def _runtask((tid, srcs, trgs, fun, args, kwargs, desc)):
r"""
Execute a single task.
"""
# initialize logger
logger = Logger.getInstance()
# check required source files
srcs_check = _check_files(srcs)
if not numpy.all(srcs_check):
raise TaskExecutionError('Task {} ({}): Required source file(s) missing: "{}"'.format(tid, desc, numpy.asarray(srcs)[~srcs_check]))
# check target files
trgs_check = _check_files(trgs)
if numpy.all(trgs_check):
logger.warning('Task {} ({}): All target files already existent; skipping task'.format(tid, desc))
return
elif numpy.any(trgs_check):
raise TaskExecutionError('Task {} ({}): Some target file(s) already exist: "{}".'.format(tid, desc, numpy.asarray(trgs)[trgs_check]))
# execute task
try:
fun(*args, **kwargs)
except Exception as e:
# remove target files (if partially created)
for trg in trgs:
try:
if os.path.isfile(trg):
os.remove(trg)
except Exception as e:
pass
raise TaskExecutionError, TaskExecutionError('Task {} ({}): Execution failed. Partial results removed. Reason signaled: {}'.format(tid, desc, e)), sys.exc_info()[2]
# check target files
trgs_check = _check_files(trgs)
if not numpy.all(srcs_check):
raise TaskExecutionError('Task {} ({}): Execution failed to create some target files: "{}".'.format(tid, desc, numpy.asarray(trgs)[~trgs_check]))
def stripskull(directory, inset, stripsequence = False):
r"""
Compute a brain mask for MR brain images.
Parameters
----------
directory : string
Where to place the results.
inset : FileSet
The input file set.
stripsequence : False or string
The sequence to use for computing the brain mask. If none supplied, the order
in `~skullstripping.SEQUENCE_PREFERENCES` is respected.
Returns
-------
resultset : FileSet
A FilSet centered on ``directory`` and representing the binary brain masks.
stripsequence : string
The sequence employed for the skull-stripping.
"""
logger = Logger.getInstance()
# decide on strip-sequence
if not stripsequence:
for sequence in SEQUENCE_PREFERENCES:
if sequence in inset.identifiers:
stripsequence = sequence
break
if not stripsequence:
stripsequence = inset.identifiers[0]
logger.warning('None of the preferred sequences for skull-stripping "{}" available. Falling back to "{}"'.format(SEQUENCE_PREFERENCES, stripsequence))
elif not stripsequence in inset.identifiers:
raise ValueError('The chosen skull-strip sequence "{}" is not available in the input image set.'.format(stripsequence))
# prepare the task machine
tm = TaskMachine(multiprocessing=True)
# prepare output
resultset = FileSet(directory, inset.cases, False, ['{}.{}'.format(cid, PREFERRED_FILE_SUFFIX) for cid in inset.cases], 'cases', False)
# prepare and register skull-stripping tasks
for case in inset.cases:
src = inset.getfile(case=case, identifier=stripsequence)
dest = resultset.getfile(case=case)
rfile = dest.replace('.{}'.format(PREFERRED_FILE_SUFFIX), '_mask.{}'.format(PREFERRED_FILE_SUFFIX))
tm.register([src], [dest], brainmask, [src, dest, rfile], dict(), 'skull-strip')
# run
tm.run()
return resultset, stripsequence
def __init__(self, multiprocessing = False, nprocesses = None) :
r"""
A class to which tasks can be registered and then executed, either sequential or in parallel.
Parameters
----------
multiprocessing : bool
Enable/disable multiprocessing.
nprocesses : int or None
The number of processes to spawn. If ``None``, the number corresponds to the processor count.
"""
self.logger = Logger.getInstance()
self.tasks = []
self.multiprocessing = multiprocessing
self.nprocesses = nprocesses
def test_SaveLoad(self):
"""
The bases essence of this test is to check if any one image format in any one
dimension can be saved and read, as this is the only base requirement for using
medpy.
Additionally checks the basic expected behaviour of the load and save
functionality.
