def extractStudyDetails(inputImageFile):
"""Reads and extracts Patient's Basic Info from a DICOM file.
"""
studyList = []
dicomfile = inputImageFile
tracker = set()
trackerID=''
for i, dfile in enumerate(dicomfile):
studyDetails = {}
ds = dicomio.read_file(dfile)
if ds[0x00200010]:
# print(ds[0x00200010])
trackerID = str(ds.StudyID)
if trackerID in tracker:
''
else:
studyDetails["StudyID"]= ds.StudyID
studyDetails["StudyDescription"]=ds.StudyDescription
studyDetails["StudyDate"]= datetime.strptime(ds.StudyDate, '%Y%m%d')
studyDetails["PatientID"]=ds.PatientID
tracker.add(str(ds.StudyID))
studyList.append(studyDetails)
else:
''
return studyList
def run(path):
# Используем Python одним потоком
start_time = time.time()
paths = find_all_files(path)
for file_path in paths:
if os.path.isdir(file_path): continue
dcm = dicomio.read_file(file_path, specific_tags=REQUIRED_TAGS)
tags_py = {
t: dcm.get(t) if t in dcm else DEFAULT_TAG_VAL
for t in REQUIRED_TAGS
}
py_long = time.time() - start_time
# ----------------------------------------
# Используем Rust
start_time = time.time()
_ = py_dcm_finder_rs.load_dcm_files_in_dir(path, REQUIRED_TAGS,
DEFAULT_TAG_VAL)
rust_long = time.time() - start_time
# ----------------------------------------
# Используем Python c multiprocessing
start_time = time.time()
find_and_read_dcm_in_dir_multiproc(path)
multi_py_long = time.time() - start_time
# ----------------------------------------
print(f"Всего файлов в папке: {len(paths)}")
print("─" * 42)
print(f"| {'Python одним процессом':25} | {f'{py_long:.5f}':10} |")
print(f"| {'Rust вызванный из python':25} | {f'{rust_long:.5f}':10} |")
print(f"| {'Python мульти процес.':25} | {f'{multi_py_long:.5f}':10} |")
print("─" * 42)
def __init__(self, dataset, memmap_pixel_array=False):
self.memmap_pixel_array = memmap_pixel_array
if isinstance(dataset, Dataset):
self.ds = dataset
elif isinstance(dataset, (string_types, BytesIO)):
try:
with open(dataset, "rb") as fp:
self.ds = read_file(fp,
defer_size=100,
force=True,
stop_before_pixels=memmap_pixel_array)
if memmap_pixel_array:
self.offset = fp.tell() + 8
except:
# Raise the error for the calling method to handle
raise
else:
# Sometimes DICOM files may not have headers,
# but they should always have a SOPClassUID
# to declare what type of file it is.
# If the file doesn't have a SOPClassUID,
# then it probably isn't DICOM.
if not "SOPClassUID" in self.ds:
raise AttributeError
else:
raise AttributeError
if memmap_pixel_array:
self.filename = dataset
self.pixel_array = self.get_pixel_array
else:
if "PixelData" in self.ds:
self.pixel_array = self.ds.pixel_array
def extractPatientDetails(inputImageFile):
"""Reads and extracts Patient's Basic Info from a DICOM file.
"""
PatientList = []
dicomfile = inputImageFile
tracker = set()
for i, dfile in enumerate(dicomfile):
patientDetails = {}
ds = dicomio.read_file(dfile)
trackerID = str(ds.PatientID)
if trackerID in tracker:
''
else:
patientDetails["PatientID"]=ds.PatientID
patientDetails["PatientName"]= str.replace(str(ds.PatientName),'^',' ')
patientDetails["PatientSex"]=ds.PatientSex
if ds[0x00101010]:
patientDetails["PatientReportedAge"]=ds.PatientAge
else:
patientDetails["PatientReportedAge"]=''
dob = datetime.strptime(ds.PatientBirthDate , '%Y%m%d')
sod = datetime.strptime(ds.StudyDate, '%Y%m%d')
patientDetails["PatientBirthDate"]= dob
patientDetails['Age_Days']= str.replace(str(sod-dob),'days, 0:00:00','')
tracker.add(str(ds.PatientID))
PatientList.append(patientDetails)
return PatientList
def test_trait_names(self):
"""Test Dataset.trait_names contains element keywords"""
test_file = get_testdata_files('CT_small.dcm')[0]
ds = read_file(test_file, force=True)
names = ds.trait_names()
assert 'PatientName' in names
assert 'save_as' in names
assert 'PixelData' in names
def test_trait_names(self):
"""Test Dataset.trait_names contains element keywords"""
test_file = os.path.join(DATA_ROOT, 'test_files', 'CT_small.dcm')
ds = read_file(test_file, force=True)
names = ds.trait_names()
assert 'PatientName' in names
assert 'save_as' in names
assert 'PixelData' in names
def read_file(*args, **kwargs):
global read_file
from pydicom.dicomio import read_file
import warnings
msg = ("The read_file function has moved to pydicom.dicomio. "
"Please use 'from pydicom import dicomio; dicomio.read_file(...)'")
warnings.warn(msg, DeprecationWarning)
return read_file(*args, **kwargs)
def getTagObject(self, index):
"""Get the object storing tag information from Dicom file at the given index."""
if index not in self.tagcache:
dcm = dicomio.read_file(self.filenames[index],
stop_before_pixels=True)
self.tagcache[index] = dcm
return self.tagcache[index]
def read_file(*args, **kwargs):
global read_file
from pydicom.dicomio import read_file
import warnings
msg = ("The read_file function has moved to pydicom.dicomio. "
"Please use 'from pydicom import dicomio; dicomio.read_file(...)'")
warnings.warn(msg, DeprecationWarning)
return read_file(*args, **kwargs)
def load_dicom_file(filename, queue):
"""Load the Dicom file `filename` and put an abbreviated tag->value map onto `queue`."""
try:
dcm = dicomio.read_file(filename, stop_before_pixels=True)
tags = {t: dcm.get(t) for t in LOAD_TAGS if t in dcm}
queue.put((filename, tags))
except errors.InvalidDicomError:
pass
def extractSeriesDetails(inputImageFile):
"""Reads and extracts Patient's Basic Info from a DICOM file.
