def get_gsps_file_metadata():
file_meta = Dataset()
file_meta.MediaStorageSOPClassUID = "1.2.840.10008.5.1.4.1.1.11.1" # Grayscale Softcopy Presentation State Storage SOP Class
file_meta.MediaStorageSOPInstanceUID = dicom.UID.generate_uid()
file_meta.ImplementationClassUID = "1.2.276.0.7230010.3.0.3.4.1"
file_meta.ImplementationVersionName = "GSPS_DEMO"
return file_meta
def OnReceiveStore(SOPClass, DS):
print "Received C-STORE"
# do something with dataset. For instance, store it on disk.
file_meta = Dataset()
file_meta.MediaStorageSOPClassUID = DS.SOPClassUID
file_meta.MediaStorageSOPInstanceUID = DS.SOPInstanceUID # Change to my own UID via dicom.UID.generate_uid() though I should make sure such genereated UIDs use my orgroot.
file_meta.ImplementationClassUID = "1.2.826.0.1.3680043.9.5066.0" # My UID for my implementation, with a '.0' appended to it to represent development testing, ie the UID I got from Medical Connections.
file_meta.ImplementationVersionName = "DICOMMETRICS-DEV" # My implementation version name. Remember to change this for each version. Remember to correspondingly change the ImplementationClassUID too.
filename = '%s/%s.dcm' % (tempfile.gettempdir(), DS.SOPInstanceUID)
ds = FileDataset(filename, {}, file_meta=file_meta, preamble="\0" * 128)
ds.update(DS)
ds.is_little_endian = True
ds.is_implicit_VR = True
ds.save_as(filename)
print "File %s written" % filename
# must return appropriate status
return SOPClass.Success
def OnReceiveStore(SOPClass, DS):
print "Received C-STORE"
# do something with dataset. For instance, store it on disk.
file_meta = Dataset()
file_meta.MediaStorageSOPClassUID = DS.SOPClassUID
file_meta.MediaStorageSOPInstanceUID = DS.SOPInstanceUID # Change to my own UID via dicom.UID.generate_uid() though I should make sure such genereated UIDs use my orgroot.
file_meta.ImplementationClassUID = "1.2.826.0.1.3680043.9.5066.0" # My UID for my implementation, with a '.0' appended to it to represent development testing, ie the UID I got from Medical Connections.
file_meta.ImplementationVersionName = "DICOMMETRICS-DEV" # My implementation version name. Remember to change this for each version. Remember to correspondingly change the ImplementationClassUID too.
filename = '%s/%s.dcm' % (tempfile.gettempdir(), DS.SOPInstanceUID)
ds = FileDataset(filename, {}, file_meta=file_meta, preamble="\0" * 128)
ds.update(DS)
ds.is_little_endian = True
ds.is_implicit_VR = True
ds.save_as(filename)
print "File %s written" % filename
# must return appropriate status
return SOPClass.Success
def fileOutput(infilename, PLOT=False):
noiseAmp = 150 #units are "HA". See file in slack.
cellLocations = read_CA_output(infilename, noiseAmp)
outfilename = datetime.now().strftime("%y-%m-%d-%H%M.dcm")
# Populate required values for file meta information
file_meta = Dataset()
file_meta.FileMetaInformationGroupLength = 190
file_meta.FileMetaInformationVersion = '\x00\x01'
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.2' # CT Image Storage
file_meta.MediaStorageSOPInstanceUID = '1.3.6.1.4.1.9590.100.1.2.115051905812620145920373971792360190180'
file_meta.TransferSyntaxUID = '1.2.840.10008.1.2'
file_meta.ImplementationClassUID = '1.2.40.0.13.1.1'
file_meta.ImplementationVersionName = 'dcm4che-2.0'
ds = FileDataset(outfilename, {}, file_meta=file_meta, preamble="\0" * 128)
# Set the transfer syntax
ds.is_little_endian = True
ds.is_implicit_VR = True
#Set the data that we copied from another dicom file
setAttributes(ds)
# Set the image's data equal to that from our CA output
ds.Rows = cellLocations.shape[0]
ds.Columns = cellLocations.shape[1]
if cellLocations.dtype != np.uint16:
ds.PixelData = cellLocations.astype(np.uint16).tostring()
else:
ds.PixelData = cellLocations.tostring()
ds.SmallestImagePixelValue = struct.pack(
"<i", nmin
) #'\\x00\\x00': struct.pack("<H",0), w/ little_endian=True https://docs.python.org/2/library/struct.html#byte-order-size-and-alignment
ds.LargestImagePixelValue = struct.pack(
"<i", nmax) #'\\xff\\xff': struct.pack("<H",65535)
ds.save_as(outfilename)
if (PLOT):
plt.imshow(ds.pixel_array, cmap=plt.cm.bone)
plt.show()
def process_file(filename):
print(os.getcwd())
from remapp.extractors.dx import dx
from remapp.extractors.mam import mam
from remapp.extractors.rdsr import rdsr
from remapp.extractors.ct_philips import ct_philips
from remapp.models import DicomDeleteSettings
from remapp.version import __netdicom_implementation_version__
from remapp.version import __version__ as openrem_version
from openremproject.settings import MEDIA_ROOT
try:
DS = read_file(filename)
except Exception as e:
logger.info('Could not load file...')
