Пример #1
0
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
Пример #2
0
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
Пример #3
0
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
Пример #4
0
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()
Пример #5
0
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