Since this usually does not make much sense, this implementation allows also to
set a switch (verboose) which causes the test to print a comprehensive overview
over which image formats with how many dimensions and which pixel data types
can be read and written.
"""
####
# VERBOOSE SETTINGS
# The following are three variables that can be used to print some nicely
# formatted additional output. When one of them is set to True, this unittest
# should be run stand-alone.
####
# Print a list of supported image types, dimensions and pixel data types
supported = True
# Print a list of image types that were tested but are not supported
notsupported = False
# Print a list of image type, dimensions and pixel data types configurations,
# that seem to work but failed the consistency tests. These should be handled
# with special care, as they might be the source of errors.
inconsistent = True
####
# OTHER SETTINGS
####
# debug settings
logger = Logger.getInstance()
#logger.setLevel(logging.DEBUG)
# run test either for most important formats or for all
#__suffixes = self.__important # (choice 1)
__suffixes = self.__pydicom + self.__nifti + self.__itk + self.__itk_more # (choice 2)
# dimensions and dtypes to check
__suffixes = list(set(__suffixes))
__ndims = [1, 2, 3, 4, 5]
__dtypes = [scipy.bool_,
scipy.int8, scipy.int16, scipy.int32, scipy.int64,
scipy.uint8, scipy.uint16, scipy.uint32, scipy.uint64,
scipy.float32, scipy.float64,
scipy.complex64, scipy.complex128]
# prepare struct to save settings that passed the test
valid_types = dict.fromkeys(__suffixes)
for k1 in valid_types:
valid_types[k1] = dict.fromkeys(__ndims)
for k2 in valid_types[k1]:
valid_types[k1][k2] = []
# prepare struct to save settings that did not
unsupported_type = dict.fromkeys(__suffixes)
for k1 in unsupported_type:
unsupported_type[k1] = dict.fromkeys(__ndims)
for k2 in unsupported_type[k1]:
unsupported_type[k1][k2] = dict.fromkeys(__dtypes)
# prepare struct to save settings that did not pass the data integrity test
invalid_types = dict.fromkeys(__suffixes)
for k1 in invalid_types:
invalid_types[k1] = dict.fromkeys(__ndims)
for k2 in invalid_types[k1]:
invalid_types[k1][k2] = dict.fromkeys(__dtypes)
# create artifical images, save them, load them again and compare them
path = tempfile.mkdtemp()
try:
for ndim in __ndims:
logger.debug('Testing for dimension {}...'.format(ndim))
arr_base = scipy.random.randint(0, 10, range(10, ndim + 10))
for dtype in __dtypes:
arr_save = arr_base.astype(dtype)
for suffix in __suffixes:
# do not run test, if in avoid array
if ndim in self.__avoid and suffix in self.__avoid[ndim]:
unsupported_type[suffix][ndim][dtype] = "Test skipped, as combination in the tests __avoid array."
continue
image = '{}/img{}'.format(path, suffix)
try:
# attempt to save the image
save(arr_save, image)
self.assertTrue(os.path.exists(image), 'Image of type {} with shape={}/dtype={} has been saved without exception, but the file does not exist.'.format(suffix, arr_save.shape, dtype))
# attempt to load the image
arr_load, header = load(image)
self.assertTrue(header, 'Image of type {} with shape={}/dtype={} has been loaded without exception, but no header has been supplied (got: {})'.format(suffix, arr_save.shape, dtype, header))
# check for data consistency
msg = self.__diff(arr_save, arr_load)
if msg:
invalid_types[suffix][ndim][dtype] = msg
#elif list == type(valid_types[suffix][ndim]):
else:
valid_types[suffix][ndim].append(dtype)
# remove image
if os.path.exists(image): os.remove(image)
except Exception as e: # clean up
unsupported_type[suffix][ndim][dtype] = e.message
if os.path.exists(image): os.remove(image)
except Exception:
if not os.listdir(path): os.rmdir(path)
else: logger.debug('Could not delete temporary directory {}. Is not empty.'.format(path))
raise
if supported:
print '\nsave() and load() support (at least) the following image configurations:'
print 'type\tndim\tdtypes'
for suffix in valid_types:
for ndim, dtypes in valid_types[suffix].iteritems():
if list == type(dtypes) and not 0 == len(dtypes):
