コード例 #1
0
ファイル: test_filereader.py プロジェクト: sidsd27/BIO-X_2020
 def testValuesIdentical(self):
     """Deferred values exactly matches normal read..............."""
     ds_norm = read_file(self.testfile_name)
     ds_defer = read_file(self.testfile_name, defer_size=2000)
     for data_elem in ds_norm:
         tag = data_elem.tag
         self.assertEqual(data_elem.value, ds_defer[tag].value, "Mismatched value for tag %r" % tag)
コード例 #2
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ファイル: test_filereader.py プロジェクト: IMAGE-ET/pydicom
 def testValuesIdentical(self):
     """Deferred values exactly matches normal read..............."""
     ds_norm = read_file(self.testfile_name)
     ds_defer = read_file(self.testfile_name, defer_size=2000)
     for data_elem in ds_norm:
         tag = data_elem.tag
         self.assertEqual(data_elem.value, ds_defer[tag].value, "Mismatched value for tag %r" % tag)
コード例 #3
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ファイル: test_filereader.py プロジェクト: IMAGE-ET/pydicom
    def testPrivateSQ(self):
        """Can read private undefined length SQ without error...................."""
        # From issues 91, 97, 98. Bug introduced by fast reading, due to VR=None
        #    in raw data elements, then an undefined length private item VR is looked up,
        #    and there is no such tag, generating an exception

        # Simply read the file, in 0.9.5 this generated an exception
        read_file(priv_SQ_name)
コード例 #4
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    def testPrivateSQ(self):
        """Can read private undefined length SQ without error...................."""
        # From issues 91, 97, 98. Bug introduced by fast reading, due to VR=None
        #    in raw data elements, then an undefined length private item VR is looked up,
        #    and there is no such tag, generating an exception

        # Simply read the file, in 0.9.5 this generated an exception
        read_file(priv_SQ_name)
コード例 #5
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 def testNoPixelsRead(self):
     """Returns all data elements before pixels using stop_before_pixels=False"""
     # Just check the tags, and a couple of values
     ctpartial = read_file(ct_name, stop_before_pixels=True)
     ctpartial_tags = sorted(ctpartial.keys())
     ctfull = read_file(ct_name)
     ctfull_tags = sorted(ctfull.keys())
     msg = "Tag list of partial CT read (except pixel tag and padding) did not match full read"
     msg += "\nExpected: %r\nGot %r" % (ctfull_tags[:-2], ctpartial_tags)
     missing = [Tag(0x7fe0, 0x10), Tag(0xfffc, 0xfffc)]
     self.assertEqual(ctfull_tags, ctpartial_tags + missing, msg)
コード例 #6
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ファイル: test_filereader.py プロジェクト: IMAGE-ET/pydicom
 def testNoPixelsRead(self):
     """Returns all data elements before pixels using stop_before_pixels=False"""
     # Just check the tags, and a couple of values
     ctpartial = read_file(ct_name, stop_before_pixels=True)
     ctpartial_tags = sorted(ctpartial.keys())
     ctfull = read_file(ct_name)
     ctfull_tags = sorted(ctfull.keys())
     msg = "Tag list of partial CT read (except pixel tag and padding) did not match full read"
     msg += "\nExpected: %r\nGot %r" % (ctfull_tags[:-2], ctpartial_tags)
     missing = [Tag(0x7fe0, 0x10), Tag(0xfffc, 0xfffc)]
     self.assertEqual(ctfull_tags, ctpartial_tags + missing, msg)
コード例 #7
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 def testReadFileGivenFileObject(self):
     """filereader: can read using already opened file............"""
     f = open(ct_name, "rb")
     ct = read_file(f)
     # Tests here simply repeat testCT -- perhaps should collapse the code together?
     got = ct.ImagePositionPatient
     DS = dicom.valuerep.DS
     expected = [DS("-158.135803"), DS("-179.035797"), DS("-75.699997")]
     self.assertTrue(got == expected, "ImagePosition(Patient) values not as expected")
     self.assertEqual(
         ct.file_meta.ImplementationClassUID, "1.3.6.1.4.1.5962.2", "ImplementationClassUID not the expected value"
     )
     self.assertEqual(
         ct.file_meta.ImplementationClassUID,
         ct.file_meta[0x2, 0x12].value,
         "ImplementationClassUID does not match the value accessed by tag number",
     )
     # (0020, 0032) Image Position (Patient)  [-158.13580300000001, -179.035797, -75.699996999999996]
     got = ct.ImagePositionPatient
     expected = [DS("-158.135803"), DS("-179.035797"), DS("-75.699997")]
     self.assertTrue(got == expected, "ImagePosition(Patient) values not as expected")
     self.assertEqual(ct.Rows, 128, "Rows not 128")
     self.assertEqual(ct.Columns, 128, "Columns not 128")
     self.assertEqual(ct.BitsStored, 16, "Bits Stored not 16")
     self.assertEqual(len(ct.PixelData), 128 * 128 * 2, "Pixel data not expected length")
     # Should also be able to close the file ourselves without exception raised:
     f.close()
コード例 #8
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    def testNestedPrivateSQ(self):
        """Can successfully read a private SQ which contains additional SQ's....."""
        # From issue 113. When a private SQ of undefined length is used, the
        #   sequence is read in and the length of the SQ is determined upon
        #   identification of the SQ termination sequence. When using nested
        #   Sequences, the first termination sequence encountered actually
        #   belongs to the nested Sequence not the parent, therefore the
        #   remainder of the file is not read in properly
        ds = read_file(nested_priv_SQ_name)

        # Make sure that the entire dataset was read in
        pixel_data_tag = TupleTag((0x7FE0, 0x10))
        self.assertTrue(pixel_data_tag in ds, "Entire dataset was not parsed properly. PixelData is not present")

        # Check that the DataElement is indeed a Sequence
        tag = TupleTag((0x01, 0x01))
        seq0 = ds[tag]
        self.assertEqual(seq0.VR, "SQ", "First level sequence not parsed properly")

        # Now verify the presence of the nested private SQ
        seq1 = seq0[0][tag]
        self.assertEqual(seq1.VR, "SQ", "Second level sequence not parsed properly")

        # Now make sure the values that are parsed are correct
        got = seq1[0][tag].value
        expected = b"Double Nested SQ"
        self.assertEqual(got, expected, "Expected a value of %s, got %s'" % (expected, got))

        got = seq0[0][0x01, 0x02].value
        expected = b"Nested SQ"
        self.assertEqual(got, expected, "Expected a value of %s, got %s'" % (expected, got))
コード例 #9
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ファイル: test_filereader.py プロジェクト: IMAGE-ET/pydicom
    def testCT(self):
        """Returns correct values for sample data elements in test CT file...."""
        ct = read_file(ct_name)
        self.assertEqual(ct.file_meta.ImplementationClassUID, '1.3.6.1.4.1.5962.2',
                         "ImplementationClassUID not the expected value")
        self.assertEqual(ct.file_meta.ImplementationClassUID,
                         ct.file_meta[0x2, 0x12].value,
                         "ImplementationClassUID does not match the value accessed by tag number")
        # (0020, 0032) Image Position (Patient)  [-158.13580300000001, -179.035797, -75.699996999999996]
        got = ct.ImagePositionPatient
        DS = dicom.valuerep.DS
        expected = [DS('-158.135803'), DS('-179.035797'), DS('-75.699997')]
        self.assertTrue(got == expected, "ImagePosition(Patient) values not as expected."
                        "got {0}, expected {1}".format(got, expected))

        self.assertEqual(ct.Rows, 128, "Rows not 128")
        self.assertEqual(ct.Columns, 128, "Columns not 128")
        self.assertEqual(ct.BitsStored, 16, "Bits Stored not 16")
        self.assertEqual(len(ct.PixelData), 128 * 128 * 2, "Pixel data not expected length")

        # Also test private elements name can be resolved:
        expected = "[Duration of X-ray on]"
        got = ct[(0x0043, 0x104e)].name
        msg = "Mismatch in private tag name, expected '%s', got '%s'"
        self.assertEqual(expected, got, msg % (expected, got))

        # Check that can read pixels - get last one in array
        if have_numpy:
            expected = 909
            got = ct.pixel_array[-1][-1]
            msg = "Did not get correct value for last pixel: expected %d, got %r" % (expected, got)
            self.assertEqual(expected, got, msg)
        else:
            print "**Numpy not available -- pixel array test skipped**"
コード例 #10
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    def testRTstruct(self):
        """Returns correct values for sample elements in test RTSTRUCT file...."""
        # RTSTRUCT test file has complex nested sequences -- see rtstruct.dump file
        # Also has no DICOM header ... so tests 'force' argument of read_file

        rtss = read_file(rtstruct_name, force=True)
        expected = '1.2.840.10008.1.2'  # implVR little endian
        got = rtss.file_meta.TransferSyntaxUID
        msg = "Expected transfer syntax %r, got %r" % (expected, got)
        self.assertEqual(expected, got, msg)
        frame_of_ref = rtss.ReferencedFrameOfReferenceSequence[0]
        study = frame_of_ref.RTReferencedStudySequence[0]
        uid = study.RTReferencedSeriesSequence[0].SeriesInstanceUID
        expected = "1.2.826.0.1.3680043.8.498.2010020400001.2.1.1"
        msg = "Expected Reference Series UID '%s', got '%s'" % (expected, uid)
        self.assertEqual(expected, uid, msg)

        got = rtss.ROIContourSequence[0].ContourSequence[2].ContourNumber
        expected = 3
        msg = "Expected Contour Number %d, got %r" % (expected, got)
        self.assertEqual(expected, got, msg)

        obs_seq0 = rtss.RTROIObservationsSequence[0]
        got = obs_seq0.ROIPhysicalPropertiesSequence[0].ROIPhysicalProperty
        expected = 'REL_ELEC_DENSITY'
        msg = "Expected Physical Property '%s', got %r" % (expected, got)
        self.assertEqual(expected, got, msg)
コード例 #11
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 def testDir(self):
     """Returns correct dir attributes for both Dataset and DICOM names (python >= 2.6).."""
     # Only python >= 2.6 calls __dir__ for dir() call
     rtss = read_file(rtstruct_name, force=True)
     # sample some expected 'dir' values
     got_dir = dir(rtss)
     expect_in_dir = [
         'pixel_array', 'add_new', 'ROIContourSequence', 'StructureSetDate',
         '__sizeof__'
     ]
     expect_not_in_dir = ['RemovePrivateTags', 'AddNew',
                          'GroupDataset']  # remove in v1.0
     for name in expect_in_dir:
         self.assertTrue(name in got_dir,
                         "Expected name '%s' in dir()" % name)
     for name in expect_not_in_dir:
         self.assertTrue(name not in got_dir,
                         "Unexpected name '%s' in dir()" % name)
     # Now check for some items in dir() of a nested item
     roi0 = rtss.ROIContourSequence[0]
     got_dir = dir(roi0)
     expect_in_dir = [
         'pixel_array', 'add_new', 'ReferencedROINumber', 'ROIDisplayColor',
         '__sizeof__'
     ]
     for name in expect_in_dir:
         self.assertTrue(name in got_dir,
                         "Expected name '%s' in dir()" % name)
コード例 #12
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ファイル: test_filereader.py プロジェクト: IMAGE-ET/pydicom
 def testDeflate(self):
     """Returns correct values for sample data elements in test compressed (zlib deflate) file"""
     # Everything after group 2 is compressed. If we can read anything else, the decompression must have been ok.
     ds = read_file(deflate_name)
     got = ds.ConversionType
     expected = "WSD"
     self.assertEqual(got, expected, "Attempted to read deflated file data element Conversion Type, expected '%s', got '%s'" % (expected, got))
コード例 #13
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ファイル: test_filereader.py プロジェクト: IMAGE-ET/pydicom
    def testRTstruct(self):
        """Returns correct values for sample elements in test RTSTRUCT file...."""
        # RTSTRUCT test file has complex nested sequences -- see rtstruct.dump file
        # Also has no DICOM header ... so tests 'force' argument of read_file

        rtss = read_file(rtstruct_name, force=True)
        expected = '1.2.840.10008.1.2'  # implVR little endian
        got = rtss.file_meta.TransferSyntaxUID
        msg = "Expected transfer syntax %r, got %r" % (expected, got)
        self.assertEqual(expected, got, msg)
        frame_of_ref = rtss.ReferencedFrameOfReferenceSequence[0]
        study = frame_of_ref.RTReferencedStudySequence[0]
        uid = study.RTReferencedSeriesSequence[0].SeriesInstanceUID
        expected = "1.2.826.0.1.3680043.8.498.2010020400001.2.1.1"
        msg = "Expected Reference Series UID '%s', got '%s'" % (expected, uid)
        self.assertEqual(expected, uid, msg)

