def test_application():
"""Test application running"""
app = use_app()
print(app) # __repr__ without app
app.create()
wrong = 'glut' if app.backend_name.lower() != 'glut' else 'pyglet'
assert_raises(RuntimeError, use_app, wrong)
app.process_events()
print(app) # test __repr__
assert_raises(ValueError, Canvas, keys='foo')
assert_raises(TypeError, Canvas, keys=dict(escape=1))
assert_raises(ValueError, Canvas, keys=dict(escape='foo')) # not an attr
pos = [0, 0] if app.backend_module.capability['position'] else None
size = (100, 100)
# Use "with" statement so failures don't leave open window
# (and test context manager behavior)
title = 'default'
with Canvas(title=title, size=size, app=app, show=True,
position=pos) as canvas:
assert_true(canvas.create_native() is None) # should be done already
assert_is(canvas.app, app)
assert_true(canvas.native)
assert_equal('swap_buffers', canvas.events.draw.callback_refs[-1])
canvas.measure_fps(0.001)
sleep(0.002)
canvas.update()
app.process_events()
assert_true(canvas.fps > 0)
# Other methods
print(canvas) # __repr__
assert_equal(canvas.title, title)
canvas.title = 'you'
with use_log_level('warning', record=True, print_msg=False) as l:
if app.backend_module.capability['position']:
# todo: disable more tests based on capability
canvas.position = pos
canvas.size = size
if 'ipynb_vnc' in canvas.app.backend_name.lower():
assert_true(len(l) >= 1)
else:
assert_true(len(l) == 0)
canvas.connect(on_mouse_move)
assert_raises(ValueError, canvas.connect, _on_mouse_move)
if sys.platform != 'darwin': # XXX knownfail, prob. needs warmup
canvas.show(False)
canvas.show()
app.process_events()
assert_raises(ValueError, canvas.connect, on_nonexist)
# deprecation of "paint"
with use_log_level('info', record=True, print_msg=False) as log:
olderr = sys.stderr
try:
with open(os.devnull, 'w') as fid:
sys.stderr = fid
@canvas.events.paint.connect
def fake(event):
pass
finally:
sys.stderr = olderr
assert_equal(len(log), 1)
assert_in('deprecated', log[0])
# screenshots
gl.glViewport(0, 0, *size)
ss = _screenshot()
assert_array_equal(ss.shape, size + (4,))
assert_equal(len(canvas._backend._vispy_get_geometry()), 4)
if (app.backend_name.lower() != 'glut' and # XXX knownfail for Almar
sys.platform != 'win32'): # XXX knownfail for windows
assert_array_equal(canvas.size, size)
assert_equal(len(canvas.position), 2) # XXX knawnfail, doesn't "take"
# GLOO: should have an OpenGL context already, so these should work
vert = VertexShader("void main (void) {gl_Position = pos;}")
frag = FragmentShader("void main (void) {gl_FragColor = pos;}")
program = Program(vert, frag)
assert_raises(RuntimeError, program.activate)
vert = VertexShader("uniform vec4 pos;"
"void main (void) {gl_Position = pos;}")
frag = FragmentShader("uniform vec4 pos;"
"void main (void) {gl_FragColor = pos;}")
program = Program(vert, frag)
#uniform = program.uniforms[0]
program['pos'] = [1, 2, 3, 4]
program.activate() # should print
#uniform.upload(program)
program.detach(vert)
program.detach(frag)
assert_raises(RuntimeError, program.detach, vert)
assert_raises(RuntimeError, program.detach, frag)
vert = VertexShader("attribute vec4 pos;"
"void main (void) {gl_Position = pos;}")
frag = FragmentShader("void main (void) {}")
program = Program(vert, frag)
#attribute = program.attributes[0]
program["pos"] = [1, 2, 3, 4]
program.activate()
#attribute.upload(program)
# cannot get element count
#assert_raises(RuntimeError, program.draw, 'POINTS')
# use a real program
vert = ("uniform mat4 u_model;"
"attribute vec2 a_position; attribute vec4 a_color;"
"varying vec4 v_color;"
"void main (void) {v_color = a_color;"
"gl_Position = u_model * vec4(a_position, 0.0, 1.0);"
"v_color = a_color;}")
frag = "void main() {gl_FragColor = vec4(0, 0, 0, 1);}"
n, p = 250, 50
T = np.random.uniform(0, 2 * np.pi, n)
position = np.zeros((n, 2), dtype=np.float32)
position[:, 0] = np.cos(T)
position[:, 1] = np.sin(T)
color = np.ones((n, 4), dtype=np.float32) * (1, 1, 1, 1)
data = np.zeros(n * p, [('a_position', np.float32, 2),
('a_color', np.float32, 4)])
data['a_position'] = np.repeat(position, p, axis=0)
data['a_color'] = np.repeat(color, p, axis=0)
program = Program(vert, frag)
program.bind(VertexBuffer(data))
program['u_model'] = np.eye(4, dtype=np.float32)
# different codepath if no call to activate()
program.draw(gl.GL_POINTS)
subset = IndexBuffer(np.arange(10, dtype=np.uint32))
