Merge pull request #2 from openworm/development

Latest notebook & all updated generated activity images
yasinthanvickneswaran · Jan 31, 2024 · b0c2620 · b0c2620
2 parents 3bb9efa + bb91a43
commit b0c2620
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Showing 551 changed files with 226 additions and 282 deletions.
diff --git a/.gitignore b/.gitignore
@@ -90,3 +90,4 @@ arm64
 /.ipynb_checkpoints
 /c302/.ipynb_checkpoints
 .ipynb_checkpoints
+/c302/data/~$*.xlsx
diff --git a/.travis.yml b/.travis.yml
diff --git a/c302/NeuroMLUtilities.py b/c302/NeuroMLUtilities.py
@@ -105,7 +105,8 @@ def analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_co
 
     print_("Found %i neurons connected to muscles: %s\n"%(len(neurons2muscles), sorted(neurons2muscles)))
     print_("Found %i muscles connected to neurons: %s\n"%(len(muscles), sorted(muscles)))
-    print_("Found %i connections between neurons and muscles, e.g. %s\n"%(len(muscle_conns), muscle_conns[0]))
+
+    print_("Found %i connections between neurons and muscles%s\n"%(len(muscle_conns), (', e.g. %s'%muscle_conns[0]) if len(muscle_conns)>0 else ''))
 
     nts = {}
     nts_tot = {}

diff --git a/c302/SpreadsheetDataReader.py b/c302/SpreadsheetDataReader.py
@@ -4,7 +4,7 @@
 
 #    A simple script to read the values in CElegansNeuronTables.xls.
 
-#    This is on of a number of interchangeable "Readers" which can 
+#    This is one of a number of interchangeable "Readers" which can 
 #    be used to get connection data for c302
 
 ############################################################
@@ -20,11 +20,13 @@
 
 from c302 import print_
 
+READER_DESCRIPTION = """Data extracted from CElegansNeuronTables.xls for neuronal connectivity"""
+
 def read_data(include_nonconnected_cells=False, neuron_connect=False):
 
 
 
-# reading the NeuronConnect.xls file if neuron_connect = True
+# reading the NeuronConnectFormatted.xls file if neuron_connect = True
     if neuron_connect:
         conns = []
         cells = []
@@ -53,7 +55,7 @@ def read_data(include_nonconnected_cells=False, neuron_connect=False):
         filename = "%sCElegansNeuronTables.xls"%spreadsheet_location
         rb = open_workbook(filename)
 
-        print_("Opened Excel file..: " + filename)
+        print_("Opened Excel file: " + filename)
 
         known_nonconnected_cells = ['CANL', 'CANR', 'VC6']
 

diff --git a/c302/c302_utils.py b/c302/c302_utils.py
@@ -12,8 +12,6 @@
 
 import c302
 
-
-
 natsort = lambda s: [int(t) if t.isdigit() else t for t in re.split(r'(\d+)', s)]
 
 
@@ -56,7 +54,8 @@ def plots(a_n, info, cells, dt):
 
     a_n_ = a_n[:,::downscale]
 
-    plot0 = ax.pcolormesh(a_n_)
+    cmap = plt.colormaps['jet']
+    plot0 = ax.pcolormesh(a_n_, cmap=cmap)
     ax.set_yticks(np.arange(a_n_.shape[0]) + 0.5, minor=False)
     ax.set_yticklabels(cells)
     ax.tick_params(axis='y', labelsize=6)
@@ -102,6 +101,7 @@ def generate_traces_plot(config,parameter_set,xvals,yvals,info,labels,save,save_
                         show_plot_already=False,
                         save_figure_to=(None if not save else save_fig_path%(file_name)),
                         cols_in_legend_box=8,
+                        legend_position = "bottom center",
                         title_above_plot=True)
 
 
@@ -370,10 +370,12 @@ def _show_conn_matrix(data, t, all_info_pre,all_info_post, type, save_figure_to=
     plt.title(title)
     fig.canvas.manager.set_window_title(title)
     import matplotlib
-    cm = matplotlib.cm.get_cmap('gist_stern_r')
+    #cm = matplotlib.cm.get_cmap('gist_stern_r')
+    cmap = plt.colormaps['gist_stern_r']
+    #cmap = plt.colormaps['gist_earth']
 
