def convert_value(VR, raw_data_element, encoding=default_encoding):
"""Return the converted value (from raw bytes) for the given VR"""
if VR not in converters:
raise NotImplementedError(
"Unknown Value Representation '{0}'".format(VR))
# Look up the function to convert that VR
# Dispatch two cases: a plain converter, or a number one which needs a format string
if isinstance(converters[VR], tuple):
converter, num_format = converters[VR]
else:
converter = converters[VR]
num_format = None
# Ensure that encoding is in the proper 3-element format
if isinstance(encoding, compat.string_types):
encoding = [
encoding,
] * 3
byte_string = raw_data_element.value
is_little_endian = raw_data_element.is_little_endian
is_implicit_VR = raw_data_element.is_implicit_VR
# Not only two cases. Also need extra info if is a raw sequence
# Pass the encoding to the converter if it is a specific VR
try:
if VR == 'PN':
value = converter(byte_string, is_little_endian, encoding=encoding)
elif VR in text_VRs:
# Text VRs use the 2nd specified encoding
value = converter(byte_string,
is_little_endian,
encoding=encoding[1])
elif VR != "SQ":
value = converter(byte_string, is_little_endian, num_format)
else:
value = convert_SQ(byte_string, is_implicit_VR, is_little_endian,
encoding, raw_data_element.value_tell)
except ValueError:
if config.enforce_valid_values:
# The user really wants an exception here
raise
logger.debug('unable to translate tag %s with VR %s' %
(raw_data_element.tag, VR))
for convert_vr in convert_retry_VR_order:
vr = convert_vr
converter = converters[vr]
if vr == VR:
continue
try:
value = convert_value(vr, raw_data_element, encoding)
break
except Exception:
pass
else:
logger.debug('converted tag %s with VR %s' %
(raw_data_element.tag, vr))
value = raw_data_element.value
return value
def read_item(fp):
"""Read and return a single Item in the fragmented data stream"""
try:
tag = fp.read_tag()
except EOFError: # already read delimiter before passing data here, so should just run out
return None
if tag == SequenceDelimiterTag: # No more items, time for sequence to stop reading
length = fp.read_UL()
logger.debug("%04x: Sequence Delimiter, length 0x%x",
fp.tell() - 8, length)
if length != 0:
logger.warning(
"Expected 0x00000000 after delimiter, found 0x%x, at data position 0x%x",
length,
fp.tell() - 4)
return None
if tag != ItemTag:
logger.warning("Expected Item with tag %s at data position 0x%x",
ItemTag,
fp.tell() - 4)
length = fp.read_UL()
else:
length = fp.read_UL()
logger.debug("%04x: Item, length 0x%x", fp.tell() - 8, length)
if length == 0xFFFFFFFF:
raise ValueError(
"Encapsulated data fragment had Undefined Length at data position 0x%x"
% fp.tell() - 4)
item_data = fp.read(length)
return item_data
def __setitem__(self, key, value):
"""Operator for dataset[key]=value. Check consistency, and deal with private tags"""
if not isinstance(
value,
(DataElement,
RawDataElement)): # ok if is subclass, e.g. DeferredDataElement
raise TypeError(
"Dataset contents must be DataElement instances.\n"
"To set a data_element value use data_element.value=val")
tag = Tag(value.tag)
if key != tag:
raise ValueError("data_element.tag must match the dictionary key")
data_element = value
if tag.is_private:
# See PS 3.5-2008 section 7.8.1 (p. 44) for how blocks are reserved
logger.debug("Setting private tag %r" % tag)
private_block = tag.elem >> 8
private_creator_tag = Tag(tag.group, private_block)
if private_creator_tag in self and tag != private_creator_tag:
if isinstance(data_element, RawDataElement):
data_element = DataElement_from_raw(
data_element, self._character_set)
data_element.private_creator = self[private_creator_tag].value
dict.__setitem__(self, tag, data_element)
def __ne__(self, other):
try:
return self.dicom_dataset.SeriesInstanceUID != \
other.dicom_dataset.SeriesInstanceUID
except Exception as e:
logger.debug("trouble comparing two Series", exc_info=e)
return True
def __repr__(self):
try:
output = "\t\t\tSOPInstanceUID = %s:\n" % (self.dicom_dataset.SOPInstanceUID, )
return output
except Exception as e:
logger.debug("trouble getting Series data", exc_info=e)
return "\t\t\tSOPInstanceUID = None\n"
def __eq__(self, other):
try:
selfuid = self.dicom_dataset.SeriesInstanceUID()
otheruid = other.dicom_dataset.SeriesInstanceUID()
return selfuid == otheruid
except Exception as e:
logger.debug("trouble comparing two Series", exc_info=e)
return False
def __ne__(self, other):
try:
selfuid = self.dicom_dataset.StudyInstanceUID()
otheruid = other.dicom_dataset.StudyInstanceUID()
return selfuid != otheruid
except Exception as e:
logger.debug("trouble comparing two Studies", exc_info=e)
return True
def __ne__(self, other):
try:
selfid = self.dicom_dataset.PatientID()
otherid = other.dicom_dataset.PatientID()
return selfid != otherid
except Exception as e:
logger.debug("trouble comparing two patients", exc_info=e)
return True
def __str__(self):
try:
return "Patient: [{0}] {1} ({2})\n".format(
self.dicom_dataset.PatientSex(),
self.dicom_dataset.PatientName(),
self.dicom_dataset.PatientBirthDate())
except Exception as e:
logger.debug("trouble getting image PatientID", exc_info=e)
return "None"
def __repr__(self):
try:
output = f"\tStudyIUID = {self.dicom_dataset.StudyInstanceUID}:\n"
for x in self.series:
output += repr(x)
return output
except Exception as e:
logger.debug("trouble getting Study data", exc_info=e)
return "\tStudyIUID = None\n"
def __repr__(self):
try:
output = "PatientID = %s:\n" % (self.dicom_dataset.PatientID, )
for x in self.studies:
output += repr(x)
return output
except Exception as e:
logger.debug("trouble getting Patient data", exc_info=e)
return "PatientID = None\n"
def __init__(self, fp, stop_when=None, force=False):
"""Read the preamble and meta info and prepare iterator for remainder of file.
Parameters
----------
fp : an open DicomFileLike object, at start of file
force : boolean
Force reading of data. See ``read_file`` for more parameter info.
