Refactor to use versions of SpreadsheetDataReader etc. in cect (ConnectomeToolbox)

.github/workflows/non_omv.yml

@@ -61,10 +61,10 @@ jobs:
         omv list -V
         omv install NEURON # Need to install NEURON
         which nrnivmodl
-        export NEURON_HOME=$RUNNER_TOOL_CACHE/Python/3.9.7/x64/
 
     - name: Run test script
       run: |
+        export NEURON_HOME=$pythonLocation
         pip install ruff
         ./test.sh
 

.gitignore

@@ -110,3 +110,13 @@ arm64
 /examples/parametersweep/LEMS_SimCanonical_X.png
 /examples/parametersweep/Canonical_X__lems.xml
 /examples/parametersweep/average_last_1percent_GenericNeuronCellX.png
+/examples/parametersweep/IClamp_GenericNeuronCellW2D.json
+/examples/parametersweep/IClamp_GenericNeuronCellW2D.net.nml
+/examples/parametersweep/IClamp_GenericNeuronCellW2D__lems.xml
+/examples/parametersweep/LEMS_SimCanonical_W2D.xml
+/examples/parametersweep/Sim_IClamp_GenericNeuronCellW2D.json
+/examples/parametersweep/Canonical_W2D__lems.xml
+/examples/parametersweep/LEMS_Sim_IClamp_GenericNeuronCellW2D.xml
+/examples/parametersweep/c302_C0_IClampMuscle.net.nml
+/examples/parametersweep/average_last_1percent_GenericNeuronCellW2D.png
+/examples/parametersweep/heatmap_GenericNeuronCellW2D.png

c302/NeuroMLUtilities.py

@@ -43,7 +43,6 @@ def fract(a, b, f):
 
 
 if __name__ == "__main__":
-    # from SpreadsheetDataReader import read_data, read_muscle_data
     from WormNeuroAtlasReader import read_data, read_muscle_data
 
     cells, neuron_conns = read_data(include_nonconnected_cells=True)

c302/__init__.py

@@ -23,6 +23,8 @@
 import neuroml.writers as writers
 import neuroml.loaders as loaders
 
+import cect
+
 # import c302.bioparameters
 
 import airspeed
@@ -36,10 +38,7 @@
 import math
 from lxml import etree
 import re
-
 import json
-
-
 import collections
 
 try:
@@ -62,6 +61,16 @@
 except Exception:
     from urllib.error import URLError  # Python 3
 
+
+from cect.Cells import BODY_WALL_MUSCLE_NAMES
+
+DEFAULT_DATA_READER = "SpreadsheetDataReader"
+#
+# DEFAULT_DATA_READER = "cect.White_whole"
+# DEFAULT_DATA_READER = "cect.Cook2019HermReader"
+DEFAULT_DATA_READER = "cect.SpreadsheetDataReader"
+FW_DATA_READER = "cect.UpdatedSpreadsheetDataReader2"
+
 logging.basicConfig()
 
 here = os.path.abspath(os.path.dirname(__file__))
@@ -85,15 +94,20 @@ def print_(msg, print_it=True):  # print_it=False when not verbose
         print("%s %s" % (pre, msg.replace("\n", "\n" + pre)))
 
 
-def load_data_reader(data_reader="SpreadsheetDataReader"):
+def load_data_reader(data_reader):
     """
     Imports and returns data reader module
     Args:
         data_reader (str): The name of the data reader
     Returns:
         reader (obj): The data reader object
     """
-    return importlib.import_module("c302.%s" % data_reader)
+    # return importlib.import_module("c302.%s" % data_reader)
+    if "cect" in data_reader:
+        dr = importlib.import_module("%s" % data_reader)
+        return dr.get_instance()
+    else:
+        return importlib.import_module("c302.%s" % data_reader)
 
 
 def get_str_from_expnotation(num):
@@ -107,7 +121,7 @@ def get_str_from_expnotation(num):
     return "{0:.15f}".format(num)
 
 
-def get_muscle_position(muscle, data_reader="SpreadsheetDataReader"):
+def get_muscle_position(muscle, data_reader):
     if muscle == "MANAL" or muscle == "MVULVA":
         return 0, 0, 0
     # TODO: Pull these positions from openworm/owmeta-data
@@ -160,8 +174,8 @@ def process_args():
         "-datareader",
         type=str,
         metavar="<data-reader>",
-        default="SpreadsheetDataReader",
-        help='Use a specific data reader. Possible values are: "SpreadsheetDataReader". (default: SpreadsheetDataReader)',
+        default=DEFAULT_DATA_READER,
+        help="Use a specific data reader. (default: %s)" % DEFAULT_DATA_READER,
     )
 
     parser.add_argument(
@@ -449,8 +463,8 @@ def get_file_name_relative_to_c302(file_name):
         return os.path.relpath(os.environ["C302_HOME"], file_name)
 
 
-def get_cell_names_and_connection(data_reader="SpreadsheetDataReader", test=False):
-    # Use the spreadsheet reader to give a list of all cells and a list of all connections
+def get_cell_names_and_connection(data_reader, test=False):
+    # Use the data reader to give a list of all cells and a list of all connections
     # This could be replaced with a call to "DatabaseReader" or "OpenWormNeuroLexReader" in future...
     # If called from unittest folder ammend path to "../../../../"
 
