Support pixelmap annotations #776
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With `layerParams.keepLower = false`, `pixelmap` layers would disappear if the viewer was zoomed in past the maximum level. (This is possible in HistomicsUI, which is where this issue was observed.
| let pixelmapData = pixelmapElement.values; | ||
| if (pixelmapElement.boundaries) { | ||
| let valuesWithBoundaries = new Array(pixelmapData.length * 2).fill(0); | ||
| pixelmapData = valuesWithBoundaries.map((d, i) => pixelmapData[Math.floor(i / 2)]); |
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You aren't using the values in the valuesWithBoundaries array. So fill is a wasted operation. This would probably be better as:
let valuesWithBoundaries = new Array(pixelmapData.length * 2);
for (let i = 0; i < pixelmapData.length; i += 1) {
valuesWithBoundaries[i * 2] = valuesWithBoundaries[i * 2 + 1] = pixelmapData[i];
}
Function calls tend to be slow, so avoiding mapping something that is potentially millions long is preferred.
| @@ -129,7 +129,6 @@ var GeojsImageViewerWidgetExtension = function (viewer) { | |||
| */ | |||
| _addPixelmapLayerParams(layerParams, pixelmapElement) { | |||
| // For pixelmap overlays, there are additional parameters to set | |||
| layerParams.keepLower = false; | |||
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I think we need this set to false, since otherwise you'll get off effects if the superpixels are transparent.
I think this was fixed in OpenGeoscience/geojs@7ea4977. Are you on the master build of geojs?
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npm is telling me that I have [email protected], which looks like the latest release.
With layerParams.keepLower = false, I was seeing a problem in HisotmicsUI where zooming in past the number of levels would cause the pixelmap to disappear until zoomed out again. For example, in my testing I was working with a whole slide image with magnification 20, so HUI allows zooming in to 40x. The pixelmap layer would not be visible when zooming between 20x and 40x.
Without setting keepLower = false, I did not see that issue. I didn't see any effects (not sure what I should be looking out for though). Is there a better way to allow this kind of zooming while keeping the layer visible?
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You should obviously see the issue if the fill color is transparent and the stroke color is opaque. We either need to change some parameters or there is a bug in GeoJS. I'll investigate.
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There will be a PR in GeoJS shortly.
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I see the issue now. I'll go ahead and add that line back. I'm still not sure how to deal with the issue of zooming "past" the pixelmap layer that I'm seeing in HistomicsUI.
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OpenGeoscience/geojs#1178. I'll merge when it passes CI and then it will be available.
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Looks like that PR did the trick. I've added keepLower = false back in 65ae579
This is actually needed in the case that the pixelmap categories contain a fully transparent fill color and opaque stroke color.
This PR updates the
large_imageplugin to support drawingpixelmapannotations (see #767).