Page MenuHomePhabricator
Create Task
Maniphest T24678

[image cropper plugin]: TimeGeometry changed for cropped 4D data sets
Closed, WontfixPublic
Actions

Description

Steps to reproduce:

  • load 4D data set with ArbitraryTimeGeometry
  • do cropping with image cropper

Cropping extent is done correctly.

TimeGeometry of original images:

TimeGeometry:     ArbitraryTimeGeometry (00000211DA794540)
       TimeSteps: 32

       GetGeometryForTimeStep(0):       SlicedGeometry3D (00000211C3623F90)
         IndexToWorldTransform: 
        Matrix: 
          0.999238 7.1306e-11 0.0390266 
          -0.00536632 0.990501 0.137399 
          -0.0386559 -0.137504 0.989746 
        Offset: [-64.0438, -75.3906, -42.3945]
        Center: [0, 0, 0]
        Translation: [-64.0438, -75.3906, -42.3945]
        Inverse: 
          0.999238 -0.00536632 -0.0386559 
          7.1306e-11 0.990501 -0.137504 
          0.0390267 0.137399 0.989747 
        Scale : 1 1 1 
         BoundingBox:         ( 0,128 0,128 0,54  )
         Origin: [-64.0438, -75.3906, -42.3945]
         ImageGeometry: 1
         Spacing: [1, 1, 0.999999]
         EvenlySpaced: 1
         DirectionVector: [0.0390267, 0.137399, 0.989747]
         Slices: 54

         GetPlaneGeometry(0):         PlaneGeometry (00000211C76F96E0)
           IndexToWorldTransform: 
          Matrix: 
            0.999238 7.1306e-11 0.0390266 
            -0.00536632 0.990501 0.137399 
            -0.0386559 -0.137504 0.989746 
          Offset: [-64.0438, -75.3906, -42.3945]
          Center: [0, 0, 0]
          Translation: [-64.0438, -75.3906, -42.3945]
          Inverse: 
            0.999238 -0.00536632 -0.0386559 
            7.1306e-11 0.990501 -0.137504 
            0.0390267 0.137399 0.989747 
          Scale : 1 1 1 
           BoundingBox:           ( 0,128 0,128 0,1  )
           Origin: [-64.0438, -75.3906, -42.3945]
           ImageGeometry: 1
           Spacing: [1, 1, 0.999999]
           ScaleFactorMMPerUnitX: 1
           ScaleFactorMMPerUnitY: 1
           Normal: [0.0390266, 0.137399, 0.989746]
       MinimumTimePoint: 0 ms
       MaximumTimePoint: 720 ms

       min TimeBounds: 
        Step 0: 0 ms
        Step 1: 22 ms
        Step 2: 45 ms
        Step 3: 67 ms
        Step 4: 89 ms
        Step 5: 112 ms
        Step 6: 134 ms
        Step 7: 157 ms
        Step 8: 180 ms
        Step 9: 202 ms
        Step 10: 227 ms
        Step 11: 250 ms
        Step 12: 272 ms
        Step 13: 295 ms
        Step 14: 317 ms
        Step 15: 339 ms
        Step 16: 362 ms
        Step 17: 384 ms
        Step 18: 407 ms
        Step 19: 430 ms
        Step 20: 452 ms
        Step 21: 475 ms
        Step 22: 497 ms
        Step 23: 519 ms
        Step 24: 542 ms
        Step 25: 564 ms
        Step 26: 587 ms
        Step 27: 610 ms
        Step 28: 632 ms
        Step 29: 655 ms
        Step 30: 677 ms
        Step 31: 700 ms

       max TimeBounds: 
        Step 0: 22 ms
        Step 1: 45 ms
        Step 2: 67 ms
        Step 3: 89 ms
        Step 4: 112 ms
        Step 5: 134 ms
        Step 6: 157 ms
        Step 7: 180 ms
        Step 8: 202 ms
        Step 9: 227 ms
        Step 10: 250 ms
        Step 11: 272 ms
        Step 12: 295 ms
        Step 13: 317 ms
        Step 14: 339 ms
        Step 15: 362 ms
        Step 16: 384 ms
        Step 17: 407 ms
        Step 18: 430 ms
        Step 19: 452 ms
        Step 20: 475 ms
        Step 21: 497 ms
        Step 22: 519 ms
        Step 23: 542 ms
        Step 24: 564 ms
        Step 25: 587 ms
        Step 26: 610 ms
        Step 27: 632 ms
        Step 28: 655 ms
        Step 29: 677 ms
        Step 30: 700 ms
        Step 31: 720 ms

TimeGeometry of cropped image:

TimeGeometry:     ProportionalTimeGeometry (00000211C76F89F0)
      TimeSteps: 32
      FirstTimePoint: 0
      StepDuration: 1 ms
      Time Bounds: 0 - 32

