# -*- coding: utf-8 -*- # imageio is distributed under the terms of the (new) BSD License. """ Plugin for reading DICOM files. """ # todo: Use pydicom: # * Note: is not py3k ready yet # * Allow reading the full meta info # I think we can more or less replace the SimpleDicomReader with a # pydicom.Dataset For series, only ned to read the full info from one # file: speed still high # * Perhaps allow writing? import sys import os import struct import logging import numpy as np logger = logging.getLogger(__name__) # Determine endianity of system sys_is_little_endian = sys.byteorder == "little" # Define a dictionary that contains the tags that we would like to know MINIDICT = { (0x7FE0, 0x0010): ("PixelData", "OB"), # Date and time (0x0008, 0x0020): ("StudyDate", "DA"), (0x0008, 0x0021): ("SeriesDate", "DA"), (0x0008, 0x0022): ("AcquisitionDate", "DA"), (0x0008, 0x0023): ("ContentDate", "DA"), (0x0008, 0x0030): ("StudyTime", "TM"), (0x0008, 0x0031): ("SeriesTime", "TM"), (0x0008, 0x0032): ("AcquisitionTime", "TM"), (0x0008, 0x0033): ("ContentTime", "TM"), # With what, where, by whom? (0x0008, 0x0060): ("Modality", "CS"), (0x0008, 0x0070): ("Manufacturer", "LO"), (0x0008, 0x0080): ("InstitutionName", "LO"), # Descriptions (0x0008, 0x1030): ("StudyDescription", "LO"), (0x0008, 0x103E): ("SeriesDescription", "LO"), # UID's (0x0008, 0x0016): ("SOPClassUID", "UI"), (0x0008, 0x0018): ("SOPInstanceUID", "UI"), (0x0020, 0x000D): ("StudyInstanceUID", "UI"), (0x0020, 0x000E): ("SeriesInstanceUID", "UI"), (0x0008, 0x0117): ("ContextUID", "UI"), # Numbers (0x0020, 0x0011): ("SeriesNumber", "IS"), (0x0020, 0x0012): ("AcquisitionNumber", "IS"), (0x0020, 0x0013): ("InstanceNumber", "IS"), (0x0020, 0x0014): ("IsotopeNumber", "IS"), (0x0020, 0x0015): ("PhaseNumber", "IS"), (0x0020, 0x0016): ("IntervalNumber", "IS"), (0x0020, 0x0017): ("TimeSlotNumber", "IS"), (0x0020, 0x0018): ("AngleNumber", "IS"), (0x0020, 0x0019): ("ItemNumber", "IS"), (0x0020, 0x0020): ("PatientOrientation", "CS"), (0x0020, 0x0030): ("ImagePosition", "CS"), (0x0020, 0x0032): ("ImagePositionPatient", "CS"), (0x0020, 0x0035): ("ImageOrientation", "CS"), (0x0020, 0x0037): ("ImageOrientationPatient", "CS"), # Patient information (0x0010, 0x0010): ("PatientName", "PN"), (0x0010, 0x0020): ("PatientID", "LO"), (0x0010, 0x0030): ("PatientBirthDate", "DA"), (0x0010, 0x0040): ("PatientSex", "CS"), (0x0010, 0x1010): ("PatientAge", "AS"), (0x0010, 0x1020): ("PatientSize", "DS"), (0x0010, 0x1030): ("PatientWeight", "DS"), # Image specific (required to construct numpy array) (0x0028, 0x0002): ("SamplesPerPixel", "US"), (0x0028, 0x0008): ("NumberOfFrames", "IS"), (0x0028, 0x0100): ("BitsAllocated", "US"), (0x0028, 0x0101): ("BitsStored", "US"), (0x0028, 0x0102): ("HighBit", "US"), (0x0028, 0x0103): ("PixelRepresentation", "US"), (0x0028, 0x0010): ("Rows", "US"), (0x0028, 0x0011): ("Columns", "US"), (0x0028, 0x1052): ("RescaleIntercept", "DS"), (0x0028, 0x1053): ("RescaleSlope", "DS"), # Image specific (for the user) (0x0028, 0x0030): ("PixelSpacing", "DS"), (0x0018, 0x0088): ("SliceSpacing", "DS"), } # Define some special tags: # See PS 3.5-2008 section 7.5 (p.40) ItemTag = (0xFFFE, 0xE000) # start of Sequence Item ItemDelimiterTag = (0xFFFE, 0xE00D) # end of Sequence Item SequenceDelimiterTag = (0xFFFE, 0xE0DD) # end of Sequence of undefined length # Define set of groups that we're interested in (so we can quickly skip others) GROUPS = set([key[0] for key in MINIDICT.keys()]) VRS = set([val[1] for val in MINIDICT.values()]) class NotADicomFile(Exception): pass class CompressedDicom(RuntimeError): pass class SimpleDicomReader(object): """ This class provides reading of pixel data from DICOM files. It is focussed on getting