DICOM-SEG only displayed when I load it first

[inikishev]

Describe the bug. What happened?

When I drag DICOM-SEG file into Weasis, and THEN drag the linked images, the segmentation panel works.

However when I first open an image, and then open the segmentation for it, nothing happens, no segmentation appears. The only change is an orange circle that appears on the linked image thumbnail:

What version of Weasis are you running?

4.4.0

On which system the problem occurs?

Windows

Relevant log output

No response

Additional contextual elements

No response

[nroduit]

There are several enhancements for reading SEG files in the next version.
Please send me an example to see if it is OK.

[nroduit]

Can you confirm whether this problem has been fixed?

[inikishev]

Can you confirm whether this problem has been fixed?

In the last version I am not able to load my segmentation at all. When I load DICOM-SEG first, then DICOMs, it doesn't display anything and seems to break the UI a little bit - some tabs have not text.

when I load DICOMs first, and then DICOM-SEG, it just doesn't display segmentation

here is the log https://gist.github.com/inikishev/9732660c0df14530da4327526a1688a1

I downloaded the DICOMs here https://github.com/datalad/example-dicom-structural, and saved some bogus segmentation, which should look like this

example DICOM-SEG.zip here is a DICOM-SEG file (I zipped it because github doesnt accept .dcm).

[nroduit]

Your SEG file is not consistent. The SEG object must be a distinct series and therefore needs a new series instance UID. The same series can only have one modality type (MR and SEG is not possible).

[inikishev]

Your SEG file is not consistent. The SEG object must be a distinct series and therefore needs a new series instance UID. The same series can only have one modality type (MR and SEG is not possible).

thank you for the information. I was using highdicom and I set series_instance_uid = source_images[0].SeriesInstanceUID,, and that must have caused the issue. I will try this method now https://razorx89.github.io/pydicom-seg/guides/write.html

[inikishev]

Your SEG file is not consistent. The SEG object must be a distinct series and therefore needs a new series instance UID. The same series can only have one modality type (MR and SEG is not possible).

Unfortunately I am not able to get it working. I followed https://razorx89.github.io/pydicom-seg/guides/write.html, this is my code

import numpy as np
import pydicom
import pydicom_seg
import SimpleITK as sitk

template = pydicom_seg.template.from_dcmqi_metainfo('metainfo.json')

writer = pydicom_seg.MultiClassWriter(
    template=template,
    # inplane_cropping=True,  # Crop image slices to the minimum bounding box on
    #                         # x and y axes
    # skip_empty_slices=True,  # Don't encode slices with only zeros
    # skip_missing_segment=False,  # If a segment definition is missing in the
    #                              # template, then raise an error instead of
    #                              # skipping it.
)

reader = sitk.ImageSeriesReader()

# https://github.com/datalad/example-dicom-structural
series_instance_uid = pydicom.dcmread('/var/mnt/hdd/Datasets/Example DICOMs/dicoms/N2D_0001.dcm').SeriesInstanceUID

dcm_files = reader.GetGDCMSeriesFileNames('/var/mnt/hdd/Datasets/Example DICOMs/dicoms', series_instance_uid)
reader.SetFileNames(dcm_files)
image = reader.Execute()
image_data = sitk.GetArrayFromImage(image)

def process_image(arr):
    arr = np.random.randint(size = arr.shape, low = 0, high = 2, dtype = np.uint8)
    assert arr.min() == 0
    assert arr.max() == 1
    return arr


segmentation_data = process_image(image_data)

segmentation = sitk.GetImageFromArray(segmentation_data)
segmentation.CopyInformation(image)

source_images = [
    pydicom.dcmread(x, stop_before_pixels=True)
    for x in dcm_files
]
dcm = writer.write(segmentation, source_images)
dcm.save_as('segmentation.dcm')

and this is metainfo.json

{
  "ContentCreatorName": "Reader1",
  "ClinicalTrialSeriesID": "Session1",
  "ClinicalTrialTimePointID": "1",
  "SeriesDescription": "Segmentation",
  "SeriesNumber": "300",
  "InstanceNumber": "1",
  "segmentAttributes": [
    [
      {
        "labelID": 1,
        "SegmentDescription": "Meningioma",
        "SegmentAlgorithmType": "AUTOMATIC",
        "SegmentAlgorithmName": "bogus",
        "SegmentedPropertyCategoryCodeSequence": {
          "CodeValue": "49755003",
          "CodingSchemeDesignator": "SCT",
          "CodeMeaning": "Morphologically Altered Structure"
        },
        "SegmentedPropertyTypeCodeSequence": {
          "CodeValue": "4147007",
          "CodingSchemeDesignator": "SCT",
          "CodeMeaning": "Mass"
        },
        "recommendedDisplayRGBValue": [
          144,
          238,
          144
        ]
      }
    ]
  ],
  "ContentLabel": "SEGMENTATION",
  "ContentDescription": "Image segmentation",
  "ClinicalTrialCoordinatingCenterName": "dcmqi",
  "BodyPartExamined": "Brain"
}

the SEG file itself is OK, I can open it with AlizaMS

segmentation.zip

However nothing seems to happen when I open it in weasis.

[nroduit]

There are always problems with this file. It lacks mandatory fields like SegmentLabel, which is used as a key by Weasis.
Please start by 'using a DICOM validation tool if you want to create data, see the Innolitics validator: