Merge branch 'xraypy:master' into struct2xasV2407

.github/workflows/test-ubuntu-mamba.yml → .github/workflows/test-ubuntu.yml

@@ -1,4 +1,4 @@
-name: Test with Ubuntu, Mamba
+name: Test with Ubuntu, Conda
 
 on: [push]
 
@@ -19,15 +19,14 @@ jobs:
       uses: conda-incubator/[email protected]
       with:
         miniconda-version: latest
-        mamba-version: "*"
         channels: conda-forge,defaults
         channel-priority: true
         activate-environment: anaconda-client-env
         python-version: ${{ matrix.python-version }}
     - name: Install conda dependencies
       run: |
         printenv
-        mamba install -y -c conda-forge python=${{ matrix.python-version }} "numpy>=1.23" "scipy>=1.8" "matplotlib>=3.6" "h5py>=3.5" "wxpython>=4.2" scikit-image scikit-learn pycifrw pandas jupyter plotly pyparsing pytest pytest-cov coverage
+        conda install -y -c conda-forge python=${{ matrix.python-version }} "numpy>=1.23" "scipy>=1.8" "matplotlib>=3.6" "h5py>=3.5" "wxpython>=4.2" scikit-image scikit-learn pandas jupyter plotly pyparsing pytest pytest-cov coverage
     - name: Install xraylarch and other dependencies with pip
       run: |
         pip install ".[all]"

.github/workflows/test-windows.yml

@@ -23,7 +23,7 @@ jobs:
     - name: Install conda dependencies
       run: |
         printenv
-        conda install -y -c conda-forge python=${{ matrix.python-version }} "numpy>=1.23" "scipy>=1.8" "matplotlib>=3.6" "h5py>=3.5" "wxpython>=4.2" scikit-image scikit-learn pycifrw pandas jupyter plotly pyparsing pytest pytest-cov coverage
+        conda install -y -c conda-forge python=${{ matrix.python-version }} "numpy>=1.23" "scipy>=1.8" "matplotlib>=3.6" "h5py>=3.5" "wxpython>=4.2" scikit-image scikit-learn pandas jupyter plotly pyparsing pytest pytest-cov coverage
     - name: Install xraylarch and other dependencies with pip
       run: |
         printenv

README.rst

@@ -1,10 +1,8 @@
 Larch:  Data Analysis Tools for X-ray Spectroscopy and More
 ============================================================
 
-.. image:: https://github.com/xraypy/xraylarch/actions/workflows/test-ubuntu-mamba.yml/badge.svg
-   :target: https://github.com/xraypy/xraylarch/actions/workflows/test-ubuntu-mamba.yml
-.. image::  https://github.com/xraypy/xraylarch/actions/workflows/test-windows-mamba.yml/badge.svg
-   :target: https://github.com/xraypy/xraylarch/actions/workflows/test-ubuntu-mamba.yml
+.. image:: https://github.com/xraypy/xraylarch/actions/workflows/test-ubuntu.yml/badge.svg
+   :target: https://github.com/xraypy/xraylarch/actions/workflows/test-ubuntu.yml
 .. image::  https://github.com/xraypy/xraylarch/actions/workflows/test-windows.yml/badge.svg
    :target: https://github.com/xraypy/xraylarch/actions/workflows/test-windows.yml
 

installers/GetLarch.bat

@@ -19,7 +19,7 @@ echo ## basic mamba installed, running updates
 set PATH=%prefix%;%prefix%\bin;%prefix%\condabin;%prefix%\Scripts;%PATH%
 
 echo ## Installing basic python scipy packages
-call %prefix%\Scripts\mamba install -yc conda-forge python==3.11.5 numpy scipy matplotlib h5py scikit-image scikit-learn pycifrw pandas jupyter plotly wxpython fabio pyfai pymatgen mkl_fft tomopy
+call %prefix%\Scripts\mamba install -yc conda-forge python==3.11.5 numpy scipy matplotlib h5py scikit-image scikit-learn pandas jupyter plotly wxpython fabio pyfai pymatgen mkl_fft tomopy
 