the pixel data, not the meta info. To use, first create an instance of this class (giving it a file object or filename). Next use the info attribute to get a dict of the meta data. The loading of pixel data is deferred until get_numpy_array() is called. Comparison with Pydicom ----------------------- This code focusses on getting the pixel data out, which allows some shortcuts, resulting in the code being much smaller. Since the processing of data elements is much cheaper (it skips a lot of tags), this code is about 3x faster than pydicom (except for the deflated DICOM files). This class does borrow some code (and ideas) from the pydicom project, and (to the best of our knowledge) has the same limitations as pydicom with regard to the type of files that it can handle. Limitations ----------- For more advanced DICOM processing, please check out pydicom. * Only a predefined subset of data elements (meta information) is read. * This is a reader; it can not write DICOM files. * (just like pydicom) it can handle none of the compressed DICOM formats except for "Deflated Explicit VR Little Endian" (1.2.840.10008.1.2.1.99). """ def __init__(self, file): # Open file if filename given if isinstance(file, str): self._filename = file self._file = open(file, "rb") else: self._filename = "" self._file = file # Init variable to store position and size of pixel data self._pixel_data_loc = None # The meta header is always explicit and little endian self.is_implicit_VR = False self.is_little_endian = True self._unpackPrefix = "<" # Dict to store data elements of interest in self._info = {} # VR Conversion self._converters = { # Numbers "US": lambda x: self._unpack("H", x), "UL": lambda x: self._unpack("L", x), # Numbers encoded as strings "DS": lambda x: self._splitValues(x, float, "\\"), "IS": lambda x: self._splitValues(x, int, "\\"), # strings "AS": lambda x: x.decode("ascii", "ignore").strip("\x00"), "DA": lambda x: x.decode("ascii", "ignore").strip("\x00"), "TM": lambda x: x.decode("ascii", "ignore").strip("\x00"), "UI": lambda x: x.decode("ascii", "ignore").strip("\x00"), "LO": lambda x: x.decode("utf-8", "ignore").strip("\x00").rstrip(), "CS": lambda x: self._splitValues(x, float, "\\"), "PN": lambda x: x.decode("utf-8", "ignore").strip("\x00").rstrip(), } # Initiate reading self._read() @property def info(self): return self._info def _splitValues(self, x, type, splitter): s = x.decode("ascii").strip("\x00") try: if splitter in s: return tuple([type(v) for v in s.split(splitter) if v.strip()]) else: return type(s) except ValueError: return s def _unpack(self, fmt, value): return struct.unpack(self._unpackPrefix + fmt, value)[0] # Really only so we need minimal changes to _pixel_data_numpy def __iter__(self): return iter(self._info.keys()) def __getattr__(self, key): info = object.__getattribute__(self, "_info") if key in info: return info[key] return object.__getattribute__(self, key) # pragma: no cover def _read(self): f = self._file # Check prefix after peamble f.seek(128) if f.read(4) != b"DICM": raise NotADicomFile("Not a valid DICOM file.") # Read self._read_header() self._read_data_elements() self._get_shape_and_sampling() # Close if done, reopen if necessary to read pixel data if os.path.isfile(self._filename): self._file.close() self._file = None def _readDataElement(self): f = self._file # Get group and element group = self._unpack("H", f.read(2)) element = self._unpack("H", f.read(2)) # Get value length if self.is_implicit_VR: vl = self._unpack("I", f.read(4)) else: vr = f.read(2) if vr in (b"OB", b"OW", b"SQ", b"UN"): reserved = f.read(2) # noqa vl = self._unpack("I", f.read(4)) else: vl = self._unpack("H", f.read(2)) # Get value if group == 0x7FE0 and