Merge pull request #65 from openworm/development

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openworm · Feb 15, 2024 · 5ee13fb · 5ee13fb
2 parents f1bfd22 + cd80249
commit 5ee13fb
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Showing 28 changed files with 167 additions and 118 deletions.
diff --git a/.github/workflows/non_omv.yml b/.github/workflows/non_omv.yml
@@ -29,13 +29,18 @@ jobs:
     - name: Install c302
       run: |
         pip install .
+        pip install WormNeuroAtlas
         pip list
         
     - name: Test OpenWormReader with owmeta
       run: |
         owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json'
         python -m c302.OpenWormReader
 
+    - name: Test WormNeuroAtlasReader
+      run: |
+        python -m c302.WormNeuroAtlasReader
+
     - name: Run some examples
       run: |
         cd c302

diff --git a/.gitignore b/.gitignore
@@ -90,3 +90,4 @@ arm64
 /.ipynb_checkpoints
 /c302/.ipynb_checkpoints
 .ipynb_checkpoints
+/c302/data/~$*.xlsx
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/examples/parametersweep/Canonical_C.json b/examples/parametersweep/Canonical_C.json
@@ -1,6 +1,6 @@
 {
     "Canonical_C": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.5.9",
         "parameters": {
             "stim_duration": "2000ms",
             "stim_amp": "3.5pA",

diff --git a/examples/parametersweep/Canonical_C.net.nml b/examples/parametersweep/Canonical_C.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="Canonical_C">
-    <notes>Generated by NeuroMLlite v0.5.7
+    <notes>Generated by NeuroMLlite v0.5.9
     Generated network: Canonical_C
     Generation seed: 1234
     NeuroMLlite parameters: 

diff --git a/examples/parametersweep/Canonical_X.json b/examples/parametersweep/Canonical_X.json
@@ -1,6 +1,6 @@
 {
     "Canonical_X": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.5.9",
         "parameters": {
             "stim_duration": "250ms",
             "stim_amp": "1pA",

diff --git a/examples/parametersweep/Canonical_X.net.nml b/examples/parametersweep/Canonical_X.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="Canonical_X">
-    <notes>Generated by NeuroMLlite v0.5.7
+    <notes>Generated by NeuroMLlite v0.5.9
     Generated network: Canonical_X
     Generation seed: 1234
     NeuroMLlite parameters: 

diff --git a/examples/parametersweep/IClamp_GenericMuscleCell.json b/examples/parametersweep/IClamp_GenericMuscleCell.json
@@ -1,6 +1,6 @@
 {
     "IClamp_GenericMuscleCell": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.5.9",
         "notes": "A network model: IClamp_GenericMuscleCell",
         "parameters": {
             "stim_amp": "4pA"

diff --git a/examples/parametersweep/IClamp_GenericMuscleCell.net.nml b/examples/parametersweep/IClamp_GenericMuscleCell.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="IClamp_GenericMuscleCell">
-    <notes>Generated by NeuroMLlite v0.5.7
+    <notes>Generated by NeuroMLlite v0.5.9
     Generated network: IClamp_GenericMuscleCell
     Generation seed: 1234
     NeuroMLlite parameters: 

diff --git a/examples/parametersweep/IClamp_GenericNeuronCell.json b/examples/parametersweep/IClamp_GenericNeuronCell.json
@@ -1,6 +1,6 @@
 {
     "IClamp_GenericNeuronCell": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.5.9",
         "notes": "A network model: IClamp_GenericNeuronCell",
         "parameters": {
             "stim_amp": "4pA"

diff --git a/examples/parametersweep/IClamp_GenericNeuronCell.net.nml b/examples/parametersweep/IClamp_GenericNeuronCell.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="IClamp_GenericNeuronCell">
-    <notes>Generated by NeuroMLlite v0.5.7
+    <notes>Generated by NeuroMLlite v0.5.9
     Generated network: IClamp_GenericNeuronCell
     Generation seed: 1234
     NeuroMLlite parameters: 