print '{}\t{}D\t{}'.format(suffix, ndim, map(lambda x: str(x).split('.')[-1][:-2], dtypes))
if notsupported:
print '\nthe following configurations are not supported:'
print 'type\tndim\tdtype\t\terror'
for suffix in unsupported_type:
for ndim in unsupported_type[suffix]:
for dtype, msg in unsupported_type[suffix][ndim].iteritems():
if msg:
print '{}\t{}D\t{}\t\t{}'.format(suffix, ndim, str(dtype).split('.')[-1][:-2], msg)
if inconsistent:
print '\nthe following configurations show inconsistent saving and loading behaviour:'
print 'type\tndim\tdtype\t\terror'
for suffix in invalid_types:
for ndim in invalid_types[suffix]:
for dtype, msg in invalid_types[suffix][ndim].iteritems():
if msg:
print '{}\t{}D\t{}\t\t{}'.format(suffix, ndim, str(dtype).split('.')[-1][:-2], msg)
def test_SaveLoad(self):
"""
The bases essence of this test is to check if any one image format in any one
dimension can be saved and read, as this is the only base requirement for using
medpy.
Additionally checks the basic expected behaviour of the load and save
functionality.
Since this usually does not make much sense, this implementation allows also to
set a switch (verboose) which causes the test to print a comprehensive overview
over which image formats with how many dimensions and which pixel data types
can be read and written.
"""
####
# VERBOOSE SETTINGS
# The following are three variables that can be used to print some nicely
# formatted additional output. When one of them is set to True, this unittest
# should be run stand-alone.
####
# Print a list of supported image types, dimensions and pixel data types
supported = True
# Print a list of image types that were tested but are not supported
notsupported = False
# Print a list of image type, dimensions and pixel data types configurations,
# that seem to work but failed the consistency tests. These should be handled
# with special care, as they might be the source of errors.
inconsistent = True
####
# OTHER SETTINGS
####
# debug settings
logger = Logger.getInstance()
#logger.setLevel(logging.DEBUG)
# run test either for most important formats or for all
#__suffixes = self.__important # (choice 1)
__suffixes = self.__pydicom + self.__nifti + self.__itk + self.__itk_more # (choice 2)
# dimensions and dtypes to check
__suffixes = list(set(__suffixes))
__ndims = [1, 2, 3, 4, 5]
__dtypes = [
scipy.bool_, scipy.int8, scipy.int16, scipy.int32, scipy.int64,
scipy.uint8, scipy.uint16, scipy.uint32, scipy.uint64,
scipy.float32, scipy.float64, scipy.complex64, scipy.complex128
]
# prepare struct to save settings that passed the test
valid_types = dict.fromkeys(__suffixes)
for k1 in valid_types:
valid_types[k1] = dict.fromkeys(__ndims)
for k2 in valid_types[k1]:
valid_types[k1][k2] = []
# prepare struct to save settings that did not
unsupported_type = dict.fromkeys(__suffixes)
for k1 in unsupported_type:
unsupported_type[k1] = dict.fromkeys(__ndims)
for k2 in unsupported_type[k1]:
unsupported_type[k1][k2] = dict.fromkeys(__dtypes)
# prepare struct to save settings that did not pass the data integrity test
invalid_types = dict.fromkeys(__suffixes)
for k1 in invalid_types:
invalid_types[k1] = dict.fromkeys(__ndims)
for k2 in invalid_types[k1]:
invalid_types[k1][k2] = dict.fromkeys(__dtypes)
# create artifical images, save them, load them again and compare them
path = tempfile.mkdtemp()
try:
for ndim in __ndims:
logger.debug('Testing for dimension {}...'.format(ndim))
arr_base = scipy.random.randint(0, 10,
list(range(10, ndim + 10)))
for dtype in __dtypes:
arr_save = arr_base.astype(dtype)
for suffix in __suffixes:
# do not run test, if in avoid array
if ndim in self.__avoid and suffix in self.__avoid[
ndim]:
unsupported_type[suffix][ndim][
dtype] = "Test skipped, as combination in the tests __avoid array."
continue
image = '{}/img{}'.format(path, suffix)
try:
# attempt to save the image
save(arr_save, image)
self.assertTrue(
os.path.exists(image),
'Image of type {} with shape={}/dtype={} has been saved without exception, but the file does not exist.'
