brats_toolkit.util package

Submodules

brats_toolkit.util.docker_functions module

brats_toolkit.util.docker_functions.start_docker(exam_import_folder=None, exam_export_folder=None, dicom_import_folder=None, nifti_export_folder=None, mode='cpu', gpuid='0')
brats_toolkit.util.docker_functions.stop_docker()
brats_toolkit.util.docker_functions.update_docker()

brats_toolkit.util.filemanager module

Module containing functions to manage the BRATS files

brats_toolkit.util.filemanager.bratsNormalize(image=None, bm=None, bias=0.0001)

Provides normalization of BRATS images to the intensity interval 0…1 and ensures that the background is entirely 0 The bias value ensures that no brain voxel becomes 0

brats_toolkit.util.filemanager.clean(root, gz=False, dir=False)

Removes all subfolders and leaves only .nii and .nii.gz input files untouched root: path to folder with subfolers gz: If True, compressed Nifti files are also removed

brats_toolkit.util.filemanager.completeclean(root)
brats_toolkit.util.filemanager.conversion(segmentations, verbose=True)
brats_toolkit.util.filemanager.convertLabels(originalFile, oldlabels, newlabels=[0, 1, 2, 4])
brats_toolkit.util.filemanager.create_files(root, gz=False)
brats_toolkit.util.filemanager.fileFinder(srcPath, filetofind, func=<function convertLabels>, verbose=True)

finds a file starting from the source path in subdirectories and runs an arbitrary function on them

brats_toolkit.util.filemanager.fileIterator(directory, gt_root, verbose=True)
brats_toolkit.util.filemanager.loadGT(path, patid, file='gt.nii.gz', verbose=True)

Loads the Ground Truth for a specified patient from a given Ground Truth root directory In: dir, path to the GT folder

patid, patient ID verbose: True/False terminal output

Out: itk image! -> convert to numpy array

brats_toolkit.util.filemanager.reduce_filesize(root, gz=False)
brats_toolkit.util.filemanager.remove_nii(root)
brats_toolkit.util.filemanager.rename_fla(root)

Renames fla.nii files to flair.nii if required

brats_toolkit.util.filemanager.rename_flair(root)

Renames flair.nii files to fla.nii if required

brats_toolkit.util.filemanager.touchAndConvert(originalFile, gt, verbose=True)

Loads the ITK image and saves it with proper header data (and conversion to 8-bit unint)

brats_toolkit.util.filemanager.validate_files(root)

Checks if all input directories contain the right files

brats_toolkit.util.own_itk module

Module containing functions enabling to read, make and write ITK images.

brats_toolkit.util.own_itk.copy_image_info(input_path, ref_path)

Copy origin, direction and spacing information from ref_path into the header in input_path.

brats_toolkit.util.own_itk.get_itk_array(path_or_image)

Get an image array given a path or itk image.

Parameters:

path_or_image (str or itk image) – Path pointing to an image file with extension among TIFF, JPEG, PNG, BMP, DICOM, GIPL, Bio-Rad, LSM, Nifti (.nii and .nii.gz), Analyze, SDT/SPR (Stimulate), Nrrd or VTK images or an itk image.

Returns:

arr – Image ndarray contained in the given path or the itk image.

Return type:

ndarray

brats_toolkit.util.own_itk.get_itk_data(path_or_image, verbose=False)

Get the image array, image size and pixel dimensions given an itk image or a path.

Parameters:

  • path_or_image (str or itk image) – Path pointing to an image file with extension among TIFF, JPEG, PNG, BMP, DICOM, GIPL, Bio-Rad, LSM, Nifti (.nii and .nii.gz), Analyze, SDT/SPR (Stimulate), Nrrd or VTK images or an itk image.

  • verbose (boolean, optional) – If true, print image shape, spacing and data type of the image corresponding to path_or_image.

Returns:

  • arr (ndarray) – Image array contained in the given path or the itk image.

  • shape (tuple) – Shape of the image array contained in the given path or the itk image.

  • spacing (tuple) – Pixel spacing (resolution) of the image array contained in the given path or the itk image.

brats_toolkit.util.own_itk.get_itk_image(path_or_image)

Get an itk image given a path.

Parameters:

path (str or itk.Image) – Path pointing to an image file with extension among TIFF, JPEG, PNG, BMP, DICOM, GIPL, Bio-Rad, LSM, Nifti (.nii and .nii.gz), Analyze, SDT/SPR (Stimulate), Nrrd or VTK images.

Returns:

image – The itk image.

Return type:

itk image

brats_toolkit.util.own_itk.load_arr_from_paths(paths)

For every str in paths (paths can consis of nested lists), load the image at this path. If any str is not a path, an error is thrown. All other objects are preserved.

brats_toolkit.util.own_itk.make_itk_image(arr, proto_image=None, verbose=True)

Create an itk image given an image array.

Parameters:

  • arr (ndarray) – Array to create an itk image with.

  • proto_image (itk image, optional) – Proto itk image to provide Origin, Spacing and Direction.

Returns:

image – The itk image containing the input array arr.

Return type:

itk image

brats_toolkit.util.own_itk.read_dicom(source_path, verbose=True)

Reads dicom series into an itk image.

Parameters:

  • source_path (string) – path to directory containing dicom series.

  • verbose (boolean) – print out all series file names.

Returns:

image – image volume.

Return type:

itk image

brats_toolkit.util.own_itk.reduce_arr_dtype(arr, verbose=False)

Change arr.dtype to a more memory-efficient dtype, without changing any element in arr.

brats_toolkit.util.own_itk.write_itk_image(image, path)

Write an itk image to a path.

Parameters:

  • image (itk image or np.ndarray) – Image to be written.

  • path (str) – Path where the image should be written to.

brats_toolkit.util.prep_utils module

brats_toolkit.util.prep_utils.tempFiler(orgFilePath, modality, tempFolder)

Module contents