<gh_stars>10-100
# ! /usr/bin/python
# -*- coding: utf-8 -*-


# import funkcí z jiného adresáře
import sys


from PyQt5.QtWidgets import *
import os.path



# imcut_path =  os.path.join(path_to_script, "../../imcut/")
# sys.path.insert(0, imcut_path)
import unittest



import numpy as np


import pytest




from lisa import organ_segmentation


import imcut.dcmreaddata as dcmr


import lisa.dataset


import io3d.datasets




# nosetests tests/organ_segmentation_test.py:OrganSegmentationTest.test_create_iparams # noqa



class CoinaudSegmentationTest(unittest.TestCase):
    interactiveTest = False
    verbose = False


    @unittest.skip("Waiting for implementation")
    def test_devel_vein_basin_segmentation(self):
        pth = r"E:\data\medical\processed\mik2018 para\P09_paraall_cropped.pklz"
        datap = io3d.read(pth)
        labels = {
            "1": 1,
            "2": 2,
            "3": 3,
            "4": 4,
            "5": 5,
            "6": 6,
        }
        from PyQt5.QtGui import QApplication, QPushButton
        app = QApplication(sys.argv)
        import seededitorqt


        se = seededitorqt.QTSeedEditor(datap["data3d"], contours=datap["segmentation"])

        def split(obj):
            import lisa.virtual_resection as vr


            print(np.max(datap["data3d"]))
            print(np.unique(se.seeds))
            out, sepobj = vr.split_vessel(datap, se.seeds, method="separate labels", input_seeds_label2=2)
            print(np.unique(out))
            se.seeds = out
            se.contours = out
            se.setView(se.actual_view)
        qpb = QPushButton("Ahoj")
        qpb.clicked.connect(split)
        wg = se.my_layout.layout().itemAt(0).itemAt(2).addWidget(qpb)

        se.exec_()

