Label Loss on repeatedly loaded and saved segmentations
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	• s349i
	Aug 30 2022, 11:22 AM

Description

Ref T29157: NCT ISSO Annotation Support with MITK Segmentation Flow

Do annotation on an existing annotation task.
Save the annotated task.
Open a new task.
Move back to the previously saved task and add a new label. Draw annotations for the new label.
Save the modified task and open again. The newly added label should be missing now.
Add the new label to the task. The previously drawn annotation for the new label is rendered.

4_new_label_not_shown.PNG (1×1 px, 917 KB)

3_back_create_new_label.PNG (1×1 px, 904 KB)

5_manually_add_again.PNG (1×1 px, 876 KB)

Revisions and Commits

rMITK MITK
	Restricted Differential Revision	rMITKb318ecba0a31 Ignore default properties when loading multilabel images
	Restricted Differential Revision	rMITKad80d98e49b5 Fix review remarks
	Restricted Differential Revision	rMITKd5f9c80dbc7b Fix typo
	Restricted Differential Revision	rMITKfa35314228ce Ignore default properties when loading multilabel images

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		Status	Assigned	Task
		Open	None	T29157 NCT ISSO Annotation Support with MITK Segmentation Flow
		Resolved	kislinsk	T29274 Label Loss on repeatedly loaded and saved segmentations

Event Timeline

• s349i created this task.Aug 30 2022, 11:22 AM

• s349i updated the task description. (Show Details)

• s349i updated the task description. (Show Details)Aug 30 2022, 11:24 AM

• s349i updated the task description. (Show Details)

• s349i updated the task description. (Show Details)Aug 30 2022, 11:27 AM

• s349i added a parent task: T29157: NCT ISSO Annotation Support with MITK Segmentation Flow.

kislinsk claimed this task.Aug 30 2022, 11:34 AM

kislinsk triaged this task as High priority.

kislinsk added a project: MITK.

• s349i removed kislinsk as the assignee of this task.Aug 30 2022, 11:34 AM

• s349i raised the priority of this task from High to Needs Triage.

• s349i changed the visibility from "Public (No Login Required)" to "Subscribers".

kislinsk claimed this task.Aug 30 2022, 11:34 AM

kislinsk triaged this task as High priority.

kislinsk updated the task description. (Show Details)

kislinsk changed the visibility from "Subscribers" to "Public (No Login Required)".

Findings:

In my example I have an image with a predefined label which works as expected.
When I add labels in the Segmentation View and draw something, everything seems fine.
Save and load again the segmentation to see that all pixels of the drawn labels are there, but only the first label appears in the Segmentation View.
So it seems like all the meta data for the extra labels were dismissed when saving the segmentation.

