morphoclass.transforms.global_features package¶
Submodules¶
- morphoclass.transforms.global_features.abstract_global_feature_extractor module
- morphoclass.transforms.global_features.average_branch_order module
- morphoclass.transforms.global_features.average_radius module
- morphoclass.transforms.global_features.extract_maximal_apical_path_length module
- morphoclass.transforms.global_features.extract_number_branch_points module
- morphoclass.transforms.global_features.extract_number_leaves module
- morphoclass.transforms.global_features.total_path_length module
Module contents¶
Global feature extractors.
All transforms in this submodule should modify the data.u attribute
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class
morphoclass.transforms.global_features.AbstractGlobalFeatureExtractor¶ Bases:
abc.ABCA morphology data transform for global feature extraction.
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abstract
extract_global_feature(data)¶ Extract a particular global feature.
Child classes should implement this function.
- Parameters
data – A morphology data sample.
- Returns
- Return type
The value of the global feature for the given data sample.
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abstract
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class
morphoclass.transforms.global_features.AverageBranchOrder(tree_hash_fn=None)¶ -
Extract average branch order.
Branch order is defined as the number of branching points one passes going from the leafs to the root. Thus the root point has branching order 0
The data should contain the field tmd_neurites, see the ExtractTMDNeurites class.
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extract_global_feature(data)¶ Extract the average branch order global feature from data sample.
- Parameters
data – A morphology data sample.
- Returns
The average branch order of the morpholgy.
- Return type
float
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class
morphoclass.transforms.global_features.AverageRadius(tree_hash_fn=None, from_morphology=False)¶ -
Extract average radius across all apicals.
The data should contain the field tmd_neurites, see the ExtractTMDNeurites class.
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extract_global_feature(data)¶ Extract the average radius global feature from data.
- Parameters
data – The input morphology.
- Returns
- Return type
The average radius of the morphology.
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class
morphoclass.transforms.global_features.ExtractMaximalApicalPathLength(tree_hash_fn=None)¶ -
Extract maximal neurite length.
Maximal path distance form soma to a tip (leaf node)
The data should contain the field tmd_neurites, see the ExtractTMDNeurites class.
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extract_global_feature(data)¶ Extract the maximal apical length global feature from data.
- Parameters
data – The input morphology.
- Returns
- Return type
The maximal apical length of the morphology.
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class
morphoclass.transforms.global_features.ExtractNumberBranchPoints¶ -
Extract number of branch points.
The data should contain the field tmd_neurites, see the ExtractTMDNeurites class.
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extract_global_feature(data)¶ Extract the number of branch points global feature from data.
- Parameters
data – The input morphology.
- Returns
- Return type
The number of branch points in the morphology.
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class
morphoclass.transforms.global_features.ExtractNumberLeaves¶ -
Extract number of leaf nodes.
The data should contain the field tmd_neurites, see the ExtractTMDNeuritess class.
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extract_global_feature(data)¶ Extract the number of leaf nodes of the morphology.
- Parameters
data – A morphology data sample.
- Returns
- Return type
The total number of leaf nodes of the morphology.
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class
morphoclass.transforms.global_features.TotalPathLength(tree_hash_fn=None, from_morphology=False)¶ -
Extract total path length of the apical.
The data should contain the field tmd_neurites, see the ExtractTMDNeurites class.
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extract_global_feature(data)¶ Extract the total path length global feature from data sample.
- Parameters
data – A morphology data sample.
- Returns
- Return type
The total path length of the morphology.
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