program.draw(gl.GL_POINTS, subset)
# bad programs
frag_bad = ("varying vec4 v_colors") # no semicolon
program = Program(vert, frag_bad)
assert_raises(RuntimeError, program.activate)
frag_bad = None # no fragment code. no main is not always enough
program = Program(vert, frag_bad)
assert_raises(ValueError, program.activate)
# Timer
timer = Timer(interval=0.001, connect=on_mouse_move, iterations=2,
start=True, app=app)
timer.start()
timer.interval = 0.002
assert_equal(timer.interval, 0.002)
assert_true(timer.running)
sleep(.003)
assert_true(timer.elapsed >= 0.002)
timer.stop()
assert_true(not timer.running)
assert_true(timer.native)
timer.disconnect()
# test that callbacks take reasonable inputs
_test_callbacks(canvas)
# cleanup
canvas.swap_buffers()
canvas.update()
app.process_events()
# put this in even though __exit__ will call it to make sure we don't
# have problems calling it multiple times
canvas.close() # done by context
def test_application():
"""Test application running"""
app = use_app()
print(app) # __repr__ without app
app.create()
wrong = 'glfw' if app.backend_name.lower() != 'glfw' else 'pyqt4'
assert_raises(RuntimeError, use_app, wrong)
app.process_events()
print(app) # test __repr__
assert_raises(ValueError, Canvas, keys='foo')
assert_raises(TypeError, Canvas, keys=dict(escape=1))
assert_raises(ValueError, Canvas, keys=dict(escape='foo')) # not an attr
pos = [0, 0] if app.backend_module.capability['position'] else None
size = (100, 100)
# Use "with" statement so failures don't leave open window
# (and test context manager behavior)
title = 'default'
with Canvas(title=title, size=size, app=app, show=True,
position=pos) as canvas:
context = canvas.context
assert_true(canvas.create_native() is None) # should be done already
assert_is(canvas.app, app)
assert_true(canvas.native)
assert_equal('swap_buffers', canvas.events.draw.callback_refs[-1])
canvas.measure_fps(0.001)
sleep(0.002)
canvas.update()
app.process_events()
assert_true(canvas.fps > 0)
# Other methods
print(canvas) # __repr__
assert_equal(canvas.title, title)
canvas.title = 'you'
with use_log_level('warning', record=True, print_msg=False) as l:
if app.backend_module.capability['position']:
# todo: disable more tests based on capability
canvas.position = pos
canvas.size = size
if 'ipynb_vnc' in canvas.app.backend_name.lower():
assert_true(len(l) >= 1)
else:
assert_true(len(l) == 0)
canvas.connect(on_mouse_move)
assert_raises(ValueError, canvas.connect, _on_mouse_move)
if sys.platform != 'darwin': # XXX knownfail, prob. needs warmup
canvas.show(False)
canvas.show()
app.process_events()
assert_raises(ValueError, canvas.connect, on_nonexist)
# deprecation of "paint"
with use_log_level('info', record=True, print_msg=False) as log:
olderr = sys.stderr
try:
fid = StringIO()
sys.stderr = fid
@canvas.events.paint.connect
def fake(event):
pass
finally:
sys.stderr = olderr
assert_equal(len(log), 1)
assert_in('deprecated', log[0])
# screenshots
gl.glViewport(0, 0, *size)
ss = _screenshot()
assert_array_equal(ss.shape, size + (4,))
assert_equal(len(canvas._backend._vispy_get_geometry()), 4)
if sys.platform != 'win32': # XXX knownfail for windows
assert_array_equal(canvas.size, size)
assert_equal(len(canvas.position), 2) # XXX knawnfail, doesn't "take"
# GLOO: should have an OpenGL context already, so these should work
vert = "void main (void) {gl_Position = pos;}"
frag = "void main (void) {gl_FragColor = pos;}"
program = Program(vert, frag)
assert_raises(RuntimeError, program.glir.flush, context.shared.parser)
vert = "uniform vec4 pos;\nvoid main (void) {gl_Position = pos;}"
frag = "uniform vec4 pos;\nvoid main (void) {gl_FragColor = pos;}"
program = Program(vert, frag)
#uniform = program.uniforms[0]
program['pos'] = [1, 2, 3, 4]
vert = "attribute vec4 pos;\nvoid main (void) {gl_Position = pos;}"
frag = "void main (void) {}"
program = Program(vert, frag)
#attribute = program.attributes[0]
program["pos"] = [1, 2, 3, 4]
# use a real program
program._glir.clear()
vert = ("uniform mat4 u_model;"
"attribute vec2 a_position; attribute vec4 a_color;"
"varying vec4 v_color;"
"void main (void) {v_color = a_color;"
"gl_Position = u_model * vec4(a_position, 0.0, 1.0);"
"v_color = a_color;}")
frag = "void main() {gl_FragColor = vec4(0, 0, 0, 1);}"
n, p = 250, 50
T = np.random.uniform(0, 2 * np.pi, n)
position = np.zeros((n, 2), dtype=np.float32)