#     def generate_data(self):
#
#         img3d = (np.random.rand(30, 30, 30)*10).astype(np.int16)
#         seeds = (np.zeros(img3d.shape)).astype(np.int8)
#         segmentation = (np.zeros(img3d.shape)).astype(np.int8)
#         segmentation[10:25, 4:24, 2:16] = 1
#         img3d = img3d + segmentation*20
#         seeds[12:18, 9:16, 3:6] = 1
#         seeds[19:22, 21:27, 19:21] = 2
#
#         voxelsize_mm = [5, 5, 5]
#         metadata = {'voxelsize_mm': voxelsize_mm}
#         return img3d, metadata, seeds, segmentation
#
#     # @unittest.skipIf(not interactiveTest, "interactive test")
#     @pytest.mark.interactive
#     def test_viewer_seeds(self):
#
#         try:
#             from imcut.seed_editor_qt import QTSeedEditor
#         except:
#             print("Deprecated of pyseg_base as submodule")
#             from seed_editor_qt import QTSeedEditor
#         from PyQt4.QtGui import QApplication
#         import numpy as np
#         img3d = (np.random.rand(30, 30, 30)*10).astype(np.int16)
#         seeds = (np.zeros(img3d.shape)).astype(np.int8)
#         seeds[3:6, 12:18, 9:16] = 1
#         seeds[3:6, 19:22, 21:27] = 2
#         # , QMainWindow
#         app = QApplication(sys.argv)
#         pyed = QTSeedEditor(img3d, seeds=seeds)
#         pyed.exec_()
#
#         # deletemask = pyed.getSeeds()
#         # import pdb; pdb.set_trace()
#
#         # pyed = QTSeedEditor(deletemask, mode='draw')
#         # pyed.exec_()
#
#         app.exit()
#     # @unittest.skip("demonstrating skipping")
#
#     @pytest.mark.interactive
#     def test_whole_organ_segmentation_interactive(self):
#         """
#         Interactive test uses dicom data for segmentation
#         """
#         dcmdir = io3d.datasets.join_path(
#             'matlab/examples/sample_data/DICOM/digest_article/'
#         )
#             # path_to_script,
#             # './../sample_data/matlab/examples/sample_data/DICOM/digest_article/') # noqa
#         oseg = organ_segmentation.OrganSegmentation(
#             dcmdir, working_voxelsize_mm=4, manualroi=False)
#
# # manual seeds setting
#         print("with left mouse button select some pixels of the brain")
#         print("with right mouse button select some pixels of other tissues\
# and background")
#
#         oseg.interactivity()
#
#         volume = oseg.get_segmented_volume_size_mm3()
#         print(volume)
#
#         self.assertGreater(volume, 50000)
#         self.assertLess(volume, 1200000)
#
#
# #        roi_mm = [[3, 3, 3], [150, 150, 50]]
# #        oseg.ni_set_roi()
# #        coordinates_mm = [[110, 50, 30], [10, 10, 10]]
# #        label = [1, 2]
# #        radius = [5, 5]
# #        oseg.ni_set_seeds(coordinates_mm, label, radius)
# #
# #        oseg.make_segmentation()
#
#
#     # @unittest.skipIf(not interactiveTest, "interactive test")
#     @unittest.skip("interactivity params are obsolete")
#     def test_organ_segmentation_with_boundary_penalties(self):
#         """
#         Interactivity is stored to file
#         """
#         dcmdir = io3d.datasets.join_path('jatra_5mm')
#
#         print("Interactive test: with left mouse button select liver, \
#             with right mouse button select other tissues")
#         # gcparams = {'pairwiseAlpha':10, 'use_boundary_penalties':True}
#         segparams = {'pairwise_alpha_per': 3,
#                      'use_boundary_penalties': True,
#                      'boundary_penalties_sigma': 200}
#         oseg = organ_segmentation.OrganSegmentation(
#             dcmdir, working_voxelsize_mm=4, segparams=segparams)
#         oseg.add_seeds_mm([120], [120], [400], label=1, radius=30)
#         oseg.add_seeds_mm([170, 220, 250], [250, 280, 200], [400], label=2,
#                           radius=30)
#
#         "boundary penalties"
#         oseg.interactivity()
#         # oseg.ninteractivity()
#
#         volume = oseg.get_segmented_volume_size_mm3()
#
#         # misc.obj_to_file(oseg.get_iparams(),'iparams.pkl', filetype='pickle')
#
#         self.assertGreater(volume, 1000000)
#     # @unittest.skipIf(not interactiveTest, "interactive test")
#
#     @unittest.skip("interactivity params are obsolete")
#     def test_create_iparams(self):
#         """
#         Interactivity is stored to file
#         """
#         if self.verbose:
#             print("test_create_iparams")
#         import misc
#         dcmdir = io3d.datasets.join_path('jatra_5mm')
#             # path_to_script, './../sample_data/jatra_5mm')
#
#         segparams = {'pairwiseAlpha': 20,
#                      'use_boundary_penalties': False,
#                      'boundary_penalties_sigma': 200}
#         # oseg = organ_segmentation.OrganSegmentation(dcmdir, working_voxelsize_mm = 4) # noqa
#         oseg = organ_segmentation.OrganSegmentation(
#             dcmdir, working_voxelsize_mm=4,
#             segparams=segparams, manualroi=False)
#         # oseg.add_seeds_mm([120, 160], [150, 120], [70], label=1, radius=20)
#         oseg.add_seeds_mm([120, 160], [150, 80], [85], label=1, radius=20)
#         oseg.add_seeds_mm([170, 220, 250, 100], [250, 300, 200, 350], [85],
#                           label=2, radius=20)
#         oseg.add_seeds_mm([170], [240], [70], label=2, radius=20)
#
#         # print "test_ipars"
#         # oseg.interactivity()
#         oseg.ninteractivity()
#
#         volume = oseg.get_segmented_volume_size_mm3()
#         # print 'vol %.3g ' %(volume)
#
#         misc.obj_to_file(oseg.get_iparams(), 'iparams.pkl', filetype='pickle')
#
#         self.assertGreater(volume, 1000000)
#
#     # @unittest.skipIf(not interactiveTest, "interactive test")
#     @pytest.mark.interactive
#     def test_stored_interactivity(self):
#         pass
#
#     def test_synth_liver(self):
#         params = {}
#         self.synthetic_liver_template(params)
#
#     def synthetic_liver(self):
#         """
#         Create synthetic data. There is some liver and porta -like object.
#         """
#         # data
#         slab = {'none': 0, 'liver': 1, 'porta': 2}
#         voxelsize_mm = np.array([1.0, 1.0, 1.2])
#
#         segm = np.zeros([80, 256, 250], dtype=np.int16)
#
#         # liver
#         segm[30:60, 70:180, 40:190] = slab['liver']
#         # porta
#         segm[40:45, 120:130, 70:190] = slab['porta']
#         segm[40:45, 80:130, 100:110] = slab['porta']
#         segm[40:44, 120:170, 130:135] = slab['porta']
#
#         data3d = np.zeros(segm.shape)
#         data3d[segm == slab['liver']] = 146
#         data3d[segm == slab['porta']] = 206
#         noise = (np.random.normal(0, 10, segm.shape))  # .astype(np.int16)
#         data3d = (data3d + noise).astype(np.int16)
#         return data3d, segm, voxelsize_mm, slab
#
#     def synthetic_liver_template(self, params):
#         """
#         Function uses organ_segmentation  for synthetic box object
#         segmentation.
#         """
#         # dcmdir = os.path.join(path_to_script,'./../sample_data/matlab/examples/sample_data/DICOM/digest_article/') # noqa
# # data
#
#         data3d, segm, voxelsize_mm, slab = self.synthetic_liver()
#
# # seeds
#         seeds = np.zeros(data3d.shape, np.int8)
#         seeds[40:55, 90:120, 70:110] = 1
#         seeds[30:45, 190:200, 40:90] = 2
# # [mm]  10 x 10 x 10        # voxelsize_mm = [1, 4, 3]
#         metadata = {'voxelsize_mm': voxelsize_mm}
#
#         oseg = organ_segmentation.OrganSegmentation(
#             None,
#             data3d=data3d,
#             metadata=metadata,
#             seeds=seeds,
#             working_voxelsize_mm=5,
#             manualroi=False,
#             autocrop=False,
#
#             **params
#         )
#
#         oseg.ninteractivity()
#
#         volume = oseg.get_segmented_volume_size_mm3()
#         oseg.portalVeinSegmentation(interactivity=False, threshold=180)
#         oseg.saveVesselTree('porta')
#
#         # print '> 0 '
#         # print np.sum(oseg.segmentation > 0)
#         # print np.sum(segm > 0)
#         # print np.sum(oseg.segmentation > 0) * np.prod(voxelsize_mm)
#         # print np.sum(segm > 0) * np.prod(voxelsize_mm)
#         # print 'computed ', volume
#         # print voxelsize_mm
#         # print oseg.voxelsize_mm
#
#         # import pdb; pdb.set_trace()
#         # import sed3
#         # ed = sed3.sed3(data3d, seeds=seeds,
#         #                contour=(oseg.segmentation))
#         # ed.show()
#         # import ipdb; ipdb.set_trace() #  noqa BREAKPOINT
#
#         # mel by to být litr. tedy milion mm3
#         # je to zvlastni. pro nekter verze knihoven je to 630, pro jine 580
#         self.assertGreater(volume, 570000)
#         self.assertLess(volume, 640000)
#
#     def test_roi(self):
#         """
#         Test setting of ROI. It is in pixels, not in mm
#         """
#
#         img3d = (np.random.rand(30, 30, 30)*10).astype(np.int16)
#         seeds = (np.zeros(img3d.shape)).astype(np.int8)
#         segmentation = (np.zeros(img3d.shape)).astype(np.int8)
#         segmentation[10:25, 4:24, 2:16] = 1
#         img3d = img3d + segmentation*20
#         seeds[12:18, 9:16, 3:6] = 1
#         seeds[19:22, 21:27, 19:21] = 2
#
#         roi = [[7, 27], [2, 29], [0, 26]]
#         # seeds = seeds[7:27, 2:29, 0:26]
#         voxelsize_mm = [5, 5, 5]
#         metadata = {'voxelsize_mm': voxelsize_mm}
#
#         oseg = organ_segmentation.OrganSegmentation(
#             None,
#             data3d=img3d,
#             metadata=metadata,
#             seeds=seeds,
#             roi=roi,
#             working_voxelsize_mm=5,
#             manualroi=False)
#
#         # from PyQt4.QtGui import QApplication
#         # app = QApplication(sys.argv)
#         # oseg.interactivity(min_val=0, max_val=30)
#         oseg.ninteractivity()
#         datap = oseg.export()
#
#         volume = oseg.get_segmented_volume_size_mm3()
#         self.assertGreater(volume, 500000)
#         self.assertIn('data3d', datap.keys())
#         self.assertIn('voxelsize_mm', datap.keys())
#
#     def test_box_segmentation(self):
#         params = {'segmentation_smoothing': False}
#         self.box_segmentation_template(params)
#
#     def test_box_segmentation_with_smoothing(self):
#         """
#         Function uses organ_segmentation  for synthetic box object
#         segmentation.
