Add score matrix report

Change-Id: I9f1581873422012135e3b791e7e5ff31dfa3b616

.pylintrc

@@ -2,7 +2,7 @@
 ignore=version.py
 
 [MESSAGES CONTROL]
-disable=bad-continuation,fixme,invalid-name,len-as-condition,no-else-return,empty-docstring
+disable=bad-continuation,fixme,invalid-name,len-as-condition,no-else-return,empty-docstring,too-many-lines
 
 [FORMAT]
 # Maximum number of characters on a single line.

MANIFEST.in

@@ -2,4 +2,4 @@ global-exclude *.py[co] .DS_Store
 
 include src/version.py
 include src/morphval/templates/*
-include src/synthesis_workflow/defaults/morphval_default_config.yaml
+include src/synthesis_workflow/defaults/*

doc/Makefile

@@ -24,6 +24,7 @@ help:
 	pdftocairo -png -r 300 -f 1 -l 1 ../tests/data/in_small_O1/out/validation/path_distance_fit.pdf source/autoapi/tasks/validation/path_distance_fit
 	pdftocairo -png -r 300 -f 1 -l 1 ../tests/data/in_vacuum/out/validation/morphometrics/morphometrics_basal_dendrite.pdf source/autoapi/tasks/validation/morphometrics
 	pdftocairo -png -r 300 -f 1 -l 1 ../tests/data/in_vacuum/out/validation/vacuum_morphologies.pdf source/autoapi/tasks/vacuum_synthesis/vacuum_morphologies
+	pdftocairo -png -r 300 -f 1 -l 1 ../tests/data/in_small_O1/out/validation/score_matrix_reports.pdf source/autoapi/tasks/validation/score_matrix_reports
 
 	# Generate dependency graphs
 	cd ../tests/data/in_small_O1; synthesis_workflow -dg ../../../doc/source/autoapi/tasks/workflows/ValidateSynthesis.dot ValidateSynthesis; cd ../../../doc

src/synthesis_workflow/defaults/score_matrix_default_config.json

@@ -0,0 +1,94 @@
+{
+    "neurite": {
+        "number_of_bifurcations": [
+            "sum"
+        ],
+        "number_of_sections_per_neurite": [
+            "mean",
+            "sum"
+        ],
+        "number_of_terminations": [
+            "sum"
+        ],
+        "partition_asymmetry": [
+            "mean",
+            "sum"
+        ],
+        "partition_asymmetry_length": [
+            "mean",
+            "sum"
+        ],
+        "remote_bifurcation_angles": [
+            "mean"
+        ],
+        "section_areas": [
+            "mean",
+            "sum"
+        ],
+        "section_bif_branch_orders": [
+            "max",
+            "mean"
+        ],
+        "section_bif_lengths": [
+            "min",
+            "max",
+            "mean"
+        ],
+        "section_bif_radial_distances": [
+            "max",
+            "mean"
+        ],
+        "section_branch_orders": [
+            "max",
+            "mean"
+        ],
+        "section_lengths": [
+            "min",
+            "max",
+            "mean",
+            "sum"
+        ],
+        "section_path_distances": [
+            "min",
+            "max",
+            "mean"
+        ],
+        "section_radial_distances": [
+            "min",
+            "max",
+            "mean"
+        ],
+        "section_strahler_orders": [
+            "mean"
+        ],
+        "section_term_branch_orders": [
+            "max",
+            "mean"
+        ],
+        "section_term_lengths": [
+            "min",
+            "max",
+            "mean"
+        ],
+        "section_term_radial_distances": [
+            "max",
+            "mean"
+        ],
+        "section_tortuosity": [
+            "min",
+            "max",
+            "mean"
+        ],
+        "section_volumes": [
+            "mean",
+            "sum"
+        ],
+        "total_length_per_neurite": [
+            "mean"
+        ]
+    },
+    "neurite_type": [
+        "APICAL_DENDRITE",
+        "BASAL_DENDRITE"
+    ]
+}

src/synthesis_workflow/tasks/validation.py

@@ -1,4 +1,5 @@
 """Luigi tasks for validation of synthesis."""
+import json
 import logging
 from pathlib import Path
 
@@ -11,16 +12,6 @@
 from voxcell import VoxelData
 
 from morphval import validation_main as morphval_validation
-from synthesis_workflow.tools import load_circuit
-from synthesis_workflow.validation import convert_mvd3_to_morphs_df
-from synthesis_workflow.validation import parse_log
-from synthesis_workflow.validation import plot_collage
-from synthesis_workflow.validation import plot_density_profiles
-from synthesis_workflow.validation import plot_morphometrics
-from synthesis_workflow.validation import plot_path_distance_fits
-from synthesis_workflow.validation import plot_scale_statistics
-from synthesis_workflow.validation import SYNTH_MORPHOLOGY_PATH
-from synthesis_workflow.validation import VacuumCircuit
 from synthesis_workflow.tasks.circuit import CreateAtlasLayerAnnotations
 from synthesis_workflow.tasks.circuit import CreateAtlasPlanes
 from synthesis_workflow.tasks.config import CircuitConfig
@@ -42,6 +33,18 @@
 from synthesis_workflow.tasks.synthesis import BuildSynthesisDistributions
 from synthesis_workflow.tasks.synthesis import Synthesize
 from synthesis_workflow.tasks.vacuum_synthesis import VacuumSynthesize
+from synthesis_workflow.tools import load_circuit
+from synthesis_workflow.vacuum_synthesis import VACUUM_SYNTH_MORPHOLOGY_PATH
+from synthesis_workflow.validation import convert_mvd3_to_morphs_df
+from synthesis_workflow.validation import parse_log
+from synthesis_workflow.validation import plot_collage
+from synthesis_workflow.validation import plot_density_profiles
+from synthesis_workflow.validation import plot_morphometrics
+from synthesis_workflow.validation import plot_path_distance_fits
+from synthesis_workflow.validation import plot_scale_statistics
+from synthesis_workflow.validation import plot_score_matrix
+from synthesis_workflow.validation import SYNTH_MORPHOLOGY_PATH
+from synthesis_workflow.validation import VacuumCircuit
 
