Merge pull request #24 from pgleeson/main

Adding Escape response circuit

.gitignore

@@ -19,3 +19,5 @@ __pycache__
 /docs/assets/WormNeuro*
 /docs/.DS_Store
 /docs/assets/RipollSanchez*
+/docs/Escape_*data_*.md
+/docs/Escape_*_data.md

cect/Cells.py

@@ -664,10 +664,10 @@
 
 
 COOK_GROUPING_1 = {
-    "Interneurons": INTERNEURONS_COOK,
-    "Sensory neurons": SENSORY_NEURONS_COOK,
-    "Motorneurons": MOTORNEURONS_COOK,
-    "Pharyngeal polymodal neurons": PHARYNGEAL_POLYMODAL_NEURONS,
+    "Pharyngeal neurons": PHARYNGEAL_NEURONS,
+    "Sensory neurons": SENSORY_NEURONS_NONPHARYNGEAL_COOK,
+    "Interneurons": INTERNEURONS_NONPHARYNGEAL_COOK,
+    "Motorneurons": MOTORNEURONS_NONPHARYNGEAL_COOK,
     "Unknown function neurons": UNKNOWN_FUNCTION_NEURONS,
 }
 
@@ -1290,12 +1290,21 @@
     cell_notes[cell] = "male ray structural cell"
 
 
+INTESTINAL_MUSCLES = [
+    "mu_intL",
+    "mu_intR",
+]
+
+for cell in INTESTINAL_MUSCLES:
+    cell_notes[cell] = "intestinal muscles"
+
 PREFERRED_MUSCLE_NAMES = (
     BODY_WALL_MUSCLE_NAMES
     + PHARYNGEAL_MUSCLE_NAMES
     + VULVAL_MUSCLE_NAMES
     + ANAL_SPHINCTER_MUSCLES
     + MALE_SPECIFIC_MUSCLES
+    + INTESTINAL_MUSCLES
     + UNSPECIFIED_BODY_WALL_MUSCLES
 )
 
@@ -1305,7 +1314,6 @@
     PHARYNGEAL_MUSCLE_NAMES
     + VULVAL_MUSCLE_NAMES
     + ANAL_SPHINCTER_MUSCLES
-    + MALE_SPECIFIC_MUSCLES
     + UNSPECIFIED_BODY_WALL_MUSCLES
 )
 
@@ -1414,15 +1422,6 @@
 ]
 cell_notes["int"] = "intestine"
 
-INTESTINAL_MUSCLES = [
-    "mu_intL",
-    "mu_intR",
-]
-
-
-for cell in INTESTINAL_MUSCLES:
-    cell_notes[cell] = "intestinal muscles"
-
 
 KNOWN_OTHER_CELLS_COOK_19 = (
     []
@@ -1436,10 +1435,9 @@
     + HEAD_MESODERMAL_CELL
     + HYPODERMIS
     + INTESTINE
-    + INTESTINAL_MUSCLES
 )
 
-COOK_GROUPING_1["Other cells"] = KNOWN_OTHER_CELLS_COOK_19
+COOK_GROUPING_1["Other cells"] = list(KNOWN_OTHER_CELLS_COOK_19)
 
 KNOWN_OTHER_CELLS = KNOWN_OTHER_CELLS_COOK_19
 
@@ -1448,6 +1446,9 @@
 )
 
 COOK_GROUPING_1["Male specific neurons"] = MALE_SPECIFIC_NEURONS
+
+COOK_GROUPING_1["Male specific muscles "] = MALE_SPECIFIC_MUSCLES
+
 COOK_GROUPING_1["Male other cells"] = (
     MALE_RAY_STRUCTURAL_CELLS + PROCTODEUM_CELL + GONAD_CELL
 )
@@ -1487,6 +1488,9 @@ def get_SIM_class(cell):
     elif cell in INTERNEURONS_COOK:
         return "Interneuron"
     else:
+        if len(cell) == 3:
+            if get_SIM_class("%sL" % cell) == get_SIM_class("%sR" % cell):
+                return get_SIM_class("%sL" % cell)
         return "Other"
 
