def mainFunction(self):
# ...randomly exchange some pixels
import numpy
for i in range(10):
self.testProject.threshold_ov._data._data[
numpy.random.randint(self.testProject.threshold_ov._data._data.
shape[0]),
numpy.random.randint(self.testProject.threshold_ov._data._data.
shape[1]),
numpy.random.randint(self.testProject.threshold_ov._data._data.
shape[2]),
numpy.random.randint(self.testProject.threshold_ov._data._data.
shape[3]),
numpy.random.randint(self.testProject.threshold_ov._data._data.
shape[4])] = numpy.random.randint(255)
self.testProject.dataMgr[
self.testProject.dataMgr.
_activeImageNumber].Connected_Components.setInputData(
self.testProject.threshold_ov._data)
self.testThread = TestThread(self.testProject.connectedComponentsMgr,
self.testProject.listOfResultOverlays,
self.testProject.listOfFilenames)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'),
self.finalizeTest)
self.testThread.start(
None) # ...compute connected components without background
class TestWholeModule_WithoutBackgroundWrongImage2D(unittest.TestCase): # tests if wrong input leads to a test fail
def setUp(self):
#print "setUp"
self.app = QtCore.QCoreApplication(sys.argv) # we need a QCoreApplication to run, otherwise the thread just gets killed
self.testProject = CCTestProject("test_image_mirrored.png", "cc_threshold_overlay.h5", "ground_truth_cc_without_background.h5")
def test_WholeModule(self):
t = QtCore.QTimer()
t.setSingleShot(True)
t.setInterval(0)
self.app.connect(t, QtCore.SIGNAL('timeout()'), self.mainFunction)
t.start()
self.app.exec_()
def mainFunction(self):
# ...randomly exchange some pixels
import numpy
for i in range(10):
self.testProject.threshold_ov._data._data[numpy.random.randint(self.testProject.threshold_ov._data._data.shape[0]), numpy.random.randint(self.testProject.threshold_ov._data._data.shape[1]), numpy.random.randint(self.testProject.threshold_ov._data._data.shape[2]), numpy.random.randint(self.testProject.threshold_ov._data._data.shape[3]), numpy.random.randint(self.testProject.threshold_ov._data._data.shape[4])] = numpy.random.randint(255)
self.testProject.dataMgr[self.testProject.dataMgr._activeImageNumber].Connected_Components.setInputData(self.testProject.threshold_ov._data)
self.testThread = TestThread(self.testProject.connectedComponentsMgr, self.testProject.listOfResultOverlays, self.testProject.listOfFilenames)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'), self.finalizeTest)
self.testThread.start(None) # ...compute connected components without background
def finalizeTest(self):
# results comparison
self.assertEqual(self.testThread.passedTest, False) # has to be different from ground truth result (wrong input data!)
self.app.quit()
class TestWholeModule_WithoutBackground2D(unittest.TestCase):
def setUp(self):
print "setUp"
self.app = QtCore.QCoreApplication(sys.argv) # we need a QCoreApplication to run, otherwise the thread just gets killed
self.testProject = CCTestProject("test_image.png", "cc_threshold_overlay.h5", "ground_truth_cc_without_background.h5")
def test_WholeModule(self):
t = QtCore.QTimer()
t.setSingleShot(True)
t.setInterval(0)
self.app.connect(t, QtCore.SIGNAL('timeout()'), self.mainFunction)
t.start()
self.app.exec_()
def mainFunction(self):
self.testThread = TestThread(self.testProject.connectedComponentsMgr, self.testProject.listOfResultOverlays, self.testProject.listOfFilenames)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'), self.finalizeTest)
self.testThread.start(None) # ...compute connected components without background
def finalizeTest(self):
# results comparison
print "finalize"
self.assertEqual(self.testThread.passedTest, True)
self.app.quit()
class TestWholeModule_WithoutBackground2D(unittest.TestCase):
def setUp(self):
print "setUp"
self.app = QtCore.QCoreApplication(
sys.argv
) # we need a QCoreApplication to run, otherwise the thread just gets killed