 
-    im = plt.imshow(data, cmap=cm, interpolation='nearest',norm=None)
+    im = plt.imshow(data, cmap=cmap, interpolation='nearest',norm=None)
 
     ax = plt.gca();
     # Gridlines based on minor ticks
@@ -551,12 +553,12 @@ def generate_conn_matrix(nml_doc, save_fig_dir=None, verbose=False):
 
     from neuroml.loaders import read_neuroml2_file
 
-    configs = ['c302_C0_Syns.net.nml', 'c302_C0_Social.net.nml','c302_C0_Muscles.net.nml','c302_C0_Pharyngeal.net.nml','c302_C0_Oscillator.net.nml','c302_C0_Full.net.nml']
     configs = ['c302_C0_Syns.net.nml', 'c302_C0_Social.net.nml']
     #
     configs = ['c302_C0_Syns.net.nml']
     configs = ['c302_C0_Oscillator.net.nml']
     configs = ['c302_C0_Muscles.net.nml']
+    configs = ['c302_C0_Syns.net.nml', 'c302_C0_Social.net.nml','c302_C0_Muscles.net.nml','c302_C0_Pharyngeal.net.nml','c302_C0_Oscillator.net.nml','c302_C0_Full.net.nml']
 
     if '-phar' in sys.argv:
 
@@ -566,7 +568,7 @@ def generate_conn_matrix(nml_doc, save_fig_dir=None, verbose=False):
 
         nml_doc = read_neuroml2_file('examples/%s'%c)
 
-        generate_conn_matrix(nml_doc, save_fig_dir='./examples/summary/')
+        generate_conn_matrix(nml_doc, save_fig_dir='./examples/summary/images')
 