      GetGeometryForTimeStep(0):       SlicedGeometry3D (00000211C7580EB0)
        IndexToWorldTransform: 
       Matrix: 
         0.999238 7.1306e-11 0.0390266 
         -0.00536632 0.990501 0.137399 
         -0.0386559 -0.137504 0.989746 
       Offset: [-32.0682, -75.5623, -43.6315]
       Center: [0, 0, 0]
       Translation: [-32.0682, -75.5623, -43.6315]
       Inverse: 
         0.999238 -0.00536632 -0.0386559 
         7.1306e-11 0.990501 -0.137504 
         0.0390267 0.137399 0.989747 
       Scale : 1 1 1 
        BoundingBox:         ( 0,68 0,128 0,54  )
        Origin: [-32.0682, -75.5623, -43.6315]
        ImageGeometry: 1
        Spacing: [1, 1, 0.999999]
        EvenlySpaced: 1
        DirectionVector: [0.0390267, 0.137399, 0.989747]
        Slices: 54

        GetPlaneGeometry(0):         PlaneGeometry (00000211C76F9770)
          IndexToWorldTransform: 
         Matrix: 
           0.999238 7.1306e-11 0.0390266 
           -0.00536632 0.990501 0.137399 
           -0.0386559 -0.137504 0.989746 
         Offset: [-32.0682, -75.5623, -43.6315]
         Center: [0, 0, 0]
         Translation: [-32.0682, -75.5623, -43.6315]
         Inverse: 
           0.999238 -0.00536632 -0.0386559 
           7.1306e-11 0.990501 -0.137504 
           0.0390267 0.137399 0.989747 
         Scale : 1 1 1 
          BoundingBox:           ( 0,68 0,128 0,1  )
          Origin: [-32.0682, -75.5623, -43.6315]
          ImageGeometry: 1
          Spacing: [1, 1, 0.999999]
          ScaleFactorMMPerUnitX: 1
          ScaleFactorMMPerUnitY: 1
          Normal: [0.0390266, 0.137399, 0.989746]

Also, some nrrd properties are not copied from the original to the cropped image.
Original image:

DICOM.0008.0018   1.3.12.2.1107.5.2.38.51016.2016102715271836593291427
 DICOM.0008.0020   20161027
 DICOM.0008.0021   20161027
 DICOM.0008.0022   20161027
 DICOM.0008.0030   144409.618000
 DICOM.0008.0031   152718.399000
 DICOM.0008.0032   152056.265000
 DICOM.0008.0050   
 DICOM.0008.0060   MR
 DICOM.0008.0070   SIEMENS
 DICOM.0008.0080   DKFZ
 DICOM.0008.0090   
 DICOM.0008.1010   MRC51016
 DICOM.0008.1030   E0202^Mann
 DICOM.0008.103E   3D_homdyn_20conc_54sl_tot
 DICOM.0008.1050   
 DICOM.0008.1090   Biograph_mMR
 DICOM.0010.0010   Phantom^HomDynCalypso
 DICOM.0010.0020   513/04
 DICOM.0010.0030   19861021
 DICOM.0010.0040   O
 DICOM.0010.1030   80
 DICOM.0018.0020   SE
 DICOM.0018.0021   SP
 DICOM.0018.0080   3000
 DICOM.0018.0081   22.5
 DICOM.0018.0087   3
 DICOM.0018.1030   3D_homdyn_20conc_54sl_tot
 DICOM.0018.1310   0\128\128\0
 DICOM.0018.5100   HFS
 DICOM.0020.000D   1.3.12.2.1107.5.2.38.51016.30000016102706422806700000003
 DICOM.0020.000E   1.3.12.2.1107.5.2.38.51016.2016102715271837582891428.0.0.0
 DICOM.0020.0010   2
 DICOM.0020.0011   5
 DICOM.0020.0013   1
 DICOM.0020.1041   -54.817855166639
 DICOM.0028.0004   MONOCHROME2
 DICOM.0028.0010   128
 DICOM.0028.0011   128
 DICOM.0028.0030   1\1
 DICOM.0028.1050   1433
 DICOM.0028.1051   2796
 DICOM.0028.1055   Algo1
 ITK.InputFilterName   NrrdImageIO
 NRRD.kinds[0]   domain
 NRRD.kinds[1]   domain
 NRRD.kinds[2]   domain
 NRRD.kinds[3]   domain
 org.mitk.timegeometry.timepoints   0 22 45 67 89 112 134 157 180 202 227 250 272 295 317 339 362 384 407 430 452 475 497 519 542 564 587 610 632 655 677 700 720
 org.mitk.timegeometry.type   ArbitraryTimeGeometry

Cropped image:

ITK.InputFilterName   NrrdImageIO
NRRD.kinds[0]   domain
NRRD.kinds[1]   domain
NRRD.kinds[2]   domain
NRRD.kinds[3]   domain

Event Timeline

hentsch triaged this task as Normal priority.Apr 18 2018, 5:13 PM
hentsch created this task.
hentsch added projects: Restricted Project, Restricted Project.
kislinsk closed this task as Wontfix.May 26 2020, 11:16 AM
kislinsk claimed this task.
kislinsk added a project: Auto-closed.
kislinsk added a subscriber: kislinsk.

Hi there! 🙂

This task was auto-closed according to our Task Lifecycle Management.
Please follow this link for more information and don't forget that you are encouraged to reasonable re-open tasks to revive them. 🚑

Best wishes,
The MITK devs

kislinsk removed kislinsk as the assignee of this task.May 26 2020, 12:05 PM
kislinsk removed a subscriber: kislinsk.
MITK · MIC · IMSY · DKFZ