def plot3Dsilx(nodeData):
from silx.gui.plot import StackView
saveType = nodeData[0]
plot = StackView()
plot.setColormap('viridis')
plot.setGraphTitle(nodeData[1] + ' ' + saveType)
plot.setLabels(nodeData[3])
savedColumns = nodeData[4]
for fname, props in savedColumns.items():
maps = read3D(saveType, fname, props)
# applied only to one (first) 3D map:
v = maps[0]
plot.setStack(v)
# plot.saveGraph('test.png')
plot.show() # end plot3Dsilx
class TestStackView(TestCaseQt):
"""Base class for tests of StackView."""
def setUp(self):
super(TestStackView, self).setUp()
self.stackview = StackView()
self.stackview.show()
self.qWaitForWindowExposed(self.stackview)
self.mystack = numpy.fromfunction(
lambda i, j, k: numpy.sin(i/15.) + numpy.cos(j/4.) + 2 * numpy.sin(k/6.),
(10, 20, 30)
)
def tearDown(self):
self.stackview.setAttribute(qt.Qt.WA_DeleteOnClose)
self.stackview.close()
del self.stackview
super(TestStackView, self).tearDown()
def testSetStack(self):
self.stackview.setStack(self.mystack)
self.stackview.setColormap("viridis", autoscale=True)
my_trans_stack, params = self.stackview.getStack()
self.assertEqual(my_trans_stack.shape, self.mystack.shape)
self.assertTrue(numpy.array_equal(self.mystack,
my_trans_stack))
self.assertEqual(params["colormap"]["name"],
"viridis")
def testSetStackPerspective(self):
self.stackview.setStack(self.mystack, perspective=1)
# my_orig_stack, params = self.stackview.getStack()
my_trans_stack, params = self.stackview.getCurrentView()
# get stack returns the transposed data, depending on the perspective
self.assertEqual(my_trans_stack.shape,
(self.mystack.shape[1], self.mystack.shape[0], self.mystack.shape[2]))
self.assertTrue(numpy.array_equal(numpy.transpose(self.mystack, axes=(1, 0, 2)),
my_trans_stack))
def testSetStackListOfImages(self):
loi = [self.mystack[i] for i in range(self.mystack.shape[0])]
self.stackview.setStack(loi)
my_orig_stack, params = self.stackview.getStack(returnNumpyArray=True)
my_trans_stack, params = self.stackview.getStack(returnNumpyArray=True)
self.assertEqual(my_trans_stack.shape, self.mystack.shape)
self.assertTrue(numpy.array_equal(self.mystack,
my_trans_stack))
self.assertTrue(numpy.array_equal(self.mystack,
my_orig_stack))
self.assertIsInstance(my_trans_stack, numpy.ndarray)
self.stackview.setStack(loi, perspective=2)
my_orig_stack, params = self.stackview.getStack(copy=False)
my_trans_stack, params = self.stackview.getCurrentView(copy=False)
# getStack(copy=False) must return the object set in setStack
self.assertIs(my_orig_stack, loi)
# getCurrentView(copy=False) returns a ListOfImages whose .images
# attr is the original data
self.assertEqual(my_trans_stack.shape,
(self.mystack.shape[2], self.mystack.shape[0], self.mystack.shape[1]))
self.assertTrue(numpy.array_equal(numpy.array(my_trans_stack),
numpy.transpose(self.mystack, axes=(2, 0, 1))))
self.assertIsInstance(my_trans_stack,
ListOfImages) # returnNumpyArray=False by default in getStack
self.assertIs(my_trans_stack.images, loi)
def testPerspective(self):
self.stackview.setStack(numpy.arange(24).reshape((2, 3, 4)))
self.assertEqual(self.stackview._perspective, 0,
"Default perspective is not 0 (dim1-dim2).")
self.stackview._StackView__planeSelection.setPerspective(1)
self.assertEqual(self.stackview._perspective, 1,
"Plane selection combobox not updating perspective")
self.stackview.setStack(numpy.arange(6).reshape((1, 2, 3)))
self.assertEqual(self.stackview._perspective, 1,
"Perspective not preserved when calling setStack "
"without specifying the perspective parameter.")
self.stackview.setStack(numpy.arange(24).reshape((2, 3, 4)), perspective=2)
self.assertEqual(self.stackview._perspective, 2,
"Perspective not set in setStack(..., perspective=2).")