     if not '-nogui' in sys.argv:
         plt.show()
diff --git a/examples/summary/images/c302_B_Full_elec_neurons_neurons.png b/examples/summary/images/c302_B_Full_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_B_Muscles_elec_neurons_neurons.png b/examples/summary/images/c302_B_Muscles_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_B_Oscillator_elec_neurons_neurons.png b/examples/summary/images/c302_B_Oscillator_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_B_Pharyngeal_elec_neurons_neurons.png b/examples/summary/images/c302_B_Pharyngeal_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_B_Social_elec_neurons_neurons.png b/examples/summary/images/c302_B_Social_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_B_Syns_elec_neurons_neurons.png b/examples/summary/images/c302_B_Syns_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C0_Full_elec_neurons_neurons.png b/examples/summary/images/c302_C0_Full_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C0_Full_exc_to_muscles.png b/examples/summary/images/c302_C0_Full_exc_to_muscles.png
diff --git a/examples/summary/images/c302_C0_Full_exc_to_neurons.png b/examples/summary/images/c302_C0_Full_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C0_Full_inh_to_muscles.png b/examples/summary/images/c302_C0_Full_inh_to_muscles.png
diff --git a/examples/summary/images/c302_C0_Full_inh_to_neurons.png b/examples/summary/images/c302_C0_Full_inh_to_neurons.png
diff --git a/examples/summary/images/c302_C0_Muscles_elec_neurons_neurons.png b/examples/summary/images/c302_C0_Muscles_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C0_Muscles_exc_to_muscles.png b/examples/summary/images/c302_C0_Muscles_exc_to_muscles.png
diff --git a/examples/summary/images/c302_C0_Muscles_exc_to_neurons.png b/examples/summary/images/c302_C0_Muscles_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C0_Muscles_inh_to_muscles.png b/examples/summary/images/c302_C0_Muscles_inh_to_muscles.png
diff --git a/examples/summary/images/c302_C0_Muscles_inh_to_neurons.png b/examples/summary/images/c302_C0_Muscles_inh_to_neurons.png
diff --git a/examples/summary/images/c302_C0_Oscillator_elec_neurons_neurons.png b/examples/summary/images/c302_C0_Oscillator_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C0_Oscillator_exc_to_neurons.png b/examples/summary/images/c302_C0_Oscillator_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C0_Oscillator_inh_to_neurons.png b/examples/summary/images/c302_C0_Oscillator_inh_to_neurons.png
diff --git a/examples/summary/images/c302_C0_Pharyngeal_elec_neurons_neurons.png b/examples/summary/images/c302_C0_Pharyngeal_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C0_Pharyngeal_exc_to_neurons.png b/examples/summary/images/c302_C0_Pharyngeal_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C0_Social_elec_neurons_neurons.png b/examples/summary/images/c302_C0_Social_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C0_Social_exc_to_neurons.png b/examples/summary/images/c302_C0_Social_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C0_Syns_elec_neurons_neurons.png b/examples/summary/images/c302_C0_Syns_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C0_Syns_exc_to_muscles.png b/examples/summary/images/c302_C0_Syns_exc_to_muscles.png
diff --git a/examples/summary/images/c302_C0_Syns_exc_to_neurons.png b/examples/summary/images/c302_C0_Syns_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C0_Syns_inh_to_neurons.png b/examples/summary/images/c302_C0_Syns_inh_to_neurons.png
diff --git a/examples/summary/images/c302_C1_Full_elec_neurons_neurons.png b/examples/summary/images/c302_C1_Full_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C1_Full_exc_to_muscles.png b/examples/summary/images/c302_C1_Full_exc_to_muscles.png
diff --git a/examples/summary/images/c302_C1_Full_exc_to_neurons.png b/examples/summary/images/c302_C1_Full_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C1_Full_inh_to_muscles.png b/examples/summary/images/c302_C1_Full_inh_to_muscles.png
diff --git a/examples/summary/images/c302_C1_Full_inh_to_neurons.png b/examples/summary/images/c302_C1_Full_inh_to_neurons.png
diff --git a/examples/summary/images/c302_C1_Muscles_elec_neurons_neurons.png b/examples/summary/images/c302_C1_Muscles_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C1_Muscles_exc_to_muscles.png b/examples/summary/images/c302_C1_Muscles_exc_to_muscles.png
diff --git a/examples/summary/images/c302_C1_Muscles_exc_to_neurons.png b/examples/summary/images/c302_C1_Muscles_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C1_Muscles_inh_to_muscles.png b/examples/summary/images/c302_C1_Muscles_inh_to_muscles.png
diff --git a/examples/summary/images/c302_C1_Muscles_inh_to_neurons.png b/examples/summary/images/c302_C1_Muscles_inh_to_neurons.png
