pytomography.io.shared.dicom#

Module Contents#

Functions#

_get_affine_multifile(files)

Computes an affine matrix corresponding the coordinate system of a CT DICOM file. Note that since CT scans consist of many independent DICOM files, ds corresponds to an individual one of these files. This is why the maximum z value is also required (across all seperate independent DICOM files).

_get_affine_single_file(filename)

Obtain the affine matrix from a 3D medical image stored in a single file.

open_multifile(files[, return_object_meta])

Given a list of seperate DICOM files, opens them up and stacks them together into a single CT image.

open_singlefile(file)

Opens data from a single DICOM file.

compute_max_slice_loc_multifile(files)

Obtains the maximum z-location from a list of DICOM slice files

compute_min_slice_loc_multifile(files)

Obtains the minimum z-location from a list of DICOM slice files

compute_slice_thickness_multifile(files)

Compute the slice thickness for files that make up a scan. Though this information is often contained in the DICOM file, it is sometimes inconsistent with the ImagePositionPatient attribute, which gives the true location of the slices.

align_images_affine(im_fixed, im_moving, affine_fixed, ...)

pytomography.io.shared.dicom._get_affine_multifile(files)[source]#

Computes an affine matrix corresponding the coordinate system of a CT DICOM file. Note that since CT scans consist of many independent DICOM files, ds corresponds to an individual one of these files. This is why the maximum z value is also required (across all seperate independent DICOM files).

Parameters:

  • ds (Dataset) – DICOM dataset of CT data

  • max_z (float) – Maximum value of z across all axial slices that make up the CT scan

  • files (Sequence[str]) –

Returns:

Affine matrix corresponding to CT scan.

Return type:

np.array

pytomography.io.shared.dicom._get_affine_single_file(filename)[source]#

Obtain the affine matrix from a 3D medical image stored in a single file.

Parameters:

filename (str) – Path of file

Returns:

Affine matrix

Return type:

np.array

pytomography.io.shared.dicom.open_multifile(files, return_object_meta=False)[source]#

Given a list of seperate DICOM files, opens them up and stacks them together into a single CT image.

Parameters:

  • files (Sequence[str]) – List of CT DICOM filepaths corresponding to different z slices of the same scan.

  • return_object_meta (bool) – Whether or not to return object metadata corresponding to opened file

Returns:

CT scan in units of Hounsfield Units at the effective CT energy.

Return type:

np.array

pytomography.io.shared.dicom.open_singlefile(file)[source]#

Opens data from a single DICOM file.

Parameters:

file (str) – Filepath

Returns:

3D Image

Return type:

torch.Tensor

pytomography.io.shared.dicom.compute_max_slice_loc_multifile(files)[source]#

Obtains the maximum z-location from a list of DICOM slice files

Parameters:

files (Sequence[str]) – List of DICOM filepaths corresponding to different z slices of the same scan.

Returns:

Maximum z location

Return type:

float

pytomography.io.shared.dicom.compute_min_slice_loc_multifile(files)[source]#

Obtains the minimum z-location from a list of DICOM slice files

Parameters:

files (Sequence[str]) – List of DICOM filepaths corresponding to different z slices of the same scan.

Returns:

Minimum location

Return type:

float

pytomography.io.shared.dicom.compute_slice_thickness_multifile(files)[source]#

Compute the slice thickness for files that make up a scan. Though this information is often contained in the DICOM file, it is sometimes inconsistent with the ImagePositionPatient attribute, which gives the true location of the slices.

Parameters:

files (Sequence[str]) – List of DICOM filepaths corresponding to different z slices of the same scan.

Returns:

Slice thickness of the scan

Return type:

float

pytomography.io.shared.dicom.align_images_affine(im_fixed, im_moving, affine_fixed, affine_moving, cval=0)[source]#