position[:, 0] = np.cos(T)
position[:, 1] = np.sin(T)
color = np.ones((n, 4), dtype=np.float32) * (1, 1, 1, 1)
data = np.zeros(n * p, [('a_position', np.float32, 2),
('a_color', np.float32, 4)])
data['a_position'] = np.repeat(position, p, axis=0)
data['a_color'] = np.repeat(color, p, axis=0)
program = Program(vert, frag)
program.bind(VertexBuffer(data))
program['u_model'] = np.eye(4, dtype=np.float32)
# different codepath if no call to activate()
program.draw(gl.GL_POINTS)
subset = IndexBuffer(np.arange(10, dtype=np.uint32))
program.draw(gl.GL_POINTS, subset)
# bad programs
frag_bad = ("varying vec4 v_colors") # no semicolon
program = Program(vert, frag_bad)
assert_raises(RuntimeError, program.glir.flush, context.shared.parser)
frag_bad = None # no fragment code. no main is not always enough
assert_raises(ValueError, Program, vert, frag_bad)
# Timer
timer = Timer(interval=0.001, connect=on_mouse_move, iterations=2,
start=True, app=app)
timer.start()
timer.interval = 0.002
assert_equal(timer.interval, 0.002)
assert_true(timer.running)
sleep(.003)
assert_true(timer.elapsed >= 0.002)
timer.stop()
assert_true(not timer.running)
assert_true(timer.native)
timer.disconnect()
# test that callbacks take reasonable inputs
_test_callbacks(canvas)
# cleanup
canvas.swap_buffers()
canvas.update()
app.process_events()
# put this in even though __exit__ will call it to make sure we don't
# have problems calling it multiple times
canvas.close() # done by context
class MainWindow(BaseQtView):
def __init__(self, title: str = "", volume_widget: Optional[QWidget] = None, slice_widget: Optional[QWidget] = None):
self.title = title
self.volume_widget = volume_widget if volume_widget else QWidget()
self.slice_widget = slice_widget if slice_widget else QWidget()
self._init()
def _init(self):
print("Building...")
self.win = QMainWindow()
self._default_window_title = self.title
widget = QWidget()
self.win.setCentralWidget(widget)
main_layout = QHBoxLayout()
widget.setLayout(main_layout)
main_layout.addWidget(self.slice_widget)
main_layout.addWidget(self.volume_widget)
side_layout = QVBoxLayout()
main_layout.addLayout(side_layout)
load_image_button = QPushButton("Load Section")
side_layout.addWidget(load_image_button)
load_image_button.clicked.connect(self.show_load_image_dialog)
# Atlas BUttons
button_hbox = QHBoxLayout()
side_layout.addLayout(button_hbox)
atlas_buttons = QButtonGroup(self.win)
atlas_buttons.setExclusive(True)
atlas_buttons.buttonToggled.connect(self.atlas_button_toggled)
for resolution in [100, 25, 10]:
atlas_button = QPushButton(f"{resolution}um")
atlas_button.setCheckable(True)
button_hbox.addWidget(atlas_button)
atlas_buttons.addButton(atlas_button)
# The 10um atlas takes way too long to download at the moment.
# It needs some kind of progress bar or async download feature to be useful.
# The disabled button here shows it as an option for the future, but keeps it from being used.
if resolution == 10:
atlas_button.setDisabled(True)
self.title_reset_timer = Timer(interval=2, connect=lambda e: self._show_default_window_title(), iterations=1,
start=False)
self._show_default_window_title()
self.statusbar = self.win.statusBar()
self.image_coord_label = QLabel(text="Image Coords")
self.statusbar.addPermanentWidget(self.image_coord_label)
self.win.show()
@property
def qt_widget(self) -> QWidget:
return self.win
def on_image_coordinate_highlighted(self, image_coords, atlas_coords):
i, j = image_coords
x, y, z = atlas_coords
self.image_coord_label.setText(f"(i={i}, j={j}) (x={x:.1f}, y={y:.1f}, z={z:.1f})")
def on_error_raised(self, msg: str):
self.show_temp_title(msg)
def atlas_button_toggled(self, button: QPushButton, is_checked: bool):
if not is_checked: # Don't do anything for the button being unselected.
return
resolution_label = button.text()
resolution = int("".join(filter(str.isdigit, resolution_label)))
self.load_atlas(resolution=resolution)
# Command Routing
def show_load_image_dialog(self):
filename, filetype = QFileDialog.getOpenFileName(
parent=self.win,
caption="Load Image",
dir="../data/RA_10X_scans/MEA",
filter="OME-TIFF (*.ome.tiff)"
)
if not filename:
return
self.load_section(filename=filename)
def load_atlas(self, resolution: int):
raise NotImplementedError("Connect to LoadAtlasCommand before using.")
def load_section(self, filename: str):
raise NotImplementedError("Connect to a LoadImageCommand before using.")