self.testProject = CCTestProject(
"test_image.png", "cc_threshold_overlay.h5",
"ground_truth_cc_without_background.h5")
def test_WholeModule(self):
t = QtCore.QTimer()
t.setSingleShot(True)
t.setInterval(0)
self.app.connect(t, QtCore.SIGNAL('timeout()'), self.mainFunction)
t.start()
self.app.exec_()
def mainFunction(self):
self.testThread = TestThread(self.testProject.connectedComponentsMgr,
self.testProject.listOfResultOverlays,
self.testProject.listOfFilenames)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'),
self.finalizeTest)
self.testThread.start(
None) # ...compute connected components without background
def finalizeTest(self):
# results comparison
print "finalize"
self.assertEqual(self.testThread.passedTest, True)
self.app.quit()
class TestWholeModuleDefaultDecomposer(unittest.TestCase): # use default decomposer
if not numpyRecentEnough:
__test__ = False
def setUp(self):
self.app = QtCore.QCoreApplication(sys.argv) # we need a QCoreApplication to run, otherwise the thread just gets killed
self.testProject = UnsupervisedDecompositionTestProject("sims_aligned_s7_32.h5")
def test_WholeModule(self):
t = QtCore.QTimer()
t.setSingleShot(True)
t.setInterval(0)
self.app.connect(t, QtCore.SIGNAL('timeout()'), self.mainFunction)
t.start()
self.app.exec_()
def mainFunction(self):
self.testThread = TestThread(self.testProject.unsupervisedMgr, self.testProject.listOfResultOverlays, self.testProject.listOfFilenames, self.testProject.tolerance)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'), self.finalizeTest)
self.testThread.start(self.testProject.inputOverlays)
self.numOverlaysBefore = len(self.testProject.dataMgr[self.testProject.dataMgr._activeImageNumber].overlayMgr.keys())
def finalizeTest(self):
# results comparison
self.assertEqual(self.testThread.passedTest, True)
self.app.quit()
def mainFunction(self):
self.testThread = TestThread(self.testProject.connectedComponentsMgr,
self.testProject.listOfResultOverlays,
self.testProject.listOfFilenames)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'),
self.finalizeTest)
self.testThread.start(
None) # ...compute connected components without background
def mainFunction(self):
self.testThread = TestThread(self.testProject.connectedComponentsMgr,
self.testProject.listOfResultOverlays,
self.testProject.listOfFilenames)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'),
self.finalizeTest)
backgroundClasses = set([1, 3]) # use a non-empty background set
self.testThread.start(
backgroundClasses
) # ...compute connected components with background
class TestWholeModulePCADecomposer(unittest.TestCase
): # use PCA decomposer with 3 components
if not numpyRecentEnough:
__test__ = False
def setUp(self):
#print "setUp"
self.app = QtCore.QCoreApplication(
sys.argv
) # we need a QCoreApplication to run, otherwise the thread just gets killed
self.numComponents = 3
self.testProject = UnsupervisedDecompositionTestProject(
"sims_aligned_s7_32.h5", UnsupervisedDecompositionPCA,
self.numComponents)
def test_WholeModule(self):
t = QtCore.QTimer()
t.setSingleShot(True)
t.setInterval(0)
self.app.connect(t, QtCore.SIGNAL('timeout()'), self.mainFunction)
t.start()
self.app.exec_()
def mainFunction(self):
self.testThread = TestThread(self.testProject.unsupervisedMgr,
self.testProject.listOfResultOverlays,
self.testProject.listOfFilenames,
self.testProject.tolerance)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'),
self.finalizeTest)
self.testThread.start(self.testProject.inputOverlays)
self.numOverlaysBefore = len(self.testProject.dataMgr[
self.testProject.dataMgr._activeImageNumber].overlayMgr.keys())
def finalizeTest(self):
'''for i in range(self.testProject.unsupervisedMethod.numComponents):
print "*************************************"
print self.testProject.listOfResultOverlays[i]
