highdicom

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Provide meaningful error message if all Segmentation frames are empty

23

When using the static method of `_omit_empty_frames`, if there are no empty frames present (frames without positive pixels), then numpy thows an exception with regard to the empty `non_empty_frames` list...

adamvonpaternos

Allow segmentations to reference multiple images

6

Applying the logic of #193 to Segmentation instances.

hackermd

Add support for instance segmentation with LABELED segmentation type

1

This PR introduces changes to support storing multiple connected components for the same segment (labeled mask) in a DICOM Segmentation instance. This is currently not supported by the DICOM standard,...

hackermd

Allow reference of optical path for annotations measurements

1

In case of intensity measurements for annotations, the microscopy image (and the optical path) need to be specified for the measurements. This PR adds allows including a reference to the...

hackermd

Add warning when empty segmentation is passed with omit_empty_frames

1

Addresses #180 When the `omit_empty_frames` option is used for a Segmentation and an empty segmentation mask is passed (i.e. a mask with all zeros), the constructor will issue a `UserWarning`...

CPBridge

DICOM SEG for CMR cine data (2D + t)

7

Trying to generate a dicom seg file based on a multiple unsigned np.array, which is of shape (#_frames, #rows, #cols). The way I've approached the task was by generating dicom...

apint0-media

Add better support for segmented LUTs

1

#139 added support for segmented LUTs in presentation states, however the user is left to themselves to construct valid lut data, which is not straightforward. We should provide utility methods...

CPBridge

Change `ParametricMap` to use new `VOILUTTransformation` class

1

Unify the API of the `ParametricMap` class with the presentation state SOPClasses by having the user provide a `VOILUTTransformation` object to the constructor. This is a backward incompatible change

CPBridge

Set up doctests to catch errors in the examples

1

Various mistakes have been found in the user guide examples. Examples that don't work are very offputting for new users. We should set up automatic testing of the documentation examples...

CPBridge

Checks that values satisfy requirements of the VR

3

This has been discussed before (e.g. [here](https://github.com/MGHComputationalPathology/highdicom/pull/130#discussion_r737957633)) but we should have an issue to track it. Pydicom is very loose in what it allows you to set as an attribute's...

CPBridge