini_science_data('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2020B-LP-104/')\n",
    "process_gemini_science_data('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GN-2021A-LP-104/')\n",
    "process_gemini_science_data('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2021A-LP-104/')\n",
    "process_gemini_science_data('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GN-2021B-LP-104/')\n",
    "process_gemini_science_data('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2021B-LP-104/')\n",
    "process_gemini_science_data('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GN-2022A-LP-104/')\n",
    "process_gemini_science_data('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2022A-LP-104/')\n",
    "process_gemini_science_data('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GN-2022B-Q-307/')\n",
    "process_gemini_science_data('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2022B-LP-104/')\n",
    "process_gemini_science_data('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2022B-Q-111/')\n",
    "process_gemini_science_data('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/')\n",
    "#process_gemini_science_data('/users/hhsieh/data/')\n",
    "\n",
    "print('Done.')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Trimming GMOS-S data with bad amp #5...\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      ">>> Trimming GMOS-S data with bad amp #5 complete.\n",
      "Trimming GMOS-S data with bad amp #5...\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      ">>> Trimming GMOS-S data with bad amp #5 complete.\n",
      "Trimming GMOS-S data with bad amp #5...\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      ">>> Trimming GMOS-S data with bad amp #5 complete.\n",
      "Trimming GMOS-S data with bad amp #5...\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      ">>> Trimming GMOS-S data with bad amp #5 complete.\n",
      "Trimming GMOS-S data with bad amp #5...\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      ">>> Trimming GMOS-S data with bad amp #5 complete.\n",
      "Trimming GMOS-S data with bad amp #5...\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      ">>> Trimming GMOS-S data with bad amp #5 complete.\n",
      "Trimming GMOS-S data with bad amp #5...\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      ">>> Trimming GMOS-S data with bad amp #5 complete.\n",
      "Trimming GMOS-S data with bad amp #5...\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      ">>> Trimming GMOS-S data with bad amp #5 complete.\n",
      "Trimming GMOS-S data with bad amp #5...\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      "INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]\n",
      ">>> Trimming GMOS-S data with bad amp #5 complete.\n"
     ]
    }
   ],
   "source": [
    "#trim_gmoss_data_with_bad_amp('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2022B-Q-111/ut20221023_geminiS/flatfits_pyt/c01_432p/')\n",
    "#trim_gmoss_data_with_bad_amp('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2022B-Q-111/ut20221023_geminiS/flatfits_pyt/c02_p2016j1b/')\n",
    "#trim_gmoss_data_with_bad_amp('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2022B-Q-111/ut20221027_geminiS/flatfits_pyt/c01_324p/')\n",
    "#trim_gmoss_data_with_bad_amp('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2022B-Q-111/ut20221118_geminiS/flatfits_pyt/c01_238p/')\n",
    "#trim_gmoss_data_with_bad_amp('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2022B-Q-111/ut20230122_geminiS/flatfits_pyt/')\n",
    "\n",
    "trim_gmoss_data_with_bad_amp('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230213_geminiS/flatfits_pyt/')\n",
    "trim_gmoss_data_with_bad_amp('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230215_geminiS/flatfits_pyt/')\n",
    "trim_gmoss_data_with_bad_amp('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230216_geminiS/flatfits_pyt/')\n",
    "trim_gmoss_data_with_bad_amp('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230217_geminiS/flatfits_pyt/c01_133p/')\n",
    "trim_gmoss_data_with_bad_amp('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230217_geminiS/flatfits_pyt/c02_439p/')\n",
    "trim_gmoss_data_with_bad_amp('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230217_geminiS/flatfits_pyt/c03_p2021a5/')\n",
    "trim_gmoss_data_with_bad_amp('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230219_geminiS/flatfits_pyt/c01_348p/')\n",
    "trim_gmoss_data_with_bad_amp('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230219_geminiS/flatfits_pyt/c02_435p/')\n",
    "trim_gmoss_data_with_bad_amp('/volumes/Fantom12a/BackupData/gemini/data_LLP/gemini_data.GS-2023A-LP-104/ut20230226_geminiS/flatfits_pyt/')\n"
   ]
  }
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