element == 0x0010: here = f.tell() self._pixel_data_loc = here, vl f.seek(here + vl) return group, element, b"Deferred loading of pixel data" else: if vl == 0xFFFFFFFF: value = self._read_undefined_length_value() else: value = f.read(vl) return group, element, value def _read_undefined_length_value(self, read_size=128): """Copied (in compacted form) from PyDicom Copyright Darcy Mason. """ fp = self._file # data_start = fp.tell() search_rewind = 3 bytes_to_find = struct.pack( self._unpackPrefix + "HH", SequenceDelimiterTag[0], SequenceDelimiterTag[1] ) found = False value_chunks = [] while not found: chunk_start = fp.tell() bytes_read = fp.read(read_size) if len(bytes_read) < read_size: # try again, # if still don't get required amount, this is last block new_bytes = fp.read(read_size - len(bytes_read)) bytes_read += new_bytes if len(bytes_read) < read_size: raise EOFError( "End of file reached before sequence " "delimiter found." ) index = bytes_read.find(bytes_to_find) if index != -1: found = True value_chunks.append(bytes_read[:index]) fp.seek(chunk_start + index + 4) # rewind to end of delimiter length = fp.read(4) if length != b"\0\0\0\0": logger.warning( "Expected 4 zero bytes after undefined length " "delimiter" ) else: fp.seek(fp.tell() - search_rewind) # rewind a bit # accumulate the bytes read (not including the rewind) value_chunks.append(bytes_read[:-search_rewind]) # if get here then have found the byte string return b"".join(value_chunks) def _read_header(self): f = self._file TransferSyntaxUID = None # Read all elements, store transferSyntax when we encounter it try: while True: fp_save = f.tell() # Get element group, element, value = self._readDataElement() if group == 0x02: if group == 0x02 and element == 0x10: TransferSyntaxUID = value.decode("ascii").strip("\x00") else: # No more group 2: rewind and break # (don't trust group length) f.seek(fp_save) break except (EOFError, struct.error): # pragma: no cover raise RuntimeError("End of file reached while still in header.") # Handle transfer syntax self._info["TransferSyntaxUID"] = TransferSyntaxUID # if TransferSyntaxUID is None: # Assume ExplicitVRLittleEndian is_implicit_VR, is_little_endian = False, True elif TransferSyntaxUID == "1.2.840.10008.1.2.1": # ExplicitVRLittleEndian is_implicit_VR, is_little_endian = False, True elif TransferSyntaxUID == "1.2.840.10008.1.2.2": # ExplicitVRBigEndian is_implicit_VR, is_little_endian = False, False elif TransferSyntaxUID == "1.2.840.10008.1.2": # implicit VR little endian is_implicit_VR, is_little_endian = True, True elif TransferSyntaxUID == "1.2.840.10008.1.2.1.99": # DeflatedExplicitVRLittleEndian: is_implicit_VR, is_little_endian = False, True self._inflate() else: # http://www.dicomlibrary.com/dicom/transfer-syntax/ t, extra_info = TransferSyntaxUID, "" if "1.2.840.10008.1.2.4.50" <= t < "1.2.840.10008.1.2.4.99": extra_info = " (JPEG)" if "1.2.840.10008.1.2.4.90" <= t < "1.2.840.10008.1.2.4.99": extra_info = " (JPEG 2000)" if t == "1.2.840.10008.1.2.5": extra_info = " (RLE)" if t == "1.2.840.10008.1.2.6.1": extra_info = " (RFC 2557)" raise CompressedDicom( "The dicom reader can only read files with " "uncompressed image data - not %r%s. You " "can try using dcmtk or gdcm to convert the " "image." % (t, extra_info) ) # From hereon, use implicit/explicit big/little endian self.is_implicit_VR = is_implicit_VR self.is_little_endian = is_little_endian self._unpackPrefix = "><"[is_little_endian] def _read_data_elements(self): info = self._info try: while True: # Get element group, element, value = self._readDataElement() # Is it a group we are interested in? if group in GROUPS: key = (group, element) name, vr = MINIDICT.get(key, (None, None)) # Is