Python pydicom.dcmread函数代码示例

 def setUp(self):
     self.mr_small = dcmread(mr_name)
     self.mr_rle = dcmread(mr_rle)
     self.emri_small = dcmread(emri_name)
     self.emri_rle = dcmread(emri_rle)
     self.original_handlers = pydicom.config.image_handlers
     pydicom.config.image_handlers = [rle_handler, numpy_handler]

    def test_charset_patient_names(self, filename, patient_name):
        """Test patient names are correctly decoded and encoded."""
        # check that patient names are correctly read
        file_path = get_charset_files(filename + '.dcm')[0]
        ds = dcmread(file_path)
        ds.decode()
        assert patient_name == ds.PatientName

        # check that patient names are correctly written back
        fp = DicomBytesIO()
        fp.is_implicit_VR = False
        fp.is_little_endian = True
        ds.save_as(fp, write_like_original=False)
        fp.seek(0)
        ds = dcmread(fp)
        assert patient_name == ds.PatientName

        # check that patient names are correctly written back
        # without original byte string (PersonName3 only)
        if hasattr(ds.PatientName, 'original_string'):
            ds.PatientName.original_string = None
            fp = DicomBytesIO()
            fp.is_implicit_VR = False
            fp.is_little_endian = True
            ds.save_as(fp, write_like_original=False)
            fp.seek(0)
            ds = dcmread(fp)
            assert patient_name == ds.PatientName

 def get_path_info_preview(self, path):
     path_lower = path.lower()
     #name
     name = os.path.basename(os.path.normpath(path))
     name_final = ("name: " + name)
     path_sl = path + "/"
     
     if ".jpg" in path_lower:
         preview = ("Used path leads to current image.")
         img = io.imread(path)
         io.imshow(img)
         io.show()
         
     elif ".png" in path_lower:
         preview = ("Used path leads to current image.")
         img = io.imread(path)
         io.imshow(img)
         io.show()
         
     elif ".dcm" in path_lower:
         preview = ("Used path leads to current image.")
         ds = pdicom.dcmread(path)
         plt.imshow(ds.pixel_array, cmap=plt.cm.bone)
         
     else:
         preview = ("Preview of files in dir: " + name) 
         only_files = [f for f in listdir(path) if isfile(join(path, f))]
         
         for x in only_files:
             if (".dcm" or ".Dcm" or ".DCM") in x:
                 ending = os.path.basename(os.path.normpath(path_sl + x))
                 preview_path = path_sl + ending
                 ds = pdicom.dcmread(preview_path)
                 plt.imshow(ds.pixel_array, cmap=plt.cm.bone)
                 break
             elif (".jpg" or ".Jpg" or ".JPG") in x:
                 ending = os.path.basename(os.path.normpath(path_sl + x))
                 preview_path = path_sl + ending
                 img = io.imread(preview_path)
                 io.imshow(img)
                 io.show()
                 break
                 
             elif (".png" or ".Png" or ".PNG") in x:
                 ending = os.path.basename(os.path.normpath(path_sl + x))
                 preview_path = path_sl + ending
                 img = io.imread(preview_path)
                 io.imshow(img)
                 io.show()
                 break
                 
             else:
                 None
                 break

 def test_changed_character_set(self):
     # Regression test for #629
     multiPN_name = get_charset_files("chrFrenMulti.dcm")[0]
     ds = dcmread(multiPN_name)  # is Latin-1
     ds.SpecificCharacterSet = 'ISO_IR 192'
     from pydicom.filebase import DicomBytesIO
     fp = DicomBytesIO()
     ds.save_as(fp, write_like_original=False)
     fp.seek(0)
     ds_out = dcmread(fp)
     # we expect UTF-8 encoding here
     assert b'Buc^J\xc3\xa9r\xc3\xb4me' == ds_out.get_item(0x00100010).value

    def test_encapsulate_single_fragment_per_frame_bot(self):
        """Test encapsulating single fragment per frame with BOT values."""
        ds = dcmread(JP2K_10FRAME_NOBOT)
        frames = decode_data_sequence(ds.PixelData)
        assert len(frames) == 10

