Feat: Ensure single axon, remove dummy dendrites and connect axon to soma (#150)

Author: Alexis Arnaudon

.pylintrc

@@ -4,7 +4,11 @@ disable=
 	fixme,
 	invalid-name,
 	len-as-condition,
-	no-else-return
+	no-else-return,
+	too-many-arguments,
+	too-many-return-statements,
+	too-many-branches,
+	too-many-statements
 
 [FORMAT]
 # Regexp for a line that is allowed to be longer than the limit.
@@ -13,19 +17,11 @@ ignore-long-lines=\bhttps?://\S
 max-line-length=100
 
 [DESIGN]
-# Maximum number of arguments for function / method
-max-args=8
 # Argument names that match this expression will be ignored. Default to name
 # with leading underscore
 ignored-argument-names=_.*
 # Maximum number of locals for function / method body
 max-locals=15
-# Maximum number of return / yield for function / method body
-max-returns=6
-# Maximum number of branch for function / method body
-max-branches=12
-# Maximum number of statements in function / method body
-max-statements=50
 # Maximum number of parents for a class (see R0901).
 max-parents=9
 # Maximum number of attributes for a class (see R0902).

src/morphology_workflows/curation.py

@@ -425,21 +425,66 @@ def fix_root_section(morph, min_length=_ZERO_LENGTH):
         morph.delete_section(sec)
 
 
-def check_neurites(
+def _ensure_single_axon(morph):
+    """Keep only the largest axon if multiple are present."""
+    sections = {}
+    for root_section in morph.root_sections:
+        if root_section.type == SectionType.axon:
+            sections[root_section] = len(list(root_section.iter()))
+    if len(sections) > 1:
+        for sec in sorted(sections, key=sections.get, reverse=True)[1:]:
+            morph.delete_section(sec, recursive=True)
+
+
+def _ensure_axon_at_soma(morph):
+    """Ensure axon is connected to soma."""
+    for root_section in morph.root_sections:
+        root_section_type = root_section.type
+        for section in root_section.iter():
+            if section.type != root_section_type:
+                morph.append_root_section(section)
+                morph.delete_section(section, recursive=True)
+                break
+
+
+def _remove_dummy_neurites(morph):
+    for root_section in morph.root_sections:
+        if (
+            not root_section.children
+            and root_section.points.shape[0] == 2
+            and np.linalg.norm(root_section.points[0] - root_section.points[1]) < 1e-5
+        ):
+            morph.delete_section(root_section)
+
+
+def check_neurites(  # noqa: PLR0913
     row,
     data_dir,
     axon_n_section_min=5,
     mock_soma_type="spherical",
     ensure_stub_axon=False,
+    ensure_single_axon=True,
+    ensure_axon_at_soma=True,
+    remove_dummy_neurites=True,
     min_length_first_section=_ZERO_LENGTH,
 ):
     """Check which neurites are present, add soma if missing and mock_soma_type is not None."""
     new_morph_path = data_dir / Path(row.morph_path).name
     morph = Morphology(row.morph_path)
     if mock_soma_type is not None:
         _add_soma(morph, mock_soma_type)
+
     if ensure_stub_axon and not _has_axon(row.morph_path, n_section_min=0):
         _add_stub_axon(morph)
+
+    if ensure_axon_at_soma:
+        _ensure_axon_at_soma(morph)
+    if ensure_single_axon:
+        _ensure_single_axon(morph)
+
+    if remove_dummy_neurites:
+        _remove_dummy_neurites(morph)
+
     fix_root_section(morph, min_length_first_section)
     morph.write(new_morph_path)
     has_axon = row.get("use_axon", _has_axon(new_morph_path, n_section_min=axon_n_section_min))

src/morphology_workflows/tasks/curation.py

@@ -1,4 +1,5 @@
 """Curation tasks."""
+
 import logging
 
 import luigi
@@ -121,6 +122,18 @@ class CheckNeurites(StrIndexMixin, ElementValidationTask):
         description=":bool: Add a stub axon if there is no axon on the morphology",
         default=False,
     )
+    ensure_single_axon = luigi.BoolParameter(
+        description=":bool: Keep only largest axon if multiple are present",
+        default=True,
+    )
+    ensure_axon_at_soma = luigi.BoolParameter(
+        description=":bool: Ensure all axons are connected to the soma, and not dendrites",
+        default=True,
+    )
+    remove_dummy_neurites = luigi.BoolParameter(
+        description=":bool: Remove neurites with two equal points",
+        default=True,
+    )
     min_length_first_section = OptionalNumericalParameter(
         description=(
             ":float: Resize the first section to be at least of the given size (do nothing if None "
@@ -138,6 +151,9 @@ def kwargs(self):
             "mock_soma_type": self.mock_soma_type,
             "axon_n_section_min": self.axon_n_section_min,
             "ensure_stub_axon": self.ensure_stub_axon,
+            "ensure_single_axon": self.ensure_single_axon,
+            "ensure_axon_at_soma": self.ensure_axon_at_soma,
+            "remove_dummy_neurites": self.remove_dummy_neurites,
             "min_length_first_section": self.min_length_first_section,
         }
 