"""
seriesList = []
dicomfile = inputImageFile
tracker = set()
for i, dfile in enumerate(dicomfile):
seriesDetails = {}
ds = dicomio.read_file(dfile)
trackerID = str(ds.SeriesInstanceUID)
if trackerID in tracker:
''
else:
seriesDetails["SeriesID"]=ds.SeriesInstanceUID
seriesDetails["SeriesDescription"]=ds.SeriesDescription
if ds[0x00080060]:
seriesDetails["Modality"]=ds.Modality
else:
seriesDetails["Modality"]=''
if ds[0x00200010]:
seriesDetails["StudyID"]=ds.StudyID
else:
seriesDetails["StudyID"]=''
# if ds[0x00181030]:
# seriesDetails["ProtocolName"]=ds.ProtocolName
# else:
# seriesDetails["ProtocolName"]=''
# if ds[0x00540500]:
# seriesDetails["SliceProgressionDirection"]=ds.SliceProgressionDirection
# else:
# seriesDetails["SliceProgressionDirection"]=''
# if ds[0x00280010]:
# seriesDetails["Rows"]=ds.Rows
# else:
# seriesDetails["Rows"]=''
# if ds[0x00280011]:
# seriesDetails["Columns"]=ds.Columns
# else:
# seriesDetails["Columns"]=''
seriesDetails["PatientID"]=ds.PatientID
tracker.add(str(ds.SeriesInstanceUID))
seriesList.append(seriesDetails)
return seriesList
def loadDicomFiles(filenames, queue):
"""Load the Dicom files `filenames' and put an abbreviated tag->value map for each onto `queue'."""
for filename in filenames:
try:
dcm = dicomio.read_file(filename, stop_before_pixels=True)
tags = {t: dcm.get(t) for t in loadTags if t in dcm}
queue.put((filename, tags))
except errors.InvalidDicomError:
pass
def testEqualityFileMeta(self):
"""Dataset: equality returns correct value if with metadata"""
d = read_file(self.test_file)
e = read_file(self.test_file)
self.assertTrue(d == e)
e.is_implicit_VR = not e.is_implicit_VR
self.assertFalse(d == e)
e.is_implicit_VR = not e.is_implicit_VR
self.assertTrue(d == e)
e.is_little_endian = not e.is_little_endian
self.assertFalse(d == e)
e.is_little_endian = not e.is_little_endian
self.assertTrue(d == e)
e.filename = 'test_filename.dcm'
self.assertFalse(d == e)
def testEqualityFileMeta(self):
"""Dataset: equality returns correct value if with metadata"""
d = read_file(self.test_file)
e = read_file(self.test_file)
self.assertTrue(d == e)
e.is_implicit_VR = not e.is_implicit_VR
self.assertFalse(d == e)
e.is_implicit_VR = not e.is_implicit_VR
self.assertTrue(d == e)
e.is_little_endian = not e.is_little_endian
self.assertFalse(d == e)
e.is_little_endian = not e.is_little_endian
self.assertTrue(d == e)
e.filename = "test_filename.dcm"
self.assertFalse(d == e)
def testLatin1(self):
"""charset: can read and decode latin_1 file........................"""
ds = dicomio.read_file(latin1_file)
ds.decode()
# Make sure don't get unicode encode error on converting to string
expected = u'Buc^J\xe9r\xf4me'
got = ds.PatientName
self.assertEqual(expected, got,
"Expected %r, got %r" % (expected, got))
def test_get_item(self):
"""Test Dataset.get_item"""
ds = Dataset()
ds.CommandGroupLength = 120 # 0000,0000
ds.SOPInstanceUID = '1.2.3.4' # 0008,0018
# Test non-deferred read
assert ds.get_item(0x00000000) == ds[0x00000000]
assert ds.get_item(0x00000000).value == 120
assert ds.get_item(0x00080018) == ds[0x00080018]
assert ds.get_item(0x00080018).value == '1.2.3.4'
# Test deferred read
test_file = get_testdata_files('MR_small.dcm')[0]
ds = read_file(test_file, force=True, defer_size='0.8 kB')
ds_ref = read_file(test_file, force=True)
# get_item will follow the deferred read branch
assert ds.get_item((0x7fe00010)).value == ds_ref.PixelData
def testLatin1(self):
"""charset: can read and decode latin_1 file........................"""
ds = dicomio.read_file(latin1_file)
ds.decode()
# Make sure don't get unicode encode error on converting to string
expected = u'Buc^J\xe9r\xf4me'
got = ds.PatientName
self.assertEqual(expected, got,
"Expected %r, got %r" % (expected, got))
def testRead(self):
"""Unicode: Can read a file with unicode characters in name..."""