# View Code
def _show_default_window_title(self):
self.win.setWindowTitle(self._default_window_title)
def show_temp_title(self, title: str) -> None:
self.win.setWindowTitle(title)
self.title_reset_timer.stop()
self.title_reset_timer.start(iterations=1)
def _test_application(backend):
"""Test application running"""
app = Application()
assert_raises(ValueError, app.use, "foo")
app.use(backend)
wrong = "Glut" if app.backend_name != "Glut" else "Pyglet"
assert_raises(RuntimeError, app.use, wrong)
app.process_events()
if backend is not None:
# "in" b/c "qt" in "PySide (qt)"
assert_in(backend, app.backend_name)
print(app) # test __repr__
# Canvas
pos = [0, 0]
size = (100, 100)
# Use "with" statement so failures don't leave open window
# (and test context manager behavior)
title = "default" if backend is None else backend
with Canvas(title=title, size=size, app=app, show=True, position=pos) as canvas:
assert_is(canvas.app, app)
assert_true(canvas.native)
assert_equal("swap_buffers", canvas.events.paint.callback_refs[-1])
print(canvas) # __repr__
assert_array_equal(canvas.size, size)
assert_equal(canvas.title, title)
canvas.title = "you"
canvas.position = pos
canvas.size = size
canvas.connect(on_mouse_move)
assert_raises(ValueError, canvas.connect, _on_mouse_move)
if sys.platform != "darwin": # XXX knownfail, prob. needs warmup
canvas.show(False)
canvas.show()
app.process_events()
assert_raises(ValueError, canvas.connect, on_nonexist)
# screenshots
gl.glViewport(0, 0, *size)
ss = _screenshot()
assert_array_equal(ss.shape, size + (3,))
assert_equal(len(canvas._backend._vispy_get_geometry()), 4)
assert_array_equal(canvas.size, size)
assert_equal(len(canvas.position), 2) # XXX knawnfail, doesn't "take"
# GLOO: should have an OpenGL context already, so these should work
vert = VertexShader("void main (void) {gl_Position = pos;}")
frag = FragmentShader("void main (void) {gl_FragColor = pos;}")
program = Program(vert, frag)
assert_raises(RuntimeError, program.activate)
vert = VertexShader("uniform vec4 pos;" "void main (void) {gl_Position = pos;}")
frag = FragmentShader("uniform vec4 pos;" "void main (void) {gl_FragColor = pos;}")
program = Program(vert, frag)
# uniform = program.uniforms[0]
program["pos"] = [1, 2, 3, 4]
program.activate() # should print
# uniform.upload(program)
program.detach(vert)
program.detach(frag)
assert_raises(RuntimeError, program.detach, vert)
assert_raises(RuntimeError, program.detach, frag)
vert = VertexShader("attribute vec4 pos;" "void main (void) {gl_Position = pos;}")
frag = FragmentShader("void main (void) {}")
program = Program(vert, frag)
# attribute = program.attributes[0]
program["pos"] = [1, 2, 3, 4]
program.activate()
# attribute.upload(program)
# cannot get element count
# assert_raises(RuntimeError, program.draw, 'POINTS')
# use a real program
vert = (
"uniform mat4 u_model;"
"attribute vec2 a_position; attribute vec4 a_color;"
"varying vec4 v_color;"
"void main (void) {v_color = a_color;"
"gl_Position = u_model * vec4(a_position, 0.0, 1.0);"
"v_color = a_color;}"
)
frag = "void main() {gl_FragColor = vec4(0, 0, 0, 1);}"
n, p = 250, 50
T = np.random.uniform(0, 2 * np.pi, n)
position = np.zeros((n, 2), dtype=np.float32)
position[:, 0] = np.cos(T)
position[:, 1] = np.sin(T)
color = np.ones((n, 4), dtype=np.float32) * (1, 1, 1, 1)
data = np.zeros(n * p, [("a_position", np.float32, 2), ("a_color", np.float32, 4)])
data["a_position"] = np.repeat(position, p, axis=0)
data["a_color"] = np.repeat(color, p, axis=0)
program = Program(vert, frag)
program.bind(VertexBuffer(data))
program["u_model"] = np.eye(4, dtype=np.float32)
# different codepath if no call to activate()
program.draw(gl.GL_POINTS)
subset = IndexBuffer(np.arange(10, dtype=np.uint32))
program.draw(gl.GL_POINTS, subset)
# bad programs
frag_bad = "varying vec4 v_colors" # no semicolon
program = Program(vert, frag_bad)
assert_raises(RuntimeError, program.activate)
frag_bad = None # no fragment code. no main is not always enough
program = Program(vert, frag_bad)
assert_raises(ValueError, program.activate)
# Timer
timer = Timer(interval=0.001, connect=on_mouse_move, iterations=2, start=True, app=app)
timer.start()
timer.interval = 0.002
assert_equal(timer.interval, 0.002)
assert_true(timer.running)
timer.stop()
assert_true(not timer.running)
assert_true(timer.native)
timer.disconnect()
# test that callbacks take reasonable inputs
_test_callbacks(canvas)
# cleanup
canvas.swap_buffers()
canvas.update()
app.process_events()
def _test_application(backend):
"""Test application running"""
app = Application()
assert_raises(ValueError, app.use, 'foo')
app.use(backend)
wrong = 'Glut' if app.backend_name != 'Glut' else 'Pyglet'
assert_raises(RuntimeError, app.use, wrong)
app.process_events()
if backend is not None:
# "in" b/c "qt" in "PySide (qt)"
assert_true(backend in app.backend_name)
print(app) # test __repr__
# Canvas
pos = [0, 0, 1, 1]
# Use "with" statement so failures don't leave open window
# (and test context manager behavior)
with Canvas(title='me', app=app, show=True, position=pos) as canvas:
assert_true(canvas.app is app)
assert_true(canvas.native)
print(canvas.size >= (1, 1))
canvas.resize(90, 90)
canvas.move(1, 1)
assert_equal(canvas.title, 'me')
canvas.title = 'you'
canvas.position = (0, 0)
canvas.size = (100, 100)
canvas.connect(on_mouse_move)
assert_raises(ValueError, canvas.connect, _on_mouse_move)
canvas.show()
assert_raises(ValueError, canvas.connect, on_nonexist)
# screenshots
ss = _screenshot()
assert_array_equal(ss.shape[2], 3) # XXX other dimensions not correct?