tests/data/test_example_1/out_annotated/Annotate/report.csv

@@ -10,7 +10,7 @@ mono-type,True,0,,,L1_AAA:C,out_annotated/HardLimit/data/mono-type.yaml,out_anno
 multiple_point_section,True,0,,,L1_AAA:C,out_annotated/HardLimit/data/multiple_point_section.yaml,,,True,0,,,out_annotated/CollectCurated/data/multiple_point_section.asc,False,L1_AAA:C,,True,0,No regex provided!,,L1_AAA:C,True,0,,,out_annotated/CollectCurated/data/multiple_point_section.asc,out_annotated/HardLimit/data/multiple_point_section.yaml,True,0,,,out_annotated/CollectCurated/data/multiple_point_section.asc,False,,True,0,No cut leaves found,,out_annotated/CollectCurated/data/multiple_point_section.asc,,,,True,0,,,out_annotated/CollectCurated/data/multiple_point_section.asc,False,,,True,0,,,,,out_annotated/CollectCurated/data/multiple_point_section.asc,,True,0,,,out_annotated/CollectCurated/data/multiple_point_section.asc,out_annotated/HardLimit/data/multiple_point_section.yaml,out_annotated/PlotHardLimit/data/multiple_point_section.html
 nested_single_children,True,0,,,L1_AAA:C,out_annotated/HardLimit/data/nested_single_children.yaml,,,True,0,,,out_annotated/CollectCurated/data/nested_single_children.asc,False,L1_AAA:C,,True,0,No regex provided!,,L1_AAA:C,True,0,,,out_annotated/CollectCurated/data/nested_single_children.asc,out_annotated/HardLimit/data/nested_single_children.yaml,True,0,,,out_annotated/CollectCurated/data/nested_single_children.asc,False,,True,0,No cut leaves found,,out_annotated/CollectCurated/data/nested_single_children.asc,,,,True,0,,,out_annotated/CollectCurated/data/nested_single_children.asc,False,,,True,0,,,,,out_annotated/CollectCurated/data/nested_single_children.asc,,True,0,,,out_annotated/CollectCurated/data/nested_single_children.asc,out_annotated/HardLimit/data/nested_single_children.yaml,out_annotated/PlotHardLimit/data/nested_single_children.html
 neurite_wrong_root_point,True,0,,,L1_AAA:C,out_annotated/HardLimit/data/neurite_wrong_root_point.yaml,,,True,0,,,out_annotated/CollectCurated/data/neurite_wrong_root_point.swc,False,L1_AAA:C,,True,0,No regex provided!,,L1_AAA:C,True,0,,,out_annotated/CollectCurated/data/neurite_wrong_root_point.swc,out_annotated/HardLimit/data/neurite_wrong_root_point.yaml,True,0,,,out_annotated/CollectCurated/data/neurite_wrong_root_point.swc,False,,True,0,No cut leaves found,,out_annotated/CollectCurated/data/neurite_wrong_root_point.swc,,,,True,0,,,out_annotated/CollectCurated/data/neurite_wrong_root_point.swc,False,,,True,0,,,,,out_annotated/CollectCurated/data/neurite_wrong_root_point.swc,,True,0,,,out_annotated/CollectCurated/data/neurite_wrong_root_point.swc,out_annotated/HardLimit/data/neurite_wrong_root_point.yaml,out_annotated/PlotHardLimit/data/neurite_wrong_root_point.html
-nrn-order-already-sorted,True,0,,,L1_AAA:C,out_annotated/HardLimit/data/nrn-order-already-sorted.yaml,out_annotated/ApicalPoint/data/nrn-order-already-sorted.yaml,out_annotated/CutLeaves/data/nrn-order-already-sorted.yaml,True,0,,,out_annotated/CollectCurated/data/nrn-order-already-sorted.h5,True,L1_AAA:C,,True,0,No regex provided!,,L1_AAA:C,True,0,,,out_annotated/CollectCurated/data/nrn-order-already-sorted.h5,out_annotated/HardLimit/data/nrn-order-already-sorted.yaml,True,0,,,out_annotated/CollectCurated/data/nrn-order-already-sorted.h5,True,out_annotated/ApicalPoint/data/nrn-order-already-sorted.yaml,True,0,,,out_annotated/CollectCurated/data/nrn-order-already-sorted.h5,,out_annotated/CutLeaves/data/nrn-order-already-sorted.yaml,"[{""axis"": ""Z"", ""side"": -1, ""quality"": 