obtained = self.testProject.dataMgr[self.testProject.dataMgr._activeImageNumber].overlayMgr[self.testProject.listOfResultOverlays[i]]
from ilastik.core import dataImpex
dataImpex.DataImpex.exportOverlay(str("c:/gt_PCA_result_component_%d" % (i+1)), "h5", obtained)'''
# results comparison
self.assertEqual(self.testThread.passedTest, True)
# other conditions
# exactly self.numComponents computed overlays + self.numComponents ground truth overlays were added
self.numOverlaysAfter = len(self.testProject.dataMgr[
self.testProject.dataMgr._activeImageNumber].overlayMgr.keys())
self.assertEqual(self.numOverlaysAfter - self.numOverlaysBefore,
self.numComponents * 2)
self.app.quit()
def mainFunction(self):
self.testThread = TestThread(self.testProject.unsupervisedMgr,
self.testProject.listOfResultOverlays,
self.testProject.listOfFilenames,
self.testProject.tolerance)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'),
self.finalizeTest)
self.testThread.start(self.testProject.inputOverlays)
self.numOverlaysBefore = len(self.testProject.dataMgr[
self.testProject.dataMgr._activeImageNumber].overlayMgr.keys())
class TestWholeModule_WithoutBackgroundWrongImage2D(
unittest.TestCase): # tests if wrong input leads to a test fail
def setUp(self):
#print "setUp"
self.app = QtCore.QCoreApplication(
sys.argv
) # we need a QCoreApplication to run, otherwise the thread just gets killed
self.testProject = CCTestProject(
"test_image_mirrored.png", "cc_threshold_overlay.h5",
"ground_truth_cc_without_background.h5")
def test_WholeModule(self):
t = QtCore.QTimer()
t.setSingleShot(True)
t.setInterval(0)
self.app.connect(t, QtCore.SIGNAL('timeout()'), self.mainFunction)
t.start()
self.app.exec_()
def mainFunction(self):
# ...randomly exchange some pixels
import numpy
for i in range(10):
self.testProject.threshold_ov._data._data[
numpy.random.randint(self.testProject.threshold_ov._data._data.
shape[0]),
numpy.random.randint(self.testProject.threshold_ov._data._data.
shape[1]),
numpy.random.randint(self.testProject.threshold_ov._data._data.
shape[2]),
numpy.random.randint(self.testProject.threshold_ov._data._data.
shape[3]),
numpy.random.randint(self.testProject.threshold_ov._data._data.
shape[4])] = numpy.random.randint(255)
self.testProject.dataMgr[
self.testProject.dataMgr.
_activeImageNumber].Connected_Components.setInputData(
self.testProject.threshold_ov._data)
self.testThread = TestThread(self.testProject.connectedComponentsMgr,
self.testProject.listOfResultOverlays,
self.testProject.listOfFilenames)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'),
self.finalizeTest)
self.testThread.start(
None) # ...compute connected components without background
def finalizeTest(self):
# results comparison
self.assertEqual(
self.testThread.passedTest, False
) # has to be different from ground truth result (wrong input data!)
self.app.quit()
class TestWholeModulePLSADecomposer(unittest.TestCase
): # pLSA with 5 components
def setUp(self):
#print "setUp"
self.app = QtCore.QCoreApplication(sys.argv)
self.numComponents = 5
self.testProject = UnsupervisedDecompositionTestProject(
"sims_aligned_s7_32.h5", UnsupervisedDecompositionPLSA,
self.numComponents)
def test_WholeModule(self):
t = QtCore.QTimer()
t.setSingleShot(True)
t.setInterval(0)
self.app.connect(t, QtCore.SIGNAL('timeout()'), self.mainFunction)
t.start()
self.app.exec_()
def mainFunction(self):
# fix random seed
from ilastik.core.randomSeed import RandomSeed
RandomSeed.setRandomSeed(42)
self.testThread = TestThread(self.testProject.unsupervisedMgr,
self.testProject.listOfResultOverlays,
self.testProject.listOfFilenames,
self.testProject.tolerance)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'),
self.finalizeTest)
self.testThread.start(self.testProject.inputOverlays)
self.numOverlaysBefore = len(self.testProject.dataMgr[
self.testProject.dataMgr._activeImageNumber].overlayMgr.keys())
def finalizeTest(self):