def testDefaultTitle(self):
"""Test that the plot title contains the proper Z information"""
self.stackview.setStack(numpy.arange(24).reshape((4, 3, 2)),
calibrations=[(0, 1), (-10, 10), (3.14, 3.14)])
self.assertEqual(self.stackview._plot.getGraphTitle(),
"Image z=0")
self.stackview.setFrameNumber(2)
self.assertEqual(self.stackview._plot.getGraphTitle(),
"Image z=2")
self.stackview._StackView__planeSelection.setPerspective(1)
self.stackview.setFrameNumber(0)
self.assertEqual(self.stackview._plot.getGraphTitle(),
"Image z=-10")
self.stackview.setFrameNumber(2)
self.assertEqual(self.stackview._plot.getGraphTitle(),
"Image z=10")
self.stackview._StackView__planeSelection.setPerspective(2)
self.stackview.setFrameNumber(0)
self.assertEqual(self.stackview._plot.getGraphTitle(),
"Image z=3.14")
self.stackview.setFrameNumber(1)
self.assertEqual(self.stackview._plot.getGraphTitle(),
"Image z=6.28")
def testCustomTitle(self):
"""Test setting the plot title with a user defined callback"""
self.stackview.setStack(numpy.arange(24).reshape((4, 3, 2)),
calibrations=[(0, 1), (-10, 10), (3.14, 3.14)])
def title_callback(frame_idx):
return "Cubed index title %d" % (frame_idx**3)
self.stackview.setTitleCallback(title_callback)
self.assertEqual(self.stackview._plot.getGraphTitle(),
"Cubed index title 0")
self.stackview.setFrameNumber(2)
self.assertEqual(self.stackview._plot.getGraphTitle(),
"Cubed index title 8")
# perspective should not matter, only frame index
self.stackview._StackView__planeSelection.setPerspective(1)
self.stackview.setFrameNumber(0)
self.assertEqual(self.stackview._plot.getGraphTitle(),
"Cubed index title 0")
self.stackview.setFrameNumber(2)
self.assertEqual(self.stackview._plot.getGraphTitle(),
"Cubed index title 8")
with self.assertRaises(TypeError):
# setTitleCallback should not accept non-callable objects like strings
self.stackview.setTitleCallback(
"Là, vous faites sirop de vingt-et-un et vous dites : "
"beau sirop, mi-sirop, siroté, gagne-sirop, sirop-grelot,"
" passe-montagne, sirop au bon goût.")
def testStackFrameNumber(self):
self.stackview.setStack(self.mystack)
self.assertEqual(self.stackview.getFrameNumber(), 0)
listener = SignalListener()
self.stackview.sigFrameChanged.connect(listener)
self.stackview.setFrameNumber(1)
self.assertEqual(self.stackview.getFrameNumber(), 1)
self.assertEqual(listener.arguments(), [(1,)])
class TestStackView(TestCaseQt):
"""Base class for tests of StackView."""
def setUp(self):
super(TestStackView, self).setUp()
self.stackview = StackView()
self.stackview.show()
self.qWaitForWindowExposed(self.stackview)
self.mystack = numpy.fromfunction(
lambda i, j, k: numpy.sin(i / 15.) + numpy.cos(j / 4.) + 2 * numpy.
