def test_segment_2d():
from keras import backend as K
K.set_image_data_format(
"channels_last"
) # Set at channels_first in test_deepseg_lesion.test_segment()
contrast_test = 't2'
model_path = os.path.join(sct.__sct_dir__, 'data', 'deepseg_sc_models',
'{}_sc.h5'.format(contrast_test))
fname_t2 = os.path.join(sct.__sct_dir__, 'sct_testing_data/t2/t2.nii.gz'
) # install: sct_download_data -d sct_testing_data
fname_t2_seg = os.path.join(
sct.__sct_dir__, 'sct_testing_data/t2/t2_seg.nii.gz'
) # install: sct_download_data -d sct_testing_data
img, gt = _preprocess_segment(fname_t2, fname_t2_seg, contrast_test)
seg = deepseg_sc.segment_2d(model_fname=model_path,
contrast_type=contrast_test,
input_size=(64, 64),
im_in=img)
assert seg.dtype == np.dtype('float32')
seg_im = img.copy()
seg_im.data = (seg > 0.5).astype(np.uint8)
assert msct_image.compute_dice(seg_im, gt) > 0.80
def test_segment_2d():
from keras import backend as K
K.set_image_data_format("channels_last") # Set at channels_first in test_deepseg_lesion.test_segment()
contrast_test = 't2'
model_path = os.path.join(sct.__sct_dir__, 'data', 'deepseg_sc_models', '{}_sc.h5'.format(contrast_test))
fname_t2 = os.path.join(sct.__sct_dir__, 'sct_testing_data/t2/t2.nii.gz') # install: sct_download_data -d sct_testing_data
fname_t2_seg = os.path.join(sct.__sct_dir__, 'sct_testing_data/t2/t2_seg.nii.gz') # install: sct_download_data -d sct_testing_data
img, gt = _preprocess_segment(fname_t2, fname_t2_seg, contrast_test)
seg = deepseg_sc.segment_2d(model_fname=model_path, contrast_type=contrast_test, input_size=(64,64), im_in=img)
seg_im = img.copy()
seg_im.data = seg
assert msct_image.compute_dice(seg_im, gt) > 0.80