ClearMap can't find my .ilp file for celldetection

[bhnrus]

Hi, I'm trying to use ilastik interfaced within ClearMap, but when trying to run detectCells on the ilastik_for some reason ClearMap says the .ilp trained in ilastik does not exist. Did it happened to anyone else?

This is the error message I get: detectCells(**ImageProcessingParameter); ChunkSize: Estimated chunk size 98.94444444444444 in 36 chunks! [(0, 98), (66, 165), (133, 232), (200, 299), (267, 366), (334, 433), (401, 500), (468, 567), (535, 634), (602, 701), (669, 768), (736, 835), (803, 902), (870, 969), (937, 1036), (1004, 1103), (1071, 1170), (1138, 1236), (1204, 1303), (1271, 1370), (1338, 1437), (1405, 1504), (1472, 1571), (1539, 1638), (1606, 1705), (1673, 1772), (1740, 1839), (1807, 1906), (1874, 1973), (1941, 2040), (2008, 2107), (2075, 2174), (2142, 2241), (2209, 2308), (2276, 2375), (2343, 2442)] ChunkSize: final chunks : [(0, 98), (66, 165), (133, 232), (200, 299), (267, 366), (334, 433), (401, 500), (468, 567), (535, 634), (602, 701), (669, 768), (736, 835), (803, 902), (870, 969), (937, 1036), (1004, 1103), (1071, 1170), (1138, 1236), (1204, 1303), (1271, 1370), (1338, 1437), (1405, 1504), (1472, 1571), (1539, 1638), (1606, 1705), (1673, 1772), (1740, 1839), (1807, 1906), (1874, 1973), (1941, 2040), (2008, 2107), (2075, 2174), (2142, 2241), (2209, 2308), (2276, 2375), (2343, 2442)] ChunkSize: final centers: [0, 82.0, 149.0, 216.0, 283.0, 350.0, 417.0, 484.0, 551.0, 618.0, 685.0, 752.0, 819.0, 886.0, 953.0, 1020.0, 1087.0, 1154.0, 1220.0, 1287.0, 1354.0, 1421.0, 1488.0, 1555.0, 1622.0, 1689.0, 1756.0, 1823.0, 1890.0, 1957.0, 2024.0, 2091.0, 2158.0, 2225.0, 2292.0, 2359.0, 2442] Process 0: processing substack 0/36 Process 0: file = /media/kupchiklab/4TBsata/TRIO/822-00-F4/r_hemi_010320/C02/For_BigStitcher/vertical/verC02Z\d{4}.tif Process 0: segmentation = <function classifyCells at 0x7f2c088c9d30> Process 0: ranges: x,y,z = ,,(0, 98) Process 0: Reading data of size (1306, 2048, 98): elapsed time: 0:00:02 Process 0: Ilastik cell detection: classifier: classifier Process 0: Ilastik cell detection: classindex: classifier Process 0: Ilastik cell detection: save : classifier Process 0: Ilastik: running: /home/kupchiklab/CM/ilastik-1.3.3post3-Linux/run_ilastik.sh --headless --project=" classifier " --output_format="hdf5" --output_filename_format="/tmp/tmphppuysc7.h5" "/tmp/tmp31g3zwl6/ilastik.npy" Warning: Ignoring your non-empty LD_LIBRARY_PATH Warning: Ignoring your non-empty PYTHONPATH/PYTHONHOME /home/kupchiklab/CM/ilastik-1.3.3post3-Linux/ilastik-meta/lazyflow/lazyflow/classifiers/init.py:20: UserWarning: init: Could not import tiktorch classifier warnings.warn("init: Could not import tiktorch classifier") Traceback (most recent call last): File "/home/kupchiklab/CM/ilastik-1.3.3post3-Linux/ilastik-meta/ilastik/ilastik.py", line 134, in main() File "/home/kupchiklab/CM/ilastik-1.3.3post3-Linux/ilastik-meta/ilastik/ilastik.py", line 128, in main hShell = ilastik_main.main(parsed_args, workflow_cmdline_args) File "/home/kupchiklab/CM/ilastik-1.3.3post3-Linux/ilastik-meta/ilastik/ilastik_main.py", line 137, in main load_fn = _prepare_auto_open_project(parsed_args) File "/home/kupchiklab/CM/ilastik-1.3.3post3-Linux/ilastik-meta/ilastik/ilastik_main.py", line 336, in _prepare_auto_open_project raise RuntimeError("Project file '" + parsed_args.project + "' does not exist.") RuntimeError: Project file ' classifier ' does not exist. Traceback (most recent call last):

File "", line 1, in detectCells(**ImageProcessingParameter);

File "/home/kupchiklab/CM/ClearMap/ImageProcessing/CellDetection.py", line 85, in detectCells result = sequentiallyProcessStack(source, sink = sink, function = detectCells, verbose = verbose, **parameter);

File "/home/kupchiklab/CM/ClearMap/ImageProcessing/StackProcessing.py", line 468, in sequentiallyProcessStack results.append(_processSubStack(argdata[i]));

File "/home/kupchiklab/CM/ClearMap/ImageProcessing/StackProcessing.py", line 89, in _processSubStack seg = sf(img, subStack = sub, out = pw, **pp);

File "/home/kupchiklab/CM/ClearMap/ImageProcessing/IlastikClassification.py", line 173, in classifyCells imgmax = ilastik.classifyPixel(classifier, img);

File "/home/kupchiklab/CM/ClearMap/ImageProcessing/Ilastik/Ilastik.py", line 314, in classifyPixel run(args);

File "/home/kupchiklab/CM/ClearMap/ImageProcessing/Ilastik/Ilastik.py", line 160, in run raise RuntimeError('runIlastik: failed executing: ' + cmd);

RuntimeError: runIlastik: failed executing: /home/kupchiklab/CM/ilastik-1.3.3post3-Linux/run_ilastik.sh --headless --project=" classifier " --output_format="hdf5" --output_filename_format="/tmp/tmphppuysc7.h5" "/tmp/tmp31g3zwl6/ilastik.npy"

Thanks!