def enable(self):
self.nav_mode = NavigateMouseMode(self.viewer,
press_callback=self._on_nav_activate)
self.rng_mode = RangeMouseMode(self.viewer)
self.nav_mode.state.add_callback('x', self._on_slider_change)
self.ui.tabs.setCurrentIndex(0)
self.ui.tabs.currentChanged.connect(self._on_tab_change)
self.ui.button_settings.clicked.connect(self._on_settings)
self.ui.button_fit.clicked.connect(self._on_fit)
self.ui.button_clear.clicked.connect(self._on_clear)
self.ui.button_collapse.clicked.connect(self._on_collapse)
font = QtGui.QFont("Courier")
font.setStyleHint(font.Monospace)
self.ui.text_log.document().setDefaultFont(font)
self.ui.text_log.setLineWrapMode(self.ui.text_log.NoWrap)
self.axes = self.viewer.axes
self.canvas = self.axes.figure.canvas
self._fit_artists = []
ProfileTools.fit_function.set_choices(self, list(fit_plugin))
ProfileTools.fit_function.set_display_func(self,
lambda fitter: fitter.label)
connect_combo_selection(self, 'fit_function',
self.ui.combosel_fit_function)
ProfileTools.collapse_function.set_choices(self, list(COLLAPSE_FUNCS))
ProfileTools.collapse_function.set_display_func(
self, COLLAPSE_FUNCS.get)
connect_combo_selection(self, 'collapse_function',
self.ui.combosel_collapse_function)
self._toolbar_connected = False
self.viewer.toolbar_added.connect(self._on_toolbar_added)
self.viewer.state.add_callback('x_att', self._on_x_att_change)
def enable(self):
self.nav_mode = NavigateMouseMode(self.viewer,
press_callback=self._on_nav_activate)
self.rng_mode = RangeMouseMode(self.viewer)
self.nav_mode.state.add_callback('x', self._on_slider_change)
self.ui.tabs.setCurrentIndex(0)
self.ui.tabs.currentChanged.connect(self._on_tab_change)
self.ui.button_settings.clicked.connect(self._on_settings)
self.ui.button_fit.clicked.connect(self._on_fit)
self.ui.button_clear.clicked.connect(self._on_clear)
self.ui.button_collapse.clicked.connect(self._on_collapse)
font = QtGui.QFont("Courier")
font.setStyleHint(font.Monospace)
self.ui.text_log.document().setDefaultFont(font)
self.ui.text_log.setLineWrapMode(self.ui.text_log.NoWrap)
self.axes = self.viewer.axes
self.canvas = self.axes.figure.canvas
self._fit_artists = []
ProfileTools.fit_function.set_choices(self, list(fit_plugin))
ProfileTools.fit_function.set_display_func(self, lambda fitter: fitter.label)
connect_combo_selection(self, 'fit_function', self.ui.combosel_fit_function)
ProfileTools.collapse_function.set_choices(self, list(COLLAPSE_FUNCS))
ProfileTools.collapse_function.set_display_func(self, COLLAPSE_FUNCS.get)
connect_combo_selection(self, 'collapse_function', self.ui.combosel_collapse_function)
self._toolbar_connected = False
self.viewer.toolbar_added.connect(self._on_toolbar_added)
self.viewer.state.add_callback('x_att', self._on_x_att_change)
class ProfileTools(QtWidgets.QWidget):
fit_function = SelectionCallbackProperty()
collapse_function = SelectionCallbackProperty()
def __init__(self, parent=None):
super(ProfileTools, self).__init__(parent=parent)
self._viewer = weakref.ref(parent)
self.ui = load_ui('profile_tools.ui', self,
directory=os.path.dirname(__file__))
fix_tab_widget_fontsize(self.ui.tabs)
self.image_viewer = None
@property
def viewer(self):
return self._viewer()
def show(self, *args):
super(ProfileTools, self).show(*args)
self._on_tab_change()
def hide(self, *args):
super(ProfileTools, self).hide(*args)
self.rng_mode.deactivate()
self.nav_mode.deactivate()
def enable(self):
self.nav_mode = NavigateMouseMode(self.viewer,
press_callback=self._on_nav_activate)