uni_name = u'test°'
# verify first that we could encode file name in this environment
try:
_ = uni_name.encode(sys.getfilesystemencoding())
except UnicodeEncodeError:
print("SKIP: Environment doesn't support unicode filenames")
return
try:
dicomio.read_file(uni_name)
except UnicodeEncodeError:
self.fail("UnicodeEncodeError generated for unicode name")
# ignore file doesn't exist error
except IOError:
pass
def testEncodingWithSpecificTags(self):
"""Encoding is correctly applied even if Specific Character Set
is not in specific tags..."""
ds = dicomio.read_file(jp_file, specific_tags=['PatientName'])
ds.decode()
self.assertEqual(1, len(ds))
expected = ('Yamada^Tarou='
'\033$B;3ED\033(B^\033$BB@O:\033(B='
'\033$B$d$^$@\033(B^\033$B$?$m$&\033(B')
self.assertEqual(expected, ds.PatientName)
def testEncodingWithSpecificTags(self):
"""Encoding is correctly applied even if Specific Character Set
is not in specific tags..."""
ds = dicomio.read_file(jp_file, specific_tags=['PatientName'])
ds.decode()
self.assertEqual(1, len(ds))
expected = ('Yamada^Tarou='
'\033$B;3ED\033(B^\033$BB@O:\033(B='
'\033$B$d$^$@\033(B^\033$B$?$m$&\033(B')
self.assertEqual(expected, ds.PatientName)
def testNestedCharacterSets(self):
"""charset: can read and decode SQ with different encodings........."""
ds = dicomio.read_file(sq_encoding_file)
ds.decode()
# These datasets inside of the SQ cannot be decoded with default_encoding
# OR UTF-8 (the parent dataset's encoding). Instead, we make sure that it
# is decoded using the (0008,0005) tag of the dataset
expected = u'\uff94\uff8f\uff80\uff9e^\uff80\uff9b\uff73=\u5c71\u7530^\u592a\u90ce=\u3084\u307e\u3060^\u305f\u308d\u3046'
got = ds[0x32, 0x1064][0].PatientName
self.assertEqual(expected, got,
"Expected %r, got %r" % (expected, got))
def test_set_convert_private_elem_from_raw(self):
"""Test Dataset.__setitem__ with a raw private element"""
test_file = get_testdata_files('CT_small.dcm')[0]
ds = read_file(test_file, force=True)
# 'tag VR length value value_tell is_implicit_VR is_little_endian'
elem = RawDataElement((0x0043, 0x1029), 'OB', 2, b'\x00\x01', 0, True,
True)
ds.__setitem__((0x0043, 0x1029), elem)
assert ds[(0x0043, 0x1029)].value == b'\x00\x01'
assert type(ds[(0x0043, 0x1029)]) == DataElement
def __init__(self, dataset, memmap_pixel_array=False):
"""Initialize DicomParser from a pydicom Dataset or DICOM file.
Parameters
----------
dataset : pydicom Dataset or filename
pydicom dataset object or DICOM file location
memmap_pixel_array : bool, optional
Enable pixel array access via memory mapping, by default False
Raises
------
AttributeError
Raised if SOPClassUID is not present in the pydicom Dataset
AttributeError
Raised if the DICOM file or pydicom Dataset cannot be read
"""
self.memmap_pixel_array = memmap_pixel_array
if isinstance(dataset, Dataset):
self.ds = dataset
elif isinstance(dataset, (string_types, BytesIO)):
try:
with open(dataset, "rb") as fp:
self.ds = read_file(fp,
defer_size=100,
force=True,
stop_before_pixels=memmap_pixel_array)
if memmap_pixel_array:
self.offset = fp.tell() + 8
except Exception:
# Raise the error for the calling method to handle
raise
else:
# Sometimes DICOM files may not have headers,
# but they should always have a SOPClassUID
# to declare what type of file it is.
# If the file doesn't have a SOPClassUID,
# then it probably isn't DICOM.
if "SOPClassUID" not in self.ds:
raise AttributeError
else:
raise AttributeError
# Remove the PixelData attribute if it is not set.
# i.e. RTStruct does not contain PixelData and its presence can confuse
# the parser
if "PixelData" in self.ds and self.ds.PixelData is None:
delattr(self.ds, 'PixelData')
if memmap_pixel_array:
self.filename = dataset
self.pixel_array = self.get_pixel_array
else:
if "PixelData" in self.ds:
self.pixel_array = self.ds.pixel_array
def getPixelData(self, index):
"""Get the pixel data array for file at position `index` in self.filenames, or None if no pixel data."""
if index not in self.imgcache:
try:
dcm = dicomio.read_file(self.filenames[index])
rslope = float(dcm.get("RescaleSlope", 1) or 1)
rinter = float(dcm.get("RescaleIntercept", 0) or 0)
img = dcm.pixel_array * rslope + rinter
except:
img = None # exceptions indicate that the pixel data doesn't exist or isn't readable so ignore
self.imgcache[index] = img
return self.imgcache[index]
def getPixelData(self, index):
'''Get the pixel data Numpy array for file at position `index` in self.filenames, or None if there is no pixel data.'''
if index not in self.imgcache:
img = None
try:
dcm = dicomio.read_file(self.filenames[index])
rslope = float(dcm.get('RescaleSlope', 1) or 1)
rinter = float(dcm.get('RescaleIntercept', 0) or 0)
img = dcm.pixel_array * rslope + rinter
except Exception:
pass # exceptions indicate that the pixel data doesn't exist or isn't readable so ignore
self.imgcache[index] = img
return self.imgcache[index]
def loadDicomZip(filename, statusfunc=lambda s, c, n: None):
"""
Load Dicom images from given zip file `filename'. This uses the status callback `statusfunc' like loadDicomDir().
