def validate_dataset(*, dataset_file, reference_file, dataset_group,
reference_group):
try:
dataset_file = ismrmrd.File(dataset_file, 'r')
except OSError as e:
return Failure, "Failed to read dataset file '{}'".format(dataset_file)
try:
reference_file = ismrmrd.File(reference_file, 'r')
except OSError as e:
return Failure, "Failed to read reference file '{}'".format(
reference_file)
header = dataset_file[dataset_group].header
ref_header = reference_file[reference_group].header
if not dataset_file[dataset_group].header == reference_file[
reference_group].header:
import deepdiff
diff = deepdiff.diff.DeepDiff(header, ref_header)
print(diff.pretty())
return Failure, "Dataset header did not match reference header"
for attribute in ['acquisitions', 'waveforms', 'images']:
dataset = getattr(dataset_file[dataset_group], attribute) or []
reference = getattr(reference_file[reference_group], attribute) or []
if not list(dataset) == list(reference):
return Failure, "Dataset {attr} did not match reference {attr}".format(
attr=attribute)
return None, "Dataset matched reference"
def test_file_cannot_write_data_on_image():
filename = os.path.join(temp_dir, "file.h5")
with ismrmrd.File(filename) as file:
dataset = file['dataset']
dataset.images = random_images(1)
with ismrmrd.File(filename) as file:
dataset = file['dataset']
dataset.acquisitions = random_acquisitions(10)
def test_file_can_access_random_acquisition():
filename = os.path.join(temp_dir, "acquisitions.h5")
acquisitions = list(random_acquisitions(256))
with ismrmrd.File(filename) as file:
dataset = file['dataset']
dataset.acquisitions = acquisitions
with ismrmrd.File(filename) as file:
dataset = file['dataset']
assert acquisitions[255] == dataset.acquisitions[255]
def test_file_can_read_and_write_headers():
filename = os.path.join(temp_dir, "file.h5")
header = ismrmrd.xsd.CreateFromDocument(example_header)
with ismrmrd.File(filename) as file:
dataset = file['dataset']
dataset.header = header
with ismrmrd.File(filename) as file:
dataset = file['dataset']
assert header.toxml() == dataset.header.toxml()
def test_file_can_read_and_write_waveforms():
filename = os.path.join(temp_dir, "waveforms.h5")
waveforms = list(random_waveforms(10))
with ismrmrd.File(filename) as file:
dataset = file['dataset']
dataset.waveforms = waveforms
with ismrmrd.File(filename) as file:
dataset = file['dataset']
for a, b in zip(waveforms, dataset.waveforms):
assert a == b
def test_file_can_read_random_image():
filename = os.path.join(temp_dir, "images.h5")
images = list(random_images(10))
with ismrmrd.File(filename) as file:
imageset = file['dataset/image_1']
imageset.images = images
with ismrmrd.File(filename) as file:
imageset = file['dataset/image_1']
assert images[8] == imageset.images[8]
def test_file_can_read_image_slice():
filename = os.path.join(temp_dir, "images.h5")
images = list(random_images(10))
with ismrmrd.File(filename) as file:
imageset = file['dataset/image_1']
imageset.images = images
with ismrmrd.File(filename) as file:
imageset = file['dataset/image_1']
for a, b in zip(images[5:10], imageset.images[5:10]):
assert a == b
def test_file_can_list_keys():
filename = os.path.join(temp_dir, "keys.h5")
with ismrmrd.File(filename) as file:
dataset = file['dataset']
dataset.acquisitions = random_acquisitions(10)
dataset2 = file['dataset2']
dataset2.acquisitions = random_acquisitions(10)
with ismrmrd.File(filename) as file:
assert (file.keys() == {'dataset', 'dataset2'})
def test_file_can_read_and_write_acquisitions():
filename = os.path.join(temp_dir, "acquisitions.h5")
acquisitions = list(random_acquisitions(10))
with ismrmrd.File(filename) as file:
dataset = file['dataset']
dataset.acquisitions = acquisitions
with ismrmrd.File(filename) as file:
dataset = file['dataset']
for a, b in zip(acquisitions, dataset.acquisitions):
assert a == b
def test_file_can_write_random_acquisition():
filename = os.path.join(temp_dir, "acquisitions.h5")
acquisitions = list(random_acquisitions(256))
acquisition = create_random_acquisition()
with ismrmrd.File(filename) as file:
dataset = file['dataset']
dataset.acquisitions = acquisitions
dataset.acquisitions[200] = acquisition
with ismrmrd.File(filename) as file:
dataset = file['dataset']
assert acquisition == dataset.acquisitions[200]
def test_file_can_access_random_acquisition_slice():
filename = os.path.join(temp_dir, "acquisitions.h5")
acquisitions = list(random_acquisitions(256))
with ismrmrd.File(filename) as file:
dataset = file['dataset']
dataset.acquisitions = acquisitions
with ismrmrd.File(filename) as file:
dataset = file['dataset']
for a, b in zip(acquisitions[250:255], dataset.acquisitions[250:255]):
assert a == b
def test_file_can_write_random_image():
filename = os.path.join(temp_dir, "images.h5")
image = create_random_image()
with ismrmrd.File(filename) as file:
imageset = file['dataset/image_1']
imageset.images = random_images(10)
imageset.images[6] = image
with ismrmrd.File(filename) as file:
imageset = file['dataset/image_1']
assert image == imageset.images[6]
def test_file_can_write_random_acquisition_slice():
filename = os.path.join(temp_dir, "acquisitions.h5")
acquisitions = list(random_acquisitions(256))
