Module Expr Str Import alias identifier ImportFrom alias ImportFrom alias ClassDef bases NameLoad body Expr Str Assign NameStore TupleLoad Str Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign NameStore AttributeLoad NameLoad attr For NameStore AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Str Expr Call NameLoad NameLoad NameLoad Call AttributeLoad NameLoad attr NameLoad Num decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr NameLoad For NameStore AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call NameLoad NameLoad NameLoad NameLoad Return NameLoad decorator_list NameLoad FunctionDef arguments args NameParam NameParam defaults body Return BoolOpAnd Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Str Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Str Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Str decorator_list FunctionDef arguments args NameParam defaults body Return Call AttributeLoad NameLoad attr NameLoad decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam defaults body Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr AttributeLoad AttributeLoad NameLoad attr attr decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr ListLoad Str Str Return NameLoad decorator_list NameLoad decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam NameParam NameParam defaults body Expr Str Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr NameLoad Num decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr ListLoad Str Str NameLoad Return NameLoad decorator_list NameLoad decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam NameParam defaults body Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr AttributeLoad AttributeLoad NameLoad attr attr decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr ListLoad Str Str Return NameLoad decorator_list NameLoad decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam NameParam defaults body Assign AttributeStore NameLoad attr NameLoad Assign NameStore AttributeLoad Call AttributeLoad NameLoad attr NameLoad Str attr Assign NameStore AttributeLoad Call AttributeLoad NameLoad attr NameLoad Str attr Assign AttributeStore NameLoad attr BinOpDiv NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Return Call NameLoad NameLoad NameLoad decorator_list NameLoad decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam NameParam defaults body Assign AttributeStore NameLoad attr NameLoad Assign NameStore AttributeLoad Call AttributeLoad NameLoad attr NameLoad Str attr Assign NameStore AttributeLoad Call AttributeLoad NameLoad attr NameLoad Str attr Assign AttributeStore NameLoad attr BinOpDiv NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Return Call NameLoad NameLoad NameLoad decorator_list NameLoad decorator_list
N/A N/A 
morphology_features.py

 N/A numpy np generic_features Feature N/A utils Widths N/A object N/A N/A 
    This is no longer used in the new code and can be deleted when ready

    Attributes
    ----------
    head :
    midbody :
    tail :
     N/A fields N/A head midbody tail __init__ N/A N/A self features_ref N/A N/A N/A 
        Parameters
        ----------
        features_ref : WormFeatures instance

        Note the current approach just computes the mean of the
        different body section widths. Eventually this should be
        computed in this class.

         N/A nw N/A features_ref nw N/A partition N/A self fields N/A N/A widths_in_partition N/A N/A nw get_partition partition widths N/A N/A setattr self partition N/A N/A np mean widths_in_partition 0 N/A from_disk N/A N/A cls width_ref N/A N/A N/A self N/A N/A cls __new__ cls N/A partition N/A self fields N/A N/A widths_in_partition N/A N/A utils _extract_time_from_disk width_ref partition N/A N/A setattr self partition widths_in_partition N/A self N/A classmethod __eq__ N/A N/A self other N/A N/A N/A N/A N/A N/A utils correlation N/A self head N/A other head morph.width.head N/A N/A utils correlation N/A self midbody N/A other midbody morph.width.midbody N/A N/A utils correlation N/A self tail N/A other tail morph.width.tail N/A __repr__ N/A N/A self N/A N/A N/A N/A N/A utils print_object self N/A N/A Length N/A Feature N/A __init__ N/A N/A self wf feature_name N/A N/A N/A N/A self name feature_name N/A N/A self value N/A N/A wf nw length N/A from_schafer_file N/A N/A cls wf feature_name N/A N/A N/A self N/A N/A cls __new__ cls N/A N/A self name feature_name N/A N/A self value N/A N/A utils get_nested_h5_field N/A wf h N/A morphology length N/A self N/A classmethod N/A WidthSection N/A Feature N/A N/A 
    This should only be called by the subclasses

    Attributes
    ----------
    partition_name
     __init__ N/A N/A self wf feature_name partition_name N/A N/A N/A 
        Parameters
        ----------
        wf : WormFeatures instance
         N/A N/A self name feature_name N/A N/A self partition_name partition_name N/A widths_in_partition N/A N/A N/A wf nw get_partition partition_name widths N/A N/A self value N/A N/A np mean widths_in_partition 0 N/A from_schafer_file N/A N/A cls wf feature_name partition_name N/A N/A N/A self N/A N/A cls __new__ cls N/A N/A self name feature_name N/A N/A self value N/A N/A utils get_nested_h5_field N/A wf h N/A morphology width partition_name N/A self N/A classmethod N/A Area N/A Feature N/A N/A 
    Feature: morphology.area
     __init__ N/A N/A self wf feature_name N/A N/A N/A N/A self name feature_name N/A N/A self value N/A N/A wf nw area N/A from_schafer_file N/A N/A cls wf feature_name N/A N/A N/A self N/A N/A cls __new__ cls N/A N/A self name feature_name N/A N/A self value N/A N/A utils get_nested_h5_field N/A wf h N/A morphology area N/A self N/A classmethod N/A AreaPerLength N/A Feature N/A N/A 
    Feature: morphology.area_per_length
     __init__ N/A N/A self wf feature_name N/A N/A N/A N/A self name feature_name N/A area N/A N/A N/A self get_feature wf morphology.area value N/A length N/A N/A N/A self get_feature wf morphology.length value N/A N/A self value N/A area length N/A from_schafer_file N/A N/A cls wf feature_name N/A N/A N/A N/A cls wf feature_name N/A classmethod N/A WidthPerLength N/A Feature N/A N/A 
    Feature: morphology.width_per_length
     __init__ N/A N/A self wf feature_name N/A N/A N/A N/A self name feature_name N/A width N/A N/A N/A self get_feature wf morphology.width.midbody value N/A length N/A N/A N/A self get_feature wf morphology.length value N/A N/A self value N/A width length N/A from_schafer_file N/A N/A cls wf feature_name N/A N/A N/A N/A cls wf feature_name N/A classmethod N/A