#         """
#         params = {'segmentation_smoothing': True}
#         self.box_segmentation_template(params, noise_sigma=4)
#         # dcmdir = os.path.join(path_to_script,'./../sample_data/matlab/examples/sample_data/DICOM/digest_article/') # noqa
#
#     def box_segmentation_template(self, params, noise_sigma=3):
#         """
#         Function uses organ_segmentation  for synthetic box object
#         segmentation.
#         """
#         # dcmdir = os.path.join(path_to_script,'./../sample_data/matlab/examples/sample_data/DICOM/digest_article/') # noqa
# # data
#         img3d = np.random.rand(32, 64, 64) * noise_sigma
#         img3d[4:24, 12:32, 5:25] = img3d[4:24, 12:32, 5:25] + 30
#
# # seeds
#         seeds = np.zeros([32, 64, 64], np.int8)
#         seeds[9:12, 13:29, 18:25] = 1
#         seeds[9:12, 4:9, 3:32] = 2
# # [mm]  10 x 10 x 10        # voxelsize_mm = [1, 4, 3]
#         voxelsize_mm = [5, 5, 5]
#         metadata = {'voxelsize_mm': voxelsize_mm}
#
#         oseg = organ_segmentation.OrganSegmentation(
#             None,
#             data3d=img3d,
#             metadata=metadata,
#             seeds=seeds,
#             working_voxelsize_mm=10,
#             manualroi=False,
#             **params
#         )
#
#         # oseg.seeds = seeds
#         # oseg.make_gc()
# # manual seeds setting
#
#         from PyQt4.QtGui import QApplication
#         app = QApplication(sys.argv)
#         # oseg.interactivity()
#         oseg.ninteractivity()
#
#         volume = oseg.get_segmented_volume_size_mm3()
#
#         # import pdb; pdb.set_trace()
#
#         # mel by to být litr. tedy milion mm3
#         self.assertGreater(volume, 800000)
#         self.assertLess(volume, 1100000)
#
#     def test_volume_resize(self):
#         # from scipy.sparse.import lil_matrix
#
#         pass
#
#     # @unittest.skipIf(True, "interactive test")
#     # @unittest.skipIf(not interactiveTest, "interactive test")
#     @pytest.mark.interactive
#     def test_vincentka_06_slice_thickness_interactive(self):
#         """
#         Interactive test. SliceThickness is not voxel depth. If it is, this
#         test will fail.
#         """
#         # dcmdir = os.path.join(path_to_script, './../sample_data/matlab/examples/sample_data/DICOM/digest_article/') #noqa
#         dcmdir = os.path.expanduser(
#             '~/data/medical/data_orig/vincentka/13021610/10200000/')
#         dcmdir = os.path.expanduser(
#             '~/data/medical/data_orig/vincentka/13021610/12460000/')
#         oseg = organ_segmentation.OrganSegmentation(dcmdir,
#                                                     working_voxelsize_mm=4,
#                                                     manualroi=False)
#
# # manual seeds setting
#         print(
#             "with left mouse button select some pixels of the bottle content")
#         print("with right mouse button select some pixels of background")
#
#         oseg.interactivity()
#
#         volume = oseg.get_segmented_volume_size_mm3()
#         # print volume
#
#         self.assertGreater(volume, 550000)
#         self.assertLess(volume, 850000)
#
#     def setUp(self):
#         """ Nastavení společných proměnných pro testy  """
#         self.assertTrue(True)
#
#     # @TODO dodělat přidávání uzlů pomocí mm
#     # @unittest.skipIf(not interactiveTest, "interactive test")
#     def test_add_seeds_mm(self):
#         """
#         Function uses organ_segmentation object for segmentation
#         """
#         dcmdir = io3d.datasets.join_path(
#             'matlab/examples/sample_data/DICOM/digest_article/'
#             # path_to_script,
#             # './../sample_data/matlab/examples/sample_data/DICOM/digest_article/'
#         )
#         oseg = organ_segmentation.OrganSegmentation(dcmdir,
#                                                     working_voxelsize_mm=4,
#                                                     manualroi=False)
#
#         oseg.add_seeds_mm([80], [120], [120], 1, 25)
#         oseg.add_seeds_mm([80], [40], [130], 2, 25)
#
#         # pro kontrolu lze odkomentovat
#         # from PyQt4.QtGui import QApplication
#         # app = QApplication(sys.argv)
#         # oseg.interactivity()
#
#         oseg.ninteractivity()
#
#         volume = oseg.get_segmented_volume_size_mm3()
#
#         # import pdb; pdb.set_trace()
#
#         # mel by to být litr. tedy milion mm3
#         self.assertGreater(volume, 800000)
#         self.assertLess(volume, 1200000)
#
#         # roi_mm = [[3, 3, 3], [150, 150, 50]]
#         # oseg.ni_set_roi()
#         # coordinates_mm = [[110, 50, 30], [10, 10, 10]]
#         # label = [1, 2]
#         # radius = [5, 5]
#         # oseg.ni_set_seeds(coordinates_mm, label, radius)
#
#         # oseg.make_segmentation()
#
#         # oseg.noninteractivity()
#         pass
#
#     @unittest.skip("demonstrating skipping")
#     def test_dicomread_and_graphcut(self):
#         """
#         Test dicomread module and graphcut module
#         """
#         from imcut import pycut
#
#         path_to_script = os.path.dirname(os.path.abspath(__file__))
#         dcmdir = os.path.join(path_to_script, './../sample_data/matlab/examples/sample_data/DICOM/digest_article/') #noqa
#         data3d, metadata = dcmr.dcm_read_from_dir(dcmdir)
#
#         # print("Data size: " + str(data3d.nbytes) + ', shape: ' + str(data3d.shape) ) #noqa
#
#         igc = pycut.ImageGraphCut(data3d, zoom=0.5)
#         seeds = igc.seeds
#         seeds[0, :, 0] = 1
#         seeds[60:66, 60:66, 5:6] = 2
#         igc.noninteractivity(seeds)
#
#         igc.make_gc()
#         segmentation = igc.segmentation
#         self.assertTrue(segmentation[14, 4, 1] == 0)
#         self.assertTrue(segmentation[127, 120, 10] == 1)
#         self.assertTrue(np.sum(segmentation == 1) > 100)
#         self.assertTrue(np.sum(segmentation == 0) > 100)
#         # igc.show_segmentation()
#
#     def test_resize_data_one_value(self):
#         datap = io3d.datasets.generate_abdominal()
#         target_voxelsize_mm = 3
#         oseg = organ_segmentation.OrganSegmentation(
#                                                     working_voxelsize_mm=4,
#                                                     manualroi=False)
#         oseg.import_dataplus(dataplus=datap)
#         orig_shape = oseg.data3d.shape
#
#         oseg.resize_to_mm(target_voxelsize_mm)
#         self.assertEqual(oseg.voxelsize_mm[0], target_voxelsize_mm)
#         self.assertEqual(oseg.voxelsize_mm[1], target_voxelsize_mm)
#         self.assertEqual(oseg.voxelsize_mm[2], target_voxelsize_mm)
#         self.assertNotEqual(orig_shape[0], oseg.data3d.shape[0])
#         self.assertNotEqual(orig_shape[1], oseg.data3d.shape[1])
#         self.assertNotEqual(orig_shape[2], oseg.data3d.shape[2])
#
#     def test_resize_data_three_values(self):
#         datap = io3d.datasets.generate_abdominal()
#         target_voxelsize_mm = [7.14, 4.1, 3]
#         oseg = organ_segmentation.OrganSegmentation(
#             working_voxelsize_mm=4,
#             manualroi=False)
#         oseg.import_dataplus(dataplus=datap)
#         orig_shape = oseg.data3d.shape
#
#         oseg.resize_to_mm(target_voxelsize_mm)
#         self.assertEqual(oseg.voxelsize_mm[0], target_voxelsize_mm[0])
#         self.assertEqual(oseg.voxelsize_mm[1], target_voxelsize_mm[1])
#         self.assertEqual(oseg.voxelsize_mm[2], target_voxelsize_mm[2])
#         self.assertNotEqual(orig_shape[0], oseg.data3d.shape[0])
#         self.assertNotEqual(orig_shape[1], oseg.data3d.shape[1])
#         self.assertNotEqual(orig_shape[2], oseg.data3d.shape[2])


