trx.workflows
=============

.. py:module:: trx.workflows


Attributes
----------

.. autoapisummary::

   trx.workflows.dipy_available


Functions
---------

.. autoapisummary::

   trx.workflows.convert_dsi_studio
   trx.workflows.convert_tractogram
   trx.workflows.tractogram_simple_compare
   trx.workflows.verify_header_compatibility
   trx.workflows.tractogram_visualize_overlap
   trx.workflows.validate_tractogram
   trx.workflows._load_streamlines_from_csv
   trx.workflows._load_streamlines_from_arrays
   trx.workflows._apply_spatial_transforms
   trx.workflows._write_header
   trx.workflows._write_streamline_data
   trx.workflows._normalize_dtype
   trx.workflows._write_data_array
   trx.workflows.generate_trx_from_scratch
   trx.workflows.manipulate_trx_datatype


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

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


.. py:function:: convert_dsi_studio(in_dsi_tractogram, in_dsi_fa, out_tractogram, remove_invalid=True, keep_invalid=False)

.. py:function:: convert_tractogram(in_tractogram, out_tractogram, reference, pos_dtype='float32', offsets_dtype='uint32')

.. py:function:: tractogram_simple_compare(in_tractograms, reference)

.. py:function:: verify_header_compatibility(in_files)

.. py:function:: tractogram_visualize_overlap(in_tractogram, reference, remove_invalid=True)

.. py:function:: validate_tractogram(in_tractogram, reference, out_tractogram, remove_identical_streamlines=True, precision=1)

.. py:function:: _load_streamlines_from_csv(positions_csv)

   
   Load streamlines from CSV file.
















   ..
       !! processed by numpydoc !!

.. py:function:: _load_streamlines_from_arrays(positions, offsets)

   
   Load streamlines from position and offset arrays.
















   ..
       !! processed by numpydoc !!

.. py:function:: _apply_spatial_transforms(streamlines, reference, space_str, origin_str, verify_invalid, offsets)

   
   Apply spatial transforms and verify streamlines.
















   ..
       !! processed by numpydoc !!

.. py:function:: _write_header(tmp_dir_name, reference, streamlines)

   
   Write header file.
















   ..
       !! processed by numpydoc !!

.. py:function:: _write_streamline_data(tmp_dir_name, streamlines, positions_dtype, offsets_dtype)

   
   Write streamline position and offset data.
















   ..
       !! processed by numpydoc !!

.. py:function:: _normalize_dtype(dtype_str)

   
   Normalize dtype string format.
















   ..
       !! processed by numpydoc !!

.. py:function:: _write_data_array(tmp_dir_name, subdir_name, args, is_dpg=False)

   
   Write data array to file.
















   ..
       !! processed by numpydoc !!

.. py:function:: generate_trx_from_scratch(reference, out_tractogram, positions_csv=False, positions=False, offsets=False, positions_dtype='float32', offsets_dtype='uint64', space_str='rasmm', origin_str='nifti', verify_invalid=True, dpv=None, dps=None, groups=None, dpg=None)

   
   Generate TRX file from scratch using various input formats.
















   ..
       !! processed by numpydoc !!

.. py:function:: manipulate_trx_datatype(in_filename, out_filename, dict_dtype)