MoritzNegwer
commented
1 year ago Hi there, nice that you want to give DELiVR a shot! Judging from the error log you posted, it looks like there is an error in the downsampling step of the preprocessing, maybe with reading the test dataset.
We are currently trying to reproduce this on our end. Meanwhile, could you please let us know the following infos? 1) System you are running this on (Windows/Linux, Processor, RAM, Disk space) 2) Are you running this from the Fiji plugin, docker container, or the code from this github repo? If you are running it via the Fiji plugin, can you save the entire log output (that includes the docker command) and post it here as .txt? If the latter two cases, can you please let us know the docker command you are using?
Many thanks in advance and all the best, Moritz
grace-fengqing-yu
Hi, very impressive work and thanks for providing the scripts for the end-to-end pipeline! Our group is trying to reproduce the results using the test dataset provided. But when I tried to run the script with the dataset, I met the "<tifffile.TiffFile 'downsampled_um_xxxxxx.tif'> contains no pages" error. Below are the full output, do you know the potential causes of this issue and how I can solve it? Thank you in advance for your help!
Loading config.json Making /data/projects/deepneuronseg/Grace_files/DeLiVR/deliver_cfos/data/output/04_atlas_alignment/collection/ HOOK:OVERALL:6 Masking HOOK:1:6:0:1 ['/tmp/tmpe0oqvfnv/downsampled_um_z0000-0004.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0004-0008.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0008-0012.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0012-0016.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0016-0020.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0020-0024.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0024-0028.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0028-0032.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0032-0036.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0036-0040.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0040-0044.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0044-0048.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0048-0052.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0052-0056.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0056-0060.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0060-0064.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0064-0068.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0068-0072.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0072-0076.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0076-0080.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0080-0084.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0084-0088.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0088-0092.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0092-0096.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0096-0100.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0100-0104.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0104-0108.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0108-0112.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0112-0116.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0116-0120.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0120-0124.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0124-0128.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0128-0132.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0132-0136.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0136-0140.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0140-0144.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0144-0148.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0148-0152.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0152-0156.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0156-0160.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0160-0164.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0164-0168.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0168-0172.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0172-0176.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0176-0180.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0180-0184.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0184-0188.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0188-0192.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0192-0196.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0196-0200.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0200-0204.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0204-0208.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0208-0212.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0212-0216.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0216-0220.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0220-0224.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0224-0228.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0228-0232.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0232-0236.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0236-0240.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0240-0244.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0244-0248.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0248-0252.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0252-0256.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0256-0260.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0260-0264.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0264-0268.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0268-0272.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0272-0276.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0276-0280.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0280-0284.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0284-0288.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0288-0292.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0292-0296.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0296-0300.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0300-0304.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0304-0308.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0308-0312.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0312-0316.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0316-0320.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0320-0324.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0324-0328.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0328-0332.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0332-0336.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0336-0340.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0340-0344.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0344-0348.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0348-0352.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0352-0356.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0356-0360.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0360-0364.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0364-0368.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0368-0372.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0372-0376.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0376-0380.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0380-0384.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0384-0388.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0388-0392.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0392-0396.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0396-0400.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0400-0404.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0404-0408.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0408-0412.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0412-0416.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0416-0420.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0420-0424.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0424-0428.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0428-0432.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0432-0436.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0436-0440.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0440-0444.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0444-0448.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0448-0452.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0452-0456.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0456-0460.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0460-0464.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0464-0468.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0468-0472.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0472-0476.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0476-0480.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0480-0484.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0484-0488.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0488-0492.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0492-0496.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0496-0500.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0500-0504.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0504-0508.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0508-0512.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0512-0516.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0516-0520.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0520-0524.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0524-0528.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0528-0532.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0532-0536.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0536-0540.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0540-0544.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0544-0548.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0548-0552.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0552-0556.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0556-0560.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0560-0564.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0564-0568.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0568-0572.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0572-0576.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0576-0580.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0580-0584.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0584-0588.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0588-0592.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0592-0596.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0596-0600.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0600-0604.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0604-0608.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0608-0612.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0612-0616.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0616-0620.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0620-0624.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0624-0628.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0628-0632.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0632-0636.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0636-0640.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0640-0644.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0644-0648.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0648-0652.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0652-0656.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0656-0660.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0660-0664.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0664-0668.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0668-0672.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0672-0676.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0676-0680.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0680-0684.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0684-0688.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0688-0692.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0692-0696.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0696-0700.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0700-0704.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0704-0708.tif', '/tmp/tmpe0oqvfnv/downsampled_um_z0708-0712.tif'] <tifffile.TiffFile 'downsampled_um_z0000-0004.tif'> contains no pages <tifffile.TiffFile 'downsampled_um_z0004-0008.tif'> contains no pages <tifffile.TiffFile 'downsampled_um_z0008-0012.tif'> contains no pages <tifffile.TiffFile 'downsampled_um_z0012-0016.tif'> contains no pages <tifffile.TiffFile 'downsampled_um_z0016-0020.tif'> contains no pages <tifffile.TiffFile 'downsampled_um_z0020-0024.tif'> contains no pages <tifffile.TiffFile 'downsampled_um_z0024-0028.tif'> contains no pages <tifffile.TiffFile 'downsampled_um_z0028-0032.tif'> contains no pages <tifffile.TiffFile 'downsampled_um_z0032-0036.tif'> contains no pages <tifffile.TiffFile 'downsampled_um_z0036-0040.tif'> contains no pages <tifffile.TiffFile 'downsampled_um_z0040-0044.tif'> contains no pages <tifffile.TiffFile 'downsampled_um_z0044-0048.tif'> contains no pages <tifffile.TiffFile 'downsampled_um_z0048-0052.tif'> contains 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"main.py", line 95, in
mouse_id, stack_shape = downsample_mask(settings, brain)
File "/data/projects/deepneuronseg/Grace_files/DeLiVR/deliver_cfos/downsample/downsample_and_mask.py", line 274, in downsample_mask
downsampled_stack_8bit = histogram_equalization_8b(downsampled_stack)
File "/data/projects/deepneuronseg/Grace_files/DeLiVR/deliver_cfos/downsample/downsample_and_mask.py", line 178, in histogram_equalization_8b
minval = round(np.percentile(stack.ravel(),1))
File "<__array_function__ internals>", line 5, in percentile
File "/home/gyu/.conda/envs/DeLiVR_env/lib/python3.8/site-packages/numpy/lib/function_base.py", line 3867, in percentile
return _quantile_unchecked(
File "/home/gyu/.conda/envs/DeLiVR_env/lib/python3.8/site-packages/numpy/lib/function_base.py", line 3986, in _quantile_unchecked
r, k = _ureduce(a, func=_quantile_ureduce_func, q=q, axis=axis, out=out,
File "/home/gyu/.conda/envs/DeLiVR_env/lib/python3.8/site-packages/numpy/lib/function_base.py", line 3564, in _ureduce
r = func(a, **kwargs)
File "/home/gyu/.conda/envs/DeLiVR_env/lib/python3.8/site-packages/numpy/lib/function_base.py", line 4098, in _quantile_ureduce_func
n = np.isnan(ap[-1])
IndexError: index -1 is out of bounds for axis 0 with size 0