def __init__(self, session, parent=None):
super(SpectraWindow, self).__init__(session, parent)
self.sub_window = SpectraMdiSubWindow()
self.sub_window.setWindowFlags(QtCore.Qt.FramelessWindowHint)
self.setCentralWidget(self.sub_window)
self.current_layer_item = None
self.model = DataTreeModel()
# Define main options widget as a tabbed widget
self.wgt_options = QtGui.QToolBox()
# Get the model editor dock widget and remove header
self.model_editor_dock = ModelDockWidget()
self.model_editor_dock.setTitleBarWidget(QtGui.QWidget(None))
# Get equivalent width and measurement info docks, remove headers
self.equiv_width_dock = EquivalentWidthDockWidget()
self.equiv_width_dock.setTitleBarWidget(QtGui.QWidget(None))
self.measurement_dock = MeasurementDockWidget()
self.measurement_dock.setTitleBarWidget(QtGui.QWidget(None))
self.smoothing_dock = SmoothingDockWidget()
self.smoothing_dock.setTitleBarWidget(QtGui.QWidget(None))
# Add docks to the tabbed widget
self.wgt_options.addItem(self.model_editor_dock, 'Model Editor')
self.wgt_options.addItem(self.equiv_width_dock, 'Equivalent Width')
self.wgt_options.addItem(self.measurement_dock, 'Measurements')
self.wgt_options.addItem(self.smoothing_dock, 'Smoothing')
self.layer_dock = LayerDataTree()
self.layer_dock.setModel(self.model)
self.client = SpectraClient(data=self._data, model=self.model,
graph=self.sub_window.graph)
self.layer_dock.set_root_item(self.client._node_parent)
self._connect()
print("New spectra widget has been created.")
class SpectraWindow(DataViewer):
LABEL = "Spectra Plot"
def __init__(self, session, parent=None):
super(SpectraWindow, self).__init__(session, parent)
self.sub_window = SpectraMdiSubWindow()
self.sub_window.setWindowFlags(QtCore.Qt.FramelessWindowHint)
self.setCentralWidget(self.sub_window)
self.current_layer_item = None
self.model = DataTreeModel()
# Define main options widget as a tabbed widget
self.wgt_options = QtGui.QToolBox()
# Get the model editor dock widget and remove header
self.model_editor_dock = ModelDockWidget()
self.model_editor_dock.setTitleBarWidget(QtGui.QWidget(None))
# Get equivalent width and measurement info docks, remove headers
self.equiv_width_dock = EquivalentWidthDockWidget()
self.equiv_width_dock.setTitleBarWidget(QtGui.QWidget(None))
self.measurement_dock = MeasurementDockWidget()
self.measurement_dock.setTitleBarWidget(QtGui.QWidget(None))
self.smoothing_dock = SmoothingDockWidget()
self.smoothing_dock.setTitleBarWidget(QtGui.QWidget(None))
# Add docks to the tabbed widget
self.wgt_options.addItem(self.model_editor_dock, 'Model Editor')
self.wgt_options.addItem(self.equiv_width_dock, 'Equivalent Width')
self.wgt_options.addItem(self.measurement_dock, 'Measurements')
self.wgt_options.addItem(self.smoothing_dock, 'Smoothing')
self.layer_dock = LayerDataTree()
self.layer_dock.setModel(self.model)
self.client = SpectraClient(data=self._data, model=self.model,
graph=self.sub_window.graph)
self.layer_dock.set_root_item(self.client._node_parent)
self._connect()
print("New spectra widget has been created.")
def register_to_hub(self, hub):
super(SpectraWindow, self).register_to_hub(hub)
self.client.register_to_hub(hub)
def unregister(self, hub):
super(SpectraWindow, self).unregister(hub)
self.client.unregister(hub)
def add_data(self, data):
print("[Debug] Adding data.")