Loaded files will have their pixel data thus avoiding the need to reload the zip file when an image is viewed but is
at the expense of load time and memory. Return value is a sequence of DicomSeries objects in no particular order.
"""
series = {}
count = 0
with zipfile.ZipFile(filename) as z:
names = z.namelist()
numfiles = len(names)
for n in names:
nfilename = "%s?%s" % (filename, n)
s = BytesIO(z.read(n))
try:
dcm = dicomio.read_file(s)
except:
pass # ignore files which aren't Dicom files, various exceptions raised so no concise way to do this
else:
seriesid = dcm.get("SeriesInstanceUID", "???")
if seriesid not in series:
series[seriesid] = DicomSeries(seriesid, nfilename)
# need to load image data now since we don't want to reload the zip file later when an image is viewed
try: # attempt to create the image matrix, store None if this doesn't work
rslope = float(dcm.get("RescaleSlope", 1) or 1)
rinter = float(dcm.get("RescaleIntercept", 0) or 0)
img = dcm.pixel_array * rslope + rinter
except:
img = None
s = series[seriesid]
s.addFile(nfilename, dcm)
s.tagcache[len(s.filenames) - 1] = dcm
s.imgcache[len(s.filenames) - 1] = img
count += 1
# update status only 100 times, doing it too frequently really slows things down
if numfiles < 100 or count % (numfiles // 100) == 0:
statusfunc("Loading DICOM files", count, numfiles)
statusfunc("", 0, 0)
return list(series.values())
def _load_dicom_files(filenames: str, queue):
"""Для DICOM-файлов из списка filenames загружаем минимальный набор тегов и помещаем в очередь."""
for filename in filenames:
try:
dcm = dicomio.read_file(filename, specific_tags=REQUIRED_TAGS)
tags = {
t: dcm.get(t) if t in dcm else DEFAULT_TAG_VAL
for t in REQUIRED_TAGS
}
queue.put((filename, tags))
except errors.InvalidDicomError:
pass
except AttributeError:
pass
except:
pass
def getPixelData(self, index):
'''Get the pixel data Numpy array for file at position `index` in self.filenames, or None if there is no pixel data.'''
if index not in self.imgcache:
img = None
try:
dcm = dicomio.read_file(self.filenames[index])
if dcm.pixel_array is not None:
rslope = float(dcm.get('RescaleSlope', 1))
rinter = float(dcm.get('RescaleIntercept', 0))
img = dcm.pixel_array * rslope + rinter
except Exception:
pass
self.imgcache[index] = img
return self.imgcache[index]
def anonymize_folder(folder, new_patient_name="Anonymous", verbose=True):
"""
Anonymizes all dicom files inside a given folder. By default,
the patient name attribute is replaced by "Anonymous" but an
alternative name can be provided as an argument to the function.
NOTE: Assumes all files in the folder belong to the same patient.
Currently, the following DICOM fields are anonymised:
RTPlanTime, ReviewTime, StudyTime, RTPlanDate, ReviewDate, StudyDate,
PatientBirthDate, PatientName, PatientID, StudyID, ReviewerName.
"""
files = match_dicom(folder)
times = ["RTPlanTime", "ReviewTime", "StudyTime"]
dates = ["RTPlanDate", "ReviewDate", "StudyDate", "PatientBirthDate"]
# Not guaranteed to be unique, but they're not UIDs so it shouldn't matter.
new_patientID = "ANON" + str(random.randint(0, 1000000))
new_studyID = "ANON" + str(random.randint(0, 1000000))
for dicomfile in files:
try:
df = dicom.read_file(dicomfile)
if verbose:
print "Anonymizing %s" % dicomfile
if "PatientName" in df:
df.PatientName = new_patient_name
if "PatientID" in df:
df.PatientID = new_patientID
if "StudyID" in df:
df.StudyID = new_studyID
if "ReviewerName" in df:
df.ReviewerName = "ANON"
for date in dates:
if date in df:
setattr(df, date, "19000101")
for time in times:
if time in df:
setattr(df, time, "111111")
df.save_as(dicomfile)
except dicom.filereader.InvalidDicomError:
pass
def anonymize_folder(folder, new_patient_name="Anonymous", verbose=True):
"""
Anonymizes all dicom files inside a given folder. By default,
the patient name attribute is replaced by "Anonymous" but an
alternative name can be provided as an argument to the function.
NOTE: Assumes all files in the folder belong to the same patient.
Currently, the following DICOM fields are anonymised:
RTPlanTime, ReviewTime, StudyTime, RTPlanDate, ReviewDate, StudyDate,
PatientBirthDate, PatientName, PatientID, StudyID, ReviewerName.