Adds flags to fp: Big/Little-endian and Implicit/Explicit VR
"""
self.fp = fp
self.stop_when = stop_when
self.preamble = preamble = read_preamble(fp, force)
self.has_header = has_header = (preamble is not None)
self.file_meta_info = Dataset()
if has_header:
self.file_meta_info = file_meta_info = _read_file_meta_info(fp)
transfer_syntax = file_meta_info.TransferSyntaxUID
if transfer_syntax == pydicom.uid.ExplicitVRLittleEndian:
self._is_implicit_VR = False
self._is_little_endian = True
elif transfer_syntax == pydicom.uid.ImplicitVRLittleEndian:
self._is_implicit_VR = True
self._is_little_endian = True
elif transfer_syntax == pydicom.uid.ExplicitVRBigEndian:
self._is_implicit_VR = False
self._is_little_endian = False
elif transfer_syntax == pydicom.uid.DeflatedExplicitVRLittleEndian:
# See PS3.6-2008 A.5 (p 71) -- when written, the entire dataset
# following the file metadata was prepared the normal way,
# then "deflate" compression applied.
# All that is needed here is to decompress and then
# use as normal in a file-like object
zipped = fp.read()
# -MAX_WBITS part is from comp.lang.python answer:
# groups.google.com/group/comp.lang.python/msg/e95b3b38a71e6799
unzipped = zlib.decompress(zipped, -zlib.MAX_WBITS)
fp = BytesIO(unzipped) # a file-like object
self.fp = fp # point to new object
self._is_implicit_VR = False
self._is_little_endian = True
else:
# Any other syntax should be Explicit VR Little Endian,
# e.g. all Encapsulated (JPEG etc) are ExplVR-LE
# by Standard PS 3.5-2008 A.4 (p63)
self._is_implicit_VR = False
self._is_little_endian = True
else: # no header -- make assumptions
fp.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
self._is_little_endian = True
self._is_implicit_VR = True
impl_expl = ("Explicit", "Implicit")[self._is_implicit_VR]
big_little = ("Big", "Little")[self._is_little_endian]
logger.debug("Using {0:s} VR, {1:s} Endian transfer syntax".format(
impl_expl, big_little))
def __init__(self, fp, stop_when=None, force=False):
"""Read the preamble and meta info and prepare iterator for remainder of file.
Parameters
----------
fp : an open DicomFileLike object, at start of file
force : boolean
Force reading of data. See ``read_file`` for more parameter info.
Adds flags to fp: Big/Little-endian and Implicit/Explicit VR
"""
self.fp = fp
self.stop_when = stop_when
self.preamble = preamble = read_preamble(fp, force)
self.has_header = has_header = (preamble is not None)
self.file_meta_info = Dataset()
if has_header:
self.file_meta_info = file_meta_info = _read_file_meta_info(fp)
transfer_syntax = file_meta_info.TransferSyntaxUID
if transfer_syntax == pydicom.uid.ExplicitVRLittleEndian:
self._is_implicit_VR = False
self._is_little_endian = True
elif transfer_syntax == pydicom.uid.ImplicitVRLittleEndian:
self._is_implicit_VR = True
self._is_little_endian = True
elif transfer_syntax == pydicom.uid.ExplicitVRBigEndian:
self._is_implicit_VR = False
self._is_little_endian = False
elif transfer_syntax == pydicom.uid.DeflatedExplicitVRLittleEndian:
# See PS3.6-2008 A.5 (p 71) -- when written, the entire dataset
# following the file metadata was prepared the normal way,
# then "deflate" compression applied.
# All that is needed here is to decompress and then
# use as normal in a file-like object
zipped = fp.read()
# -MAX_WBITS part is from comp.lang.python answer:
# groups.google.com/group/comp.lang.python/msg/e95b3b38a71e6799
unzipped = zlib.decompress(zipped, -zlib.MAX_WBITS)
fp = BytesIO(unzipped) # a file-like object
self.fp = fp # point to new object
self._is_implicit_VR = False
self._is_little_endian = True
else:
# Any other syntax should be Explicit VR Little Endian,
# e.g. all Encapsulated (JPEG etc) are ExplVR-LE
# by Standard PS 3.5-2008 A.4 (p63)
self._is_implicit_VR = False
self._is_little_endian = True
else: # no header -- make assumptions
fp.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
self._is_little_endian = True
self._is_implicit_VR = True
impl_expl = ("Explicit", "Implicit")[self._is_implicit_VR]
big_little = ("Big", "Little")[self._is_little_endian]
logger.debug("Using {0:s} VR, {1:s} Endian transfer syntax".format(
impl_expl, big_little))
def __str__(self):
try:
return "\tStudy: [{0}] {1} ({2})\n".format(
self.dicom_dataset.StudyID(),
self.dicom_dataset.StudyDescription(),
self.dicom_dataset.StudyDate(),
)
except Exception as e:
logger.debug("trouble getting image StudyInstanceUID", exc_info=e)
return "None"
def convert_pixel_data(self):
"""Convert the Pixel Data to a numpy array internally.
Returns
-------
None
Converted pixel data is stored internally in the dataset.
If a compressed image format, the image is decompressed,
and any related data elements are changed accordingly.
"""
# Check if already have converted to a NumPy array
# Also check if self.PixelData has changed. If so, get new NumPy array
already_have = True
if not hasattr(self, "_pixel_array"):
already_have = False
elif self._pixel_id != id(self.PixelData):
already_have = False
if not already_have:
last_exception = None
successfully_read_pixel_data = False
for x in [
h for h in pydicom.config.image_handlers
if h and h.supports_transfer_syntax(self)
]:
try:
pixel_array = x.get_pixeldata(self)
self._pixel_array = self._reshape_pixel_array(pixel_array)
if x.needs_to_convert_to_RGB(self):
self._pixel_array = self._convert_YBR_to_RGB(
self._pixel_array)
successfully_read_pixel_data = True
break
except Exception as e:
logger.debug("Trouble with", exc_info=e)
last_exception = e
continue
if not successfully_read_pixel_data:
handlers_tried = " ".join(
[str(x) for x in pydicom.config.image_handlers])
logger.info("%s did not support this transfer syntax",
handlers_tried)
self._pixel_array = None
self._pixel_id = None
if last_exception:
raise last_exception
else:
msg = ("No available image handler could "
"decode this transfer syntax {}".format(
self.file_meta.TransferSyntaxUID.name))
raise NotImplementedError(msg)