6.0}]",True,0,,,out_annotated/CollectCurated/data/nrn-order-already-sorted.h5,True,out_annotated/ApicalPoint/data/nrn-order-already-sorted.yaml,out_annotated/PlotApicalPoint/data/nrn-order-already-sorted.html,True,0,,,out_annotated/CutLeaves/data/nrn-order-already-sorted.yaml,"[{""axis"": ""Z"", ""side"": -1, ""quality"": 6.0}]",out_annotated/CollectCurated/data/nrn-order-already-sorted.h5,out_annotated/PlotCutLeaves/data/nrn-order-already-sorted.html,True,0,,,out_annotated/CollectCurated/data/nrn-order-already-sorted.h5,out_annotated/HardLimit/data/nrn-order-already-sorted.yaml,out_annotated/PlotHardLimit/data/nrn-order-already-sorted.html
+nrn-order-already-sorted,True,0,,,L1_AAA:C,out_annotated/HardLimit/data/nrn-order-already-sorted.yaml,out_annotated/ApicalPoint/data/nrn-order-already-sorted.yaml,out_annotated/CutLeaves/data/nrn-order-already-sorted.yaml,True,0,,,out_annotated/CollectCurated/data/nrn-order-already-sorted.h5,True,L1_AAA:C,,True,0,No regex provided!,,L1_AAA:C,True,0,,,out_annotated/CollectCurated/data/nrn-order-already-sorted.h5,out_annotated/HardLimit/data/nrn-order-already-sorted.yaml,True,0,,,out_annotated/CollectCurated/data/nrn-order-already-sorted.h5,True,out_annotated/ApicalPoint/data/nrn-order-already-sorted.yaml,True,0,,,out_annotated/CollectCurated/data/nrn-order-already-sorted.h5,,out_annotated/CutLeaves/data/nrn-order-already-sorted.yaml,"[{""axis"": ""Z"", ""side"": -1, ""quality"": 5.0}]",True,0,,,out_annotated/CollectCurated/data/nrn-order-already-sorted.h5,True,out_annotated/ApicalPoint/data/nrn-order-already-sorted.yaml,out_annotated/PlotApicalPoint/data/nrn-order-already-sorted.html,True,0,,,out_annotated/CutLeaves/data/nrn-order-already-sorted.yaml,"[{""axis"": ""Z"", ""side"": -1, ""quality"": 5.0}]",out_annotated/CollectCurated/data/nrn-order-already-sorted.h5,out_annotated/PlotCutLeaves/data/nrn-order-already-sorted.html,True,0,,,out_annotated/CollectCurated/data/nrn-order-already-sorted.h5,out_annotated/HardLimit/data/nrn-order-already-sorted.yaml,out_annotated/PlotHardLimit/data/nrn-order-already-sorted.html
 nrn_ordering,True,0,,,L1_AAA:C,out_annotated/HardLimit/data/nrn_ordering.yaml,out_annotated/ApicalPoint/data/nrn_ordering.yaml,out_annotated/CutLeaves/data/nrn_ordering.yaml,True,0,,,out_annotated/CollectCurated/data/nrn_ordering.swc,True,L1_AAA:C,,True,0,No regex provided!,,L1_AAA:C,True,0,,,out_annotated/CollectCurated/data/nrn_ordering.swc,out_annotated/HardLimit/data/nrn_ordering.yaml,True,0,,,out_annotated/CollectCurated/data/nrn_ordering.swc,True,out_annotated/ApicalPoint/data/nrn_ordering.yaml,True,0,,,out_annotated/CollectCurated/data/nrn_ordering.swc,,out_annotated/CutLeaves/data/nrn_ordering.yaml,"[{""axis"": ""Z"", ""side"": 1, ""quality"": 14.8}]",True,0,,,out_annotated/CollectCurated/data/nrn_ordering.swc,True,out_annotated/ApicalPoint/data/nrn_ordering.yaml,out_annotated/PlotApicalPoint/data/nrn_ordering.html,True,0,,,out_annotated/CutLeaves/data/nrn_ordering.yaml,"[{""axis"": ""Z"", ""side"": 1, ""quality"": 14.8}]",out_annotated/CollectCurated/data/nrn_ordering.swc,out_annotated/PlotCutLeaves/data/nrn_ordering.html,True,0,,,out_annotated/CollectCurated/data/nrn_ordering.swc,out_annotated/HardLimit/data/nrn_ordering.yaml,out_annotated/PlotHardLimit/data/nrn_ordering.html
