def setUp(self):
self.focus = TMCLController(name="test_focus",
role="focus",
port="/dev/fake3",
axes=["z"],
ustepsize=[1e-6],
rng=[
[-3000e-6, 3000e-6],
],
refproc="Standard")
def test_cryo_feature_overlay(self):
"""
Test behavior of CryoFeatureOverlay
"""
cnvs = miccanvas.DblMicroscopeCanvas(self.panel)
self.add_control(cnvs, wx.EXPAND, proportion=1, clear=True)
tab_mod = self.create_cryo_tab_model()
# Create a dummy stage & focus to attach to the view
stage = TMCLController(name="test_stage",
role="stage",
port="/dev/fake3",
axes=["x", "y"],
ustepsize=[1e-6, 1e-6],
rng=[[-3e-3, 3e-3], [-3e-3, 3e-3]],
refproc="Standard")
focus = TMCLController(name="test_focus",
role="focus",
port="/dev/fake3",
axes=["z"],
ustepsize=[1e-6],
rng=[[-3e-3, 3e-3]],
refproc="Standard")
tab_mod.main.stage = stage
tab_mod.main.focus = focus
fview = FeatureOverviewView("fakeview", stage=stage)
tab_mod.views.value.append(fview)
tab_mod.focussedView.value = fview
cnvs.setView(fview, tab_mod)
# Save current empty canvas
img = wx.Bitmap.ConvertToImage(cnvs._bmp_buffer)
buffer_clear = wxImage2NDImage(img)
cryofeature_overlay = wol.CryoFeatureOverlay(cnvs, tab_mod)
cnvs.add_world_overlay(cryofeature_overlay)
cryofeature_overlay.active.value = True
# Add features to the tab's features list
tab_mod.add_new_feature(0, 0)
tab_mod.add_new_feature(0.001, 0.001)
cnvs._dc_buffer.SelectObject(wx.NullBitmap) # Flush the buffer
cnvs._dc_buffer.SelectObject(cnvs._bmp_buffer)
img = wx.Bitmap.ConvertToImage(cnvs._bmp_buffer)
buffer_feature = wxImage2NDImage(img)
# Compare empty canvas with the added _features_va
assert_array_not_equal(
buffer_clear,
buffer_feature,
msg=
"Buffers are equal, which means the added _features_va didn't appear on the canvas."
)
test.gui_loop()
def test_current_pos_crosshair_overlay(self):
"""
Test behaviour of CurrentPosCrossHairOverlay
"""
cnvs = miccanvas.DblMicroscopeCanvas(self.panel)
self.add_control(cnvs, wx.EXPAND, proportion=1, clear=True)
tab_mod = self.create_simple_tab_model()
# create a dummy stage to attach to the view
stage = TMCLController(name="test",
role="test",
port="/dev/fake3",
axes=["x", "y"],
ustepsize=[1e-6, 1e-6],
rng=[[-3e-3, 3e-3], [-3e-3, 3e-3]],
refproc="Standard")
# Add a tiled area view to the tab model
logging.debug(stage.position.value)
fview = FeatureOverviewView("fakeview", stage=stage)
tab_mod.views.value.append(fview)
tab_mod.focussedView.value = fview
cnvs.setView(fview, tab_mod)
cnvs.view.show_crosshair.value = False
slol = wol.CurrentPosCrossHairOverlay(cnvs)
slol.active.value = True
cnvs.add_world_overlay(slol)
# stage start at 0,0 (cross hair at center) -> move bt 1mm, 1mm -> then back to 0,0
stage.moveAbs({'x': 1e-3, 'y': 1e-3}).result()
img = wx.Bitmap.ConvertToImage(cnvs._bmp_buffer)
buffer_ch_move = wxImage2NDImage(img)
test.gui_loop(1)
stage.moveAbs({'x': 0, 'y': 0}).result()
cnvs.update_drawing()
cnvs._dc_buffer.SelectObject(wx.NullBitmap) # Flush the buffer
cnvs._dc_buffer.SelectObject(cnvs._bmp_buffer)
img = wx.Bitmap.ConvertToImage(cnvs._bmp_buffer)
buffer_ch_center = wxImage2NDImage(img)
assert_array_not_equal(
buffer_ch_center,
buffer_ch_move,
msg=
"Buffers are equal, which means the crosshair didn't change on stage movement."