@@ -463,17 +477,28 @@ def get_cell_names_and_connection(data_reader="SpreadsheetDataReader", test=Fals
     return cell_names, conns
 
 
-def get_cell_muscle_names_and_connection(
-    data_reader="SpreadsheetDataReader", test=False
-):
+def get_cell_muscle_names_and_connection(data_reader, test=False):
     mneurons, all_muscles, muscle_conns = load_data_reader(
         data_reader
     ).read_muscle_data()
     if "MANAL" in all_muscles:
         all_muscles.remove("MANAL")
     if "MVULVA" in all_muscles:
         all_muscles.remove("MVULVA")
-    return mneurons, sorted(all_muscles), muscle_conns
+
+    all_known_muscles = []
+    if len(all_muscles) == 0:
+        all_known_muscles = BODY_WALL_MUSCLE_NAMES
+    else:
+        for m in all_muscles:
+            if m in BODY_WALL_MUSCLE_NAMES:
+                all_known_muscles.append(m)
+
+    all_known_muscles = sorted(all_known_muscles)
+
+    print(" --- Using for muscles: %s" % all_known_muscles)
+
+    return mneurons, all_known_muscles, muscle_conns
 
 
 def is_cond_based_cell(params):
@@ -629,7 +654,7 @@ def mirror_param(params, k, v):
 def generate(
     net_id,
     params,
-    data_reader="SpreadsheetDataReader",
+    data_reader=DEFAULT_DATA_READER,
     cells=None,
     cells_to_plot=None,
     cells_to_stimulate=None,
@@ -707,6 +732,11 @@ def generate(
         "\n\nParameters and setting used to generate this network:\n\n"
         + "    Data reader:                    %s\n" % data_reader
         + "    c302 version:                   %s\n" % __version__
+        + (
+            "    cect version:                   %s\n" % (cect.__version__)
+            if "cect" in data_reader
+            else ""
+        )
         + "    owmeta version:                 %s\n"
         % ("- not installed -" if not owmeta_installed else owmeta_version)
         + "    owmeta_core version:            %s\n"
@@ -1006,10 +1036,6 @@ def generate(
         data_reader
     )
 
-    # print(all_muscles)
-    # if data_reader == "SpreadsheetDataReader":
-    #    all_muscles = get_muscle_names()
-
     if muscles_to_include is None or muscles_to_include is True:
         muscles_to_include = all_muscles
     elif muscles_to_include is False:

c302/__version__.py

@@ -1 +1 @@
-__version__ = "0.9.1"
+__version__ = "0.10.0"

c302/c302_FW.py

@@ -17,7 +17,7 @@ def setup(
     duration=2000,
     dt=0.05,
     target_directory="examples",
-    data_reader="UpdatedSpreadsheetDataReader2",
+    data_reader=c302.FW_DATA_READER,
     param_overrides={},
     verbose=True,
     config_param_overrides={},
@@ -256,6 +256,6 @@ def setup(
 
 if __name__ == "__main__":
     parameter_set = sys.argv[1] if len(sys.argv) == 2 else "C2"
-    data_reader = sys.argv[2] if len(sys.argv) == 3 else "UpdatedSpreadsheetDataReader2"
+    data_reader = sys.argv[2] if len(sys.argv) == 3 else c302.FW_DATA_READER
 
     setup(parameter_set, generate=True, data_reader=data_reader)

c302/c302_Full.py

@@ -11,7 +11,7 @@ def setup(
     dt=0.05,
     target_directory="examples",
     muscles_to_include=None,  # None => All!
-    data_reader="SpreadsheetDataReader",
+    data_reader=c302.DEFAULT_DATA_READER,
     param_overrides={},
     config_param_overrides={},
     verbose=True,
@@ -79,7 +79,7 @@ def setup(
 
     reference = "c302_%s_Full" % parameter_set
 
-    cell_names, conns = c302.get_cell_names_and_connection()
+    cell_names, conns = c302.get_cell_names_and_connection(data_reader)
 
     nml_doc = None
 

c302/c302_IClamp.py

@@ -11,7 +11,7 @@ def setup(
     duration=None,
     dt=0.05,
     target_directory="examples",
-    data_reader="SpreadsheetDataReader",
+    data_reader=c302.DEFAULT_DATA_READER,
     param_overrides={},
     config_param_overrides={},
     verbose=True,

c302/c302_IClampMuscle.py

@@ -10,7 +10,7 @@ def setup(
     duration=2000,
     dt=0.05,
     target_directory="examples",
-    data_reader="SpreadsheetDataReader",
+    data_reader=c302.DEFAULT_DATA_READER,
     param_overrides={},
     verbose=True,
 ):

c302/c302_MuscleTest.py

@@ -17,7 +17,7 @@ def setup(
     duration=2000,
     dt=0.05,
     target_directory="examples",
-    data_reader="SpreadsheetDataReader",
+    data_reader=c302.DEFAULT_DATA_READER,
     param_overrides={},
     verbose=True,
     config_param_overrides={},

