Source code for pydicom.filereader

# Copyright 2008-2018 pydicom authors. See LICENSE file for details.
"""Read a dicom media file"""

from __future__ import absolute_import

# Need zlib and io.BytesIO for deflate-compressed file
from io import BytesIO
import os
from struct import (Struct, unpack)
from sys import byteorder
import warnings
import zlib

from pydicom import compat  # don't import datetime_conversion directly
from pydicom import config
from pydicom.charset import (default_encoding, convert_encodings)
from pydicom.compat import in_py2
from pydicom.config import logger
from pydicom.datadict import dictionary_VR, tag_for_keyword
from pydicom.dataelem import (DataElement, RawDataElement,
                              DataElement_from_raw)
from pydicom.dataset import (Dataset, FileDataset)
from pydicom.dicomdir import DicomDir
from pydicom.errors import InvalidDicomError
from pydicom.filebase import DicomFile
from pydicom.fileutil import read_undefined_length_value
from pydicom.misc import size_in_bytes
from pydicom.sequence import Sequence
from pydicom.tag import (ItemTag, SequenceDelimiterTag, TupleTag, Tag, BaseTag)
import pydicom.uid
from pydicom.util.hexutil import bytes2hex
from pydicom.valuerep import extra_length_VRs


[docs]class DicomIter(object): """Iterator over DICOM data elements created from a file-like object""" 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 & 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) # a file-like object fp = BytesIO(unzipped) # point to new object self.fp = fp 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 __iter__(self): tags = sorted(self.file_meta_info.keys()) for tag in tags: yield self.file_meta_info[tag] for data_element in data_element_generator(self.fp, self._is_implicit_VR, self._is_little_endian, stop_when=self.stop_when): yield data_element
[docs]def data_element_generator(fp, is_implicit_VR, is_little_endian, stop_when=None, defer_size=None, encoding=default_encoding, specific_tags=None): """Create a generator to efficiently return the raw data elements. Parameters ---------- fp : file-like object is_implicit_VR : boolean is_little_endian : boolean stop_when : None, callable, optional If None (default), then the whole file is read. A callable which takes tag, VR, length, and returns True or False. If it returns True, read_data_element will just return. defer_size : int, str, None, optional See ``dcmread`` for parameter info. encoding : Encoding scheme specific_tags : list or None See ``dcmread`` for parameter info. Returns ------- VR : None if implicit VR, otherwise the VR read from the file length : the length as in the DICOM data element (could be DICOM "undefined length" 0xffffffffL) value_bytes : the raw bytes from the DICOM file (not parsed into python types) is_little_endian : boolean True if transfer syntax is little endian; else False. """ # Summary of DICOM standard PS3.5-2008 chapter 7: # If Implicit VR, data element is: # tag, 4-byte length, value. # The 4-byte length can be FFFFFFFF (undefined length)* # # If Explicit VR: # if OB, OW, OF, SQ, UN, or UT: # tag, VR, 2-bytes reserved (both zero), 4-byte length, value # For all but UT, the length can be FFFFFFFF (undefined length)* # else: (any other VR) # tag, VR, (2 byte length), value # * for undefined length, a Sequence Delimitation Item marks the end # of the Value Field. # Note, except for the special_VRs, both impl and expl VR use 8 bytes; # the special VRs follow the 8 bytes with a 4-byte length # With a generator, state is stored, so we can break down # into the individual cases, and not have to check them again for each # data element if is_little_endian: endian_chr = "<" else: endian_chr = ">" if is_implicit_VR: element_struct = Struct(endian_chr + "HHL") else: # Explicit VR # tag, VR, 2-byte length (or 0 if special VRs) element_struct = Struct(endian_chr + "HH2sH") extra_length_struct = Struct(endian_chr + "L") # for special VRs extra_length_unpack = extra_length_struct.unpack # for lookup speed # Make local variables so have faster lookup fp_read = fp.read fp_tell = fp.tell logger_debug = logger.debug debugging = config.debugging element_struct_unpack = element_struct.unpack defer_size = size_in_bytes(defer_size) tag_set = set() if specific_tags is not None: for tag in specific_tags: if isinstance(tag, (str, compat.text_type)): tag = Tag(tag_for_keyword(tag)) if isinstance(tag, BaseTag): tag_set.add(tag) tag_set.add(Tag(0x08, 0x05)) has_tag_set = len(tag_set) > 0 while True: # Read tag, VR, length, get ready to read value bytes_read = fp_read(8) if len(bytes_read) < 8: return # at end of file if debugging: debug_msg = "{0:08x}: {1}".format(fp.tell() - 8, bytes2hex(bytes_read)) if is_implicit_VR: # must reset VR each time; could have set last iteration (e.g. SQ) VR = None group, elem, length = element_struct_unpack(bytes_read) else: # explicit VR group, elem, VR, length = element_struct_unpack(bytes_read) if not in_py2: VR = VR.decode(default_encoding) if VR in extra_length_VRs: bytes_read = fp_read(4) length = extra_length_unpack(bytes_read)[0] if debugging: debug_msg += " " + bytes2hex(bytes_read) if debugging: debug_msg = "%-47s (%04x, %04x)" % (debug_msg, group, elem) if not is_implicit_VR: debug_msg += " %s " % VR if length != 0xFFFFFFFF: debug_msg += "Length: %d" % length else: debug_msg += "Length: Undefined length (FFFFFFFF)" logger_debug(debug_msg) # Positioned to read the value, but may not want to -- check stop_when value_tell = fp_tell() tag = TupleTag((group, elem)) if stop_when is not None: # XXX VR may be None here!! Should stop_when just take tag? if stop_when(tag, VR, length): if debugging: logger_debug("Reading ended by stop_when callback. " "Rewinding to start of data element.") rewind_length = 8 if not is_implicit_VR and VR in extra_length_VRs: rewind_length += 4 fp.seek(value_tell - rewind_length) return # Reading the value # First case (most common): reading a value with a defined length if length != 0xFFFFFFFF: # don't defer loading of Specific Character Set value as it is # needed immediately to get the character encoding for other tags if has_tag_set and tag not in tag_set: # skip the tag if not in specific tags fp.seek(fp_tell() + length) continue if (defer_size is not None and length > defer_size and tag != BaseTag(0x00080005)): # Flag as deferred by setting value to None, and skip bytes value = None logger_debug("Defer size exceeded. " "Skipping forward to next data element.") fp.seek(fp_tell() + length) else: value = fp_read(length) if debugging: dotdot = " " if length > 12: dotdot = "..." logger_debug("%08x: %-34s %s %r %s" % (value_tell, bytes2hex( value[:12]), dotdot, value[:12], dotdot)) # If the tag is (0008,0005) Specific Character Set, then store it if tag == BaseTag(0x00080005): from pydicom.values import convert_string encoding = convert_string(value, is_little_endian) # Store the encoding value in the generator # for use with future elements (SQs) encoding = convert_encodings(encoding) yield RawDataElement(tag, VR, length, value, value_tell, is_implicit_VR, is_little_endian) # Second case: undefined length - must seek to delimiter, # unless is SQ type, in which case is easier to parse it, because # undefined length SQs and items of undefined lengths can be nested # and it would be error-prone to read to the correct outer delimiter else: # Try to look up type to see if is a SQ # if private tag, won't be able to look it up in dictionary, # in which case just ignore it and read the bytes unless it is # identified as a Sequence if VR is None: try: VR = dictionary_VR(tag) except KeyError: # Look ahead to see if it consists of items # and is thus a SQ next_tag = TupleTag(unpack(endian_chr + "HH", fp_read(4))) # Rewind the file fp.seek(fp_tell() - 4) if next_tag == ItemTag: VR = 'SQ' if VR == 'SQ': if debugging: msg = "{0:08x}: Reading/parsing undefined length sequence" logger_debug(msg.format(fp_tell())) seq = read_sequence(fp, is_implicit_VR, is_little_endian, length, encoding) if has_tag_set and tag not in tag_set: continue yield DataElement(tag, VR, seq, value_tell, is_undefined_length=True) else: delimiter = SequenceDelimiterTag if debugging: logger_debug("Reading undefined length data element") value = read_undefined_length_value(fp, is_little_endian, delimiter, defer_size) # If the tag is (0008,0005) Specific Character Set, # then store it if tag == (0x08, 0x05): from pydicom.values import convert_string encoding = convert_string(value, is_little_endian) # Store the encoding value in the generator for use # with future elements (SQs) encoding = convert_encodings(encoding) # tags with undefined length are skipped after read if has_tag_set and tag not in tag_set: continue yield RawDataElement(tag, VR, length, value, value_tell, is_implicit_VR, is_little_endian)
[docs]def read_dataset(fp, is_implicit_VR, is_little_endian, bytelength=None, stop_when=None, defer_size=None, parent_encoding=default_encoding, specific_tags=None): """Return a Dataset instance containing the next dataset in the file. Parameters ---------- fp : an opened file object is_implicit_VR : boolean True if file transfer syntax is implicit VR. is_little_endian : boolean True if file has little endian transfer syntax. bytelength : int, None, optional None to read until end of file or ItemDeliterTag, else a fixed number of bytes to read stop_when : None, optional optional call_back function which can terminate reading. See help for data_element_generator for details defer_size : int, None, optional Size to avoid loading large elements in memory. See ``dcmread`` for more parameter info. parent_encoding : optional encoding to use as a default in case a Specific Character Set (0008,0005) isn't specified specific_tags : list or None See ``dcmread`` for parameter info. Returns ------- a Dataset instance See Also -------- pydicom.dataset.Dataset A collection (dictionary) of Dicom `DataElement` instances. """ raw_data_elements = dict() fpStart = fp.tell() de_gen = data_element_generator(fp, is_implicit_VR, is_little_endian, stop_when, defer_size, parent_encoding, specific_tags) try: while (bytelength is None) or (fp.tell() - fpStart < bytelength): raw_data_element = next(de_gen) # Read data elements. Stop on some errors, but return what was read tag = raw_data_element.tag # Check for ItemDelimiterTag --dataset is an item in a sequence if tag == BaseTag(0xFFFEE00D): break raw_data_elements[tag] = raw_data_element except StopIteration: pass except EOFError as details: # XXX is this error visible enough to user code with just logging? logger.error(str(details) + " in file " + getattr(fp, "name", "<no filename>")) except NotImplementedError as details: logger.error(details) ds = Dataset(raw_data_elements) if 0x00080005 in raw_data_elements: char_set = DataElement_from_raw(raw_data_elements[0x00080005]) encoding = convert_encodings(char_set) else: encoding = parent_encoding ds.set_original_encoding(is_implicit_VR, is_little_endian, encoding) return ds
[docs]def read_sequence(fp, is_implicit_VR, is_little_endian, bytelength, encoding, offset=0): """Read and return a Sequence -- i.e. a list of Datasets""" seq = [] # use builtin list to start for speed, convert to Sequence at end is_undefined_length = False if bytelength != 0: # SQ of length 0 possible (PS 3.5-2008 7.5.1a (p.40) if bytelength == 0xffffffff: is_undefined_length = True bytelength = None fp_tell = fp.tell # for speed in loop fpStart = fp_tell() while (not bytelength) or (fp_tell() - fpStart < bytelength): file_tell = fp.tell() dataset = read_sequence_item(fp, is_implicit_VR, is_little_endian, encoding, offset) if dataset is None: # None is returned if hit Sequence Delimiter break dataset.file_tell = file_tell + offset seq.append(dataset) seq = Sequence(seq) seq.is_undefined_length = is_undefined_length return seq