if __name__ == "__main__":
    unittest.main()

# ! /usr/bin/python
# -*- coding: utf-8 -*-


# import funkcí z jiného adresáře
import sys


from PyQt5.QtWidgets import *
import os.path



# imcut_path =  os.path.join(path_to_script, "../../imcut/")
# sys.path.insert(0, imcut_path)
import unittest



import numpy as np


import pytest




from lisa import organ_segmentation


import imcut.dcmreaddata as dcmr


import lisa.dataset


import io3d.datasets




# nosetests tests/organ_segmentation_test.py:OrganSegmentationTest.test_create_iparams # noqa



class CoinaudSegmentationTest(unittest.TestCase):
    interactiveTest = False
    verbose = False


    @unittest.skip("Waiting for implementation")
    def test_devel_vein_basin_segmentation(self):
        pth = r"E:\data\medical\processed\mik2018 para\P09_paraall_cropped.pklz"
        datap = io3d.read(pth)
        labels = {
            "1": 1,
            "2": 2,
            "3": 3,
            "4": 4,
            "5": 5,
            "6": 6,
        }
        from PyQt5.QtGui import QApplication, QPushButton
        app = QApplication(sys.argv)
        import seededitorqt


        se = seededitorqt.QTSeedEditor(datap["data3d"], contours=datap["segmentation"])

        def split(obj):
            import lisa.virtual_resection as vr


            print(np.max(datap["data3d"]))
            print(np.unique(se.seeds))
            out, sepobj = vr.split_vessel(datap, se.seeds, method="separate labels", input_seeds_label2=2)
            print(np.unique(out))
            se.seeds = out
            se.contours = out
            se.setView(se.actual_view)
        qpb = QPushButton("Ahoj")
        qpb.clicked.connect(split)
        wg = se.my_layout.layout().itemAt(0).itemAt(2).addWidget(qpb)

        se.exec_()