# is this guaranteed to work if memory is re-used??
self._pixel_id = id(self.PixelData)
def __str__(self):
try:
return "\t\tSeries: [{0} {1}] {2} ({3} {4})\n".format(
self.dicom_dataset.Modality(),
self.dicom_dataset.ProtoclName(),
self.dicom_dataset.SeriesDescription(),
self.dicom_dataset.BodyPasrtExamined(),
self.dicom_dataset.PatientPosition())
except Exception as e:
logger.debug("trouble getting image SeriesInstanceUID", exc_info=e)
return "None"
def __str__(self):
try:
return "\t\t\tImage:[{0} {1} {2}] {3} ({4} {5})\n".format(
self.dicom_dataset.SliceLocation(),
self.dicom_dataset.ImagePositionPatient(),
self.dicom_dataset.ImageOrientationPatient(),
self.dicom_dataset.Shape(),
self.dicom_dataset.ImageSpacing(),
)
except Exception as e:
logger.debug("trouble getting image SOPInstanceUID", exc_info=e)
return "None"
def convert_value(VR, raw_data_element, encoding=default_encoding):
"""Return the converted value (from raw bytes) for the given VR"""
if VR not in converters:
raise NotImplementedError("Unknown Value Representation '{0}'".format(VR))
# Look up the function to convert that VR
# Dispatch two cases: a plain converter, or a number one which needs a format string
if isinstance(converters[VR], tuple):
converter, num_format = converters[VR]
else:
converter = converters[VR]
num_format = None
# Ensure that encoding is in the proper 3-element format
if isinstance(encoding, compat.string_types):
encoding = [encoding, ] * 3
byte_string = raw_data_element.value
is_little_endian = raw_data_element.is_little_endian
is_implicit_VR = raw_data_element.is_implicit_VR
# Not only two cases. Also need extra info if is a raw sequence
# Pass the encoding to the converter if it is a specific VR
try:
if VR == 'PN':
value = converter(byte_string, is_little_endian, encoding=encoding)
elif VR in text_VRs:
# Text VRs use the 2nd specified encoding
value = converter(byte_string, is_little_endian, encoding=encoding[1])
elif VR != "SQ":
value = converter(byte_string, is_little_endian, num_format)
else:
value = convert_SQ(byte_string, is_implicit_VR, is_little_endian,
encoding, raw_data_element.value_tell)
except ValueError:
if config.enforce_valid_values:
# The user really wants an exception here
raise
logger.debug('unable to translate tag %s with VR %s' % (raw_data_element.tag, VR))
for convert_vr in convert_retry_VR_order:
vr = convert_vr
converter = converters[vr]
if vr == VR:
continue
try:
value = convert_value(vr, raw_data_element, encoding)
break
except Exception:
pass
else:
logger.debug('converted tag %s with VR %s' % (raw_data_element.tag, vr))
value = raw_data_element.value
return value
def __repr__(self):
try:
output = "Patient: [{0}] {1} ({2})\n".format(
self.dicom_dataset.PatientSex(),
self.dicom_dataset.PatientName(),
self.dicom_dataset.PatientBirthDate())
for x in self.studies:
output += repr(x)
return output
except Exception as e:
logger.debug("trouble getting Patient data", exc_info=e)
return "Patient: N/A\n"
def convert_pixel_data(self):
"""Convert the Pixel Data to a numpy array internally.
Returns
-------
None
Converted pixel data is stored internally in the dataset.
If a compressed image format, the image is decompressed,
and any related data elements are changed accordingly.
"""
# Check if already have converted to a NumPy array
# Also check if self.PixelData has changed. If so, get new NumPy array
already_have = True
if not hasattr(self, "_pixel_array"):
already_have = False
elif self._pixel_id != id(self.PixelData):
already_have = False
if not already_have:
last_exception = None
successfully_read_pixel_data = False
for x in [h for h in pydicom.config.image_handlers
if h and h.supports_transfer_syntax(self)]:
try:
pixel_array = x.get_pixeldata(self)
self._pixel_array = self._reshape_pixel_array(pixel_array)
if x.needs_to_convert_to_RGB(self):
self._pixel_array = self._convert_YBR_to_RGB(
self._pixel_array
)
successfully_read_pixel_data = True
break
except Exception as e:
logger.debug("Trouble with", exc_info=e)
last_exception = e
continue
if not successfully_read_pixel_data:
handlers_tried = " ".join(
[str(x) for x in pydicom.config.image_handlers])
logger.info("%s did not support this transfer syntax",
handlers_tried)
self._pixel_array = None
self._pixel_id = None
if last_exception:
raise last_exception
else:
msg = ("No available image handler could "
"decode this transfer syntax {}".format(
self.file_meta.TransferSyntaxUID))
raise NotImplementedError(msg)
# is this guaranteed to work if memory is re-used??
self._pixel_id = id(self.PixelData)
def __repr__(self):
try:
output = "\tStudy: [{0}] {1} ({2})\n".format(
self.dicom_dataset.StudyID(),
self.dicom_dataset.StudyDescription(),
self.dicom_dataset.StudyDate(),
)
for x in self.series:
output += repr(x)
return output
except Exception as e:
logger.debug("trouble getting Study data", exc_info=e)
return "\tStudy: N/A\n"
def __repr__(self):
try:
output = "\t\t\tImage:[{0}] {1} {2} {3} ({4} {5})\n".format(
self.dicom_dataset.SliceLocation(),
self.dicom_dataset.ImagePositionPatient(),
self.dicom_dataset.ImageOrientationPatient(),
self.dicom_dataset.Shape(),
self.dicom_dataset.ImageSpacing(),
self.dicom_dataset.VoxelSize(),
)
return output
except Exception as e:
logger.debug("trouble getting Series data", exc_info=e)
return "\t\t\tImage: N/A\n"
def __repr__(self):
try:
output = "\t\tSeries: [{0} {1}] {2} ({3} {4})\n".format(
self.dicom_dataset.Modality(),
self.dicom_dataset.ProtocolName(),
self.dicom_dataset.SeriesDescription(),
self.dicom_dataset.BodyPartExamined(),
self.dicom_dataset.PatientPosition())
for x in self.images:
output += repr(x)
return output
except Exception as e:
logger.debug("trouble getting Series data", exc_info=e)
return "\t\tSeries: N/A\n"
def read_preamble(fp: BinaryIO, force: bool) -> Optional[bytes]:
"""Return the 128-byte DICOM preamble in `fp` if present.
`fp` should be positioned at the start of the file-like. If the preamble
and prefix are found then after reading `fp` will be positioned at the
first byte after the prefix (byte offset 133). If either the preamble or
prefix are missing and `force` is ``True`` then after reading `fp` will be
positioned at the start of the file-like.
Parameters
----------
fp : file-like object
The file-like to read the preamble from.
force : bool
Flag to force reading of a file even if no header is found.
Returns
-------
preamble : bytes or None
The 128-byte DICOM preamble will be returned if the appropriate prefix
('DICM') is found at byte offset 128. Returns ``None`` if the 'DICM'
prefix is not found and `force` is ``True``.
Raises
------
InvalidDicomError
If `force` is ``False`` and no appropriate header information found.
Notes
-----
Also reads past the 'DICM' marker. Rewinds file to the beginning if
no header found.