"""
files = match_dicom(folder)
times = ["RTPlanTime", "ReviewTime", "StudyTime"]
dates = ["RTPlanDate", "ReviewDate", "StudyDate", "PatientBirthDate"]
# Not guaranteed to be unique, but they're not UIDs so it shouldn't matter.
new_patientID = "ANON" + str(random.randint(0, 1000000))
new_studyID = "ANON" + str(random.randint(0, 1000000))
for dicomfile in files:
try:
df = dicom.read_file(dicomfile)
if verbose:
print "Anonymizing %s" % dicomfile
if "PatientName" in df:
df.PatientName = new_patient_name
if "PatientID" in df:
df.PatientID = new_patientID
if "StudyID" in df:
df.StudyID = new_studyID
if "ReviewerName" in df:
df.ReviewerName = "ANON"
for date in dates:
if date in df:
setattr(df, date, "19000101")
for time in times:
if time in df:
setattr(df, time, "111111")
df.save_as(dicomfile)
except dicom.filereader.InvalidDicomError:
pass
def _imread_dcm(filename):
"""Open DICOM image with pydicom and return a NumPy array"""
try:
# pydicom 1.0
from pydicom import dicomio
except ImportError:
# pydicom 0.9
import dicom as dicomio
dcm = dicomio.read_file(filename, force=True)
# **********************************************************************
# The following is necessary until pydicom numpy support is improved:
# (after that, a simple: 'arr = dcm.PixelArray' will work the same)
format_str = "%sint%s" % (
("u", "")[dcm.PixelRepresentation], dcm.BitsAllocated)
try:
dtype = np.dtype(format_str)
except TypeError:
raise TypeError("Data type not understood by NumPy: "
"PixelRepresentation=%d, BitsAllocated=%d" %
(dcm.PixelRepresentation, dcm.BitsAllocated))
arr = np.fromstring(dcm.PixelData, dtype)
try:
# pydicom 0.9.3:
dcm_is_little_endian = dcm.isLittleEndian
except AttributeError:
# pydicom 0.9.4:
dcm_is_little_endian = dcm.is_little_endian
if dcm_is_little_endian != (sys.byteorder == "little"):
arr.byteswap(True)
if hasattr(dcm, "NumberofFrames") and dcm.NumberofFrames > 1:
if dcm.SamplesperPixel > 1:
arr = arr.reshape(dcm.SamplesperPixel, dcm.NumberofFrames,
dcm.Rows, dcm.Columns)
else:
arr = arr.reshape(dcm.NumberofFrames, dcm.Rows, dcm.Columns)
else:
if dcm.SamplesperPixel > 1:
if dcm.BitsAllocated == 8:
arr = arr.reshape(dcm.SamplesperPixel, dcm.Rows, dcm.Columns)
else:
raise NotImplementedError(
"This code only handles "
"SamplesPerPixel > 1 if Bits Allocated = 8")
else:
arr = arr.reshape(dcm.Rows, dcm.Columns)
# **********************************************************************
return arr
def get_tag(dicomPath1, dicomPath2):
dcm = pydicom.dcmread(dicomPath1) # 选择一个普通的非压缩dcm文件作为转换模板
image = sitk.ReadImage(dicomPath2)
image_array = sitk.GetArrayFromImage(image)
np_array = np.int16(image_array)
image_array = np.squeeze(np_array) # 读取有压缩分段的dcm图像数据
dataset = pydicom.dcmread(dicomPath2) # 用来修改Tag，图像读写相关的tag都要改
dcm.data_element('PixelSpacing').value = dataset.data_element(
'PixelSpacing').value
dcm.data_element('RescaleIntercept').value = dataset.data_element(
'RescaleIntercept').value
dcm.data_element('RescaleSlope').value = dataset.data_element(
'RescaleSlope').value
dcm.PixelData = image_array.tobytes()
dcm.save_as(dicomPath2)
dcm = dicomio.read_file(dicomPath2)
return dcm.StudyDescription
def _imread_dcm(filename):
"""Open DICOM image with pydicom and return a NumPy array"""
try:
# pydicom 1.0
from pydicom import dicomio
except ImportError:
# pydicom 0.9
import dicom as dicomio
dcm = dicomio.read_file(filename, force=True)
# **********************************************************************
# The following is necessary until pydicom numpy support is improved:
# (after that, a simple: 'arr = dcm.PixelArray' will work the same)
format_str = '%sint%s' % (('u', '')[dcm.PixelRepresentation],
dcm.BitsAllocated)
try:
dtype = np.dtype(format_str)
except TypeError:
raise TypeError("Data type not understood by NumPy: "
"PixelRepresentation=%d, BitsAllocated=%d" % (
dcm.PixelRepresentation, dcm.BitsAllocated))
arr = np.fromstring(dcm.PixelData, dtype)
try:
# pydicom 0.9.3:
dcm_is_little_endian = dcm.isLittleEndian
except AttributeError:
# pydicom 0.9.4:
dcm_is_little_endian = dcm.is_little_endian
if dcm_is_little_endian != (sys.byteorder == 'little'):
arr.byteswap(True)
if hasattr(dcm, 'NumberofFrames') and dcm.NumberofFrames > 1:
if dcm.SamplesperPixel > 1:
arr = arr.reshape(dcm.SamplesperPixel, dcm.NumberofFrames,
dcm.Rows, dcm.Columns)
else:
arr = arr.reshape(dcm.NumberofFrames, dcm.Rows, dcm.Columns)
else:
if dcm.SamplesperPixel > 1:
if dcm.BitsAllocated == 8:
arr = arr.reshape(dcm.SamplesperPixel, dcm.Rows, dcm.Columns)
else:
raise NotImplementedError("This code only handles "
"SamplesPerPixel > 1 if Bits Allocated = 8")
else:
arr = arr.reshape(dcm.Rows, dcm.Columns)
# **********************************************************************
return arr
def build_dcm_dict(dcmpath, fn_dict, image_dict_pkl="image_dict.pkl"):
slice_location = []
trigger_time = []
image_dict = {}
hash_value = hashlib.sha1(dcmpath).hexdigest()
#count = 0
for dirname, subdirlist, filelist in os.walk(dcmpath):
for filen in filelist:
filePath = os.path.join(dirname,filen)
#print(filePath)
#print(dirname, subdirlist, filelist)
#print(filePath)
#print(f.SliceLocation)
try:
f = dicomio.read_file(filePath, stop_before_pixels=True)
except Exception as e:
print(str(e))
print("error: {0}".format(filen))
continue
#dictionary of images
if (f.TriggerTime not in image_dict.keys()):
image_dict[f.TriggerTime] = {}
if (f.SliceLocation not in image_dict[f.TriggerTime].keys()):
image_dict[f.TriggerTime][f.SliceLocation] = {}
for fn_key in fn_dict.keys():
if( fn_key not in image_dict[f.TriggerTime][f.SliceLocation].keys()):
image_dict[f.TriggerTime][f.SliceLocation][fn_key] = {}
#print(fn_key, filen, fn_dict[fn_key])
if (fnmatch.fnmatch(filen, fn_dict[fn_key])):
#print('did i get here')
if (f.SOPInstanceUID not in image_dict[f.TriggerTime][f.SliceLocation][fn_key].keys()):
image_dict[f.TriggerTime][f.SliceLocation][fn_key][f.SOPInstanceUID] = [filePath]
#print(image_dict[fn_key])
if (f.TriggerTime not in trigger_time):
trigger_time.append(f.TriggerTime)
if (f.SliceLocation not in slice_location):
slice_location.append(f.SliceLocation)
print("writing {0} to current working directory".format(image_dict_pkl))
with open(os.path.join(os.getcwd(), image_dict_pkl), "wb") as pkl_f:
pickle.dump(hash_value, pkl_f, -1)
pickle.dump(image_dict, pkl_f, -1)
return image_dict
def convert_dcm_to_csv(id_label_map, input_filename, output_filename):
print("Start to convert dcm: {} to csv: {}".format(input_filename,
output_filename))
ds = dicomio.read_file(input_filename)
image_ndarray = ds.pixel_array
label = id_label_map[ds.PatientID]
csv_content = "{},".format(label)
# Example: 512 * 512
for i in image_ndarray:
for j in i:
csv_content += "{},".format(j)
csv_content = csv_content[:-1] + "\n"
with open(output_filename, "w") as f:
f.write(csv_content)
print("Successfully convert dcm: {} to csv: {}".format(
input_filename, output_filename))
def convert_dcm_to_csv(id_label_map, input_filename, output_filename):
print("Start to convert dcm: {} to csv: {}".format(input_filename,
output_filename))
ds = dicomio.read_file(input_filename)
image_ndarray = ds.pixel_array
label = id_label_map[ds.PatientID]
csv_content = "{},".format(label)
# Example: 512 * 512
for i in image_ndarray:
for j in i:
csv_content += "{},".format(j)
csv_content = csv_content[:-1] + "\n"
with open(output_filename, "w") as f:
f.write(csv_content)
print("Successfully convert dcm: {} to csv: {}".format(input_filename,
output_filename))
def __init__(self, dataset):
if isinstance(dataset, Dataset):
self.ds = dataset
elif isinstance(dataset, (string_types, BytesIO)):
try:
self.ds = \
read_file(dataset, defer_size=100, force=True)
except:
# Raise the error for the calling method to handle
raise
else:
# Sometimes DICOM files may not have headers,
# but they should always have a SOPClassUID
# to declare what type of file it is.
# If the file doesn't have a SOPClassUID,
# then it probably isn't DICOM.
if not "SOPClassUID" in self.ds:
raise AttributeError
else:
raise AttributeError
def __init__(self, dataset):
if isinstance(dataset, Dataset):
self.ds = dataset
elif isinstance(dataset, string_types):
try:
self.ds = \
read_file(dataset, defer_size=100, force=True)
except:
# Raise the error for the calling method to handle
raise
else:
# Sometimes DICOM files may not have headers,
# but they should always have a SOPClassUID
# to declare what type of file it is.
# If the file doesn't have a SOPClassUID,
# then it probably isn't DICOM.
if not "SOPClassUID" in self.ds:
raise AttributeError
else:
raise AttributeError
def loadDicomZip(filename, statusfunc=lambda s, c, n: None):
series = {}
count = 0
with zipfile.ZipFile(filename) as z:
names = z.namelist()
numfiles = len(names)
for n in names:
nfilename = '%s?%s' % (filename, n)
s = StringIO(z.read(n))
try:
dcm = dicomio.read_file(s)
except:
pass # ignore files which aren't Dicom files
else:
seriesid = dcm.get('SeriesInstanceUID', '???')