sin(k / 6.), (10, 20, 30))
def tearDown(self):
self.stackview.setAttribute(qt.Qt.WA_DeleteOnClose)
self.stackview.close()
del self.stackview
super(TestStackView, self).tearDown()
def testSetStack(self):
self.stackview.setStack(self.mystack)
self.stackview.setColormap("viridis", autoscale=True)
my_trans_stack, params = self.stackview.getStack()
self.assertEqual(my_trans_stack.shape, self.mystack.shape)
self.assertTrue(numpy.array_equal(self.mystack, my_trans_stack))
self.assertEqual(params["colormap"]["name"], "viridis")
def testSetStackPerspective(self):
self.stackview.setStack(self.mystack, perspective=1)
# my_orig_stack, params = self.stackview.getStack()
my_trans_stack, params = self.stackview.getCurrentView()
# get stack returns the transposed data, depending on the perspective
self.assertEqual(my_trans_stack.shape,
(self.mystack.shape[1], self.mystack.shape[0],
self.mystack.shape[2]))
self.assertTrue(
numpy.array_equal(numpy.transpose(self.mystack, axes=(1, 0, 2)),
my_trans_stack))
def testSetStackListOfImages(self):
loi = [self.mystack[i] for i in range(self.mystack.shape[0])]
self.stackview.setStack(loi)
my_orig_stack, params = self.stackview.getStack(returnNumpyArray=True)
my_trans_stack, params = self.stackview.getStack(returnNumpyArray=True)
self.assertEqual(my_trans_stack.shape, self.mystack.shape)
self.assertTrue(numpy.array_equal(self.mystack, my_trans_stack))
self.assertTrue(numpy.array_equal(self.mystack, my_orig_stack))
self.assertIsInstance(my_trans_stack, numpy.ndarray)
self.stackview.setStack(loi, perspective=2)
my_orig_stack, params = self.stackview.getStack(copy=False)
my_trans_stack, params = self.stackview.getCurrentView(copy=False)
# getStack(copy=False) must return the object set in setStack
self.assertIs(my_orig_stack, loi)
# getCurrentView(copy=False) returns a ListOfImages whose .images
# attr is the original data
self.assertEqual(my_trans_stack.shape,
(self.mystack.shape[2], self.mystack.shape[0],
self.mystack.shape[1]))
self.assertTrue(
numpy.array_equal(numpy.array(my_trans_stack),
numpy.transpose(self.mystack, axes=(2, 0, 1))))
self.assertIsInstance(
my_trans_stack,
ListOfImages) # returnNumpyArray=False by default in getStack
self.assertIs(my_trans_stack.images, loi)
def testPerspective(self):
self.stackview.setStack(numpy.arange(24).reshape((2, 3, 4)))
self.assertEqual(self.stackview._perspective, 0,
"Default perspective is not 0 (dim1-dim2).")
self.stackview._StackView__planeSelection.setPerspective(1)
self.assertEqual(self.stackview._perspective, 1,
"Plane selection combobox not updating perspective")
self.stackview.setStack(numpy.arange(6).reshape((1, 2, 3)))
self.assertEqual(self.stackview._perspective, 0,
"Default perspective not restored in setStack.")
self.stackview.setStack(numpy.arange(24).reshape((2, 3, 4)),
perspective=2)
self.assertEqual(
self.stackview._perspective, 2,
"Perspective not set in setStack(..., perspective=2).")
def testDefaultTitle(self):
"""Test that the plot title contains the proper Z information"""
self.stackview.setStack(numpy.arange(24).reshape((4, 3, 2)),
calibrations=[(0, 1), (-10, 10), (3.14, 3.14)])
self.assertEqual(self.stackview._plot.getGraphTitle(), "Image z=0")
self.stackview.setFrameNumber(2)
self.assertEqual(self.stackview._plot.getGraphTitle(), "Image z=2")
self.stackview._StackView__planeSelection.setPerspective(1)
self.stackview.setFrameNumber(0)
self.assertEqual(self.stackview._plot.getGraphTitle(), "Image z=-10")
self.stackview.setFrameNumber(2)
self.assertEqual(self.stackview._plot.getGraphTitle(), "Image z=10")
self.stackview._StackView__planeSelection.setPerspective(2)
self.stackview.setFrameNumber(0)
self.assertEqual(self.stackview._plot.getGraphTitle(), "Image z=3.14")
self.stackview.setFrameNumber(1)
self.assertEqual(self.stackview._plot.getGraphTitle(), "Image z=6.28")
def testCustomTitle(self):
"""Test setting the plot title with a user defined callback"""
self.stackview.setStack(numpy.arange(24).reshape((4, 3, 2)),
calibrations=[(0, 1), (-10, 10), (3.14, 3.14)])
def title_callback(frame_idx):
return "Cubed index title %d" % (frame_idx**3)
self.stackview.setTitleCallback(title_callback)
self.assertEqual(self.stackview._plot.getGraphTitle(),
"Cubed index title 0")
self.stackview.setFrameNumber(2)
self.assertEqual(self.stackview._plot.getGraphTitle(),
"Cubed index title 8")
# perspective should not matter, only frame index
self.stackview._StackView__planeSelection.setPerspective(1)
self.stackview.setFrameNumber(0)
self.assertEqual(self.stackview._plot.getGraphTitle(),
"Cubed index title 0")
self.stackview.setFrameNumber(2)
self.assertEqual(self.stackview._plot.getGraphTitle(),
"Cubed index title 8")
with self.assertRaises(TypeError):
# setTitleCallback should not accept non-callable objects like strings
self.stackview.setTitleCallback(
"Là, vous faites sirop de vingt-et-un et vous dites : "
"beau sirop, mi-sirop, siroté, gagne-sirop, sirop-grelot,"
" passe-montagne, sirop au bon goût.")
