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ggirelli / pygpseq

Python3 package to analyse GPSeq images and manage TIFF files.
MIT License
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Crashed for unknown reasons #18

Open ggirelli opened 5 years ago

ggirelli commented 5 years ago

Before submitting an issue, please be sure to

This issue affects

What did you do (e.g., steps to reproduce)

Ran as in iFISH-singLoc-snakemake.

What happened instead?

...........................................................................
.../pygpseq/fish/image.py in analyze_field_of_view(sid=4, data=               x            y          z ...   x...6723 ...  564   954  26

[1958 rows x 15 columns], im2fov={1: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_001_cmle.tif', 2: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_002_cmle.tif', 3: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_003_cmle.tif', 4: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_004_cmle.tif', 5: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_005_cmle.tif', 6: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_006_cmle.tif', 7: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_007_cmle.tif', 8: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_008_cmle.tif', 9: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_009_cmle.tif', 10: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_010_cmle.tif', ...}, dilate_factor=5, istruct=array([[[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
     ...[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]]], dtype=uint8), aspect=[300.0, 130.0, 130.0], mask_dir='/media/MiSo/iFISH-singleLocus-analysis/input/cmask/iAM196_20180830_002/', mask_prefix='cmask_', plotCompartments=True, pole_fraction=0.25, outdir='/media/MiSo/iFISH-singleLocus-DOTTER/output/iFIS...orrected-preFitting/fromfish/iAM196_20180830_002/', noplot=False, labeled=False, compressed=True, dist_type=1, nbins=200, discard_dilation_mode=False, an_type=2, seg_type=2, mask2d_dir=None, verbose=False, debug=False, debug_dir='')
    158 
    159     # Export mask as PNG
    160     if not noplot:
    161         # Create png masks output directory
    162         maskdir = os.path.join(outdir, 'masks/')
--> 163         if not os.path.isdir(maskdir): os.mkdir(maskdir)
        maskdir = '/media/MiSo/iFISH-singleLocus-DOTTER/output/iFIS...ed-preFitting/fromfish/iAM196_20180830_002/masks/'
    164         imbname = os.path.splitext(os.path.basename(im2fov[sid]))[0]
    165 
    166         # Save default mask
    167         msg += printout("Saving default binary mask...", 3, v)

FileExistsError: [Errno 17] File exists: '/media/MiSo/iFISH-singleLocus-DOTTER/output/iFISH-singLoc-snakemake-rootOutput-CAcorrected-preFitting/fromfish/iAM196_20180830_002/masks/'
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Additional information

stale[bot] commented 5 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.