Esempio n. 1
0
 def test_vessel_tree_lar(self):
     import lisa.gt_lar
     tvg = TreeGenerator(lisa.gt_lar.GTLar)
     yaml_path = os.path.join(path_to_script, "./hist_stats_test.yaml")
     tvg.importFromYaml(yaml_path)
     tvg.voxelsize_mm = [1, 1, 1]
     tvg.shape = [100, 100, 100]
     output = tvg.generateTree() # noqa
     if self.interactiveTests:
         tvg.show()
Esempio n. 2
0
    def test_synthetic_data_vessel_tree_evaluation(self):
        """
        Generovani umeleho stromu do 3D a jeho evaluace.
        V testu dochazi ke kontrole predpokladaneho objemu a deky cev


        """
        # import segmentation
        # import misc

        # generate 3d data from yaml for testing
        tvg = TreeGenerator()
        yaml_path = os.path.join(path_to_script, "./hist_stats_test.yaml")
        tvg.importFromYaml(yaml_path)
        tvg.voxelsize_mm = [1, 1, 1]
        tvg.shape = [100, 100, 100]
        data3d = tvg.generateTree()

        # init histology Analyser
        metadata = {'voxelsize_mm': tvg.voxelsize_mm}
        data3d = data3d * 10
        threshold = 2.5
        ha = HistologyAnalyser(data3d, metadata, threshold)

        # segmented data
        ha.data_to_binar()
        ha.data_to_skeleton()

        # get statistics
        ha.data_to_statistics()
        yaml_new = os.path.join(path_to_script, "hist_stats_new.yaml")
        ha.writeStatsToYAML(filename=yaml_new)

        # get histology reports
        hr = HistologyReport()
        hr.importFromYaml(yaml_path)
        hr.generateStats()
        stats_orig = hr.stats['Report']

        hr = HistologyReport()
        hr.importFromYaml(yaml_new)
        hr.generateStats()
        stats_new = hr.stats['Report']

        ha.writeStatsToCSV(filename=yaml_new)
        # compare
        self.assertGreater(stats_orig['Other']['Total length mm'],stats_new['Other']['Total length mm']*0.9)  # noqa
        self.assertLess(stats_orig['Other']['Total length mm'],stats_new['Other']['Total length mm']*1.1)  # noqa

        self.assertGreater(stats_orig['Other']['Avg length mm'],stats_new['Other']['Avg length mm']*0.9)  # noqa
        self.assertLess(stats_orig['Other']['Avg length mm'],stats_new['Other']['Avg length mm']*1.1)  # noqa

        self.assertGreater(stats_orig['Other']['Avg radius mm'],stats_new['Other']['Avg radius mm']*0.9)  # noqa
        self.assertLess(stats_orig['Other']['Avg radius mm'],stats_new['Other']['Avg radius mm']*1.1)  # noqa
Esempio n. 3
0
    def test_surface_measurement_find_edge(self):
        import lisa.surface_measurement as sm
        tvg = TreeGenerator()
        yaml_path = os.path.join(path_to_script, "./hist_stats_test.yaml")
        tvg.importFromYaml(yaml_path)
        tvg.voxelsize_mm = [1, 1, 1]
        tvg.shape = [100, 100, 100]
        data3d = tvg.generateTree()

        # init histology Analyser
        # metadata = {'voxelsize_mm': tvg.voxelsize_mm}
        # data3d = data3d * 10
        # threshold = 2.5

        im_edg = sm.find_edge(data3d, 0)
        # in this area should be positive edge
        self.assertGreater(
            np.sum(im_edg[25:30, 25:30, 30]),
            3
        )