 
@@ -1576,7 +1580,7 @@ def convert_to_preferred_muscle_name(muscle):
     elif muscle == "pm7d":
         return "pm7D"
     else:
-        if is_muscle(muscle):
+        if is_known_muscle(muscle):
             return muscle
         else:
             return muscle + "???"
@@ -1625,13 +1629,19 @@ def get_body_wall_muscle_prefixes():
     return ["BWM-D", "BWM-V", "LegacyBodyWallMuscles", "vBWM", "dBWM"]
 
 
-def is_muscle(cell):
+def is_potential_muscle(cell):
     if cell in PREFERRED_MUSCLE_NAMES:
         return True
     known_muscle_prefixes = get_all_muscle_prefixes()
     return cell.startswith(tuple(known_muscle_prefixes))
 
 
+def is_known_muscle(cell):
+    if cell in PREFERRED_MUSCLE_NAMES:
+        return True
+    return False
+
+
 def is_potential_body_wall_muscle(cell):
     known_muscle_prefixes = get_body_wall_muscle_prefixes()
     return cell.startswith(tuple(known_muscle_prefixes))
@@ -1821,7 +1831,7 @@ def get_cell_internal_link(cell_name, html=False, text=None, use_color=False):
 
         return '<a href="%s" title="%s">%s</a>' % (
             url,
-            get_short_description(cell_name),
+            (cell_name + " (%s)" if text else "%s") % get_short_description(cell_name),
             link_text,
         )
     else:
@@ -1912,6 +1922,7 @@ def _generate_cell_table(cell_type, cells):
     fig_md = ""
 
     verbose = False
+    some_cells = False
 
     for syn_summary in syn_summaries:
         fig = go.Figure()
@@ -1955,6 +1966,7 @@ def _generate_cell_table(cell_type, cells):
                     line=dict(dash=dash),
                 )
                 nonempty_fig_present = True
+                some_cells = True
 
         if nonempty_fig_present:
             asset_filename = "assets/%s_%s_hist.json" % (
@@ -1997,7 +2009,14 @@ def _generate_cell_table(cell_type, cells):
 
     table_md = df_all.to_markdown()
 
-    return "%s\n%s\n\n" % (fig_md, table_md)
+    title = cell_type[0].upper() + cell_type[1:]
+    title = ("%s" if some_cells else "<i>%s</i>") % title
+
+    title_md = "#### ![#{0}](https://via.placeholder.com/15/{0}/{0}.png) {1}\n".format(
+        color, title
+    )
+
+    return "%s\n%s\n%s\n\n" % (title_md, fig_md, table_md)
 
 
 if __name__ == "__main__":
@@ -2010,9 +2029,9 @@ def _generate_cell_table(cell_type, cells):
     filename = "docs/Cells.md"
 
     with open(filename, "w") as f:
-        for sex in WA_COLORS:
-            f.write("---\ntitle: <C. elegans> cells\n---\n\n")
+        f.write("---\ntitle: <i>C. elegans</i> cells\n---\n\n")
 
+        for sex in WA_COLORS:
             f.write("\n## %s\n" % sex)
 
             for cell_class in WA_COLORS[sex]:
@@ -2021,15 +2040,15 @@ def _generate_cell_table(cell_type, cells):
                 for cell_type in WA_COLORS[sex][cell_class]:
                     if "General code" not in cell_type:
                         color = WA_COLORS[sex][cell_class][cell_type][1:]
-                        f.write(
-                            "#### ![#{0}](https://via.placeholder.com/15/{0}/{0}.png) {1}\n".format(
-                                color, cell_type[0].upper() + cell_type[1:]
-                            )
-                        )
+
                         if cell_type == "body wall muscle":
                             f.write(
                                 _generate_cell_table(cell_type, BODY_WALL_MUSCLE_NAMES)
                             )
+                        elif cell_type == "vulval muscle":
+                            f.write(
+                                _generate_cell_table(cell_type, VULVAL_MUSCLE_NAMES)
+                            )
                         elif cell_type == "interneuron":
                             f.write(
                                 _generate_cell_table(

