Options

Some plugins accept options which modify the plugin behaviour. These options can be provided by adding them to the opts dictionary on the Series() read. The can also be given as **kwargs on the object instantiation. E.g.:

from imagedata import Series
a = Series('in_dir', opts={'accept_duplicate_tag': True})
b = Series('in_dir', accept_duplicate_tag=True)

Options can be given to the Cohort(), Patient(), Study() and Series() objects.

The following plugin options are known at the time of writing:

Plugin	Option Name	Type	Usage
Collections
read	strict_values	bool	Require study attributes to match in each series/study. Default: True
All Plugins
read	input_shape	str or iter	Set shape of input data. Give as string ‘4x5’ or as iterable (4,5) or [4,5]. Default: None
write	output_sort	str	Which tag will sort the output images, ‘slice’ or ‘tag’
write	output_dir	str	Store all images in a single or multiple directories, ‘single’ or ‘multi’
DICOMPlugin
read	skip_broken_series	bool	Skip broken series in a study. Do not raise exception. Default: False
read	accept_uneven_slices	bool	Accept series with uneven number of slices. Keep last image for each position only. Default: False
read	sort_on_slice_location	bool	Sort stack on slice location, not on distance along normal vector. Default: False
read	accept_duplicate_tag	bool	Accept series where tag is duplicated. Each image is added to image list at slice position. Default: False
read	split_acquisitions	bool	Split series on DICOM Acquisition Number. Default: False
read	split_echo_numbers	bool	Split series on DICOM Echo Numbers. Default: False
read	headers_only	bool	Skip pixel data. Default: False
read	correct_acq	bool	Correct acquisition times for dynamic series. Default: False
read	ignore_series_uid	bool	Ignore Series Instance UID, i.e. do not sort images into different Series. Default: False
read	input_serinsuid	str	Filter input files on specified Series Instance UID
read	input_echo	int	Filter input files on specified Echo Numbers
read	input_acquisition	int	Filter input files on specified Acquisition Number
read	slice_tolerance	float	Slice distance tolerance when sorting. Default: 1E-5
read	dir_cosine_tolerance	float	Tolerance for difference in directional cosine tolerance. Default: 0.0
read	<input_order>	str	User-defined input order
write	keep_uid	bool	When False, create new Instance UIDs when writing. Default: False
ITKPlugin
read	input_sort	int	Sort images on SORT_ON_SLICE or SORT_ON_TAG. Useful for image formats that do not provide geometry data
MatPlugin
read	input_sort	int	Sort images on SORT_ON_SLICE or SORT_ON_TAG. Useful for image formats that do not provide geometry data
NiftiPlugin
No options used