.format(suffix, arr_save.shape, dtype))
# attempt to load the image
arr_load, header = load(image)
self.assertTrue(
header,
'Image of type {} with shape={}/dtype={} has been loaded without exception, but no header has been supplied (got: {})'
.format(suffix, arr_save.shape, dtype, header))
# check for data consistency
msg = self.__diff(arr_save, arr_load)
if msg:
invalid_types[suffix][ndim][dtype] = msg
#elif list == type(valid_types[suffix][ndim]):
else:
valid_types[suffix][ndim].append(dtype)
# remove image
if os.path.exists(image): os.remove(image)
except Exception as e: # clean up
unsupported_type[suffix][ndim][dtype] = e.message
if os.path.exists(image): os.remove(image)
except Exception:
if not os.listdir(path): os.rmdir(path)
else:
logger.debug(
'Could not delete temporary directory {}. Is not empty.'.
format(path))
raise
if supported:
print(
'\nsave() and load() support (at least) the following image configurations:'
)
print('type\tndim\tdtypes')
for suffix in valid_types:
for ndim, dtypes in list(valid_types[suffix].items()):
if list == type(dtypes) and not 0 == len(dtypes):
print(('{}\t{}D\t{}'.format(
suffix, ndim,
[str(x).split('.')[-1][:-2] for x in dtypes])))
if notsupported:
print('\nthe following configurations are not supported:')
print('type\tndim\tdtype\t\terror')
for suffix in unsupported_type:
for ndim in unsupported_type[suffix]:
for dtype, msg in list(
unsupported_type[suffix][ndim].items()):
if msg:
print(('{}\t{}D\t{}\t\t{}'.format(
suffix, ndim,
str(dtype).split('.')[-1][:-2], msg)))
if inconsistent:
print(
'\nthe following configurations show inconsistent saving and loading behaviour:'
)
print('type\tndim\tdtype\t\terror')
for suffix in invalid_types:
for ndim in invalid_types[suffix]:
for dtype, msg in list(
invalid_types[suffix][ndim].items()):
if msg:
print(('{}\t{}D\t{}\t\t{}'.format(
suffix, ndim,
str(dtype).split('.')[-1][:-2], msg)))
def test_MetadataConsistency(self):
"""
This test checks the ability of different image formats to consistently save
meta-data information. Especially if a conversion between formats is required,
that involves different 3rd party modules, this is not always guaranteed.
The images are saved in one format, loaded and then saved in another format.
Subsequently the differences in the meta-data is checked.
Currently this test can only check:
- voxel spacing
- image offset
Note that some other test are inherently performed by the
loadsave.TestIOFacilities class:
- data type
- shape
- content
With the verboose switches, a comprehensive list of the results can be obtianed.
"""
####
# VERBOOSE SETTINGS
# The following are two variables that can be used to print some nicely
# formatted additional output. When one of them is set to True, this unittest
# should be run stand-alone.
####
# Print a list of format to format conversion which preserve meta-data
consistent = True
# Print a list of format to format conversion which do not preserve meta-data
inconsistent = False
# Print a list of formats that failed conversion in general
unsupported = False
####
# OTHER SETTINGS
####
# debug settings
logger = Logger.getInstance()
#logger.setLevel(logging.DEBUG)
# run test either for most important formats or for all (see loadsave.TestIOFacilities)
#__suffixes = self.__important # (choice 1)
__suffixes = self.__important + self.__itk # (choice 2)
# dimensions and dtypes to check
__suffixes = list(set(__suffixes))
__ndims = [1, 2, 3, 4, 5]
__dtypes = [
scipy.bool_,
scipy.int8,
scipy.int16,
scipy.int32,
scipy.int64,
scipy.uint8,
scipy.uint16,
scipy.uint32,
scipy.uint64,
scipy.float32,
scipy.
