{"action":"opened","issue":{"url":"https://api.github.com/repos/bigdataviewer/SPIM_Registration/issues/54","labels_url":"https://api.github.com/repos/bigdataviewer/SPIM_Registration/issues/54/labels{/name}","comments_url":"https://api.github.com/repos/bigdataviewer/SPIM_Registration/issues/54/comments","events_url":"https://api.github.com/repos/bigdataviewer/SPIM_Registration/issues/54/events","html_url":"https://github.com/bigdataviewer/SPIM_Registration/issues/54","id":82395890,"number":54,"title":"Exception DualChannel Multiview Deconvolution","user":{"login":"schmiedc","id":10744409,"avatar_url":"https://avatars.githubusercontent.com/u/10744409?v=3","gravatar_id":"","url":"https://api.github.com/users/schmiedc","html_url":"https://github.com/schmiedc","followers_url":"https://api.github.com/users/schmiedc/followers","following_url":"https://api.github.com/users/schmiedc/following{/other_user}","gists_url":"https://api.github.com/users/schmiedc/gists{/gist_id}","starred_url":"https://api.github.com/users/schmiedc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/schmiedc/subscriptions","organizations_url":"https://api.github.com/users/schmiedc/orgs","repos_url":"https://api.github.com/users/schmiedc/repos","events_url":"https://api.github.com/users/schmiedc/events{/privacy}","received_events_url":"https://api.github.com/users/schmiedc/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-05-29T11:49:48Z","updated_at":"2015-05-29T11:49:48Z","closed_at":null,"body":"Hi Stephan,\r\n\r\nI get an exception using deconvolution with dual channel. 1 channel contains the beads.\r\nThe 1st time point and the channel that contains the beads (Channel1) gets made successfully. The channel (Channel 0) without beads however not. \r\n\r\nI will send you the xml file and the interest points. \r\n\r\nCheers\r\nChristopher\r\n\r\n\r\nException:\r\n---\r\n\r\n\r\n(Fiji Is Just) ImageJ 2.0.0-rc-30/1.49s; Java 1.6.0_24 [64-bit]; Linux 2.6.32-431.5.1.el6.x86_64; 7842MB of 124962MB (6%)\r\n \r\njava.lang.NullPointerException\r\n\tat mpicbg.imglib.wrapper.ImgLib2.wrapFloatToImgLib1(ImgLib2.java:63)\r\n\tat mpicbg.spim.postprocessing.deconvolution2.LRFFT.wrap(LRFFT.java:83)\r\n\tat mpicbg.spim.postprocessing.deconvolution2.LRFFT.<init>(LRFFT.java:61)\r\n\tat spim.process.fusion.deconvolution.EfficientBayesianBased.fuseData(EfficientBayesianBased.java:206)\r\n\tat spim.fiji.plugin.Image_Fusion.fuse(Image_Fusion.java:173)\r\n\tat spim.fiji.plugin.Image_Fusion.run(Image_Fusion.java:76)\r\n\tat ij.IJ.runUserPlugIn(IJ.java:199)\r\n\tat ij.IJ.runPlugIn(IJ.java:163)\r\n\tat ij.Executer.runCommand(Executer.java:131)\r\n\tat ij.Executer.run(Executer.java:64)\r\n\tat java.lang.Thread.run(Thread.java:662)\r\n\r\nLog file \r\n---\r\n\r\nUsing spimdata version: 0.9-revision\r\nUsing spimreconstruction version: 2.3.9-SNAPSHOT\r\nangles selected: 0, 1, 2, 3, 4\r\nchannels selected: 0, 1\r\nilluminations selected: 0\r\nTimepoints selected: 0, 1\r\nFri May 29 13:26:12 CEST 2015: Estimating Bounding Box for Fusion. If size of images is not known (they were never opened before), some of them need to be opened once to determine their size.