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 |