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
DICOMPlugin
read	accept_uneven_slices	bool	Accept series with uneven number of slices
read	accept_duplicate_tag	bool	Accept series where tag is duplicated
read	select_thickness	str	Select “thin” or “thick” series. Used for some CT acquisitions.
read	headers_only	bool	Skip pixel data
read	correct_acq	bool	Correct acquisition times for dynamic series
read	separate_series	bool	Sort by Series Instance UID. Used by Collections
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	<input_order>	str	User-defined input order
write	keep_uid	bool	When True, create new Instance UIDs when writing
write	window	str	Acquisition Number
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