class TestStackView(TestCaseQt):
"""Base class for tests of StackView."""
def setUp(self):
super(TestStackView, self).setUp()
self.stackview = StackView()
self.stackview.show()
self.qWaitForWindowExposed(self.stackview)
self.mystack = numpy.fromfunction(
lambda i, j, k: numpy.sin(i / 15.) + numpy.cos(j / 4.) + 2 * numpy.
sin(k / 6.), (10, 20, 30))
def tearDown(self):
self.stackview.setAttribute(qt.Qt.WA_DeleteOnClose)
self.stackview.close()
del self.stackview
super(TestStackView, self).tearDown()
def testSetStack(self):
self.stackview.setStack(self.mystack)
self.stackview.setColormap("viridis", autoscale=True)
my_trans_stack, params = self.stackview.getStack()
self.assertEqual(my_trans_stack.shape, self.mystack.shape)
self.assertTrue(numpy.array_equal(self.mystack, my_trans_stack))
self.assertEqual(params["colormap"]["name"], "viridis")
def testSetStackPerspective(self):
self.stackview.setStack(self.mystack, perspective=1)
# my_orig_stack, params = self.stackview.getStack()
my_trans_stack, params = self.stackview.getCurrentView()
# get stack returns the transposed data, depending on the perspective
self.assertEqual(my_trans_stack.shape,
(self.mystack.shape[1], self.mystack.shape[0],
self.mystack.shape[2]))
self.assertTrue(
numpy.array_equal(numpy.transpose(self.mystack, axes=(1, 0, 2)),
my_trans_stack))
def testSetStackListOfImages(self):
loi = [self.mystack[i] for i in range(self.mystack.shape[0])]
self.stackview.setStack(loi)
my_orig_stack, params = self.stackview.getStack(returnNumpyArray=True)
my_trans_stack, params = self.stackview.getStack(returnNumpyArray=True)
self.assertEqual(my_trans_stack.shape, self.mystack.shape)
self.assertTrue(numpy.array_equal(self.mystack, my_trans_stack))
self.assertTrue(numpy.array_equal(self.mystack, my_orig_stack))
self.assertIsInstance(my_trans_stack, numpy.ndarray)
self.stackview.setStack(loi, perspective=2)
my_orig_stack, params = self.stackview.getStack(copy=False)
my_trans_stack, params = self.stackview.getCurrentView(copy=False)
# getStack(copy=False) must return the object set in setStack
self.assertIs(my_orig_stack, loi)
# getCurrentView(copy=False) returns a ListOfImages whose .images
# attr is the original data
self.assertEqual(my_trans_stack.shape,
(self.mystack.shape[2], self.mystack.shape[0],
self.mystack.shape[1]))
self.assertTrue(
numpy.array_equal(numpy.array(my_trans_stack),
numpy.transpose(self.mystack, axes=(2, 0, 1))))
self.assertIsInstance(
my_trans_stack,
ListOfImages) # returnNumpyArray=False by default in getStack
self.assertIs(my_trans_stack.images, loi)
def testPerspective(self):
self.stackview.setStack(numpy.arange(24).reshape((2, 3, 4)))
self.assertEqual(self.stackview._perspective, 0,
"Default perspective is not 0 (dim1-dim2).")
self.stackview._StackView__planeSelection.setPerspective(1)
self.assertEqual(self.stackview._perspective, 1,
"Plane selection combobox not updating perspective")
self.stackview.setStack(numpy.arange(6).reshape((1, 2, 3)))
self.assertEqual(self.stackview._perspective, 0,
"Default perspective not restored in setStack.")
self.stackview.setStack(numpy.arange(24).reshape((2, 3, 4)),
perspective=2)
self.assertEqual(
self.stackview._perspective, 2,
"Perspective not set in setStack(..., perspective=2).")