def test_log_file(self):
configure('test', filename=RESULT)
logger('test').info("Test info log message.")
logger('test').debug("Test debug log message.")
assert_true(os.path.exists(RESULT),
"The log file was not created: %s" % RESULT)
with open(RESULT) as fs:
msgs = fs.readlines()
assert_true(not not msgs, "No log messages in %s" % RESULT)
assert_equal(len(msgs), 1, "Extraneous log messages: %s" % msgs)
def __iter__(self):
"""
Iterates over each DICOM data set.
:yield: the next pydicom dicom object
"""
for f in super(DicomIterator, self).__iter__():
with qiutil.file.open(f) as fp:
try:
yield dicom.read_file(fp, **self.opts)
except InvalidDicomError:
logger(__name__).info("Skipping non-DICOM file %s" % f)
def __iter__(self):
"""
Iterates over each DICOM data set.
:yield: the next pydicom dicom object
"""
for f in super(DicomIterator, self).__iter__():
with qiutil.file.open(f) as fp:
try:
yield dicom.read_file(fp, **self.opts)
except InvalidDicomError:
logger(__name__).info("Skipping non-DICOM file %s" % f)
def test_config_file(self):
os.makedirs(RESULTS)
# Since the config fixture specifies a relative log file 'log/test.log',
# run this test in the context of the results directory.
with cd(RESULTS):
configure('test', config=FIXTURE)
logger('test').info("Test info log message.")
assert_true(os.path.exists(RESULT), "The log file was not created: %s" %
RESULT)
with open(RESULT) as fs:
msgs = fs.readlines()
assert_true(not not msgs, "No log messages in %s" % RESULT)
msg = msgs[0]
assert_true(msg.startswith('Custom: '), "The log message format is"
" incorrect: %s" % msg)
def _disconnect():
"""
Closes the xnat connection and deletes the cache directory.
"""
connect.xnat.close()
cachedir = connect.cachedir
# If this connection created a cache directory, then delete it.
if cachedir:
# Unset the cachedir first so that it can be safely deleted.
connect.cachedir = None
# Delete the cache directory
try:
shutil.rmtree(cachedir)
except Exception:
# Issue a warning and move on.
logger(__name__).warn("Could not delete the XNAT cache"
" directory %s" % cachedir)
logger(__name__).debug('Closed the XNAT connection.')
def edit(*in_files, **opts):
"""
Edits the given DICOM files. The *dest* option can be either the
destination directory path or an output file namer function.
If *dest* is a directory path, then the output file location is
a file in the given destination directory with the same unqualified
file name as the input file. If the *dest* option is a function,
then the output file location is the result of calling that
function with the input file path as an argument. The default is
to edit the file in-place.
:param in_files: the input DICOM files or directories containing
DICOM files
:param opts: the following options:
:keyword dest: the destination directory or file namer function
:yield: the :meth`qidicom.reader.next` pydicom dicom object
"""
# Prepare the destination directory.
dest = opts.get('dest')
if dest:
if isinstance(dest, str):
dest = os.path.abspath(dest)
if not os.path.exists(dest):
os.makedirs(dest)
else:
dest = os.getcwd()
if isinstance(dest, str):
logger(__name__).debug("The edited DICOM files will be saved to %s." %
dest)
# Open the DICOM store on each DICOM file (skipping non-DICOM files),
# yield to the edit callback and save to the file in the destination
# directory.
logger(__name__).debug("Editing %d DICOM files..." % len(in_files))
for ds in reader.iter_dicom(*in_files):
# Delegate the edit.
yield ds
# Make the output file name.
if isinstance(dest, str):
# The dest option is a parent directory.
_, fname = os.path.split(ds.filename)
out_file = os.path.join(dest, fname)
else:
# The dest option is a function.
out_file = dest(ds.filename)
# Save the modified dataset.
ds.save_as(out_file)
logger(__name__).debug("Saved the edited DICOM files.")
def _connect(config=None, **opts):
"""
Opens a XNAT connection.
:param config: the XNAT configuration file, or None
for the :meth:`qixnat.configuration.load` default
:param opts: the :class:`qixnat.facade.XNAT`
initialization options
"""
# Load the configuration file or default.
opts.update(configuration.load(config))
# If the pyxnat cachedir is not set, then make a new temp
# directory for the exclusive use of this execution process.
cachedir = opts.get('cachedir')
if not cachedir:
cachedir = tempfile.mkdtemp()
connect.cachedir = opts['cachedir'] = cachedir
logger(__name__).debug("The XNAT cache directory is %s" % cachedir)
logger(__name__).debug('Connecting to XNAT...')
connect.xnat = XNAT(**opts)
logger(__name__).debug('Connected to XNAT.')
def __init__(self, **opts):
"""
:param opts: the XNAT configuration options
"""
self._logger = logger(__name__)
self.interface = pyxnat.Interface(**opts)