#     def generate_data(self):
#
#         img3d = (np.random.rand(30, 30, 30)*10).astype(np.int16)
#         seeds = (np.zeros(img3d.shape)).astype(np.int8)
#         segmentation = (np.zeros(img3d.shape)).astype(np.int8)
#         segmentation[10:25, 4:24, 2:16] = 1
#         img3d = img3d + segmentation*20
#         seeds[12:18, 9:16, 3:6] = 1
#         seeds[19:22, 21:27, 19:21] = 2
#
#         voxelsize_mm = [5, 5, 5]
#         metadata = {'voxelsize_mm': voxelsize_mm}
#         return img3d, metadata, seeds, segmentation
#
#     # @unittest.skipIf(not interactiveTest, "interactive test")
#     @pytest.mark.interactive
#     def test_viewer_seeds(self):
#
#         try:
#             from imcut.seed_editor_qt import QTSeedEditor
#         except:
#             print("Deprecated of pyseg_base as submodule")
#             from seed_editor_qt import QTSeedEditor
#         from PyQt4.QtGui import QApplication
#         import numpy as np
#         img3d = (np.random.rand(30, 30, 30)*10).astype(np.int16)
#         seeds = (np.zeros(img3d.shape)).astype(np.int8)
#         seeds[3:6, 12:18, 9:16] = 1
#         seeds[3:6, 19:22, 21:27] = 2
#         # , QMainWindow
#         app = QApplication(sys.argv)
#         pyed = QTSeedEditor(img3d, seeds=seeds)
#         pyed.exec_()
#
#         # deletemask = pyed.getSeeds()
#         # import pdb; pdb.set_trace()
#
#         # pyed = QTSeedEditor(deletemask, mode='draw')
#         # pyed.exec_()
#
#         app.exit()
#     # @unittest.skip("demonstrating skipping")
#
#     @pytest.mark.interactive
#     def test_whole_organ_segmentation_interactive(self):
#         """
#         Interactive test uses dicom data for segmentation
#         """
#         dcmdir = io3d.datasets.join_path(
#             'matlab/examples/sample_data/DICOM/digest_article/'
#         )
#             # path_to_script,
#             # './../sample_data/matlab/examples/sample_data/DICOM/digest_article/') # noqa
#         oseg = organ_segmentation.OrganSegmentation(
#             dcmdir, working_voxelsize_mm=4, manualroi=False)
#
# # manual seeds setting
#         print("with left mouse button select some pixels of the brain")
#         print("with right mouse button select some pixels of other tissues\
# and background")
#
#         oseg.interactivity()
#
#         volume = oseg.get_segmented_volume_size_mm3()
#         print(volume)
#
#         self.assertGreater(volume, 50000)
#         self.assertLess(volume, 1200000)
#
#
# #        roi_mm = [[3, 3, 3], [150, 150, 50]]
# #        oseg.ni_set_roi()
# #        coordinates_mm = [[110, 50, 30], [10, 10, 10]]
# #        label = [1, 2]
# #        radius = [5, 5]
# #        oseg.ni_set_seeds(coordinates_mm, label, radius)
# #
# #        oseg.make_segmentation()
#
#
#     # @unittest.skipIf(not interactiveTest, "interactive test")
#     @unittest.skip("interactivity params are obsolete")
#     def test_organ_segmentation_with_boundary_penalties(self):
#         """
#         Interactivity is stored to file
#         """
#         dcmdir = io3d.datasets.join_path('jatra_5mm')
#
#         print("Interactive test: with left mouse button select liver, \
#             with right mouse button select other tissues")
#         # gcparams = {'pairwiseAlpha':10, 'use_boundary_penalties':True}
#         segparams = {'pairwise_alpha_per': 3,
#                      'use_boundary_penalties': True,
#                      'boundary_penalties_sigma': 200}
#         oseg = organ_segmentation.OrganSegmentation(
#             dcmdir, working_voxelsize_mm=4, segparams=segparams)
#         oseg.add_seeds_mm([120], [120], [400], label=1, radius=30)
#         oseg.add_seeds_mm([170, 220, 250], [250, 280, 200], [400], label=2,
#                           radius=30)
#
#         "boundary penalties"
#         oseg.interactivity()
#         # oseg.ninteractivity()
#
#         volume = oseg.get_segmented_volume_size_mm3()
#
#         # misc.obj_to_file(oseg.get_iparams(),'iparams.pkl', filetype='pickle')
#
#         self.assertGreater(volume, 1000000)
#     # @unittest.skipIf(not interactiveTest, "interactive test")
#
#     @unittest.skip("interactivity params are obsolete")
#     def test_create_iparams(self):
#         """
#         Interactivity is stored to file
#         """
#         if self.verbose:
#             print("test_create_iparams")
#         import misc
#         dcmdir = io3d.datasets.join_path('jatra_5mm')
#             # path_to_script, './../sample_data/jatra_5mm')
#
#         segparams = {'pairwiseAlpha': 20,
#                      'use_boundary_penalties': False,
#                      'boundary_penalties_sigma': 200}
#         # oseg = organ_segmentation.OrganSegmentation(dcmdir, working_voxelsize_mm = 4) # noqa
#         oseg = organ_segmentation.OrganSegmentation(
#             dcmdir, working_voxelsize_mm=4,
#             segparams=segparams, manualroi=False)
#         # oseg.add_seeds_mm([120, 160], [150, 120], [70], label=1, radius=20)
#         oseg.add_seeds_mm([120, 160], [150, 80], [85], label=1, radius=20)
#         oseg.add_seeds_mm([170, 220, 250, 100], [250, 300, 200, 350], [85],
#                           label=2, radius=20)
#         oseg.add_seeds_mm([170], [240], [70], label=2, radius=20)
#
#         # print "test_ipars"
#         # oseg.interactivity()
#         oseg.ninteractivity()
#
#         volume = oseg.get_segmented_volume_size_mm3()
#         # print 'vol %.3g ' %(volume)
#
#         misc.obj_to_file(oseg.get_iparams(), 'iparams.pkl', filetype='pickle')
#
#         self.assertGreater(volume, 1000000)
#
#     # @unittest.skipIf(not interactiveTest, "interactive test")
#     @pytest.mark.interactive
#     def test_stored_interactivity(self):
#         pass
#
#     def test_synth_liver(self):
#         params = {}
#         self.synthetic_liver_template(params)
#
#     def synthetic_liver(self):
#         """
#         Create synthetic data. There is some liver and porta -like object.
#         """
#         # data
#         slab = {'none': 0, 'liver': 1, 'porta': 2}
#         voxelsize_mm = np.array([1.0, 1.0, 1.2])
#
#         segm = np.zeros([80, 256, 250], dtype=np.int16)
#
#         # liver
#         segm[30:60, 70:180, 40:190] = slab['liver']
#         # porta
#         segm[40:45, 120:130, 70:190] = slab['porta']
#         segm[40:45, 80:130, 100:110] = slab['porta']
#         segm[40:44, 120:170, 130:135] = slab['porta']
#
#         data3d = np.zeros(segm.shape)
#         data3d[segm == slab['liver']] = 146
#         data3d[segm == slab['porta']] = 206
#         noise = (np.random.normal(0, 10, segm.shape))  # .astype(np.int16)
#         data3d = (data3d + noise).astype(np.int16)
#         return data3d, segm, voxelsize_mm, slab
#
#     def synthetic_liver_template(self, params):
#         """
#         Function uses organ_segmentation  for synthetic box object
#         segmentation.
#         """
#         # dcmdir = os.path.join(path_to_script,'./../sample_data/matlab/examples/sample_data/DICOM/digest_article/') # noqa
# # data
#
#         data3d, segm, voxelsize_mm, slab = self.synthetic_liver()
#
# # seeds
#         seeds = np.zeros(data3d.shape, np.int8)
#         seeds[40:55, 90:120, 70:110] = 1
#         seeds[30:45, 190:200, 40:90] = 2
# # [mm]  10 x 10 x 10        # voxelsize_mm = [1, 4, 3]
#         metadata = {'voxelsize_mm': voxelsize_mm}
#
#         oseg = organ_segmentation.OrganSegmentation(
#             None,
#             data3d=data3d,
#             metadata=metadata,
#             seeds=seeds,
#             working_voxelsize_mm=5,
#             manualroi=False,
#             autocrop=False,
#
#             **params
#         )
#
#         oseg.ninteractivity()
#
#         volume = oseg.get_segmented_volume_size_mm3()
#         oseg.portalVeinSegmentation(interactivity=False, threshold=180)
#         oseg.saveVesselTree('porta')
#
#         # print '> 0 '
#         # print np.sum(oseg.segmentation > 0)
#         # print np.sum(segm > 0)
#         # print np.sum(oseg.segmentation > 0) * np.prod(voxelsize_mm)
#         # print np.sum(segm > 0) * np.prod(voxelsize_mm)
#         # print 'computed ', volume
#         # print voxelsize_mm
#         # print oseg.voxelsize_mm
#
#         # import pdb; pdb.set_trace()
#         # import sed3
#         # ed = sed3.sed3(data3d, seeds=seeds,
#         #                contour=(oseg.segmentation))
#         # ed.show()
#         # import ipdb; ipdb.set_trace() #  noqa BREAKPOINT
#
#         # mel by to být litr. tedy milion mm3
#         # je to zvlastni. pro nekter verze knihoven je to 630, pro jine 580
#         self.assertGreater(volume, 570000)
#         self.assertLess(volume, 640000)
#
#     def test_roi(self):
#         """
#         Test setting of ROI. It is in pixels, not in mm
#         """
#
#         img3d = (np.random.rand(30, 30, 30)*10).astype(np.int16)
#         seeds = (np.zeros(img3d.shape)).astype(np.int8)
#         segmentation = (np.zeros(img3d.shape)).astype(np.int8)
#         segmentation[10:25, 4:24, 2:16] = 1
#         img3d = img3d + segmentation*20
#         seeds[12:18, 9:16, 3:6] = 1
#         seeds[19:22, 21:27, 19:21] = 2
#
#         roi = [[7, 27], [2, 29], [0, 26]]
#         # seeds = seeds[7:27, 2:29, 0:26]
#         voxelsize_mm = [5, 5, 5]
#         metadata = {'voxelsize_mm': voxelsize_mm}
#
#         oseg = organ_segmentation.OrganSegmentation(
#             None,
#             data3d=img3d,
#             metadata=metadata,
#             seeds=seeds,
#             roi=roi,
#             working_voxelsize_mm=5,
#             manualroi=False)
#
#         # from PyQt4.QtGui import QApplication
#         # app = QApplication(sys.argv)
#         # oseg.interactivity(min_val=0, max_val=30)
#         oseg.ninteractivity()
#         datap = oseg.export()
#
#         volume = oseg.get_segmented_volume_size_mm3()
#         self.assertGreater(volume, 500000)
#         self.assertIn('data3d', datap.keys())
#         self.assertIn('voxelsize_mm', datap.keys())
#
#     def test_box_segmentation(self):
#         params = {'segmentation_smoothing': False}
#         self.box_segmentation_template(params)
#
#     def test_box_segmentation_with_smoothing(self):
#         """
#         Function uses organ_segmentation  for synthetic box object
#         segmentation.
