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cytomine / Cytomine-IMS

Cytomine-IMS: Image Management System
GNU Lesser General Public License v2.1
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Displaying ventana tiff image fails #31

Open anttikos opened 3 years ago

anttikos commented 3 years ago

I'm able to upload a Ventana tiff to Cytomine without issues, and can even see the metadata, thumbnail and the slide preview images. However, when I try to display the image itself, I run into issues / the viewer is unable to load the tile data.

I'm not sure how to continue to debug the root cause of this issue. The image data seems fine, I'm able to display it with

Here is what is caught on the logs:

ims:/var/log/tomcat7/catalina.out 2021-03-15 08:55:48,180 [http-bio-8080-exec-2] INFO image.ImageUtilsController - url=http://cyto-iip/fcgi-bin/iipsrv.fcgi?zoomify=%2Fdata%2Fimages%2F30%2F%2F1615797725208%2Ftest_image.tif/TileGroupTileGroup0/0-0-0.jpg 2021-03-15 08:55:48,187 [http-bio-8080-exec-2] ERROR errors.GrailsExceptionResolver - FileNotFoundException occurred when processing request: [GET] /image/tile http://cyto-iip/fcgi-bin/iipsrv.fcgi?zoomify=%2Fdata%2Fimages%2F30%2F%2F1615797725208%2Ftest_image.tif/TileGroupTileGroup0/0-0-0.jpg. Stacktrace follows: java.io.FileNotFoundException: http://cyto-iip/fcgi-bin/iipsrv.fcgi?zoomify=%2Fdata%2Fimages%2F30%2F%2F1615797725208%2Ftest_image.tif/TileGroupTileGroup0/0-0-0.jpg at java.net.URLConnection.getHeaderFieldLong(URLConnection.java:629) at java.net.URLConnection.getContentLengthLong(URLConnection.java:501) at java.net.URLConnection.getContentLength(URLConnection.java:485) at be.cytomine.image.ImageUtilsController.responseImageFromUrl(ImageUtilsController.groovy:109) at be.cytomine.image.ImageController.tile(ImageController.groovy:399) at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:165) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)

iipCyto:/tmp/iip-openslide.out Full Request is zoomify=%2Fdata%2Fimages%2F30%2F%2F1615797725208%2Ftest_image.tif/TileGroupTileGroup0/0-0-0.jpg [1/1]: Command / Argument is zoomify : 2Fdata%2Fimages%2F30%2F%2F1615797725208%2Ftest_image.tif/TileGroupTileGroup0/0-0-0.jpg Zoomify handler reached FIF handler reached FIF :: URL decoding/filtering: %2Fdata%2Fimages%2F30%2F%2F1615797725208%2Ftest_image.tif => /data/images/30//1615797725208/test_image.tif FIF :: Image cache miss FIF :: TIFF image detected TIFF image is not tiled Sending HTTP 404 Not Found Total Request Time: 1935 microseconds image closed and deleted Server count is 17

...and here is the metadata of the same image (openslide-show-properties.exe test_image.tif): openslide.comment: 'level=0 mag=40 quality=95' openslide.level-count: '10' openslide.level[0].downsample: '1' openslide.level[0].height: '103424' openslide.level[0].tile-height: '1024' openslide.level[0].tile-width: '1024' openslide.level[0].width: '45056' openslide.level[1].downsample: '2' openslide.level[1].height: '51712' openslide.level[1].tile-height: '1024' openslide.level[1].tile-width: '1024' openslide.level[1].width: '22528' openslide.level[2].downsample: '4' openslide.level[2].height: '25856' openslide.level[2].tile-height: '1024' openslide.level[2].tile-width: '1024' openslide.level[2].width: '11264' openslide.level[3].downsample: '8' openslide.level[3].height: '12928' openslide.level[3].tile-height: '1024' openslide.level[3].tile-width: '1024' openslide.level[3].width: '5632' openslide.level[4].downsample: '16' openslide.level[4].height: '6464' openslide.level[4].tile-height: '1024' openslide.level[4].tile-width: '1024' openslide.level[4].width: '2816' openslide.level[5].downsample: '32' openslide.level[5].height: '3232' openslide.level[5].tile-height: '1024' openslide.level[5].tile-width: '1024' openslide.level[5].width: '1408' openslide.level[6].downsample: '64' openslide.level[6].height: '1616' openslide.level[6].tile-height: '1024' openslide.level[6].tile-width: '1024' openslide.level[6].width: '704' openslide.level[7].downsample: '128' openslide.level[7].height: '808' openslide.level[7].tile-height: '1024' openslide.level[7].tile-width: '1024' openslide.level[7].width: '352' openslide.level[8].downsample: '256' openslide.level[8].height: '404' openslide.level[8].tile-height: '1024' openslide.level[8].tile-width: '1024' openslide.level[8].width: '176' openslide.level[9].downsample: '512' openslide.level[9].height: '202' openslide.level[9].tile-height: '1024' openslide.level[9].tile-width: '1024' openslide.level[9].width: '88' openslide.mpp-x: '0.25' openslide.mpp-y: '0.25' openslide.objective-power: '40' openslide.quickhash-1: '588c6cb0fcf53fec9b7d0ba25ef14381089c3ab96424703af9f30514722a3084' openslide.vendor: 'ventana' tiff.DateTime: '2021:03:02 20:35:43' tiff.ImageDescription: 'level=0 mag=40 quality=95' tiff.ResolutionUnit: 'centimeter' tiff.Software: 'ScanOutputManager 1.1.0.15854' tiff.XResolution: '40000' tiff.YResolution: '40000' ventana.Anonymization: '0' ventana.BuildDate: '11/27/2019 11:6:28 AM' ventana.BuildVersion: '1.1.0.15854' ventana.FocusMode: '0' ventana.FocusQuality: '1' ventana.LabelBoundary: '0' ventana.Magnification: '40' ventana.Mode: 'brightfield' ventana.ScanMode: '1' ventana.ScanRes: '0.25' ventana.ScanWhitePoint: '235' ventana.ScannerModel: 'VENTANA DP 200' ventana.ShowLabel: '1' ventana.UserName: 'Operator' ventana.Z-layers: '1' ventana.Z-spacing: '1'