)
test.gui_loop()
def test_stage_point_select_mode_overlay(self):
"""
Test behavior of StagePointSelectOverlay
"""
cnvs = miccanvas.DblMicroscopeCanvas(self.panel)
self.add_control(cnvs, wx.EXPAND, proportion=1, clear=True)
tab_mod = self.create_simple_tab_model()
# create a dummy stage to attach to the view
stage = TMCLController(name="test",
role="test",
port="/dev/fake3",
axes=["x", "y"],
ustepsize=[1e-6, 1e-6],
rng=[[-3e-3, 3e-3], [-3e-3, 3e-3]],
refproc="Standard")
# Add a tiled area view to the tab model
logging.debug(stage.position.value)
fview = FeatureOverviewView("fakeview", stage=stage)
tab_mod.views.value.append(fview)
tab_mod.focussedView.value = fview
cnvs.setView(fview, tab_mod)
slol = wol.StagePointSelectOverlay(cnvs)
slol.active.value = True
cnvs.add_world_overlay(slol)
initial_pos = copy.deepcopy(stage.position.value)
# simulate double click by passing the mouse event to on_dbl_click
evt = wx.MouseEvent()
evt.x = 10
evt.y = 10
slol.on_dbl_click(evt)
test.gui_loop(1)
# stage should have been moved from initial position
assert_pos_not_almost_equal(stage.position.value, initial_pos)
logging.debug(stage.position.value)
test.gui_loop()
class TestGenerateZlevels(unittest.TestCase):
def setUp(self):
self.focus = TMCLController(name="test_focus",
role="focus",
port="/dev/fake3",
axes=["z"],
ustepsize=[1e-6],
rng=[
[-3000e-6, 3000e-6],
],
refproc="Standard")
def test_zero_zstep(self):
self.focus.moveAbsSync({"z": 1300e-6})
zMin = -500e-6
zMax = 500e-6
zrange = [zMin, zMax]
zStep = 0e-6
with self.assertRaises(ZeroDivisionError):
generate_zlevels(self.focus, zrange, zStep)
def test_zmax_and_zmin_both_zeros(self):
self.focus.moveAbsSync({"z": 1300e-6})
zMin = -0e-6
zMax = 0e-6
zrange = [zMin, zMax]
zStep = 10e-6
actual = generate_zlevels(self.focus, zrange, zStep)
expected = self.focus.position.value
self.assertAlmostEqual(expected["z"], actual)
def test_zrange_not_in_proper_order(self):
self.focus.moveAbsSync({"z": 1300e-6})
zMin = -10e-6
zMax = 10e-6
zrange = [zMax, zMin]
zStep = 10e-6
with self.assertRaises(ValueError):
generate_zlevels(self.focus, zrange, zStep)
def test_zstep_greater_than_zmax_and_zmin(self):
self.focus.moveAbsSync({"z": 1300e-6})
zMin = -10e-6
zMax = 10e-6
zrange = [zMin, zMax]
zStep = 70e-6
actual = generate_zlevels(self.focus, zrange, zStep)
expected = numpy.asarray([-10e-6, 10e-6
]) + self.focus.position.value["z"]
numpy.testing.assert_array_almost_equal(actual, expected)
def test_normal_zlevels_output_with_positive_zstep(self):
self.focus.moveAbsSync({"z": 1000e-6})
zMax = 100e-6
zMin = -250e-6
zrange = [zMin, zMax]
zStep = 50e-6
expected = numpy.asarray([
-250e-6, -200e-6, -150e-6, -100e-6, -50e-6, 0e-6, 50e-6, 100e-6
]) + self.focus.position.value["z"]
actual = generate_zlevels(self.focus, zrange, zStep)
numpy.testing.assert_array_almost_equal(expected, actual)
def test_normal_zlevels_output_with_negative_zstep(self):
self.focus.moveAbsSync({"z": 1000e-6})
zMax = 100e-6
zMin = -250e-6
zrange = [zMin, zMax]
zStep = -50e-6
expected = numpy.asarray([
1.0e-04, 5.0e-05, 0.0, -5.0e-05, -1.0e-04, -1.5e-04, -2.0e-04,
-2.5e-04
]) + self.focus.position.value["z"]
actual = generate_zlevels(self.focus, zrange, zStep)
numpy.testing.assert_array_almost_equal(expected, actual)
def test_normal_zlevels_output_with_rounding_down(self):
self.focus.moveAbsSync({"z": 1000e-6})
zMax = 10e-6
zMin = -10e-6
zrange = [zMin, zMax]
zStep = 6e-6
expected = numpy.asarray([-10e-6, -3.33e-6, 3.33e-6, 10e-6
]) + self.focus.position.value["z"]
actual = generate_zlevels(self.focus, zrange, zStep)
numpy.testing.assert_array_almost_equal(expected, actual)
def test_normal_zlevels_output_with_rounding_up(self):
self.focus.moveAbsSync({"z": 1000e-6})
zMax = 24e-6
zMin = -24e-6
zrange = [zMin, zMax]
zStep = 17e-6
expected = numpy.asarray([-24e-6, -8e-6, 8e-6, 24e-6]) + \
self.focus.position.value["z"]
actual = generate_zlevels(self.focus, zrange, zStep)
numpy.testing.assert_array_almost_equal(expected, actual)
def test_large_number_of_levels(self):
self.focus.moveAbsSync({"z": 1000e-6})
zMax = 100e-6
zMin = -100e-6
zrange = [zMin, zMax]
zStep = 0.5e-6
output = generate_zlevels(self.focus, zrange, zStep)
self.assertEqual(len(output), 401)
def test_clipping_zmin_on_actuator_lower_limit(self):
self.focus.moveAbsSync({"z": -2800e-6})
zMax = 0e-6
zMin = -300e-6
zrange = [zMin, zMax]
zStep = 100e-6
expected = numpy.asarray([-200e-6, -100e-6, 0e-6]) + \
self.focus.position.value["z"]
actual = generate_zlevels(self.focus, zrange, zStep)
numpy.testing.assert_array_almost_equal(expected, actual)
def test_clipping_zmax_on_actuator_upper_limit(self):
self.focus.moveAbsSync({"z": 2800e-6})
zMax = 300e-6
zMin = 0e-6
zrange = [zMin, zMax]
zStep = 100e-6
expected = numpy.asarray([0e-6, 100e-6, 200e-6]) + \
self.focus.position.value["z"]
actual = generate_zlevels(self.focus, zrange, zStep)
numpy.testing.assert_array_almost_equal(expected, actual)