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)
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)
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)
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)
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)
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)
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()
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))
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**"
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)
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)
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))
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)
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()
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))
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**")
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)
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")
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
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
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)
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
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)
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
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))
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))
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
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")
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()
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)
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)
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
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()
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")
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")
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")
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()
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)
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)")
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)")
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)
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)")
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()
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)
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))
def data(self):
if not self._data:
self._data = read_file(self.path)
return self._data
def setUp(self):
self.jpeg = read_file(jpeg_lossless_name)
def setUp(self):
self.jpeg = read_file(jpeg2000_name)
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
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
def setUp(self):
self.jpeg = read_file(jpeg_lossless_name)
def setUp(self):
self.jpeg = read_file(jpeg2000_name)
#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
def data(self):
"""Lazy evaluated DICOM file data."""
if not self._data:
self._data = read_file(self.path)
return self._data