\r\n(Fri May 29 13:26:20 CEST 2015): Reserving memory for fused image.\r\n(Fri May 29 13:26:20 CEST 2015): Requesting Img from ImgLoader (tp=0, setup=0)\r\n(Fri May 29 13:26:25 CEST 2015): Requesting Img from ImgLoader (tp=0, setup=1)\r\n(Fri May 29 13:26:31 CEST 2015): Requesting Img from ImgLoader (tp=0, setup=2)\r\n(Fri May 29 13:26:36 CEST 2015): Requesting Img from ImgLoader (tp=0, setup=3)\r\n(Fri May 29 13:26:42 CEST 2015): Requesting Img from ImgLoader (tp=0, setup=4)\r\n(Fri May 29 13:26:47 CEST 2015): Starting fusion process.\r\n(Fri May 29 13:26:48 CEST 2015): Reserving memory for fused image.\r\n(Fri May 29 13:26:48 CEST 2015): Requesting Img from ImgLoader (tp=0, setup=5)\r\n(Fri May 29 13:26:52 CEST 2015): Requesting Img from ImgLoader (tp=0, setup=6)\r\n(Fri May 29 13:26:57 CEST 2015): Requesting Img from ImgLoader (tp=0, setup=7)\r\n(Fri May 29 13:27:02 CEST 2015): Requesting Img from ImgLoader (tp=0, setup=8)\r\n(Fri May 29 13:27:07 CEST 2015): Requesting Img from ImgLoader (tp=0, setup=9)\r\n(Fri May 29 13:27:12 CEST 2015): Starting fusion process.\r\n(Fri May 29 13:27:13 CEST 2015): Reserving memory for fused image.\r\n(Fri May 29 13:27:13 CEST 2015): Requesting Img from ImgLoader (tp=1, setup=0)\r\n(Fri May 29 13:27:18 CEST 2015): Requesting Img from ImgLoader (tp=1, setup=1)\r\n(Fri May 29 13:27:25 CEST 2015): Requesting Img from ImgLoader (tp=1, setup=2)\r\n(Fri May 29 13:27:30 CEST 2015): Requesting Img from ImgLoader (tp=1, setup=3)\r\n(Fri May 29 13:27:34 CEST 2015): Requesting Img from ImgLoader (tp=1, setup=4)\r\n(Fri May 29 13:27:38 CEST 2015): Starting fusion process.\r\n(Fri May 29 13:27:39 CEST 2015): Reserving memory for fused image.\r\n(Fri May 29 13:27:39 CEST 2015): Requesting Img from ImgLoader (tp=1, setup=5)\r\n(Fri May 29 13:27:44 CEST 2015): Requesting Img from ImgLoader (tp=1, setup=6)\r\n(Fri May 29 13:27:48 CEST 2015): Requesting Img from ImgLoader (tp=1, setup=7)\r\n(Fri May 29 13:27:52 CEST 2015): Requesting Img from ImgLoader (tp=1, setup=8)\r\n(Fri May 29 13:27:56 CEST 2015): Requesting Img from ImgLoader (tp=1, setup=9)\r\n(Fri May 29 13:28:01 CEST 2015): Starting fusion process.\r\n(Fri May 29 13:28:02 CEST 2015): Fusion finished.\r\nUsing spimdata version: 0.9-revision\r\nUsing spimreconstruction version: 2.3.9-SNAPSHOT\r\nangles selected: 0, 1, 2, 3, 4\r\nchannels selected: 0, 1\r\nilluminations selected: 0\r\nTimepoints selected: 0, 1\r\nFri May 29 13:28:56 CEST 2015: Estimating Bounding Box for Fusion. If size of images is not known (they were never opened before), some of them need to be opened once to determine their size.\r\nLooking for native libraries ending with '.so', '.lib' in directory: '/home/schmied/Desktop/2015-05-29_Fiji(2.3.9-SNAP).app.cuda/lib' ... \r\nTrying to load following library: /home/schmied/Desktop/2015-05-29_Fiji(2.3.9-SNAP).app.cuda/lib/libFourierConvolutionCUDALib.so\r\nUsing an outdated version of the CUDA libs, cannot query free memory. Assuming total memory.