diff --git a/examples/summary/images/c302_C1_Oscillator_elec_neurons_neurons.png b/examples/summary/images/c302_C1_Oscillator_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C1_Oscillator_exc_to_neurons.png b/examples/summary/images/c302_C1_Oscillator_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C1_Oscillator_inh_to_neurons.png b/examples/summary/images/c302_C1_Oscillator_inh_to_neurons.png
diff --git a/examples/summary/images/c302_C1_Pharyngeal_elec_neurons_neurons.png b/examples/summary/images/c302_C1_Pharyngeal_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C1_Pharyngeal_exc_to_neurons.png b/examples/summary/images/c302_C1_Pharyngeal_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C1_Social_elec_neurons_neurons.png b/examples/summary/images/c302_C1_Social_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C1_Social_exc_to_neurons.png b/examples/summary/images/c302_C1_Social_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C1_Syns_elec_neurons_neurons.png b/examples/summary/images/c302_C1_Syns_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C1_Syns_exc_to_muscles.png b/examples/summary/images/c302_C1_Syns_exc_to_muscles.png
diff --git a/examples/summary/images/c302_C1_Syns_exc_to_neurons.png b/examples/summary/images/c302_C1_Syns_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C1_Syns_inh_to_neurons.png b/examples/summary/images/c302_C1_Syns_inh_to_neurons.png
diff --git a/examples/summary/images/c302_C2_Full_elec_neurons_neurons.png b/examples/summary/images/c302_C2_Full_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C2_Full_exc_to_muscles.png b/examples/summary/images/c302_C2_Full_exc_to_muscles.png
diff --git a/examples/summary/images/c302_C2_Full_exc_to_neurons.png b/examples/summary/images/c302_C2_Full_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C2_Full_inh_to_muscles.png b/examples/summary/images/c302_C2_Full_inh_to_muscles.png
diff --git a/examples/summary/images/c302_C2_Full_inh_to_neurons.png b/examples/summary/images/c302_C2_Full_inh_to_neurons.png
diff --git a/examples/summary/images/c302_C2_Muscles_elec_neurons_neurons.png b/examples/summary/images/c302_C2_Muscles_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C2_Muscles_exc_to_muscles.png b/examples/summary/images/c302_C2_Muscles_exc_to_muscles.png
diff --git a/examples/summary/images/c302_C2_Muscles_exc_to_neurons.png b/examples/summary/images/c302_C2_Muscles_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C2_Muscles_inh_to_muscles.png b/examples/summary/images/c302_C2_Muscles_inh_to_muscles.png
diff --git a/examples/summary/images/c302_C2_Muscles_inh_to_neurons.png b/examples/summary/images/c302_C2_Muscles_inh_to_neurons.png
diff --git a/examples/summary/images/c302_C2_Oscillator_elec_neurons_neurons.png b/examples/summary/images/c302_C2_Oscillator_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C2_Oscillator_exc_to_neurons.png b/examples/summary/images/c302_C2_Oscillator_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C2_Oscillator_inh_to_neurons.png b/examples/summary/images/c302_C2_Oscillator_inh_to_neurons.png
diff --git a/examples/summary/images/c302_C2_Pharyngeal_elec_neurons_neurons.png b/examples/summary/images/c302_C2_Pharyngeal_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C2_Pharyngeal_exc_to_neurons.png b/examples/summary/images/c302_C2_Pharyngeal_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C2_Social_elec_neurons_neurons.png b/examples/summary/images/c302_C2_Social_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C2_Social_exc_to_neurons.png b/examples/summary/images/c302_C2_Social_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C2_Syns_elec_neurons_neurons.png b/examples/summary/images/c302_C2_Syns_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C2_Syns_exc_to_muscles.png b/examples/summary/images/c302_C2_Syns_exc_to_muscles.png
diff --git a/examples/summary/images/c302_C2_Syns_exc_to_neurons.png b/examples/summary/images/c302_C2_Syns_exc_to_neurons.png
diff --git a/examples/summary/images/c302_C2_Syns_inh_to_neurons.png b/examples/summary/images/c302_C2_Syns_inh_to_neurons.png
diff --git a/examples/summary/images/c302_C_Full_elec_neurons_neurons.png b/examples/summary/images/c302_C_Full_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C_Muscles_elec_neurons_neurons.png b/examples/summary/images/c302_C_Muscles_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C_Oscillator_elec_neurons_neurons.png b/examples/summary/images/c302_C_Oscillator_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C_Pharyngeal_elec_neurons_neurons.png b/examples/summary/images/c302_C_Pharyngeal_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C_Social_elec_neurons_neurons.png b/examples/summary/images/c302_C_Social_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_C_Syns_elec_neurons_neurons.png b/examples/summary/images/c302_C_Syns_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_D1_Full_elec_neurons_neurons.png b/examples/summary/images/c302_D1_Full_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_D1_Full_exc_to_muscles.png b/examples/summary/images/c302_D1_Full_exc_to_muscles.png
