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rename feature names with ambiguity #98

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merged 3 commits into from
Aug 29, 2023
Merged

rename feature names with ambiguity #98

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1b8ab62
rename feature names with ambiguity
anilbey Aug 28, 2023
9c2cab8
update feature names in sscx tests
anilbey Aug 28, 2023
709b08f
add build.os to readthedocs yml
anilbey Aug 29, 2023
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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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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
Expand Down
40 changes: 20 additions & 20 deletions tests/sscx_tests/test_factsheets_output.py
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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]
Expand Down
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