From fulviofulvioni55 at gmail.com Thu Jan 19 10:16:41 2023 From: fulviofulvioni55 at gmail.com (Fulvio Fulvioni) Date: Thu, 19 Jan 2023 16:16:41 +0100 Subject: Performance issue Message-ID: Hi, We are having some trouble opening some .ndpi images in our medical viewer. We are trying to open a file with the following characteristics: hamamatsu.AHEX[0] 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 hamamatsu.AHEX[0].fluorescence 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 hamamatsu.AHEX[0].ploidy 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 hamamatsu.AHEX[1] 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 hamamatsu.AHEX[1].fluorescence 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 hamamatsu.AHEX[1].ploidy 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 hamamatsu.AHEX[2] 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 hamamatsu.AHEX[2].fluorescence 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 hamamatsu.AHEX[2].ploidy 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 hamamatsu.Created 2019/07/12 hamamatsu.Macro.S/N 000903 hamamatsu.NDP.S/N 000128 hamamatsu.Objective.Lens.Magnificant 35.16 hamamatsu.PSHV 100 hamamatsu.PSHV.10x 100 hamamatsu.PSHV.40x 100 hamamatsu.PSHV.ploidy 100 hamamatsu.PSHV.ploidy.10x 100 hamamatsu.Product C13239-01 hamamatsu.Reference A-220000004-A-01-001 hamamatsu.SourceLens 20 hamamatsu.Updated 2021/01/18 hamamatsu.XOffsetFromSlideCentre 5617940 hamamatsu.YOffsetFromSlideCentre -727733 hamamatsu.YRNP[0] 0,0,0,0 hamamatsu.YRNP[1] 0,0,0,0 hamamatsu.YRNP[2] 0,0,0,0 hamamatsu.calibration.version 3519 hamamatsu.ccd.height 0 hamamatsu.ccd.width 8449 hamamatsu.ccd.width.ploidy 8449 hamamatsu.coarse.focus.pitch 10000 hamamatsu.colorfilterID 0 hamamatsu.cube.kind 0 hamamatsu.exposure.barcode.macro 740 hamamatsu.exposure.slide.darkfield.macro 10 hamamatsu.exposure.slide.macro 20 hamamatsu.fine.focus.pitch 250 hamamatsu.focalplane.leftbottom 88914,689278,87825 hamamatsu.focalplane.lefttop 88914,489278,88404 hamamatsu.focalplane.rightbottom 488914,689278,86827 hamamatsu.focalplane.righttop 488914,489278,87429 hamamatsu.lane.shift.amount -1 hamamatsu.roi.barcode.macro 948,253,1272,672 hamamatsu.roi.slide.macro 59,257,1264,668 hamamatsu.slant.leftbottom 0,0,0 hamamatsu.slant.lefttop 0,0,0 hamamatsu.slant.rightbottom 0,0,0 hamamatsu.slant.righttop 0,0,0 hamamatsu.slide.tickness 0 hamamatsu.stage.center 178914,589278 hamamatsu.system.version 1.0 hamamatsu.target.white.intensity 235 hamamatsu.valid.DDKP 0 hamamatsu.valid.DLTP 0 hamamatsu.valid.DSHP 0 hamamatsu.variable.exposuretime 0 hamamatsu.zCoarse[0] 0,0,0,0 hamamatsu.zCoarse[1] 0,0,0,0 hamamatsu.zCoarse[2] 0,0,0,0 hamamatsu.zFine[0] 0,0,0,0 hamamatsu.zFine[1] 0,0,0,0 hamamatsu.zFine[2] 0,0,0,0 openslide.level-count 8 openslide.level[0].downsample 1 openslide.level[0].height 53504 openslide.level[0].tile-height 8 openslide.level[0].tile-width 1920 openslide.level[0].width 69120 openslide.level[1].downsample 2 openslide.level[1].height 26752 openslide.level[1].tile-height 4 openslide.level[1].tile-width 960 openslide.level[1].width 34560 openslide.level[2].downsample 4 openslide.level[2].height 13376 openslide.level[2].tile-height 8 openslide.level[2].tile-width 480 openslide.level[2].width 17280 openslide.level[3].downsample 8 openslide.level[3].height 6688 openslide.level[3].tile-height 4 openslide.level[3].tile-width 240 openslide.level[3].width 8640 openslide.level[4].downsample 16 openslide.level[4].height 3344 openslide.level[4].tile-height 8 openslide.level[4].tile-width 120 openslide.level[4].width 4320 openslide.level[5].downsample 32 openslide.level[5].height 1672 openslide.level[5].tile-height 4 openslide.level[5].tile-width 60 openslide.level[5].width 2160 openslide.level[6].downsample 64 openslide.level[6].height 836 openslide.level[6].tile-height 2 openslide.level[6].tile-width 30 openslide.level[6].width 1080 openslide.level[7].downsample 128 openslide.level[7].height 418 openslide.level[7].tile-height 1 openslide.level[7].tile-width 15 openslide.level[7].width 540 openslide.mpp-x 0.44006336912515404 openslide.mpp-y 0.44006336912515404 openslide.objective-power 20 openslide.quickhash-1 edd079959828875e175c886ffeb8d11cd2067b744d461333367a6afe4ac8d6df openslide.vendor hamamatsu tiff.DateTime 2022:09:21 13:27:41 tiff.Make Hamamatsu tiff.Model C13239-01 tiff.ResolutionUnit centimeter tiff.Software NDP.scan 3.3.2 tiff.XResolution 22724 tiff.YResolution 22724 The following is the code we are using to test the performances (using the openslide java wrapper): ``` File file = new File("C:/path/to/file"); OpenSlide slide = new OpenSlide(file); long t0 = System.currentTimeMillis(); slide.createThumbnailImage(512); System.out.println("thumb extracted in: " + (System.currentTimeMillis() - t0)); ``` Trying to compute said thumbnail from a local file on an SSD it takes around 2 seconds, while accessing it from a remote HDD archive it takes around 70 seconds. Just as a reference, doing the same test with an .svs it take at most 700 ms on the remote HDD. Is this image strange in any way? Is there anything we can do to improve the reading performance of openslide? Thanks a lot! -------------- next part -------------- An HTML attachment was scrubbed... URL: