def setUp(self):
self.msi = helpers.getFakeMsi()
self.specialmsi = helpers.getFakeMsi()
# set one pixel to special values
self.specialValue = np.arange(self.specialmsi.get_image().shape[-1]) * 2
self.specialmsi.get_image()[2, 2, :] = self.specialValue
# create a segmentation which sets all elements to invalid but the
# one pixel with the special value
self.segmentation = np.zeros(self.specialmsi.get_image().shape[0:-1])
self.segmentation[2, 2] = 1
def test_imageWriterCreatesCorrectFile(self):
writer = TiffWriter(self.msi, convert_to_nm=False)
writer.write(self.fileUriToWrite)
reader = TiffReader(shift_bits=0)
msi = reader.read(self.fileUriToWrite)
self.assertTrue(msi == helpers.getFakeMsi(),
"image correctly written and read")
def test_imageWriterCreatesCorrectFile(self):
writer = TiffWriter(self.msi, convert_to_nm=False)
writer.write(self.fileUriToWrite)
reader = TiffReader(shift_bits=0)
msi = reader.read(self.fileUriToWrite)
self.assertTrue(msi == helpers.getFakeMsi(),
"image correctly written and read")
def test_imageWriterCreatesCorrectFile(self):
writer = NrrdWriter(self.msi)
writer.write(self.fileUriToWrite)
reader = NrrdReader()
msi = reader.read(self.fileUriToWrite)
self.assertTrue(msi == helpers.getFakeMsi(),
"image correctly written and read")
def setUp(self):
# setup file and the path where it shall be written to
self.msi = helpers.getFakeMsi()
self.fileUriToWrite = "testfile.nrrd"
def setUp(self):
self.msi = helpers.getFakeMsi()
self.test_file_path = "test_msi.msi"
def setUp(self):
# setup file and the path where it shall be written to
self.msi = helpers.getFakeMsi()
self.msi.set_image(self.msi.get_image())
self.fileUriToWrite = os.path.join(os.getcwd(), "testfiles")
def setUp(self):
self.specialmsi = helpers.getFakeMsi()
# set one pixel to special values
self.specialValue = np.arange(
self.specialmsi.get_image().shape[-1]) * 2
self.specialmsi.get_image()[2, 2, :] = self.specialValue
def setUp(self):
self.msi = helpers.getFakeMsi()
def setUp(self):
self.specialmsi = helpers.getFakeMsi()
# set one pixel to special values
self.specialValue = np.arange(self.specialmsi.get_image().shape[-1]) * 2
self.specialmsi.get_image()[2, 2, :] = self.specialValue