Merge pull request #18 from pgleeson/main

Randi et al. 2023 Func connectome reader

.gitignore

@@ -6,3 +6,4 @@ __pycache__
 /cect/.DS_Store
 /.DS_Store
 /cect/data/~$*
+/pdfs/*.pdf

cect/Cells.py

@@ -13,6 +13,20 @@
 from cect.WormAtlasInfo import WA_COLORS
 from cect import print_
 
+
+ALL_KNOWN_CHEMICAL_NEUROTRANSMITTERS = [
+    "Acetylcholine",
+    "Acetylcholine_Tyramine",
+    "Dopamine",
+    "FMRFamide",
+    "GABA",
+    "Glutamate",
+    "Octapamine",
+    "Serotonin",
+    "Serotonin_Acetylcholine",
+    "Serotonin_Glutamate",
+]
+
 cell_notes = {}
 
 connectomes = None
@@ -1410,6 +1424,42 @@
     MALE_RAY_STRUCTURAL_CELLS + PROCTODEUM_CELL + GONAD_CELL
 )
 
+ALL_PREFERRED_CELL_NAMES = (
+    PREFERRED_NEURON_NAMES + PREFERRED_MUSCLE_NAMES + KNOWN_OTHER_CELLS
+)
+
+
+def is_bilateral_left(cell):
+    if (
+        cell in ALL_PREFERRED_CELL_NAMES
+        and cell.endswith("L")
+        and cell[:-1] + "R" in ALL_PREFERRED_CELL_NAMES
+    ):
+        return True
+    else:
+        return False
+
+
+def is_bilateral_right(cell):
+    if (
+        cell in ALL_PREFERRED_CELL_NAMES
+        and cell.endswith("R")
+        and cell[:-1] + "L" in ALL_PREFERRED_CELL_NAMES
+    ):
+        return True
+    else:
+        return False
+
+
+def are_bilateral_pair(cell_a, cell_b):
+    if cell_a[:-1] == cell_b[:-1] and (
+        (cell_a[-1] == "L" and cell_b[-1] == "R")
+        or (cell_b[-1] == "L" and cell_a[-1] == "R")
+    ):
+        return True
+    else:
+        return False
+
 
 def get_standard_color(cell):
     from cect.WormAtlasInfo import WA_COLORS
@@ -1645,13 +1695,15 @@ def _generate_cell_table(cell_type, cells):
     print_(" - Adding table for %s" % cell_type)
 
     syn_summaries = {
-        "Chemical conns in": ["Acetylcholine", "Generic_CS", "GABA"],
-        "Chemical conns out": ["Acetylcholine", "Generic_CS", "GABA"],
+        "Chemical conns in": ["Generic_CS"] + ALL_KNOWN_CHEMICAL_NEUROTRANSMITTERS,
+        "Chemical conns out": ["Generic_CS"] + ALL_KNOWN_CHEMICAL_NEUROTRANSMITTERS,
         "Electrical conns": ["Generic_GJ"],
     }
 
     fig_md = ""
 
+    verbose = False
+
     for syn_summary in syn_summaries:
         fig = go.Figure()
         fig.layout.showlegend = True
@@ -1673,10 +1725,11 @@ def _generate_cell_table(cell_type, cells):
                         conns_here = connectome.get_connections_from(cell, syn_type)
                     else:
                         conns_here = connectome.get_connections_to(cell, syn_type)
-                    print_(
-                        "Conns: %i for %s of type %s (%s)"
-                        % (len(conns_here), cell, syn_type, syn_summary)
-                    )
+                    if verbose:
+                        print_(
+                            "Conns: %i for %s of type %s (%s)"
+                            % (len(conns_here), cell, syn_type, syn_summary)
+                        )
                     total_y += len(conns_here)
 
                 y.append(total_y)

cect/Comparison.py

@@ -29,6 +29,10 @@
     "Cook2019Herm": "Cook2019Herm_data",
     "Cook2019Male": "Cook2019Male_data",
     "Cook2020": "Cook2020_data",
+    "Randi2023": "Randi2023_data",
+    "SSData": "SSDR_data",
+    "UpdSSData": "UpdSSData_data",
+    "UpdSSData2": "UpdSSData2_data",
 }
 
 all_data[""] = [
@@ -64,6 +68,9 @@ def _format_json(json_str):
 def get_2d_graph_markdown(reader_name, view, connectome, synclass, indent="    "):
     view_name = view.name
 