diff --git a/examples/parametersweep/README.md b/examples/parametersweep/README.md
@@ -21,6 +21,27 @@
     <img alt="?" src="mean_spike_frequency_dt_GenericNeuronCell.png" height="160"/></a>
   </td>
 <tr>
+<tr>
+  <td width=30><b>GenericNeuronCellX</b></td>
+  <td><a href="mean_spike_frequency_GenericNeuronCellX.png">
+    <img alt="?" src="mean_spike_frequency_GenericNeuronCellX.png" height="160"/></a>
+  </td>
+  <td><a href="firing_rates_GenericNeuronCellX.png">
+    <img alt="?" src="firing_rates_GenericNeuronCellX.png" height="160"/></a>
+  </td>
+  <td><a href="heatmap_GenericNeuronCellX.png">
+    <img alt="?" src="heatmap_GenericNeuronCellX.png" height="160"/></a>
+  </td>
+  <td><a href="dt_traces_GenericNeuronCellX.png">
+    <img alt="?" src="dt_traces_GenericNeuronCellX.png" height="160"/></a>
+  </td>
+  <td><a href="heatmap_dt_GenericNeuronCellX.png">
+    <img alt="?" src="heatmap_dt_GenericNeuronCellX.png" height="160"/></a>
+  </td>
+  <td><a href="mean_spike_frequency_dt_GenericNeuronCellX.png">
+    <img alt="?" src="mean_spike_frequency_dt_GenericNeuronCellX.png" height="160"/></a>
+  </td>
+<tr>
 <tr>
   <td width=30><b>GenericMuscleCell</b></td>
   <td><a href="mean_spike_frequency_GenericMuscleCell.png">

diff --git a/examples/parametersweep/SimCanonical_C.json b/examples/parametersweep/SimCanonical_C.json
@@ -1,6 +1,6 @@
 {
     "SimCanonical_C": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.5.9",
         "network": "Canonical_C.json",
         "duration": 3000.0,
         "dt": 0.1,

diff --git a/examples/parametersweep/SimCanonical_X.json b/examples/parametersweep/SimCanonical_X.json
@@ -1,6 +1,6 @@
 {
     "SimCanonical_X": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.5.9",
         "network": "Canonical_X.json",
         "duration": 3000.0,
         "dt": 0.1,

diff --git a/examples/parametersweep/Sim_IClamp_GenericMuscleCell.json b/examples/parametersweep/Sim_IClamp_GenericMuscleCell.json
@@ -1,6 +1,6 @@
 {
     "Sim_IClamp_GenericMuscleCell": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.5.9",
         "network": "IClamp_GenericMuscleCell.json",
         "duration": 3000.0,
         "dt": 0.025,

diff --git a/examples/parametersweep/Sim_IClamp_GenericNeuronCell.json b/examples/parametersweep/Sim_IClamp_GenericNeuronCell.json
@@ -1,6 +1,6 @@
 {
     "Sim_IClamp_GenericNeuronCell": {
-        "version": "NeuroMLlite v0.5.7",
+        "version": "NeuroMLlite v0.5.9",
         "network": "IClamp_GenericNeuronCell.json",
         "duration": 3000.0,
         "dt": 0.025,

diff --git a/examples/parametersweep/Sweep.py b/examples/parametersweep/Sweep.py
@@ -12,7 +12,7 @@
 
     heatmap_lims=[-110,20]
 
-    standard_stim_amps = ['%spA'%(i/10.0) for i in xrange(-5,70,1)]
+    standard_stim_amps = ['%spA'%(i/10.0) for i in range(-5,70,1)]
 
     if '-all' in sys.argv:
 
@@ -24,7 +24,7 @@
 
 
         vary = {'stim_amp':standard_stim_amps}
-        #vary = {'stim_amp':['%spA'%(i/10.0) for i in xrange(-10,20,5)]}
+        #vary = {'stim_amp':['%spA'%(i/10.0) for i in range(-10,20,5)]}
         #vary = {'stim_amp':['-100pA','0pA','100pA','200pA','300pA','400pA']}
 
         cells = colors.keys()
@@ -146,9 +146,9 @@
 
         vary = {'stim_amp':standard_stim_amps}
 
-        #vary = {'number_per_cell':[i for i in xrange(0,250,10)]}
+        #vary = {'number_per_cell':[i for i in range(0,250,10)]}
         vary = {'stim_amp':['-1pA','0pA','1.5pA','2pA']}
-        vary = {'stim_amp':['%spA'%(i/10.0) for i in xrange(-20,60,5)]}
+        vary = {'stim_amp':['%spA'%(i/10.0) for i in range(-20,60,5)]}
 
         type = 'GenericMuscleCell'
         type = 'GenericNeuronCell'
@@ -197,9 +197,9 @@
         vary = {'dt':[0.1,0.05,0.025,0.01,0.005,0.0025,0.001]}
         vary = {'dt':[0.1,0.05,0.025,0.01,0.005]}
 
