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rename feature names with ambiguity (#98)
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* rename feature names with ambiguity

* update feature names in sscx tests

* add build.os to readthedocs yml
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@anilbey
anilbey authored Aug 29, 2023
1 parent adf8bac commit ebc89db
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Showing 7 changed files with 119 additions and 114 deletions.
5 changes: 5 additions & 0 deletions .readthedocs.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,11 @@
# Required
version: 2

build:
os: ubuntu-22.04
tools:
python: "3.11"

sphinx:
configuration: doc/source/conf.py
fail_on_warning: true
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28 changes: 14 additions & 14 deletions emodelrunner/factsheets/morphology_features.py
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Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,7 @@ def __init__(self, morphology, neurite_name, neurite_type):
neurite_type (NeuriteType): enum for neurite type encoding
"""
super().__init__()
self.name = f"average diameter of {neurite_name}"
self.name = f"average diameter, {neurite_name}"
self.unit = "\u00b5m"

neurites = list(iter_neurites(morphology, filt=is_type(neurite_type)))
Expand Down Expand Up @@ -117,7 +117,7 @@ def __init__(self, morphology, neurite_name, neurite_type):
neurite_type (NeuriteType): enum for neurite type encoding
"""
super().__init__()
self.name = f"total {neurite_name} length"
self.name = f"total length, {neurite_name}"
self.unit = "\u00b5m"
feature_value = nm.get("total_length", morphology, neurite_type=neurite_type)
self.value = self.replace_empty_value(feature_value)
Expand All @@ -141,7 +141,7 @@ def __init__(self, morphology, neurite_name, neurite_type):
neurite_type (NeuriteType): enum for neurite type encoding
"""
super().__init__()
self.name = f"total {neurite_name} height"
self.name = f"total height, {neurite_name}"
self.unit = "\u00b5m"
feature_value = nm.get("total_height", morphology, neurite_type=neurite_type)
self.value = self.replace_empty_value(feature_value)
Expand All @@ -165,7 +165,7 @@ def __init__(self, morphology, neurite_name, neurite_type):
neurite_type (NeuriteType): enum for neurite type encoding
"""
super().__init__()
self.name = f"total {neurite_name} width"
self.name = f"total width, {neurite_name}"
self.unit = "\u00b5m"
feature_value = nm.get("total_width", morphology, neurite_type=neurite_type)
self.value = self.replace_empty_value(feature_value)
Expand All @@ -189,7 +189,7 @@ def __init__(self, morphology, neurite_name, neurite_type):
neurite_type (NeuriteType): enum for neurite type encoding
"""
super().__init__()
self.name = f"total {neurite_name} depth"
self.name = f"total depth, {neurite_name}"
self.unit = "\u00b5m"
feature_value = nm.get("total_depth", morphology, neurite_type=neurite_type)
self.value = self.replace_empty_value(feature_value)
Expand All @@ -213,7 +213,7 @@ def __init__(self, morphology, neurite_name, neurite_type):
neurite_type (NeuriteType): enum for neurite type encoding
"""
super().__init__()
self.name = f"total {neurite_name} area"
self.name = f"total area, {neurite_name}"
self.unit = "\u00b5m\u00b2"
feature_value = nm.get("total_area", morphology, neurite_type=neurite_type)
self.value = self.replace_empty_value(feature_value)
Expand All @@ -237,7 +237,7 @@ def __init__(self, morphology, neurite_name, neurite_type):
neurite_type (NeuriteType): enum for neurite type encoding
"""
super().__init__()
self.name = f"total {neurite_name} volume"
self.name = f"total volume, {neurite_name}"
self.unit = "\u00b5m\u00b3"
feature_value = nm.get("total_volume", morphology, neurite_type=neurite_type)
self.value = self.replace_empty_value(feature_value)
Expand All @@ -261,7 +261,7 @@ def __init__(self, morphology, neurite_name, neurite_type):
neurite_type (NeuriteType): enum for neurite type encoding
"""
super().__init__()
self.name = f"number of {neurite_name} sections"
self.name = f"number of sections, {neurite_name}"
