scikit-image version fix

[haoxusci]

scikit-image version 0.18.0 and 0.18.1 doesn't work. For example, if you run register(imgs, dots, method = 'translation'), it will throw error AttributeError: 'DataArray' object has no attribute 'flags'

[ttung]

I think the tests are passing, which does exercise registration. Do you have a full stacktrace?

[haoxusci]

I think the tests are passing, which does exercise registration. Do you have a full stacktrace?

I got the error when I run the quick-start tutorial--the function of def register(imgs, dots, method = 'translation') https://spacetx-starfish.readthedocs.io/en/latest/gallery/quick_start/plot_quick_start.html#quick-start

AttributeError                            Traceback (most recent call last)
<ipython-input-13-19514b63df4a> in <module>
----> 1 register(imgs, dots, method = 'translation')

<ipython-input-12-c6bc49a02aa3> in register(imgs, dots, method)
      6     mip_dots = dots.reduce(dims = [Axes.CH, Axes.ZPLANE], func="max")
      7     learn_translation = LearnTransform.Translation(reference_stack=mip_dots, axes=Axes.ROUND, upsampling=1000)
----> 8     transforms_list = learn_translation.run(mip_imgs)
      9     warp = ApplyTransform.Warp()
     10     registered_imgs = warp.run(imgs, transforms_list=transforms_list, in_place=False, verbose=True)

~/opt/miniconda3/envs/starfish/lib/python3.7/site-packages/starfish/core/pipeline/algorithmbase.py in helper(*args, **kwargs)
     21         @functools.wraps(func)
     22         def helper(*args, **kwargs):
---> 23             result = func(*args, **kwargs)
     24             if result is not None:
     25                 method_class_str = str(args[0].__class__)

~/opt/miniconda3/envs/starfish/lib/python3.7/site-packages/starfish/core/image/_registration/LearnTransform/translation.py in run(self, stack, verbose, *args)
     66             shift, error, phasediff = register_translation(src_image=target_image,
     67                                                            target_image=reference_image,
---> 68                                                            upsample_factor=self.upsampling)
     69             if verbose:
     70                 print(f"For {self.axes}: {a}, Shift: {shift}, Error: {error}")

~/opt/miniconda3/envs/starfish/lib/python3.7/site-packages/skimage/_shared/utils.py in wrapped(*args, **kwargs)
    203             elif self.behavior == 'raise':
    204                 raise skimage_deprecation(msg)
--> 205             return func(*args, **kwargs)
    206 
    207         # modify doc string to display deprecation warning

~/opt/miniconda3/envs/starfish/lib/python3.7/site-packages/skimage/feature/__init__.py in register_translation(src_image, target_image, upsample_factor, space, return_error)
     49     return phase_cross_correlation(src_image, target_image,
     50                                    upsample_factor=upsample_factor,
---> 51                                    space=space, return_error=return_error)
     52 
     53 

~/opt/miniconda3/envs/starfish/lib/python3.7/site-packages/skimage/registration/_phase_cross_correlation.py in phase_cross_correlation(reference_image, moving_image, upsample_factor, space, return_error, reference_mask, moving_mask, overlap_ratio)
    202     # real data needs to be fft'd.
    203     elif space.lower() == 'real':
--> 204         src_freq = fft.fftn(reference_image)
    205         target_freq = fft.fftn(moving_image)
    206     else:

~/opt/miniconda3/envs/starfish/lib/python3.7/site-packages/scipy/fft/_backend.py in __ua_function__(method, args, kwargs)
     21         if fn is None:
     22             return NotImplemented
---> 23         return fn(*args, **kwargs)
     24 
     25 

~/opt/miniconda3/envs/starfish/lib/python3.7/site-packages/scipy/fft/_pocketfft/basic.py in c2cn(forward, x, s, axes, norm, overwrite_x, workers, plan)
    178         raise NotImplementedError('Passing a precomputed plan is not yet '
    179                                   'supported by scipy.fft functions')
--> 180     tmp = _asfarray(x)
    181 
    182     shape, axes = _init_nd_shape_and_axes(tmp, s, axes)

~/opt/miniconda3/envs/starfish/lib/python3.7/site-packages/scipy/fft/_pocketfft/helper.py in _asfarray(x)
     95     dtype = x.dtype.newbyteorder('=')
     96     # Always align input
---> 97     copy = not x.flags['ALIGNED']
     98     return np.array(x, dtype=dtype, copy=copy)
     99 

~/opt/miniconda3/envs/starfish/lib/python3.7/site-packages/xarray/core/common.py in __getattr__(self, name)
    238                     return source[name]
    239         raise AttributeError(
--> 240             "{!r} object has no attribute {!r}".format(type(self).__name__, name)
    241         )
    242 

AttributeError: 'DataArray' object has no attribute 'flags'

[ttung]

Ahh! The reason the tests did not catch this is because scikit-image 0.18.x was not released for python3.6.

[haoxusci]

Ahh! The reason the tests did not catch this is because scikit-image 0.18.x was not released for python3.6.

Great. Thanks for answering that. That makes sense. Feel free to close the PR then.

[neuromusic]

1963 should have fixed these issues