def test_get_testdata_file_network_outage(self, download_failure):
"""Test a network outage when using get_testdata_file."""
fname = "693_UNCI.dcm"
msg = (r"A download failure occurred while attempting to "
r"retrieve 693_UNCI.dcm")
with pytest.warns(UserWarning, match=msg):
assert get_testdata_file(fname) is None
def test_get_testdata_file_no_download(self, recwarn):
"""
Test that `data_path_with_download`
is not called when `download=False`.
"""
fname = "693_UNCI.dcm"
assert get_testdata_file(fname, download=False) is None
assert not recwarn.list
def test_get_testdata_file_external_hash_match(self):
"""Test that external source is used when hash is OK."""
fname = "693_UNCI.dcm"
p = self.dpath / fname
ext_hash = calculate_file_hash(p)
ref_hash = get_cached_filehash(p.name)
assert ext_hash == ref_hash
fpath = self.as_posix(get_testdata_file(fname))
assert "data_store/data" in fpath
def test_get_testdata_file_external_hash_mismatch(self):
"""Test that the external source is not used when hash is not OK."""
p = self.dpath / "693_UNCI.dcm"
with open(p, 'wb') as f:
f.write(b"\x00\x01")
ext_hash = calculate_file_hash(p)
ref_hash = get_cached_filehash(p.name)
assert ext_hash != ref_hash
fpath = self.as_posix(get_testdata_file(p.name))
assert ".pydicom/data" in fpath
def test_get_testdata_file_external_ignore_hash(self):
"""Test that non-pydicom-data external source ignores hash check."""
EXTERNAL_DATA_SOURCES['mylib'] = EXTERNAL_DATA_SOURCES['pydicom-data']
p = self.dpath / "693_UNCI.dcm"
with open(p, 'wb') as f:
f.write(b"\x00\x01")
ext_hash = calculate_file_hash(p)
ref_hash = get_cached_filehash(p.name)
assert ext_hash != ref_hash
fpath = self.as_posix(get_testdata_file(p.name))
assert "data_store/data" in fpath
def test_get_testdata_file(self):
"""Test that file name is working properly."""
p = Path(get_testdata_file('DICOMDIR'))
assert "DICOMDIR" == p.name.upper()
def test_get_testdata_file_missing(self):
"""Test no such file available."""
fname = "MY_MISSING_FILE.dcm"
assert get_testdata_file(fname) is None
def test_get_testdata_file_external(self):
"""Test that external data source preferred over cache."""
fname = "693_UNCI.dcm"
fpath = self.as_posix(get_testdata_file(fname))
assert "data_store/data" in fpath
def test_get_testdata_file_local(self):
"""Test that local data path retrieved OK."""
fname = "CT_small.dcm"
fpath = self.as_posix(get_testdata_file(fname))
assert "pydicom/data/test_files" in fpath
def filespec_parser(filespec: str):
"""Utility to return a dataset and an optional data element value within it
Note: this is used as an argparse 'type' for adding parsing arguments.
Parameters
----------
filespec: str
A filename with optional `pydicom::` prefix and optional data element,
in format:
[pydicom::]<filename>[::<element>]
If an element is specified, it must be a path to a data element,
sequence item (dataset), or a sequence.
Examples:
your_file.dcm
your_file.dcm::StudyDate
pydicom::rtplan.dcm::BeamSequence[0]
pydicom::rtplan.dcm::BeamSequence[0].BeamLimitingDeviceSequence
Returns
-------
List[Tuple[Dataset, Any]]
Matching pairs of (dataset, data element value)
This usually is a single pair, but a list is returned for future
ability to work across multiple files.
Note
----
This function is meant to be used in a call to an `argparse` libary's
`add_argument` call for subparsers, with name="filespec" and
`type=filespec_parser`. When used that way, the resulting args.filespec
will contain the return values of this function
(e.g. use `ds, element_val = args.filespec` after parsing arguments)
See the `pydicom.cli.show` module for an example.
Raises
------
argparse.ArgumentTypeError
If the filename does not exist in local path or in pydicom test files,
or if the optional element is not a valid expression,
or if the optional element is a valid expression but does not exist
within the dataset
"""
prefix, filename, element = filespec_parts(filespec)
# Get the pydicom test filename even without prefix, in case user forgot it
try:
pydicom_filename = cast(str, get_testdata_file(filename))
except NotImplementedError: # will get this if absolute path passed
pydicom_filename = ""
if prefix == "pydicom":
filename = pydicom_filename
# Check element syntax first to avoid unnecessary load of file
if element and not re_file_spec_object.match(element):
raise argparse.ArgumentTypeError(
f"Component '{element}' is not valid syntax for a "
"data element, sequence, or sequence item")
# Read DICOM file
try:
ds = dcmread(filename, force=True)
except FileNotFoundError:
extra = ((f", \nbut 'pydicom::{filename}' test data file is available")
if pydicom_filename else "")
raise argparse.ArgumentTypeError(f"File '{filename}' not found{extra}")
except Exception as e:
raise argparse.ArgumentTypeError(
f"Error reading '{filename}': {str(e)}")
if not element:
return [(ds, None)]
data_elem_val = eval_element(ds, element)
return [(ds, data_elem_val)]
def test_get_testdata_file(self):
"""Test that file name is working properly."""
name = 'DICOMDIR'
filename = get_testdata_file(name)
assert filename and filename.endswith('DICOMDIR')
