kwneuro.io
==========

.. py:module:: kwneuro.io


Classes
-------

.. autoapisummary::

   kwneuro.io.NiftiVolumeResource
   kwneuro.io.FslBvalResource
   kwneuro.io.FslBvecResource
   kwneuro.io.JsonResponseFunctionResource


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

.. py:class:: NiftiVolumeResource

   Bases: :py:obj:`kwneuro.resource.VolumeResource`


   A volume or volume stack that is saved to disk in the nifti file format.


   .. py:attribute:: is_loaded
      :type:  ClassVar[bool]
      :value: False


      Whether a resource corresponds to in-memory data, rather than for example on-disk data.


   .. py:attribute:: path_in
      :type:  dataclasses.InitVar[kwneuro.util.PathLike]

      Path to the underlying volume nifti file


   .. py:attribute:: path
      :type:  pathlib.Path


   .. py:method:: load() -> kwneuro.resource.InMemoryVolumeResource

      Load volume into memory



   .. py:method:: get_array() -> numpy.typing.NDArray[numpy.number]

      Get the underlying volume data array



   .. py:method:: get_affine() -> numpy.typing.NDArray[numpy.floating]

      Get the 4x4 affine matrix that maps index space to patient/scanner space



   .. py:method:: get_metadata() -> dict[str, Any]

      Get the volume image metadata



   .. py:method:: save(vol: kwneuro.resource.VolumeResource, path: kwneuro.util.PathLike) -> NiftiVolumeResource
      :staticmethod:


      Save volume data to a path, creating a NiftiVolumeResource.



.. py:class:: FslBvalResource

   Bases: :py:obj:`kwneuro.resource.BvalResource`


   A b-value list that is saved to disk in the FSL text file format.


   .. py:attribute:: is_loaded
      :type:  ClassVar[bool]
      :value: False


      Whether a resource corresponds to in-memory data, rather than for example on-disk data.


   .. py:attribute:: path_in
      :type:  dataclasses.InitVar[kwneuro.util.PathLike]

      Path to the underlying bval txt file


   .. py:attribute:: path
      :type:  pathlib.Path


   .. py:method:: load() -> kwneuro.resource.InMemoryBvalResource

      Load b-values into memory



   .. py:method:: get() -> numpy.typing.NDArray[numpy.floating]

      Get the underlying array of b-values



   .. py:method:: save(bvals: kwneuro.resource.BvalResource, path: kwneuro.util.PathLike) -> FslBvalResource
      :staticmethod:


      Save data to a path, creating a FslBvalResource.



.. py:class:: FslBvecResource

   Bases: :py:obj:`kwneuro.resource.BvecResource`


   A b-vector list that is saved to disk in the FSL text file format.


   .. py:attribute:: is_loaded
      :type:  ClassVar[bool]
      :value: False


      Whether a resource corresponds to in-memory data, rather than for example on-disk data.


   .. py:attribute:: path_in
      :type:  dataclasses.InitVar[kwneuro.util.PathLike]

      Path to the underlying bvec txt file


   .. py:attribute:: path
      :type:  pathlib.Path


   .. py:method:: load() -> kwneuro.resource.InMemoryBvecResource

      Load b-vectors into memory



   .. py:method:: get() -> numpy.typing.NDArray[numpy.floating]

      Get the underlying array of b-vectors of shape (N,3)



   .. py:method:: save(bvecs: kwneuro.resource.BvecResource, path: kwneuro.util.PathLike) -> FslBvecResource
      :staticmethod:


      Save data to a path, creating a FslBvecResource.



.. py:class:: JsonResponseFunctionResource

   Bases: :py:obj:`kwneuro.resource.ResponseFunctionResource`


   A response function that is saved to disk in a json file.


   .. py:attribute:: is_loaded
      :type:  ClassVar[bool]
      :value: False


      Whether a resource corresponds to in-memory data, rather than for example on-disk data.


   .. py:attribute:: path_in
      :type:  dataclasses.InitVar[kwneuro.util.PathLike]

      Path to the underlying json file


   .. py:attribute:: path
      :type:  pathlib.Path


   .. py:method:: get() -> tuple[numpy.typing.NDArray, numpy.floating]

      Get the underlying response function



   .. py:method:: get_dipy_object() -> dipy.reconst.csdeconv.AxSymShResponse

      Get the underlying response function in a format compatible with Dipy



   .. py:method:: load() -> kwneuro.resource.InMemoryResponseFunctionResource

      Load volume into memory



   .. py:method:: save(response: kwneuro.resource.ResponseFunctionResource, path: kwneuro.util.PathLike) -> JsonResponseFunctionResource
      :staticmethod:


      Save response function data to a path, creating a JsonResponseFunctionResource.