# XXX it would be good to do real checks, but sometimes the
# repositionings don't "take" (i.e., lead to random errors)
assert_equal(len(canvas._backend._vispy_get_geometry()), 4)
assert_equal(len(canvas.size), 2)
assert_equal(len(canvas.position), 2)
# GLOO: should have an OpenGL context already, so these should work
vert = VertexShader("void main (void) {gl_Position = pos;}")
frag = FragmentShader("void main (void) {gl_FragColor = pos;}")
program = Program(vert, frag)
assert_raises(ShaderError, program.activate)
vert = VertexShader("uniform vec4 pos;"
"void main (void) {gl_Position = pos;}")
frag = FragmentShader("uniform vec4 pos;"
"void main (void) {gl_FragColor = pos;}")
program = Program(vert, frag)
uniform = program.uniforms[0]
uniform.set_data([1, 2, 3, 4])
program.activate() # should print
uniform.upload(program)
program.detach(vert, frag)
assert_raises(ShaderError, program.detach, vert)
assert_raises(ShaderError, program.detach, frag)
vert = VertexShader("attribute vec4 pos;"
"void main (void) {gl_Position = pos;}")
frag = FragmentShader("void main (void) {}")
program = Program(vert, frag)
attribute = program.attributes[0]
attribute.set_data([1, 2, 3, 4])
program.activate()
attribute.upload(program)
# cannot get element count
assert_raises(ProgramError, program.draw, 'POINTS')
# use a real program
vert = ("uniform mat4 u_model;"
"attribute vec2 a_position; attribute vec4 a_color;"
"varying vec4 v_color;"
"void main (void) {v_color = a_color;"
"gl_Position = u_model * vec4(a_position, 0.0, 1.0);"
"v_color = a_color;}")
frag = "void main() {gl_FragColor = vec4(0, 0, 0, 1);}"
n, p = 250, 50
T = np.random.uniform(0, 2 * np.pi, n)
position = np.zeros((n, 2), dtype=np.float32)
position[:, 0] = np.cos(T)
position[:, 1] = np.sin(T)
color = np.ones((n, 4), dtype=np.float32) * (1, 1, 1, 1)
data = np.zeros(n * p, [('a_position', np.float32, 2),
('a_color', np.float32, 4)])
data['a_position'] = np.repeat(position, p, axis=0)
data['a_color'] = np.repeat(color, p, axis=0)
program = Program(vert, frag)
program.set_vars(VertexBuffer(data))
program['u_model'] = np.eye(4, dtype=np.float32)
program.draw('POINTS') # different codepath if no call to activate()
subset = ElementBuffer(np.arange(10, dtype=np.uint32))
program.draw('POINTS', subset=subset)
# bad programs
frag_bad = ("varying vec4 v_colors") # no semicolon
program = Program(vert, frag_bad)
assert_raises(ShaderError, program.activate)
frag_bad = None # no fragment code. no main is not always enough
program = Program(vert, frag_bad)
assert_raises(ProgramError, program.activate)
# Timer
timer = Timer(interval=0.001, connect=on_mouse_move, iterations=2,
start=True, app=app)
timer.start()
timer.interval = 0.002
assert_equal(timer.interval, 0.002)
assert_true(timer.running)
timer.stop()
assert_true(not timer.running)
assert_true(timer.native)
timer.disconnect()
# test that callbacks take reasonable inputs
_test_callbacks(canvas)
# cleanup
canvas.swap_buffers()
canvas.update()
# put this in even though __exit__ will call it to make sure we don't
# have problems calling it multiple times
canvas.close()
app.quit()
app.quit() # make sure it doesn't break if a user does something silly
class SourceInspectCamera(PanZoomCamera):
"""
"""
_state_props = PanZoomCamera._state_props + ('index', )
def __init__(self, image, img_data, sources, poslist, index=0, **kwargs):
PanZoomCamera.__init__(self, **kwargs)
self.index = index
self.image = image
self.img_data = img_data
self.sources = sources
self.poslist = poslist
#self.smin = 0.9*np.nanmin(self.img_data)
#self.smax = 1.02*np.nanmax(self.img_data)
