def test_compute_intensity_features(self):
expected_feature_list = [
'Intensity.Min',
'Intensity.Max',
'Intensity.Mean',
'Intensity.Median',
'Intensity.MeanMedianDiff',
'Intensity.Std',
'Intensity.IQR',
'Intensity.MAD',
'Intensity.Skewness',
'Intensity.Kurtosis',
'Intensity.HistEnergy',
'Intensity.HistEntropy',
]
fdata = htk_features.compute_intensity_features(
self.im_nuclei_seg_mask, self.im_nuclei_stain)
self.check_fdata_sanity(fdata, expected_feature_list)
self.check_fdata_sanity(self.fdata_nuclei,
expected_feature_list,
prefix='Nucleus.',
match_feature_count=False)
self.check_fdata_sanity(self.fdata_nuclei,
expected_feature_list,
prefix='Cytoplasm.',
match_feature_count=False)
def test_compute_intensity_features(self):
expected_feature_list = [
'Intensity.Min',
'Intensity.Max',
'Intensity.Mean',
'Intensity.Median',
'Intensity.MeanMedianDiff',
'Intensity.Std',
'Intensity.IQR',
'Intensity.MAD',
'Intensity.Skewness',
'Intensity.Kurtosis',
'Intensity.HistEnergy',
'Intensity.HistEntropy',
]
fdata = htk_features.compute_intensity_features(
cfg.im_nuclei_seg_mask, cfg.im_nuclei_stain)
check_fdata_sanity(fdata, expected_feature_list)
check_fdata_sanity(cfg.fdata_nuclei,
expected_feature_list,
prefix='Nucleus.',
match_feature_count=False)
check_fdata_sanity(cfg.fdata_nuclei,
expected_feature_list,
prefix='Cytoplasm.',
match_feature_count=False)
if GENERATE_GROUNDTRUTH:
fdata.to_csv(os.path.join(tempfile.gettempdir(),
'Easy1_nuclei_intensity_features.csv'),
index=False)
fdata_gtruth = pd.read_csv(
utilities.getTestFilePath('Easy1_nuclei_intensity_features.csv'),
index_col=None)
pd.testing.assert_frame_equal(fdata,
fdata_gtruth,
check_less_precise=2)
def test_compute_intensity_features(self):
expected_feature_list = [
'Intensity.Min',
'Intensity.Max',
'Intensity.Mean',
'Intensity.Median',
'Intensity.MeanMedianDiff',
'Intensity.Std',
'Intensity.IQR',
'Intensity.MAD',
'Intensity.Skewness',
'Intensity.Kurtosis',
'Intensity.HistEnergy',
'Intensity.HistEntropy',
]
fdata = htk_features.compute_intensity_features(
self.im_nuclei_seg_mask, self.im_nuclei_stain)
self.check_fdata_sanity(fdata, expected_feature_list)
self.check_fdata_sanity(self.fdata_nuclei,
expected_feature_list,
prefix='Nucleus.',
match_feature_count=False)
self.check_fdata_sanity(self.fdata_nuclei,
expected_feature_list,
prefix='Cytoplasm.',
match_feature_count=False)
# Uncomment to generate ground truth
# fdata.to_csv(os.path.join(
# TEST_DATA_DIR, 'Easy1_nuclei_intensity_features.csv'),
# index=False)
fdata_gtruth = pd.read_csv(os.path.join(
TEST_DATA_DIR, 'Easy1_nuclei_intensity_features.csv'),
index_col=None)
pd.testing.assert_frame_equal(fdata, fdata_gtruth)