Added readmes for matrices

.gitignore

@@ -95,3 +95,13 @@ arm64
 /examples/test/images/c302_C1_Oscillator.net.nml
 /examples/test/images/LEMS_c302_C1_Oscillator.xml
 /c302/VarshneyDataReader2.py
+/
+/examples/test/images/LEMS_c302_C1_Full.xml
+/examples/test/images/LEMS_c302_C1_Muscles.xml
+/examples/test/images/LEMS_c302_C1_Social.xml
+/examples/test/images/LEMS_c302_C1_Syns.xml
+/examples/test/images/c302_C1_Full.net.nml
+/examples/test/images/c302_C1_Muscles.net.nml
+/examples/test/images/c302_C1_Pharyngeal.net.nml
+/examples/test/images/c302_C1_Social.net.nml
+/examples/test/images/c302_C1_Syns.net.nml

c302/Cook2019DataReader.py

@@ -47,7 +47,9 @@ def get_synclass(cell, syntype):
             return "GABA"
         return "Acetylcholine"
 
-class Cook2019DataReaderReader():
+class Cook2019DataReader():
+
+    verbose = False
 
     def __init__(self):
 
@@ -69,12 +71,12 @@ def __init__(self):
             for i in pre_range[conn_type]:
                 self.pre_cells[conn_type].append(sheet['C%i'%i].value)
 
-            print(' - Pre cells for %s (%i):\n%s'%(conn_type, len(self.pre_cells[conn_type]), self.pre_cells[conn_type]))
+            if self.verbose: print(' - Pre cells for %s (%i):\n%s'%(conn_type, len(self.pre_cells[conn_type]), self.pre_cells[conn_type]))
 
             for i in post_range[conn_type]:
                 self.post_cells[conn_type].append(sheet.cell(row=3, column=i).value)
 
-            print(' - Post cells for %s (%i):\n%s'%(conn_type, len(self.post_cells[conn_type]), self.post_cells[conn_type]))
+            if self.verbose: print(' - Post cells for %s (%i):\n%s'%(conn_type, len(self.post_cells[conn_type]), self.post_cells[conn_type]))
 
             self.conn_nums[conn_type] = np.zeros([len(self.pre_cells[conn_type]),len(self.post_cells[conn_type])], dtype=int)
 
@@ -87,8 +89,7 @@ def __init__(self):
                     if val is not None:
                         self.conn_nums[conn_type][i,j] = int(val)
 
-            print()
-            print(' - Conns for %s (%s):\n%s'%(conn_type, self.conn_nums[conn_type].shape, self.conn_nums[conn_type]))
+            if self.verbose: print(' - Conns for %s (%s):\n%s'%(conn_type, self.conn_nums[conn_type].shape, self.conn_nums[conn_type]))
 
 
 
@@ -167,14 +168,14 @@ def read_muscle_data(self):
                 elif is_body_wall_muscle(pre) and pre not in muscles:
                     muscles.append(pre)
                 if post not in muscles:
-                    muscles.append(post)'''
+                    muscles.append(post)''' 
 
         return neurons, muscles, conns
 
 
 def main():
 
-    cdr = Cook2019DataReaderReader()
+    cdr = Cook2019DataReader()
     read_data = cdr.read_data
     read_muscle_data = cdr.read_muscle_data
 

c302/Cook2019HermReader.py

@@ -0,0 +1,19 @@
+# Temporary class to allow this to be used in comparison notebook. 
+# Should be tidied up.
+
+from c302.Cook2019DataReader import Cook2019DataReader
+
+from c302.ConnectomeReader import analyse_connections
+
+cdr = Cook2019DataReader()
+read_data = cdr.read_data
+read_muscle_data = cdr.read_muscle_data
+
+def main1():
+    cells, neuron_conns = read_data(include_nonconnected_cells=True)
+    neurons2muscles, muscles, muscle_conns = read_muscle_data()
+    analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns)
+
+
+if __name__ == '__main__':
+    main1()

c302/__init__.py

@@ -465,7 +465,7 @@ def _get_cell_info(bnd, cells):
     for name in fixed_up_names:
         cell = next(ctx(Cell).query(name=name).load(), None)
         if cell is None:
-            print_("No matching cell for %s" % name)
+            #print_("No matching cell for %s" % name)
             continue
 
         normalized_name = cell.name()

c302/c302_utils.py

@@ -577,6 +577,8 @@ def generate_conn_matrix(nml_doc, save_fig_dir=None, verbose=False, figsize=defa
     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']
 
+    figsize=(6.4,4.8)
+
     if '-phar' in sys.argv:
 
         configs = ['c302_C0_Pharyngeal.net.nml']
@@ -585,11 +587,21 @@ def generate_conn_matrix(nml_doc, save_fig_dir=None, verbose=False, figsize=defa
 
         configs = ['c302_C1_Oscillator.net.nml']
 
+    elif '-musc' in sys.argv:
+
+        configs = ['c302_C1_Muscles.net.nml']
+        figsize=(10,10)
+
+    elif '-full' in sys.argv:
+
+        configs = ['c302_C1_Full.net.nml']
+        figsize=(10,10)
+
     for c in configs:
 
         nml_doc = read_neuroml2_file('examples/%s'%c)
 
-        generate_conn_matrix(nml_doc, save_fig_dir='./examples/summary/images', figsize=(6.4,4.8))
+        generate_conn_matrix(nml_doc, save_fig_dir='./examples/summary/images', figsize=figsize)
 
     if not '-nogui' in sys.argv:
         plt.show()