"""
logger.debug("Reading File Meta Information preamble...")
preamble = fp.read(128)
if config.debugging:
sample = bytes2hex(preamble[:8]) + "..." + bytes2hex(preamble[-8:])
logger.debug(f"{fp.tell() - 128:08x}: {sample}")
logger.debug("Reading File Meta Information prefix...")
magic = fp.read(4)
if magic != b"DICM" and force:
logger.info(
"File is not conformant with the DICOM File Format: 'DICM' "
"prefix is missing from the File Meta Information header "
"or the header itself is missing. Assuming no header and "
"continuing.")
fp.seek(0)
return None
if magic != b"DICM" and not force:
raise InvalidDicomError(
"File is missing DICOM File Meta Information header or the 'DICM' "
"prefix is missing from the header. Use force=True to force "
"reading.")
else:
logger.debug(f"{fp.tell() - 4:08x}: 'DICM' prefix found")
return preamble
def add_dataset(self, dataset):
try:
if self.dicom_dataset.SeriesInstanceUID == dataset.SeriesInstanceUID:
for x in self.images:
if x.SOPInstanceUID == dataset.SOPInstanceUID:
logger.debug("Image is already part of this series")
break
else:
self.images.append(Image(dicom_dataset=dataset))
else:
raise KeyError("Not the same SeriesInstanceUIDs")
except Exception as e:
logger.debug("trouble adding image to series", exc_info=e)
raise KeyError("Not the same SeriesInstanceUIDs")
def read_preamble(fp, force):
"""Return the 128-byte DICOM preamble in `fp` if present.
`fp` should be positioned at the start of the file-like. If the preamble
and prefix are found then after reading `fp` will be positioned at the
first byte after the prefix (byte offset 133). If either the preamble or
prefix are missing and `force` is True then after reading `fp` will be
positioned at the start of the file-like.
Parameters
----------
fp : file-like object
The file-like to read the preamble from.
force : bool
Flag to force reading of a file even if no header is found.
Returns
-------
preamble : str/bytes or None
The 128-byte DICOM preamble will be returned if the appropriate prefix
('DICM') is found at byte offset 128. Returns None if the 'DICM' prefix
is not found and `force` is True.
Raises
------
InvalidDicomError
If `force` is False and no appropriate header information found.
Notes
-----
Also reads past the 'DICM' marker. Rewinds file to the beginning if
no header found.
"""
logger.debug("Reading File Meta Information preamble...")
preamble = fp.read(128)
if config.debugging:
sample = bytes2hex(preamble[:8]) + "..." + bytes2hex(preamble[-8:])
logger.debug("{0:08x}: {1}".format(fp.tell() - 128, sample))
logger.debug("Reading File Meta Information prefix...")
magic = fp.read(4)
if magic != b"DICM" and force:
logger.info(
"File is not conformant with the DICOM File Format: 'DICM' "
"prefix is missing from the File Meta Information header "
"or the header itself is missing. Assuming no header and "
"continuing.")
preamble = None
fp.seek(0)
elif magic != b"DICM" and not force:
raise InvalidDicomError("File is missing DICOM File Meta Information "
"header or the 'DICM' prefix is missing from "
"the header. Use force=True to force reading.")
else:
logger.debug("{0:08x}: 'DICM' prefix found".format(fp.tell() - 4))
return preamble
def __setitem__(self, key, value):
"""Operator for Dataset[key] = value.
Check consistency, and deal with private tags.
Parameters
----------
key : int
The tag for the element to be added to the Dataset.
value : pydicom.dataelem.DataElement or pydicom.dataelem.RawDataElement
The element to add to the Dataset.
Raises
------
NotImplementedError
If `key` is a slice.
ValueError
If the `key` value doesn't match DataElement.tag.
"""
if isinstance(key, slice):
raise NotImplementedError('Slicing is not supported for setting '
'Dataset elements.')
# OK if is subclass, e.g. DeferredDataElement
if not isinstance(value, (DataElement, RawDataElement)):
raise TypeError("Dataset contents must be DataElement instances.")
if isinstance(value.tag, BaseTag):
tag = value.tag
else:
tag = Tag(value.tag)
if key != tag:
raise ValueError("DataElement.tag must match the dictionary key")
data_element = value
if tag.is_private:
# See PS 3.5-2008 section 7.8.1 (p. 44) for how blocks are reserved
logger.debug("Setting private tag %r" % tag)
private_block = tag.elem >> 8
private_creator_tag = Tag(tag.group, private_block)
if private_creator_tag in self and tag != private_creator_tag:
if isinstance(data_element, RawDataElement):
data_element = DataElement_from_raw(
data_element, self._character_set)
data_element.private_creator = self[private_creator_tag].value
dict.__setitem__(self, tag, data_element)
def read_deferred_data_element(fileobj_type, filename, timestamp,
raw_data_elem):
"""Read the previously deferred value from the file into memory
and return a raw data element"""
logger.debug("Reading deferred element %r" % str(raw_data_elem.tag))
# If it wasn't read from a file, then return an error
if filename is None:
raise IOError("Deferred read -- original filename not stored. "
"Cannot re-open")
# Check that the file is the same as when originally read
if not os.path.exists(filename):
raise IOError(u"Deferred read -- original file "
"{0:s} is missing".format(filename))
if timestamp is not None:
statinfo = os.stat(filename)
if statinfo.st_mtime != timestamp:
warnings.warn("Deferred read warning -- file modification time "
"has changed.")
# Open the file, position to the right place
# fp = self.typefileobj(self.filename, "rb")
fp = fileobj_type(filename, 'rb')
is_implicit_VR = raw_data_elem.is_implicit_VR
is_little_endian = raw_data_elem.is_little_endian
offset = data_element_offset_to_value(is_implicit_VR, raw_data_elem.VR)
fp.seek(raw_data_elem.value_tell - offset)
elem_gen = data_element_generator(fp,
is_implicit_VR,
is_little_endian,
defer_size=None)
# Read the data element and check matches what was stored before
data_elem = next(elem_gen)
fp.close()
if data_elem.VR != raw_data_elem.VR:
raise ValueError("Deferred read VR {0:s} does not match "
"original {1:s}".format(data_elem.VR,
raw_data_elem.VR))
if data_elem.tag != raw_data_elem.tag:
raise ValueError("Deferred read tag {0!r} does not match "
"original {1!r}".format(data_elem.tag,
raw_data_elem.tag))
# Everything is ok, now this object should act like usual DataElement
return data_elem
def read_deferred_data_element(fileobj_type, filename, timestamp,
raw_data_elem):
"""Read the previously deferred value from the file into memory
and return a raw data element"""
logger.debug("Reading deferred element %r" % str(raw_data_elem.tag))
# If it wasn't read from a file, then return an error
if filename is None:
raise IOError("Deferred read -- original filename not stored. "
"Cannot re-open")
# Check that the file is the same as when originally read
if not os.path.exists(filename):
raise IOError(u"Deferred read -- original file "
"{0:s} is missing".format(filename))
if timestamp is not None:
statinfo = os.stat(filename)
if statinfo.st_mtime != timestamp:
warnings.warn("Deferred read warning -- file modification time "
"has changed.")
