trx.utils
=========

.. py:module:: trx.utils


Attributes
----------

.. autoapisummary::

   trx.utils.dipy_available


Functions
---------

.. autoapisummary::

   trx.utils.close_or_delete_mmap
   trx.utils.split_name_with_gz
   trx.utils.get_reference_info_wrapper
   trx.utils.is_header_compatible
   trx.utils.get_axis_shift_vector
   trx.utils.get_axis_flip_vector
   trx.utils.get_shift_vector
   trx.utils.flip_sft
   trx.utils.load_matrix_in_any_format
   trx.utils.get_reverse_enum
   trx.utils.convert_data_dict_to_tractogram
   trx.utils.append_generator_to_dict
   trx.utils.verify_trx_dtype


Module Contents
---------------

.. py:data:: dipy_available
   :value: True


.. py:function:: close_or_delete_mmap(obj)

   
   Close the memory-mapped file if it exists, otherwise set the object to None.
















   ..
       !! processed by numpydoc !!

.. py:function:: split_name_with_gz(filename)

   
   Returns the clean basename and extension of a file.
   Means that this correctly manages the ".nii.gz" extensions.


   :Parameters:

       **filename: str**
           The filename to clean

   :Returns:

       **base, ext** : tuple(str, str)
           ..

       Clean basename and the full extension
           ..













   ..
       !! processed by numpydoc !!

.. py:function:: get_reference_info_wrapper(reference)

   
   Will compare the spatial attribute of 2 references.


   :Parameters:

       **reference** : Nifti or Trk filename, Nifti1Image or TrkFile, Nifti1Header or
           trk.header (dict), TrxFile or trx.header (dict)
           Reference that provides the spatial attribute.

       **Returns**
           ..

       **-------**
           ..

       **output** : tuple
           - affine ndarray (4,4), np.float32, tranformation of VOX to RASMM
           - dimensions ndarray (3,), int16, volume shape for each axis
           - voxel_sizes  ndarray (3,), float32, size of voxel for each axis
           - voxel_order, string, Typically 'RAS' or 'LPS'














   ..
       !! processed by numpydoc !!

.. py:function:: is_header_compatible(reference_1, reference_2)

   
   Will compare the spatial attribute of 2 references.


   :Parameters:

       **reference_1** : Nifti or Trk filename, Nifti1Image or TrkFile,
           Nifti1Header or trk.header (dict)
           Reference that provides the spatial attribute.

       **reference_2** : Nifti or Trk filename, Nifti1Image or TrkFile,
           Nifti1Header or trk.header (dict)
           Reference that provides the spatial attribute.

       **Returns**
           ..

       **-------**
           ..

       **output** : bool
           Does all the spatial attribute match














   ..
       !! processed by numpydoc !!

.. py:function:: get_axis_shift_vector(flip_axes)

   



   :Parameters:

       **flip_axes** : list of str
           String containing the axis to flip.
           Possible values are 'x', 'y', 'z'

       **Returns**
           ..

       **-------**
           ..

       **flip_vector** : np.ndarray (3,)
           Vector containing the axis to flip.
           Possible values are -1, 1














   ..
       !! processed by numpydoc !!

.. py:function:: get_axis_flip_vector(flip_axes)

   



   :Parameters:

       **flip_axes** : list of str
           String containing the axis to flip.
           Possible values are 'x', 'y', 'z'

       **Returns**
           ..

       **-------**
           ..

       **flip_vector** : np.ndarray (3,)
           Vector containing the axis to flip.
           Possible values are -1, 1














   ..
       !! processed by numpydoc !!

.. py:function:: get_shift_vector(sft)

   
   When flipping a tractogram the shift vector is used to change the origin
   of the grid from the corner to the center of the grid.


   :Parameters:

       **sft** : StatefulTractogram
           StatefulTractogram object

       **Returns**
           ..

       **-------**
           ..

       **shift_vector** : ndarray
           Shift vector to apply to the streamlines














   ..
       !! processed by numpydoc !!

.. py:function:: flip_sft(sft, flip_axes)

   
   Flip the streamlines in the StatefulTractogram according to the
   flip_axes. Uses the spatial information to flip according to the center
   of the grid.


   :Parameters:

       **sft** : StatefulTractogram
           StatefulTractogram to flip

       **flip_axes** : list of str
           Axes to flip.
           Possible values are 'x', 'y', 'z'

       **Returns**
           ..

       **-------**
           ..

       **sft** : StatefulTractogram
           StatefulTractogram with flipped axes














   ..
       !! processed by numpydoc !!

.. py:function:: load_matrix_in_any_format(filepath)

   
   Load a matrix from a txt file OR a npy file.


   :Parameters:

       **filepath** : str
           Path to the matrix file.

       **Returns**
           ..

       **-------**
           ..

       **matrix** : numpy.ndarray
           The matrix.














   ..
       !! processed by numpydoc !!

.. py:function:: get_reverse_enum(space_str, origin_str)

   
   Convert string representation to enums for the StatefulTractogram.


   :Parameters:

       **space_str** : str
           String representing the space.

       **origin_str** : str
           String representing the origin.

       **Returns**
           ..

       **-------**
           ..

       **output** : str
           Space and Origin as Enums.














   ..
       !! processed by numpydoc !!

.. py:function:: convert_data_dict_to_tractogram(data)

   
   Convert a data from a lazy tractogram to a tractogram

   Keyword arguments:
       data -- The data dictionary to convert into a nibabel tractogram

   Returns:
       A Tractogram object















   ..
       !! processed by numpydoc !!

.. py:function:: append_generator_to_dict(gen, data)

.. py:function:: verify_trx_dtype(trx, dict_dtype)

   
   Verify if the dtype of the data in the trx is the same as the one in
   the dict.


   :Parameters:

       **trx** : Tractogram
           Tractogram to verify.

       **dict_dtype** : dict
           Dictionary containing all elements dtype to verify.

       **Returns**
           ..

       **-------**
           ..

       **output** : bool
           True if the dtype is the same, False otherwise.














   ..
       !! processed by numpydoc !!