def setUp(self):
# TODO: change to test_data
self.pl1 = ParsePipeline('./final_data')
self.valid_dicom_file = './test_data/dicoms/study-1/48.dcm'
self.invalid_dicom_file = './test_data/dicoms/study-1/invalid.dcm'
self.valid_icontour_file = './test_data/contourfiles/cf-1/i-contours/IM-0001-0048-icontour-manual.txt'
self.invalid_icontour_file = './test_data/contourfiles/cf-1/i-contours/invalid-icontour.txt'
def test_new_ipoch(self):
ppl = ParsePipeline('./test_data')
result = list(ppl.pair_dicom_contour_file())
fpl1 = FeedPipeline(result, 1)
for img, mask in iter(fpl1.next_batch, None):
print img
print mask
class TestParsePipeline(unittest.TestCase):
def setUp(self):
# TODO: change to test_data
self.pl1 = ParsePipeline('./final_data')
self.valid_dicom_file = './test_data/dicoms/study-1/48.dcm'
self.invalid_dicom_file = './test_data/dicoms/study-1/invalid.dcm'
self.valid_icontour_file = './test_data/contourfiles/cf-1/i-contours/IM-0001-0048-icontour-manual.txt'
self.invalid_icontour_file = './test_data/contourfiles/cf-1/i-contours/invalid-icontour.txt'
def test_patient_data(self):
self.assertTrue(len(self.pl1.patient_data) == 5)
def test_find_dicom_file_for_icontour_file_invalid_icontour_file_hyphen(self):
pl = ParsePipeline('./test_data')
ret = pl.find_dicom_file_for_icontour_file('./test_data/dicoms/study-2', './test_data/contourfiles/cf-2/i-contours/invalid-icontour.txt')
self.assertIsNone(ret)
def test_find_dicom_file_for_icontour_file_invalid_icontour_file_nohyphen(self):
pl = ParsePipeline('./test_data')
ret = pl.find_dicom_file_for_icontour_file('./test_data/dicoms/study-2', './test_data/contourfiles/cf-2/i-contours/invalidicontour.txt')
self.assertIsNone(ret)
def test_find_dicom_file_for_icontour_file_non_existent(self):
pl = ParsePipeline('./test_data')
ret = pl.find_dicom_file_for_icontour_file('./test_data/dicoms/study-2', './test_data/contourfiles/cf-2/i-contours/IM-0001-0147-icontour-manual.txt.txt')
self.assertIsNone(ret)
def test_find_dicom_file_for_icontour_file(self):
pl = ParsePipeline('./test_data')
ret = pl.find_dicom_file_for_icontour_file('./test_data/dicoms/study-2', './test_data/contourfiles/cf-2/i-contours/IM-0001-0140-icontour-manual.txt.txt')
self.assertEqual(ret, './test_data/dicoms/study-2/140.dcm')
ret = pl.find_dicom_file_for_icontour_file('./test_data/dicoms/study-2', './test_data/contourfiles/cf-2/i-contours/IM-0001-0127-icontour-manual.txt.txt')
self.assertEqual(ret, './test_data/dicoms/study-2/127.dcm')
def test_pair_dicom_contour_file(self):
#TODO: add corresponding test data
pair = self.pl1.pair_dicom_contour_file()
for i in range(10):
dicom_image, boolean_mask = next(pair)
self.assertEqual(boolean_mask.shape, dicom_image.shape)
def test_convert_tuple_to_img_boolean_mask_invalid_dicom(self):
(dicom_img, boolean_mask) = self.pl1.convert_tuple_to_img_boolean_mask(self.invalid_dicom_file, self.valid_icontour_file)
self.assertIsNone(dicom_img)
self.assertIsNone(boolean_mask)
def test_convert_tuple_to_img_boolean_mask_invalid_icontour(self):
(dicom_img, boolean_mask) = self.pl1.convert_tuple_to_img_boolean_mask(self.valid_dicom_file, self.invalid_icontour_file)
self.assertIsNone(dicom_img)
self.assertIsNone(boolean_mask)
def test_convert_tuple_to_img_boolean_mask(self):
(dicom_img, boolean_mask) = self.pl1.convert_tuple_to_img_boolean_mask(self.valid_dicom_file, self.valid_icontour_file)
self.assertEqual(dicom_img.shape, boolean_mask.shape)
def test_find_dicom_file_for_icontour_file(self):
pl = ParsePipeline('./test_data')
ret = pl.find_dicom_file_for_icontour_file('./test_data/dicoms/study-2', './test_data/contourfiles/cf-2/i-contours/IM-0001-0140-icontour-manual.txt.txt')
self.assertEqual(ret, './test_data/dicoms/study-2/140.dcm')
ret = pl.find_dicom_file_for_icontour_file('./test_data/dicoms/study-2', './test_data/contourfiles/cf-2/i-contours/IM-0001-0127-icontour-manual.txt.txt')
self.assertEqual(ret, './test_data/dicoms/study-2/127.dcm')
def test_find_dicom_file_for_icontour_file_non_existent(self):
pl = ParsePipeline('./test_data')
ret = pl.find_dicom_file_for_icontour_file('./test_data/dicoms/study-2', './test_data/contourfiles/cf-2/i-contours/IM-0001-0147-icontour-manual.txt.txt')
self.assertIsNone(ret)
def test_find_dicom_file_for_icontour_file_invalid_icontour_file_nohyphen(self):
pl = ParsePipeline('./test_data')
ret = pl.find_dicom_file_for_icontour_file('./test_data/dicoms/study-2', './test_data/contourfiles/cf-2/i-contours/invalidicontour.txt')
self.assertIsNone(ret)
def setUp(self):
ppl = ParsePipeline('./final_data')
self.result = list(ppl.pair_dicom_contour_file())
self.fpl1 = FeedPipeline(self.result, 8)
from parse_pipeline import ParsePipeline
from feed_pipeline import FeedPipeline
p = ParsePipeline('./final_data')
result = list(p.pair_dicom_contour_file())
f = FeedPipeline(result, 8)
for img,mask in iter(f.next_batch, None):
print img
print mask