class StraditizerWidgets(QWidget, DockMixin):
"""A widget that contains widgets to control the straditization in a GUI
This widget is the basis of the straditize GUI and implemented as a
plugin into the psyplot gui. The open straditizers are handled in the
:attr:`_straditizer` attribute.
The central parts of this widget are
- The combobox to manage the open straditizers
- The QTreeWidget in the :attr:`tree` attribute that contains all the
controls to interface the straditizer
- the tutorial area
- the :guilabel:`Apply` and :guilabel:`Cancel` button"""
#: Boolean that is True if all dialogs should be answered with `Yes`
always_yes = False
#: The QTreeWidget that contains the different widgets for the digitization
tree = None
#: The apply button
apply_button = None
#: The cancel button
cancel_button = None
#: The button to edit the straditizer attributes
attrs_button = None
#: The button to start a tutorial
tutorial_button = None
#: An :class:`InfoButton` to display the docs
info_button = None
#: A QComboBox to select the current straditizer
stradi_combo = None
#: A button to open a new straditizer
btn_open_stradi = None
#: A button to close the current straditizer
btn_close_stradi = None
#: A button to reload the last autosaved state
btn_reload_autosaved = None
#: The :class:`straditize.widgets.progress_widget.ProgressWidget` to
#: display the progress of the straditization
progress_widget = None
#: The :class:`straditize.widgets.data.DigitizingControl` to interface
#: the :straditize.straditizer.Straditizer.data_reader`
digitizer = None
#: The :class:`straditize.widgets.colnames.ColumnNamesManager` to interface
#: the :straditize.straditizer.Straditizer.colnames_reader`
colnames_manager = None
#: The :class:`straditize.widgets.axes_translations.AxesTranslations` to
#: handle the y- and x-axis conversions
axes_translations = None
#: The :class:`straditize.widgets.image_correction.ImageRescaler` class to
#: rescale the image
image_rescaler = None
#: The :class:`straditize.widgets.image_correction.ImageRotator` class to
#: rotate the image
image_rotator = None
#: The :class:`straditize.widgets.plots.PlotControl` to display additional
#: information on the diagram
plot_control = None
#: The :class:`straditize.widgets.marker_control.MarkerControl` to modify
#: the appearance of the :class:`~straditize.straditizer.Straditizer.marks`
#: of the current straditizer
marker_control = None
#: The :class:`straditize.widgets.selection_toolbar.SelectionToolbar` to
#: select features in the stratigraphic diagram
selection_toolbar = None
#: The :class:`straditize.straditizer.Straditizer` instance
straditizer = None
#: open straditizers
_straditizers = []
#: The :class:`straditize.widgets.tutorial.Tutorial` class
tutorial = None
dock_position = Qt.LeftDockWidgetArea
#: Auto-saved straditizers
autosaved = []
hidden = True
title = 'Stratigraphic diagram digitization'
window_layout_action = None
open_external = QtCore.pyqtSignal(list)
def __init__(self, *args, **kwargs):
from straditize.widgets.menu_actions import StraditizerMenuActions
from straditize.widgets.progress_widget import ProgressWidget
from straditize.widgets.data import DigitizingControl
from straditize.widgets.selection_toolbar import SelectionToolbar
from straditize.widgets.marker_control import MarkerControl
from straditize.widgets.plots import PlotControl
from straditize.widgets.axes_translations import AxesTranslations
from straditize.widgets.image_correction import (ImageRotator,
ImageRescaler)
from straditize.widgets.colnames import ColumnNamesManager
self._straditizers = []
super(StraditizerWidgets, self).__init__(*args, **kwargs)
self.tree = QTreeWidget(parent=self)
self.tree.setSelectionMode(QTreeWidget.NoSelection)
self.refresh_button = QToolButton(self)
