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AllenInstitute / AllenSDK

code for reading and processing Allen Institute for Brain Science data
https://allensdk.readthedocs.io/en/latest/
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latest scikit image has broken some tests #238

Open dyf opened 6 years ago

dyf commented 6 years ago 
new_file = 'natural_movie_three_track_plot.png' natural_movie = <test_observatory_plots.AnalysisSingleton object at 0x7f5bae9627d0> cell_specimen_id = 517446551, shape = [500, 500]      @pytest.mark.skipif(data_file == 'skip', reason='NWB Data files not configured')     @pytest.mark.parametrize("new_file,natural_movie,cell_specimen_id",                              [ ("natural_movie_one_a_track_plot.png", NATURAL_MOVIE_ONE_A, CELL_SPECIMEN_ID),                                ("natural_movie_one_b_track_plot.png", NATURAL_MOVIE_ONE_B, CELL_SPECIMEN_ID),                                ("natural_movie_one_c_track_plot.png", NATURAL_MOVIE_ONE_C, CELL_SPECIMEN_ID),                                ("natural_movie_two_track_plot.png", NATURAL_MOVIE_TWO, CELL_SPECIMEN_ID),                                ("natural_movie_three_track_plot.png", NATURAL_MOVIE_THREE, CELL_SPECIMEN_ID) ])     def test_track_plot(new_file, natural_movie, cell_specimen_id, shape=[500,500]):         with oplots.figure_in_px(shape[1], shape[0], new_file) as fig: >           natural_movie().open_track_plot(cell_specimen_id)  allensdk/test/brain_observatory/test_observatory_plots.py:233:  _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _  allensdk/brain_observatory/natural_movie.py:182: in open_track_plot     clim=[0, data.mean() + data.std()*3]) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _   self = <allensdk.brain_observatory.circle_plots.TrackPlotter object at 0x7f5b89e8c190> data = array([[ 0.00268703,  0.01976048, -0.00307827, ...,  0.03682319,          0.05....02512315, ..., -0.04575663,         -0.05276261, -0.10325079]], dtype=float32) clim = [0, 0.2936495216563344] cmap = <matplotlib.colors.LinearSegmentedColormap object at 0x7f5b8f271dd0> mean_cmap = <matplotlib.colors.LinearSegmentedColormap object at 0x7f5b8f271d90> norm = None      def plot(self, data,              clim=None,              cmap=DEFAULT_COLOR_MAP,              mean_cmap=DEFAULT_MEAN_RESP_COLOR_MAP,              norm=None):              ax = plt.gca()              clim = self._clim(clim, data)         if self.ring_length:             data = skimage.transform.resize(data.astype(np.float64),                                             (data.shape[0], self.ring_length),                                             mode='constant', >                                           anti_aliasing=False) E           TypeError: resize() got an unexpected keyword argument 'anti_aliasing'  allensdk/brain_observatory/circle_plots.py:385: TypeError
new_file = 'natural_movie_three_track_plot.png'
natural_movie = <test_observatory_plots.AnalysisSingleton object at 0x7f5bae9627d0>
cell_specimen_id = 517446551, shape = [500, 500]

    @pytest.mark.skipif(data_file == 'skip', reason='NWB Data files not configured')
    @pytest.mark.parametrize("new_file,natural_movie,cell_specimen_id",
                             [ ("natural_movie_one_a_track_plot.png", NATURAL_MOVIE_ONE_A, CELL_SPECIMEN_ID),
                               ("natural_movie_one_b_track_plot.png", NATURAL_MOVIE_ONE_B, CELL_SPECIMEN_ID),
                               ("natural_movie_one_c_track_plot.png", NATURAL_MOVIE_ONE_C, CELL_SPECIMEN_ID),
                               ("natural_movie_two_track_plot.png", NATURAL_MOVIE_TWO, CELL_SPECIMEN_ID),
                               ("natural_movie_three_track_plot.png", NATURAL_MOVIE_THREE, CELL_SPECIMEN_ID) ])
    def test_track_plot(new_file, natural_movie, cell_specimen_id, shape=[500,500]):
        with oplots.figure_in_px(shape[1], shape[0], new_file) as fig:
>           natural_movie().open_track_plot(cell_specimen_id)

allensdk/test/brain_observatory/test_observatory_plots.py:233: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
allensdk/brain_observatory/natural_movie.py:182: in open_track_plot
    clim=[0, data.mean() + data.std()*3])
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <allensdk.brain_observatory.circle_plots.TrackPlotter object at 0x7f5b89e8c190>
data = array([[ 0.00268703,  0.01976048, -0.00307827, ...,  0.03682319,
         0.05....02512315, ..., -0.04575663,
        -0.05276261, -0.10325079]], dtype=float32)
clim = [0, 0.2936495216563344]
cmap = <matplotlib.colors.LinearSegmentedColormap object at 0x7f5b8f271dd0>
mean_cmap = <matplotlib.colors.LinearSegmentedColormap object at 0x7f5b8f271d90>
norm = None

    def plot(self, data,
             clim=None,
             cmap=DEFAULT_COLOR_MAP,
             mean_cmap=DEFAULT_MEAN_RESP_COLOR_MAP,
             norm=None):

        ax = plt.gca()

        clim = self._clim(clim, data)
        if self.ring_length:
            data = skimage.transform.resize(data.astype(np.float64),
                                            (data.shape[0], self.ring_length),
                                            mode='constant',
>                                           anti_aliasing=False)
E           TypeError: resize() got an unexpected keyword argument 'anti_aliasing'

allensdk/brain_observatory/circle_plots.py:385: TypeError
JFPerkins commented 6 years ago

What version of scikit-image is this against? anti_aliasing has been a keyword argument to skimage.transform.resize supposedly since 0.14.0 which should be the minimum requirement on current allensdk.