[docs]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 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) ds.is_undefined_length_sequence_item = True else: ds = read_dataset(fp, is_implicit_VR, is_little_endian, length, parent_encoding=encoding) 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_command_set_elements(fp): """Return a Dataset containing any Command Set (0000,eeee) elements in `fp`. Command Set elements are always Implicit VR Little Endian (as per PS3.7 Section 6.3). Once any Command Set elements are read `fp` will be positioned at the start of the next group of elements. Parameters ---------- fp : file-like The file-like positioned at the start of any command set elements. Returns ------- pydicom.dataset.Dataset The command set elements as a Dataset instance. May be empty if no command set elements are present. """ def _not_group_0000(tag, VR, length): """Return True if the tag is not in group 0x0000, False otherwise.""" return (tag.group != 0) command_set = read_dataset(fp, is_implicit_VR=True, is_little_endian=True, stop_when=_not_group_0000) return command_set def _read_file_meta_info(fp): """Return a Dataset containing any File Meta (0002,eeee) elements in `fp`. File Meta elements are always Explicit VR Little Endian (as per PS3.10 Section 7). Once any File Meta elements are read `fp` will be positioned at the start of the next group of elements. Parameters ---------- fp : file-like The file-like positioned at the start of any File Meta Information group elements. Returns ------- pydicom.dataset.Dataset The File Meta elements as a Dataset instance. May be empty if no File Meta are present. """ def _not_group_0002(tag, VR, length): """Return True if the tag is not in group 0x0002, False otherwise.""" return tag.group != 2 start_file_meta = fp.tell() file_meta = read_dataset(fp, is_implicit_VR=False, is_little_endian=True, stop_when=_not_group_0002) if not file_meta: return file_meta # Test the file meta for correct interpretation by requesting the first # data element: if it fails, retry loading the file meta with an # implicit VR (issue #503) try: file_meta[list(file_meta.elements())[0].tag] except NotImplementedError: fp.seek(start_file_meta) file_meta = read_dataset(fp, is_implicit_VR=True, is_little_endian=True, stop_when=_not_group_0002) # Log if the Group Length doesn't match actual length if 'FileMetaInformationGroupLength' in file_meta: # FileMetaInformationGroupLength must be 12 bytes long and its value # counts from the beginning of the next element to the end of the # file meta elements length_file_meta = fp.tell() - (start_file_meta + 12) if file_meta.FileMetaInformationGroupLength != length_file_meta: logger.info("_read_file_meta_info: (0002,0000) 'File Meta " "Information Group Length' value doesn't match the " "actual File Meta Information length ({0} vs {1} " "bytes)." .format(file_meta.FileMetaInformationGroupLength, length_file_meta)) return file_meta
[docs]def read_file_meta_info(filename): """Read and return the DICOM file meta information only. This function is meant to be used in user code, for quickly going through a series of files to find one which is referenced to a particular SOP, without having to read the entire files. """ with DicomFile(filename, 'rb') as fp: read_preamble(fp, False) # if no header, raise exception return _read_file_meta_info(fp)
[docs]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 _at_pixel_data(tag, VR, length): return tag == (0x7fe0, 0x0010)
[docs]def read_partial(fileobj, stop_when=None, defer_size=None, force=False, specific_tags=None): """Parse a DICOM file until a condition is met. Parameters ---------- fileobj : a file-like object Note that the file will not close when the function returns. stop_when : Stop condition. See ``read_dataset`` for more info. defer_size : int, str, None, optional See ``dcmread`` for parameter info. force : boolean See ``dcmread`` for parameter info. specific_tags : list or None See ``dcmread`` for parameter info. Notes ----- Use ``dcmread`` unless you need to stop on some condition other than reaching pixel data. Returns ------- FileDataset instance or DicomDir instance. See Also -------- dcmread More generic file reading function. """ # Read File Meta Information # Read preamble (if present) preamble = read_preamble(fileobj, force) # Read any File Meta Information group (0002,eeee) elements (if present) file_meta_dataset = _read_file_meta_info(fileobj) # Read Dataset # Read any Command Set group (0000,eeee) elements (if present) command_set = _read_command_set_elements(fileobj) # Check to see if there's anything left to read peek = fileobj.read(1) fileobj.seek(-1, 1) # `filobj` should be positioned at the start of the dataset by this point. # Ensure we have appropriate values for `is_implicit_VR` and # `is_little_endian` before we try decoding. We assume an initial # transfer syntax of implicit VR little endian and correct it as necessary is_implicit_VR = True is_little_endian = True transfer_syntax = file_meta_dataset.get("TransferSyntaxUID") if peek == b'': # EOF pass elif transfer_syntax is None: # issue 258 # If no TransferSyntaxUID element then we have to try and figure out # the correct values for `is_little_endian` and `is_implicit_VR`. # Peek at the first 6 bytes to get the first element's tag group and # (possibly) VR group, _, VR = unpack("<HH2s", fileobj.read(6)) fileobj.seek(-6, 1) # Test the VR to see if it's valid, and if so then assume explicit VR from pydicom.values import converters if not in_py2: VR = VR.decode(default_encoding) if VR in converters.keys(): is_implicit_VR = False # Big endian encoding can only be explicit VR # Big endian 0x0004 decoded as little endian will be 1024 # Big endian 0x0100 decoded as little endian will be 1 # Therefore works for big endian tag groups up to 0x00FF after # which it will fail, in which case we leave it as little endian # and hope for the best (big endian is retired anyway) if group >= 1024: is_little_endian = False elif transfer_syntax == pydicom.uid.ImplicitVRLittleEndian: pass elif transfer_syntax == pydicom.uid.ExplicitVRLittleEndian: is_implicit_VR = False elif transfer_syntax == pydicom.uid.ExplicitVRBigEndian: is_implicit_VR = False 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 = fileobj.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) fileobj = BytesIO(unzipped) # a file-like object is_implicit_VR = False 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) is_implicit_VR = False # Try and decode the dataset # By this point we should be at the start of the dataset and have # the transfer syntax (whether read from the file meta or guessed at) try: dataset = read_dataset(fileobj, is_implicit_VR, is_little_endian, stop_when=stop_when, defer_size=defer_size, specific_tags=specific_tags) except EOFError: pass # error already logged in read_dataset # Add the command set elements to the dataset (if any) dataset.update(command_set) class_uid = file_meta_dataset.get("MediaStorageSOPClassUID", None) if class_uid and class_uid.name == "Media Storage Directory Storage": dataset_class = DicomDir else: dataset_class = FileDataset new_dataset = dataset_class(fileobj, dataset, preamble, file_meta_dataset, is_implicit_VR, is_little_endian) # save the originally read transfer syntax properties in the dataset new_dataset.set_original_encoding(is_implicit_VR, is_little_endian, dataset._character_set) return new_dataset
[docs]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
read_file = dcmread # used read_file until pydicom 1.0. Kept for compatibility
[docs]def read_dicomdir(filename="DICOMDIR"): """Read a DICOMDIR file and return a DicomDir instance. This is a wrapper around dcmread, which gives a default file name. Parameters ---------- filename : str, optional Full path and name to DICOMDIR file to open Returns ------- DicomDir Raises ------ InvalidDicomError Raised if filename is not a DICOMDIR file. """ # dcmread will return a DicomDir instance if file is one. # Read the file as usual. ds = dcmread(filename) # Here, check that it is in fact DicomDir if not isinstance(ds, DicomDir): msg = u"File '{0}' is not a Media Storage Directory file".format( filename) raise InvalidDicomError(msg) return ds
[docs]def data_element_offset_to_value(is_implicit_VR, VR): """Return number of bytes from start of data element to start of value""" if is_implicit_VR: offset = 8 # tag of 4 plus 4-byte length else: if VR in extra_length_VRs: offset = 12 # tag 4 + 2 VR + 2 reserved + 4 length else: offset = 8 # tag 4 + 2 VR + 2 length return offset
[docs]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