 echo ## Installing xraylarch and dependencies from PyPI
 call %prefix%\Scripts\pip install xraylarch[larix]

installers/GetLarch.sh

@@ -20,7 +20,7 @@ condafile="Mambaforge-$uname-x86_64.sh"
 logfile=GetLarch.log
 
 ## set list of conda packages to install from conda-forge
-cforge_pkgs="python=>3.12.3 numpy scipy matplotlib h5py scikit-image scikit-learn pycifrw pandas jupyter plotly wxpython fabio pyfai pymatgen mkl_fft tomopy"
+cforge_pkgs="python=>3.12.3 numpy scipy matplotlib h5py scikit-image scikit-learn pandas jupyter plotly wxpython fabio pyfai pymatgen mkl_fft tomopy"
 
 unset CONDA_EXE CONDA_PYTHON_EXE CONDA_PREFIX PROJ_LIB
 

installers/conda_constructor/construct.yaml

@@ -54,5 +54,4 @@ specs:
     - wxpython>=4.2.0
     - tomopy
     - pymatgen
-    - pycifrw
     - numdifftools

larch/interpreter.py

@@ -14,7 +14,8 @@
 import numpy
 from pathlib import Path
 from copy import deepcopy
-
+from functools import partial
+from inspect import signature
 from . import site_config
 from asteval import valid_symbol_name
 from .symboltable import SymbolTable, Group, isgroup
@@ -154,9 +155,8 @@ def __init__(self, symtable=None, input=None, writer=None,
                 group = self.symtable.set_symbol(groupname,
                                                  value=Group(__name__=groupname))
             for fname, fcn in list(entries.items()):
-                if callable(fcn):
-                    setattr(group, fname,
-                            Closure(func=fcn, _larch=self, _name=fname))
+                if callable(fcn) and '_larch' in signature(fcn).parameters:
+                    setattr(group, fname, Closure(func=fcn, _larch=self))
                 else:
                     setattr(group, fname, fcn)
 

larch/io/athena_project.py

@@ -18,6 +18,7 @@
 from larch import Group, repr_value
 from larch import __version__ as larch_version
 from larch.utils import bytes2str, str2bytes, fix_varname, asfloat, unixpath
+from larch.math import remove_dups
 
 from xraydb import guess_edge
 import asteval
@@ -760,6 +761,8 @@ def read(self, filename=None, match=None, do_preedge=True, do_bkg=False,
             raise IOError("%s '%s': cannot find file" % (ERR_MSG, self.filename))
 
         from larch.xafs import pre_edge, autobk, xftf
+        from larch.xafs.xafsutils import TINY_ENERGY
+
 
         if not Path(filename).exists():
             raise IOError("file '%s' not found" % filename)
@@ -797,6 +800,17 @@ def read(self, filename=None, match=None, do_preedge=True, do_bkg=False,
                 if not fnmatch(gname.lower(), match):
                     continue
             this = getattr(data, gname)
+            this.energy = remove_dups(this.energy, tiny=TINY_ENERGY)
+            eorder = np.argsort(this.energy)
+            has_nan = False
+            for aname in dir(this):
+                obj = getattr(this, aname)
+                if isinstance(obj, np.ndarray) and len(eorder) == len(obj):
+                    setattr(this, aname, obj[eorder])
+                    has_nan = has_nan or any(np.isnan(obj))
+            this.energy = remove_dups(this.energy, tiny=TINY_ENERGY)
+            if has_nan:
+                print("NOTE: nans seen!!")
 
             this.athena_id = this.athena_params.id
             if use_hashkey:
@@ -835,15 +849,18 @@ def read(self, filename=None, match=None, do_preedge=True, do_bkg=False,
             if is_chi:
                 this.k = this.energy*1.0
                 this.chi = this.mu*1.0
+                this.xdat = this.energy*1.0
+                this.ydat = this.mu*1.0
                 del this.energy
                 del this.mu
+            else:
+                this.xdat = 1.0*this.energy
+                this.ydat = 1.0*this.mu
 