c302/c302_Muscles.py

@@ -10,7 +10,7 @@ def setup(
     duration=1000,
     dt=0.05,
     target_directory="examples",
-    data_reader="SpreadsheetDataReader",
+    data_reader=c302.DEFAULT_DATA_READER,
     param_overrides={},
     config_param_overrides={},
     verbose=True,

c302/c302_MusclesSine.py

@@ -9,7 +9,7 @@ def setup(
     duration=1000,
     dt=0.05,
     target_directory="examples",
-    data_reader="SpreadsheetDataReader",
+    data_reader=c302.DEFAULT_DATA_READER,
     param_overrides={},
     config_param_overrides={},
     verbose=True,

c302/c302_Oscillator.py

@@ -9,7 +9,7 @@ def setup(
     duration=1000,
     dt=0.05,
     target_directory="examples",
-    data_reader="SpreadsheetDataReader",
+    data_reader="cect.SpreadsheetDataReader",
     param_overrides={},
     config_param_overrides={},
     verbose=True,

c302/c302_OscillatorM.py

@@ -9,7 +9,7 @@ def setup(
     duration=1000,
     dt=0.05,
     target_directory="examples",
-    data_reader="SpreadsheetDataReader",
+    data_reader=c302.DEFAULT_DATA_READER,
     param_overrides={},
     config_param_overrides={},
     verbose=True,

c302/c302_Pharyngeal.py

@@ -9,7 +9,7 @@ def setup(
     duration=500,
     dt=0.01,
     target_directory="examples",
-    data_reader="SpreadsheetDataReader",
+    data_reader=c302.DEFAULT_DATA_READER,
     param_overrides={},
     config_param_overrides={},
     verbose=True,

c302/c302_RIA.py

@@ -10,7 +10,7 @@ def setup(
     duration=1000,
     dt=0.05,
     target_directory="examples",
-    data_reader="SpreadsheetDataReader",
+    data_reader=c302.DEFAULT_DATA_READER,
     param_overrides={},
     verbose=True,
 ):

c302/c302_Social.py

@@ -23,7 +23,7 @@ def setup(
     duration=2500,
     dt=0.05,
     target_directory="examples",
-    data_reader="SpreadsheetDataReader",
+    data_reader=c302.DEFAULT_DATA_READER,
     param_overrides={},
     config_param_overrides={},
     verbose=True,

c302/c302_Syns.py

@@ -10,7 +10,7 @@ def setup(
     duration=500,
     dt=0.05,
     target_directory="examples",
-    data_reader="SpreadsheetDataReader",
+    data_reader=c302.DEFAULT_DATA_READER,
     param_overrides={},
     config_param_overrides={},
     verbose=True,

c302/c302_TapWithdrawal.py

@@ -19,7 +19,7 @@ def setup(
     duration=400,
     dt=0.05,
     target_directory="examples",
-    data_reader="UpdatedSpreadsheetDataReader",
+    data_reader=c302.FW_DATA_READER,
     param_overrides={},
     config_param_overrides={},
     verbose=True,
@@ -469,4 +469,4 @@ def setup(
 if __name__ == "__main__":
     parameter_set = sys.argv[1] if len(sys.argv) == 2 else "C2"
 
-    setup(parameter_set, generate=True, data_reader="UpdatedSpreadsheetDataReader")
+    setup(parameter_set, generate=True, data_reader=c302.FW_DATA_READER)

c302/c302_TargetMuscle.py

@@ -9,7 +9,7 @@ def setup(
     duration=3000,
     dt=0.05,
     target_directory="examples",
-    data_reader="SpreadsheetDataReader",
+    data_reader=c302.DEFAULT_DATA_READER,
     param_overrides={},
     config_param_overrides={},
     verbose=True,

c302/c302_utils.py

@@ -126,7 +126,7 @@ def plot_c302_results(
     directory="./",
     save=True,
     show_plot_already=True,
-    data_reader="SpreadsheetDataReader",
+    data_reader=c302.DEFAULT_DATA_READER,
     plot_ca=True,
 ):
     params = {"legend.fontsize": 8, "font.size": 10}

c302/custom_synapses.xml

@@ -3,6 +3,10 @@
     <!-- Definition of new synapse model types-->
 
 
+    <ComponentType name="baseGradedSynapseDL"
+                   extends="baseSynapseDL"
+                   description="Base type for dimensionless graded synapses">
+    </ComponentType>
 
     <ComponentType name="outputSynapse"
                    extends="baseGradedSynapse"
@@ -14,12 +18,12 @@
 
         <Exposure name="i" dimension="current"/>
 
-        <Requirement name="state" dimension="none"/>
+        <Requirement name="output" dimension="none"/>
 
         <InstanceRequirement name="peer" type="outputSynapse"/>
 
         <Dynamics>
-            <DerivedVariable name="outputpeer" dimension="none" select="peer/state"/>
+            <DerivedVariable name="outputpeer" dimension="none" select="peer/output"/>
             <DerivedVariable name="i" exposure="i"  value="weight * outputpeer * PAMP_SCALE"/>
         </Dynamics>
     </ComponentType>