tract_querier.tractography

Classes

tract_querier.tractography.Tractography([...])

Class to represent a tractography dataset

Functions

tract_querier.tractography.tractography_from_vtk_files(...)
tract_querier.tractography.tractography_to_vtk_file(...)

tract_querier.tractography.tractography_from_files(filenames)

tract_querier.tractography.tractography_from_file(filename)

tract_querier.tractography.tractography_to_file(filename, tractography, **kwargs)

class tract_querier.tractography.Tractography(tracts=None, tracts_data=None, validate=True, **kwargs)

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)

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

append(tracts, tracts_data=None, validate=True)

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

are_tracts_filtered()

are_tracts_subsampled()

extra_args

filter_tracts(criterium)

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

filtered_tracts_map()

Tract indices included after the filtering

Returns:List of tract indices included after the filtering

original_tracts()

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

original_tracts_data()

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.

subsample_tracts(points_per_tract)

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

tracts()

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

tracts_data()

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.

unfilter_tracts()

Reset any filtering applied to the tracts

unsubsample_tracts()

Reset any subsampling applied to the tracts

tract_querier.tractography.tractography_from_trackvis_file(filename)

tract_querier.tractography.tractography_to_trackvis_file(filename, tractography, affine=None, image_dimensions=None)

tract_querier.tractography.tractography_from_vtk_files(vtk_file_names)

tract_querier.tractography.tractography_to_vtk_file(vtk_file_name, tractography)

tract_querier.tractography.vtkPolyData_to_tracts(polydata, return_tractography_object=True)

Reads a VTKPolyData object and outputs a tracts/tracts_data pair

Parameters:

polydata : vtkPolyData

VTKPolyData Object

Returns:

tracts : list of float array N_ix3

Each element of the list is a tract represented as point array, the length of the i-th tract is N_i

tract_data : dict of <data name>= list of float array of N_ixM

Each element in the list corresponds to a tract, N_i is the length of the i-th tract and M is the number of components of that data type.

tract_querier.tractography.tracts_to_vtkPolyData(tracts, tracts_data={}, lines_indices=None)