             # add a selection flag and XAS datatypes, as used by Larix
             this.sel = 1
             this.datatype = 'xas'
             this.filename = getattr(this, 'label', 'unknown')
-            this.xdat = 1.0*this.energy
-            this.ydat = 1.0*this.mu
             this.yerr = 1.0
             this.plot_xlabel = 'energy'
             this.plot_ylabel = 'mu'

larch/io/mergegroups.py

@@ -5,7 +5,7 @@
 import os
 import numpy as np
 from larch import Group
-from larch.math import interp, interp1d, index_of, remove_dups
+from larch.math import interp, interp1d, index_of, remove_dups, remove_nans
 from larch.utils.logging import getLogger
 
 _logger = getLogger("larch.io.mergegroups")
@@ -32,14 +32,20 @@ def merge_groups(grouplist, master=None, xarray='energy', yarray='mu',
     if master is None:
         master = grouplist[0]
 
-    xout = remove_dups(getattr(master, xarray))
+    xarr = getattr(master, xarray)
+    dxperc = np.percentile(abs(np.diff(xarr)), [1, 2, 25])
+    dxmin = min(0.01*dxperc[1], 1.e-4*dxperc[2])
+
+
+    xout = remove_dups(xarr, dxmin)
+    xout = remove_nans(xout, interp=True)
     xmins = [min(xout)]
     xmaxs = [max(xout)]
     yvals = []
 
     for g in grouplist:
-        x = getattr(g, xarray)
-        y = getattr(g, yarray)
+        x = remove_nans(remove_dups(getattr(g, xarray), dxmin), interp=True)
+        y = remove_nans(getattr(g, yarray), interp=True)
         yvals.append(interp(x, y, xout, kind=kind))
         xmins.append(min(x))
         xmaxs.append(max(x))

larch/wxlib/cif_browser.py

@@ -23,9 +23,10 @@
 from xraydb import atomic_number
 
 import larch
+
 from larch import Group
 from larch.xafs import feff8l, feff6l
-from larch.xrd.cif2feff import cif_sites
+from larch.xrd.cif2feff import cif2feffinp, cif_cluster, site_label, fcompact
 from larch.utils import read_textfile, mkdir
 from larch.utils.paths import unixpath
 from larch.utils.strutils import fix_filename, unique_name, strict_ascii
@@ -227,8 +228,8 @@ def createMainPanel(self):
             wids['feffvers']      = Choice(panel, choices=['6', '8'], default=1,
                                            size=(80, -1),
                                           action=self.onGetFeff)
-            wids['feff_site']         = Choice(panel, choices=['1', '2', '3', '4'],
-                                          size=(80, -1),
+            wids['feff_site']         = Choice(panel, choices=[' ', ' ', ' ', ' '],
+                                          size=(200, -1),
                                           action=self.onGetFeff)
             wids['feff_cluster_size'] = FloatSpin(panel, value=7.0, digits=2,
                                              increment=0.1, max_val=10,
@@ -244,10 +245,10 @@ def createMainPanel(self):
 
             sizer.Add(SimpleText(panel, ' Absorbing Atom: '),  (ir, 0), (1, 1), LEFT, 3)
             sizer.Add(wids['feff_central_atom'], (ir, 1), (1, 1), LEFT, 3)
-            sizer.Add(SimpleText(panel, ' Crystal Site: '), (ir, 2), (1, 1), LEFT, 3)
-            sizer.Add(wids['feff_site'],     (ir, 3), (1, 1), LEFT, 3)
-            sizer.Add(SimpleText(panel, ' Edge: '),  (ir, 4), (1, 1), LEFT, 3)
-            sizer.Add(wids['feff_edge'],     (ir, 5), (1, 1), LEFT, 3)
+            sizer.Add(SimpleText(panel, ' Edge: '),  (ir, 2), (1, 1), LEFT, 3)
+            sizer.Add(wids['feff_edge'],     (ir, 3), (1, 1), LEFT, 3)
+            sizer.Add(SimpleText(panel, ' Crystal Site: '), (ir, 4), (1, 1), LEFT, 3)
+            sizer.Add(wids['feff_site'],     (ir, 5), (1, 1), LEFT, 3)
 