pcts = np.nanpercentile(self.img_data, [5.0, 99.0])
if np.all(np.isfinite(pcts)):
self.smin = pcts[0]
self.smax = pcts[1]
self.accelerator = 5.0
self.nsrc = len(poslist)
self._keymap = {
keys.UP: +1,
keys.DOWN: -1,
keys.LEFT: -1,
keys.RIGHT: +1,
keys.SPACE: +1
}
self._timer = Timer(0.2, start=False, connect=self.on_timer)
@property
def keymap(self):
"""
"""
return self._keymap
def update_index(self, val):
self.index += val
if (self.index > self.nsrc-1):
self.index = 0
if (self.index < 0):
self.index = self.nsrc - 1
def update_pan(self):
newX = self.poslist[self.index][0]
newY = self.poslist[self.index][1]
curX = self.rect.left + self.rect.width/2.0
curY = self.rect.bottom + self.rect.height/2.0
self.pan((newX-curX,newY-curY))
# update image data
imsect = self.img_data[int(self.rect.bottom):int(self.rect.top),
int(self.rect.left):int(self.rect.right)]
pcts = np.nanpercentile(imsect, [5.0, 99.0])
if np.all(np.isfinite(pcts)):
self.smin = pcts[0]
#cmin = -0.01 + 1.2*self.sources['background'][self.sources.index==self.index].values[0]
if (is_pacs):
self.smax = 1.2*self.sources['susflux']\
[self.sources.index==self.index].values[0]/1000.0/10.0 + self.smin
else:
self.smax = 1.2*self.sources['fluxtml']\
[self.sources.index==self.index].values[0]/1000.0/0.95 + self.smin
self.update_scale()
def update_scale(self):
self.image.set_data(bytescale(self.img_data, cmin=self.smin, cmax=self.smax))
self.view_changed()
def on_timer(self, event):
"""Timer event handler
Parameters
----------
event : instance of Event
The event.
"""
self.update_index(1)
self.update_pan()
self.view_changed()
def viewbox_key_event(self, event):
"""ViewBox key event handler
Parameters
----------
event : instance of Event
The event.
"""
PanZoomCamera.viewbox_key_event(self, event)
if event.handled or not self.interactive:
return
if event.type == 'key_press':
if event.key in self._keymap:
val = self._keymap[event.key]
self.update_index(val)
self.update_pan()
self.view_changed()
elif event.key == 'M':
self._timer.start()
elif event.key == 'S':
self._timer.stop()
#elif event.key == 'X':
# ind = np.argsort(self.poslist[:,0])
# self.poslist = self.poslist[ind]
#elif event.key == 'Y':
# ind = np.argsort(self.poslist[:,1])
# self.poslist = self.poslist[ind]
elif event.key == 'L':
print(self.sources[self.sources.sourceid==self.sources['sourceid'][self.index]])
elif event.key == 'T':
sdiff = self.accelerator*(self.smax - self.smin)/255.0
self.smax += sdiff
self.smin += sdiff
self.update_scale()
elif event.key == 'B':
sdiff = self.accelerator*(self.smax - self.smin)/255.0
self.smax -= sdiff
self.smin -= sdiff
self.update_scale()
elif event.key == 'N':
sdiff = self.accelerator*(self.smax - self.smin)/255.0
self.smax -= sdiff
self.smin += sdiff
self.update_scale()
elif event.key == 'W':
sdiff = self.accelerator*(self.smax - self.smin)/255.0
self.smax += sdiff
self.smin -= sdiff
self.update_scale()
elif event.key == 'U':
print("Current stretch limits: %10.4g, %10.4g"%(self.smin, self.smax))
self.smin = float(input("New lower value?"))
self.smax = float(input("New upper value?"))
self.update_scale()
class MainWindow(BaseQtView):
def __init__(
self,
title: str = "",
volume_widget: Optional[QWidget] = None,
slice_widget: Optional[QWidget] = None,
side_controls: Optional[QWidget] = None,
):
self.title = title
self.volume_widget = volume_widget if volume_widget else QWidget()
self.slice_widget = slice_widget if slice_widget else QWidget()
self.side_widget = side_controls if side_controls else QWidget()
self._init()
def _init(self):
print("Building...")