self.refresh_button.setIcon(QIcon(get_psy_icon('refresh.png')))
self.refresh_button.setToolTip('Refresh from the straditizer')
self.apply_button = EnableButton('Apply', parent=self)
self.cancel_button = EnableButton('Cancel', parent=self)
self.attrs_button = QPushButton('Attributes', parent=self)
self.tutorial_button = QPushButton('Tutorial', parent=self)
self.tutorial_button.setCheckable(True)
self.error_msg = PyErrorMessage(self)
self.stradi_combo = QComboBox()
self.btn_open_stradi = QToolButton()
self.btn_open_stradi.setIcon(QIcon(get_psy_icon('run_arrow.png')))
self.btn_close_stradi = QToolButton()
self.btn_close_stradi.setIcon(QIcon(get_psy_icon('invalid.png')))
self.btn_reload_autosaved = QPushButton("Reload")
self.btn_reload_autosaved.setToolTip(
"Close the straditizer and reload the last autosaved project")
# ---------------------------------------------------------------------
# --------------------------- Tree widgets ----------------------------
# ---------------------------------------------------------------------
self.tree.setHeaderLabels(['', ''])
self.tree.setColumnCount(2)
self.progress_item = QTreeWidgetItem(0)
self.progress_item.setText(0, 'ToDo list')
self.progress_widget = ProgressWidget(self, self.progress_item)
self.menu_actions_item = QTreeWidgetItem(0)
self.menu_actions_item.setText(0, 'Images import/export')
self.tree.addTopLevelItem(self.menu_actions_item)
self.menu_actions = StraditizerMenuActions(self)
self.digitizer_item = item = QTreeWidgetItem(0)
item.setText(0, 'Digitization control')
self.digitizer = DigitizingControl(self, item)
self.col_names_item = item = QTreeWidgetItem(0)
item.setText(0, 'Column names')
self.colnames_manager = ColumnNamesManager(self, item)
self.add_info_button(item, 'column_names.rst')
self.axes_translations_item = item = QTreeWidgetItem(0)
item.setText(0, 'Axes translations')
self.axes_translations = AxesTranslations(self, item)
self.image_transform_item = item = QTreeWidgetItem(0)
item.setText(0, 'Transform source image')
self.image_rescaler = ImageRescaler(self, item)
self.image_rotator_item = item = QTreeWidgetItem(0)
item.setText(0, 'Rotate image')
self.image_rotator = ImageRotator(self)
self.image_transform_item.addChild(item)
self.image_rotator.setup_children(item)
self.plot_control_item = item = QTreeWidgetItem(0)
item.setText(0, 'Plot control')
self.plot_control = PlotControl(self, item)
self.add_info_button(item, 'plot_control.rst')
self.marker_control_item = item = QTreeWidgetItem(0)
item.setText(0, 'Marker control')
self.marker_control = MarkerControl(self, item)
self.add_info_button(item, 'marker_control.rst')
# ---------------------------------------------------------------------
# ----------------------------- Toolbars ------------------------------
# ---------------------------------------------------------------------
self.selection_toolbar = SelectionToolbar(self, 'Selection toolbar')
# ---------------------------------------------------------------------
# ----------------------------- InfoButton ----------------------------
# ---------------------------------------------------------------------
self.info_button = InfoButton(self, get_doc_file('straditize.rst'))
# ---------------------------------------------------------------------
# --------------------------- Layouts ---------------------------------
# ---------------------------------------------------------------------
stradi_box = QHBoxLayout()
stradi_box.addWidget(self.stradi_combo, 1)
stradi_box.addWidget(self.btn_open_stradi)
stradi_box.addWidget(self.btn_close_stradi)
attrs_box = QHBoxLayout()
attrs_box.addWidget(self.attrs_button)
attrs_box.addStretch(0)
attrs_box.addWidget(self.tutorial_button)
btn_box = QHBoxLayout()
btn_box.addWidget(self.refresh_button)
btn_box.addWidget(self.info_button)