             ir += 1
             sizer.Add(SimpleText(panel, ' Cluster Size (\u212B): '),  (ir, 0), (1, 1), LEFT, 3)
@@ -292,16 +293,17 @@ def _swallow_plot_messages(s, panel=0):
         self.plotpanel.SetMaxSize((675, 400))
         self.plotpanel.onPanelExposed = self.showXRD1D
 
+        fw_font = wx.Font(FONTSIZE,  wx.MODERN, wx.NORMAL, wx.BOLD)
+
         cif_panel = wx.Panel(rightpanel)
         wids['cif_text'] = wx.TextCtrl(cif_panel, value='<CIF TEXT>',
                                        style=wx.TE_MULTILINE|wx.TE_READONLY,
-                                       size=(700, 450))
-        wids['cif_text'].SetFont(Font(FONTSIZE+1))
+                                       size=(725, 450))
+        wids['cif_text'].SetFont(fw_font)
         cif_sizer = wx.BoxSizer(wx.VERTICAL)
         cif_sizer.Add(wids['cif_text'], 0, LEFT, 1)
         pack(cif_panel, cif_sizer)
 
-
         self.nbpages = []
         for label, page in (('CIF Text',  cif_panel),
                             ('1-D XRD Pattern', self.plotpanel),
@@ -318,11 +320,12 @@ def _swallow_plot_messages(s, panel=0):
             wids['feff_text'] = wx.TextCtrl(feffinp_panel,
                                            value='<Feff Input Text>',
                                            style=wx.TE_MULTILINE,
-                                           size=(700, 450))
+                                           size=(725, 450))
+            wids['feff_text'].SetFont(fw_font)
             wids['feff_text'].CanCopy()
 
             feffinp_panel.onPanelExposed = self.onGetFeff
-            wids['feff_text'].SetFont(Font(FONTSIZE+1))
+            # wids['feff_text'].SetFont(Font(FONTSIZE+1))
             feff_sizer = wx.BoxSizer(wx.VERTICAL)
             feff_sizer.Add(wids['feff_text'], 0, LEFT, 1)
             pack(feffinp_panel, feff_sizer)
@@ -331,9 +334,10 @@ def _swallow_plot_messages(s, panel=0):
             wids['feffout_text'] = wx.TextCtrl(feffout_panel,
                                                value='<Feff Output>',
                                                style=wx.TE_MULTILINE,
-                                               size=(700, 450))
+                                               size=(725, 450))
             wids['feffout_text'].CanCopy()
-            wids['feffout_text'].SetFont(Font(FONTSIZE+1))
+            wids['feffout_text'].SetFont(fw_font)
+            # wids['feffout_text'].SetFont(Font(FONTSIZE+1))
             feffout_sizer = wx.BoxSizer(wx.VERTICAL)
             feffout_sizer.Add(wids['feffout_text'], 0, LEFT, 1)
             pack(feffout_panel, feffout_sizer)
@@ -448,13 +452,14 @@ def onShowCIF(self, event=None, cif_id=None):
             self.wids['feff_central_atom'].AppendItems(list(elems.keys()))
             self.wids['feff_central_atom'].Select(0)
 
-            el0 = list(elems.keys())[0]
-            edge_val = 'K' if atomic_number(el0) < 60 else 'L3'
+            catom = list(elems.keys())[0]
+            edge_val = 'K' if atomic_number(catom) < 60 else 'L3'
             self.wids['feff_edge'].SetStringSelection(edge_val)
 
