major restructure

- template notebooks moved to /templates folder - all template notebooks have been fully updated and commented - minor edits to studies notebooks
teanijarv · Dec 16, 2022 · a57e0c2 · a57e0c2
1 parent 29eede6
commit a57e0c2
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Showing 18 changed files with 2,524 additions and 9,699 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/oddball_data_visualisation.ipynb b/oddball_data_visualisation.ipynb
diff --git a/oddball_erp_analysis.ipynb b/oddball_erp_analysis.ipynb
diff --git a/oddball_erp_preprocessing.ipynb b/oddball_erp_preprocessing.ipynb
diff --git a/resting_aperiodicfit_bp_analysis.ipynb b/resting_aperiodicfit_bp_analysis.ipynb
diff --git a/resting_classic_bp_analysis.ipynb b/resting_classic_bp_analysis.ipynb
diff --git a/resting_preprocessing.ipynb b/resting_preprocessing.ipynb
diff --git a/signal_processing/erp_analysis.py b/signal_processing/erp_analysis.py
@@ -52,7 +52,7 @@ def find_all_peaks(evoked_obj,epochs,thresh=None,subject_name='',verbose=False,p
     return minpeak_times,minpeak_mags,maxpeak_times,maxpeak_mags
 
 def identify_erps(evoked_obj,erp_wins,minpeak_times,minpeak_mags,maxpeak_times,maxpeak_mags,subject_name='',
-                  verbose=False,plot=False,savefig=False,results_foldername = "Results/"):
+                  verbose=False,plot=False,savefig=False,results_foldername = "Results/",exp_folder=''):
     # Pre-define variables
     erp_peaks = {}
     not_erp_peaks = {}
@@ -129,13 +129,14 @@ def identify_erps(evoked_obj,erp_wins,minpeak_times,minpeak_mags,maxpeak_times,m
             plt.plot(erp_peaks[erp_name][0], erp_peaks[erp_name][1], marker='*', linestyle='None', color=color)
             plt.annotate(erp_name, (erp_peaks[erp_name][0]+15,erp_peaks[erp_name][1]-0.15))
         if savefig == True:
-            plt.savefig(fname='{}/ERP plots/{}_erpfig.png'.format(results_foldername,subject_name)) # add ERP plots to precreation function
+            plt.savefig(fname='{}/{}/ERP analysis/{}_erpfig.png'.format(results_foldername,
+                                                                        exp_folder, subject_name)) # add ERP plots to precreation function
         plt.show()
 
     return erp_peaks, not_erp_peaks
 
 def find_minmax_erp(evoked_obj,erp_peaks,erp_tochange,new_time_win,subject_name='',
-                    verbose=False,plot=False,savefig=False,results_foldername = "Results/"):
+                    verbose=False,plot=False,savefig=False,results_foldername = "Results/",exp_folder=''):
     time_coef = 1e3
     amplitude_coef= 1e6
 
@@ -188,7 +189,8 @@ def find_minmax_erp(evoked_obj,erp_peaks,erp_tochange,new_time_win,subject_name=
             plt.plot(erp_peaks[erp_name][0], erp_peaks[erp_name][1], marker='*', linestyle='None', color=color)
             plt.annotate(erp_name, (erp_peaks[erp_name][0]+15,erp_peaks[erp_name][1]-0.15))
         if savefig == True:
-            plt.savefig(fname='{}/ERP plots/{}_erpfig.png'.format(results_foldername,subject_name)) # add ERP plots to precreation function
+            plt.savefig(fname='{}/{}/ERP analysis/{}_erpfig.png'.format(results_foldername,
+                                                                        exp_folder, subject_name)) # add ERP plots to precreation function
         plt.show()
 
     return erp_peaks

diff --git a/studies/LABS-LEISURE_rsEEG_aperiodic+iaf.ipynb b/studies/LABS-LEISURE_rsEEG_aperiodic+iaf.ipynb
@@ -16,7 +16,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -31,7 +31,7 @@
     "from fooof.plts.periodic import plot_peak_params\n",
     "\n",
     "# Set the current working directory to be the project main folder\n",
-    "os.chdir('/Users/tanijarv/Documents/GitHub/EEG-pipeline-TI')\n",
+    "os.chdir('/Users/tanijarv/Documents/GitHub/EEG-pyline')\n",
     "plt.rc('axes', axisbelow=True)\n",
     "\n",
     "import basic.arrange_data as arrange\n",
@@ -1546,12 +1546,12 @@
     "                                '\\nAbs. PSD: '+str(np.round(abs_bp, 4))+'\\nRel. PSD: '+str(np.round(rel_bp, 4)),\n",
     "                                (0.75, 0.16), xycoords='figure fraction', color='green', fontsize=8.5)\n",
     "            \n",
-    "            plt.suptitle('{} region ({})'.format(region,subject_names[i]))\n",
+    "            plt.suptitle('{} region ({})'.format(region, subject_names[i]))\n",
     "            plt.tight_layout()\n",
     "            if savefig == True:\n",
     "                plt.savefig(fname='{}/{}/FOOOF/{}_{}_{}_fooof.png'.format(results_folder, exp_folder[exp],\n",
-    "                                                                        exp_condition[exp], subject_names[i],\n",
-    "                                                                        region))\n",
+    "                                                                          exp_condition[exp], subject_names[i],\n",
+    "                                                                          region), dpi=300)\n",
     "            plt.show()\n",
     "\n",
     "            # Add model parameters to dataframe\n",

