opengate.image
==============

.. py:module:: opengate.image


Functions
---------

.. autoapisummary::

   opengate.image.update_image_py_to_cpp
   opengate.image.itk_dir_to_rotation
   opengate.image.create_3d_image
   opengate.image.create_image_like
   opengate.image.create_image_like_info
   opengate.image.get_info_from_image
   opengate.image.read_image_info
   opengate.image.get_translation_between_images_center
   opengate.image.get_origin_wrt_images_g4_position
   opengate.image.get_cpp_image
   opengate.image.itk_image_view_from_array
   opengate.image.get_image_center
   opengate.image.get_translation_from_iso_center
   opengate.image.align_image_with_physical_volume
   opengate.image.create_image_with_extent
   opengate.image.create_image_with_volume_extent
   opengate.image.voxelize_volume
   opengate.image.transform_images_point
   opengate.image.compute_image_3D_CDF
   opengate.image.scale_itk_image
   opengate.image.divide_itk_images
   opengate.image.split_spect_projections
   opengate.image.compare_itk_image_info
   opengate.image.compare_itk_image_content
   opengate.image.compare_itk_image


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

.. py:function:: update_image_py_to_cpp(py_img, cpp_img, copy_data=False)

.. py:function:: itk_dir_to_rotation(dir)

.. py:function:: create_3d_image(size, spacing, pixel_type='float', allocate=True, fill_value=0)

.. py:function:: create_image_like(like_image, allocate=True, pixel_type='')

.. py:function:: create_image_like_info(info, allocate=True)

.. py:function:: get_info_from_image(image)

.. py:function:: read_image_info(path_to_image)

.. py:function:: get_translation_between_images_center(img_name1, img_name2)

   The two images are considered in the same physical space (coordinate system).
   This function computes the translation between their centers.
   Warning, the ITK image origin consider the center of the first voxel, we thus
   consider half a pixel shift for the center.


.. py:function:: get_origin_wrt_images_g4_position(img_info1, img_info2, translation)

   The two images are considered in the same GATE physical space (coordinate system), so according to the
   centers of both images (+translation).
   This function computes the origin for the second image such as the two images will be in the same
   physical space of the first image.
   Warning, the ITK image origin considers the center of the first voxel, we thus
   consider half a pixel shift for the center.


.. py:function:: get_cpp_image(cpp_image)

.. py:function:: itk_image_view_from_array(arr)

   When the input numpy array is of shape [1,1,x], the conversion to itk image fails:
   the output image size is with the wrong dimensions.
   We thus 'patch' itk.image_view_from_array to correct the size.

   Not fully sure if this is the way to go.


.. py:function:: get_image_center(image)

.. py:function:: get_translation_from_iso_center(img_info, rot, iso_center, centered)

.. py:function:: align_image_with_physical_volume(volume, image, initial_translation=None, initial_rotation=Rotation.identity(), copy_index=0)

.. py:function:: create_image_with_extent(extent, spacing=(1, 1, 1), margin=0)

.. py:function:: create_image_with_volume_extent(volume, spacing=(1, 1, 1), margin=0)

.. py:function:: voxelize_volume(se, image)

   The voxelization do not check which volume is voxelized.
   Every voxel will be assigned an ID corresponding to the material at this position
   in the world.


.. py:function:: transform_images_point(p, img1, img2)

.. py:function:: compute_image_3D_CDF(image)

   Compute the three CDF (Cumulative Density Function) for the given image
   Warning; numpy order is ZYX

   :param image: itk image


.. py:function:: scale_itk_image(img, scale)

.. py:function:: divide_itk_images(img1_numerator, img2_denominator, filterVal=0, replaceFilteredVal=0)

.. py:function:: split_spect_projections(input_filenames, nb_ene)

   The inputs are filenames of several images containing projections for a given spect head
   Each image is composed of nb_ene energy windows and XX angles.
   The number of angles is found by looking at the number of slices.

   The function computes nb_ene itk image with all angles and all heads merged into a list of
   projections stored as a 3D image, to make it easy to reconstruct with RTK.



.. py:function:: compare_itk_image_info(image1, image2)

.. py:function:: compare_itk_image_content(image1, image2)

.. py:function:: compare_itk_image(filename1, filename2)