if seriesid not in series:
series[seriesid] = DicomSeries(seriesid, nfilename)
try: # attempt to create the image matrix, store None if this doesn't work
rslope = float(dcm.get('RescaleSlope', 1) or 1)
rinter = float(dcm.get('RescaleIntercept', 0) or 0)
img = dcm.pixel_array * rslope + rinter
except:
img = None
s = series[seriesid]
s.addFile(nfilename, dcm)
s.tagcache[len(s.filenames) - 1] = dcm
s.imgcache[len(s.filenames) - 1] = img
count += 1
# update status only 100 times, doing it too frequently really slows things down
if numfiles < 100 or count % (numfiles // 100) == 0:
statusfunc('Loading DICOM files', count, numfiles)
statusfunc('', 0, 0)
return list(series.values())
def read_file(*args, **kwargs):
global read_file
from pydicom.dicomio import read_file
return read_file(*args, **kwargs)
def create_image_volume(image_dict, mri_2_cfd_map, image_type, return_coord=True):
trigger_t = mri_2_cfd_map[0]
slice_location = image_dict[trigger_t].keys()
dcm_files = []
for loc in slice_location:
for image_id in image_dict[trigger_t][loc][image_type].keys():
dcm_files.append(image_dict[trigger_t][loc][image_type][image_id][0])
path_loc = zip(dcm_files, slice_location)
path_loc.sort(key=lambda x: x[1])
dcm_files, slice_location = zip(*path_loc)
#print(slice_location)
# get reference image
#print(len(dcm_files), dcm_files)
ref_image = dicomio.read_file(dcm_files[0])
# load dimensions based on the number of rows columns and slices
const_pixel_dims = (int(ref_image.Rows), int(ref_image.Columns), len(dcm_files))
#check it whether image has been interpolated
if (hasattr(ref_image, 'SpacingBetweenSlices')):
if(ref_image.SpacingBetweenSlices < ref_image.SliceThickness):
z_spacing = float(ref_image.SpacingBetweenSlices)
else:
z_spacing = float(ref_image.SliceThickness)
else:
z_spacing = float(ref_image.SliceThickness)
# the array is sized based on 'const_pixel_dims
array_dicom = np.zeros(const_pixel_dims, dtype=np.float64) #ref_image.pixel_array.dtype)
print(array_dicom.shape)
#loop through all the DICOM FILES
for filenamedcm in dcm_files:
#read the file
ds = dicomio.read_file(filenamedcm)
#store the raw image data
array_dicom[:, :, dcm_files.index(filenamedcm)] = (
np.asarray(ds.pixel_array, dtype=np.float64) * (
np.float64(ds.RescaleSlope)) + np.float64(ds.RescaleIntercept))
#testindx = np.where(array_dicom !=0)
#minx = np.min(testindx[0])
#miny = np.min(testindx[1])
#minz = np.min(testindx[2])
#maxx = np.max(testindx[0])
#maxy = np.max(testindx[1])
#maxz = np.max(testindx[2])
if (return_coord == True):
# load spacing values in mm
const_pixel_spacing = (float(ref_image.PixelSpacing[0]),
float(ref_image.PixelSpacing[1]), z_spacing)
x = np.arange(const_pixel_spacing[0]/2.0, (const_pixel_dims[0]+1)*const_pixel_spacing[0]-1.0,
const_pixel_spacing[0])
y = np.arange(const_pixel_spacing[1]/2.0, (const_pixel_dims[1]+1)*const_pixel_spacing[1]-1.0,
const_pixel_spacing[1])
z = np.arange(const_pixel_spacing[2]/2.0, (const_pixel_dims[2]+1)*const_pixel_spacing[2]-1.0,
const_pixel_spacing[2])
return array_dicom, x,y,z
else:
return array_dicom
dicom_test = np.testing.dec.skipif(not have_dicom, "could not import pydicom")
from .. import dicomwrappers as didw
from .. import dicomreaders as didr
from ...volumeutils import endian_codes
from unittest import TestCase
from nose.tools import assert_true, assert_false, assert_equal, assert_not_equal, assert_raises
from numpy.testing import assert_array_equal, assert_array_almost_equal
IO_DATA_PATH = pjoin(dirname(__file__), "data")
DATA_FILE = pjoin(IO_DATA_PATH, "siemens_dwi_1000.dcm.gz")
DATA_FILE_PHILIPS = pjoin(IO_DATA_PATH, "philips_mprage.dcm.gz")
if have_dicom:
DATA = read_file(gzip.open(DATA_FILE))
DATA_PHILIPS = read_file(gzip.open(DATA_FILE_PHILIPS))
else:
DATA = None
DATA_PHILIPS = None
DATA_FILE_B0 = pjoin(IO_DATA_PATH, "siemens_dwi_0.dcm.gz")
DATA_FILE_SLC_NORM = pjoin(IO_DATA_PATH, "csa_slice_norm.dcm")
DATA_FILE_DEC_RSCL = pjoin(IO_DATA_PATH, "decimal_rescale.dcm")
DATA_FILE_4D = pjoin(IO_DATA_PATH, "4d_multiframe_test.dcm")
# This affine from our converted image was shown to match our image spatially
# with an image from SPM DICOM conversion. We checked the matching with SPM
# check reg. We have flipped the first and second rows to allow for rows, cols
# transpose in current return compared to original case.
EXPECTED_AFFINE = np.array( # do this for philips?
[
def de_sensitive(path, write_to):
dc = dicomio.read_file(path, force=True)
for tag in info_deleted:
if tag in dc:
del dc[dc.data_element(tag).tag]
dicomio.write_file(write_to, dc)
from .. import dicomwrappers as didw
from .. import dicomreaders as didr
from ...volumeutils import endian_codes
from unittest import TestCase
from nose.tools import (assert_true, assert_false, assert_equal,
assert_not_equal, assert_raises)
from numpy.testing import assert_array_equal, assert_array_almost_equal
IO_DATA_PATH = pjoin(dirname(__file__), 'data')
DATA_FILE = pjoin(IO_DATA_PATH, 'siemens_dwi_1000.dcm.gz')
DATA_FILE_PHILIPS = pjoin(IO_DATA_PATH, 'philips_mprage.dcm.gz')
if have_dicom:
DATA = read_file(gzip.open(DATA_FILE))
DATA_PHILIPS = read_file(gzip.open(DATA_FILE_PHILIPS))
else:
DATA = None
DATA_PHILIPS = None
DATA_FILE_B0 = pjoin(IO_DATA_PATH, 'siemens_dwi_0.dcm.gz')
DATA_FILE_SLC_NORM = pjoin(IO_DATA_PATH, 'csa_slice_norm.dcm')
DATA_FILE_DEC_RSCL = pjoin(IO_DATA_PATH, 'decimal_rescale.dcm')
DATA_FILE_4D = pjoin(IO_DATA_PATH, '4d_multiframe_test.dcm')