\r\nUsing an outdated version of the CUDA libs, cannot query free memory. Assuming total memory.\r\nUsing device Quadro 4000 (id=0, mem=2047MB (2047MB free), CUDA capability 2.0)\r\nUsing device Quadro 4000 (id=1, mem=2047MB (2047MB free), CUDA capability 2.0)\r\nbeads --- channel: 1 angle: 0 illum: 0 timepoint: 0: 727 correspondences.\r\nbeads --- channel: 1 angle: 1 illum: 0 timepoint: 0: 667 correspondences.\r\nbeads --- channel: 1 angle: 2 illum: 0 timepoint: 0: 871 correspondences.\r\nbeads --- channel: 1 angle: 3 illum: 0 timepoint: 0: 729 correspondences.\r\nbeads --- channel: 1 angle: 4 illum: 0 timepoint: 0: 779 correspondences.\r\nbeads --- channel: 1 angle: 0 illum: 0 timepoint: 1: 731 correspondences.\r\nbeads --- channel: 1 angle: 1 illum: 0 timepoint: 1: 653 correspondences.\r\nbeads --- channel: 1 angle: 2 illum: 0 timepoint: 1: 860 correspondences.\r\nbeads --- channel: 1 angle: 3 illum: 0 timepoint: 1: 717 correspondences.\r\nbeads --- channel: 1 angle: 4 illum: 0 timepoint: 1: 812 correspondences.\r\n\r\nFound 0 label(s) with correspondences for channel 0: \r\n\r\nFound 1 label(s) with correspondences for channel 1: \r\nLabel 'beads' (channel 1) has 10/10 views with corresponding detections.\r\nChannel 0: uses same PSF as channel 1\r\nChannel 1: extract PSF from label 'beads'\r\nFusing view 0 of 4\r\n(Fri May 29 13:29:49 CEST 2015): Reserving memory for fused & weight image.\r\nExtracting PSF for viewsetup 5 using label 'beads' (474 corresponding detections available)\r\nPSF size: (19, 19, 25)\r\nFusing view 1 of 4\r\n(Fri May 29 13:30:14 CEST 2015): Reserving memory for fused & weight image.\r\nExtracting PSF for viewsetup 6 using label 'beads' (404 corresponding detections available)\r\nPSF size: (19, 19, 25)\r\nFusing view 2 of 4\r\n(Fri May 29 13:30:39 CEST 2015): Reserving memory for fused & weight image.\r\nExtracting PSF for viewsetup 7 using label 'beads' (529 corresponding detections available)\r\nPSF size: (19, 19, 25)\r\nFusing view 3 of 4\r\n(Fri May 29 13:31:05 CEST 2015): Reserving memory for fused & weight image.\r\nExtracting PSF for viewsetup 8 using label 'beads' (477 corresponding detections available)\r\nPSF size: (19, 19, 25)\r\nFusing view 4 of 4\r\n(Fri May 29 13:31:32 CEST 2015): Reserving memory for fused & weight image.\r\nExtracting PSF for viewsetup 9 using label 'beads' (468 corresponding detections available)\r\nPSF size: (19, 19, 25)\r\nMinimal number of overlapping views: 0, using 1\r\nAverage number of overlapping views: 2.539770276690097, using 2.539770276690097\r\nType of iteration: OPTIMIZATION_I\r\nNumber iterations: 10\r\nOSEM speedup: 1.0\r\nUsing blocks: true\r\nBlock size: (256, 256, 256)\r\nUsing CUDA: true\r\nBlending border: 9x9x5\r\nBlending range: 25x25x25\r\nPSF size (extracting): 19x19x25\r\nChannel 0 uses same PSF as channel '1'. \r\nChannel 1 extracts from label 'beads'. \r\nImgLib container (deconvolved): ArrayImgFactory\r\nUsing Tikhonov regularization (lambda = 0.0060)\r\nmaxSize: (63, 11, 63)\r\nNumber of blocks: 24\r\nNumber of blocks: 24\r\nNumber of blocks: 24\r\nNumber of blocks: 24\r\nNumber of blocks: 24\r\nFri May 29 13:32:03 CEST 2015: numThreads = 24\r\nFri May 29 13:32:18 CEST 2015: done normalizing.