self.rng_mode = RangeMouseMode(self.viewer)
self.nav_mode.state.add_callback('x', self._on_slider_change)
self.ui.tabs.setCurrentIndex(0)
self.ui.tabs.currentChanged.connect(self._on_tab_change)
self.ui.button_settings.clicked.connect(self._on_settings)
self.ui.button_fit.clicked.connect(self._on_fit)
self.ui.button_clear.clicked.connect(self._on_clear)
self.ui.button_collapse.clicked.connect(self._on_collapse)
font = QtGui.QFont("Courier")
font.setStyleHint(font.Monospace)
self.ui.text_log.document().setDefaultFont(font)
self.ui.text_log.setLineWrapMode(self.ui.text_log.NoWrap)
self.axes = self.viewer.axes
self.canvas = self.axes.figure.canvas
self._fit_artists = []
ProfileTools.fit_function.set_choices(self, list(fit_plugin))
ProfileTools.fit_function.set_display_func(self, lambda fitter: fitter.label)
self._connection_fit = connect_combo_selection(self, 'fit_function', self.ui.combosel_fit_function)
ProfileTools.collapse_function.set_choices(self, list(COLLAPSE_FUNCS))
ProfileTools.collapse_function.set_display_func(self, COLLAPSE_FUNCS.get)
self._connection_collapse = connect_combo_selection(self, 'collapse_function', self.ui.combosel_collapse_function)
self._toolbar_connected = False
self.viewer.toolbar_added.connect(self._on_toolbar_added)
self.viewer.state.add_callback('x_att', self._on_x_att_change)
def _on_x_att_change(self, *event):
self.nav_mode.clear()
self.rng_mode.clear()
def _on_nav_activate(self, *args):
self._nav_data = self._visible_data()
self._nav_viewers = {}
for data in self._nav_data:
pix_cid = is_convertible_to_single_pixel_cid(data, self.viewer.state.x_att_pixel)
self._nav_viewers[data] = self._viewers_with_data_slice(data, pix_cid)
def _on_slider_change(self, *args):
x = self.nav_mode.state.x
if x is None:
return
for data in self._nav_data:
axis, slc = self._get_axis_and_pixel_slice(data, x)
for viewer in self._nav_viewers[data]:
slices = list(viewer.state.slices)
slices[axis] = slc
viewer.state.slices = tuple(slices)
def _get_axis_and_pixel_slice(self, data, x):
if self.viewer.state.x_att in data.pixel_component_ids:
axis = self.viewer.state.x_att.axis
slc = int(round(x))
else:
pix_cid = is_convertible_to_single_pixel_cid(data, self.viewer.state.x_att_pixel)
axis = pix_cid.axis
axis_view = [0] * data.ndim
axis_view[pix_cid.axis] = slice(None)
axis_values = data[self.viewer.state.x_att, axis_view]
slc = int(np.argmin(np.abs(axis_values - x)))
return axis, slc
def _on_settings(self):
d = FitSettingsWidget(self.fit_function())
d.exec_()
def _on_fit(self):
"""
Fit a model to the data
The fitting happens on a dedicated thread, to keep the UI
responsive
"""
if self.rng_mode.state.x_min is None or self.rng_mode.state.x_max is None:
return
x_range = self.rng_mode.state.x_range
fitter = self.fit_function()
def on_success(result):
fit_results, x, y = result
report = ""
normalize = {}
for layer_artist in fit_results:
report += ("<b><font color='{0}'>{1}</font>"
"</b>".format(color2hex(layer_artist.state.color),
layer_artist.layer.label))
report += "<pre>" + fitter.summarize(fit_results[layer_artist], x, y) + "</pre>"
if self.viewer.state.normalize:
normalize[layer_artist] = layer_artist.state.normalize_values
self._report_fit(report)
self._plot_fit(fitter, fit_results, x, y, normalize)
def on_fail(exc_info):
exc = '\n'.join(traceback.format_exception(*exc_info))
self._report_fit("Error during fitting:\n%s" % exc)
def on_done():
self.ui.button_fit.setText("Fit")
self.ui.button_fit.setEnabled(True)
self.canvas.draw_idle()
self.ui.button_fit.setText("Running...")
self.ui.button_fit.setEnabled(False)
w = Worker(self._fit, fitter, xlim=x_range)
w.result.connect(on_success)
w.error.connect(on_fail)
w.finished.connect(on_done)
self._fit_worker = w # hold onto a reference
w.start()
def wait_for_fit(self):
self._fit_worker.wait()
def _report_fit(self, report):
self.ui.text_log.document().setHtml(report)
def _on_clear(self):
self.ui.text_log.document().setPlainText('')
self._clear_fit()
self.canvas.draw_idle()
def _fit(self, fitter, xlim=None):
# We cycle through all the visible layers and get the plotted data
# for each one of them.
results = {}
for layer in self.viewer.layers:
if layer.enabled and layer.visible:
x, y = layer.state.profile
x = np.asarray(x)
y = np.asarray(y)
keep = (x >= min(xlim)) & (x <= max(xlim))
if len(x) > 0:
results[layer] = fitter.build_and_fit(x[keep], y[keep])
return results, x, y
def _clear_fit(self):
for artist in self._fit_artists[:]:
artist.remove()
self._fit_artists.remove(artist)
def _plot_fit(self, fitter, fit_result, x, y, normalize):
self._clear_fit()
for layer in fit_result:
# y_model = fitter.predict(fit_result[layer], x)
self._fit_artists.append(fitter.plot(fit_result[layer], self.axes, x,
alpha=layer.state.alpha,
linewidth=layer.state.linewidth * 0.5,
color=layer.state.color,
normalize=normalize.get(layer, None))[0])
self.canvas.draw_idle()
def _visible_data(self):
datasets = set()
for layer_artist in self.viewer.layers:
if layer_artist.enabled and layer_artist.visible:
if isinstance(layer_artist.state.layer, BaseData):
datasets.add(layer_artist.state.layer)
elif isinstance(layer_artist.state.layer, Subset):
datasets.add(layer_artist.state.layer.data)
return list(datasets)
def _viewers_with_data_slice(self, data, xatt):
if self.viewer.session.application is None:
return []
viewers = []
for tab in self.viewer.session.application.viewers:
for viewer in tab:
if isinstance(viewer, ImageViewer):
for layer_artist in viewer._layer_artist_container[data]:
if layer_artist.enabled and layer_artist.visible:
if len(viewer.state.slices) >= xatt.axis:
viewers.append(viewer)
return viewers
def _on_collapse(self):
if self.rng_mode.state.x_min is None or self.rng_mode.state.x_max is None:
return
func = self.collapse_function
x_range = self.rng_mode.state.x_range
for data in self._visible_data():
pix_cid = is_convertible_to_single_pixel_cid(data, self.viewer.state.x_att_pixel)
for viewer in self._viewers_with_data_slice(data, pix_cid):
slices = list(viewer.state.slices)
# TODO: don't need to fetch axis twice
axis, imin = self._get_axis_and_pixel_slice(data, x_range[0])
axis, imax = self._get_axis_and_pixel_slice(data, x_range[1])
current_slice = slices[axis]
if isinstance(current_slice, AggregateSlice):
current_slice = current_slice.center
imin, imax = min(imin, imax), max(imin, imax)
slices[axis] = AggregateSlice(slice(imin, imax),
current_slice,
func)
viewer.state.slices = tuple(slices)
@property
def mode(self):
return MODES[self.tabs.currentIndex()]
def _on_toolbar_added(self, *event):
self.viewer.toolbar.tool_activated.connect(self._on_toolbar_activate)
self.viewer.toolbar.tool_deactivated.connect(self._on_tab_change)
def _on_toolbar_activate(self, *event):
self.rng_mode.deactivate()
self.nav_mode.deactivate()
def _on_tab_change(self, *event):
mode = self.mode
if mode == 'navigate':
self.rng_mode.deactivate()
self.nav_mode.activate()
else:
self.rng_mode.activate()
self.nav_mode.deactivate()
class ProfileTools(QtWidgets.QWidget):
fit_function = SelectionCallbackProperty()
collapse_function = SelectionCallbackProperty()
def __init__(self, parent=None):
super(ProfileTools, self).__init__(parent=parent)
self.ui = load_ui('profile_tools.ui', self,
directory=os.path.dirname(__file__))
fix_tab_widget_fontsize(self.ui.tabs)
self._viewer = weakref.ref(parent)
self.image_viewer = None
@property