-        #vary = {'number_per_cell':[i for i in xrange(0,250,10)]}
+        #vary = {'number_per_cell':[i for i in range(0,250,10)]}
         #vary = {'stim_amp':['1pA','1.5pA','2pA']}
-        vary = {'stim_amp':['%spA'%(i/10.0) for i in xrange(-3,60,1)]}
+        vary = {'stim_amp':['%spA'%(i/10.0) for i in range(-3,60,1)]}
 
         type = 'GenericMuscleCell'
         type = 'GenericNeuronCell'

diff --git a/examples/parametersweep/firing_rates_GenericMuscleCell.png b/examples/parametersweep/firing_rates_GenericMuscleCell.png
diff --git a/examples/parametersweep/firing_rates_GenericNeuronCell.png b/examples/parametersweep/firing_rates_GenericNeuronCell.png
diff --git a/examples/parametersweep/firing_rates_GenericNeuronCellX.png b/examples/parametersweep/firing_rates_GenericNeuronCellX.png
diff --git a/examples/parametersweep/heatmap_GenericMuscleCell.png b/examples/parametersweep/heatmap_GenericMuscleCell.png
diff --git a/examples/parametersweep/heatmap_GenericNeuronCell.png b/examples/parametersweep/heatmap_GenericNeuronCell.png
diff --git a/examples/parametersweep/heatmap_GenericNeuronCellX.png b/examples/parametersweep/heatmap_GenericNeuronCellX.png
diff --git a/examples/parametersweep/info.html b/examples/parametersweep/info.html
@@ -21,6 +21,27 @@
     <img alt="?" src="mean_spike_frequency_dt_GenericNeuronCell.png" height="160"/></a>
   </td>
 <tr>
+<tr>
+  <td width=30><b>GenericNeuronCellX</b></td>
+  <td><a href="mean_spike_frequency_GenericNeuronCellX.png">
+    <img alt="?" src="mean_spike_frequency_GenericNeuronCellX.png" height="160"/></a>
+  </td>
+  <td><a href="firing_rates_GenericNeuronCellX.png">
+    <img alt="?" src="firing_rates_GenericNeuronCellX.png" height="160"/></a>
+  </td>
+  <td><a href="heatmap_GenericNeuronCellX.png">
+    <img alt="?" src="heatmap_GenericNeuronCellX.png" height="160"/></a>
+  </td>
+  <td><a href="dt_traces_GenericNeuronCellX.png">
+    <img alt="?" src="dt_traces_GenericNeuronCellX.png" height="160"/></a>
+  </td>
+  <td><a href="heatmap_dt_GenericNeuronCellX.png">
+    <img alt="?" src="heatmap_dt_GenericNeuronCellX.png" height="160"/></a>
+  </td>
+  <td><a href="mean_spike_frequency_dt_GenericNeuronCellX.png">
+    <img alt="?" src="mean_spike_frequency_dt_GenericNeuronCellX.png" height="160"/></a>
+  </td>
+<tr>
 <tr>
   <td width=30><b>GenericMuscleCell</b></td>
   <td><a href="mean_spike_frequency_GenericMuscleCell.png">

diff --git a/examples/parametersweep/mean_spike_frequency_GenericMuscleCell.png b/examples/parametersweep/mean_spike_frequency_GenericMuscleCell.png
diff --git a/examples/parametersweep/mean_spike_frequency_GenericNeuronCell.png b/examples/parametersweep/mean_spike_frequency_GenericNeuronCell.png
diff --git a/examples/parametersweep/mean_spike_frequency_GenericNeuronCellX.png b/examples/parametersweep/mean_spike_frequency_GenericNeuronCellX.png