tract_querier.tractography¶
Classes
tract_querier.tractography.Tractography ([...]) |
Class to represent a tractography dataset |
Functions
tract_querier.tractography.tractography_from_vtk_files |
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tract_querier.tractography.tractography_to_vtk_file |
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class
tract_querier.tractography.
Tractography
(tracts=None, tracts_data=None, validate=True, **kwargs)[source]¶ Class to represent a tractography dataset
Parameters: tracts : list of float array
Each element of the list is a tract represented as point array, the length of the i-th tract is
tracts_data : dict of <data name>= list of float array of
Each element in the list corresponds to a tract, is the length of the i-th tract and M is the number of components of that data type.
validate : bool
Check that tracts and tracts_data are valid
Attributes
extra_args
Methods
add_tract_data_from_array
(name, array)Add a new data element reproducing a constant data value for each of the tracts. append
(tracts[, tracts_data, validate])Append tracts and corresponding data to the current set are_tracts_filtered
()are_tracts_subsampled
()filter_tracts
(criterium)Filter the tracts in the set according to a criterium function filtered_tracts_map
()Tract indices included after the filtering original_tracts
()Tract set used to original construct this original_tracts_data
()Tract data contained of the original dataset of this tractography object subsample_tracts
(points_per_tract)Subsample the tracts in the dataset to a maximum number of tracts
()Tracts contained in this tractography object after filtering and tracts_data
()Tract data contained in this tractography object after filtering and unfilter_tracts
()Reset any filtering applied to the tracts unsubsample_tracts
()Reset any subsampling applied to the tracts -
add_tract_data_from_array
(name, array)[source]¶ Add a new data element reproducing a constant data value for each of the tracts.
After execution, the tract data will have a new set original_tracts_data()[name][i][:] == array[i]
Parameters: name : str
Name of the new data element
array : array of length
Data value for each tract
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append
(tracts, tracts_data=None, validate=True)[source]¶ Append tracts and corresponding data to the current set
Parameters: tracts : list of float array
Each element of the list is a tract represented as point array, the length of the i-th tract is
tracts_data : dict of <data name>= list of float array of
Each element in the list corresponds to a tract, is the length of the i-th tract and M is the number of components of that data type.
validate : bool
Check that tracts and tracts_data are valid
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extra_args
¶
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filter_tracts
(criterium)[source]¶ Filter the tracts in the set according to a criterium function
Parameters: criterium : function of array -> Bool
A function taking a tract as an array of 3D points and returning True or False with specifying if it should be included
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filtered_tracts_map
()[source]¶ Tract indices included after the filtering
Returns: List of tract indices included after the filtering
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original_tracts
()[source]¶ Tract set used to original construct this tractography object, no subsampling or filtering applied
Returns: tracts : list of float array
Each element of the list is a tract represented as point array, the length of the i-th tract is
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original_tracts_data
()[source]¶ Tract data contained of the original dataset of this tractography object
Returns: tract data : dict of <data name>= list of float array of
Each element in the list corresponds to a tract, is the length of the i-th tract and M is the number of components of that data type.
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subsample_tracts
(points_per_tract)[source]¶ Subsample the tracts in the dataset to a maximum number of points per tract
Parameters: points_per_tract: int
Maximum number of points per tract after the operation is executed
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tracts
()[source]¶ Tracts contained in this tractography object after filtering and subsampling if these operations have been applied
Returns: tracts : list of float array
Each element of the list is a tract represented as point array, the length of the i-th tract is
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tracts_data
()[source]¶ Tract data contained in this tractography object after filtering and subsampling if these operations have been applied
Returns: tract data : dict of <data name>= list of float array of
Each element in the list corresponds to a tract, is the length of the i-th tract and M is the number of components of that data type.
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