if 'cube' in [x.label for x in data.components]:
layer_data_item = self.client.add_data(data.data['cube'],
data.label)
self.current_layer_item = layer_data_item
# self.model_editor_dock.wgt_model_tree.set_root_item(layer_data_item)
return True
else:
layer_data_item = self.client.add_data(data.data['spec1d'],
"Spectrum 1D")
self.current_layer_item = layer_data_item
# self.model_editor_dock.wgt_model_tree.set_root_item(layer_data_item)
return True
return False
def set_data(self, data, layer_data_item=None):
if layer_data_item is None:
return self.client.add_data(data, "Hover spectrum")
layer_data_item.update_data(item=data)
self.sub_window.graph.update_item(layer_data_item)
def update_data(self, data):
print("Updating data")
pass
def add_subset(self, subset):
print("Adding subset")
return True
def layer_view(self):
return self.layer_dock
def options_widget(self):
return self.wgt_options
def _connect(self):
# Set model editor's model
self.model_editor_dock.wgt_model_tree.setModel(self.model)
# Set view model
self.layer_dock.setModel(self.model)
self.layer_dock.sig_current_changed.connect(
self.set_selected_item)
# Get the model selector combobox
model_selector = self.model_editor_dock.wgt_model_selector
# Connect the combobox signal to a lambda slot for generating fit
model_selector.activated.connect(lambda:
self.model.create_fit_model(
self.current_layer_item,
self.model_editor_dock,
str(model_selector.currentText())))
# Connect perform fit button
self.model_editor_dock.btn_perform_fit.clicked.connect(lambda:
self._perform_fit(self.layer_dock.current_item))
# Connect Read and Save model buttons
self.model_editor_dock.btn_read.clicked.connect(lambda:
self._read_model(self.layer_dock.current_item))
self.model_editor_dock.btn_save.clicked.connect(lambda:
self._save_model(self.layer_dock.current_item))
# Connect removing layers
self.model.sig_removed_item.connect(self.sub_window.graph.remove_item)
self.model.sig_removed_item.connect(self._reconfigureSpectralModel)
# Connect toggling layer visibility on graphs
self.model.sig_set_visibility.connect(
self.sub_window.graph.set_visibility)
# Connect toggling error display in plot
self.sub_window.plot_toolbar.atn_toggle_errs.triggered.connect(lambda:
self.sub_window.graph.set_error_visibility(
# self.layer_dock.current_item,
show=self.sub_window.plot_toolbar.atn_toggle_errs.isChecked()))
# Connect smoothing functionality
self.smoothing_dock.btn_perform.clicked.connect(lambda:
self._perform_smoothing(self.layer_dock.current_item))
# It's not enough that we remove an item. The internal structure
# of the spectral model may require further processing. For now,
# it just needs to report a new model expression in the GUI, but
# future enhancements may need more work in here.
def _reconfigureSpectralModel(self):
self.model.updateModelExpression(self.model_editor_dock, self.layer_dock.current_item)
def _read_model(self, layer):
# any pre-existing compound model must be deleted before adding
# new spectral components. Although it would be nice to be able
# to add new components defined in a file to the existing compound
# model, that operation cannot be done if the existing compound
# model resulted from a previous fitting operation. The following
# example can be used to verify this at the command-line level:
#
# % python
# Python 2.7.10 |Continuum Analytics, Inc.| (default, May 28 2015, 17:04:42)
# [GCC 4.2.1 (Apple Inc. build 5577)] on darwin
# Type "help", "copyright", "credits" or "license" for more information.
# Anaconda is brought to you by Continuum Analytics.
# Please check out: http://continuum.io/thanks and https://binstar.org
# >>> from astropy.modeling import models, fitting
# >>> import numpy as np
# >>> fitter = fitting.LevMarLSQFitter()
# >>> g1 = models.Gaussian1D(1.,1.,1.)
# >>> g2 = models.Gaussian1D(2.,2.,2.)
# >>> initial_model = g1 + g2
# >>> initial_model
# <CompoundModel0(amplitude_0=1.0, mean_0=1.0, stddev_0=1.0, amplitude_1=2.0, mean_1=2.0, stddev_1=2.0)>
# >>> x = np.array([1.,2.,3.,4.,5.,6.,7.])
# >>> y = np.array([0.1,0.2,0.35,0.43,0.56,0.61,0.69])
# >>> fit_result = fitter(initial_model, x, y)
# >>> fit_result
# <CompoundModel0(amplitude_0=-0.738532388970048, mean_0=-1.7107256329301135, stddev_0=4.13731791035706, amplitude_1=0.8553623423732329, mean_1=23.06935094019223, stddev_1=33.944748624197345)>
# >>> g3 = models.Gaussian1D(3.,3.,3.)
# >>> modified_result = fit_result + g3
# >>> modified_result
# <CompoundModel2(amplitude_0=1.0, mean_0=1.0, stddev_0=1.0, amplitude_1=2.0, mean_1=2.0, stddev_1=2.0, amplitude_2=3.0, mean_2=3.0, stddev_2=3.0)>
# >>>
#
# Note the problem here: adding a new component to the compound model created
# by the fitter erases the fitted values and returns them to whatever values
# they have in the initial model.
length = len(layer._model_items)
for model_item in layer._model_items:
layer.remove_model(model_item)