def viewer(self):
return self._viewer()
def show(self, *args):
super(ProfileTools, self).show(*args)
self._on_tab_change()
def hide(self, *args):
super(ProfileTools, self).hide(*args)
self.rng_mode.deactivate()
self.nav_mode.deactivate()
def enable(self):
self.nav_mode = NavigateMouseMode(self.viewer,
press_callback=self._on_nav_activate)
self.rng_mode = RangeMouseMode(self.viewer)
self.nav_mode.state.add_callback('x', self._on_slider_change)
self.ui.tabs.setCurrentIndex(0)
self.ui.tabs.currentChanged.connect(self._on_tab_change)
self.ui.button_settings.clicked.connect(self._on_settings)
self.ui.button_fit.clicked.connect(self._on_fit)
self.ui.button_clear.clicked.connect(self._on_clear)
self.ui.button_collapse.clicked.connect(self._on_collapse)
font = QtGui.QFont("Courier")
font.setStyleHint(font.Monospace)
self.ui.text_log.document().setDefaultFont(font)
self.ui.text_log.setLineWrapMode(self.ui.text_log.NoWrap)
self.axes = self.viewer.axes
self.canvas = self.axes.figure.canvas
self._fit_artists = []
ProfileTools.fit_function.set_choices(self, list(fit_plugin))
ProfileTools.fit_function.set_display_func(self, lambda fitter: fitter.label)
connect_combo_selection(self, 'fit_function', self.ui.combosel_fit_function)
ProfileTools.collapse_function.set_choices(self, list(COLLAPSE_FUNCS))
ProfileTools.collapse_function.set_display_func(self, COLLAPSE_FUNCS.get)
connect_combo_selection(self, 'collapse_function', self.ui.combosel_collapse_function)
self._toolbar_connected = False
self.viewer.toolbar_added.connect(self._on_toolbar_added)
self.viewer.state.add_callback('x_att', self._on_x_att_change)
def _on_x_att_change(self, *event):
self.nav_mode.clear()
self.rng_mode.clear()
def _on_nav_activate(self, *args):
self._nav_data = self._visible_data()
self._nav_viewers = {}
for data in self._nav_data:
pix_cid = is_convertible_to_single_pixel_cid(data, self.viewer.state.x_att)
self._nav_viewers[data] = self._viewers_with_data_slice(data, pix_cid)
def _on_slider_change(self, *args):
x = self.nav_mode.state.x
if x is None:
return
for data in self._nav_data:
axis, slc = self._get_axis_and_pixel_slice(data, x)
for viewer in self._nav_viewers[data]:
slices = list(viewer.state.slices)
slices[axis] = slc
viewer.state.slices = tuple(slices)
def _get_axis_and_pixel_slice(self, data, x):
if self.viewer.state.x_att in data.pixel_component_ids:
axis = self.viewer.state.x_att.axis
slc = int(round(x))
else:
pix_cid = is_convertible_to_single_pixel_cid(data, self.viewer.state.x_att)
axis = pix_cid.axis
axis_view = [0] * data.ndim
axis_view[pix_cid.axis] = slice(None)
axis_values = data[self.viewer.state.x_att, axis_view]
slc = int(np.argmin(np.abs(axis_values - x)))
return axis, slc
def _on_settings(self):
d = FitSettingsWidget(self.fit_function())
d.exec_()
def _on_fit(self):
"""
Fit a model to the data
The fitting happens on a dedicated thread, to keep the UI
responsive
"""
if self.rng_mode.state.x_min is None or self.rng_mode.state.x_max is None:
return
x_range = self.rng_mode.state.x_range
fitter = self.fit_function()
def on_success(result):
fit_results, x, y = result
report = ""
normalize = {}
for layer_artist in fit_results:
report += ("<b><font color='{0}'>{1}</font>"
"</b>".format(color2hex(layer_artist.state.color),
layer_artist.layer.label))
report += "<pre>" + fitter.summarize(fit_results[layer_artist], x, y) + "</pre>"
if self.viewer.state.normalize:
normalize[layer_artist] = layer_artist.state.normalize_values
self._report_fit(report)
self._plot_fit(fitter, fit_results, x, y, normalize)
def on_fail(exc_info):
exc = '\n'.join(traceback.format_exception(*exc_info))
self._report_fit("Error during fitting:\n%s" % exc)
def on_done():
self.ui.button_fit.setText("Fit")
self.ui.button_fit.setEnabled(True)
self.canvas.draw()
self.ui.button_fit.setText("Running...")