Image header for the working case with 2 labels

NRRD0004
# Complete NRRD file format specification at:
# http://teem.sourceforge.net/nrrd/format.html
type: unsigned short
dimension: 3
space: left-posterior-superior
sizes: 256 256 49
space directions: (1,0,0) (0,1,0) (0,0,3)
kinds: domain domain domain
endian: little
encoding: gzip
space origin: (0,0,0)
DICOM_0008_0060:={"values":[{"z":0, "t":0, "value":"SEG"}]}
DICOM_0008_103E:={"values":[{"z":0, "t":0, "value":"MITK Segmentation"}]}
layer_000:=3
layers:=1
modality:=org.mitk.image.multilabel
org.mitk.label_000_00000:=<?xml version="1.0" encoding="UTF-8"?>\n<Label>\n    <property key="DICOM.0062.0002.0062.0004" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"0"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0005" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"Exterior"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0008" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"SEMIAUTOMATIC"}]}</temporo_spatial_string>\n    </property>\n    <property key="center.coordinates" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="center.index" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="color" type="ColorProperty">\n        <color r="0" g="0" b="0"/>\n    </property>\n    <property key="layer" type="UIntProperty">\n        <unsigned value="0"/>\n    </property>\n    <property key="locked" type="BoolProperty">\n        <bool value="false"/>\n    </property>\n    <property key="name" type="StringProperty">\n        <string value="Exterior"/>\n    </property>\n    <property key="opacity" type="FloatProperty">\n        <float value="0"/>\n    </property>\n    <property key="value" type="UShortProperty">\n        <unsigned value="0"/>\n    </property>\n    <property key="visible" type="BoolProperty">\n        <bool value="true"/>\n    </property>\n</Label>\n
org.mitk.label_000_00001:=<?xml version="1.0" encoding="UTF-8"?>\n<Label>\n    <property key="DICOM.0062.0002.0062.0003.0008.0100" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"T-D000A"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0003.0008.0102" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"SRT"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0003.0008.0104" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"Anatomical Structure"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0004" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"1"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0005" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"Liver"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0008" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"SEMIAUTOMATIC"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.000F.0008.0100" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"T-62000"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.000F.0008.0102" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"SRT"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.000F.0008.0104" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"Liver"}]}</temporo_spatial_string>\n    </property>\n    <property key="center.coordinates" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="center.index" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="color" type="ColorProperty">\n        <color r="0.745098054" g="0" b="0.196078435"/>\n    </property>\n    <property key="layer" type="UIntProperty">\n        <unsigned value="0"/>\n    </property>\n    <property key="locked" type="BoolProperty">\n        <bool value="true"/>\n    </property>\n    <property key="name" type="StringProperty">\n        <string value="Liver"/>\n    </property>\n    <property key="opacity" type="FloatProperty">\n        <float value="0.600000024"/>\n    </property>\n    <property key="value" type="UShortProperty">\n        <unsigned value="1"/>\n    </property>\n    <property key="visible" type="BoolProperty">\n        <bool value="true"/>\n    </property>\n</Label>\n
org.mitk.label_000_00002:=<?xml version="1.0" encoding="UTF-8"?>\n<Label>\n    <property key="DICOM.0062.0002.0062.0004" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"2"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0005" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"Label 1"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0008" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"SEMIAUTOMATIC"}]}</temporo_spatial_string>\n    </property>\n    <property key="center.coordinates" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="center.index" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="color" type="ColorProperty">\n        <color r="0.952941179" g="0.764705896" b="0"/>\n    </property>\n    <property key="layer" type="UIntProperty">\n        <unsigned value="0"/>\n    </property>\n    <property key="locked" type="BoolProperty">\n        <bool value="true"/>\n    </property>\n    <property key="name" type="StringProperty">\n        <string value="Label 1"/>\n    </property>\n    <property key="opacity" type="FloatProperty">\n        <float value="0.600000024"/>\n    </property>\n    <property key="value" type="UShortProperty">\n        <unsigned value="2"/>\n    </property>\n    <property key="visible" type="BoolProperty">\n        <bool value="true"/>\n    </property>\n</Label>\n
org_mitk_uid:=2a0c52f7-1b2e-4a46-88ca-f4ff9344a7e4