-            sites = cif_sites(cif.ciftext, absorber=el0)
+            cluster = cif_cluster(ciftext=cif.ciftext, absorber=catom)
+            self.absorber_sites = cluster.all_sites[catom]
             try:
-                sites = ['%d' % (i+1) for i in range(len(sites))]
+                sites = list(self.absorber_sites.keys())
             except:
                 title = "Could not make sense of atomic sites"
                 message = [f"Elements: {list(elems.keys())}",
@@ -482,11 +487,14 @@ def onFeffCentralAtom(self, event=None):
             return
         catom = event.GetString()
         try:
-            sites = cif_sites(cif.ciftext, absorber=catom)
-            sites = ['%d' % (i+1) for i in range(len(sites))]
+            cluster = cif_cluster(ciftext=cif.ciftext, absorber=catom)
+            self.absorber_sites = cluster.all_sites[catom]
+
+            sites = list(self.absorber_sites.keys())
             self.wids['feff_site'].Clear()
             self.wids['feff_site'].AppendItems(sites)
             self.wids['feff_site'].Select(0)
+
         except:
             self.write_message(f"could not get sites for central atom '{catom}'")
             title = f"Could not get sites for central atom '{catom}'"
@@ -505,16 +513,37 @@ def onGetFeff(self, event=None):
         edge  = self.wids['feff_edge'].GetStringSelection()
         version8 = '8' == self.wids['feffvers'].GetStringSelection()
         catom = self.wids['feff_central_atom'].GetStringSelection()
-        asite = int(self.wids['feff_site'].GetStringSelection())
+        label = self.wids['feff_site'].GetStringSelection()
+        site_index = self.absorber_sites[label]
         csize = self.wids['feff_cluster_size'].GetValue()
         with_h = not self.wids['feff_without_h'].IsChecked()
         mineral = cif.get_mineralname()
-        folder = f'{catom:s}{asite:d}_{edge:s}_{mineral}_cif{cif.ams_id:d}'
+
+        folder = f'{catom:s}{site_index:d}_{edge:s}_{mineral}_cif{cif.ams_id:d}'
         folder = unique_name(fix_filename(folder), self.feffruns_list)
 
-        fefftext = cif.get_feffinp(catom, edge=edge, cluster_size=csize,
-                                   absorber_site=asite, version8=version8,
-                                   with_h=with_h)
+        # extra titles from CIF
+        etitles = [f'CIF Source: Am Min Crystal Structure Database ID {cif.ams_id}',
+                  f'Mineral Name: {cif.mineral.name.lower()}']
+        pub = getattr(cif, 'publication', None)
+        if pub is not None:
+            authors = ', '.join(pub.authors)
+            ptext = f'{pub.journalname} {pub.volume} [{pub.page_first}:{pub.page_last}] ({pub.year})'
+            etitles.append(f'Publication: {ptext}')
+            etitles.append(f'Authors: {authors}')
+
+        cell = [f'a={fcompact(cif.a)}', f'b={fcompact(cif.b)}', f'c={fcompact(cif.c)}',
+                f'alpha={fcompact(cif.alpha)}', f'beta={fcompact(cif.beta)}',
+                f'gamma={fcompact(cif.gamma)}']
+
+        etitles.append(f'Cell Parameters (A, degrees): {", ".join(cell)}')
+        etitles.append(f'Cell Volume (A^3): {cif.cell_volume:.5f}')
+        etitles.append(f'Crystal Density (gr/cm^3): {cif.crystal_density:.5f}')
+        etitles.append(f'Compound: {cif.compound}')
+
+        fefftext = cif2feffinp(cif.ciftext, catom, edge=edge, cluster_size=csize,
+                               absorber_site=site_index, version8=version8,
+                               with_h=with_h, extra_titles=etitles)
 
         self.wids['feff_runfolder'].SetValue(folder)
         self.wids['feff_text'].SetValue(fefftext)
@@ -570,7 +599,6 @@ def onRunFeff(self, event=None):
         wx.CallAfter(self.run_feff, folder, version8=version8)
 
     def run_feff(self, folder=None, version8=True):
-        # print("RUN FEFF ", folder)
         dname = Path(folder).name
         prog, cmd = feff8l, 'feff8l'
         if not version8: