[BUG]: Cannot decompress jpeg error for SpaceNet Rio imagery

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Summary of the bug

I’m receiving ValueError: cannot decompress jpeg after trying to run a command. I’m point the .yml file to 500x500px .tif files. Just as the API Tiling Tutorial.

I’m not sure what should I put as input for this command. TIFF, PNG, JPG images? From which size?

Steps to reproduce the bug

import solaris as sol
config = sol.utils.config.parse('path/to/file.yml')
inferer = sol.nets.infer.Inferer(config)
inference_data = sol.nets.infer.get_infer_df(config)
inferer(inference_data)

Steps to reproduce the behavior: Run this on Jupyter after installing solaris.

Buggy behavior and/or error message

Please describe the buggy behavior and/or paste output here.

ValueError                                Traceback (most recent call last)
<ipython-input-7-cd090e093ecc> in <module>
      3 inferer = sol.nets.infer.Inferer(config)
      4 inference_data = sol.nets.infer.get_infer_df(config)
----> 5 inferer(inference_data)

~/miniconda3/envs/project-v1-nogpu/lib/python3.6/site-packages/solaris/nets/infer.py in __call__(self, infer_df)
     62         for idx, im_path in enumerate(infer_df['image']):
     63             inf_input, idx_refs, (
---> 64                 src_im_height, src_im_width) = inf_tiler(im_path)
     65 
     66             if self.framework == 'keras':

~/miniconda3/envs/project-v1-nogpu/lib/python3.6/site-packages/solaris/nets/datagen.py in __call__(self, im)
    259         # read in the image if it's a path
    260         if isinstance(im, str):
--> 261             im = imread(im)
    262         # determine how many samples will be generated with the sliding window
    263         src_im_height = im.shape[0]

~/miniconda3/envs/project-v1-nogpu/lib/python3.6/site-packages/solaris/utils/io.py in imread(path, make_8bit, rescale, rescale_min, rescale_max)
     50 
     51     """
---> 52     im_arr = skimage.io.imread(path)
     53     # check dtype for preprocessing
     54     if im_arr.dtype == np.uint8:

~/miniconda3/envs/project-v1-nogpu/lib/python3.6/site-packages/skimage/io/_io.py in imread(fname, as_gray, plugin, flatten, **plugin_args)
     59 
     60     with file_or_url_context(fname) as fname:
---> 61         img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
     62 
     63     if not hasattr(img, 'ndim'):

~/miniconda3/envs/project-v1-nogpu/lib/python3.6/site-packages/skimage/io/manage_plugins.py in call_plugin(kind, *args, **kwargs)
    208                                (plugin, kind))
    209 
--> 210     return func(*args, **kwargs)
    211 
    212 

~/miniconda3/envs/project-v1-nogpu/lib/python3.6/site-packages/skimage/io/_plugins/tifffile_plugin.py in imread(fname, dtype, **kwargs)
     36     # read and return tiff as numpy array
     37     with TiffFile(fname, **kwargs_tiff) as tif:
---> 38         return tif.asarray(**kwargs)

~/miniconda3/envs/project-v1-nogpu/lib/python3.6/site-packages/skimage/external/tifffile/tifffile.py in asarray(self, key, series, memmap, tempdir)
   1505                                      colormapped=False, squeeze=False)
   1506         elif len(pages) == 1:
-> 1507             result = pages[0].asarray(memmap=memmap)
   1508         elif self.is_ome:
   1509             assert not self.is_indexed, "color mapping disabled for ome-tiff"

~/miniconda3/envs/project-v1-nogpu/lib/python3.6/site-packages/skimage/external/tifffile/tifffile.py in asarray(self, squeeze, colormapped, rgbonly, scale_mdgel, memmap, reopen, maxsize)
   2482                 self.sample_format, self.bits_per_sample))
   2483         if self.compression not in TIFF_DECOMPESSORS:
-> 2484             raise ValueError("cannot decompress %s" % self.compression)
   2485         if 'sample_format' in self.tags:
   2486             tag = self.tags['sample_format']

ValueError: cannot decompress jpeg

Environment information

• OS: Ubuntu 18.10
• solaris version: 0.1.2
• python version: 3.7
• version of any relevant dependencies (optional - we may ask for this information later if not provided)

[nrweir]

Thanks @jacquesmats for the clarification and glad it worked.

I’m going to re-name the issue and flag it to help with tracking. My guess is that the issue is related to the formatting of those images being incompatible with scikit-image’s default TIFF loading schema. I’ll try to explore what’s going on if I get around to it, but feel free to explore yourself and drop your findings here.

[AH-Merii]

@nrweir I was facing the same issue, in order to resolve it I pip installed imagecodecs. Note: I had to pip install it as it wasn’t being resolved when I attempted to conda install. After installing imagecodecs, everything seemed to work as expected.

I myself am developing using the docker environment that you provided, so in I added this requirement to the Dockerfile by doing the following:

# activate conda environment
SHELL ["conda", "run", "-n", "solaris", "/bin/bash", "-c"]

# pip install imagecodecs in conda environment
RUN pip install imagecodecs