it an element we are interested in? if name: # Store value converter = self._converters.get(vr, lambda x: x) info[name] = converter(value) except (EOFError, struct.error): pass # end of file ... def get_numpy_array(self): """Get numpy arra for this DICOM file, with the correct shape, and pixel values scaled appropriately. """ # Is there pixel data at all? if "PixelData" not in self: raise TypeError("No pixel data found in this dataset.") # Load it now if it was not already loaded if self._pixel_data_loc and len(self.PixelData) < 100: # Reopen file? close_file = False if self._file is None: close_file = True self._file = open(self._filename, "rb") # Read data self._file.seek(self._pixel_data_loc[0]) if self._pixel_data_loc[1] == 0xFFFFFFFF: value = self._read_undefined_length_value() else: value = self._file.read(self._pixel_data_loc[1]) # Close file if close_file: self._file.close() self._file = None # Overwrite self._info["PixelData"] = value # Get data data = self._pixel_data_numpy() data = self._apply_slope_and_offset(data) # Remove data again to preserve memory # Note that the data for the original file is loaded twice ... self._info["PixelData"] = ( b"Data converted to numpy array, " + b"raw data removed to preserve memory" ) return data def _get_shape_and_sampling(self): """Get shape and sampling without actuall using the pixel data. In this way, the user can get an idea what's inside without having to load it. """ # Get shape (in the same way that pydicom does) if "NumberOfFrames" in self and self.NumberOfFrames > 1: if self.SamplesPerPixel > 1: shape = ( self.SamplesPerPixel, self.NumberOfFrames, self.Rows, self.Columns, ) else: shape = self.NumberOfFrames, self.Rows, self.Columns elif "SamplesPerPixel" in self: if self.SamplesPerPixel > 1: if self.BitsAllocated == 8: shape = self.SamplesPerPixel, self.Rows, self.Columns else: raise NotImplementedError( "DICOM plugin only handles " "SamplesPerPixel > 1 if Bits " "Allocated = 8" ) else: shape = self.Rows, self.Columns else: raise RuntimeError( "DICOM file has no SamplesPerPixel " "(perhaps this is a report?)" ) # Try getting sampling between pixels if "PixelSpacing" in self: sampling = float(self.PixelSpacing[0]), float(self.PixelSpacing[1]) else: sampling = 1.0, 1.0 if "SliceSpacing" in self: sampling = (abs(self.SliceSpacing),) + sampling # Ensure that sampling has as many elements as shape sampling = (1.0,) * (len(shape) - len(sampling)) + sampling[-len(shape) :] # Set shape and sampling self._info["shape"] = shape self._info["sampling"] = sampling def _pixel_data_numpy(self): """Return a NumPy array of the pixel data.""" # Taken from pydicom # Copyright (c) 2008-2012 Darcy Mason if "PixelData" not in self: raise TypeError("No pixel data found in this dataset.") # determine the type used for the array need_byteswap = self.is_little_endian != sys_is_little_endian # Make NumPy format code, e.g. "uint16", "int32" etc # from two pieces of info: # self.PixelRepresentation -- 0 for unsigned, 1 for signed; # self.BitsAllocated -- 8, 16, or 32 format_str = "%sint%d" % ( ("u", "")[self.PixelRepresentation], self.BitsAllocated, ) try: numpy_format = np.dtype(format_str) except TypeError: # pragma: no cover raise TypeError( "Data type not understood by NumPy: format='%s', " " PixelRepresentation=%d, BitsAllocated=%d" % (numpy_format, self.PixelRepresentation, self.BitsAllocated) ) # Have correct Numpy format, so create the NumPy array arr = np.frombuffer(self.PixelData, numpy_format).copy() # XXX byte swap - may later handle this in read_file!!? if need_byteswap: arr.byteswap(True) # True means swap in-place, don't make new copy # Note the following reshape operations return a new *view* onto arr, # but