328 lines
12 KiB
Python
328 lines
12 KiB
Python
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# -*- coding: utf-8 -*-
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# imageio is distributed under the terms of the (new) BSD License.
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""" Plugin for reading DICOM files.
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"""
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# todo: Use pydicom:
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# * Note: is not py3k ready yet
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# * Allow reading the full meta info
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# I think we can more or less replace the SimpleDicomReader with a
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# pydicom.Dataset For series, only ned to read the full info from one
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# file: speed still high
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# * Perhaps allow writing?
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import os
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import sys
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import logging
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import subprocess
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from .. import formats
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from ..core import Format, BaseProgressIndicator, StdoutProgressIndicator
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from ..core import read_n_bytes
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_dicom = None # lazily loaded in load_lib()
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logger = logging.getLogger(__name__)
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def load_lib():
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global _dicom
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from . import _dicom
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return _dicom
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# Determine endianity of system
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sys_is_little_endian = sys.byteorder == "little"
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def get_dcmdjpeg_exe():
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fname = "dcmdjpeg" + ".exe" * sys.platform.startswith("win")
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for dir in (
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"c:\\dcmtk",
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"c:\\Program Files",
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"c:\\Program Files\\dcmtk",
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"c:\\Program Files (x86)\\dcmtk",
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):
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filename = os.path.join(dir, fname)
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if os.path.isfile(filename):
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return [filename]
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try:
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subprocess.check_call([fname, "--version"])
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return [fname]
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except Exception:
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return None
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def get_gdcmconv_exe():
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fname = "gdcmconv" + ".exe" * sys.platform.startswith("win")
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# Maybe it's on the path
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try:
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subprocess.check_call([fname, "--version"])
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return [fname, "--raw"]
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except Exception:
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pass
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# Select directories where it could be
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candidates = []
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base_dirs = [r"c:\Program Files"]
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for base_dir in base_dirs:
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if os.path.isdir(base_dir):
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for dname in os.listdir(base_dir):
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if dname.lower().startswith("gdcm"):
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suffix = dname[4:].strip()
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candidates.append((suffix, os.path.join(base_dir, dname)))
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# Sort, so higher versions are tried earlier
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candidates.sort(reverse=True)
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# Select executable
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filename = None
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for _, dirname in candidates:
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exe1 = os.path.join(dirname, "gdcmconv.exe")
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exe2 = os.path.join(dirname, "bin", "gdcmconv.exe")
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if os.path.isfile(exe1):
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filename = exe1
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break
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if os.path.isfile(exe2):
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filename = exe2
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break
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else:
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return None
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return [filename, "--raw"]
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class DicomFormat(Format):
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""" A format for reading DICOM images: a common format used to store
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medical image data, such as X-ray, CT and MRI.
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This format borrows some code (and ideas) from the pydicom project. However,
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only a predefined subset of tags are extracted from the file. This allows
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for great simplifications allowing us to make a stand-alone reader, and
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also results in a much faster read time.
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By default, only uncompressed and deflated transfer syntaxes are supported.
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If gdcm or dcmtk is installed, these will be used to automatically convert
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the data. See https://github.com/malaterre/GDCM/releases for installing GDCM.
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This format provides functionality to group images of the same
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series together, thus extracting volumes (and multiple volumes).
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Using volread will attempt to yield a volume. If multiple volumes
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are present, the first one is given. Using mimread will simply yield
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all images in the given directory (not taking series into account).
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Parameters for reading
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----------------------
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progress : {True, False, BaseProgressIndicator}
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Whether to show progress when reading from multiple files.
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Default True. By passing an object that inherits from
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BaseProgressIndicator, the way in which progress is reported
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can be costumized.
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"""
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def _can_read(self, request):
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# If user URI was a directory, we check whether it has a DICOM file
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if os.path.isdir(request.filename):
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files = os.listdir(request.filename)
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for fname in sorted(files): # Sorting make it consistent
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filename = os.path.join(request.filename, fname)
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if os.path.isfile(filename) and "DICOMDIR" not in fname:
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with open(filename, "rb") as f:
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first_bytes = read_n_bytes(f, 140)
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return first_bytes[128:132] == b"DICM"
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else:
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return False
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# Check
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return request.firstbytes[128:132] == b"DICM"
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def _can_write(self, request):
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# We cannot save yet. May be possible if we will used pydicom as
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# a backend.
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return False
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# --
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class Reader(Format.Reader):
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_compressed_warning_dirs = set()
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def _open(self, progress=True):
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if not _dicom:
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load_lib()
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if os.path.isdir(self.request.filename):
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# A dir can be given if the user used the format explicitly
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self._info = {}
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self._data = None
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else:
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# Read the given dataset now ...
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try:
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dcm = _dicom.SimpleDicomReader(self.request.get_file())
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except _dicom.CompressedDicom as err:
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# We cannot do this on our own. Perhaps with some help ...