float64, #scipy.float128, # last one removed, as not present on every machine
scipy.complex64,
scipy.complex128,
] #scipy.complex256 ## removed, as not present on every machine
# prepare struct to save settings that passed the test
consistent_types = dict.fromkeys(__suffixes)
for k0 in consistent_types:
consistent_types[k0] = dict.fromkeys(__suffixes)
for k1 in consistent_types[k0]:
consistent_types[k0][k1] = dict.fromkeys(__ndims)
for k2 in consistent_types[k0][k1]:
consistent_types[k0][k1][k2] = []
# prepare struct to save settings that did not
inconsistent_types = dict.fromkeys(__suffixes)
for k0 in inconsistent_types:
inconsistent_types[k0] = dict.fromkeys(__suffixes)
for k1 in inconsistent_types[k0]:
inconsistent_types[k0][k1] = dict.fromkeys(__ndims)
for k2 in inconsistent_types[k0][k1]:
inconsistent_types[k0][k1][k2] = dict.fromkeys(__dtypes)
# prepare struct to save settings that did not pass the data integrity test
unsupported_types = dict.fromkeys(__suffixes)
for k0 in consistent_types:
unsupported_types[k0] = dict.fromkeys(__suffixes)
for k1 in unsupported_types[k0]:
unsupported_types[k0][k1] = dict.fromkeys(__ndims)
for k2 in unsupported_types[k0][k1]:
unsupported_types[k0][k1][k2] = dict.fromkeys(__dtypes)
# create artifical images, save them, load them again and compare them
path = tempfile.mkdtemp()
try:
for ndim in __ndims:
logger.debug('Testing for dimension {}...'.format(ndim))
arr_base = scipy.random.randint(0, 10,
list(range(10, ndim + 10)))
for dtype in __dtypes:
arr_save = arr_base.astype(dtype)
for suffix_from in __suffixes:
# do not run test, if in avoid array
if ndim in self.__avoid and suffix_from in self.__avoid[
ndim]:
unsupported_types[suffix_from][suffix_from][ndim][
dtype] = "Test skipped, as combination in the tests __avoid array."
continue
# save array as file, load again to obtain header and set the meta-data
image_from = '{}/img{}'.format(path, suffix_from)
try:
save(arr_save, image_from, None, True)
if not os.path.exists(image_from):
raise Exception(
'Image of type {} with shape={}/dtype={} has been saved without exception, but the file does not exist.'
.format(suffix_from, arr_save.shape,
dtype))
except Exception as e:
unsupported_types[suffix_from][suffix_from][
ndim][dtype] = e.message if hasattr(
e, 'message') else str(e.args)
continue
try:
img_from, hdr_from = load(image_from)
img_from = img_from.astype(
dtype
) # change dtype of loaded image again, as sometimes the type is higher (e.g. int64 instead of int32) after loading!
except Exception as e:
_message = e.message if hasattr(
e, 'message') else str(e.args)
unsupported_types[suffix_from][suffix_from][ndim][
dtype] = 'Saved reference image of type {} with shape={}/dtype={} could not be loaded. Reason: {}'.format(
suffix_from, arr_save.shape, dtype,
_message)
continue
header.set_pixel_spacing(hdr_from, [
scipy.random.rand() * scipy.random.randint(1, 10)
for _ in range(img_from.ndim)
])
try:
header.set_pixel_spacing(hdr_from, [
scipy.random.rand() *
scipy.random.randint(1, 10)
for _ in range(img_from.ndim)
])
header.set_offset(hdr_from, [
scipy.random.rand() *
scipy.random.randint(1, 10)
for _ in range(img_from.ndim)
])
except Exception as e:
logger.error(
'Could not set the header meta-data for image of type {} with shape={}/dtype={}. This should not happen and hints to a bug in the code. Signaled reason is: {}'
.format(suffix_from, arr_save.shape, dtype, e))
unsupported_types[suffix_from][suffix_from][
ndim][dtype] = e.message if hasattr(
e, 'message') else str(e.args)
continue
for suffix_to in __suffixes:
# do not run test, if in avoid array
if ndim in self.__avoid and suffix_to in self.__avoid[
ndim]:
unsupported_types[suffix_from][suffix_to][ndim][
dtype] = "Test skipped, as combination in the tests __avoid array."