diff --git a/examples/summary/images/c302_D1_Full_exc_to_neurons.png b/examples/summary/images/c302_D1_Full_exc_to_neurons.png
diff --git a/examples/summary/images/c302_D1_Full_inh_to_muscles.png b/examples/summary/images/c302_D1_Full_inh_to_muscles.png
diff --git a/examples/summary/images/c302_D1_Full_inh_to_neurons.png b/examples/summary/images/c302_D1_Full_inh_to_neurons.png
diff --git a/examples/summary/images/c302_D1_Muscles_elec_neurons_neurons.png b/examples/summary/images/c302_D1_Muscles_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_D1_Muscles_exc_to_muscles.png b/examples/summary/images/c302_D1_Muscles_exc_to_muscles.png
diff --git a/examples/summary/images/c302_D1_Muscles_exc_to_neurons.png b/examples/summary/images/c302_D1_Muscles_exc_to_neurons.png
diff --git a/examples/summary/images/c302_D1_Muscles_inh_to_muscles.png b/examples/summary/images/c302_D1_Muscles_inh_to_muscles.png
diff --git a/examples/summary/images/c302_D1_Muscles_inh_to_neurons.png b/examples/summary/images/c302_D1_Muscles_inh_to_neurons.png
diff --git a/examples/summary/images/c302_D1_Oscillator_elec_neurons_neurons.png b/examples/summary/images/c302_D1_Oscillator_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_D1_Oscillator_exc_to_neurons.png b/examples/summary/images/c302_D1_Oscillator_exc_to_neurons.png
diff --git a/examples/summary/images/c302_D1_Oscillator_inh_to_neurons.png b/examples/summary/images/c302_D1_Oscillator_inh_to_neurons.png
diff --git a/examples/summary/images/c302_D1_Pharyngeal_elec_neurons_neurons.png b/examples/summary/images/c302_D1_Pharyngeal_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_D1_Pharyngeal_exc_to_neurons.png b/examples/summary/images/c302_D1_Pharyngeal_exc_to_neurons.png
diff --git a/examples/summary/images/c302_D1_Social_elec_neurons_neurons.png b/examples/summary/images/c302_D1_Social_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_D1_Social_exc_to_neurons.png b/examples/summary/images/c302_D1_Social_exc_to_neurons.png
diff --git a/examples/summary/images/c302_D1_Syns_elec_neurons_neurons.png b/examples/summary/images/c302_D1_Syns_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_D1_Syns_exc_to_muscles.png b/examples/summary/images/c302_D1_Syns_exc_to_muscles.png
diff --git a/examples/summary/images/c302_D1_Syns_exc_to_neurons.png b/examples/summary/images/c302_D1_Syns_exc_to_neurons.png
diff --git a/examples/summary/images/c302_D1_Syns_inh_to_neurons.png b/examples/summary/images/c302_D1_Syns_inh_to_neurons.png
diff --git a/examples/summary/images/c302_D_Full_elec_neurons_neurons.png b/examples/summary/images/c302_D_Full_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_D_Muscles_elec_neurons_neurons.png b/examples/summary/images/c302_D_Muscles_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_D_Oscillator_elec_neurons_neurons.png b/examples/summary/images/c302_D_Oscillator_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_D_Pharyngeal_elec_neurons_neurons.png b/examples/summary/images/c302_D_Pharyngeal_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_D_Social_elec_neurons_neurons.png b/examples/summary/images/c302_D_Social_elec_neurons_neurons.png
diff --git a/examples/summary/images/c302_D_Syns_elec_neurons_neurons.png b/examples/summary/images/c302_D_Syns_elec_neurons_neurons.png
diff --git a/examples/summary/images/muscle_activity_B_Full.png b/examples/summary/images/muscle_activity_B_Full.png
diff --git a/examples/summary/images/muscle_activity_B_IClamp.png b/examples/summary/images/muscle_activity_B_IClamp.png
diff --git a/examples/summary/images/muscle_activity_B_Muscles.png b/examples/summary/images/muscle_activity_B_Muscles.png
diff --git a/examples/summary/images/muscle_activity_B_Syns.png b/examples/summary/images/muscle_activity_B_Syns.png
diff --git a/examples/summary/images/muscle_activity_C0_Full.png b/examples/summary/images/muscle_activity_C0_Full.png
diff --git a/examples/summary/images/muscle_activity_C0_IClamp.png b/examples/summary/images/muscle_activity_C0_IClamp.png
diff --git a/examples/summary/images/muscle_activity_C0_Muscles.png b/examples/summary/images/muscle_activity_C0_Muscles.png
diff --git a/examples/summary/images/muscle_activity_C0_Syns.png b/examples/summary/images/muscle_activity_C0_Syns.png
diff --git a/examples/summary/images/muscle_activity_C1_Full.png b/examples/summary/images/muscle_activity_C1_Full.png
diff --git a/examples/summary/images/muscle_activity_C1_IClamp.png b/examples/summary/images/muscle_activity_C1_IClamp.png
diff --git a/examples/summary/images/muscle_activity_C1_Muscles.png b/examples/summary/images/muscle_activity_C1_Muscles.png
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