# Open the file, position to the right place
# fp = self.typefileobj(self.filename, "rb")
fp = fileobj_type(filename, 'rb')
is_implicit_VR = raw_data_elem.is_implicit_VR
is_little_endian = raw_data_elem.is_little_endian
offset = data_element_offset_to_value(is_implicit_VR, raw_data_elem.VR)
fp.seek(raw_data_elem.value_tell - offset)
elem_gen = data_element_generator(fp, is_implicit_VR, is_little_endian,
defer_size=None)
# Read the data element and check matches what was stored before
data_elem = next(elem_gen)
fp.close()
if data_elem.VR != raw_data_elem.VR:
raise ValueError("Deferred read VR {0:s} does not match "
"original {1:s}".format(data_elem.VR,
raw_data_elem.VR))
if data_elem.tag != raw_data_elem.tag:
raise ValueError("Deferred read tag {0!r} does not match "
"original {1!r}".format(data_elem.tag,
raw_data_elem.tag))
# Everything is ok, now this object should act like usual DataElement
return data_elem
def __setitem__(self, key, value):
"""Operator for Dataset[key] = value.
Check consistency, and deal with private tags.
Parameters
----------
key : int
The tag for the element to be added to the Dataset.
value : pydicom.dataelem.DataElement or pydicom.dataelem.RawDataElement
The element to add to the Dataset.
Raises
------
NotImplementedError
If `key` is a slice.
ValueError
If the `key` value doesn't match DataElement.tag.
"""
if isinstance(key, slice):
raise NotImplementedError('Slicing is not supported for setting '
'Dataset elements.')
# OK if is subclass, e.g. DeferredDataElement
if not isinstance(value, (DataElement, RawDataElement)):
raise TypeError("Dataset contents must be DataElement instances.")
tag = Tag(value.tag)
if key != tag:
raise ValueError("DataElement.tag must match the dictionary key")
data_element = value
if tag.is_private:
# See PS 3.5-2008 section 7.8.1 (p. 44) for how blocks are reserved
logger.debug("Setting private tag %r" % tag)
private_block = tag.elem >> 8
private_creator_tag = Tag(tag.group, private_block)
if private_creator_tag in self and tag != private_creator_tag:
if isinstance(data_element, RawDataElement):
data_element = DataElement_from_raw(
data_element, self._character_set)
data_element.private_creator = self[private_creator_tag].value
dict.__setitem__(self, tag, data_element)
def __setitem__(self, key, value):
"""Operator for dataset[key]=value. Check consistency, and deal with private tags"""
if not isinstance(value, (DataElement, RawDataElement)): # ok if is subclass, e.g. DeferredDataElement
raise TypeError("Dataset contents must be DataElement instances.\n"
"To set a data_element value use data_element.value=val")
tag = Tag(value.tag)
if key != tag:
raise ValueError("data_element.tag must match the dictionary key")
data_element = value
if tag.is_private:
# See PS 3.5-2008 section 7.8.1 (p. 44) for how blocks are reserved
logger.debug("Setting private tag %r" % tag)
private_block = tag.elem >> 8
private_creator_tag = Tag(tag.group, private_block)
if private_creator_tag in self and tag != private_creator_tag:
if isinstance(data_element, RawDataElement):
data_element = DataElement_from_raw(data_element, self._character_set)
data_element.private_creator = self[private_creator_tag].value
dict.__setitem__(self, tag, data_element)
def absorb_delimiter_item(
fp: BinaryIO, is_little_endian: bool, delimiter: BaseTag
) -> None:
"""Read (and ignore) undefined length sequence or item terminators."""
if is_little_endian:
struct_format = "<HHL"
else:
struct_format = ">HHL"
group, elem, length = unpack(struct_format, fp.read(8))
tag = TupleTag((group, elem))
if tag != delimiter:
logger.warn(
"Did not find expected delimiter "
f"'{dictionary_description(delimiter)}', instead found "
f"{tag} at file position 0x{fp.tell() - 8:X}"
)
fp.seek(fp.tell() - 8)
return
logger.debug("%04x: Found Delimiter '%s'", fp.tell() - 8,
dictionary_description(delimiter))
if length == 0:
logger.debug("%04x: Read 0 bytes after delimiter", fp.tell() - 4)
else:
logger.debug("%04x: Expected 0x00000000 after delimiter, found 0x%x",
fp.tell() - 4, length)
def read_sequence_item(fp: BinaryIO,
is_implicit_VR: bool,
is_little_endian: bool,
encoding: Union[str, MutableSequence[str]],
offset: int = 0) -> Optional[Dataset]:
"""Read and return a single :class:`~pydicom.sequence.Sequence` item, i.e.
a :class:`~pydicom.dataset.Dataset`.