self.win = QMainWindow()
self._default_window_title = self.title
widget = QWidget()
self.win.setCentralWidget(widget)
main_layout = QHBoxLayout()
widget.setLayout(main_layout)
main_layout.addWidget(self.slice_widget)
main_layout.addWidget(self.volume_widget)
main_layout.addWidget(self.side_widget)
self.title_reset_timer = Timer(
interval=2,
connect=lambda e: self._show_default_window_title(),
iterations=1,
start=False)
self._show_default_window_title()
self.statusbar = self.win.statusBar()
self.image_coord_label = QLabel(text="Image Coords")
self.statusbar.addPermanentWidget(self.image_coord_label)
self.win.show()
@property
def qt_widget(self) -> QWidget:
return self.win
def on_image_coordinate_highlighted(self, image_coords, atlas_coords):
i, j = image_coords
x, y, z = atlas_coords
self.image_coord_label.setText(
f"(i={i}, j={j}) (x={x:.1f}, y={y:.1f}, z={z:.1f})")
def on_error_raised(self, msg: str):
self.show_temp_title(msg)
# View Code
def _show_default_window_title(self):
self.win.setWindowTitle(self._default_window_title)
def show_temp_title(self, title: str) -> None:
self.win.setWindowTitle(title)
self.title_reset_timer.stop()
self.title_reset_timer.start(iterations=1)
scene.add_to_subplot(brain_obj, row=0, col=0, rotate='left', use_this_cam=True)
# Finally, add the colorbar :
colorbar = ColorbarObj(source_object,
cblabel='Projection of niEEG data',
**CBAR_STATE)
scene.add_to_subplot(colorbar, row=0, col=1, width_max=200, rotate='up')
# Animation
app_timer = Timer(app=CONFIG['VISPY_APP'], interval='auto', iterations=-1)
def on_timer(*args, **kwargs):
if hasattr(brain_obj, 'camera'):
brain_obj.camera.azimuth += 1
t = app_timer.elapsed
frame = int(np.floor(t * sampling_frequency))
new_data = data[:, frame % data.shape[1]].ravel()
source_object._data = vispy_array(new_data)
source_object.update()
source_object.project_sources(brain_obj)
source_object.color_sources()
app_timer.connect(on_timer)
app_timer.start()
scene.preview()
class VisbrainObject(_VisbrainObj):
"""Base class inherited by all of the Visbrain objects.
Parameters
----------
name : string
Object name.
parent : VisPy.parent | None
Markers object parent.
transform : VisPy.visuals.transforms | None
VisPy transformation to set to the parent node.
verbose : string
Verbosity level.
"""
def __init__(self, name, parent=None, transform=None, verbose=None, **kw):
"""Init."""
_VisbrainObj.__init__(self, **kw)
self._node = vispy.scene.Node(name=name)
self._node.parent = parent
self._csize = None # canvas size
self._shortcuts = {}
# Name :
assert isinstance(name, str)
self._name = name
# Transformation :
if transform is None:
transform = vist.STTransform()
self._node.transform = transform
# Verbose :
set_log_level(verbose)
logger.info('%s created' % repr(self))
def __repr__(self):
"""Represent ClassName(name='object_name')."""
return type(self).__name__ + "(name='" + self._name + "')"
def __str__(self):
"""Return the object name."""
return self._name
def _get_parent(self, bgcolor, axis, show, obj=None, **kwargs):
"""Get the object parent for preview and screenshot."""
if hasattr(obj, '_get_camera'):
camera = obj._get_camera()
else:
camera = self._get_camera()
canvas = VisbrainCanvas(axis=axis, show=show, name=self._name,
bgcolor=color2vb(bgcolor), camera=camera,
shortcuts=self._shortcuts, **kwargs)
self._csize = canvas.canvas.size
self.set_shortcuts_to_canvas(canvas)
if not hasattr(self._node.parent, 'name'):
self._node.parent = canvas.wc.scene
return canvas
def preview(self, bgcolor='black', axis=False, xyz=False, show=True,
obj=None, size=(1200, 800), mpl=False, **kwargs):
"""Previsualize the result.
Parameters
----------
bgcolor : array_like/string/tuple | 'black'
Background color for the preview.
axis : bool | False
Add x and y axis with ticks.
xyz : bool | False
Add an (x, y, z) axis to the scene.
obj : VisbrainObj | None
Pass a Visbrain object if you want to use the camera of an other
object.
size : tuple | (1200, 800)
Default size of the window.
mpl : bool | False
Use Matplotlib to display the object. This result in a non
interactive figure.
kwargs : dict | {}
Optional arguments are passed to the VisbrainCanvas class.
"""
if CONFIG['MPL_RENDER'] or mpl:
canvas = self._get_parent(bgcolor, False, False, obj, **kwargs)
mpl_preview(canvas.canvas, widget=canvas.canvas.central_widget)
else:
parent_bck = self._node.parent
kwargs['cargs'] = {'size': size}
canvas = self._get_parent(bgcolor, axis, show, obj, **kwargs)
if xyz:
vispy.scene.visuals.XYZAxis(parent=canvas.wc.scene)
# view.camera = camera
if (sys.flags.interactive != 1) and show:
CONFIG['VISPY_APP'].run()
# Reset orignial parent :
self._node.parent = parent_bck
def describe_tree(self):
"""Tree description."""
return self._node.describe_tree()
def animate(self, step=1., interval='auto', iterations=-1):
"""Animate the object.