+    if np.sum(connectome.connections[synclass]) == 0:
+        return None
+
     fig = connectome.to_plotly_graph_fig(synclass, view)
 
     asset_filename = "assets/%s_%s_%s_graph.json" % (
@@ -75,14 +82,6 @@ def get_2d_graph_markdown(reader_name, view, connectome, synclass, indent="    "
     with open("./docs/%s" % asset_filename, "w") as asset_file:
         asset_file.write(_format_json(fig.to_json()))
 
-    if np.sum(connectome.connections[synclass]) == 0:
-        return "\n%sNo connections of type **%s** in the **%s** for **%s**...\n" % (
-            indent,
-            synclass,
-            view_name,
-            reader_name,
-        )
-
     return '\n%s```plotly\n%s---8<-- "./%s"\n%s```\n' % (
         indent,
         indent,
@@ -94,6 +93,9 @@ def get_2d_graph_markdown(reader_name, view, connectome, synclass, indent="    "
 def get_matrix_markdown(reader_name, view, connectome, synclass, indent="    "):
     view_name = view.name
 
+    if np.sum(connectome.connections[synclass]) == 0:
+        return None
+
     fig = connectome.to_plotly_matrix_fig(synclass, view)
 
     asset_filename = "assets/%s_%s_%s.json" % (
@@ -105,14 +107,6 @@ def get_matrix_markdown(reader_name, view, connectome, synclass, indent="    "):
     with open("./docs/%s" % asset_filename, "w") as asset_file:
         asset_file.write(_format_json(fig.to_json()))
 
-    if np.sum(connectome.connections[synclass]) == 0:
-        return "\n%sNo connections of type **%s** in the **%s** for **%s**...\n" % (
-            indent,
-            synclass,
-            view_name,
-            reader_name,
-        )
-
     return '\n%s```plotly\n%s---8<-- "./%s"\n%s```\n' % (
         indent,
         indent,
@@ -121,7 +115,7 @@ def get_matrix_markdown(reader_name, view, connectome, synclass, indent="    "):
     )
 
 
-def generate_comparison_page(quick: bool, color_table=False):
+def generate_comparison_page(quick: bool, color_table=True):
     connectomes = {}
     all_connectomes = {}
 
@@ -136,6 +130,8 @@ def generate_comparison_page(quick: bool, color_table=False):
         "Witvliet1": ["cect.WitvlietDataReader1", "Witvliet_2021"],
     }
 
+    readers["Randi2023"] = ["cect.WormNeuroAtlasFuncReader", "Randi_2023"]
+
     if not quick:
         readers["Witvliet2"] = ["cect.WitvlietDataReader2", "Witvliet_2021"]
         readers["Witvliet3"] = ["cect.WitvlietDataReader3", "Witvliet_2021"]
@@ -218,28 +214,27 @@ def generate_comparison_page(quick: bool, color_table=False):
                             f.write('=== "%s"\n' % view.name)
 
                             for sc in view.synclass_sets:
-                                f.write(indent + '=== "%s"\n' % sc)
-
                                 if matrix:
-                                    f.write(
-                                        get_matrix_markdown(
-                                            reader_name,
-                                            view,
-                                            cv,
-                                            sc,
-                                            indent=indent + indent,
-                                        )
+                                    mkdown_fig = get_matrix_markdown(
+                                        reader_name,
+                                        view,
+                                        cv,
+                                        sc,
+                                        indent=indent + indent,
                                     )
 
                                 else:
+                                    mkdown_fig = get_2d_graph_markdown(
+                                        reader_name,
+                                        view,
+                                        cv,
+                                        sc,
+                                        indent=indent + indent,
+                                    )
+
+                                if mkdown_fig is not None:
                                     f.write(
-                                        get_2d_graph_markdown(
-                                            reader_name,
-                                            view,
-                                            cv,
-                                            sc,
-                                            indent=indent + indent,
-                                        )
+                                        indent + '=== "%s"\n%s\n' % (sc, mkdown_fig)
                                     )
 
                     cell_types = {