slice = list(random_acquisitions(3))
with ismrmrd.File(filename) as file:
dataset = file['dataset']
dataset.acquisitions = acquisitions
dataset.acquisitions[150:153] = slice
with ismrmrd.File(filename) as file:
dataset = file['dataset']
for a, b in zip(slice, dataset.acquisitions[150:153]):
assert a == b
def test_file_can_rewrite_data_and_images():
filename = os.path.join(temp_dir, "file.h5")
with ismrmrd.File(filename) as file:
dataset = file['dataset']
dataset.acquisitions = random_acquisitions(20)
dataset.acquisitions = random_acquisitions(10)
dataset.waveforms = random_waveforms(10)
dataset.waveforms = random_waveforms(5)
dataset.acquisitions = random_acquisitions(5)
with ismrmrd.File(filename) as file:
imageset = file['dataset/images']
imageset.images = random_images(1)
imageset.images = random_images(2)
imageset.images = random_images(3)
def test_file_returns_none_when_no_acquisitions_present():
filename = os.path.join(temp_dir, "acquisitions.h5")
acquisitions = list(random_acquisitions(10))
with ismrmrd.File(filename) as file:
dataset = file['dataset']
assert not dataset.has_acquisitions()
assert dataset.acquisitions is None
dataset.acquisitions = acquisitions
with ismrmrd.File(filename) as file:
dataset = file['dataset']
assert dataset.has_acquisitions()
assert dataset.acquisitions is not None
def test_file_cannot_write_mismatched_slice():
filename = os.path.join(temp_dir, "acquisitions.h5")
acquisitions = list(random_acquisitions(256))
slice = list(random_acquisitions(3))
with ismrmrd.File(filename) as file:
dataset = file['dataset']
dataset.acquisitions = acquisitions
dataset.acquisitions[150:155] = slice
def test_file_can_list_contained_images():
filename = os.path.join(temp_dir, "find_file.h5")
with ismrmrd.File(filename) as file:
dataset = file['dataset']
dataset.acquisitions = random_acquisitions(10)
imageset = file['dataset/image_1']
imageset.images = random_images(1)
imageset = file['dataset/image_2']
imageset.images = random_images(2)
imageset = file['dataset/nested/image_3']
imageset.images = [create_random_image(3)]
with ismrmrd.File(filename) as file:
assert (file.find_images() == {
'dataset/image_1', 'dataset/image_2', 'dataset/nested/image_3'
})
assert (file.find_data() == {'dataset'})
def __init__(self, parent, file_name):
super().__init__(parent)
self.tree = QtWidgets.QTreeWidget(self)
self.tree.setHeaderHidden(True)
self.tree.itemClicked.connect(lambda widget, _: self.set_viewer(widget.container, widget.viewer))
FileWidget.__populate_tree(self.tree, ismrmrd.File(file_name, mode='r'))
self.viewer = QtWidgets.QListWidget(self)
self.addWidget(self.tree)
self.addWidget(self.viewer)
self.__balance()
def test_file_can_delete_acquisitions():
filename = os.path.join(temp_dir, "acquisitions.h5")
with ismrmrd.File(filename) as file:
dataset = file['dataset']
assert dataset.acquisitions is None
del dataset.acquisitions
assert dataset.acquisitions is None
dataset.acquisitions = random_acquisitions(10)
assert dataset.acquisitions is not None
del dataset.acquisitions
assert dataset.acquisitions is None
def validate_image_header(*, output_file, reference_file, output_group,
reference_group):
def equals():
return lambda out, ref: out == ref
def approx(threshold=1e-6):
return lambda out, ref: abs(out - ref) <= threshold
def ignore():
return lambda out, ref: True
def each(rule):
return lambda out, ref: all(
rule(out, ref) for out, ref in itertools.zip_longest(out, ref))
header_rules = {
'version': equals(),
'data_type': equals(),
'flags': equals(),
'measurement_uid': equals(),
'matrix_size': each(equals()),
'field_of_view': each(approx()),
'channels': equals(),
'position': each(approx()),
'read_dir': each(approx()),
'phase_dir': each(approx()),
'slice_dir': each(approx()),
'patient_table_position': each(approx()),
'average': equals(),
'slice': equals(),
'contrast': equals(),
'phase': equals(),
'repetition': equals(),
'set': equals(),
'acquisition_time_stamp': ignore(),
'physiology_time_stamp': each(ignore()),
'image_type': equals(),
'image_index': equals(),
'image_series_index': ignore(),
'user_int': each(equals()),
'user_float': each(approx()),
'attribute_string_len': ignore()
}
def check_image_header(output, reference):
if not output:
raise RuntimeError("Missing output")
if not reference:
raise RuntimeError("Missing reference")
output = output.getHead()
reference = reference.getHead()
for attribute, rule in header_rules.items():
if not rule(getattr(output, attribute),
getattr(reference, attribute)):
print(output)
print(reference)
raise RuntimeError(
"Image header '{}' does not match reference. [index {}, series {}]"
.format(attribute, output.image_index,
output.image_series_index))
try:
with ismrmrd.File(output_file, 'r') as output_file:
with ismrmrd.File(reference_file, 'r') as reference_file:
output_images = output_file[output_group].images or []
reference_images = reference_file[reference_group].images or []
for output_image, reference_image in itertools.zip_longest(
output_images, reference_images):
check_image_header(output_image, reference_image)
except OSError as e:
return Failure, str(e)
except RuntimeError as e:
return Failure, str(e)
return None, "Output headers matched reference"