Note that this method can only be used with 3D objects.
Parameters
----------
step : float | 1.
Rotation step.
interval : float | 'auto'
Time between events in seconds. The default is ‘auto’, which
attempts to find the interval that matches the refresh rate of the
current monitor. Currently this is simply 1/60.
iterations : int | -1
Number of iterations. Can be -1 for infinite.
"""
from vispy.app import Timer
def on_timer(*args, **kwargs): # noqa
if hasattr(self, 'camera'):
self.camera.azimuth += step # noqa
kw = dict(connect=on_timer, app=CONFIG['VISPY_APP'],
interval=interval, iterations=iterations)
self._app_timer = Timer(**kw)
self._app_timer.start()
def record_animation(self, name, n_pic=10, bgcolor=None):
"""Record an animated object and save as a *.gif file.
Note that this method :
* Can only be used with 3D objects.
* Requires the python package imageio
Parameters
----------
name : string
Name of the gif file (e.g 'myfile.gif')
n_pic : int | 10
Number of pictures to use to render the gif.
bgcolor : string, tuple, list | None
Background color.
"""
import imageio
writer = imageio.get_writer(name)
canvas = self._get_parent(bgcolor, False, False)
for k in range(n_pic):
im = canvas.canvas.render()
writer.append_data(im)
self.camera.azimuth += 360. / n_pic
writer.close()
def render(self):
"""Render the canvas.
Returns
-------
img : array_like
Array of shape (n_rows, n_columns, 4) where 4 describes the RGBA
components.
"""
canvas = self._get_parent(None, False, False)
return canvas.canvas.render()
def screenshot(self, saveas, print_size=None, dpi=300., unit='centimeter',
factor=None, region=None, autocrop=False, bgcolor=None,
transparent=False, obj=None, line_width=1., **kwargs):
"""Take a screeshot of the scene.
By default, the rendered canvas will have the size of your screen.
The screenshot() method provides two ways to increase to exported image
resolution :
* Using print_size, unit and dpi inputs : specify the size of the
image at a specific dpi level. For example, you might want to
have an (10cm, 15cm) image at 300 dpi.
* Using the factor input : multiply the default image size by this
factor. For example, if you have a (1920, 1080) monitor and if
factor is 2, the exported image should have a shape of
(3840, 2160) pixels.
Parameters
----------
saveas : str
The name of the file to be saved. This file must contains a
extension like .png, .tiff, .jpg...
print_size : tuple | None
The desired print size. This argument should be used in association
with the dpi and unit inputs. print_size describe should be a tuple
of two floats describing (width, height) of the exported image for
a specific dpi level. The final image might not have the exact
desired size but will try instead to find a compromize
regarding to the proportion of width/height of the original image.
dpi : float | 300.
Dots per inch for printing the image.
unit : {'centimeter', 'millimeter', 'pixel', 'inch'}
Unit of the printed size.
factor : float | None
If you don't want to use the print_size input, factor simply
multiply the resolution of your screen.
region : tuple | None
Select a specific region. Must be a tuple of four integers each one
describing (x_start, y_start, width, height).
autocrop : bool | False
Automaticaly crop the figure in order to have the smallest
space between the brain and the border of the picture.
bgcolor : array_like/string | None
The background color of the image.
transparent : bool | False
Specify if the exported figure have to contains a transparent
background.
obj : VisbrainObj | None
Pass a Visbrain object if you want to use the camera of an other
object for the sceen rendering.
kwargs : dict | {}
Optional arguments are passed to the VisbrainCanvas class.
"""
kw = dict(print_size=print_size, dpi=dpi, factor=factor,
autocrop=autocrop, unit=unit, region=region,
bgcolor=bgcolor, transparent=transparent)
canvas = self._get_parent(bgcolor, False, False, obj, **kwargs)
write_fig_canvas(saveas, canvas.canvas,
widget=canvas.canvas.central_widget, **kw)
self._node.parent = None
def copy(self):
"""Get a copy of the object."""
from copy import copy
return copy(self)
# ----------- PARENT -----------
@property
def parent(self):
"""Get the parent value."""
p_isnn = self._node.parent is not None
return self._node.parent if p_isnn else self._node
@parent.setter
def parent(self, value):
"""Set parent value."""
self._node.parent = value
# ----------- TRANSFORM -----------
@property
def transform(self):
"""Get the transform value."""
return self._node.transform
@transform.setter
def transform(self, value):
"""Set transform value."""
self._node.transform = value
# ----------- NAME -----------
@property
def name(self):
"""Get the name value."""
return self._name
# ----------- VISIBLE_OBJ -----------
@property
def visible_obj(self):
"""Get the visible_obj value."""
return self._node.visible
@visible_obj.setter
def visible_obj(self, value):
"""Set visible_obj value."""
assert isinstance(value, bool)
self._node.visible = value