jgamper / compay-syntax Goto Github PK

slide = Slide(slide_path=dataset[0])

pipeline = Pipeline([OtsuTissueMask(), SimpleTiling(magnification=40,
                                                  tile_size=224,
                                                  max_per_class=10)])
slide = pipeline.fit_transform(slide)
visualize_pipeline_results(slide=slide,
                           transformer_list=pipeline.transformers,
                           title_list=['Tissue Mask', 'Random Tile Sampling'])

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
/opt/conda/lib/python3.6/site-packages/syntax/slide/slide.py in __init__(self, slide_path, level0, verbose)
     44             try:
---> 45                 self.level0 = float(self.properties['openslide.objective-power'])
     46                 if self.verbose:

/opt/conda/lib/python3.6/site-packages/openslide/__init__.py in __getitem__(self, key)
    250         if v is None:
--> 251             raise KeyError()
    252         return v

KeyError: 

During handling of the above exception, another exception occurred:

Exception                                 Traceback (most recent call last)
<ipython-input-7-d399eadbf4ad> in <module>
      4 from syntax.transformers import Pipeline, visualize_pipeline_results
      5 
----> 6 slide = Slide(slide_path=dataset[0])
      7 
      8 pipeline = Pipeline([OtsuTissueMask(), SimpleTiling(magnification=40,

/opt/conda/lib/python3.6/site-packages/typeguard/__init__.py in wrapper(*args, **kwargs)
    838         memo = _CallMemo(python_func, _localns, args=args, kwargs=kwargs)
    839         check_argument_types(memo)
--> 840         retval = func(*args, **kwargs)
    841         check_return_type(retval, memo)
    842 

/opt/conda/lib/python3.6/site-packages/syntax/slide/slide.py in __init__(self, slide_path, level0, verbose)
     47                     print('Level 0 found @ {}X'.format(self.level0))
     48             except:
---> 49                 raise Exception('Slide does not have property objective-power.')
     50         else:
     51             self.level0 = float(level0)

Exception: Slide does not have property objective-power.