# for an unknown reason, the loop above won't exhaust the layer._model_items list.
# One element is left behind in the list and has to be forcibly removed. Why????
if len(layer._model_items) > 0:
model_item = layer._model_items[0]
layer.remove_model(model_item)
layer.removeRows(0, length)
# Now we can read from file.
global _model_directory # retains memory of last visited directory
fname = QtGui.QFileDialog.getOpenFileName(self, 'Open file', _model_directory)
# note that under glue, QFileDialog.getOpenFileName returns a tuple.
# Under plain PyQt it returns a simple QString. It is like it's
# overriding getOpenFileNameAndFilter, but why?? So, under glue we
# need to get the first element in the tuple.
compound_model, _model_directory = model_io.buildModelFromFile(fname[0])
self._model_items = model_registry.getComponents(compound_model)
for model_item in self._model_items:
model_name = model_registry.get_component_name(model_item)
model_data_item = ModelDataTreeItem(layer, model_item, model_name)
layer.add_model_item(model_data_item)
# model_data_item.setIcon(QtGui.QIcon(path.join(PATH, 'model_item.png')))
layer.appendRow(model_data_item)
# It's not clear that signals must be emitted at this point.
# self.sig_added_item.emit(model_data_item.index())
# self.sig_added_fit_model.emit(model_data_item)
layer.setCompoundModel(compound_model)
self.model.updateModelExpression(self.model_editor_dock, layer)
def _save_model(self, layer):
global _model_directory # retains memory of last visited directory
model_io.saveModelToFile(self, layer.model, _model_directory)
def _perform_fit(self, layer_data_item):
mask = self.sub_window.graph.get_roi_mask(layer_data_item)
fit_spec_data = model_fitting.fit_model(
layer_data_item,
fitter_name=str(
self.model_editor_dock.wgt_fit_selector.currentText()),
roi_mask=mask)
new_spec_data_item = self.model.create_spec_data_item(fit_spec_data)
# Display
self.client.add_layer(new_spec_data_item,
filter_mask=mask,
name="Model Fit ({}: {})".format(
layer_data_item.parent.text(),
layer_data_item.text()))
def _perform_smoothing(self, layer_data_item):
name, kwargs = self.smoothing_dock.get_kwargs()
new_spec_data = spectral_smoothing(
layer_data_item.item, method=name, kwargs=kwargs)
new_spec_data_item = self.model.create_spec_data_item(new_spec_data)
self.client.add_layer(new_spec_data_item,
name="Smoothed " + layer_data_item.text())
def display_graph(self, data_item, sub_window=None, set_active=True,
style='line'):
if not isinstance(data_item, LayerDataTreeItem):
layer_data_item = self.model.create_layer_item(data_item)
self.sub_window.graph.add_item(layer_data_item, style=style)
@QtCore.Slot(QtCore.QModelIndex)
def set_selected_item(self, index):
layer_data_item = self.model.itemFromIndex(index)
print("Setting new root item {}".format(layer_data_item))
self.model_editor_dock.wgt_model_tree.set_root_item(layer_data_item)
self.current_layer_item = layer_data_item
if type(layer_data_item.model) == type([]):
compound_model = self.model.buildSummedCompoundModel(layer_data_item.model)
else:
compound_model = layer_data_item.model
if self.model_editor_dock:
if hasattr(compound_model, '_format_expression'):
self.model_editor_dock.expression_field.setText(compound_model._format_expression())
else:
self.model_editor_dock.expression_field.setText('')
class SpectraWindow(DataViewer):
LABEL = "Spectra Plot"
def __init__(self, session, parent=None):
super(SpectraWindow, self).__init__(session, parent)
self.sub_window = SpectraMdiSubWindow()
self.sub_window.setWindowFlags(QtCore.Qt.FramelessWindowHint)
self.setCentralWidget(self.sub_window)
self.current_layer_item = None
self.model = DataTreeModel()
# Define main options widget as a tabbed widget
self.wgt_options = QtGui.QToolBox()
# Get the model editor dock widget and remove header
self.model_editor_dock = ModelDockWidget()
self.model_editor_dock.setTitleBarWidget(QtGui.QWidget(None))
# Get equivalent width and measurement info docks, remove headers
self.equiv_width_dock = EquivalentWidthDockWidget()
self.equiv_width_dock.setTitleBarWidget(QtGui.QWidget(None))
self.measurement_dock = MeasurementDockWidget()
self.measurement_dock.setTitleBarWidget(QtGui.QWidget(None))
self.smoothing_dock = SmoothingDockWidget()
self.smoothing_dock.setTitleBarWidget(QtGui.QWidget(None))
# Add docks to the tabbed widget
self.wgt_options.addItem(self.model_editor_dock, 'Model Editor')
self.wgt_options.addItem(self.equiv_width_dock, 'Equivalent Width')
self.wgt_options.addItem(self.measurement_dock, 'Measurements')
self.wgt_options.addItem(self.smoothing_dock, 'Smoothing')
self.layer_dock = LayerDataTree()
self.layer_dock.setModel(self.model)
self.client = SpectraClient(data=self._data, model=self.model,
graph=self.sub_window.graph)
self.layer_dock.set_root_item(self.client._node_parent)
self._connect()
print("New spectra widget has been created.")