cect/Comparison.py

@@ -31,7 +31,9 @@
     "Witvliet8": "Witvliet8_data",
     "WormNeuroAtlas": "WormNeuroAtlas_data",
     "Randi2023": "Randi2023_data",
-    "RipollSanchez": "RipollSanchez_data",
+    "RipollSanchezShortRange": "RipollSanchezShortRange_data",
+    "RipollSanchezMidRange": "RipollSanchezMidRange_data",
+    "RipollSanchezLongRange": "RipollSanchezLongRange_data",
     "Test": "Test_data",
     "SSData": "SSData_data",
     "UpdSSData": "UpdSSData_data",
@@ -149,39 +151,55 @@ def generate_comparison_page(quick: bool, color_table=True):
     readers = {}
 
     if not quick:
-        readers["SSData"] = ["cect.SpreadsheetDataReader", None]
-        readers["UpdSSData"] = ["cect.UpdatedSpreadsheetDataReader", None]
-        readers["UpdSSData2"] = ["cect.UpdatedSpreadsheetDataReader2", None]
+        readers["White_A"] = ["cect.White_A", "White_1986"]
+        readers["White_L4"] = ["cect.White_L4", "White_1986"]
 
-    readers["Varshney"] = ["cect.VarshneyDataReader", "Varshney_2011"]
     readers["White_whole"] = ["cect.White_whole", "White_1986"]
-    readers["Test"] = ["cect.TestDataReader", None]
-    readers["Cook2020"] = ["cect.Cook2020DataReader", "Cook_2020"]
-    readers["Witvliet1"] = ["cect.WitvlietDataReader1", "Witvliet_2021"]
+    readers["Varshney"] = ["cect.VarshneyDataReader", "Varshney_2011"]
 
     if not quick:
-        readers["RipollSanchez"] = [
-            "cect.RipollSanchezDataReader",
-            "RipollSanchez_2023",
-        ]
         readers["Bentley2016_MA"] = ["cect.WormNeuroAtlasMAReader", "Bentley_2016"]
         readers["Bentley2016_PEP"] = ["cect.WormNeuroAtlasPepReader", "Bentley_2016"]
+        readers["Witvliet1"] = ["cect.WitvlietDataReader1", "Witvliet_2021"]
         readers["Witvliet2"] = ["cect.WitvlietDataReader2", "Witvliet_2021"]
         readers["Witvliet3"] = ["cect.WitvlietDataReader3", "Witvliet_2021"]
         readers["Witvliet4"] = ["cect.WitvlietDataReader4", "Witvliet_2021"]
         readers["Witvliet5"] = ["cect.WitvlietDataReader5", "Witvliet_2021"]
         readers["Witvliet6"] = ["cect.WitvlietDataReader6", "Witvliet_2021"]
         readers["Witvliet7"] = ["cect.WitvlietDataReader7", "Witvliet_2021"]
         readers["Witvliet8"] = ["cect.WitvlietDataReader8", "Witvliet_2021"]
-        readers["White_A"] = ["cect.White_A", "White_1986"]
-        readers["White_L4"] = ["cect.White_L4", "White_1986"]
-        readers["Cook2019Herm"] = ["cect.Cook2019HermReader", "Cook_2019"]
+
+    readers["Cook2019Herm"] = ["cect.Cook2019HermReader", "Cook_2019"]
+
+    if not quick:
         readers["Cook2019Male"] = ["cect.Cook2019MaleReader", "Cook_2019"]
+
+        readers["Cook2020"] = ["cect.Cook2020DataReader", "Cook_2020"]
         readers["WormNeuroAtlas"] = ["cect.WormNeuroAtlasReader", "Randi_2023"]
         readers["Randi2023"] = ["cect.WormNeuroAtlasFuncReader", "Randi_2023"]
 