 
 L = logging.getLogger(__name__)
@@ -601,3 +604,83 @@ def run(self):
     def output(self):
         """"""
         return ValidationLocalTarget(self.output_path)
+
+
+@copy_params(
+    mtypes=ParamLink(SynthesisConfig),
+    morphology_path=ParamLink(PathConfig),
+    nb_jobs=ParamLink(RunnerConfig),
+)
+class PlotScoreMatrix(WorkflowTask):
+    """Create score matrix reports.
+
+    The generated images are like the following:
+
+    .. image:: score_matrix_reports-1.png
+
+    Attributes:
+        mtypes (list(str)): List of mtypes to plot.
+        morphology_path (str): Column name to use in the DF from ApplySubstitutionRules.
+        nb_jobs (int): Number of jobs.
+    """
+
+    config_path = luigi.OptionalParameter(default=None)
+    """str: (optional) Path to the configuration file. Use default configuration if not provided."""
+
+    output_path = luigi.Parameter(default="score_matrix_reports.pdf")
+    """str: Path to the output file."""
+
+    in_atlas = BoolParameter(default=False)
+    """bool: Trigger atlas case."""
+
+    def requires(self):
+        """"""
+        if self.in_atlas:
+            test_task = ConvertMvd3()
+        else:
+            test_task = VacuumSynthesize()
+        return {
+            "ref": ApplySubstitutionRules(),
+            "test": test_task,
+        }
+
+    def run(self):
+        """"""
+        L.debug("Score matrix output path = %s", self.output().path)
+
+        ref_morphs_df = pd.read_csv(self.input()["ref"].path)
+        if self.in_atlas:
+            test_morphs_df = pd.read_csv(self.input()["test"].path)
+            file_path_col_name = SYNTH_MORPHOLOGY_PATH
+        else:
+            test_morphs_df = pd.read_csv(self.input()["test"]["out_morphs_df"].path)
+            file_path_col_name = VACUUM_SYNTH_MORPHOLOGY_PATH
+
+        if self.config_path is not None:
+            with open(self.config_path) as f:
+                config = json.load(f)
+        else:
+            with pkg_resources.resource_stream(
+                "synthesis_workflow", "defaults/score_matrix_default_config.json"
+            ) as f:
+                config = json.load(f)
+
+        ref_morphs_df = ref_morphs_df[["name", "mtype", self.morphology_path]].rename(
+            columns={self.morphology_path: "filepath"}
+        )
+        test_morphs_df = test_morphs_df[["name", "mtype", file_path_col_name]].rename(
+            columns={file_path_col_name: "filepath"}
+        )
+
+        plot_score_matrix(
+            ref_morphs_df,
+            test_morphs_df,
+            self.output().ppath,
+            config,
+            mtypes=self.mtypes,
+            nb_jobs=self.nb_jobs,
+        )
+
+    def output(self):
+        """"""
+        return ValidationLocalTarget(self.output_path)

src/synthesis_workflow/tasks/workflows.py

@@ -15,6 +15,7 @@
 from synthesis_workflow.tasks.validation import PlotMorphometrics
 from synthesis_workflow.tasks.validation import PlotPathDistanceFits
 from synthesis_workflow.tasks.validation import PlotScales
+from synthesis_workflow.tasks.validation import PlotScoreMatrix
 from synthesis_workflow.validation import plot_morphometrics
 
 
@@ -54,6 +55,11 @@ class ValidateSynthesis(WorkflowWrapperTask):
     )
     """bool: Trigger morphology validation reports."""
 
+    with_score_matrix_reports = BoolParameter(
+        default=True, description="Trigger score matrix reports."
+    )
+    """bool: Trigger score matrix reports."""
+
     def requires(self):
         """"""
         tasks = [GetSynthesisInputs()]
@@ -69,6 +75,8 @@ def requires(self):
             tasks.append(PlotScales())
         if self.with_morphology_validation_reports:
             tasks.append(MorphologyValidationReports())
+        if self.with_score_matrix_reports:
+            tasks.append(PlotScoreMatrix())
         return tasks
 
 
@@ -95,6 +103,11 @@ class ValidateVacuumSynthesis(WorkflowWrapperTask):
     )
     """bool: Trigger density profiles."""
 
+    with_score_matrix_reports = BoolParameter(
+        default=True, description="Trigger score matrix reports."
+    )
+    """bool: Trigger score matrix reports."""
+
     def requires(self):
         """"""
         tasks = [GetSynthesisInputs()]
@@ -104,6 +117,8 @@ def requires(self):
             tasks.append(PlotVacuumMorphologies())
         if self.with_density_profiles:
             tasks.append(PlotDensityProfiles(in_atlas=False))
+        if self.with_score_matrix_reports:
+            tasks.append(PlotScoreMatrix(in_atlas=False))
         return tasks