don't copy the data arr = arr.reshape(*self._info["shape"]) return arr def _apply_slope_and_offset(self, data): """ If RescaleSlope and RescaleIntercept are present in the data, apply them. The data type of the data is changed if necessary. """ # Obtain slope and offset slope, offset = 1, 0 needFloats, needApplySlopeOffset = False, False if "RescaleSlope" in self: needApplySlopeOffset = True slope = self.RescaleSlope if "RescaleIntercept" in self: needApplySlopeOffset = True offset = self.RescaleIntercept if int(slope) != slope or int(offset) != offset: needFloats = True if not needFloats: slope, offset = int(slope), int(offset) # Apply slope and offset if needApplySlopeOffset: # Maybe we need to change the datatype? if data.dtype in [np.float32, np.float64]: pass elif needFloats: data = data.astype(np.float32) else: # Determine required range minReq, maxReq = data.min(), data.max() minReq = min([minReq, minReq * slope + offset, maxReq * slope + offset]) maxReq = max([maxReq, minReq * slope + offset, maxReq * slope + offset]) # Determine required datatype from that dtype = None if minReq < 0: # Signed integer type maxReq = max([-minReq, maxReq]) if maxReq < 2**7: dtype = np.int8 elif maxReq < 2**15: dtype = np.int16 elif maxReq < 2**31: dtype = np.int32 else: dtype = np.float32 else: # Unsigned integer type if maxReq < 2**8: dtype = np.int8 elif maxReq < 2**16: dtype = np.int16 elif maxReq < 2**32: dtype = np.int32 else: dtype = np.float32 # Change datatype if dtype != data.dtype: data = data.astype(dtype) # Apply slope and offset data *= slope data += offset # Done return data def _inflate(self): # Taken from pydicom # Copyright (c) 2008-2012 Darcy Mason import zlib from io import BytesIO # 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 = self._file.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) self._file = BytesIO(unzipped) # a file-like object class DicomSeries(object): """DicomSeries This class represents a serie of dicom files (SimpleDicomReader objects) that belong together. If these are multiple files, they represent the slices of a volume (like for CT or MRI). """ def __init__(self, suid, progressIndicator): # Init dataset list and the callback self._entries = [] # Init props self._suid = suid self._info = {} self._progressIndicator = progressIndicator def __len__(self): return len(self._entries) def __iter__(self): return iter(self._entries) def __getitem__(self, index): return self._entries[index] @property def suid(self): return self._suid @property def shape(self): """The shape of the data (nz, ny, nx).""" return self._info["shape"] @property def sampling(self): """The sampling (voxel distances) of the data (dz, dy, dx).""" return self._info["sampling"] @property def info(self): """A dictionary containing the information as present in the first dicomfile of this serie. None if there are no entries.""" return self._info @property def description(self): """A description of the dicom series. Used fields are PatientName, shape of the data, SeriesDescription, and ImageComments. """ info = self.info # If no info available, return simple description if not info: # pragma: no cover return "DicomSeries containing %i images" % len(self) fields = [] # Give patient name if "PatientName" in info: fields.append("" + info["PatientName"]) # Also add dimensions if self.shape: tmp = [str(d) for d in self.shape] fields.append("x".join(tmp)) # Try adding more fields if "SeriesDescription" in info: fields.append("'" + info["SeriesDescription"] + "'") if "ImageComments" in info: fields.append("'" + info["ImageComments"] + "'") # Combine return " ".join(fields) def __repr__(self): adr = hex(id(self)).upper() return "" % (len(self), adr) def