+        readers["RipollSanchezShortRange"] = [
+            "cect.RipollSanchezShortRangeReader",
+            "RipollSanchez_2023",
+        ]
+        readers["RipollSanchezMidRange"] = [
+            "cect.RipollSanchezMidRangeReader",
+            "RipollSanchez_2023",
+        ]
+        readers["RipollSanchezLongRange"] = [
+            "cect.RipollSanchezLongRangeReader",
+            "RipollSanchez_2023",
+        ]
+
+    if not quick:
+        readers["SSData"] = ["cect.SpreadsheetDataReader", None]
+        readers["UpdSSData"] = ["cect.UpdatedSpreadsheetDataReader", None]
+        readers["UpdSSData2"] = ["cect.UpdatedSpreadsheetDataReader2", None]
+
+    readers["Test"] = ["cect.TestDataReader", None]
+
     main_mk = "# Comparison between data readers\n"
-    table = ""
+    table_html = ""
 
     for reader_name, reader_info in readers.items():
         reader = reader_info[0]
@@ -494,7 +512,7 @@ def generate_comparison_page(quick: bool, color_table=True):
 
     if color_table:
         STYLE = '"width:80px"'
-        table += f"<table>\n  <tr>\n    <th style={STYLE}>Group</th>\n"
+        table_html += f'<table>\n  <tr>\n    <th style={STYLE}><span style="font-size:150%"> </span></th>\n'
 
         readers_to_include = []
 
@@ -503,10 +521,19 @@ def generate_comparison_page(quick: bool, color_table=True):
                 readers_to_include.append(reader_name)
 
         for reader_name in readers_to_include:
-            table += f"    <th style={STYLE}>{reader_name}</th>\n"
+            better_name = (
+                reader_name.replace("_", " ")
+                .replace("201", " 201")
+                .replace("chez", "chez ")
+                .replace("19", "19 ")
+                .replace("liet", "liet ")
+                .replace("MA", "Monoamin.")
+                .replace("PEP", "Peptid.")
+            )
+            table_html += f'    <th style={STYLE}><span style="font-size:150%">{better_name}</span></th>\n'
 
         for group in COOK_GROUPING_1:
-            table += f"  <tr>\n<td >{group}</th>\n"
+            table_html += f'  <tr>\n<td ><b><span style="font-size:150%">{group}</span></b></th>\n'
 
             for reader_name in readers_to_include:
                 connectome = all_connectomes[reader_name]
@@ -519,16 +546,16 @@ def generate_comparison_page(quick: bool, color_table=True):
                     else:
                         pass  # cells_here+='<s>%s</s>&nbsp;'%cell
 
-                    if (cells_here.split("<br/>")[-1]).count("&nbsp;") > 5:
+                    if (cells_here.split("<br/>")[-1]).count("&nbsp;") > 9:
                         cells_here += "<br/>\n"
 
-                table += f"    <td >{cells_here}</th>\n"
+                table_html += f"    <td >{cells_here}</th>\n"
 
-            table += "  </tr>\n"
+            table_html += "  </tr>\n"
 
-        table += "  </tr>\n</table>\n"
+        table_html += "  </tr>\n</table>\n"
 
-        main_mk += table
+        main_mk += table_html.replace("150%", "100%")
 
     main_mk += df_all.to_markdown()
 
@@ -538,6 +565,27 @@ def generate_comparison_page(quick: bool, color_table=True):
 
     print_("Written page: %s" % filename)
 
+    filename = "docs/Comparison_table.html"
+    with open(filename, "w") as f:
+        f.write(
+            """<html>
+  <head>
+    <style>
+    table, th, td {
+      border: 1px solid black;
+      border-collapse: collapse;
+    }
+    </style>
+    </head>
+    <body>
+    %s
+    </body>
+</html>"""
+            % table_html
+        )
+
+    print_("Written page: %s" % filename)
+
     return connectomes