def register_to_hub(self, hub):
super(SpectraWindow, self).register_to_hub(hub)
self.client.register_to_hub(hub)
def unregister(self, hub):
super(SpectraWindow, self).unregister(hub)
self.client.unregister(hub)
def add_data(self, data):
print("[Debug] Adding data.")
if 'cube' in [x.label for x in data.components]:
layer_data_item = self.client.add_data(data.data['cube'],
data.label)
self.current_layer_item = layer_data_item
self.model_editor_dock.wgt_model_tree.set_root_item(layer_data_item)
return True
return False
def set_data(self, data, layer_data_item=None):
if layer_data_item is None:
return self.client.add_data(data, "Hover spectrum")
layer_data_item.update_data(item=data)
self.sub_window.graph.update_item(layer_data_item)
def update_data(self, data):
print("Updating data")
pass
def add_subset(self, subset):
print("Adding subset")
return True
def layer_view(self):
return self.layer_dock
def options_widget(self):
return self.wgt_options
def _connect(self):
# Set model editor's model
self.model_editor_dock.wgt_model_tree.setModel(self.model)
# Set view model
self.layer_dock.setModel(self.model)
self.layer_dock.sig_current_changed.connect(
self.set_selected_item)
# Get the model selector combobox
model_selector = self.model_editor_dock.wgt_model_selector
# Connect the combobox signal to a lambda slot for generating fit
model_selector.activated.connect(lambda:
self.model.create_fit_model(
self.current_layer_item,
str(model_selector.currentText())))
# Connect perform fit button
self.model_editor_dock.btn_perform_fit.clicked.connect(lambda:
self._perform_fit(self.layer_dock.current_item))
# Connect removing layers
self.model.sig_removed_item.connect(self.sub_window.graph.remove_item)
# Connect toggling layer visibility on graphs
self.model.sig_set_visibility.connect(
self.sub_window.graph.set_visibility)
# Connect toggling error display in plot
self.sub_window.plot_toolbar.atn_toggle_errs.triggered.connect(lambda:
self.sub_window.graph.set_all_errors_visibility(
# self.layer_dock.current_item,
self.sub_window.plot_toolbar.atn_toggle_errs.isChecked()))
# Connect smoothing functionality
self.smoothing_dock.btn_perform.clicked.connect(lambda:
self._perform_smoothing(self.layer_dock.current_item))
def _perform_fit(self, layer_data_item):
mask = self.sub_window.graph.get_roi_mask(layer_data_item)
fit_spec_data = model_fitting.fit_model(
layer_data_item,
fitter_name=str(
self.model_editor_dock.wgt_fit_selector.currentText()),
roi_mask=mask)
new_spec_data_item = self.model.create_spec_data_item(fit_spec_data)
# Display
self.client.add_layer(new_spec_data_item,
filter_mask=mask,
name="Model Fit ({}: {})".format(
layer_data_item.parent.text(),
layer_data_item.text()))
def _perform_smoothing(self, layer_data_item):
name, kwargs = self.smoothing_dock.get_kwargs()
new_spec_data = spectral_smoothing(
layer_data_item.item, method=name, kwargs=kwargs)
new_spec_data_item = self.model.create_spec_data_item(new_spec_data)
self.client.add_layer(new_spec_data_item,
name="Smoothed " + layer_data_item.text())
def display_graph(self, data_item, sub_window=None, set_active=True,
style='line'):
if not isinstance(data_item, LayerDataTreeItem):
layer_data_item = self.model.create_layer_item(data_item)
self.sub_window.graph.add_item(layer_data_item, style=style,
set_active=False)
@QtCore.Slot(QtCore.QModelIndex)
def set_selected_item(self, index):
layer_data_item = self.model.itemFromIndex(index)
print("Setting new root item {}".format(layer_data_item))
self.model_editor_dock.wgt_model_tree.set_root_item(layer_data_item)
self.current_layer_item = layer_data_item