"""
seq_item_tell = fp.tell() + offset
if is_little_endian:
tag_length_format = "<HHL"
else:
tag_length_format = ">HHL"
try:
bytes_read = fp.read(8)
group, element, length = unpack(tag_length_format, bytes_read)
except BaseException:
raise IOError(
f"No tag to read at file position {fp.tell() + offset:X}")
tag = (group, element)
if tag == SequenceDelimiterTag: # No more items, time to stop reading
logger.debug(f"{fp.tell() - 8 + offset:08x}: End of Sequence")
if length != 0:
logger.warning(
f"Expected 0x00000000 after delimiter, found 0x{length:X}, "
f"at position 0x{fp.tell() - 4 + offset:X}")
return None
if tag != ItemTag:
logger.warning(
f"Expected sequence item with tag {ItemTag} at file position "
f"0x{fp.tell() - 4 + offset:X}")
else:
logger.debug(f"{fp.tell() - 4 + offset:08x}: {bytes2hex(bytes_read)} "
"Found Item tag (start of item)")
if length == 0xFFFFFFFF:
ds = read_dataset(fp,
is_implicit_VR,
is_little_endian,
bytelength=None,
parent_encoding=encoding,
at_top_level=False)
ds.is_undefined_length_sequence_item = True
else:
ds = read_dataset(fp,
is_implicit_VR,
is_little_endian,
length,
parent_encoding=encoding,
at_top_level=False)
ds.is_undefined_length_sequence_item = False
logger.debug(f"{fp.tell() + offset:08X}: Finished sequence item")
ds.seq_item_tell = seq_item_tell
return ds
def read_item(fp):
"""Read and return a single Item in the fragmented data stream"""
try:
tag = fp.read_tag()
except EOFError: # already read delimiter before passing data here, so should just run out
return None
if tag == SequenceDelimiterTag: # No more items, time for sequence to stop reading
length = fp.read_UL()
logger.debug("%04x: Sequence Delimiter, length 0x%x", fp.tell() - 8, length)
if length != 0:
logger.warning("Expected 0x00000000 after delimiter, found 0x%x, at data position 0x%x", length, fp.tell() - 4)
return None
if tag != ItemTag:
logger.warning("Expected Item with tag %s at data position 0x%x", ItemTag, fp.tell() - 4)
length = fp.read_UL()
else:
length = fp.read_UL()
logger.debug("%04x: Item, length 0x%x", fp.tell() - 8, length)
if length == 0xFFFFFFFF:
raise ValueError("Encapsulated data fragment had Undefined Length at data position 0x%x" % fp.tell() - 4)
item_data = fp.read(length)
return item_data
def convert_value(VR, raw_data_element, encodings=None):
"""Return the converted value (from raw bytes) for the given VR"""
if VR not in converters:
message = "Unknown Value Representation '{0}'".format(VR)
raise NotImplementedError(message)
# Look up the function to convert that VR
# Dispatch two cases: a plain converter,
# or a number one which needs a format string
if isinstance(converters[VR], tuple):
converter, num_format = converters[VR]
else:
converter = converters[VR]
num_format = None
# Ensure that encodings is a list
encodings = encodings or [default_encoding]
if isinstance(encodings, compat.string_types):
encodings = [encodings]
byte_string = raw_data_element.value
is_little_endian = raw_data_element.is_little_endian
is_implicit_VR = raw_data_element.is_implicit_VR
# Not only two cases. Also need extra info if is a raw sequence
# Pass all encodings to the converter if needed
try:
if VR in text_VRs or VR == 'PN':
value = converter(byte_string, encodings=encodings)
elif VR != "SQ":
value = converter(byte_string, is_little_endian, num_format)
else:
value = convert_SQ(byte_string, is_implicit_VR, is_little_endian,
encodings, raw_data_element.value_tell)
except ValueError:
if config.enforce_valid_values:
# The user really wants an exception here
raise
logger.debug('unable to translate tag %s with VR %s' %
(raw_data_element.tag, VR))
for vr in convert_retry_VR_order:
if vr == VR:
continue
try:
value = convert_value(vr, raw_data_element, encodings)
logger.debug('converted value for tag %s with VR %s' %
(raw_data_element.tag, vr))
break
except Exception:
pass
else:
logger.debug('Could not convert value for tag %s with any VR '
'in the convert_retry_VR_order list' %
raw_data_element.tag)
value = raw_data_element.value
return value
def read_sequence_item(fp,
is_implicit_VR,
is_little_endian,
encoding,
offset=0):
"""Read and return a single :class:`~pydicom.sequence.Sequence` item, i.e.
a :class:`~pydicom.dataset.Dataset`.
"""
seq_item_tell = fp.tell() + offset
if is_little_endian:
tag_length_format = "<HHL"
else:
tag_length_format = ">HHL"
try:
bytes_read = fp.read(8)
group, element, length = unpack(tag_length_format, bytes_read)
except BaseException:
raise IOError("No tag to read at file position "
"{0:05x}".format(fp.tell() + offset))
tag = (group, element)
if tag == SequenceDelimiterTag: # No more items, time to stop reading
logger.debug("{0:08x}: {1}".format(fp.tell() - 8 + offset,
"End of Sequence"))
if length != 0:
logger.warning("Expected 0x00000000 after delimiter, found 0x%x, "
"at position 0x%x" %
(length, fp.tell() - 4 + offset))
return None
if tag != ItemTag:
logger.warning("Expected sequence item with tag %s at file position "
"0x%x" % (ItemTag, fp.tell() - 4 + offset))
else:
logger.debug("{0:08x}: {1} Found Item tag (start of item)".format(
fp.tell() - 4 + offset, bytes2hex(bytes_read)))
if length == 0xFFFFFFFF:
ds = read_dataset(fp,
is_implicit_VR,
is_little_endian,
bytelength=None,
parent_encoding=encoding,
at_top_level=False)
ds.is_undefined_length_sequence_item = True
else:
ds = read_dataset(fp,
is_implicit_VR,
is_little_endian,
length,
parent_encoding=encoding,
at_top_level=False)
ds.is_undefined_length_sequence_item = False
logger.debug("%08x: Finished sequence item" % (fp.tell() + offset, ))
ds.seq_item_tell = seq_item_tell
return ds
def read_preamble(fp, force):
"""Return the 128-byte DICOM preamble in `fp` if present.
Parameters
----------
fp : file-like object
The file-like to read the preamble from.
force : bool
Flag to force reading of a file even if no header is found.
Returns
-------
preamble : str/bytes or None
The 128-byte DICOM preamble will be returned if the appropriate prefix
('DICM') is found at byte offset 128. Returns None if the 'DICM' prefix
is not found and `force` is True.
Raises
------
InvalidDicomError
If `force` is False and no appropriate header information found.
Notes
-----
Also reads past the 'DICM' marker. Rewinds file to the beginning if
no header found.
"""
logger.debug("Reading preamble...")
preamble = fp.read(0x80)
if config.debugging:
sample = bytes2hex(preamble[:8]) + "..." + bytes2hex(preamble[-8:])
logger.debug("{0:08x}: {1}".format(fp.tell() - 0x80, sample))
magic = fp.read(4)
if magic != b"DICM":
if force:
logger.info(
"File is not a conformant DICOM file; 'DICM' prefix is "
"missing from the file header or the header is "
"missing. Assuming no header and continuing.")
preamble = None
fp.seek(0)
else:
raise InvalidDicomError("File is missing DICOM header or 'DICM' "
"prefix is missing from the header. Use "
"force=True to force reading.")
else:
logger.debug("{0:08x}: 'DICM' prefix found".format(fp.tell() - 4))
return preamble
def add_dataset(self, dataset):
try:
if self.dicom_dataset.StudyInstanceUID == dataset.StudyInstanceUID:
for x in self.series:
try:
x.add_dataset(dataset)
logger.debug("Part of this series")
break
except Exception as e:
logger.debug("Not part of this series")
else:
self.series.append(Series(dicom_dataset=dataset))
else:
raise KeyError("Not the same StudyInstanceUIDs")
except Exception as e:
logger.debug("trouble adding series to study", exc_info=e)
raise KeyError("Not the same StudyInstanceUIDs")
def read_preamble(fp, force):
"""Read and return the DICOM preamble.
