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_image_file_serializer(self):
image_file = ImageFile(path='/my_path')
serialized = ImageFileSerializer(image_file)
# we construct the preview url, so test it here
self.assertEqual(serialized['preview_url'].value,
'/api/images/preview?dicom_location=/my_path')
for s in serialized:
self.assertIsNone(s.errors)
def get(self, request):
'''
Get metadata of a DICOM image that is not yet imported into the database. This can
be used to preview the DICOM images before creating the model (e.g., during selection).
Example: .../api/images/metadata?dicom_location=FULL_PATH_TO_IMAGE
---
parameters:
- name: dicom_location
description: full location of the image
required: true
type: string
'''
path = request.GET['dicom_location']
try:
return Response(ImageFile.load_dicom_data_from_disk(path, encode_image_data=True))
except IOError as err:
raise NotFound(f"DICOM file not found on disk with path '{path}'")
def test_invalid_path_on_image_file_create(self):
with self.assertRaises(PermissionDenied):
ImageFile(path='/not_valid/path').save()
with self.assertRaises(FileNotFoundError):
ImageFile(path='/images/LIDC-IDRI-0001/not_valid/path').save()
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')