        got = rtss.ROIContourSequence[0].ContourSequence[2].ContourNumber
        expected = 3
        msg = "Expected Contour Number %d, got %r" % (expected, got)
        self.assertEqual(expected, got, msg)

        obs_seq0 = rtss.RTROIObservationsSequence[0]
        got = obs_seq0.ROIPhysicalPropertiesSequence[0].ROIPhysicalProperty
        expected = 'REL_ELEC_DENSITY'
        msg = "Expected Physical Property '%s', got %r" % (expected, got)
        self.assertEqual(expected, got, msg)
コード例 #14
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 def testReadFileGivenFileObject(self):
     """filereader: can read using already opened file............"""
     f = open(ct_name, 'rb')
     ct = read_file(f)
     # Tests here simply repeat testCT -- perhaps should collapse the code together?
     got = ct.ImagePositionPatient
     DS = dicom.valuerep.DS
     expected = [DS('-158.135803'), DS('-179.035797'), DS('-75.699997')]
     self.assertTrue(got == expected,
                     "ImagePosition(Patient) values not as expected")
     self.assertEqual(ct.file_meta.ImplementationClassUID,
                      '1.3.6.1.4.1.5962.2',
                      "ImplementationClassUID not the expected value")
     self.assertEqual(
         ct.file_meta.ImplementationClassUID, ct.file_meta[0x2, 0x12].value,
         "ImplementationClassUID does not match the value accessed by tag number"
     )
     # (0020, 0032) Image Position (Patient)  [-158.13580300000001, -179.035797, -75.699996999999996]
     got = ct.ImagePositionPatient
     expected = [DS('-158.135803'), DS('-179.035797'), DS('-75.699997')]
     self.assertTrue(got == expected,
                     "ImagePosition(Patient) values not as expected")
     self.assertEqual(ct.Rows, 128, "Rows not 128")
     self.assertEqual(ct.Columns, 128, "Columns not 128")
     self.assertEqual(ct.BitsStored, 16, "Bits Stored not 16")
     self.assertEqual(len(ct.PixelData), 128 * 128 * 2,
                      "Pixel data not expected length")
     # Should also be able to close the file ourselves without exception raised:
     f.close()
コード例 #15
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ファイル: test_filereader.py プロジェクト: sidsd27/BIO-X_2020
 def testDeflate(self):
     """Returns correct values for sample data elements in test compressed (zlib deflate) file"""
     # Everything after group 2 is compressed. If we can read anything else, the decompression must have been ok.
     ds = read_file(deflate_name)
     got = ds.ConversionType
     expected = "WSD"
     self.assertEqual(got, expected, "Attempted to read deflated file data element Conversion Type, expected '%s', got '%s'" % (expected, got))
コード例 #16
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ファイル: test_filereader.py プロジェクト: sidsd27/BIO-X_2020
    def testCT(self):
        """Returns correct values for sample data elements in test CT file...."""
        ct = read_file(ct_name)
        self.assertEqual(ct.file_meta.ImplementationClassUID, '1.3.6.1.4.1.5962.2',
                         "ImplementationClassUID not the expected value")
        self.assertEqual(ct.file_meta.ImplementationClassUID,
                         ct.file_meta[0x2, 0x12].value,
                         "ImplementationClassUID does not match the value accessed by tag number")
        # (0020, 0032) Image Position (Patient)  [-158.13580300000001, -179.035797, -75.699996999999996]
        got = ct.ImagePositionPatient
        DS = dicom.valuerep.DS
        expected = [DS('-158.135803'), DS('-179.035797'), DS('-75.699997')]
        self.assertTrue(got == expected, "ImagePosition(Patient) values not as expected."
                        "got {0}, expected {1}".format(got, expected))

        self.assertEqual(ct.Rows, 128, "Rows not 128")
        self.assertEqual(ct.Columns, 128, "Columns not 128")
        self.assertEqual(ct.BitsStored, 16, "Bits Stored not 16")
        self.assertEqual(len(ct.PixelData), 128 * 128 * 2, "Pixel data not expected length")

        # Also test private elements name can be resolved:
        expected = "[Duration of X-ray on]"
        got = ct[(0x0043, 0x104e)].name
        msg = "Mismatch in private tag name, expected '%s', got '%s'"
        self.assertEqual(expected, got, msg % (expected, got))