get_numpy_array(self): """Get (load) the data that this DicomSeries represents, and return it as a numpy array. If this serie contains multiple images, the resulting array is 3D, otherwise it's 2D. """ # It's easy if no file or if just a single file if len(self) == 0: raise ValueError("Serie does not contain any files.") elif len(self) == 1: return self[0].get_numpy_array() # Check info if self.info is None: raise RuntimeError("Cannot return volume if series not finished.") # Init data (using what the dicom packaged produces as a reference) slice = self[0].get_numpy_array() vol = np.zeros(self.shape, dtype=slice.dtype) vol[0] = slice # Fill volume self._progressIndicator.start("loading data", "", len(self)) for z in range(1, len(self)): vol[z] = self[z].get_numpy_array() self._progressIndicator.set_progress(z + 1) self._progressIndicator.finish() # Done import gc gc.collect() return vol def _append(self, dcm): self._entries.append(dcm) def _sort(self): self._entries.sort( key=lambda k: ( k.InstanceNumber, ( k.ImagePositionPatient[2] if hasattr(k, "ImagePositionPatient") else None ), ) ) def _finish(self): """ Evaluate the series of dicom files. Together they should make up a volumetric dataset. This means the files should meet certain conditions. Also some additional information has to be calculated, such as the distance between the slices. This method sets the attributes for "shape", "sampling" and "info". This method checks: * that there are no missing files * that the dimensions of all images match * that the pixel spacing of all images match """ # The datasets list should be sorted by instance number L = self._entries if len(L) == 0: return elif len(L) == 1: self._info = L[0].info return # Get previous ds1 = L[0] # Init measures to calculate average of distance_sum = 0.0 # Init measures to check (these are in 2D) dimensions = ds1.Rows, ds1.Columns # sampling = float(ds1.PixelSpacing[0]), float(ds1.PixelSpacing[1]) sampling = ds1.info["sampling"][:2] # row, column for index in range(len(L)): # The first round ds1 and ds2 will be the same, for the # distance calculation this does not matter # Get current ds2 = L[index] # Get positions pos1 = float(ds1.ImagePositionPatient[2]) pos2 = float(ds2.ImagePositionPatient[2]) # Update distance_sum to calculate distance later distance_sum += abs(pos1 - pos2) # Test measures dimensions2 = ds2.Rows, ds2.Columns # sampling2 = float(ds2.PixelSpacing[0]), float(ds2.PixelSpacing[1]) sampling2 = ds2.info["sampling"][:2] # row, column if dimensions != dimensions2: # We cannot produce a volume if the dimensions match raise ValueError("Dimensions of slices does not match.") if sampling != sampling2: # We can still produce a volume, but we should notify the user self._progressIndicator.write("Warn: sampling does not match.") # Store previous ds1 = ds2 # Finish calculating average distance # (Note that there are len(L)-1 distances) distance_mean = distance_sum / (len(L) - 1) # Set info dict self._info = L[0].info.copy() # Store information that is specific for the serie self._info["shape"] = (len(L),) + ds2.info["shape"] self._info["sampling"] = (distance_mean,) + ds2.info["sampling"] def list_files(files, path): """List all files in the directory, recursively.""" for item in os.listdir(path): item = os.path.join(path, item) if os.path.isdir(item): list_files(files, item) elif os.path.isfile(item): files.append(item) def process_directory(request, progressIndicator, readPixelData=False): """ Reads dicom files and returns a list of DicomSeries objects, which contain information about the data, and can be used to load the image or volume data. if readPixelData is True, the pixel data of all series is read. By default the loading of