        data = encapsulate(frames, fragments_per_frame=1, has_bot=True)
        test_frames = decode_data_sequence(data)
        for a, b in zip(test_frames, frames):
            assert a == b

        fp = DicomBytesIO(data)
        fp.is_little_endian = True
        offsets = get_frame_offsets(fp)
        assert offsets == [
            0x0000,  # 0
            0x0eee,  # 3822
            0x1df6,  # 7670
            0x2cf8,  # 11512
            0x3bfc,  # 15356
            0x4ade,  # 19166
            0x59a2,  # 22946
            0x6834,  # 26676
            0x76e2,  # 30434
            0x8594  # 34196
        ]

 def is_CT_slice(file: str) -> bool:
     """Test if the file is a CT Image storage DICOM file."""
     try:
         ds = pydicom.dcmread(file, force=True, stop_before_pixels=True)
         return ds.SOPClassUID.name == 'CT Image Storage'
     except (InvalidDicomError, AttributeError, MemoryError):
         return False

    def setup(self):
        # MONOCHROME2, 64x64, 1 sample/pixel, 16 bits allocated, 12 bits stored
        self.ds = dcmread(EMRI_RLE_10F)
        self.frames = decode_data_sequence(self.ds.PixelData)
        assert len(self.frames) == 10

        self.no_runs = 100

 def test_trait_names(self):
     """Test Dataset.trait_names contains element keywords"""
     test_file = get_testdata_files('CT_small.dcm')[0]
     ds = dcmread(test_file, force=True)
     names = ds.trait_names()
     assert 'PatientName' in names
     assert 'save_as' in names
     assert 'PixelData' in names

def is_dicom(path):
    """Whether the file is a readable DICOM file via pydicom."""
    try:
        ds = pydicom.dcmread(path, force=True)
        ds.pixel_array
        return True
    except:
        return False

 def test_decoding_with_specific_tags(self):
     """Decoding is correctly applied even if  Specific Character Set
     is not in specific tags..."""
     rus_file = get_charset_files("chrRuss.dcm")[0]
     ds = dcmread(rus_file, specific_tags=['PatientName'])
     ds.decode()
     assert 2 == len(ds)  # specific character set is always decoded
     assert u'Люкceмбypг' == ds.PatientName

 def test_invalid_character_set_enforce_valid(self):
     """charset: raise on invalid encoding"""
     config.enforce_valid_values = True
     ds = dcmread(get_testdata_files("CT_small.dcm")[0])
     ds.read_encoding = None
     ds.SpecificCharacterSet = 'Unsupported'
     with pytest.raises(LookupError, match='unknown encoding: Unsupported'):
         ds.decode()

    def test_equality_file_meta(self):
        """Dataset: equality returns correct value if with metadata"""
        d = dcmread(self.test_file)
        e = dcmread(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 test_latin1(self):
     """charset: can read and decode latin_1 file........................"""
     ds = dcmread(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:
            dcmread(uni_name)
        except UnicodeEncodeError:
            self.fail("UnicodeEncodeError generated for unicode name")
        # ignore file doesn't exist error
        except IOError:
            pass

def assign2machine(source_file: str, machine_file: str):
    """Assign a DICOM RT Plan file to a specific machine. The source file is overwritten to contain
    the machine of the machine file.

    Parameters
    ----------
    source_file : str
        Path to the DICOM RTPlan file that contains the fields/plan desired
        (e.g. a Winston Lutz set of fields or Varian's default PF files).
    machine_file : str
        Path to a DICOM RTPlan file that has the desired machine. This is easily obtained from pushing a plan from the TPS
        for that specific machine. The file must contain at least one valid field.
    """
    dcm_source = pydicom.dcmread(source_file)
    dcm_machine = pydicom.dcmread(machine_file)
    for beam in dcm_source.BeamSequence:
        beam.TreatmentMachineName = dcm_machine.BeamSequence[0].TreatmentMachineName
    dcm_source.save_as(source_file)