continue
# for each other format, try format to format conversion an check if the meta-data is consistent
image_to = '{}/img_to{}'.format(path, suffix_to)
try:
save(img_from, image_to, hdr_from, True)
if not os.path.exists(image_to):
raise Exception(
'Image of type {} with shape={}/dtype={} has been saved without exception, but the file does not exist.'
.format(suffix_to, arr_save.shape,
dtype))
except Exception as e:
unsupported_types[suffix_from][suffix_from][
ndim][dtype] = e.message if hasattr(
e, 'message') else str(e.args)
continue
try:
_, hdr_to = load(image_to)
except Exception as e:
_message = e.message if hasattr(
e, 'message') else str(e.args)
unsupported_types[suffix_from][suffix_to][ndim][
dtype] = 'Saved testing image of type {} with shape={}/dtype={} could not be loaded. Reason: {}'.format(
suffix_to, arr_save.shape, dtype,
_message)
continue
msg = self.__diff(hdr_from, hdr_to)
if msg:
inconsistent_types[suffix_from][suffix_to][
ndim][dtype] = msg
else:
consistent_types[suffix_from][suffix_to][
ndim].append(dtype)
# remove testing image
if os.path.exists(image_to): os.remove(image_to)
# remove reference image
if os.path.exists(image_to): os.remove(image_to)
except Exception:
if not os.listdir(path): os.rmdir(path)
else:
logger.debug(
'Could not delete temporary directory {}. Is not empty.'.
format(path))
raise
if consistent:
print(
'\nthe following format conversions are meta-data consistent:')
print('from\tto\tndim\tdtypes')
for suffix_from in consistent_types:
for suffix_to in consistent_types[suffix_from]:
for ndim, dtypes in list(
consistent_types[suffix_from][suffix_to].items()):
if list == type(dtypes) and not 0 == len(dtypes):
print(('{}\t{}\t{}D\t{}'.format(
suffix_from, suffix_to, ndim,
[str(x).split('.')[-1][:-2] for x in dtypes])))
if inconsistent:
print(
'\nthe following form conversions are not meta-data consistent:'
)
print('from\tto\tndim\tdtype\t\terror')
for suffix_from in inconsistent_types:
for suffix_to in inconsistent_types[suffix_from]:
for ndim in inconsistent_types[suffix_from][suffix_to]:
for dtype, msg in list(inconsistent_types[suffix_from]
[suffix_to][ndim].items()):
if msg:
print(('{}\t{}\t{}D\t{}\t\t{}'.format(
suffix_from, suffix_to, ndim,
str(dtype).split('.')[-1][:-2], msg)))
if unsupported:
print(
'\nthe following form conversions could not be tested due to errors:'
)
print('from\tto\tndim\tdtype\t\terror')
for suffix_from in unsupported_types:
for suffix_to in unsupported_types[suffix_from]:
for ndim in unsupported_types[suffix_from][suffix_to]:
for dtype, msg in list(unsupported_types[suffix_from]
[suffix_to][ndim].items()):
if msg:
print(('{}\t{}\t{}D\t{}\t\t{}'.format(
suffix_from, suffix_to, ndim,
str(dtype).split('.')[-1][:-2], msg)))
def test_MetadataConsistency(self):
"""
This test checks the ability of different image formats to consistently save
meta-data information. Especially if a conversion between formats is required,
that involves different 3rd party modules, this is not always guaranteed.
The images are saved in one format, loaded and then saved in another format.
Subsequently the differences in the meta-data is checked.
Currently this test can only check:
- voxel spacing
- image offset
Note that some other test are inherently performed by the
loadsave.TestIOFacilities class:
- data type
- shape
- content
With the verboose switches, a comprehensive list of the results can be obtianed.
