forked from 170010011/fr
328 lines
12 KiB
Python
328 lines
12 KiB
Python
|
# -*- 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 os
|
||
|
|
import sys
|
||
|
|
import logging
|
||
|
|
import subprocess
|
||
|
|
|
||
|
|
from .. import formats
|
||
|
|
from ..core import Format, BaseProgressIndicator, StdoutProgressIndicator
|
||
|
|
from ..core import read_n_bytes
|
||
|
|
|
||
|
|
_dicom = None # lazily loaded in load_lib()
|
||
|
|
|
||
|
|
logger = logging.getLogger(__name__)
|
||
|
|
|
||
|
|
|
||
|
|
def load_lib():
|
||
|
|
global _dicom
|
||
|
|
from . import _dicom
|
||
|
|
|
||
|
|
return _dicom
|
||
|
|
|
||
|
|
|
||
|
|
# Determine endianity of system
|
||
|
|
sys_is_little_endian = sys.byteorder == "little"
|
||
|
|
|
||
|
|
|
||
|
|
def get_dcmdjpeg_exe():
|
||
|
|
fname = "dcmdjpeg" + ".exe" * sys.platform.startswith("win")
|
||
|
|
for dir in (
|
||
|
|
"c:\\dcmtk",
|
||
|
|
"c:\\Program Files",
|
||
|
|
"c:\\Program Files\\dcmtk",
|
||
|
|
"c:\\Program Files (x86)\\dcmtk",
|
||
|
|
):
|
||
|
|
filename = os.path.join(dir, fname)
|
||
|
|
if os.path.isfile(filename):
|
||
|
|
return [filename]
|
||
|
|
|
||
|
|
try:
|
||
|
|
subprocess.check_call([fname, "--version"])
|
||
|
|
return [fname]
|
||
|
|
except Exception:
|
||
|
|
return None
|
||
|
|
|
||
|
|
|
||
|
|
def get_gdcmconv_exe():
|
||
|
|
fname = "gdcmconv" + ".exe" * sys.platform.startswith("win")
|
||
|
|
# Maybe it's on the path
|
||
|
|
try:
|
||
|
|
subprocess.check_call([fname, "--version"])
|
||
|
|
return [fname, "--raw"]
|
||
|
|
except Exception:
|
||
|
|
pass
|
||
|
|
# Select directories where it could be
|
||
|
|
candidates = []
|
||
|
|
base_dirs = [r"c:\Program Files"]
|
||
|
|
for base_dir in base_dirs:
|
||
|
|
if os.path.isdir(base_dir):
|
||
|
|
for dname in os.listdir(base_dir):
|
||
|
|
if dname.lower().startswith("gdcm"):
|
||
|
|
suffix = dname[4:].strip()
|
||
|
|
candidates.append((suffix, os.path.join(base_dir, dname)))
|
||
|
|
# Sort, so higher versions are tried earlier
|
||
|
|
candidates.sort(reverse=True)
|
||
|
|
# Select executable
|
||
|
|
filename = None
|
||
|
|
for _, dirname in candidates:
|
||
|
|
exe1 = os.path.join(dirname, "gdcmconv.exe")
|
||
|
|
exe2 = os.path.join(dirname, "bin", "gdcmconv.exe")
|
||
|
|
if os.path.isfile(exe1):
|
||
|
|
filename = exe1
|
||
|
|
break
|
||
|
|
if os.path.isfile(exe2):
|
||
|
|
filename = exe2
|
||
|
|
break
|
||
|
|
else:
|
||
|
|
return None
|
||
|
|
return [filename, "--raw"]
|
||
|
|
|
||
|
|
|
||
|
|
class DicomFormat(Format):
|
||
|
|
""" A format for reading DICOM images: a common format used to store
|
||
|
|
medical image data, such as X-ray, CT and MRI.
|
||
|
|
|
||
|
|
This format borrows some code (and ideas) from the pydicom project. However,
|
||
|
|
only a predefined subset of tags are extracted from the file. This allows
|
||
|
|
for great simplifications allowing us to make a stand-alone reader, and
|
||
|
|
also results in a much faster read time.
|
||
|
|
|
||
|
|
By default, only uncompressed and deflated transfer syntaxes are supported.
|
||
|
|
If gdcm or dcmtk is installed, these will be used to automatically convert
|
||
|
|
the data. See https://github.com/malaterre/GDCM/releases for installing GDCM.
|
||
|
|
|
||
|
|
This format provides functionality to group images of the same
|
||
|
|
series together, thus extracting volumes (and multiple volumes).
|
||
|
|
Using volread will attempt to yield a volume. If multiple volumes
|
||
|
|
are present, the first one is given. Using mimread will simply yield
|
||
|
|
all images in the given directory (not taking series into account).
|
||
|
|
|
||
|
|
Parameters for reading
|
||
|
|
----------------------
|
||
|
|
progress : {True, False, BaseProgressIndicator}
|
||
|
|
Whether to show progress when reading from multiple files.
|
||
|
|
Default True. By passing an object that inherits from
|
||
|
|
BaseProgressIndicator, the way in which progress is reported
|
||
|
|
can be costumized.
|
||
|
|
|
||
|
|
"""
|
||
|
|
|
||
|
|
def _can_read(self, request):
|
||
|
|
# If user URI was a directory, we check whether it has a DICOM file
|
||
|
|
if os.path.isdir(request.filename):
|
||
|
|
files = os.listdir(request.filename)
|
||
|
|
for fname in sorted(files): # Sorting make it consistent
|
||
|
|
filename = os.path.join(request.filename, fname)
|
||
|
|
if os.path.isfile(filename) and "DICOMDIR" not in fname:
|
||
|
|
with open(filename, "rb") as f:
|
||
|
|
first_bytes = read_n_bytes(f, 140)
|
||
|
|
return first_bytes[128:132] == b"DICM"
|
||
|
|
else:
|
||
|
|
return False
|
||
|
|
# Check
|
||
|
|
return request.firstbytes[128:132] == b"DICM"
|
||
|
|
|
||
|
|
def _can_write(self, request):
|
||
|
|
# We cannot save yet. May be possible if we will used pydicom as
|
||
|
|
# a backend.
|
||
|
|
return False
|
||
|
|
|
||
|
|
# --
|
||
|
|
|
||
|
|
class Reader(Format.Reader):
|
||
|
|
|
||
|
|
_compressed_warning_dirs = set()
|
||
|
|
|
||
|
|
def _open(self, progress=True):
|
||
|
|
if not _dicom:
|
||
|
|
load_lib()
|
||
|
|
if os.path.isdir(self.request.filename):
|
||
|
|
# A dir can be given if the user used the format explicitly
|
||
|
|
self._info = {}
|
||
|
|
self._data = None
|
||
|
|
else:
|
||
|
|
# Read the given dataset now ...
|
||
|
|
try:
|
||
|
|
dcm = _dicom.SimpleDicomReader(self.request.get_file())
|
||
|
|
except _dicom.CompressedDicom as err:
|
||
|
|
# We cannot do this on our own. Perhaps with some help ...
|
||
|
|
cmd = get_gdcmconv_exe()
|
||
|
|
if not cmd and "JPEG" in str(err):
|
||
|
|
cmd = get_dcmdjpeg_exe()
|
||
|
|
if not cmd:
|
||
|
|
msg = err.args[0].replace("using", "installing")
|
||
|
|
msg = msg.replace("convert", "auto-convert")
|
||
|
|
err.args = (msg,)
|
||
|
|
raise
|
||
|
|
else:
|
||
|
|
fname1 = self.request.get_local_filename()
|
||
|
|
fname2 = fname1 + ".raw"
|
||
|
|
try:
|
||
|
|
subprocess.check_call(cmd + [fname1, fname2])
|
||
|
|
except Exception:
|
||
|
|
raise err
|
||
|
|
d = os.path.dirname(fname1)
|
||
|
|
if d not in self._compressed_warning_dirs:
|
||
|
|
self._compressed_warning_dirs.add(d)
|
||
|
|
logger.warning(
|
||
|
|
"DICOM file contained compressed data. "
|
||
|
|
+ "Autoconverting with "
|
||
|
|
+ cmd[0]
|
||
|
|
+ " (this warning is shown once for each directory)"
|
||
|
|
)
|
||
|
|
dcm = _dicom.SimpleDicomReader(fname2)
|
||
|
|
|
||
|
|
self._info = dcm._info
|
||
|
|
self._data = dcm.get_numpy_array()
|
||
|
|
|
||
|
|
# Initialize series, list of DicomSeries objects
|
||
|
|
self._series = None # only created if needed
|
||
|
|
|
||
|
|
# Set progress indicator
|
||
|
|
if isinstance(progress, BaseProgressIndicator):
|
||
|
|
self._progressIndicator = progress
|
||
|
|
elif progress is True:
|
||
|
|
p = StdoutProgressIndicator("Reading DICOM")
|
||
|
|
self._progressIndicator = p
|
||
|
|
elif progress in (None, False):
|
||
|
|
self._progressIndicator = BaseProgressIndicator("Dummy")
|
||
|
|
else:
|
||
|
|
raise ValueError("Invalid value for progress.")