 pia,True,0,,,L1_AAA:C,out_annotated/HardLimit/data/pia.yaml,,,True,0,,,out_annotated/CollectCurated/data/pia.asc,False,L1_AAA:C,,True,0,No regex provided!,,L1_AAA:C,True,0,,,out_annotated/CollectCurated/data/pia.asc,out_annotated/HardLimit/data/pia.yaml,True,0,,,out_annotated/CollectCurated/data/pia.asc,False,,True,0,No cut leaves found,,out_annotated/CollectCurated/data/pia.asc,,,,True,0,,,out_annotated/CollectCurated/data/pia.asc,False,,,True,0,,,,,out_annotated/CollectCurated/data/pia.asc,,True,0,,,out_annotated/CollectCurated/data/pia.asc,out_annotated/HardLimit/data/pia.yaml,out_annotated/PlotHardLimit/data/pia.html
 reversed_NRN_neurite_order,True,0,,,L1_AAA:C,out_annotated/HardLimit/data/reversed_NRN_neurite_order.yaml,out_annotated/ApicalPoint/data/reversed_NRN_neurite_order.yaml,,True,0,,,out_annotated/CollectCurated/data/reversed_NRN_neurite_order.swc,True,L1_AAA:C,,True,0,No regex provided!,,L1_AAA:C,True,0,,,out_annotated/CollectCurated/data/reversed_NRN_neurite_order.swc,out_annotated/HardLimit/data/reversed_NRN_neurite_order.yaml,True,0,,,out_annotated/CollectCurated/data/reversed_NRN_neurite_order.swc,True,out_annotated/ApicalPoint/data/reversed_NRN_neurite_order.yaml,True,0,No cut leaves found,,out_annotated/CollectCurated/data/reversed_NRN_neurite_order.swc,,,,True,0,,,out_annotated/CollectCurated/data/reversed_NRN_neurite_order.swc,True,out_annotated/ApicalPoint/data/reversed_NRN_neurite_order.yaml,out_annotated/PlotApicalPoint/data/reversed_NRN_neurite_order.html,True,0,,,,,out_annotated/CollectCurated/data/reversed_NRN_neurite_order.swc,,True,0,,,out_annotated/CollectCurated/data/reversed_NRN_neurite_order.swc,out_annotated/HardLimit/data/reversed_NRN_neurite_order.yaml,out_annotated/PlotHardLimit/data/reversed_NRN_neurite_order.html
@@ -20,7 +20,9 @@ simple,True,0,,,L1_AAA:C,out_annotated/HardLimit/data/simple.yaml,,,True,0,,,out
 simple-with-font,True,0,,,L1_AAA:C,out_annotated/HardLimit/data/simple-with-font.yaml,,,True,0,,,out_annotated/CollectCurated/data/simple-with-font.asc,False,L1_AAA:C,,True,0,No regex provided!,,L1_AAA:C,True,0,,,out_annotated/CollectCurated/data/simple-with-font.asc,out_annotated/HardLimit/data/simple-with-font.yaml,True,0,,,out_annotated/CollectCurated/data/simple-with-font.asc,False,,True,0,No cut leaves found,,out_annotated/CollectCurated/data/simple-with-font.asc,,,,True,0,,,out_annotated/CollectCurated/data/simple-with-font.asc,False,,,True,0,,,,,out_annotated/CollectCurated/data/simple-with-font.asc,,True,0,,,out_annotated/CollectCurated/data/simple-with-font.asc,out_annotated/HardLimit/data/simple-with-font.yaml,out_annotated/PlotHardLimit/data/simple-with-font.html
 simple-with-image-coord,True,0,,,L1_AAA:C,out_annotated/HardLimit/data/simple-with-image-coord.yaml,,,True,0,,,out_annotated/CollectCurated/data/simple-with-image-coord.asc,False,L1_AAA:C,,True,0,No regex provided!,,L1_AAA:C,True,0,,,out_annotated/CollectCurated/data/simple-with-image-coord.asc,out_annotated/HardLimit/data/simple-with-image-coord.yaml,True,0,,,out_annotated/CollectCurated/data/simple-with-image-coord.asc,False,,True,0,No cut leaves found,,out_annotated/CollectCurated/data/simple-with-image-coord.asc,,,,True,0,,,out_annotated/CollectCurated/data/simple-with-image-coord.asc,False,,,True,0,,,,,out_annotated/CollectCurated/data/simple-with-image-coord.asc,,True,0,,,out_annotated/CollectCurated/data/simple-with-image-coord.asc,out_annotated/HardLimit/data/simple-with-image-coord.yaml,out_annotated/PlotHardLimit/data/simple-with-image-coord.html