"""
####
# VERBOOSE SETTINGS
# The following are two variables that can be used to print some nicely
# formatted additional output. When one of them is set to True, this unittest
# should be run stand-alone.
####
# Print a list of format to format conversion which preserve meta-data
consistent = True
# Print a list of format to format conversion which do not preserve meta-data
inconsistent = True
# Print a list of formats that failed conversion in general
unsupported = False
####
# OTHER SETTINGS
####
# debug settings
logger = Logger.getInstance()
#logger.setLevel(logging.DEBUG)
# run test either for most important formats or for all (see loadsave.TestIOFacilities)
#__suffixes = self.__important # (choice 1)
__suffixes = self.__pydicom + self.__nifti + self.__itk + self.__itk_more # (choice 2)
# dimensions and dtypes to check
__suffixes = list(set(__suffixes))
__ndims = [1, 2, 3, 4, 5]
__dtypes = [scipy.bool_,
scipy.int8, scipy.int16, scipy.int32, scipy.int64,
scipy.uint8, scipy.uint16, scipy.uint32, scipy.uint64,
scipy.float32, scipy.float64, #scipy.float128, # last one removed, as not present on every machine
scipy.complex64, scipy.complex128, ] #scipy.complex256 ## removed, as not present on every machine
# prepare struct to save settings that passed the test
consistent_types = dict.fromkeys(__suffixes)
for k0 in consistent_types:
consistent_types[k0] = dict.fromkeys(__suffixes)
for k1 in consistent_types[k0]:
consistent_types[k0][k1] = dict.fromkeys(__ndims)
for k2 in consistent_types[k0][k1]:
consistent_types[k0][k1][k2] = []
# prepare struct to save settings that did not
inconsistent_types = dict.fromkeys(__suffixes)
for k0 in inconsistent_types:
inconsistent_types[k0] = dict.fromkeys(__suffixes)
for k1 in inconsistent_types[k0]:
inconsistent_types[k0][k1] = dict.fromkeys(__ndims)
for k2 in inconsistent_types[k0][k1]:
inconsistent_types[k0][k1][k2] = dict.fromkeys(__dtypes)
# prepare struct to save settings that did not pass the data integrity test
unsupported_types = dict.fromkeys(__suffixes)
for k0 in consistent_types:
unsupported_types[k0] = dict.fromkeys(__suffixes)
for k1 in unsupported_types[k0]:
unsupported_types[k0][k1] = dict.fromkeys(__ndims)
for k2 in unsupported_types[k0][k1]:
unsupported_types[k0][k1][k2] = dict.fromkeys(__dtypes)
# create artifical images, save them, load them again and compare them
path = tempfile.mkdtemp()
try:
for ndim in __ndims:
logger.debug('Testing for dimension {}...'.format(ndim))
arr_base = scipy.random.randint(0, 10, range(10, ndim + 10))
for dtype in __dtypes:
arr_save = arr_base.astype(dtype)
for suffix_from in __suffixes:
# do not run test, if in avoid array
if ndim in self.__avoid and suffix_from in self.__avoid[ndim]:
unsupported_types[suffix_from][suffix_from][ndim][dtype] = "Test skipped, as combination in the tests __avoid array."
continue
# save array as file, load again to obtain header and set the meta-data
image_from = '{}/img{}'.format(path, suffix_from)
try:
save(arr_save, image_from, None, True)
if not os.path.exists(image_from):
raise Exception('Image of type {} with shape={}/dtype={} has been saved without exception, but the file does not exist.'.format(suffix_from, arr_save.shape, dtype))
except Exception as e:
unsupported_types[suffix_from][suffix_from][ndim][dtype] = e.message
continue
try:
img_from, hdr_from = load(image_from)
img_from = img_from.astype(dtype) # change dtype of loaded image again, as sometimes the type is higher (e.g. int64 instead of int32) after loading!
