Python getFakeMsi Examples

Example #1

File: test_msimanipulations.py Project: 151706061/MITK

    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

Example #2

    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")

Example #3

File: test_tiffwriter.py Project: 151706061/MITK

    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")

Example #4

File: test_nrrdwriter.py Project: 151706061/MITK

    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")

Example #5

File: test_nrrdwriter.py Project: 151706061/MITK

 def setUp(self):
     # setup file and the path where it shall be written to
     self.msi = helpers.getFakeMsi()
     self.fileUriToWrite = "testfile.nrrd"

Example #6

File: test_msireaderwriter.py Project: araex/MITK

 def setUp(self):
     self.msi = helpers.getFakeMsi()
     self.test_file_path = "test_msi.msi"

Example #7

File: test_tiffwriter.py Project: 151706061/MITK

 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")

Example #8

File: test_normalize.py Project: dishamishra/MITKats

 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

Example #9

File: test_msi.py Project: swirkert/ipcai2016

 def setUp(self):
     self.msi = helpers.getFakeMsi()

Example #10

File: test_normalize.py Project: swirkert/ipcai2016

 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