        # Check that can read pixels - get last one in array
        if have_numpy:
            expected = 909
            got = ct.pixel_array[-1][-1]
            msg = "Did not get correct value for last pixel: expected %d, got %r" % (expected, got)
            self.assertEqual(expected, got, msg)
        else:
            print("**Numpy not available -- pixel array test skipped**")
コード例 #17
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 def testFileExists(self):
     """Deferred read raises error if file no longer exists....."""
     ds = read_file(self.testfile_name, defer_size=2000)
     os.remove(self.testfile_name)
     def read_value():
         data_elem = ds.PixelData
     self.assertRaises(IOError, read_value)
コード例 #18
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 def testMR(self):
     """Returns correct values for sample data elements in test MR file....."""
     mr = read_file(mr_name)
     # (0010, 0010) Patient's Name           'CompressedSamples^MR1'
     self.assertEqual(mr.PatientsName, 'CompressedSamples^MR1', "Wrong patient name")
     self.assertEqual(mr.PatientsName, mr[0x10,0x10].value,
             "Name does not match value found when accessed by tag number")
     self.assert_(isClose(mr.PixelSpacing, [0.3125, 0.3125]), "Wrong pixel spacing")
コード例 #19
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 def testZippedDeferred(self):
     """Deferred values from a gzipped file works.............."""
     # Arose from issue 103 "Error for defer_size read of gzip file object"
     fobj = gzip.open(gzip_name)
     ds = read_file(fobj, defer_size=1)
     # before the fix, this threw an error as file reading was not in right place,
     #    it was re-opened as a normal file, not zip file
     num = ds.InstanceNumber
コード例 #20
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ファイル: test_filereader.py プロジェクト: psy2013GitHub/Atom
 def testZippedDeferred(self):
     """Deferred values from a gzipped file works.............."""
     # Arose from issue 103 "Error for defer_size read of gzip file object"
     fobj = gzip.open(gzip_name)
     ds = read_file(fobj, defer_size=1)
     # before the fix, this threw an error as file reading was not in right place,
     #    it was re-opened as a normal file, not zip file
     num = ds.InstanceNumber
コード例 #21
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ファイル: test_filewriter.py プロジェクト: psy2013GitHub/Atom
 def testListItemWriteBack(self):
     """Change item in a list and confirm it is written to file      .."""
     DS_expected = 0
     CS_expected = "new"
     SS_expected = 999
     ds = read_file(ct_name)
     ds.ImagePositionPatient[2] = DS_expected
     ds.ImageType[1] = CS_expected
     ds[(0x0043, 0x1012)].value[0] = SS_expected
     ds.save_as(ct_out)
     # Now read it back in and check that the values were changed
     ds = read_file(ct_out)
     self.assert_(ds.ImageType[1] == CS_expected, "Item in a list not written correctly to file (VR=CS)")
     self.assert_(ds[0x00431012].value[0] == SS_expected, "Item in a list not written correctly to file (VR=SS)")
     self.assert_(ds.ImagePositionPatient[2] == DS_expected, "Item in a list not written correctly to file (VR=DS)")
     if os.path.exists(ct_out):
         os.remove(ct_out)
コード例 #22
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 def compare(self, in_, out_):
     """Read file1, write file2, then compare. Return value as for files_identical"""
     dataset = read_file(in_)
     write_file(out_, dataset)
     same, pos = files_identical(in_, out_)
     self.assert_(same, "Files are not identical - first difference at 0x%x" % pos)
     if os.path.exists(out_):
         os.remove(out_)  # get rid of the file
コード例 #23
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    def testFileExists(self):
        """Deferred read raises error if file no longer exists....."""
        ds = read_file(self.testfile_name, defer_size=2000)
        os.remove(self.testfile_name)

        def read_value():
            data_elem = ds.PixelData

        self.assertRaises(IOError, read_value)
コード例 #24
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def image_processing(file, value, rect_mask, circle_mask, len_files):
    
    """ Do the processing of an image to obtain the skull. """
    
    line = currentframe().f_back.f_lineno
    if file.__class__ != str:
        print 'Line', line, '- Error: First argument must be str.'
        exit()
    elif value.__class__ != int:
        print 'Line', line, '- Error: Second argument must be int.'
        exit()
    else:
        
        plt.close('all')
        
        image_begin_time = time.time()
        
        # ----------------------------
        # ----- 1. DICOM OPENING -----
        # ----------------------------
        
        dicom_file = dicomio.read_file(file)
        dicom_array = dicom_file.pixel_array
        image_number = dicom_file.InstanceNumber
        if image_number < 10:
            image_number = '0000' + str(image_number)
        if image_number >= 10 and image_number < 100:
            image_number = '000' + str(image_number)
        if image_number >= 100 and image_number < 1000:
            image_number = '00' + str(image_number)
        if image_number >= 1000:
            image_number = '0' + str(image_number)
        
        # Two ways to give back the initial dimensions to the segmented images:
        # - Use the MedPy library which seems really easy to use, but which does not work now
        #   Website: https://pypi.python.org/pypi/MedPy
        # - Use the Pydicom library with .PixelSpacing, which seems to be a bit more difficult to use
        #   Website: https://pyscience.wordpress.com/2014/09/08/dicom-in-python-importing-medical-image-data-into-numpy-with-pydicom-and-vtk/
        
        #pixel_dims = (int(dicom_file.Rows), int(dicom_file.Columns), len_files)
        pixel_spacing = [float(dicom_file.PixelSpacing[0]), float(dicom_file.PixelSpacing[1]), float(dicom_file.SliceThickness)]     
#        print 'slice_thickness :', float(dicom_file.SliceThickness)
        
        new_dicom_array = normalize(dicom_array)
        new_dicom_array2 = convert_from_uint16_to_uint8(normalize(double_threshold(new_dicom_array, value, int(array_max(new_dicom_array)))))
        # Value was equal to 2200 for the skull only, and 1500 seems 'good' for "living persons".
        
        grayskull_image = array2image(new_dicom_array2)
        
        skull_array = threshold(new_dicom_array2, 1)
        skull_image = array2image(skull_array)

        
        image_end_time = time.time()
        print 'Image execution time:', round(image_end_time - image_begin_time, 3), 'seconds'
        