Image header for the corrupt case with 2 labels

NRRD0004
# Complete NRRD file format specification at:
# http://teem.sourceforge.net/nrrd/format.html
type: unsigned short
dimension: 3
space: left-posterior-superior
sizes: 256 256 49
space directions: (1,0,0) (0,1,0) (0,0,3)
kinds: domain domain domain
endian: little
encoding: gzip
space origin: (0,0,0)
DICOM_0008_0060:={"values":[{"z":0, "t":0, "value":"SEG"}]}
DICOM_0008_103E:={"values":[{"z":0, "t":0, "value":"MITK Segmentation"}]}
ITK_InputFilterName:=NrrdImageIO
MITK_IO_reader_description:=MITK Multilabel Image
MITK_IO_reader_inputlocation:=C:\\Users\\Stefan\\Desktop\\segmentation_task_lists\\results/liver.interim.nrrd
MITK_IO_reader_mime_category:=Images
MITK_IO_reader_mime_name:=application/vnd.mitk.image.nrrd
MITK_IO_reader_version:=2022.04.99-4e5d077f
layer_000:=2
layers:=1
modality:=org.mitk.image.multilabel
org.mitk.label_000_00000:=<?xml version="1.0" encoding="UTF-8"?>\n<Label>\n    <property key="DICOM.0062.0002.0062.0004" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"0"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0005" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"Exterior"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0008" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"SEMIAUTOMATIC"}]}</temporo_spatial_string>\n    </property>\n    <property key="center.coordinates" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="center.index" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="color" type="ColorProperty">\n        <color r="0" g="0" b="0"/>\n    </property>\n    <property key="layer" type="UIntProperty">\n        <unsigned value="0"/>\n    </property>\n    <property key="locked" type="BoolProperty">\n        <bool value="false"/>\n    </property>\n    <property key="name" type="StringProperty">\n        <string value="Exterior"/>\n    </property>\n    <property key="opacity" type="FloatProperty">\n        <float value="0"/>\n    </property>\n    <property key="value" type="UShortProperty">\n        <unsigned value="0"/>\n    </property>\n    <property key="visible" type="BoolProperty">\n        <bool value="true"/>\n    </property>\n</Label>\n
org.mitk.label_000_00001:=<?xml version="1.0" encoding="UTF-8"?>\n<Label>\n    <property key="DICOM.0062.0002.0062.0003.0008.0100" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"T-D000A"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0003.0008.0102" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"SRT"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0003.0008.0104" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"Anatomical Structure"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0004" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"1"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0005" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"Liver"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0008" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"SEMIAUTOMATIC"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.000F.0008.0100" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"T-62000"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.000F.0008.0102" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"SRT"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.000F.0008.0104" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"Liver"}]}</temporo_spatial_string>\n    </property>\n    <property key="center.coordinates" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="center.index" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="color" type="ColorProperty">\n        <color r="0.745098054" g="0" b="0.196078435"/>\n    </property>\n    <property key="layer" type="UIntProperty">\n        <unsigned value="0"/>\n    </property>\n    <property key="locked" type="BoolProperty">\n        <bool value="true"/>\n    </property>\n    <property key="name" type="StringProperty">\n        <string value="Liver"/>\n    </property>\n    <property key="opacity" type="FloatProperty">\n        <float value="0.600000024"/>\n    </property>\n    <property key="value" type="UShortProperty">\n        <unsigned value="1"/>\n    </property>\n    <property key="visible" type="BoolProperty">\n        <bool value="true"/>\n    </property>\n</Label>\n
org.mitk.label_000_00002:=<?xml version="1.0" encoding="UTF-8"?>\n<Label>\n    <property key="DICOM.0062.0002.0062.0004" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"2"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0005" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"Label 1"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0008" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"SEMIAUTOMATIC"}]}</temporo_spatial_string>\n    </property>\n    <property key="center.coordinates" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="center.index" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="color" type="ColorProperty">\n        <color r="0.952941179" g="0.764705896" b="0"/>\n    </property>\n    <property key="layer" type="UIntProperty">\n        <unsigned value="0"/>\n    </property>\n    <property key="locked" type="BoolProperty">\n        <bool value="true"/>\n    </property>\n    <property key="name" type="StringProperty">\n        <string value="Label 1"/>\n    </property>\n    <property key="opacity" type="FloatProperty">\n        <float value="0.600000024"/>\n    </property>\n    <property key="value" type="UShortProperty">\n        <unsigned value="2"/>\n    </property>\n    <property key="visible" type="BoolProperty">\n        <bool value="true"/>\n    </property>\n</Label>\n
org_mitk_uid:=25facd2e-7f9a-4366-b5e3-8da72f1e0bdd

Pushed new branch to rMITK MITK: bugfix/T29274-IgnoreDefaultPropertiesOnLoad.

The solution is to ignore default properties when loading multilabel images as it was already intended:

Add forgotten call of InitializeDefaultMetaDataKeys() to ctor
Fix names of default properties (. instead of _)

kislinsk added a revision: Restricted Differential Revision.Sep 2 2022, 2:49 PM

kislinsk renamed this task from Label Loss on Saved Tasks for Flow Bench to Label Loss on repeatedly loaded and saved segmentations.Sep 6 2022, 7:38 AM

kislinsk closed this task as Resolved by committing rMITKfa35314228ce: Ignore default properties when loading multilabel images.Sep 6 2022, 10:58 AM

kislinsk added a commit: rMITKfa35314228ce: Ignore default properties when loading multilabel images.

kislinsk added a commit: rMITKd5f9c80dbc7b: Fix typo.

kislinsk added a commit: rMITKad80d98e49b5: Fix review remarks.

kislinsk added a commit: rMITKb318ecba0a31: Ignore default properties when loading multilabel images.

Deleted branch from rMITK MITK: bugfix/T29274-IgnoreDefaultPropertiesOnLoad.

kislinsk mentioned this in T29291: 2022 Week 36 (Early September).Sep 9 2022, 10:31 AM

kislinsk mentioned this in T29431: [worklist] mitk-flow: save changed dicom segmentation not possible.Dec 12 2022, 11:21 AM

	F2564299: 6_its_back.PNG
	Aug 30 2022, 11:23 AM

	F2564301: 2_open_new_task.PNG
	Aug 30 2022, 11:23 AM

	F2564302: 1_save_results.PNG
	Aug 30 2022, 11:23 AM

Label Loss on repeatedly loaded and saved segmentationsClosed, ResolvedPublicActions

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Label Loss on repeatedly loaded and saved segmentations
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