|
||
|
|
|
||
|
|
def _close(self):
|
||
|
|
# Clean up
|
||
|
|
self._info = None
|
||
|
|
self._data = None
|
||
|
|
self._series = None
|
||
|
|
|
||
|
|
@property
|
||
|
|
def series(self):
|
||
|
|
if self._series is None:
|
||
|
|
pi = self._progressIndicator
|
||
|
|
self._series = _dicom.process_directory(self.request, pi)
|
||
|
|
return self._series
|
||
|
|
|
||
|
|
def _get_length(self):
|
||
|
|
if self._data is None:
|
||
|
|
dcm = self.series[0][0]
|
||
|
|
self._info = dcm._info
|
||
|
|
self._data = dcm.get_numpy_array()
|
||
|
|
|
||
|
|
nslices = self._data.shape[0] if (self._data.ndim == 3) else 1
|
||
|
|
|
||
|
|
if self.request.mode[1] == "i":
|
||
|
|
# User expects one, but lets be honest about this file
|
||
|
|
return nslices
|
||
|
|
elif self.request.mode[1] == "I":
|
||
|
|
# User expects multiple, if this file has multiple slices, ok.
|
||
|
|
# Otherwise we have to check the series.
|
||
|
|
if nslices > 1:
|
||
|
|
return nslices
|
||
|
|
else:
|
||
|
|
return sum([len(serie) for serie in self.series])
|
||
|
|
elif self.request.mode[1] == "v":
|
||
|
|
# User expects a volume, if this file has one, ok.
|
||
|
|
# Otherwise we have to check the series
|
||
|
|
if nslices > 1:
|
||
|
|
return 1
|
||
|
|
else:
|
||
|
|
return len(self.series) # We assume one volume per series
|
||
|
|
elif self.request.mode[1] == "V":
|
||
|
|
# User expects multiple volumes. We have to check the series
|
||
|
|
return len(self.series) # We assume one volume per series
|
||
|
|
else:
|
||
|
|
raise RuntimeError("DICOM plugin should know what to expect.")
|
||
|
|
|
||
|
|
def _get_data(self, index):
|
||
|
|
if self._data is None:
|
||
|
|
dcm = self.series[0][0]
|
||
|
|
self._info = dcm._info
|
||
|
|
self._data = dcm.get_numpy_array()
|
||
|
|
|
||
|
|
nslices = self._data.shape[0] if (self._data.ndim == 3) else 1
|
||
|
|
|
||
|
|
if self.request.mode[1] == "i":
|
||
|
|
# Allow index >1 only if this file contains >1
|
||
|
|
if nslices > 1:
|
||
|
|
return self._data[index], self._info
|
||
|
|
elif index == 0:
|
||
|
|
return self._data, self._info
|
||
|
|
else:
|
||
|
|
raise IndexError("Dicom file contains only one slice.")
|
||
|
|
elif self.request.mode[1] == "I":
|
||
|
|
# Return slice from volume, or return item from series
|
||
|
|
if index == 0 and nslices > 1:
|
||
|
|
return self._data[index], self._info
|
||
|
|
else:
|
||
|
|
L = []
|
||
|
|
for serie in self.series:
|
||
|
|
L.extend([dcm_ for dcm_ in serie])
|
||
|
|
return L[index].get_numpy_array(), L[index].info
|
||
|
|
elif self.request.mode[1] in "vV":
|
||
|
|
# Return volume or series
|
||
|
|
if index == 0 and nslices > 1:
|
||
|
|
return self._data, self._info
|
||
|
|
else:
|
||
|
|
return (
|
||
|
|
self.series[index].get_numpy_array(),
|
||
|
|
self.series[index].info,
|
||
|
|
)
|
||
|
|
else: # pragma: no cover
|
||
|
|
raise ValueError("DICOM plugin should know what to expect.")
|
||
|
|
|
||
|
|
def _get_meta_data(self, index):
|
||
|
|
if self._data is None:
|
||
|
|
dcm = self.series[0][0]
|
||
|
|
self._info = dcm._info
|
||
|
|
self._data = dcm.get_numpy_array()
|
||
|
|
|
||
|
|
nslices = self._data.shape[0] if (self._data.ndim == 3) else 1
|
||
|
|
|
||
|
|
# Default is the meta data of the given file, or the "first" file.
|
||
|
|
if index is None:
|
||
|
|
return self._info
|
||
|
|
|
||
|
|
if self.request.mode[1] == "i":
|
||
|
|
return self._info
|
||
|
|
elif self.request.mode[1] == "I":
|
||
|
|
# Return slice from volume, or return item from series
|
||
|
|
if index == 0 and nslices > 1:
|
||
|
|
return self._info
|
||
|
|
else:
|
||
|
|
L = []
|
||
|
|
for serie in self.series:
|
||
|
|
L.extend([dcm_ for dcm_ in serie])
|
||
|
|
return L[index].info
|
||
|
|
elif self.request.mode[1] in "vV":
|
||
|
|
# Return volume or series
|
||
|
|
if index == 0 and nslices > 1:
|
||
|
|
return self._info
|
||
|
|
else:
|
||
|
|
return self.series[index].info
|
||
|
|
else: # pragma: no cover
|
||
|
|
raise ValueError("DICOM plugin should know what to expect.")
|
||
|
|
|
||
|
|
|
||
|
|
# Add this format
|
||
|
|
formats.add_format(
|
||
|
|
DicomFormat(
|
||
|
|
"DICOM",
|
||
|
|
"Digital Imaging and Communications in Medicine",
|
||
|
|
".dcm .ct .mri",
|
||
|
|
"iIvV",
|
||
|
|
)
|
||
|
|
) # Often DICOM files have weird or no extensions
|