Parameters
----------
fp : file-like object
force : boolean
Flag to force reading of a file even if no header is found.
Returns
-------
preamble : DICOM preamble, None
The DICOM preamble will be returned if appropriate
header ('DICM') is found. Returns None if no header
is found.
Raises
------
InvalidDicomError
If force flag is false and no appropriate header information
found.
Notes
-----
Also reads past the 'DICM' marker. Rewinds file to the beginning if
no header found.
"""
logger.debug("Reading preamble...")
preamble = fp.read(0x80)
if config.debugging:
sample = bytes2hex(preamble[:8]) + "..." + bytes2hex(preamble[-8:])
logger.debug("{0:08x}: {1}".format(fp.tell() - 0x80, sample))
magic = fp.read(4)
if magic != b"DICM":
if force:
logger.info("File is not a standard DICOM file; 'DICM' header is "
"missing. Assuming no header and continuing")
preamble = None
fp.seek(0)
else:
raise InvalidDicomError("File is missing 'DICM' marker. "
"Use force=True to force reading")
else:
logger.debug("{0:08x}: 'DICM' marker found".format(fp.tell() - 4))
return preamble
def absorb_delimiter_item(fp, is_little_endian, delimiter):
"""Read (and ignore) undefined length sequence or item terminators."""
if is_little_endian:
struct_format = "<HHL"
else:
struct_format = ">HHL"
group, elem, length = unpack(struct_format, fp.read(8))
tag = TupleTag((group, elem))
if tag != delimiter:
msg = "Did not find expected delimiter '%s'" % dictionary_description(delimiter)
msg += ", instead found %s at file position 0x%x" % (str(tag), fp.tell() - 8)
logger.warn(msg)
fp.seek(fp.tell() - 8)
return
logger.debug("%04x: Found Delimiter '%s'", fp.tell() - 8, dictionary_description(delimiter))
if length == 0:
logger.debug("%04x: Read 0 bytes after delimiter", fp.tell() - 4)
else:
logger.debug("%04x: Expected 0x00000000 after delimiter, found 0x%x", fp.tell() - 4, length)
def read_sequence_item(fp, is_implicit_VR, is_little_endian, encoding, offset=0):
"""Read and return a single sequence item, i.e. a Dataset"""
seq_item_tell = fp.tell() + offset
if is_little_endian:
tag_length_format = "<HHL"
else:
tag_length_format = ">HHL"
try:
bytes_read = fp.read(8)
group, element, length = unpack(tag_length_format, bytes_read)
except:
raise IOError("No tag to read at file position " "{0:05x}".format(fp.tell() + offset))
tag = (group, element)
if tag == SequenceDelimiterTag: # No more items, time to stop reading
logger.debug("{0:08x}: {1}".format(fp.tell() - 8 + offset, "End of Sequence"))
if length != 0:
logger.warning(
"Expected 0x00000000 after delimiter, found 0x%x, "
"at position 0x%x" % (length, fp.tell() - 4 + offset)
)
return None
if tag != ItemTag:
logger.warning(
"Expected sequence item with tag %s at file position " "0x%x" % (ItemTag, fp.tell() - 4 + offset)
)
else:
logger.debug(
"{0:08x}: {1} Found Item tag (start of item)".format(fp.tell() - 4 + offset, bytes2hex(bytes_read))
)
if length == 0xFFFFFFFF:
ds = read_dataset(
fp, is_implicit_VR, is_little_endian, bytelength=None, parent_encoding=encoding, value_tell_offset=offset
)
ds.is_undefined_length_sequence_item = True
else:
ds = read_dataset(
fp, is_implicit_VR, is_little_endian, length, parent_encoding=encoding, value_tell_offset=offset
)
ds.is_undefined_length_sequence_item = False
logger.debug("%08x: Finished sequence item" % (fp.tell() + offset,))
ds.seq_item_tell = seq_item_tell
return ds
def keyword_for_tag(tag):
"""Return the DICOM keyword for the given tag.
Will return GroupLength for group length tags,
and returns empty string ("") if the tag
doesn't exist in the dictionary.
"""
try:
return dictionary_keyword(tag)
except KeyError:
return ""
# Provide for the 'reverse' lookup. Given the keyword, what is the tag?
logger.debug("Reversing DICOM dictionary so can look up tag from a keyword...")
keyword_dict = dict([(dictionary_keyword(tag), tag)
for tag in DicomDictionary])
def tag_for_keyword(keyword):
"""Return the dicom tag corresponding to keyword,
or None if none exist."""
return keyword_dict.get(keyword)
def repeater_has_tag(tag):
"""Return True if the DICOM repeaters dictionary
has an entry for `tag`."""
return (mask_match(tag) in RepeatersDictionary)
def dcmread(fp, defer_size=None, stop_before_pixels=False,
force=False, specific_tags=None):
"""Read and parse a DICOM dataset stored in the DICOM File Format.
Read a DICOM dataset stored in accordance with the DICOM File Format
(DICOM Standard Part 10 Section 7). If the dataset is not stored in
accordance with the File Format (i.e. the preamble and prefix are missing,
there are missing required Type 1 File Meta Information Group elements
or the entire File Meta Information is missing) then you will have to
set `force` to True.
Parameters
----------
fp : str or file-like
Either a file-like object, or a string containing the file name. If a
file-like object, the caller is responsible for closing it.
defer_size : int or str or None
If None (default), all elements read into memory. If specified, then if
a data element's stored value is larger than `defer_size`, the value is
not read into memory until it is accessed in code. Specify an integer
(bytes), or a string value with units, e.g. "512 KB", "2 MB".
stop_before_pixels : bool
If False (default), the full file will be read and parsed. Set True to
stop before reading (7FE0,0010) 'Pixel Data' (and all subsequent
elements).
force : bool
If False (default), raises an InvalidDicomError if the file is missing
the File Meta Information header. Set to True to force reading even if
no File Meta Information header is found.
specific_tags : list or None
If not None, only the tags in the list are returned. The list
elements can be tags or tag names. Note that the tag Specific
Character Set is always returned if present - this ensures correct
decoding of returned text values.
Returns
-------
FileDataset
An instance of FileDataset that represents a parsed DICOM file.
Raises
------
InvalidDicomError
If `force` is True and the file is not a valid DICOM file.
See Also
--------
pydicom.dataset.FileDataset
Data class that is returned.
pydicom.filereader.read_partial
Only read part of a DICOM file, stopping on given conditions.