#         """
#         params = {'segmentation_smoothing': True}
#         self.box_segmentation_template(params, noise_sigma=4)
#         # dcmdir = os.path.join(path_to_script,'./../sample_data/matlab/examples/sample_data/DICOM/digest_article/') # noqa
#
#     def box_segmentation_template(self, params, noise_sigma=3):
#         """
#         Function uses organ_segmentation  for synthetic box object
#         segmentation.
#         """
#         # dcmdir = os.path.join(path_to_script,'./../sample_data/matlab/examples/sample_data/DICOM/digest_article/') # noqa
# # data
#         img3d = np.random.rand(32, 64, 64) * noise_sigma
#         img3d[4:24, 12:32, 5:25] = img3d[4:24, 12:32, 5:25] + 30
#
# # seeds
#         seeds = np.zeros([32, 64, 64], np.int8)
#         seeds[9:12, 13:29, 18:25] = 1
#         seeds[9:12, 4:9, 3:32] = 2
# # [mm]  10 x 10 x 10        # voxelsize_mm = [1, 4, 3]
#         voxelsize_mm = [5, 5, 5]
#         metadata = {'voxelsize_mm': voxelsize_mm}
#
#         oseg = organ_segmentation.OrganSegmentation(
#             None,
#             data3d=img3d,
#             metadata=metadata,
#             seeds=seeds,
#             working_voxelsize_mm=10,
#             manualroi=False,
#             **params
#         )
#
#         # oseg.seeds = seeds
#         # oseg.make_gc()
# # manual seeds setting
#
#         from PyQt4.QtGui import QApplication
#         app = QApplication(sys.argv)
#         # oseg.interactivity()
#         oseg.ninteractivity()
#
#         volume = oseg.get_segmented_volume_size_mm3()
#
#         # import pdb; pdb.set_trace()
#
#         # mel by to být litr. tedy milion mm3
#         self.assertGreater(volume, 800000)
#         self.assertLess(volume, 1100000)
#
#     def test_volume_resize(self):
#         # from scipy.sparse.import lil_matrix
#
#         pass
#
#     # @unittest.skipIf(True, "interactive test")
#     # @unittest.skipIf(not interactiveTest, "interactive test")
#     @pytest.mark.interactive
#     def test_vincentka_06_slice_thickness_interactive(self):
#         """
#         Interactive test. SliceThickness is not voxel depth. If it is, this
#         test will fail.
#         """
#         # dcmdir = os.path.join(path_to_script, './../sample_data/matlab/examples/sample_data/DICOM/digest_article/') #noqa
#         dcmdir = os.path.expanduser(
#             '~/data/medical/data_orig/vincentka/13021610/10200000/')
#         dcmdir = os.path.expanduser(
#             '~/data/medical/data_orig/vincentka/13021610/12460000/')
#         oseg = organ_segmentation.OrganSegmentation(dcmdir,
#                                                     working_voxelsize_mm=4,
#                                                     manualroi=False)
#
# # manual seeds setting
#         print(
#             "with left mouse button select some pixels of the bottle content")
#         print("with right mouse button select some pixels of background")
#
#         oseg.interactivity()
#
#         volume = oseg.get_segmented_volume_size_mm3()
#         # print volume
#
#         self.assertGreater(volume, 550000)
#         self.assertLess(volume, 850000)
#
#     def setUp(self):
#         """ Nastavení společných proměnných pro testy  """
#         self.assertTrue(True)
#
#     # @TODO dodělat přidávání uzlů pomocí mm
#     # @unittest.skipIf(not interactiveTest, "interactive test")
#     def test_add_seeds_mm(self):
#         """
#         Function uses organ_segmentation object for segmentation
#         """
#         dcmdir = io3d.datasets.join_path(
#             'matlab/examples/sample_data/DICOM/digest_article/'
#             # path_to_script,
#             # './../sample_data/matlab/examples/sample_data/DICOM/digest_article/'
#         )
#         oseg = organ_segmentation.OrganSegmentation(dcmdir,
#                                                     working_voxelsize_mm=4,
#                                                     manualroi=False)
#
#         oseg.add_seeds_mm([80], [120], [120], 1, 25)
#         oseg.add_seeds_mm([80], [40], [130], 2, 25)
#
#         # pro kontrolu lze odkomentovat
#         # from PyQt4.QtGui import QApplication
#         # app = QApplication(sys.argv)
#         # oseg.interactivity()
#
#         oseg.ninteractivity()
#
#         volume = oseg.get_segmented_volume_size_mm3()
#
#         # import pdb; pdb.set_trace()
#
#         # mel by to být litr. tedy milion mm3
#         self.assertGreater(volume, 800000)
#         self.assertLess(volume, 1200000)
#
#         # roi_mm = [[3, 3, 3], [150, 150, 50]]
#         # oseg.ni_set_roi()
#         # coordinates_mm = [[110, 50, 30], [10, 10, 10]]
#         # label = [1, 2]
#         # radius = [5, 5]
#         # oseg.ni_set_seeds(coordinates_mm, label, radius)
#
#         # oseg.make_segmentation()
#
#         # oseg.noninteractivity()
#         pass
#
#     @unittest.skip("demonstrating skipping")
#     def test_dicomread_and_graphcut(self):
#         """
#         Test dicomread module and graphcut module
#         """
#         from imcut import pycut
#
#         path_to_script = os.path.dirname(os.path.abspath(__file__))
#         dcmdir = os.path.join(path_to_script, './../sample_data/matlab/examples/sample_data/DICOM/digest_article/') #noqa
#         data3d, metadata = dcmr.dcm_read_from_dir(dcmdir)
#
#         # print("Data size: " + str(data3d.nbytes) + ', shape: ' + str(data3d.shape) ) #noqa
#
#         igc = pycut.ImageGraphCut(data3d, zoom=0.5)
#         seeds = igc.seeds
#         seeds[0, :, 0] = 1
#         seeds[60:66, 60:66, 5:6] = 2
#         igc.noninteractivity(seeds)
#
#         igc.make_gc()
#         segmentation = igc.segmentation
#         self.assertTrue(segmentation[14, 4, 1] == 0)
#         self.assertTrue(segmentation[127, 120, 10] == 1)
#         self.assertTrue(np.sum(segmentation == 1) > 100)
#         self.assertTrue(np.sum(segmentation == 0) > 100)
#         # igc.show_segmentation()
#
#     def test_resize_data_one_value(self):
#         datap = io3d.datasets.generate_abdominal()
#         target_voxelsize_mm = 3
#         oseg = organ_segmentation.OrganSegmentation(
#                                                     working_voxelsize_mm=4,
#                                                     manualroi=False)
#         oseg.import_dataplus(dataplus=datap)
#         orig_shape = oseg.data3d.shape
#
#         oseg.resize_to_mm(target_voxelsize_mm)
#         self.assertEqual(oseg.voxelsize_mm[0], target_voxelsize_mm)
#         self.assertEqual(oseg.voxelsize_mm[1], target_voxelsize_mm)
#         self.assertEqual(oseg.voxelsize_mm[2], target_voxelsize_mm)
#         self.assertNotEqual(orig_shape[0], oseg.data3d.shape[0])
#         self.assertNotEqual(orig_shape[1], oseg.data3d.shape[1])
#         self.assertNotEqual(orig_shape[2], oseg.data3d.shape[2])
#
#     def test_resize_data_three_values(self):
#         datap = io3d.datasets.generate_abdominal()
#         target_voxelsize_mm = [7.14, 4.1, 3]
#         oseg = organ_segmentation.OrganSegmentation(
#             working_voxelsize_mm=4,
#             manualroi=False)
#         oseg.import_dataplus(dataplus=datap)
#         orig_shape = oseg.data3d.shape
#
#         oseg.resize_to_mm(target_voxelsize_mm)
#         self.assertEqual(oseg.voxelsize_mm[0], target_voxelsize_mm[0])
#         self.assertEqual(oseg.voxelsize_mm[1], target_voxelsize_mm[1])
#         self.assertEqual(oseg.voxelsize_mm[2], target_voxelsize_mm[2])
#         self.assertNotEqual(orig_shape[0], oseg.data3d.shape[0])
#         self.assertNotEqual(orig_shape[1], oseg.data3d.shape[1])
#         self.assertNotEqual(orig_shape[2], oseg.data3d.shape[2])