diff --git a/studies/LEISURE_rsEEG_aperiodic.ipynb b/studies/LEISURE_rsEEG_aperiodic.ipynb
@@ -27,7 +27,7 @@
     "from fooof.plts.spectra import plot_spectrum\n",
     "\n",
     "# Set the current working directory to be the project main folder\n",
-    "os.chdir('/Users/tanijarv/Documents/GitHub/EEG-pipeline-TI')\n",
+    "os.chdir('/Users/tanijarv/Documents/GitHub/EEG-pyline')\n",
     "\n",
     "import basic.arrange_data as arrange\n",
     "import signal_processing.pre_process as pre_process\n",
@@ -921,7 +921,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13 | packaged by conda-forge | (main, May 27 2022, 17:00:52) \n[Clang 13.0.1 ]"
+   "version": "3.9.13"
   },
   "orig_nbformat": 4,
   "vscode": {

diff --git a/studies/OKTOS_rsEEG_classic_bp.ipynb b/studies/OKTOS_rsEEG_classic_bp.ipynb
@@ -15,7 +15,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -26,7 +26,7 @@
     "#mne.set_log_level('error')\n",
     "\n",
     "# Set the current working directory to be the project main folder\n",
-    "os.chdir('/Users/tanijarv/Documents/GitHub/EEG-pipeline-TI')\n",
+    "os.chdir('/Users/tanijarv/Documents/GitHub/EEG-pyline')\n",
     "\n",
     "import basic.arrange_data as arrange\n",
     "import signal_processing.pre_process as pre_process\n",

diff --git a/templates/auditory_oddball/oddball_data_visualisation.ipynb b/templates/auditory_oddball/oddball_data_visualisation.ipynb
diff --git a/templates/auditory_oddball/oddball_erp_analysis.ipynb b/templates/auditory_oddball/oddball_erp_analysis.ipynb
diff --git a/templates/auditory_oddball/oddball_erp_preprocessing.ipynb b/templates/auditory_oddball/oddball_erp_preprocessing.ipynb
diff --git a/templates/resting_state/resting_aperiodicfit_bp_analysis.ipynb b/templates/resting_state/resting_aperiodicfit_bp_analysis.ipynb
diff --git a/templates/resting_state/resting_classic_bp_analysis.ipynb b/templates/resting_state/resting_classic_bp_analysis.ipynb
diff --git a/resting_data_visualisation.ipynb → ...ng_state/resting_data_visualisation.ipynb b/resting_data_visualisation.ipynb → ...ng_state/resting_data_visualisation.ipynb
@@ -1,26 +1,27 @@
 {
  "cells": [
   {
-   "cell_type": "code",
-   "execution_count": 2,
+   "attachments": {},
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "import pandas as pd\n",
-    "import basic.arrange_data as arrange\n",
-    "from basic.stats import apply_stat_test\n",
-    "import data_visualisation as dataviz"
+    "### (DISCONTINUED) Resting State EEG: data visualisation"
    ]
   },
   {
-   "cell_type": "markdown",
+   "cell_type": "code",
+   "execution_count": 2,
    "metadata": {},
+   "outputs": [],
    "source": [
-    "**Spectral analysis data visualisation**\n",
+    "import pandas as pd\n",
+    "import os\n",
     "\n",
-    "Change these parameters! Set the folder of EEG power spectrum density files\n",
+    "os.chdir('/Users/tanijarv/Documents/GitHub/EEG-pyline')\n",
     "\n",
-    "*NB! The path has to be relative to this notebook.*"
+    "import basic.arrange_data as arrange\n",
+    "from basic.stats import apply_stat_test\n",
+    "import data_visualisation as dataviz"
    ]
   },
   {
@@ -55,13 +56,6 @@
     "# condition_codes_comparisons_eo = [['EO_00','EO_06'],['EO_06','EO_07'],['EO_00','EO_07']]"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Run this script to load in all the necessary data for plotting. Also it will display you all the significant changes which will help you choose what regions and bands to plot."
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 7,
@@ -335,7 +329,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.9.13 | packaged by conda-forge | (main, May 27 2022, 17:00:52) \n[Clang 13.0.1 ]"
   },
   "orig_nbformat": 4,
   "vscode": {

diff --git a/templates/resting_state/resting_preprocessing.ipynb b/templates/resting_state/resting_preprocessing.ipynb