 simple2,True,0,,,L1_AAA:C,out_annotated/HardLimit/data/simple2.yaml,,,True,0,,,out_annotated/CollectCurated/data/simple2.asc,False,L1_AAA:C,,True,0,No regex provided!,,L1_AAA:C,True,0,,,out_annotated/CollectCurated/data/simple2.asc,out_annotated/HardLimit/data/simple2.yaml,True,0,,,out_annotated/CollectCurated/data/simple2.asc,False,,True,0,No cut leaves found,,out_annotated/CollectCurated/data/simple2.asc,,,,True,0,,,out_annotated/CollectCurated/data/simple2.asc,False,,,True,0,,,,,out_annotated/CollectCurated/data/simple2.asc,,True,0,,,out_annotated/CollectCurated/data/simple2.asc,out_annotated/HardLimit/data/simple2.yaml,out_annotated/PlotHardLimit/data/simple2.html
-soma_cylinders,True,0,,,L1_AAA:C,out_annotated/HardLimit/data/soma_cylinders.yaml,,,True,0,,,out_annotated/CollectCurated/data/soma_cylinders.swc,False,L1_AAA:C,,True,0,No regex provided!,,L1_AAA:C,True,0,,,out_annotated/CollectCurated/data/soma_cylinders.swc,out_annotated/HardLimit/data/soma_cylinders.yaml,True,0,,,out_annotated/CollectCurated/data/soma_cylinders.swc,False,,True,0,No cut leaves found,,out_annotated/CollectCurated/data/soma_cylinders.swc,,,,True,0,,,out_annotated/CollectCurated/data/soma_cylinders.swc,False,,,True,0,,,,,out_annotated/CollectCurated/data/soma_cylinders.swc,,True,0,,,out_annotated/CollectCurated/data/soma_cylinders.swc,out_annotated/HardLimit/data/soma_cylinders.yaml,out_annotated/PlotHardLimit/data/soma_cylinders.html
+soma_cylinders,False,1,,,L1_AAA:C,out_annotated/HardLimit/data/soma_cylinders.yaml,,,True,0,,,out_annotated/CollectCurated/data/soma_cylinders.swc,False,L1_AAA:C,,True,0,No regex provided!,,L1_AAA:C,True,0,,,out_annotated/CollectCurated/data/soma_cylinders.swc,out_annotated/HardLimit/data/soma_cylinders.yaml,True,0,,,out_annotated/CollectCurated/data/soma_cylinders.swc,False,,False,1,,"Traceback  ... ValueError: Can not search for cut leaves for a neuron with no neurites.
+",out_annotated/CollectCurated/data/soma_cylinders.swc,,,,True,0,,,out_annotated/CollectCurated/data/soma_cylinders.swc,False,,,False,1,,,,,out_annotated/CollectCurated/data/soma_cylinders.swc,,False,1,,"Traceback  ... ValueError: Can not plot axis marker for a neuron with no neurites.
+",out_annotated/CollectCurated/data/soma_cylinders.swc,out_annotated/HardLimit/data/soma_cylinders.yaml,
 soma_multiple_frustums,False,1,,,L1_AAA:C,out_annotated/HardLimit/data/soma_multiple_frustums.yaml,,,True,0,,,out_annotated/CollectCurated/data/soma_multiple_frustums.swc,False,L1_AAA:C,,True,0,No regex provided!,,L1_AAA:C,True,0,,,out_annotated/CollectCurated/data/soma_multiple_frustums.swc,out_annotated/HardLimit/data/soma_multiple_frustums.yaml,True,0,,,out_annotated/CollectCurated/data/soma_multiple_frustums.swc,False,,False,1,,"Traceback  ... ValueError: Can not search for cut leaves for a neuron with no neurites.
 ",out_annotated/CollectCurated/data/soma_multiple_frustums.swc,,,,True,0,,,out_annotated/CollectCurated/data/soma_multiple_frustums.swc,False,,,False,1,,,,,out_annotated/CollectCurated/data/soma_multiple_frustums.swc,,False,1,,"Traceback  ... ValueError: Can not plot axis marker for a neuron with no neurites.
 ",out_annotated/CollectCurated/data/soma_multiple_frustums.swc,out_annotated/HardLimit/data/soma_multiple_frustums.yaml,