'''for i in range(self.testProject.unsupervisedMethod.numComponents):
obtained = self.testProject.dataMgr[self.testProject.dataMgr._activeImageNumber].overlayMgr[self.testProject.listOfResultOverlays[i]]
from ilastik.core import dataImpex
dataImpex.DataImpex.exportOverlay(str("c:/gt_pLSA_result_component_%d" % (i+1)), "h5", obtained)'''
# results comparison
self.assertEqual(self.testThread.passedTest, True)
# exactly self.numComponents computed overlays + self.numComponents ground truth overlays were added
self.numOverlaysAfter = len(self.testProject.dataMgr[
self.testProject.dataMgr._activeImageNumber].overlayMgr.keys())
self.assertEqual(self.numOverlaysAfter - self.numOverlaysBefore,
self.numComponents * 2)
self.app.quit()
class TestWholeModulePCADecomposer(unittest.TestCase): # use PCA decomposer with 3 components
if not numpyRecentEnough:
__test__ = False
def setUp(self):
#print "setUp"
self.app = QtCore.QCoreApplication(sys.argv) # we need a QCoreApplication to run, otherwise the thread just gets killed
self.numComponents = 3
self.testProject = UnsupervisedDecompositionTestProject("sims_aligned_s7_32.h5", UnsupervisedDecompositionPCA, self.numComponents)
def test_WholeModule(self):
t = QtCore.QTimer()
t.setSingleShot(True)
t.setInterval(0)
self.app.connect(t, QtCore.SIGNAL('timeout()'), self.mainFunction)
t.start()
self.app.exec_()
def mainFunction(self):
self.testThread = TestThread(self.testProject.unsupervisedMgr, self.testProject.listOfResultOverlays, self.testProject.listOfFilenames, self.testProject.tolerance)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'), self.finalizeTest)
self.testThread.start(self.testProject.inputOverlays)
self.numOverlaysBefore = len(self.testProject.dataMgr[self.testProject.dataMgr._activeImageNumber].overlayMgr.keys())
def finalizeTest(self):
'''for i in range(self.testProject.unsupervisedMethod.numComponents):
print "*************************************"
print self.testProject.listOfResultOverlays[i]
obtained = self.testProject.dataMgr[self.testProject.dataMgr._activeImageNumber].overlayMgr[self.testProject.listOfResultOverlays[i]]
from ilastik.core import dataImpex
dataImpex.DataImpex.exportOverlay(str("c:/gt_PCA_result_component_%d" % (i+1)), "h5", obtained)'''
# results comparison
self.assertEqual(self.testThread.passedTest, True)
# other conditions
# exactly self.numComponents computed overlays + self.numComponents ground truth overlays were added
self.numOverlaysAfter = len(self.testProject.dataMgr[self.testProject.dataMgr._activeImageNumber].overlayMgr.keys())
self.assertEqual(self.numOverlaysAfter - self.numOverlaysBefore, self.numComponents*2)
self.app.quit()
def mainFunction(self):
# ...randomly exchange some pixels
import numpy
for i in range(10):
self.testProject.threshold_ov._data._data[numpy.random.randint(self.testProject.threshold_ov._data._data.shape[0]), numpy.random.randint(self.testProject.threshold_ov._data._data.shape[1]), numpy.random.randint(self.testProject.threshold_ov._data._data.shape[2]), numpy.random.randint(self.testProject.threshold_ov._data._data.shape[3]), numpy.random.randint(self.testProject.threshold_ov._data._data.shape[4])] = numpy.random.randint(255)
self.testProject.dataMgr[self.testProject.dataMgr._activeImageNumber].Connected_Components.setInputData(self.testProject.threshold_ov._data)
self.testThread = TestThread(self.testProject.connectedComponentsMgr, self.testProject.listOfResultOverlays, self.testProject.listOfFilenames)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'), self.finalizeTest)
self.testThread.start(None) # ...compute connected components without background
def mainFunction(self):
# fix random seed
from ilastik.core.randomSeed import RandomSeed
RandomSeed.setRandomSeed(42)
self.testThread = TestThread(self.testProject.unsupervisedMgr, self.testProject.listOfResultOverlays, self.testProject.listOfFilenames, self.testProject.tolerance)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'), self.finalizeTest)
