def test_get_create_image_series(self):
uri = '/images/LIDC-IDRI-0001/' \
'1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178/' \
'1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192'
image_series, created = ImageSeries.get_or_create(uri)
assert created
assert image_series.patient_id == 'LIDC-IDRI-0001'
assert image_series.series_instance_uid == '1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192'
assert image_series.uri == uri
auto_loaded_images = image_series.images.all()
self.assertEqual(len(auto_loaded_images), 16)
for img in auto_loaded_images:
self.assertTrue(os.path.exists(img.path))
image_series, created = ImageSeries.get_or_create(uri)
assert not created
assert image_series.patient_id == 'LIDC-IDRI-0001'
assert image_series.series_instance_uid == '1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192'
assert image_series.uri == uri
# assert all the images are not recreated
for old, new in zip(auto_loaded_images, image_series.images.all()):
self.assertEqual(old.id, new.id)
def test_get_create_image_series(self):
uri = '/images/LIDC-IDRI-0001/1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178/' \
'1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192'
image_series, created = ImageSeries.get_or_create(uri)
assert created
assert image_series.patient_id == 'LIDC-IDRI-0001'
assert image_series.series_instance_uid == '1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192'
assert image_series.uri == uri
image_series, created = ImageSeries.get_or_create(uri)
assert not created
assert image_series.patient_id == 'LIDC-IDRI-0001'
assert image_series.series_instance_uid == '1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192'
assert image_series.uri == uri
def test_non_existant_dicom_property(self):
uri = '/images/LIDC-IDRI-0001/' \
'1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178/' \
'1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192'
path = os.path.join(uri, '-132.500000.dcm')
image_series, created = ImageSeries.get_or_create(uri)
# Monkey patch
ImageFile.DICOM_PROPERTIES.update({
'RescaleSlope':
lambda x: NotImplemented,
})
# expected behavior is to log a warning that parsing for this
# property fails
with self.assertLogs(level='WARN') as cm:
ImageFile(path=path, series=image_series).save()
# just one warning
self.assertEqual(len(cm.output), 1)
self.assertIn('RescaleSlope', cm.output[0])
self.assertIn(path, cm.output[0])
# reset for other tests
ImageFile.DICOM_PROPERTIES.update({
'RescaleSlope': lambda x: {
'rescale_slope': int(x)
},
})
def test_create_image_file(self):
uri = '/images/LIDC-IDRI-0001/' \
'1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178/' \
'1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192'
# no warnings should be logged
try:
with self.assertLogs(level='WARN'):
image_series, created = ImageSeries.get_or_create(uri)
except AssertionError as e:
self.assertEqual(
str(e), "no logs of level WARNING or higher triggered on root")
image = image_series.images.all()[0]
expected_metdata = {
'slice_thickness': 2.5,
'slice_location': -132.5,
'rescale_slope': 1,
'rows': 512,
'columns': 512,
'pixel_spacing_col': 0.703125,
'pixel_spacing_row': 0.703125,
'path': os.path.join(uri, '-132.500000.dcm'),
}
for prop, expected in expected_metdata.items():
self.assertEqual(getattr(image, prop), expected)
def create(self, request):
# construct full path to file
series_uri = request.data['uri'].strip('/')
full_uri = safe_join(settings.DATASOURCE_DIR, series_uri)
# get case if this uri and image series ex
series, _ = ImageSeries.get_or_create(full_uri)
new_case = Case.objects.create(series=series)
serialized = self.serializer_class(new_case, context={'request': None}).data
return Response(serialized)
def test_image_series_serializer(self):
image_series = ImageSeries(uri='/images/LIDC-IDRI-0001/'
'1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178/'
'1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192')
serialized = ImageSeriesSerializer(image_series, context={'request': None})
for img in serialized['images'].value:
self.assertTrue(os.path.exists(img.path))
for s in serialized:
self.assertIsNone(s.errors)
# get, don't create if it exists
orig_id = serialized.instance.id
serialized = ImageSeriesSerializer(image_series, context={'request': None})
self.assertEqual(orig_id, serialized.instance.id)
def create(self, validated_data):
series, _ = ImageSeries.get_or_create(validated_data['uri'])
return series
def test_parsed_property_no_model_attribute(self):
uri = '/images/LIDC-IDRI-0001/' \
'1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178/' \
'1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192'
path = os.path.join(uri, '-132.500000.dcm')
image_series, created = ImageSeries.get_or_create(uri)
# CASE ONE, Dicom prop does not exist, attr is not field
ImageFile.DICOM_PROPERTIES.update({
'DoesNotExist1': 'no_attribute',
})
# expected behavior is to log a warning
with self.assertLogs(level='WARN') as cm:
ImageFile(path=path, series=image_series).save()
self.assertEqual(len(cm.output), 1)
self.assertIn("'no_attribute' not a field", cm.output[0])
# reset
ImageFile.DICOM_PROPERTIES.pop('DoesNotExist1')
# CASE TWO, Dicom prop exists, attr is not field
ImageFile.DICOM_PROPERTIES.update({
'RescaleSlope': 'no_attribute2',
})
# expected behavior is to log a warning
with self.assertLogs(level='WARN') as cm:
ImageFile(path=path, series=image_series).save()
self.assertEqual(len(cm.output), 1)
self.assertIn("'no_attribute2' not a field", cm.output[0])
ImageFile.DICOM_PROPERTIES.update({
'RescaleSlope': lambda x: {
'rescale_slope': int(x)
},
})
# CASE THREE, Dicom prop does not exist, field does exist
ImageFile.DICOM_PROPERTIES.pop('Rows')
ImageFile.DICOM_PROPERTIES.update({
'DoesNotExist2': 'rows',
})
# no warnings should be logged
try:
with self.assertLogs(level='WARN') as cm:
img_file = ImageFile(path=path, series=image_series)
img_file.save()
except AssertionError as e:
self.assertEqual(
str(e), "no logs of level WARNING or higher triggered on root")
self.assertIsNone(img_file.rows)
# reset
ImageFile.DICOM_PROPERTIES['Rows'] = 'rows'
# CASE FOUR, Dicom prop does not exist, rows set multiple times
ImageFile.DICOM_PROPERTIES.update({
'DoesNotExist2': 'rows',
})
# expected behavior is to log a warning
with self.assertLogs(level='WARN') as cm:
ImageFile(path=path, series=image_series).save()
self.assertEqual(len(cm.output), 1)
self.assertIn("Tried to set 'rows' more than once", cm.output[0])
ImageFile.DICOM_PROPERTIES.pop('DoesNotExist2')