Examples
--------
Read and return a dataset stored in accordance with the DICOM File Format:
>>> ds = pydicom.dcmread("rtplan.dcm")
>>> ds.PatientName
Read and return a dataset not in accordance with the DICOM File Format:
>>> ds = pydicom.dcmread("rtplan.dcm", force=True)
>>> ds.PatientName
Use within a context manager:
>>> with pydicom.dcmread("rtplan.dcm") as ds:
>>> ds.PatientName
"""
# Open file if not already a file object
caller_owns_file = True
if isinstance(fp, compat.string_types):
# caller provided a file name; we own the file handle
caller_owns_file = False
try:
logger.debug(u"Reading file '{0}'".format(fp))
except Exception:
logger.debug("Reading file '{0}'".format(fp))
fp = open(fp, 'rb')
if config.debugging:
logger.debug("\n" + "-" * 80)
logger.debug("Call to dcmread()")
msg = ("filename:'%s', defer_size='%s', "
"stop_before_pixels=%s, force=%s, specific_tags=%s")
logger.debug(msg % (fp.name, defer_size, stop_before_pixels,
force, specific_tags))
if caller_owns_file:
logger.debug("Caller passed file object")
else:
logger.debug("Caller passed file name")
logger.debug("-" * 80)
# Convert size to defer reading into bytes
defer_size = size_in_bytes(defer_size)
# Iterate through all items and store them --include file meta if present
stop_when = None
if stop_before_pixels:
stop_when = _at_pixel_data
try:
dataset = read_partial(fp, stop_when, defer_size=defer_size,
force=force, specific_tags=specific_tags)
finally:
if not caller_owns_file:
fp.close()
# XXX need to store transfer syntax etc.
return dataset
def _read_file_meta_info(fp):
"""Return the file meta information.
fp must be set after the 128 byte preamble and 'DICM' marker
"""
# File meta info always LittleEndian, Explicit VR. After will change these
# to the transfer syntax values set in the meta info
# Get group length data element, whose value is the length of the meta_info
fp_save = fp.tell() # in case need to rewind
debugging = config.debugging
if debugging:
logger.debug("Try to read group length info...")
bytes_read = fp.read(8)
group, elem, VR, length = unpack("<HH2sH", bytes_read)
if debugging:
debug_msg = "{0:08x}: {1}".format(fp.tell() - 8, bytes2hex(bytes_read))
if not in_py2:
VR = VR.decode(default_encoding)
if VR in extra_length_VRs:
bytes_read = fp.read(4)
length = unpack("<L", bytes_read)[0]
if debugging:
debug_msg += " " + bytes2hex(bytes_read)
if debugging:
debug_msg = "{0:<47s} ({1:04x}, {2:04x}) {3:2s} Length: {4:d}".format(
debug_msg, group, elem, VR, length)
logger.debug(debug_msg)
# Store meta group length if it exists, then read until not group 2
if group == 2 and elem == 0:
bytes_read = fp.read(length)
if debugging:
logger.debug("{0:08x}: {1}".format(fp.tell() - length,
bytes2hex(bytes_read)))
group_length = unpack("<L", bytes_read)[0]
expected_ds_start = fp.tell() + group_length
if debugging:
msg = "value (group length) = {0:d}".format(group_length)
msg += " regular dataset should start at {0:08x}".format(
expected_ds_start)
logger.debug(" " * 10 + msg)
else:
expected_ds_start = None
if debugging:
logger.debug(" " * 10 + "(0002,0000) Group length not found.")
# Changed in pydicom 0.9.7 -- don't trust the group length, just read
# until no longer group 2 data elements. But check the length and
# give a warning if group 2 ends at different location.
# Rewind to read the first data element as part of the file_meta dataset
if debugging:
logger.debug("Rewinding and reading whole dataset "
"including this first data element")
fp.seek(fp_save)
file_meta = read_dataset(fp, is_implicit_VR=False,
is_little_endian=True, stop_when=not_group2)
fp_now = fp.tell()
if expected_ds_start and fp_now != expected_ds_start:
logger.info("*** Group length for file meta dataset "
"did not match end of group 2 data ***")
else:
if debugging:
logger.debug("--- End of file meta data found "
"as expected ---------")
return file_meta
def read_file(fp, defer_size=None, stop_before_pixels=False, force=False, toad=True):
"""Read and parse a DICOM file.
Parameters
----------
fp : file-like object, str
Either a file-like object, or a string containing the file name.
If a file-like object, the caller is responsible for closing it.
defer_size : int, str, None, optional
If None (default), all elements read into memory.
If specified, if a data element value is larger than defer_size,
then the value is not read into memory until it is accessed in code.
Specify an integer (bytes), or a string value with units, e.g.
"512 KB", "2 MB".
stop_before_pixels : boolean, optional
If False (default), the full file will be read and parsed.
Set True to stop before reading pixels (and anything after them).
force : boolean, optional
If False (default), raises an InvalidDicomError if the file
is not valid DICOM.
Set to True to force reading even if no header is found.
Returns
-------
FileDataset
An instance of FileDataset that represents a parsed DICOM file.
Raises
------
InvalidDicomError
If the force flag is True and the file is not a valid DICOM file.
See Also
--------
pydicom.dataset.FileDataset
Data class that is returned.
pydicom.filereader.read_partial
Only read part of a DICOM file, stopping on given conditions.
Examples
--------
Read file and return file dataset:
>>> rtplan = pydicom.read_file("rtplan.dcm")
>>> rtplan.PatientName
Use within a context manager:
>>> with pydicom.read_file("rtplan.dcm") as rtplan:
>>> rtplan.PatientName
"""
# Open file if not already a file object
caller_owns_file = True
if isinstance(fp, compat.string_types):
# caller provided a file name; we own the file handle
caller_owns_file = False
logger.debug(u"Reading file '{0}'".format(fp))
fp = open(fp, 'rb')
if config.debugging:
logger.debug("\n" + "-" * 80)
logger.debug("Call to read_file()")
msg = ("filename:'%s', defer_size='%s', "
"stop_before_pixels=%s, force=%s")
logger.debug(msg % (fp.name, defer_size, stop_before_pixels, force))
if caller_owns_file:
logger.debug("Caller passed file object")
else:
logger.debug("Caller passed file name")
logger.debug("-" * 80)
# Convert size to defer reading into bytes, and store in file object
# if defer_size is not None:
# defer_size = size_in_bytes(defer_size)
# fp.defer_size = defer_size
# Iterate through all items and store them --include file meta if present
stop_when = None
if stop_before_pixels:
def _at_TOAD_convenience(tag, VR, length):
return tag == (0x0020, 0x0018)
if toad:
stop_when = _at_TOAD_convenience
else:
stop_when = _at_pixel_data
try:
dataset = read_partial(fp, stop_when, defer_size=defer_size, force=force)
finally:
if not caller_owns_file:
fp.close()
# XXX need to store transfer syntax etc.
return dataset