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cmd = get_gdcmconv_exe()
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if not cmd and "JPEG" in str(err):
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cmd = get_dcmdjpeg_exe()
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if not cmd:
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msg = err.args[0].replace("using", "installing")
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msg = msg.replace("convert", "auto-convert")
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err.args = (msg,)
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raise
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else:
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fname1 = self.request.get_local_filename()
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fname2 = fname1 + ".raw"
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try:
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subprocess.check_call(cmd + [fname1, fname2])
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except Exception:
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raise err
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d = os.path.dirname(fname1)
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if d not in self._compressed_warning_dirs:
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self._compressed_warning_dirs.add(d)
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logger.warning(
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"DICOM file contained compressed data. "
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+ "Autoconverting with "
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+ cmd[0]
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+ " (this warning is shown once for each directory)"
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)
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dcm = _dicom.SimpleDicomReader(fname2)
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self._info = dcm._info
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self._data = dcm.get_numpy_array()
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# Initialize series, list of DicomSeries objects
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self._series = None # only created if needed
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# Set progress indicator
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if isinstance(progress, BaseProgressIndicator):
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self._progressIndicator = progress
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elif progress is True:
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p = StdoutProgressIndicator("Reading DICOM")
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self._progressIndicator = p
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elif progress in (None, False):
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self._progressIndicator = BaseProgressIndicator("Dummy")
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else:
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raise ValueError("Invalid value for progress.")
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def _close(self):
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# Clean up
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self._info = None
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self._data = None
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self._series = None
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@property
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def series(self):
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if self._series is None:
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pi = self._progressIndicator
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self._series = _dicom.process_directory(self.request, pi)
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return self._series
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def _get_length(self):
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if self._data is None:
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dcm = self.series[0][0]
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self._info = dcm._info
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self._data = dcm.get_numpy_array()
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nslices = self._data.shape[0] if (self._data.ndim == 3) else 1
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if self.request.mode[1] == "i":
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# User expects one, but lets be honest about this file
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return nslices
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elif self.request.mode[1] == "I":
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# User expects multiple, if this file has multiple slices, ok.
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# Otherwise we have to check the series.
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if nslices > 1:
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return nslices
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else:
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return sum([len(serie) for serie in self.series])
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elif self.request.mode[1] == "v":
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# User expects a volume, if this file has one, ok.
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# Otherwise we have to check the series
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if nslices > 1:
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return 1
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else:
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return len(self.series) # We assume one volume per series
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elif self.request.mode[1] == "V":
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# User expects multiple volumes. We have to check the series
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return len(self.series) # We assume one volume per series
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else:
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raise RuntimeError("DICOM plugin should know what to expect.")
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def _get_data(self, index):
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if self._data is None:
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dcm = self.series[0][0]
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self._info = dcm._info
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self._data = dcm.get_numpy_array()
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nslices = self._data.shape[0] if (self._data.ndim == 3) else 1
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if self.request.mode[1] == "i":
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# Allow index >1 only if this file contains >1
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if nslices > 1:
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return self._data[index], self._info
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elif index == 0:
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return self._data, self._info
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else:
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raise IndexError("Dicom file contains only one slice.")
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elif self.request.mode[1] == "I":
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# Return slice from volume, or return item from series
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if index == 0 and nslices > 1:
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return self._data[index], self._info
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else:
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L = []
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for serie in self.series:
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L.extend([dcm_ for dcm_ in serie])
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return L[index].get_numpy_array(), L[index].info
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elif self.request.mode[1] in "vV":
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# Return volume or series
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if index == 0 and nslices > 1:
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return self._data, self._info
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else:
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return (
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self.series[index].get_numpy_array(),
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self.series[index].info,
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)
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else: # pragma: no cover
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raise ValueError("DICOM plugin should know what to expect.")
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def _get_meta_data(self, index):
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if self._data is None:
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dcm = self.series[0][0]
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self._info = dcm._info
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self._data = dcm.get_numpy_array()
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nslices = self._data.shape[0] if (self._data.ndim == 3) else 1
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# Default is the meta data of the given file, or the "first" file.
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if index is None:
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return self._info
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if self.request.mode[1] == "i":
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return self._info
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elif self.request.mode[1] == "I":
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# Return slice from volume, or return item from series
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if index == 0 and nslices > 1:
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return self._info
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else:
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L = []
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for serie in self.series:
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L.extend([dcm_ for dcm_ in serie])
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return L[index].info
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elif self.request.mode[1] in "vV":
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# Return volume or series
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if index == 0 and nslices > 1:
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return self._info
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else:
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return self.series[index].info
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else: # pragma: no cover
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raise ValueError("DICOM plugin should know what to expect.")
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# Add this format
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formats.add_format(
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DicomFormat(
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"DICOM",
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"Digital Imaging and Communications in Medicine",
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".dcm .ct .mri",
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"iIvV",
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)
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) # Often DICOM files have weird or no extensions
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