print('did not work' + str(e))
return
try:
logger.info(
u"Received C-Store. Stn name %s, Modality %s, SOPClassUID %s, Study UID %s and Instance UID %s",
DS.StationName, DS.Modality, DS.SOPClassUID, DS.StudyInstanceUID,
DS.SOPInstanceUID)
except AttributeError:
try:
logger.info(
u"Received C-Store - station name missing. Modality %s, SOPClassUID %s, Study UID %s and "
u"Instance UID %s", DS.Modality, DS.SOPClassUID,
DS.StudyInstanceUID, DS.SOPInstanceUID)
except AttributeError:
logger.info(u"Received C-Store - error in logging details")
if 'TransferSyntaxUID' in DS:
del DS.TransferSyntaxUID # Don't know why this has become necessary
del_settings = DicomDeleteSettings.objects.get()
file_meta = Dataset()
file_meta.MediaStorageSOPClassUID = DS.SOPClassUID
file_meta.MediaStorageSOPInstanceUID = DS.SOPInstanceUID
file_meta.ImplementationClassUID = "1.3.6.1.4.1.45593.1.{0}".format(
__netdicom_implementation_version__)
file_meta.ImplementationVersionName = "OpenREM_{0}".format(openrem_version)
path = os.path.join(MEDIA_ROOT, "dicom_in")
mkdir_p(path)
#new_filename = os.path.join(path, u"{0}.dcm".format(DS.SOPInstanceUID))
ds_new = FileDataset(filename, {},
file_meta=file_meta,
preamble="\0" * 128)
ds_new.update(DS)
ds_new.is_little_endian = True
ds_new.is_implicit_VR = True
while True:
try:
station_name = DS.StationName
except:
station_name = u"missing"
try:
ds_new.save_as(filename)
break
except ValueError as e:
# Black magic pydicom method suggested by Darcy Mason:
# https://groups.google.com/forum/?hl=en-GB#!topic/pydicom/x_WsC2gCLck
if "Invalid tag (0018, 7052)" in e.message or "Invalid tag (0018, 7054)" in e.message:
logger.debug(
u"Found illegal use of multiple values of filter thickness using comma. "
u"Changing before saving.")