if __name__ == "__main__":
    unittest.main()
# ! /usr/bin/python # -*- coding: utf-8 -*- # import funkcí z jiného adresáře # imcut_path =  os.path.join(path_to_script, "../../imcut/") # sys.path.insert(0, imcut_path) # nosetests tests/organ_segmentation_test.py:OrganSegmentationTest.test_create_iparams # noqa #     def generate_data(self): # #         img3d = (np.random.rand(30, 30, 30)*10).astype(np.int16) #         seeds = (np.zeros(img3d.shape)).astype(np.int8) #         segmentation = (np.zeros(img3d.shape)).astype(np.int8) #         segmentation[10:25, 4:24, 2:16] = 1 #         img3d = img3d + segmentation*20 #         seeds[12:18, 9:16, 3:6] = 1 #         seeds[19:22, 21:27, 19:21] = 2 # #         voxelsize_mm = [5, 5, 5] #         metadata = {'voxelsize_mm': voxelsize_mm} #         return img3d, metadata, seeds, segmentation # #     # @unittest.skipIf(not interactiveTest, "interactive test") #     @pytest.mark.interactive #     def test_viewer_seeds(self): # #         try: #             from imcut.seed_editor_qt import QTSeedEditor #         except: #             print("Deprecated of pyseg_base as submodule") #             from seed_editor_qt import QTSeedEditor #         from PyQt4.QtGui import QApplication #         import numpy as np #         img3d = (np.random.rand(30, 30, 30)*10).astype(np.int16) #         seeds = (np.zeros(img3d.shape)).astype(np.int8) #         seeds[3:6, 12:18, 9:16] = 1 #         seeds[3:6, 19:22, 21:27] = 2 #         # , QMainWindow #         app = QApplication(sys.argv) #         pyed = QTSeedEditor(img3d, seeds=seeds) #         pyed.exec_() # #         # deletemask = pyed.getSeeds() #         # import pdb; pdb.set_trace() # #         # pyed = QTSeedEditor(deletemask, mode='draw') #         # pyed.exec_() # #         app.exit() #     # @unittest.skip("demonstrating skipping") # #     @pytest.mark.interactive #     def test_whole_organ_segmentation_interactive(self): #         """ #         Interactive test uses dicom data for segmentation #         """ #         dcmdir = io3d.datasets.join_path( #             'matlab/examples/sample_data/DICOM/digest_article/' #         ) #             # path_to_script, #             # './../sample_data/matlab/examples/sample_data/DICOM/digest_article/') # noqa #         oseg = organ_segmentation.OrganSegmentation( #             dcmdir, working_voxelsize_mm=4, manualroi=False) # # # manual seeds setting #         print("with left mouse button select some pixels of the brain") #         print("with right mouse button select some pixels of other tissues\ # and background") # #         oseg.interactivity() # #         volume = oseg.get_segmented_volume_size_mm3() #         print(volume) # #         self.assertGreater(volume, 50000) #         self.assertLess(volume, 1200000) # # # #        roi_mm = [[3, 3, 3], [150, 150, 50]] # #        oseg.ni_set_roi() # #        coordinates_mm = [[110, 50, 30], [10, 10, 10]] # #        label = [1, 2] # #        radius = [5, 5] # #        oseg.ni_set_seeds(coordinates_mm, label, radius) # # # #        oseg.make_segmentation() # # #     # @unittest.skipIf(not interactiveTest, "interactive test") #     @unittest.skip("interactivity params are obsolete") #     def test_organ_segmentation_with_boundary_penalties(self): #         """ #         Interactivity is stored to file #         """ #         dcmdir = io3d.datasets.join_path('jatra_5mm') # #         print("Interactive test: with left mouse button select liver, \ #             with right mouse button select other tissues") #         # gcparams = {'pairwiseAlpha':10, 'use_boundary_penalties':True} #         segparams = {'pairwise_alpha_per': 3, #                      'use_boundary_penalties': True, #                      'boundary_penalties_sigma': 200} #         oseg = organ_segmentation.OrganSegmentation( #             dcmdir, working_voxelsize_mm=4, segparams=segparams) #         oseg.add_seeds_mm([120], [120], [400], label=1, radius=30) #         oseg.add_seeds_mm([170, 220, 250], [250, 280, 200], [400], label=2, #                           radius=30) # #         "boundary penalties" #         oseg.interactivity() #         # oseg.ninteractivity() # #         volume = oseg.get_segmented_volume_size_mm3() # #         # misc.obj_to_file(oseg.get_iparams(),'iparams.pkl', filetype='pickle') # #         self.assertGreater(volume, 1000000) #     # @unittest.skipIf(not interactiveTest, "interactive test") # #     @unittest.skip("interactivity params are obsolete") #     def test_create_iparams(self): #         """ #         Interactivity is stored to file #         """ #         if self.verbose: #             print("test_create_iparams") #         import misc #         dcmdir = io3d.datasets.join_path('jatra_5mm') #             # path_to_script, './../sample_data/jatra_5mm') # #         segparams = {'pairwiseAlpha': 20, #                      'use_boundary_penalties': False, #                      'boundary_penalties_sigma': 200} #         # oseg = organ_segmentation.OrganSegmentation(dcmdir, working_voxelsize_mm = 4) # noqa #         oseg = organ_segmentation.OrganSegmentation( #             dcmdir, working_voxelsize_mm=4, #             segparams=segparams, manualroi=False) #         # oseg.add_seeds_mm([120, 160], [150, 120], [70], label=1, radius=20) #         oseg.add_seeds_mm([120, 160], [150, 80], [85], label=1, radius=20) #         oseg.add_seeds_mm([170, 220, 250, 100], [250, 300, 200, 350], [85], #                           label=2, radius=20) #         oseg.add_seeds_mm([170], [240], [70], label=2, radius=20) # #         # print "test_ipars" #         # oseg.interactivity() #         oseg.ninteractivity() # #         volume = oseg.get_segmented_volume_size_mm3() #         # print 'vol %.3g ' %(volume) # #         misc.obj_to_file(oseg.get_iparams(), 'iparams.pkl', filetype='pickle') # #         self.assertGreater(volume, 1000000) # #     # @unittest.skipIf(not interactiveTest, "interactive test") #     @pytest.mark.interactive #     def test_stored_interactivity(self): #         pass # #     def test_synth_liver(self): #         params = {} #         self.synthetic_liver_template(params) # #     def synthetic_liver(self): #         """ #         Create synthetic data. There is some liver and porta -like object. #         """ #         # data #         slab = {'none': 0, 'liver': 1, 'porta': 2} #         voxelsize_mm = np.array([1.0, 1.0, 1.2]) # #         segm = np.zeros([80, 256, 250], dtype=np.int16) # #         # liver #         segm[30:60, 70:180, 40:190] = slab['liver'] #         # porta #         segm[40:45, 120:130, 70:190] = slab['porta'] #         segm[40:45, 80:130, 100:110] = slab['porta'] #         segm[40:44, 120:170, 130:135] = slab['porta'] # #         data3d = np.zeros(segm.shape) #         data3d[segm == slab['liver']] = 146 #         data3d[segm == slab['porta']] = 206 #         noise = (np.random.normal(0, 10, segm.shape))  # .astype(np.int16) #         data3d = (data3d + noise).astype(np.int16) #         return data3d, segm, voxelsize_mm, slab # #     def synthetic_liver_template(self, params): #         """ #         Function uses organ_segmentation  for synthetic box object #         segmentation. #         """ #         # dcmdir = os.path.join(path_to_script,'./../sample_data/matlab/examples/sample_data/DICOM/digest_article/') # noqa # # data # #         data3d, segm, voxelsize_mm, slab = self.synthetic_liver() # # # seeds #         seeds = np.zeros(data3d.shape, np.int8) #         seeds[40:55, 90:120, 70:110] = 1 #         seeds[30:45, 190:200, 40:90] = 2 # # [mm]  10 x 10 x 10        # voxelsize_mm = [1, 4, 3] #         metadata = {'voxelsize_mm': voxelsize_mm} # #         oseg = organ_segmentation.OrganSegmentation( #             None, #             data3d=data3d, #             metadata=metadata, #             seeds=seeds, #             working_voxelsize_mm=5, #             manualroi=False, #             autocrop=False, # #             **params #         ) # #         oseg.ninteractivity() # #         volume = oseg.get_segmented_volume_size_mm3() #         oseg.portalVeinSegmentation(interactivity=False, threshold=180) #         oseg.saveVesselTree('porta') # #         # print '> 0 ' #         # print np.sum(oseg.segmentation > 0) #         # print np.sum(segm > 0) #         # print np.sum(oseg.segmentation > 0) * np.prod(voxelsize_mm) #         # print np.sum(segm > 0) * np.prod(voxelsize_mm) #         # print 'computed ', volume #         # print voxelsize_mm #         # print oseg.voxelsize_mm # #         # import pdb; pdb.set_trace() #         # import sed3 #         # ed = sed3.sed3(data3d, seeds=seeds, #         #                contour=(oseg.segmentation)) #         # ed.show() #         # import ipdb; ipdb.set_trace() #  noqa BREAKPOINT # #         # mel by to být litr. tedy milion mm3 #         # je to zvlastni. pro nekter verze knihoven je to 630, pro jine 580 #         self.assertGreater(volume, 570000) #         self.assertLess(volume, 640000) # #     def test_roi(self): #         """ #         Test setting of ROI. It is in pixels, not in mm #         """ # #         img3d = (np.random.rand(30, 30, 30)*10).astype(np.int16) #         seeds = (np.zeros(img3d.shape)).astype(np.int8) #         segmentation = (np.zeros(img3d.shape)).astype(np.int8) #         segmentation[10:25, 4:24, 2:16] = 1 #         img3d = img3d + segmentation*20 #         seeds[12:18, 9:16, 3:6] = 1 #         seeds[19:22, 21:27, 19:21] = 2 # #         roi = [[7, 27], [2, 29], [0, 26]] #         # seeds = seeds[7:27, 2:29, 0:26] #         voxelsize_mm = [5, 5, 5] #         metadata = {'voxelsize_mm': voxelsize_mm} # #         oseg = organ_segmentation.OrganSegmentation( #             None, #             data3d=img3d, #             metadata=metadata, #             seeds=seeds, #             roi=roi, #             working_voxelsize_mm=5, #             manualroi=False) # #         # from PyQt4.QtGui import QApplication #         # app = QApplication(sys.argv) #         # oseg.interactivity(min_val=0, max_val=30) #         oseg.ninteractivity() #         datap = oseg.export() # #         volume = oseg.get_segmented_volume_size_mm3() #         self.assertGreater(volume, 500000) #         self.assertIn('data3d', datap.keys()) #         self.assertIn('voxelsize_mm', datap.keys()) # #     def test_box_segmentation(self): #         params = {'segmentation_smoothing': False} #         self.box_segmentation_template(params) # #     def test_box_segmentation_with_smoothing(self): #         """ #         Function uses organ_segmentation  for synthetic box object #         segmentation. #         """ #         params = {'segmentation_smoothing': True} #         self.box_segmentation_template(params, noise_sigma=4) #         # dcmdir = os.path.join(path_to_script,'./../sample_data/matlab/examples/sample_data/DICOM/digest_article/') # noqa # #     def box_segmentation_template(self, params, noise_sigma=3): #         """ #         Function uses organ_segmentation  for synthetic box object #         segmentation. #         """ #         # dcmdir = os.path.join(path_to_script,'./../sample_data/matlab/examples/sample_data/DICOM/digest_article/') # noqa # # data #         img3d = np.random.rand(32, 64, 64) * noise_sigma #         img3d[4:24, 12:32, 5:25] = img3d[4:24, 12:32, 5:25] + 30 # # # seeds #         seeds = np.zeros([32, 64, 64], np.int8) #         seeds[9:12, 13:29, 18:25] = 1 #         seeds[9:12, 4:9, 3:32] = 2 # # [mm]  10 x 10 x 10        # voxelsize_mm = [1, 4, 3] #         voxelsize_mm = [5, 5, 5] #         metadata = {'voxelsize_mm': voxelsize_mm} # #         oseg = organ_segmentation.OrganSegmentation( #             None, #             data3d=img3d, #             metadata=metadata, #             seeds=seeds, #             working_voxelsize_mm=10, #             manualroi=False, #             **params #         ) # #         # oseg.seeds = seeds #         # oseg.make_gc() # # manual seeds setting # #         from PyQt4.QtGui import QApplication #         app = QApplication(sys.argv) #         # oseg.interactivity() #         oseg.ninteractivity() # #         volume = oseg.get_segmented_volume_size_mm3() # #         # import pdb; pdb.set_trace() # #         # mel by to být litr. tedy milion mm3 #         self.assertGreater(volume, 800000) #         self.assertLess(volume, 1100000) # #     def test_volume_resize(self): #         # from scipy.sparse.import lil_matrix # #         pass # #     # @unittest.skipIf(True, "interactive test") #     # @unittest.skipIf(not interactiveTest, "interactive test") #     @pytest.mark.interactive #     def test_vincentka_06_slice_thickness_interactive(self): #         """ #         Interactive test. SliceThickness is not voxel depth. If it is, this #         test will fail. #         """ #         # dcmdir = os.path.join(path_to_script, './../sample_data/matlab/examples/sample_data/DICOM/digest_article/') #noqa #         dcmdir = os.path.expanduser( #             '~/data/medical/data_orig/vincentka/13021610/10200000/') #         dcmdir = os.path.expanduser( #             '~/data/medical/data_orig/vincentka/13021610/12460000/') #         oseg = organ_segmentation.OrganSegmentation(dcmdir, #                                                     working_voxelsize_mm=4, #                                                     manualroi=False) # # # manual seeds setting #         print( #             "with left mouse button select some pixels of the bottle content") #         print("with right mouse button select some pixels of background") # #         oseg.interactivity() # #         volume = oseg.get_segmented_volume_size_mm3() #         # print volume # #         self.assertGreater(volume, 550000) #         self.assertLess(volume, 850000) # #     def setUp(self): #         """ Nastavení společných proměnných pro testy  """ #         self.assertTrue(True) # #     # @TODO dodělat přidávání uzlů pomocí mm #     # @unittest.skipIf(not interactiveTest, "interactive test") #     def test_add_seeds_mm(self): #         """ #         Function uses organ_segmentation object for segmentation #         """ #         dcmdir = io3d.datasets.join_path( #             'matlab/examples/sample_data/DICOM/digest_article/' #             # path_to_script, #             # './../sample_data/matlab/examples/sample_data/DICOM/digest_article/' #         ) #         oseg = organ_segmentation.OrganSegmentation(dcmdir, #                                                     working_voxelsize_mm=4, #                                                     manualroi=False) # #         oseg.add_seeds_mm([80], [120], [120], 1, 25) #         oseg.add_seeds_mm([80], [40], [130], 2, 25) # #         # pro kontrolu lze odkomentovat #         # from PyQt4.QtGui import QApplication #         # app = QApplication(sys.argv) #         # oseg.interactivity() # #         oseg.ninteractivity() # #         volume = oseg.get_segmented_volume_size_mm3() # #         # import pdb; pdb.set_trace() # #         # mel by to být litr. tedy milion mm3 #         self.assertGreater(volume, 800000) #         self.assertLess(volume, 1200000) # #         # roi_mm = [[3, 3, 3], [150, 150, 50]] #         # oseg.ni_set_roi() #         # coordinates_mm = [[110, 50, 30], [10, 10, 10]] #         # label = [1, 2] #         # radius = [5, 5] #         # oseg.ni_set_seeds(coordinates_mm, label, radius) # #         # oseg.make_segmentation() # #         # oseg.noninteractivity() #         pass # #     @unittest.skip("demonstrating skipping") #     def test_dicomread_and_graphcut(self): #         """ #         Test dicomread module and graphcut module #         """ #         from imcut import pycut # #         path_to_script = os.path.dirname(os.path.abspath(__file__)) #         dcmdir = os.path.join(path_to_script, './../sample_data/matlab/examples/sample_data/DICOM/digest_article/') #noqa #         data3d, metadata = dcmr.dcm_read_from_dir(dcmdir) # #         # print("Data size: " + str(data3d.nbytes) + ', shape: ' + str(data3d.shape) ) #noqa # #         igc = pycut.ImageGraphCut(data3d, zoom=0.5) #         seeds = igc.seeds #         seeds[0, :, 0] = 1 #         seeds[60:66, 60:66, 5:6] = 2 #         igc.noninteractivity(seeds) # #         igc.make_gc() #         segmentation = igc.segmentation #         self.assertTrue(segmentation[14, 4, 1] == 0) #         self.assertTrue(segmentation[127, 120, 10] == 1) #         self.assertTrue(np.sum(segmentation == 1) > 100) #         self.assertTrue(np.sum(segmentation == 0) > 100) #         # igc.show_segmentation() # #     def test_resize_data_one_value(self): #         datap = io3d.datasets.generate_abdominal() #         target_voxelsize_mm = 3 #         oseg = organ_segmentation.OrganSegmentation( #                                                     working_voxelsize_mm=4, #                                                     manualroi=False) #         oseg.import_dataplus(dataplus=datap) #         orig_shape = oseg.data3d.shape # #         oseg.resize_to_mm(target_voxelsize_mm) #         self.assertEqual(oseg.voxelsize_mm[0], target_voxelsize_mm) #         self.assertEqual(oseg.voxelsize_mm[1], target_voxelsize_mm) #         self.assertEqual(oseg.voxelsize_mm[2], target_voxelsize_mm) #         self.assertNotEqual(orig_shape[0], oseg.data3d.shape[0]) #         self.assertNotEqual(orig_shape[1], oseg.data3d.shape[1]) #         self.assertNotEqual(orig_shape[2], oseg.data3d.shape[2]) # #     def test_resize_data_three_values(self): #         datap = io3d.datasets.generate_abdominal() #         target_voxelsize_mm = [7.14, 4.1, 3] #         oseg = organ_segmentation.OrganSegmentation( #             working_voxelsize_mm=4, #             manualroi=False) #         oseg.import_dataplus(dataplus=datap) #         orig_shape = oseg.data3d.shape # #         oseg.resize_to_mm(target_voxelsize_mm) #         self.assertEqual(oseg.voxelsize_mm[0], target_voxelsize_mm[0]) #         self.assertEqual(oseg.voxelsize_mm[1], target_voxelsize_mm[1]) #         self.assertEqual(oseg.voxelsize_mm[2], target_voxelsize_mm[2]) #         self.assertNotEqual(orig_shape[0], oseg.data3d.shape[0]) #         self.assertNotEqual(orig_shape[1], oseg.data3d.shape[1]) #         self.assertNotEqual(orig_shape[2], oseg.data3d.shape[2])