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	DICOM Attribute Name	Type	Usage
Collections
read	strict_values	bool	Require study attributes to match in each series/study. Default: True
DICOMPlugin
read	skip_broken_series	bool	Skip broken series in a study. Do not raise exception.
read	accept_uneven_slices	bool	Accept series with uneven number of slices. Keep last image for each position only.
read	accept_duplicate_tag	bool	Accept series where tag is duplicated. Each image is added to image list at slice position.
read	split_acquisitions	str	Split series on DICOM Acquisition Number.
read	split_echo_numbers	str	Split series on DICOM Echo Numbers.
read	headers_only	bool	Skip pixel data
read	correct_acq	bool	Correct acquisition times for dynamic series
read	ignore_series_uid	str	Ignore Series Instance UID, i.e. do not sort images into different Series
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	use_cross_product	bool	Always use vector cross product to calculate z column of the transformation matrix
read	<input_order>	str	User-defined input order
write	keep_uid	bool	When True, create new Instance UIDs when writing
write	window	str	When “original”: keep original center/level values. Otherwise, calculate window center/level from present data.
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’
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
write	output_sort	str	Which tag will sort the output images, ‘slice’ or ‘tag’
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
write	output_sort	str	Which tag will sort the output images, ‘slice’ or ‘tag’
NiftiPlugin
No options used