# This affine from our converted image was shown to match our image spatially
# with an image from SPM DICOM conversion. We checked the matching with SPM
# check reg. We have flipped the first and second rows to allow for rows, cols
# transpose in current return compared to original case.
EXPECTED_AFFINE = np.array( # do this for philips?
[[-1.796875, 0, 0, 115], [0, -1.79684984, -0.01570896, 135.028779],
def transform2(iminfo1):
cos = iminfo1.ImageOrientationPatient
cosines = [np.float64(val) for val in cos]
ipp = iminfo1.ImagePositionPatient
normal = [0., 0., 0.]
normal[0] = cosines[1]*cosines[5] - cosines[2]*cosines[4]
normal[1] = cosines[2]*cosines[3] - cosines[0]*cosines[5]
normal[2] = cosines[0]*cosines[4] - cosines[1]*cosines[3]
#print(normal)
dist = 0.0
for i in range(3):
dist += normal[i]*np.float64(ipp[i])
#print(dist)
return dist
if __name__ == '__main__':
dcm_path = "/home/ksansom/caseFiles/mri/images/0.4/102"
#dcm_path = "/Users/sansomk/caseFiles/mri/E431791260_merge/0.4/102"
ds1 = dicomio.read_file(os.path.join(dcm_path, 'E431791260S201I001.dcm'))
ds2 = dicomio.read_file(os.path.join(dcm_path, 'E431791260S201I002.dcm'))
M, Rot = getTransformMatrix(ds1, ds2)
print(M)
print(Rot)
dist1 = transform2(ds1)
dist2 = transform2(ds2)
print(dist2-dist1)
def testExplicitISO2022_IR6(self):
"""charset: can decode file with multi-valued data elements........."""
ds = dicomio.read_file(explicit_ir6_file)
ds.decode()
from pydicom import dicomio
directory = "/media/carlos/CE2CDDEF2CDDD317/concursos/cancer/stage 1 samples/"
patient = "0a0c32c9e08cc2ea76a71649de56be6d"
ds = dicomio.read_file(directory + patient +
"/0a67f9edb4915467ac16a565955898d3.dcm") # plan dataset
print "name:", ds.PatientName
print "dir setup:", ds.dir(
"setup") # get a list of tags with "setup" somewhere in the name
print ds
#print ds.PatientSetupSequence[0]
#ds.PatientSetupSequence[0].PatientPosition = "HFP"
#ds.save_as("rtplan2.dcm")
('?' lines from difflib removed - no use here)
"""
#import sys
from pydicom import dicomio
import difflib
# only used as a script
#if len(sys.argv) != 3:
# print(usage)
# sys.exit()
file1 = "/Users/sansomk/caseFiles/mri/E431791260_FlowVol_01/flow/FlowX_001.dcm"
file2 = "/Users/sansomk/caseFiles/mri/E431791260_FlowVol_01/flow/FlowZ_001.dcm"
datasets = (dicomio.read_file(file1, force=True),
dicomio.read_file(file2, force=True))
# diflib compare functions require a list of lines, each terminated with newline character
# massage the string representation of each dicom dataset into this form:
rep = []
for dataset in datasets:
lines = str(dataset).split("\n")
lines = [line + "\n" for line in lines] # add the newline to end
rep.append(lines)
diff = difflib.Differ()
for line in diff.compare(rep[0], rep[1]):
if line[0] != "?":
print(line)
def testStandardFile(self):
"""charset: can read and decode standard file without special char.."""
ds = dicomio.read_file(normal_file)
ds.decode()
def testMultiPN(self):
"""charset: can decode file with multi-valued data elements........."""
ds = dicomio.read_file(multiPN_file)
ds.decode()
################################################################################
if __name__ == '__main__':
#dcm_path = "/home/sansomk/caseFiles/mri/images/E431791260_Merge/0.4/102"
#dcm_path = "/home/sansomk/caseFiles/mri/images/E431791260_FlowVol_01/mag"
#dcm_path = "/home/ksansom/caseFiles/mri/images/0.4/102/"
dcm_path = "/Users/sansomk/caseFiles/mri/E431791260_merge/0.4/102"
dcm_files = []
slice_location = []
acq_N = []
trig_count = 0
for dirname, subdirlist, filelist in os.walk(dcm_path):
for filen in filelist:
filePath = os.path.join(dirname, filen)
try:
#print(filePath)
f = dicomio.read_file(filePath, stop_before_pixels=True)
except Exception as e:
print(str(e))
print("error: {0}".format(filen))
if (hasattr(f, "TriggerTime")):
if (f.TriggerTime < 1.0 and filePath not in dcm_files):
dcm_files.append(filePath)
slice_location.append(f.SliceLocation)
acq_N.append(f.AcquisitionNumber)
else:
trig_count += 1
dcm_files.append(filePath)
slice_location.append(f.SliceLocation)
acq_N.append(f.AcquisitionNumber)
if (trig_count > 0):