self.ui.button_fit.setEnabled(False)
w = Worker(self._fit, fitter, xlim=x_range)
w.result.connect(on_success)
w.error.connect(on_fail)
w.finished.connect(on_done)
self._fit_worker = w # hold onto a reference
w.start()
def wait_for_fit(self):
self._fit_worker.wait()
def _report_fit(self, report):
self.ui.text_log.document().setHtml(report)
def _on_clear(self):
self.ui.text_log.document().setPlainText('')
self._clear_fit()
self.canvas.draw()
def _fit(self, fitter, xlim=None):
# We cycle through all the visible layers and get the plotted data
# for each one of them.
results = {}
for layer in self.viewer.layers:
if layer.enabled and layer.visible:
x, y = layer.state.profile
x = np.asarray(x)
y = np.asarray(y)
keep = (x >= min(xlim)) & (x <= max(xlim))
if len(x) > 0:
results[layer] = fitter.build_and_fit(x[keep], y[keep])
return results, x, y
def _clear_fit(self):
for artist in self._fit_artists[:]:
artist.remove()
self._fit_artists.remove(artist)
def _plot_fit(self, fitter, fit_result, x, y, normalize):
self._clear_fit()
for layer in fit_result:
# y_model = fitter.predict(fit_result[layer], x)
self._fit_artists.append(fitter.plot(fit_result[layer], self.axes, x,
alpha=layer.state.alpha,
linewidth=layer.state.linewidth * 0.5,
color=layer.state.color,
normalize=normalize.get(layer, None))[0])
self.canvas.draw()
def _visible_data(self):
datasets = set()
for layer_artist in self.viewer.layers:
if layer_artist.enabled and layer_artist.visible:
if isinstance(layer_artist.state.layer, BaseData):
datasets.add(layer_artist.state.layer)
elif isinstance(layer_artist.state.layer, Subset):
datasets.add(layer_artist.state.layer.data)
return list(datasets)
def _viewers_with_data_slice(self, data, xatt):
if self.viewer.session.application is None:
return []
viewers = []
for tab in self.viewer.session.application.viewers:
for viewer in tab:
if isinstance(viewer, ImageViewer):
for layer_artist in viewer._layer_artist_container[data]:
if layer_artist.enabled and layer_artist.visible:
if len(viewer.state.slices) >= xatt.axis:
viewers.append(viewer)
return viewers
def _on_collapse(self):
if self.rng_mode.state.x_min is None or self.rng_mode.state.x_max is None:
return
func = self.collapse_function
x_range = self.rng_mode.state.x_range
for data in self._visible_data():
pix_cid = is_convertible_to_single_pixel_cid(data, self.viewer.state.x_att)
for viewer in self._viewers_with_data_slice(data, pix_cid):
slices = list(viewer.state.slices)
# TODO: don't need to fetch axis twice
axis, imin = self._get_axis_and_pixel_slice(data, x_range[0])
axis, imax = self._get_axis_and_pixel_slice(data, x_range[1])
current_slice = slices[axis]
if isinstance(current_slice, AggregateSlice):
current_slice = current_slice.center
slices[axis] = AggregateSlice(slice(imin, imax),
current_slice,
func)
viewer.state.slices = tuple(slices)
@property
def mode(self):
return MODES[self.tabs.currentIndex()]
def _on_toolbar_added(self, *event):
self.viewer.toolbar.tool_activated.connect(self._on_toolbar_activate)
self.viewer.toolbar.tool_deactivated.connect(self._on_tab_change)
def _on_toolbar_activate(self, *event):
self.rng_mode.deactivate()
self.nav_mode.deactivate()
def _on_tab_change(self, *event):
mode = self.mode
if mode == 'navigate':
self.rng_mode.deactivate()
self.nav_mode.activate()
else:
self.rng_mode.activate()
self.nav_mode.deactivate()
