Missing dependency: imagecodecs

[alvrogd]

When trying to open a GeoTIFF file w/ LZW compression using this package, it raised an internal error about the imagecodecs package not being available. I believe that it may need to be added as a dependency in order to run properly on any platforms that do not have the package by default.

I was running Python inside a Docker container based on nvcr.io/nvidia/pytorch:21.02-py3, and I installed both packages through pip in order to be able to read the file:

RUN pip install geotiff==0.1.1
RUN pip install imagecodecs==2021.2.26

[alvrogd]

This is the full traceback of the error:

Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/IPython/core/interactiveshell.py", line 3427, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-3-01155a6fbd98>", line 1, in <module>
    image = GeoTiff("datasets/z1/z1_nir.tif")
  File "/opt/conda/lib/python3.8/site-packages/geotiff/__init__.py", line 113, in __init__
    self.tifShape: List[int] = tif.asarray().shape
  File "/opt/conda/lib/python3.8/site-packages/tifffile/tifffile.py", line 3106, in asarray
    result = pages[0].asarray(out=out, maxworkers=maxworkers)
  File "/opt/conda/lib/python3.8/site-packages/tifffile/tifffile.py", line 6247, in asarray
    for _ in self.segments(
  File "/opt/conda/lib/python3.8/site-packages/tifffile/tifffile.py", line 6129, in segments
    yield from executor.map(decode, segments)
  File "/opt/conda/lib/python3.8/concurrent/futures/_base.py", line 611, in result_iterator
    yield fs.pop().result()
  File "/opt/conda/lib/python3.8/concurrent/futures/_base.py", line 432, in result
    return self.__get_result()
  File "/opt/conda/lib/python3.8/concurrent/futures/_base.py", line 388, in __get_result
    raise self._exception
  File "/opt/conda/lib/python3.8/concurrent/futures/thread.py", line 57, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/opt/conda/lib/python3.8/site-packages/tifffile/tifffile.py", line 6101, in decode
    result = keyframe.decode(*args, **decodeargs)
  File "/opt/conda/lib/python3.8/site-packages/tifffile/tifffile.py", line 5755, in decode
    raise ValueError(f'TiffPage {self.index}: {exc}')
ValueError: TiffPage 0: <COMPRESSION.LZW: 5> requires the 'imagecodecs' package

[KipCrossing]

Thanks for submitting this.

imagecodecs is a dep of tifffile. See here

I could not reproduce this error, both in a venv (fresh install) and during a recent run https://github.com/Open-Source-Agriculture/geotiff/runs/2159682261

Edit: I also did a fresh install in a conda env (I noticed you are using one) and it's all g.

I'll leave this here a while in case it comes up again

P.S. feel free to use the new version 0.1.2

[alvrogd]

Thanks for the info! Given that tifffile is indeed in the requirements file, the dependency should be automatically installed, so I'm starting to think that it might just be an issue with the Docker image that I'm using.

I'll try using another image later this week when I have some free time, and I'll let you know if I find out anything new.

P.S. I'll also try out the new version!

[KipCrossing]

@alvrogd how did you go the re-try?

[Vishu9519]

I'm also getting the same error. Even though I've installed imagecodecs, tiffile and any other required dependencies (imagecodecs-lite etc etc).

I don't understand why this is happening. I'm trying to reshape a .tiff file, and the same code worked for other tiff files earlier. This is the full traceback: Traceback (most recent call last): File "c:\Users\vishawjeet\Documents\Dataset\reshape.py", line 60, in <module> img=imread(path) ^^^^^^^^^^^^ File "C:\Users\vishawjeet\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\skimage\io\_io.py", line 53, in imread img = call_plugin('imread', fname, plugin=plugin, **plugin_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\vishawjeet\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\skimage\io\manage_plugins.py", line 205, in call_plugin return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\vishawjeet\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\skimage\io\_plugins\tifffile_plugin.py", line 74, in imread return tifffile_imread(fname, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\vishawjeet\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\tifffile\tifffile.py", line 1086, in imread return tif.asarray( ^^^^^^^^^^^^ File "C:\Users\vishawjeet\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\tifffile\tifffile.py", line 4267, in asarray result = stack_pages(pages, out=out, maxworkers=maxworkers) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\vishawjeet\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\tifffile\tifffile.py", line 22180, in stack_pages func(page, index) File "C:\Users\vishawjeet\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\tifffile\tifffile.py", line 22175, in func page.asarray(lock=lock, out=out[index], **kwargs) File "C:\Users\vishawjeet\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\tifffile\tifffile.py", line 8923, in asarray for _ in self.segments( File "C:\Users\vishawjeet\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\tifffile\tifffile.py", line 8724, in segments yield decode(segment) ^^^^^^^^^^^^^^^ File "C:\Users\vishawjeet\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\tifffile\tifffile.py", line 8712, in decode return func(decode(*args, **decodeargs)) # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\vishawjeet\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\tifffile\tifffile.py", line 8190, in decode_raise_compression raise ValueError(f'{exc}') ValueError: <COMPRESSION.LZW: 5> requires the 'imagecodecs' package