        return grayskull_image, skull_image, pixel_spacing, image_number
コード例 #25
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ファイル: test_filereader.py プロジェクト: sidsd27/BIO-X_2020
 def testNoMetaGroupLength(self):
     """Read file with no group length in file meta..........................."""
     # Issue 108 -- iView example file with no group length (0002,0002)
     # Originally crashed, now check no exception, but also check one item
     #     in file_meta, and second one in followinsg dataset
     ds = read_file(no_meta_group_length)
     got = ds.InstanceCreationDate
     expected = "20111130"
     self.assertEqual(got, expected, "Sample data element after file meta with no group length failed, expected '%s', got '%s'" % (expected, got))
コード例 #26
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ファイル: test_filereader.py プロジェクト: IMAGE-ET/pydicom
 def testNoMetaGroupLength(self):
     """Read file with no group length in file meta..........................."""
     # Issue 108 -- iView example file with no group length (0002,0002)
     # Originally crashed, now check no exception, but also check one item
     #     in file_meta, and second one in followinsg dataset
     ds = read_file(no_meta_group_length)
     got = ds.InstanceCreationDate
     expected = "20111130"
     self.assertEqual(got, expected, "Sample data element after file meta with no group length failed, expected '%s', got '%s'" % (expected, got))
コード例 #27
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 def compare(self, in_filename, out_filename):
     """Read file1, write file2, then compare. Return value as for files_identical"""
     dataset = read_file(in_filename)
     dataset.save_as(out_filename)
     same, pos = files_identical(in_filename, out_filename)
     self.assert_(
         same, "Files are not identical - first difference at 0x%x" % pos)
     if os.path.exists(out_filename):
         os.remove(out_filename)  # get rid of the file
コード例 #28
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ファイル: test_filereader.py プロジェクト: njvack/yadda
 def testMR(self):
     """Returns correct values for sample data elements in test MR file....."""
     mr = read_file(mr_name)
     # (0010, 0010) Patient's Name           'CompressedSamples^MR1'
     self.assertEqual(mr.PatientName, 'CompressedSamples^MR1', "Wrong patient name")
     self.assertEqual(mr.PatientName, mr[0x10, 0x10].value,
             "Name does not match value found when accessed by tag number")
     got = mr.PixelSpacing
     expected = [Decimal('0.3125'), Decimal('0.3125')]
     self.assertTrue(got == expected, "Wrong pixel spacing")
コード例 #29
0
ファイル: test_filereader.py プロジェクト: njvack/yadda
 def testReadFileGivenFileLikeObject(self):
     """filereader: can read using a file-like (BytesIO) file...."""
     file_like = BytesIO(open(ct_name, 'rb').read())
     ct = read_file(file_like)
     # Tests here simply repeat some of testCT test
     got = ct.ImagePositionPatient
     expected = [Decimal('-158.135803'), Decimal('-179.035797'), Decimal('-75.699997')]
     self.assertTrue(got == expected, "ImagePosition(Patient) values not as expected")
     self.assertEqual(len(ct.PixelData), 128 * 128 * 2, "Pixel data not expected length")
     # Should also be able to close the file ourselves without exception raised:
     file_like.close()
コード例 #30
0
 def testListItemWriteBack(self):
     """Change item in a list and confirm it is written to file      .."""
     DS_expected = 0
     CS_expected = "new"
     SS_expected = 999
     ds = read_file(ct_name)
     ds.ImagePositionPatient[2] = DS_expected
     ds.ImageType[1] = CS_expected
     ds[(0x0043, 0x1012)].value[0] = SS_expected
     ds.save_as(ct_out)
     # Now read it back in and check that the values were changed
     ds = read_file(ct_out)
     self.assert_(ds.ImageType[1] == CS_expected,
                  "Item in a list not written correctly to file (VR=CS)")
     self.assert_(ds[0x00431012].value[0] == SS_expected,
                  "Item in a list not written correctly to file (VR=SS)")
     self.assert_(ds.ImagePositionPatient[2] == DS_expected,
                  "Item in a list not written correctly to file (VR=DS)")
     if os.path.exists(ct_out):
         os.remove(ct_out)
コード例 #31
0
 def testTimeCheck(self):
     """Deferred read warns if file has been modified..........."""
     if stat_available:
         ds = read_file(self.testfile_name, defer_size=2000)
         from time import sleep
         sleep(1)
         open(self.testfile_name, "r+").write('\0') # "touch" the file
         warning_start = "Deferred read warning -- file modification time "
         def read_value():
             data_elem = ds.PixelData
         assertWarns(self, warning_start, read_value)
コード例 #32
0
ファイル: test_filewriter.py プロジェクト: njvack/yadda
 def compare(self, in_filename, out_filename):
     """Read file1, write file2, then compare.
     Return value as for files_identical.
     """
     dataset = read_file(in_filename)
     dataset.save_as(out_filename)
     same, pos = files_identical(in_filename, out_filename)
     self.assertTrue(same,
         "Files are not identical - first difference at 0x%x" % pos)
     if os.path.exists(out_filename):
         os.remove(out_filename)  # get rid of the file
コード例 #33
0
 def testReadFileGivenFileLikeObject(self):
     """filereader: can read using a file-like (StringIO) file...."""
     file_like = StringIO(open(ct_name, 'rb').read())
     ct = read_file(file_like)
     # Tests here simply repeat some of testCT test
     imagepos = ct.ImagePositionPatient
     self.assert_(isClose(imagepos, [-158.135803, -179.035797, -75.699997]),
             "ImagePosition(Patient) values not as expected")
     self.assertEqual(len(ct.PixelData), 128*128*2, "Pixel data not expected length")
     # Should also be able to close the file ourselves without exception raised:
     file_like.close()
コード例 #34
0
ファイル: test_filereader.py プロジェクト: sidsd27/BIO-X_2020
    def testRTDose(self):
        """Returns correct values for sample data elements in test RT Dose file"""
        dose = read_file(rtdose_name)
        self.assertEqual(dose.FrameIncrementPointer, Tag((0x3004, 0x000c)),
                         "Frame Increment Pointer not the expected value")
        self.assertEqual(dose.FrameIncrementPointer, dose[0x28, 9].value,
                         "FrameIncrementPointer does not match the value accessed by tag number")

        # try a value that is nested the deepest (so deep I break it into two steps!)
        fract = dose.ReferencedRTPlanSequence[0].ReferencedFractionGroupSequence[0]
        beamnum = fract.ReferencedBeamSequence[0].ReferencedBeamNumber
        self.assertEqual(beamnum, 1, "Beam number not the expected value")
コード例 #35
0
ファイル: test_filereader.py プロジェクト: IMAGE-ET/pydicom
    def testRTDose(self):
        """Returns correct values for sample data elements in test RT Dose file"""
        dose = read_file(rtdose_name)
        self.assertEqual(dose.FrameIncrementPointer, Tag((0x3004, 0x000c)),
                         "Frame Increment Pointer not the expected value")
        self.assertEqual(dose.FrameIncrementPointer, dose[0x28, 9].value,
                         "FrameIncrementPointer does not match the value accessed by tag number")

        # try a value that is nested the deepest (so deep I break it into two steps!)
        fract = dose.ReferencedRTPlanSequence[0].ReferencedFractionGroupSequence[0]
        beamnum = fract.ReferencedBeamSequence[0].ReferencedBeamNumber
        self.assertEqual(beamnum, 1, "Beam number not the expected value")
コード例 #36
0
 def testMR(self):
     """Returns correct values for sample data elements in test MR file....."""
     mr = read_file(mr_name)
     # (0010, 0010) Patient's Name           'CompressedSamples^MR1'
     self.assertEqual(mr.PatientName, 'CompressedSamples^MR1',
                      "Wrong patient name")
     self.assertEqual(
         mr.PatientName, mr[0x10, 0x10].value,
         "Name does not match value found when accessed by tag number")
     got = mr.PixelSpacing
     expected = [Decimal('0.3125'), Decimal('0.3125')]
     self.assert_(got == expected, "Wrong pixel spacing")
コード例 #37
0
ファイル: test_filereader.py プロジェクト: sidsd27/BIO-X_2020
 def testReadFileGivenFileLikeObject(self):
     """filereader: can read using a file-like (BytesIO) file...."""
     with open(ct_name, 'rb') as f:
         file_like = BytesIO(f.read())
     ct = read_file(file_like)
     # Tests here simply repeat some of testCT test
     got = ct.ImagePositionPatient
     DS = dicom.valuerep.DS
     expected = [DS('-158.135803'), DS('-179.035797'), DS('-75.699997')]
     self.assertTrue(got == expected, "ImagePosition(Patient) values not as expected")
     self.assertEqual(len(ct.PixelData), 128 * 128 * 2, "Pixel data not expected length")
     # Should also be able to close the file ourselves without exception raised:
     file_like.close()
コード例 #38
0
    def testTimeCheck(self):
        """Deferred read warns if file has been modified..........."""
        if stat_available:
            ds = read_file(self.testfile_name, defer_size=2000)
            from time import sleep
            sleep(1)
            open(self.testfile_name, "r+").write('\0')  # "touch" the file
            warning_start = "Deferred read warning -- file modification time "

