dicom2nifti.common module

dicom2nifti

@author: abrys

dicom2nifti.common.apply_scaling(data, dicom_headers)

Rescale the data based on the RescaleSlope and RescaleOffset Based on the scaling from pydicomseries

Parameters:

• dicom_headers – dicom headers to use to retreive the scaling factors
• data – the input data

dicom2nifti.common.create_affine(sorted_dicoms)

Function to generate the affine matrix for a dicom series This method was based on (http://nipy.org/nibabel/dicom/dicom_orientation.html)

Parameters:sorted_dicoms – list with sorted dicom files

dicom2nifti.common.do_scaling(data, rescale_slope, rescale_intercept, private_scale_slope=1.0, private_scale_intercept=0.0)

dicom2nifti.common.get_fd_array_value(tag, count)

Getters for data that also work with implicit transfersyntax

Parameters:

• count – number of items in the array
• tag – the tag to read

dicom2nifti.common.get_fd_value(tag)

Getters for data that also work with implicit transfersyntax

Parameters:tag – the tag to read

dicom2nifti.common.get_fl_value(tag)

Getters for data that also work with implicit transfersyntax

Parameters:tag – the tag to read

dicom2nifti.common.get_is_value(tag)

Getters for data that also work with implicit transfersyntax

Parameters:tag – the tag to read

dicom2nifti.common.get_numpy_type(dicom_header)

Make NumPy format code, e.g. “uint16”, “int32” etc from two pieces of info: mosaic.PixelRepresentation – 0 for unsigned, 1 for signed; mosaic.BitsAllocated – 8, 16, or 32

Parameters:dicom_header – the read dicom file/headers Returns:numpy format string

dicom2nifti.common.get_ss_value(tag)

Getters for data that also work with implicit transfersyntax

Parameters:tag – the tag to read

dicom2nifti.common.get_volume_pixeldata(sorted_slices)

the slice and intercept calculation can cause the slices to have different dtypes we should get the correct dtype that can cover all of them

Parameters:sorted_slices (list of slices) – sliced sored in the correct order to create volume

dicom2nifti.common.is_ge(dicom_input)

Use this function to detect if a dicom series is a GE dataset

Parameters:dicom_input – list with dicom objects

dicom2nifti.common.is_hitachi(dicom_input)

Use this function to detect if a dicom series is a hitachi dataset

Parameters:dicom_input – directory with dicom files for 1 scan of a dicom_header

dicom2nifti.common.is_multiframe_dicom(dicom_input)

Use this function to detect if a dicom series is a siemens 4D dataset NOTE: Only the first slice will be checked so you can only provide an already sorted dicom directory (containing one series)

Parameters:dicom_input – directory with dicom files for 1 scan

dicom2nifti.common.is_orthogonal(dicoms, log_details=False)

Validate that volume is orthonormal

Parameters:dicoms – check that we have a volume without skewing

dicom2nifti.common.is_philips(dicom_input)

Use this function to detect if a dicom series is a philips dataset

Parameters:dicom_input – directory with dicom files for 1 scan of a dicom_header

dicom2nifti.common.is_siemens(dicom_input)

Use this function to detect if a dicom series is a siemens dataset

Parameters:dicom_input – directory with dicom files for 1 scan

dicom2nifti.common.is_valid_imaging_dicom(dicom_header)

Function will do some basic checks to see if this is a valid imaging dicom

dicom2nifti.common.read_dicom_directory(dicom_directory, stop_before_pixels=False)

Read all dicom files in a given directory (stop before pixels)

Parameters:

• stop_before_pixels (bool) – Should we stop reading before the pixeldata (handy if we only want header info)
• dicom_directory (six.string_types) – Directory with dicom data

Returns:

List of dicom objects

dicom2nifti.common.set_fd_value(tag, value)

Setters for data that also work with implicit transfersyntax

Parameters:

• value – the value to set on the tag
• tag – the tag to read

dicom2nifti.common.set_ss_value(tag, value)

Setter for data that also work with implicit transfersyntax

Parameters:

• value – the value to set on the tag
• tag – the tag to read

dicom2nifti.common.set_tr_te(nifti_image, repetition_time, echo_time)

Set the tr and te in the nifti headers

Parameters:

• echo_time – echo time
• repetition_time – repetition time
• nifti_image – nifti image to set the info to

dicom2nifti.common.sort_dicoms(dicoms)

Sort the dicoms based om the image possition patient

Parameters:dicoms – list of dicoms

dicom2nifti.common.validate_orientation(dicoms)

Validate that all dicoms have the same orientation

Parameters:dicoms – list of dicoms

dicom2nifti.common.validate_orthogonal(dicoms)

Validate that volume is orthonormal

Parameters:dicoms – check that we have a volume without skewing

dicom2nifti.common.validate_slicecount(dicoms)

Validate that volume is big enough to create a meaningfull volume This will also skip localizers and alike

Parameters:dicoms – list of dicoms

dicom2nifti.common.validate_sliceincrement(dicoms)

Validate that the distance between all slices is equal (of very close to)

Parameters:dicoms – list of dicoms

dicom2nifti.common.write_bval_file(bvals, bval_file)

Write an array of bvals to a bval file

Parameters:

• bvals – array with the values
• bval_file – filepath to write to

dicom2nifti.common.write_bvec_file(bvecs, bvec_file)

Write an array of bvecs to a bvec file

Parameters:

• bvecs – array with the vectors
• bvec_file – filepath to write to