\r\nMin number of overlapping views: 1\r\nAverage number of overlapping views: 2.593306022741662\r\nAverage intensity in overlapping area: 0.0029975544\r\nOSEM acceleration: 1.0\r\nDeconvolved image container: ArrayContainerFactory\r\niteration: 0 (Fri May 29 13:32:20 CEST 2015)\r\niteration: 0 --- sum change: 119824.38779413141 --- max change per pixel: 4.4350481033325195\r\niteration: 1 (Fri May 29 13:32:52 CEST 2015)\r\niteration: 1 --- sum change: 37834.8018238715 --- max change per pixel: 5.253229141235352\r\niteration: 2 (Fri May 29 13:33:24 CEST 2015)\r\niteration: 2 --- sum change: 15678.437912661233 --- max change per pixel: 3.511646270751953\r\niteration: 3 (Fri May 29 13:33:55 CEST 2015)\r\niteration: 3 --- sum change: 9907.13806076214 --- max change per pixel: 2.482752799987793\r\niteration: 4 (Fri May 29 13:34:26 CEST 2015)\r\niteration: 4 --- sum change: 7959.7276595482035 --- max change per pixel: 1.900740623474121\r\niteration: 5 (Fri May 29 13:34:57 CEST 2015)\r\niteration: 5 --- sum change: 6902.634071748602 --- max change per pixel: 1.5311756134033203\r\niteration: 6 (Fri May 29 13:35:28 CEST 2015)\r\niteration: 6 --- sum change: 6197.028420455368 --- max change per pixel: 1.2675895690917969\r\niteration: 7 (Fri May 29 13:35:58 CEST 2015)\r\niteration: 7 --- sum change: 5683.947972657719 --- max change per pixel: 1.0649070739746094\r\niteration: 8 (Fri May 29 13:36:30 CEST 2015)\r\niteration: 8 --- sum change: 5290.334145328299 --- max change per pixel: 0.9026699066162109\r\niteration: 9 (Fri May 29 13:37:01 CEST 2015)\r\niteration: 9 --- sum change: 4976.176993982874 --- max change per pixel: 0.7701091766357422\r\nDONE (Fri May 29 13:37:31 CEST 2015).\r\nFri May 29 13:37:37 CEST 2015: Saving file /home/schmied/Desktop/Test_Pipeline_3.0/Dual_Channel/czi/TP0_Ch1_Ill0_Ang0,1,2,3,4.tif\r\nFusing view 0 of 4\r\n(Fri May 29 13:37:38 CEST 2015): Reserving memory for fused & weight image.\r\nFusing view 1 of 4\r\n(Fri May 29 13:38:00 CEST 2015): Reserving memory for fused & weight image.\r\nFusing view 2 of 4\r\n(Fri May 29 13:38:24 CEST 2015): Reserving memory for fused & weight image.\r\nFusing view 3 of 4\r\n(Fri May 29 13:38:47 CEST 2015): Reserving memory for fused & weight image.\r\nFusing view 4 of 4\r\n(Fri May 29 13:39:12 CEST 2015): Reserving memory for fused & weight image.\r\nMinimal number of overlapping views: 0, using 1\r\nAverage number of overlapping views: 2.539770276690097, using 2.539770276690097\r\nType of iteration: OPTIMIZATION_I\r\nNumber iterations: 10\r\nOSEM speedup: 1.0\r\nUsing blocks: true\r\nBlock size: (256, 256, 256)\r\nUsing CUDA: true\r\nBlending border: 9x9x5\r\nBlending range: 25x25x25\r\nPSF size (extracting): 19x19x25\r\nChannel 0 uses same PSF as channel '1'. \r\nChannel 1 extracts from label 'beads'. \r\nImgLib container (deconvolved): ArrayImgFactory\r\nUsing Tikhonov regularization (lambda = 0.0060)\r\n"}}