Image offset and oriented incorrectly

[LeoReubelt]

I have attached a series that I am testing with. When I open it, the image is oriented offset incorrectly. When I load the files, the screen is blank. But if I zoom out, eventually, it shows up. This file used to work in a previous version of dwv.
dicom_test.zip

[ivmartel]

I need to check the flips the code does when creating a view (see application.js#L1552), its logic does not seem to handle your data...

[LeoReubelt]

If I comment out that entire section that performs the flipping (effectively just removes layerGroup.flipScaleZ()), the image shows up in the correct location and correct orientation, but when I zoom, it flips. Does that indicate anything to you?

[LeoReubelt]

Thanks @ivmartel. I have a few files that have this problem. I made the following change to #addViewLayer(dataIndex, dataViewConfig) in application.js, which fixes it for my test cases, but I don't know the results for all orientations. I am putting it here in case it helps.

// view layer scale
// only flip scale for base layers
if (isBaseLayer) {
  if (typeof dataViewConfig.orientation !== "undefined") {
    if (major === 0 || major === 2) {
      // scale flip Z for oriented views...
      layerGroup.flipScaleZ();
    } else {
      viewLayer.setScale(layerGroup.getScale());
      if (typeof drawLayer !== "undefined") {
        drawLayer.setScale(layerGroup.getScale());
      }
    }
  } else {
    //BEGIN ADDED ******************************************
    const orientation = imageGeometry.getOrientation();
    if (
      orientation.get(0, 0) < 0 ||
      orientation.get(0, 1) < 0 ||
      orientation.get(0, 2) < 0
    ) {
      layerGroup.flipScaleX();
    }

    if (
      orientation.get(1, 0) < 0 ||
      orientation.get(1, 1) < 0 ||
      orientation.get(1, 2) < 0
    ) {
      layerGroup.flipScaleY();
    }
    if (
      orientation.get(2, 0) < 0 ||
      orientation.get(2, 1) < 0 ||
      orientation.get(2, 2) < 0
    ) {
      layerGroup.flipScaleZ();
    }
    //END ADDED **********************************

    if (major === 0) {
      // scale flip Z for sagittal and undefined target orientation

      //COMMENTED OUT ****************************
      //layerGroup.flipScaleZ();
    } else {
      viewLayer.setScale(layerGroup.getScale());
      if (typeof drawLayer !== "undefined") {
        drawLayer.setScale(layerGroup.getScale());
      }
    }
  }
} else {
  viewLayer.setScale(layerGroup.getScale());
  if (typeof drawLayer !== "undefined") {
    drawLayer.setScale(layerGroup.getScale());
  }
}

[LeoReubelt]

@ivmartel - I was modifying a fork at... v0.32.e. Is seems to work with all my test cases. All the changes (except the creation of new flip functions) are in app.js. The changes are in the same place where the flips occur along with a few helper functions. it won't work for image patient orientations that have decimal values, but maybe the logic will still help.

[ivmartel]

Thanks for all this. How did you validate the code? Do you have data for every possible orientation?

[LeoReubelt]

At this stage it was just round 1 validation.

1. assembled a group of files with different orientations - i think i covered them all, but i would have to double check that.
2. visually checked that the image was in the correct location on load and in each mpr orientation.
3. i compared some of them with osyrix to make sure the orientation was correct
4. i used the zoom/pan tools with some of them to make sure everything worked there. in one of my earlier attempts, when i tried to pan, the image filpped.

I think we do have data for every orientation but only orientations with -1's, 1's, and 0's. if you need files, i can see if i can get them for you.

[ivmartel]

Yes, if you can share the data, that would be very helpful.