pixeldata is deferred until it is requested using the DicomSeries.get_pixel_array() method. In general, both methods should be equally fast. """ # Get directory to examine if os.path.isdir(request.filename): path = request.filename elif os.path.isfile(request.filename): path = os.path.dirname(request.filename) else: # pragma: no cover - tested earlier raise ValueError("Dicom plugin needs a valid filename to examine the directory") # Check files files = [] list_files(files, path) # Find files recursively # Gather file data and put in DicomSeries series = {} count = 0 progressIndicator.start("examining files", "files", len(files)) for filename in files: # Show progress (note that we always start with a 0.0) count += 1 progressIndicator.set_progress(count) # Skip DICOMDIR files if filename.count("DICOMDIR"): # pragma: no cover continue # Try loading dicom ... try: dcm = SimpleDicomReader(filename) except NotADicomFile: continue # skip non-dicom file except Exception as why: # pragma: no cover progressIndicator.write(str(why)) continue # Get SUID and register the file with an existing or new series object try: suid = dcm.SeriesInstanceUID except AttributeError: # pragma: no cover continue # some other kind of dicom file if suid not in series: series[suid] = DicomSeries(suid, progressIndicator) series[suid]._append(dcm) # Finish progress # progressIndicator.finish('Found %i series.' % len(series)) # Make a list and sort, so that the order is deterministic series = list(series.values()) series.sort(key=lambda x: x.suid) # Split series if necessary for serie in reversed([serie for serie in series]): splitSerieIfRequired(serie, series, progressIndicator) # Finish all series # progressIndicator.start('analyse series', '', len(series)) series_ = [] for i in range(len(series)): try: series[i]._finish() series_.append(series[i]) except Exception as err: # pragma: no cover progressIndicator.write(str(err)) pass # Skip serie (probably report-like file without pixels) # progressIndicator.set_progress(i+1) progressIndicator.finish("Found %i correct series." % len(series_)) # Done return series_ def splitSerieIfRequired(serie, series, progressIndicator): """ Split the serie in multiple series if this is required. The choice is based on examing the image position relative to the previous image. If it differs too much, it is assumed that there is a new dataset. This can happen for example in unspitted gated CT data. """ # Sort the original list and get local name serie._sort() L = serie._entries # Init previous slice ds1 = L[0] # Check whether we can do this if "ImagePositionPatient" not in ds1: return # Initialize a list of new lists L2 = [[ds1]] # Init slice distance estimate distance = 0 for index in range(1, len(L)): # Get current slice ds2 = L[index] # Get positions pos1 = float(ds1.ImagePositionPatient[2]) pos2 = float(ds2.ImagePositionPatient[2]) # Get distances newDist = abs(pos1 - pos2) # deltaDist = abs(firstPos-pos2) # If the distance deviates more than 2x from what we've seen, # we can agree it's a new dataset. if distance and newDist > 2.1 * distance: L2.append([]) distance = 0 else: # Test missing file if distance and newDist > 1.5 * distance: progressIndicator.write( "Warning: missing file after %r" % ds1._filename ) distance = newDist # Add to last list L2[-1].append(ds2) # Store previous ds1 = ds2 # Split if we should if len(L2) > 1: # At what position are we now? i = series.index(serie) # Create new series series2insert = [] for L in L2: newSerie = DicomSeries(serie.suid, progressIndicator) newSerie._entries = L series2insert.append(newSerie) # Insert series and remove self for newSerie in reversed(series2insert): series.insert(i, newSerie) series.remove(serie)