except Exception as e:
unsupported_types[suffix_from][suffix_from][ndim][dtype] = 'Saved reference image of type {} with shape={}/dtype={} could not be loaded. Reason: {}'.format(suffix_from, arr_save.shape, dtype, e.message)
continue
header.set_pixel_spacing(hdr_from, [scipy.random.rand() * scipy.random.randint(1, 10) for _ in range(img_from.ndim)])
try:
header.set_pixel_spacing(hdr_from, [scipy.random.rand() * scipy.random.randint(1, 10) for _ in range(img_from.ndim)])
header.set_offset(hdr_from, [scipy.random.rand() * scipy.random.randint(1, 10) for _ in range(img_from.ndim)])
except Exception as e:
logger.error('Could not set the header meta-data for image of type {} with shape={}/dtype={}. This should not happen and hints to a bug in the code. Signaled reason is: {}'.format(suffix_from, arr_save.shape, dtype, e))
unsupported_types[suffix_from][suffix_from][ndim][dtype] = e.message
continue
for suffix_to in __suffixes:
# do not run test, if in avoid array
if ndim in self.__avoid and suffix_to in self.__avoid[ndim]:
unsupported_types[suffix_from][suffix_to][ndim][dtype] = "Test skipped, as combination in the tests __avoid array."
continue
# for each other format, try format to format conversion an check if the meta-data is consistent
image_to = '{}/img_to{}'.format(path, suffix_to)
try:
save(img_from, image_to, hdr_from, True)
if not os.path.exists(image_to):
raise Exception('Image of type {} with shape={}/dtype={} has been saved without exception, but the file does not exist.'.format(suffix_to, arr_save.shape, dtype))
except Exception as e:
unsupported_types[suffix_from][suffix_from][ndim][dtype] = e.message
continue
try:
_, hdr_to = load(image_to)
except Exception as e:
unsupported_types[suffix_from][suffix_to][ndim][dtype] = 'Saved testing image of type {} with shape={}/dtype={} could not be loaded. Reason: {}'.format(suffix_to, arr_save.shape, dtype, e.message)
continue
msg = self.__diff(hdr_from, hdr_to)
if msg:
inconsistent_types[suffix_from][suffix_to][ndim][dtype] = msg
else:
consistent_types[suffix_from][suffix_to][ndim].append(dtype)
# remove testing image
if os.path.exists(image_to): os.remove(image_to)
# remove reference image
if os.path.exists(image_to): os.remove(image_to)
except Exception:
if not os.listdir(path): os.rmdir(path)
else: logger.debug('Could not delete temporary directory {}. Is not empty.'.format(path))
raise
if consistent:
print '\nthe following format conversions are meta-data consistent:'
print 'from\tto\tndim\tdtypes'
for suffix_from in consistent_types:
for suffix_to in consistent_types[suffix_from]:
for ndim, dtypes in consistent_types[suffix_from][suffix_to].iteritems():
if list == type(dtypes) and not 0 == len(dtypes):
print '{}\t{}\t{}D\t{}'.format(suffix_from, suffix_to, ndim, map(lambda x: str(x).split('.')[-1][:-2], dtypes))
if inconsistent:
print '\nthe following form conversions are not meta-data consistent:'
print 'from\tto\tndim\tdtype\t\terror'
for suffix_from in inconsistent_types:
for suffix_to in inconsistent_types[suffix_from]:
for ndim in inconsistent_types[suffix_from][suffix_to]:
for dtype, msg in inconsistent_types[suffix_from][suffix_to][ndim].iteritems():
if msg:
print '{}\t{}\t{}D\t{}\t\t{}'.format(suffix_from, suffix_to, ndim, str(dtype).split('.')[-1][:-2], msg)
if unsupported:
print '\nthe following form conversions could not be tested due to errors:'
print 'from\tto\tndim\tdtype\t\terror'
for suffix_from in unsupported_types:
for suffix_to in unsupported_types[suffix_from]:
for ndim in unsupported_types[suffix_from][suffix_to]:
for dtype, msg in unsupported_types[suffix_from][suffix_to][ndim].iteritems():
if msg:
print '{}\t{}\t{}D\t{}\t\t{}'.format(suffix_from, suffix_to, ndim, str(dtype).split('.')[-1][:-2], msg)