self.unit = ""
feature_value = nm.get(
"number_of_sections", morphology, neurite_type=neurite_type
Expand All @@ -287,7 +287,7 @@ def __init__(self, morphology, neurite_name, neurite_type):
neurite_type (NeuriteType): enum for neurite type encoding
"""
super().__init__()
self.name = f"number of {neurite_name} segments"
self.name = f"number of segments, {neurite_name}"
self.unit = ""
feature_values = nm.get(
"number_of_segments", morphology, neurite_type=neurite_type
Expand All @@ -313,7 +313,7 @@ def __init__(self, morphology, neurite_name, neurite_type):
neurite_type (NeuriteType): enum for neurite type encoding
"""
super().__init__()
self.name = f"mean {neurite_name} volume"
self.name = f"mean volume, {neurite_name}"
self.unit = "\u00b5m\u00b3"
feature_values = nm.get(
"total_volume_per_neurite", morphology, neurite_type=neurite_type
Expand All @@ -340,7 +340,7 @@ def __init__(self, morphology, neurite_name, neurite_type):
neurite_type (NeuriteType): enum for neurite type encoding
"""
super().__init__()
self.name = f"average {neurite_name} section length"
self.name = f"average section length, {neurite_name}"
self.unit = "\u00b5m"
feature_values = nm.get(
"section_lengths", morphology, neurite_type=neurite_type
Expand All @@ -367,7 +367,7 @@ def __init__(self, morphology, neurite_name, neurite_type):
neurite_type (NeuriteType): enum for neurite type encoding
"""
super().__init__()
self.name = f"average {neurite_name} segment length"
self.name = f"average segment length, {neurite_name}"
self.unit = "\u00b5m"
feature_values = nm.get(
"segment_lengths", morphology, neurite_type=neurite_type
Expand All @@ -394,7 +394,7 @@ def __init__(self, morphology, neurite_name, neurite_type):
neurite_type (NeuriteType): enum for neurite type encoding
"""
super().__init__()
self.name = f"{neurite_name} maximum branch order"
self.name = f"maximum branch order, {neurite_name}"
self.unit = ""
feature_values = nm.get(
"section_branch_orders", morphology, neurite_type=neurite_type
Expand All @@ -421,7 +421,7 @@ def __init__(self, morphology, neurite_name, neurite_type):
neurite_type (NeuriteType): enum for neurite type encoding
"""
super().__init__()
self.name = f"{neurite_name} maximum section length"
self.name = f"maximum section length, {neurite_name}"
self.unit = "\u00b5m"
feature_values = nm.get(
"section_lengths", morphology, neurite_type=neurite_type
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40 changes: 20 additions & 20 deletions tests/sscx_tests/test_factsheets_output.py
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Original file line number Diff line number Diff line change
Expand Up @@ -182,29 +182,29 @@ def test_anatomy_features():
ana_dict = morph_factsheet_builder.get_feature_values()
ana_dict = {"values": ana_dict, "name": "Anatomy"}
left_to_check_1 = [
"total axon length",
"mean axon volume",
"axon maximum branch order",
"axon maximum section length",
"total apical length",
"mean apical volume",
"apical maximum branch order",
"apical maximum section length",
"total basal length",
"mean basal volume",
"basal maximum branch order",
"basal maximum section length",
"total length, axon",
"mean volume, axon",
"maximum branch order, axon",
"maximum section length, axon",
"total length, apical",
"mean volume, apical",
"maximum branch order, apical",
"maximum section length, apical",
"total length, basal",
"mean volume, basal",
"maximum branch order, basal",
"maximum section length, basal",
"soma diameter",
]
left_to_check_2 = [
"total axon length",
"mean axon volume",
"axon maximum branch order",
"axon maximum section length",
"total dendrite length",
"mean dendrite volume",
"dendrite maximum branch order",
"dendrite maximum section length",
"total length, axon",
"mean volume, axon",
"maximum branch order, axon",
"maximum section length, axon",
"total length, dendrite",
"mean volume, dendrite",
"maximum branch order, dendrite",
"maximum section length, dendrite",
"soma diameter",
]
lists_to_check = [left_to_check_1, left_to_check_2]
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