            def read_value():
                data_elem = ds.PixelData

            assertWarns(self, warning_start, read_value)
コード例 #39
0
    def testRTPlan(self):
        """Returns correct values for sample data elements in test RT Plan file"""
        plan = read_file(rtplan_name)
        beam = plan.Beams[0]
        cp0, cp1 = beam.ControlPoints # if not two controlpoints, then this would raise exception

        self.assertEqual(beam.TreatmentMachineName, "unit001", "Incorrect unit name")
        self.assertEqual(beam.TreatmentMachineName, beam[0x300a, 0x00b2].value,
                "beam TreatmentMachineName does not match the value accessed by tag number")

        cumDoseRef = cp1.ReferencedDoseReferences[0].CumulativeDoseReferenceCoefficient
        self.assert_(isClose(cumDoseRef, 0.9990268),
                "Cum Dose Ref Coeff not the expected value (CP1, Ref'd Dose Ref")
        JawX = cp0.BLDPositions[0].LeafJawPositions
        self.assert_(isClose(JawX[0], -100.0) and isClose(JawX[1], 100.0),
                "X jaws not as expected (control point 0)")
コード例 #40
0
ファイル: test_filereader.py プロジェクト: psy2013GitHub/Atom
    def testRTPlan(self):
        """Returns correct values for sample data elements in test RT Plan file"""
        plan = read_file(rtplan_name)
        beam = plan.BeamSequence[0]
        cp0, cp1 = beam.ControlPointSequence # if not two controlpoints, then this would raise exception

        self.assertEqual(beam.TreatmentMachineName, "unit001", "Incorrect unit name")
        self.assertEqual(beam.TreatmentMachineName, beam[0x300a, 0x00b2].value,
                "beam TreatmentMachineName does not match the value accessed by tag number")

        got = cp1.ReferencedDoseReferenceSequence[0].CumulativeDoseReferenceCoefficient
        expected = Decimal('0.9990268')
        self.assert_(got == expected,
                "Cum Dose Ref Coeff not the expected value (CP1, Ref'd Dose Ref")
        got = cp0.BeamLimitingDevicePositionSequence[0].LeafJawPositions
        self.assert_(got[0] == Decimal('-100') and got[1] == Decimal('100.0'),
                "X jaws not as expected (control point 0)")
コード例 #41
0
 def testDir(self):
     """Returns correct dir attributes for both Dataset and DICOM names (python >= 2.6).."""
     # Only python >= 2.6 calls __dir__ for dir() call
     rtss = read_file(rtstruct_name, force=True)
     # sample some expected 'dir' values
     got_dir = dir(rtss)
     expect_in_dir = ["pixel_array", "add_new", "ROIContourSequence", "StructureSetDate", "__sizeof__"]
     expect_not_in_dir = ["RemovePrivateTags", "AddNew", "GroupDataset"]  # remove in v1.0
     for name in expect_in_dir:
         self.assertTrue(name in got_dir, "Expected name '%s' in dir()" % name)
     for name in expect_not_in_dir:
         self.assertTrue(name not in got_dir, "Unexpected name '%s' in dir()" % name)
     # Now check for some items in dir() of a nested item
     roi0 = rtss.ROIContourSequence[0]
     got_dir = dir(roi0)
     expect_in_dir = ["pixel_array", "add_new", "ReferencedROINumber", "ROIDisplayColor", "__sizeof__"]
     for name in expect_in_dir:
         self.assertTrue(name in got_dir, "Expected name '%s' in dir()" % name)
コード例 #42
0
ファイル: test_filereader.py プロジェクト: sidsd27/BIO-X_2020
    def testRTPlan(self):
        """Returns correct values for sample data elements in test RT Plan file"""
        plan = read_file(rtplan_name)
        beam = plan.BeamSequence[0]
        cp0, cp1 = beam.ControlPointSequence  # if not two controlpoints, then this would raise exception

        self.assertEqual(beam.TreatmentMachineName, "unit001", "Incorrect unit name")
        self.assertEqual(beam.TreatmentMachineName, beam[0x300a, 0x00b2].value,
                         "beam TreatmentMachineName does not match the value accessed by tag number")

        got = cp1.ReferencedDoseReferenceSequence[0].CumulativeDoseReferenceCoefficient
        DS = dicom.valuerep.DS
        expected = DS('0.9990268')
        self.assertTrue(got == expected,
                        "Cum Dose Ref Coeff not the expected value (CP1, Ref'd Dose Ref")
        got = cp0.BeamLimitingDevicePositionSequence[0].LeafJawPositions
        self.assertTrue(got[0] == DS('-100') and got[1] == DS('100.0'),
                        "X jaws not as expected (control point 0)")
コード例 #43
0
ファイル: viewdcm.py プロジェクト: scumer/python
 def __init__(self, parent=None, flags=Qt.Widget):
     super(DCMWidget,self).__init__(parent, flags)
     
