Exemple #1
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    def test_calculate_mean_spectrum_masked_image(self):

        mani.apply_segmentation(self.specialmsi, self.segmentation)
        mani.calculate_mean_spectrum(self.specialmsi)

        np.testing.assert_equal(self.specialValue, self.specialmsi.get_image(),
                        "mean spectrum is correctly calculated on image with " +
                        "mask applied")
    def test_calculate_mean_spectrum_masked_image(self):

        mani.apply_segmentation(self.specialmsi, self.segmentation)
        mani.calculate_mean_spectrum(self.specialmsi)

        np.testing.assert_equal(self.specialValue, self.specialmsi.get_image(),
                        "mean spectrum is correctly calculated on image with " +
                        "mask applied")
Exemple #3
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    def test_apply_segmentation(self):

        mani.apply_segmentation(self.specialmsi, self.segmentation)

        validImageEntries = self.specialmsi.get_image() \
            [~self.specialmsi.get_image().mask]

        np.testing.assert_equal(validImageEntries, self.specialValue,
                        "image has been correctly segmented")
    def test_apply_segmentation(self):

        mani.apply_segmentation(self.specialmsi, self.segmentation)

        validImageEntries = self.specialmsi.get_image() \
            [~self.specialmsi.get_image().mask]

        np.testing.assert_equal(validImageEntries, self.specialValue,
                        "image has been correctly segmented")
Exemple #5
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 def setUp(self):
     self.msi = helpers.getFakeMsi()
     # set one pixel to special values
     self.specialValue = np.arange(self.msi.get_image().shape[-1]) * 2
     self.msi.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.msi.get_image().shape[0:-1])
     self.segmentation[2, 2] = 1
     # apply this segmentation to the msi
     msimani.apply_segmentation(self.msi, self.segmentation)
     self.image = self.msi.get_image()
Exemple #6
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 def setUp(self):
     self.msi = helpers.getFakeMsi()
     # set one pixel to special values
     self.specialValue = np.arange(self.msi.get_image().shape[-1]) * 2
     self.msi.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.msi.get_image().shape[0:-1])
     self.segmentation[2, 2] = 1
     # apply this segmentation to the msi
     msimani.apply_segmentation(self.msi, self.segmentation)
     self.image = self.msi.get_image()