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haesleinhuepf avatar haesleinhuepf commented on May 29, 2024

Hi Johannes @jo-mueller ,

can you paste the error message here and also let me know which function you called (example code welcome)? It's otherwise hard to guess what went wrong.

Thanks!
Robert

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jo-mueller avatar jo-mueller commented on May 29, 2024

Hi @haesleinhuepf ,

the code is from the train_on_folder_of_images notebook, particularly this cell:

# setup classifer and where it should be saved

cl_filename = "test_object_segmenter_from_folders.cl"
apoc.erase_classifier(cl_filename)
segmenter = apoc.PixelClassifier(opencl_filename=cl_filename)

# setup feature set used for training
features = apoc.PredefinedFeatureSet.object_size_1_to_5_px.value

# train classifier on folders
apoc.train_classifier_from_image_folders(
    segmenter, 
    features, 
    image = image_folder, 
    ground_truth = masks_folder)

Full traceback:

FileNotFoundError                         Traceback (most recent call last)
Input In [5], in <cell line: 10>()
      7 features = apoc.PredefinedFeatureSet.object_size_1_to_5_px.value
      9 # train classifier on folders
---> 10 apoc.train_classifier_from_image_folders(
     11     segmenter, 
     12     features, 
     13     image = image_folder, 
     14     ground_truth = masks_folder)

File ~\Anaconda3\envs\pdo_ana_env\lib\site-packages\apoc\_utils.py:216, in train_classifier_from_image_folders(classifier, features, **kwargs)
    211 kwargs_to_pass = {
    212     'features': features,
    213     'continue_training': continue_training
    214 }
    215 for key, value in kwargs.items():
--> 216     kwargs_to_pass[key] = imread(kwargs[key] + filename)
    218 # run training
    219 classifier.train(**kwargs_to_pass)

File ~\Anaconda3\envs\pdo_ana_env\lib\site-packages\skimage\io\_io.py:53, in imread(fname, as_gray, plugin, **plugin_args)
     50         plugin = 'tifffile'
     52 with file_or_url_context(fname) as fname:
---> 53     img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
     55 if not hasattr(img, 'ndim'):
     56     return img

File ~\Anaconda3\envs\pdo_ana_env\lib\site-packages\skimage\io\manage_plugins.py:207, in call_plugin(kind, *args, **kwargs)
    203     except IndexError:
    204         raise RuntimeError('Could not find the plugin "%s" for %s.' %
    205                            (plugin, kind))
--> 207 return func(*args, **kwargs)

File ~\Anaconda3\envs\pdo_ana_env\lib\site-packages\skimage\io\_plugins\tifffile_plugin.py:30, in imread(fname, **kwargs)
     27 if 'img_num' in kwargs:
     28     kwargs['key'] = kwargs.pop('img_num')
---> 30 return tifffile_imread(fname, **kwargs)

File ~\Anaconda3\envs\pdo_ana_env\lib\site-packages\tifffile\tifffile.py:891, in imread(files, aszarr, **kwargs)
    888     files = files[0]
    890 if isinstance(files, (str, os.PathLike)) or hasattr(files, 'seek'):
--> 891     with TiffFile(files, **kwargs_file) as tif:
    892         if aszarr:
    893             return tif.aszarr(**kwargs)

File ~\Anaconda3\envs\pdo_ana_env\lib\site-packages\tifffile\tifffile.py:3131, in TiffFile.__init__(self, arg, mode, name, offset, size, _multifile, _useframes, _parent, **kwargs)
   3128 if mode not in (None, 'rb', 'r+b'):
   3129     raise ValueError(f'invalid mode {mode!r}')
-> 3131 fh = FileHandle(arg, mode=mode, name=name, offset=offset, size=size)
   3132 self._fh = fh
   3133 self._multifile = bool(_multifile)

File ~\Anaconda3\envs\pdo_ana_env\lib\site-packages\tifffile\tifffile.py:10447, in FileHandle.__init__(self, file, mode, name, offset, size)
  10445 self.is_file = None
  10446 self._lock = NullContext()
> 10447 self.open()

File ~\Anaconda3\envs\pdo_ana_env\lib\site-packages\tifffile\tifffile.py:10460, in FileHandle.open(self)
  10458 self._file = os.path.realpath(self._file)
  10459 self._dir, self._name = os.path.split(self._file)
> 10460 self._fh = open(self._file, self._mode)
  10461 self._close = True
  10462 if self._offset is None:

FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\saja957d\\Desktop\\DD282\\imagesimage_1_1.tif'

A simple fix to this error is to simply pass masks_folder + '\\' and image_folder + '\\' to the train_classifier_from_image_folders to make it work. It would be nice though, to just take care of this stuff under the hood.

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