     #self.painter = QPainter(self)        
     
     self.dcmdata = read_file(filenamec)
     self.row = self.dcmdata.Rows  # width
     self.column = self.dcmdata.Columns  # height
     self.modality = self.dcmdata.Modality
     
     self.slope = self.dcmdata.RescaleSlope
     self.interceprt = self.dcmdata.RescaleIntercept
     
     print 'Rows,Column:',self.row,self.column
     print 'Modality:',self.modality
     
     if type(self.dcmdata.WindowWidth) == dicom.multival.MultiValue:
         self.winw = self.dcmdata.WindowWidth[0] 
         self.winc = self.dcmdata.WindowCenter[0]
     else:
         self.winw = self.dcmdata.WindowWidth 
         self.winc = self.dcmdata.WindowCenter            
     
     print 'winw,winc:',self.winw,self.winc  
     print 'pixel array shape:',self.dcmdata.pixel_array.shape
     
     self.win_width = QApplication.desktop().width()
     self.win_height = QApplication.desktop().height()
     
     self.resize(800, 600)
     #self.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
     
     self.image = None
     self.pmin = None
     self.pmax = None
     
     #self.pix = QPixmap(filenameb)
     
     self.pixel_array_ori = self.dcmdata.pixel_array*self.slope+self.interceprt
     self.pixel_array_lut = self.get_LUT_value(self.pixel_array_ori,self.winw,self.winc)
     
     self.genImage()
コード例 #44
0
ファイル: test_filereader.py プロジェクト: psy2013GitHub/Atom
 def testDir(self):
     """Returns correct dir attributes for both Dataset and DICOM names (python >= 2.6).."""
     # Only python >= 2.6 calls __dir__ for dir() call
     if sys.version_info >= (2,6):
         rtss = read_file(rtstruct_name, force=True)        
         # sample some expected 'dir' values
         got_dir = dir(rtss)
         expect_in_dir = ['pixel_array', 'add_new', 'ROIContourSequence', 
                          'StructureSetDate', '__sizeof__']
         expect_not_in_dir = ['RemovePrivateTags', 'AddNew', 'GroupDataset'] # remove in v1.0
         for name in expect_in_dir:
             self.assert_(name in got_dir, "Expected name '%s' in dir()" % name)
         for name in expect_not_in_dir:
             self.assert_(name not in got_dir, "Unexpected name '%s' in dir()" % name)
         # Now check for some items in dir() of a nested item
         roi0 = rtss.ROIContourSequence[0]
         got_dir = dir(roi0)
         expect_in_dir = ['pixel_array', 'add_new', 'ReferencedROINumber', 
                          'ROIDisplayColor', '__sizeof__']
         for name in expect_in_dir:
             self.assert_(name in got_dir, "Expected name '%s' in dir()" % name)               
コード例 #45
0
    def testNestedPrivateSQ(self):
        """Can successfully read a private SQ which contains additional SQ's....."""
        # From issue 113. When a private SQ of undefined length is used, the
        #   sequence is read in and the length of the SQ is determined upon
        #   identification of the SQ termination sequence. When using nested
        #   Sequences, the first termination sequence encountered actually
        #   belongs to the nested Sequence not the parent, therefore the
        #   remainder of the file is not read in properly
        ds = read_file(nested_priv_SQ_name)

        # Make sure that the entire dataset was read in
        pixel_data_tag = TupleTag((0x7fe0, 0x10))
        self.assertTrue(
            pixel_data_tag in ds,
            "Entire dataset was not parsed properly. PixelData is not present")

        # Check that the DataElement is indeed a Sequence
        tag = TupleTag((0x01, 0x01))
        seq0 = ds[tag]
        self.assertEqual(seq0.VR, 'SQ',
                         "First level sequence not parsed properly")

        # Now verify the presence of the nested private SQ
        seq1 = seq0[0][tag]
        self.assertEqual(seq1.VR, 'SQ',
                         "Second level sequence not parsed properly")

        # Now make sure the values that are parsed are correct
        got = seq1[0][tag].value
        expected = b'Double Nested SQ'
        self.assertEqual(got, expected,
                         "Expected a value of %s, got %s'" % (expected, got))

        got = seq0[0][0x01, 0x02].value
        expected = b'Nested SQ'
        self.assertEqual(got, expected,
                         "Expected a value of %s, got %s'" % (expected, got))
コード例 #46
0
 def data(self):
     if not self._data:
         self._data = read_file(self.path)
     return self._data
コード例 #47
0
ファイル: test_filereader.py プロジェクト: IMAGE-ET/pydicom
 def setUp(self):
     self.jpeg = read_file(jpeg_lossless_name)
コード例 #48
0
ファイル: test_filereader.py プロジェクト: IMAGE-ET/pydicom
 def setUp(self):
     self.jpeg = read_file(jpeg2000_name)
コード例 #49
0
ファイル: dicomparser.py プロジェクト: bpinsard/toad
    def __initialized(self):

        try:
            header = read_file(self.__filename,
                               defer_size=None,
                               stop_before_pixels=True,
                               force=True)

        except InvalidDicomError:
            self.__isDicom = False
            return
        try:

            # find the manufacturer
            self.__manufacturer = 'UNKNOWN'
            if 'Manufacturer' in header:
                for manufacturer in manufacturers:
                    if manufacturer in header.Manufacturer:
                        self.__manufacturer = manufacturer

            self.__patientName = util.slugify(header.PatientName)
            self.__seriesDescription = util.slugify(header.SeriesDescription)
            self.__seriesNumber = header.SeriesNumber
            self.__instanceNumber = header.InstanceNumber
            self.__mrModel = header.ManufacturerModelName
            self.__magneticFieldStrength = header.MagneticFieldStrength
            self.__studyUID = header.StudyInstanceUID

            self.__tr = float(header.RepetitionTime)  # TR Repetition Time
            self.__te = float(header.EchoTime)  # TE Echo Time
            self.__flipAngle = float(header.FlipAngle)  # Flip Angle

            self.__matrixSize = [
                value for value in header.AcquisitionMatrix if value != 0
            ]  # Matrix Size
            self.__voxelSize = map(
                float,
                [
                    header.PixelSpacing[0],  # Voxel size
                    header.PixelSpacing[1],
                    header.SliceThickness
                ])
            self.__fov = self.__matrixSize[0] * self.__voxelSize[
                0]  # Compute FOV

            self.__isDicom = True

        except AttributeError as a:
            if "EchoTime" in a.message:
                try:
                    self.__te = header[Tag((0x2001, 0x1025))].value
                    self.__isDicom = True
                except KeyError as k:
                    self.__isDicom = False
            else:
                self.__isDicom = False

        if self.isSiemens():
            if 'DIFFUSION' and 'MOSAIC' in header.ImageType:  # If Diffusion Acquistion
                self.__SequenceName = 'Diffusion'
            elif 'DIFFUSION' in header.ImageType:  # If b0 Acquistion
                self.__SequenceName = 'b0'
            elif 'M' and 'NORM' in header.ImageType:  # If T1 Acquisition
                self.__SequenceName = 'Structural T1'
                self.__ti = float(header.InversionTime)
            elif 'P' in header.ImageType:  # If Phase acquisition
                self.__SequenceName = 'Phase'
            else:  # If Magnitude acquisition
                self.__SequenceName = 'Magnitude'