thickmin = dict.__getitem__(ds_new, 0x187052)
thickvalmin = thickmin.__getattribute__('value')
if ',' in thickvalmin:
thickvalmin = thickvalmin.replace(',', '\\')
thicknewmin = thickmin._replace(value=thickvalmin)
dict.__setitem__(ds_new, 0x187052, thicknewmin)
thickmax = dict.__getitem__(ds_new, 0x187054)
thickvalmax = thickmax.__getattribute__('value')
if ',' in thickvalmax:
thickvalmax = thickvalmax.replace(',', '\\')
thicknewmax = thickmax._replace(value=thickvalmax)
dict.__setitem__(ds_new, 0x187054, thicknewmax)
elif "Invalid tag (01f1, 1027)" in e.message:
logger.warning(
u"Invalid value in tag (01f1,1027), 'exposure time per rotation'. Tag value deleted. "
u"Stn name {0}, modality {1}, SOPClass UID {2}, Study UID {3}, Instance UID {4}"
.format(station_name, DS.Modality, DS.SOPClassUID,
DS.StudyInstanceUID, DS.SOPInstanceUID))
priv_exp_time = dict.__getitem__(ds_new, 0x1f11027)
blank_val = priv_exp_time._replace(value='')
dict.__setitem__(ds_new, 0x1f11027, blank_val)
elif "Invalid tag (01f1, 1033)" in e.message:
logger.warning(
u"Invalid value in unknown private tag (01f1,1033). Tag value deleted. "
u"Stn name {0}, modality {1}, SOPClass UID {2}, Study UID {3}, Instance UID {4}"
.format(station_name, DS.Modality, DS.SOPClassUID,
DS.StudyInstanceUID, DS.SOPInstanceUID))
priv_tag = dict.__getitem__(ds_new, 0x1f11033)
blank_val = priv_tag._replace(value='')
dict.__setitem__(ds_new, 0x1f11033, blank_val)
else:
logger.error(
u"ValueError on DCM save {0}. Stn name {1}, modality {2}, SOPClass UID {3}, Study UID {4}, "
u"Instance UID {5}".format(e.message, station_name,
DS.Modality, DS.SOPClassUID,
DS.StudyInstanceUID,
DS.SOPInstanceUID))
return
except IOError as e:
logger.error(
u"IOError on DCM save {0} - does the user running storescp have write rights in the {1} "
u"folder?".format(e.message, path))
return
except:
logger.error(
u"Unexpected error on DCM save: {0}. Stn name {1}, modality {2}, SOPClass UID {3}, Study UID {4}, "
u"Instance UID {5}".format(sys.exc_info()[0], DS.StationName,
DS.Modality, DS.SOPClassUID,
DS.StudyInstanceUID,
DS.SOPInstanceUID))
return
logger.info(u"File %s rewritten", filename)
if (DS.SOPClassUID ==
'1.2.840.10008.5.1.4.1.1.88.67' # X-Ray Radiation Dose SR
or DS.SOPClassUID ==
'1.2.840.10008.5.1.4.1.1.88.22' # Enhanced SR, as used by GE
):
logger.info(u"Processing as RDSR")
rdsr(filename)
elif (DS.SOPClassUID == '1.2.840.10008.5.1.4.1.1.1' # CR Image Storage
or DS.SOPClassUID ==
'1.2.840.10008.5.1.4.1.1.1.1' # Digital X-Ray Image Storage for Presentation
or DS.SOPClassUID ==
'1.2.840.10008.5.1.4.1.1.1.1.1' # Digital X-Ray Image Storage for Processing
):
logger.info(u"Processing as DX")
dx(filename)
elif (DS.SOPClassUID ==
'1.2.840.10008.5.1.4.1.1.1.2' # Digital Mammography X-Ray Image Storage for Presentation
or DS.SOPClassUID ==
'1.2.840.10008.5.1.4.1.1.1.2.1' # Digital Mammography X-Ray Image Storage for Processing
or
(DS.SOPClassUID ==
'1.2.840.10008.5.1.4.1.1.7' # Secondary Capture Image Storage, for processing
and
DS.Modality == 'MG' # Selenia proprietary DBT projection objects
and 'ORIGINAL' in DS.ImageType)):
logger.info(u"Processing as MG")
mam(filename)
elif DS.SOPClassUID == '1.2.840.10008.5.1.4.1.1.7':
try:
manufacturer = DS.Manufacturer
series_description = DS.SeriesDescription
except AttributeError:
if del_settings.del_no_match:
os.remove(filename)
logger.info(
u"Secondary capture object with either no manufacturer or series description. Deleted."
)
return
if manufacturer == 'Philips' and series_description == 'Dose Info':
logger.info(u"Processing as Philips Dose Info series")
ct_philips(filename)
elif del_settings.del_no_match:
os.remove(filename)
logger.info(
u"Can't find anything to do with this file - it has been deleted"
)
elif del_settings.del_no_match:
os.remove(filename)
logger.info(
u"Can't find anything to do with this file - it has been deleted")
# must return appropriate status
return