A None value for mtypes means that all mtypes are taken

Change-Id: I4f5fd144fff77b3fc699a4e7d78c875f1701226e

examples/luigi_cfg/luigi_vacuum.cfg

@@ -44,7 +44,6 @@ morphology_path = repaired_morphology_path_h5
 vacuum_synth_morphology_path = out_vacuum/vacuum_synth_morphologies
 vacuum_synth_morphs_df_path = out_vacuum/vacuum_synth_morphs_df.csv
 n_cells = 10
-mtypes = ["all"]
 
 # validation plots
 [ValidateVacuumSynthesis]

src/synthesis_workflow/tasks/circuit.py

@@ -209,20 +209,12 @@ def requires(self):
 
     def run(self):
         """"""
-        mtypes = self.mtypes
-        if (
-            # pylint: disable=unsupported-membership-test
-            mtypes is None
-            or "all" in mtypes
-        ):
-            mtypes = None
-
         planes = load_planes_centerline(self.input()["atlas_planes"].path)["planes"]
 
         _slicer = partial(
             circuit_slicer,
             n_cells=self.n_cells,
-            mtypes=mtypes,
+            mtypes=self.mtypes,
             planes=planes,
             hemisphere=self.hemisphere,
         )

src/synthesis_workflow/tasks/config.py

@@ -93,7 +93,11 @@ class SynthesisConfig(luigi.Config):
         description="The list of cortical thicknesses",
     )
     mtypes = luigi.ListParameter(
-        default=None, description="The list of mtypes to process"
+        default=None,
+        description=(
+            "The list of mtypes to process (default is None, which means that all found "
+            "mtypes are taken)"
+        ),
     )
 
 

src/synthesis_workflow/tasks/synthesis.py

@@ -156,7 +156,7 @@ def requires(self):
     def run(self):
         """"""
         morphs_df = pd.read_csv(self.input()["morphologies"].path)
-        mtypes = morphs_df.mtype.unique()
+        mtypes = sorted(morphs_df.mtype.unique())
         neurite_types = get_neurite_types(morphs_df, mtypes)
 
         if self.input_tmd_parameters_path is not None:

src/synthesis_workflow/tasks/vacuum_synthesis.py

@@ -54,11 +54,7 @@ def run(self):
         tmd_parameters = json.load(self.input()["tmd_parameters"].open())
         tmd_distributions = json.load(self.input()["tmd_distributions"].open())
 
-        if (
-            # pylint: disable=unsubscriptable-object
-            self.mtypes is None
-            or self.mtypes[0] == "all"
-        ):
+        if self.mtypes is None:
             mtypes = list(tmd_parameters.keys())
         else:
             mtypes = self.mtypes

src/synthesis_workflow/tasks/validation.py

@@ -215,14 +215,11 @@ def requires(self):
 
     def run(self):
         """"""
-        if (
-            # pylint: disable=unsubscriptable-object
-            self.mtypes is None
-            or self.mtypes[0] == "all"
-        ):
-            mtypes = pd.read_csv(self.input().path).mtype.unique()
+        if self.mtypes is None:
+            mtypes = sorted(pd.read_csv(self.input().path).mtype.unique())
         else:
             mtypes = self.mtypes
+
         for mtype in mtypes:
             yield PlotSingleCollage(
                 collage_base_path=self.collage_base_path,
@@ -336,11 +333,8 @@ def requires(self):
     def run(self):
         """"""
         morphs_df = pd.read_csv(self.input().path)
-        if (
-            self.mtypes is None
-            or self.mtypes[0] == "all"  # pylint: disable=unsubscriptable-object
-        ):
-            mtypes = morphs_df.mtype.unique()
+        if self.mtypes is None:
+            mtypes = sorted(morphs_df.mtype.unique())
         else:
             mtypes = self.mtypes
 
@@ -474,14 +468,11 @@ def run(self):
         ref_morphs_df = pd.read_csv(self.input()["ref"].path)
         test_morphs_df = pd.read_csv(self.input()["test"].path)
 
-        if self.mtypes is None or "all" in self.mtypes:
-            mtypes = None
-        else:
-            mtypes = self.mtypes
-
-        if mtypes is not None:
-            ref_morphs_df = ref_morphs_df.loc[ref_morphs_df["mtype"].isin(mtypes)]
-            test_morphs_df = test_morphs_df.loc[test_morphs_df["mtype"].isin(mtypes)]
+        if self.mtypes is not None:
+            ref_morphs_df = ref_morphs_df.loc[ref_morphs_df["mtype"].isin(self.mtypes)]
+            test_morphs_df = test_morphs_df.loc[
+                test_morphs_df["mtype"].isin(self.mtypes)
+            ]
 
         if self.config_path is not None:
             with open(self.config_path) as f:

src/synthesis_workflow/validation.py

@@ -640,7 +640,7 @@ def plot_path_distance_fits(
     # Read morphology DataFrame
     morphs_df = pd.read_csv(morphs_df_path)
 
-    if mtypes is None or mtypes[0] == "all":
+    if mtypes is None:
         mtypes = sorted(
             [
                 mtype
@@ -837,14 +837,16 @@ def plot_scale_statistics(mtypes, scale_data, output_dir="scales", dpi=100):
             plt.close(fig)
 
         if mtypes is None:
-            mtypes = scale_data["mtype"].unique().tolist()
+            mtypes = sorted(scale_data["mtype"].unique())
 
         for col in scale_data.drop(
             columns=["worker_task_id", "mtype", "x", "y", "z"], errors="ignore"
         ).columns:
             fig = plt.figure(figsize=(10, 20))
             ax = plt.gca()
-            scale_data[["mtype", col]].boxplot(by="mtype", vert=False, ax=ax)
+            scale_data.loc[scale_data["mtype"].isin(mtypes), ["mtype", col]].boxplot(
+                by="mtype", vert=False, ax=ax
+            )
 
             ax.grid(True)
             fig.suptitle("")

tests/data/in_small_O1/luigi.cfg

@@ -15,9 +15,6 @@ neurite_types = ["basal", "apical"]
 trunk_max_tries = 100
 s_samples = 5
 
-[SynthesisConfig]
-mtypes = ["all"]
-
 [CircuitConfig]
 circuit_somata_path = circuit_somata.mvd3
 atlas_path = <path_to_atlas_directory>

tests/data/in_vacuum/luigi.cfg

@@ -36,7 +36,6 @@ morphology_path = repaired_morphology_path
 # synthesize in vacuum
 [VacuumSynthesize]
 n_cells = 10
-mtypes = ["all"]
 
 ####################################
 # ########## Validation ########## #