            # inherith Siemens ascconv properties
            Ascconv.__init__(self, self.__filename)
            bandwidthPerPixelPhaseEncodeTag = Tag((0x0019, 0x1028))

            try:
                if header.has_key(bandwidthPerPixelPhaseEncodeTag):
                    val = header[bandwidthPerPixelPhaseEncodeTag].value
                    try:
                        self.__bandwidthPerPixelPhaseEncode = float(val)
                    except ValueError:
                        # some data have wrong VR in dicomparser, try to unpack
                        self.__bandwidthPerPixelPhaseEncode = struct.unpack(
                            'd', val)[0]

                self.__echoSpacing = 1 / (self.__bandwidthPerPixelPhaseEncode * self.getEpiFactor()) * 1000.0 * \
                                     self.getPatFactor() * self.getPhaseResolution() * \
                                     self.getPhaseOversampling()

            except (KeyError, IndexError, TypeError, ValueError):
                self.__echoSpacing = None
コード例 #50
0
ファイル: dicomparser.py プロジェクト: UNFmontreal/toad
    def __initialized(self):

        try:
            header = read_file(self.__filename, defer_size=None, stop_before_pixels=True, force=True)

        except InvalidDicomError:
            self.__isDicom = False
            return
        try:

            # find the manufacturer
            self.__manufacturer = 'UNKNOWN'
            if 'Manufacturer' in header:
                for manufacturer in manufacturers:
                    if manufacturer in header.Manufacturer:
                        self.__manufacturer = manufacturer

            self.__patientName = util.slugify(header.PatientName)
            self.__seriesDescription = util.slugify(header.SeriesDescription)
            self.__seriesNumber = header.SeriesNumber
            self.__instanceNumber = header.InstanceNumber
            self.__mrModel = header.ManufacturerModelName
            self.__magneticFieldStrength = header.MagneticFieldStrength
            self.__studyUID = header.StudyInstanceUID

            self.__tr = float(header.RepetitionTime)  # TR Repetition Time
            self.__te = float(header.EchoTime)  # TE Echo Time
            self.__flipAngle = float(header.FlipAngle)  # Flip Angle

            self.__matrixSize = [value for value in header.AcquisitionMatrix if value != 0]  # Matrix Size
            self.__voxelSize = map(float, [header.PixelSpacing[0],  # Voxel size
                                           header.PixelSpacing[1],
                                           header.SliceThickness])
            self.__fov = self.__matrixSize[0] * self.__voxelSize[0]  # Compute FOV

            self.__isDicom = True

        except AttributeError as a:
            if "EchoTime" in a.message:
                try:
                    self.__te = header[Tag((0x2001, 0x1025))].value
                    self.__isDicom = True
                except KeyError as k:
                    self.__isDicom = False
            else:
                self.__isDicom = False

        if self.isSiemens():
            if 'DIFFUSION' and 'MOSAIC' in header.ImageType:  # If Diffusion Acquistion
                self.__SequenceName = 'Diffusion'
            elif 'DIFFUSION' in header.ImageType:  # If b0 Acquistion
                self.__SequenceName = 'b0'
            elif 'M' and 'NORM' in header.ImageType:  # If T1 Acquisition
                self.__SequenceName = 'Structural T1'
                self.__ti = float(header.InversionTime)
            elif 'P' in header.ImageType:  # If Phase acquisition
                self.__SequenceName = 'Phase'
            else:  # If Magnitude acquisition
                self.__SequenceName = 'Magnitude'

            # inherith Siemens ascconv properties
            Ascconv.__init__(self, self.__filename)
            bandwidthPerPixelPhaseEncodeTag = Tag((0x0019, 0x1028))

            try:
                if header.has_key(bandwidthPerPixelPhaseEncodeTag):
                    val = header[bandwidthPerPixelPhaseEncodeTag].value
                    try:
                        self.__bandwidthPerPixelPhaseEncode = float(val)
                    except ValueError:
                        # some data have wrong VR in dicomparser, try to unpack
                        self.__bandwidthPerPixelPhaseEncode = struct.unpack('d', val)[0]

                self.__echoSpacing = 1 / (self.__bandwidthPerPixelPhaseEncode * self.getEpiFactor()) * 1000.0 * \
                                     self.getPatFactor() * self.getPhaseResolution() * \
                                     self.getPhaseOversampling()

            except (KeyError, IndexError, TypeError, ValueError):
                self.__echoSpacing = None
コード例 #51
0
 def setUp(self):
     self.jpeg = read_file(jpeg_lossless_name)
コード例 #52
0
 def setUp(self):
     self.jpeg = read_file(jpeg2000_name)
コード例 #53
0
ファイル: dicom_fileop.py プロジェクト: scumer/python
#logger.setLevel(logging.DEBUG)

#dicom.debug(True)
#print type(logger.handlers[0])

#H:unsigned short
#s:string (array of char)
#L:unsigned long
#HHL
#struct(endian_chr + "HH2sH")

#group, elem, VR, length = element_struct_unpack(bytes_read) explict
#group, elem, length = element_struct_unpack(bytes_read) implict
filename = r'E:\Project\Python\dicom\306.dcm'

dcm = read_file(filename)
#print dcm[(0x0010, 0x0010)].name
#print dcm[(0x0010, 0x0010)].value
#dcm.decode()
#print dcm.PatientName
#print dcm.get_item(key)
#print dcm.
#print dcm.pixel_array
#print dcm.PixelData
#print dcm.SamplesPerPixel
#print dcm.BitsStored
#print dcm.BitsAllocated
#print dcm.HighBit
#print dcm.SliceLocation
#print dcm.SliceThickness
#print dcm.PixelRepresentation
コード例 #54
0
 def data(self):
     """Lazy evaluated DICOM file data."""
     if not self._data:
         self._data = read_file(self.path)
     return self._data