self.testThread.start(self.testProject.inputOverlays)
self.numOverlaysBefore = len(self.testProject.dataMgr[self.testProject.dataMgr._activeImageNumber].overlayMgr.keys())
class TestWholeModulePLSADecomposer(unittest.TestCase): # pLSA with 5 components
def setUp(self):
#print "setUp"
self.app = QtCore.QCoreApplication(sys.argv)
self.numComponents = 5
self.testProject = UnsupervisedDecompositionTestProject("sims_aligned_s7_32.h5", UnsupervisedDecompositionPLSA, self.numComponents)
def test_WholeModule(self):
t = QtCore.QTimer()
t.setSingleShot(True)
t.setInterval(0)
self.app.connect(t, QtCore.SIGNAL('timeout()'), self.mainFunction)
t.start()
self.app.exec_()
def mainFunction(self):
# fix random seed
from ilastik.core.randomSeed import RandomSeed
RandomSeed.setRandomSeed(42)
self.testThread = TestThread(self.testProject.unsupervisedMgr, self.testProject.listOfResultOverlays, self.testProject.listOfFilenames, self.testProject.tolerance)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'), self.finalizeTest)
self.testThread.start(self.testProject.inputOverlays)
self.numOverlaysBefore = len(self.testProject.dataMgr[self.testProject.dataMgr._activeImageNumber].overlayMgr.keys())
def finalizeTest(self):
'''for i in range(self.testProject.unsupervisedMethod.numComponents):
obtained = self.testProject.dataMgr[self.testProject.dataMgr._activeImageNumber].overlayMgr[self.testProject.listOfResultOverlays[i]]
from ilastik.core import dataImpex
dataImpex.DataImpex.exportOverlay(str("c:/gt_pLSA_result_component_%d" % (i+1)), "h5", obtained)'''
# results comparison
self.assertEqual(self.testThread.passedTest, True)
# exactly self.numComponents computed overlays + self.numComponents ground truth overlays were added
self.numOverlaysAfter = len(self.testProject.dataMgr[self.testProject.dataMgr._activeImageNumber].overlayMgr.keys())
self.assertEqual(self.numOverlaysAfter - self.numOverlaysBefore, self.numComponents*2)
self.app.quit()
class TestWholeModuleDefaultDecomposer(unittest.TestCase
): # use default decomposer
if not numpyRecentEnough:
__test__ = False
def setUp(self):
self.app = QtCore.QCoreApplication(
sys.argv
) # we need a QCoreApplication to run, otherwise the thread just gets killed
self.testProject = UnsupervisedDecompositionTestProject(
"sims_aligned_s7_32.h5")
def test_WholeModule(self):
t = QtCore.QTimer()
t.setSingleShot(True)
t.setInterval(0)
self.app.connect(t, QtCore.SIGNAL('timeout()'), self.mainFunction)
t.start()
self.app.exec_()
def mainFunction(self):
self.testThread = TestThread(self.testProject.unsupervisedMgr,
self.testProject.listOfResultOverlays,
self.testProject.listOfFilenames,
self.testProject.tolerance)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'),
self.finalizeTest)
self.testThread.start(self.testProject.inputOverlays)
self.numOverlaysBefore = len(self.testProject.dataMgr[
self.testProject.dataMgr._activeImageNumber].overlayMgr.keys())
def finalizeTest(self):
# results comparison
self.assertEqual(self.testThread.passedTest, True)
self.app.quit()
def mainFunction(self):
self.testThread = TestThread(self.testProject.connectedComponentsMgr, self.testProject.listOfResultOverlays, self.testProject.listOfFilenames)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'), self.finalizeTest)
self.testThread.start(None) # ...compute connected components without background
def mainFunction(self):
self.testThread = TestThread(self.testProject.connectedComponentsMgr, self.testProject.listOfResultOverlays, self.testProject.listOfFilenames)
QtCore.QObject.connect(self.testThread, QtCore.SIGNAL('done()'), self.finalizeTest)
backgroundClasses = set([1, 3]) # use a non-empty background set
self.testThread.start(backgroundClasses) # ...compute connected components with background