btn_box.addStretch(0)
btn_box.addWidget(self.apply_button)
btn_box.addWidget(self.cancel_button)
reload_box = QHBoxLayout()
reload_box.addWidget(self.btn_reload_autosaved)
reload_box.addStretch(0)
vbox = QVBoxLayout()
vbox.addLayout(stradi_box)
vbox.addWidget(self.tree)
vbox.addLayout(attrs_box)
vbox.addLayout(btn_box)
vbox.addLayout(reload_box)
self.setLayout(vbox)
self.apply_button.setEnabled(False)
self.cancel_button.setEnabled(False)
self.tree.expandItem(self.progress_item)
self.tree.expandItem(self.digitizer_item)
# ---------------------------------------------------------------------
# --------------------------- Connections -----------------------------
# ---------------------------------------------------------------------
self.stradi_combo.currentIndexChanged.connect(self.set_current_stradi)
self.refresh_button.clicked.connect(self.refresh)
self.attrs_button.clicked.connect(self.edit_attrs)
self.tutorial_button.clicked.connect(self.start_tutorial)
self.open_external.connect(self._create_straditizer_from_args)
self.btn_open_stradi.clicked.connect(
self.menu_actions.open_straditizer)
self.btn_close_stradi.clicked.connect(self.close_straditizer)
self.btn_reload_autosaved.clicked.connect(self.reload_autosaved)
self.refresh()
header = self.tree.header()
header.setStretchLastSection(False)
header.setSectionResizeMode(0, QHeaderView.Stretch)
def disable_apply_button(self):
"""Method that is called when the :attr:`cancel_button` is clicked"""
for w in [self.apply_button, self.cancel_button]:
try:
w.clicked.disconnect()
except TypeError:
pass
w.setEnabled(False)
self.apply_button.setText('Apply')
self.cancel_button.setText('Cancel')
self.refresh_button.setEnabled(True)
def switch_to_straditizer_layout(self):
"""Switch to the straditizer layout
This method makes this widget visible and stacks it with the psyplot
content widget"""
mainwindow = self.dock.parent()
mainwindow.figures_tree.hide_plugin()
mainwindow.ds_tree.hide_plugin()
mainwindow.fmt_widget.hide_plugin()
self.show_plugin()
mainwindow.tabifyDockWidget(mainwindow.project_content.dock, self.dock)
hsize = self.marker_control.sizeHint().width() + 50
self.menu_actions.setup_shortcuts(mainwindow)
if with_qt5:
mainwindow.resizeDocks([self.dock], [hsize], Qt.Horizontal)
self.tree.resizeColumnToContents(0)
self.tree.resizeColumnToContents(1)
self.info_button.click()
def to_dock(self, main, *args, **kwargs):
ret = super(StraditizerWidgets, self).to_dock(main, *args, **kwargs)
if self.menu_actions.window_layout_action is None:
main.window_layouts_menu.addAction(self.window_layout_action)
main.callbacks['straditize'] = self.open_external.emit
main.addToolBar(self.selection_toolbar)
self.dock.toggleViewAction().triggered.connect(
self.show_or_hide_toolbar)
self.menu_actions.setup_menu_actions(main)
self.menu_actions.setup_children(self.menu_actions_item)
try:
main.open_file_options['Straditize project'] = \
self.create_straditizer_from_args
except AttributeError: # psyplot-gui <= 1.1.0
pass
return ret
def show_or_hide_toolbar(self):
"""Show or hide the toolbar depending on the visibility of this widget
"""
self.selection_toolbar.setVisible(self.is_shown)
def _create_straditizer_from_args(self, args):
"""A method that is called when the :attr:`psyplot_gui.main.mainwindow`
receives a 'straditize' callback"""
self.create_straditizer_from_args(*args)
def create_straditizer_from_args(self,
fnames,
project=None,
xlim=None,
ylim=None,
full=False,
reader_type='area'):
"""Create a straditizer from the given file name
This method is called when the :attr:`psyplot_gui.main.mainwindow`
receives a 'straditize' callback"""
fname = fnames[0]
if fname is not None:
self.menu_actions.open_straditizer(fname)
stradi = self.straditizer
if stradi is None:
return
if xlim is not None:
stradi.data_xlim = xlim
if ylim is not None:
stradi.data_ylim = ylim
if xlim is not None or ylim is not None or full:
if stradi.data_xlim is None:
stradi.data_xlim = [0, np.shape(stradi.image)[1]]
if stradi.data_ylim is None:
stradi.data_ylim = [0, np.shape(stradi.image)[0]]
stradi.init_reader(reader_type)
stradi.data_reader.digitize()
self.refresh()
if not self.is_shown:
self.switch_to_straditizer_layout()
return fname is not None
def start_tutorial(self, state, tutorial_cls=None):
"""Start or stop the tutorial
Parameters
----------
state: bool
If False, the tutorial is stopped. Otherwise it is started
tutorial_cls: straditize.widgets.tutorial.beginner.Tutorial
The tutorial class to use. If None, it will be asked in a
QInputDialog"""
if self.tutorial is not None or not state:
self.tutorial.close()
self.tutorial_button.setText('Tutorial')
elif state:
if tutorial_cls is None:
tutorial_cls, ok = QInputDialog.getItem(
self,
'Start tutorial',
"Select the tutorial type",
["Beginner", "Advanced (Hoya del Castillo)"],
editable=False)
if not ok:
self.tutorial_button.blockSignals(True)
self.tutorial_button.setChecked(False)
self.tutorial_button.blockSignals(False)
return
if tutorial_cls == 'Beginner':
from straditize.widgets.tutorial import Tutorial
else:
from straditize.widgets.tutorial import (
HoyaDelCastilloTutorial as Tutorial)
else:
Tutorial = tutorial_cls
self.tutorial = Tutorial(self)
self.tutorial_button.setText('Stop tutorial')
def edit_attrs(self):
"""Edit the attributes of the current straditizer
This creates a new dataframe editor to edit the
:attr:`straditize.straditizer.Straditizer.attrs` meta informations"""
def add_attr(key):
model = editor.table.model()
n = len(attrs)
model.insertRow(n)
model.setData(model.index(n, 0), key)
model.setData(model.index(n, 1), '', change_type=six.text_type)
from psyplot_gui.main import mainwindow
from straditize.straditizer import common_attributes
attrs = self.straditizer.attrs
editor = mainwindow.new_data_frame_editor(attrs,
'Straditizer attributes')
editor.table.resizeColumnToContents(1)
editor.table.horizontalHeader().setVisible(False)
editor.table.frozen_table_view.horizontalHeader().setVisible(False)
combo = QComboBox()
combo.addItems([''] + common_attributes)
combo.currentTextChanged.connect(add_attr)
hbox = QHBoxLayout()
hbox.addWidget(QLabel('Common attributes:'))
hbox.addWidget(combo)
hbox.addStretch(0)
editor.layout().insertLayout(1, hbox)
return editor, combo
def refresh(self):
"""Refresh from the straditizer"""
for i, stradi in enumerate(self._straditizers):
self.stradi_combo.setItemText(
i,
self.get_attr(stradi, 'project_file')
or self.get_attr(stradi, 'image_file') or '')
# toggle visibility of close button and attributes button
enable = self.straditizer is not None
self.btn_close_stradi.setVisible(enable)
self.attrs_button.setEnabled(enable)
# refresh controls
self.menu_actions.refresh()
self.progress_widget.refresh()
self.digitizer.refresh()
self.selection_toolbar.refresh()
self.plot_control.refresh()
self.marker_control.refresh()
self.axes_translations.refresh()
if self.tutorial is not None:
self.tutorial.refresh()
self.image_rotator.refresh()
self.image_rescaler.refresh()
self.colnames_manager.refresh()
self.btn_reload_autosaved.setEnabled(bool(self.autosaved))
def get_attr(self, stradi, attr):
try:
return stradi.get_attr(attr)
except KeyError:
pass
docstrings.delete_params('InfoButton.parameters', 'parent')
@docstrings.get_sectionsf('StraditizerWidgets.add_info_button')
@docstrings.with_indent(8)
def add_info_button(self,
child,
fname=None,
rst=None,
name=None,
connections=[]):
"""Add an infobutton to the :attr:`tree` widget
Parameters
----------
child: QTreeWidgetItem
The item to which to add the infobutton
%(InfoButton.parameters.no_parent)s
connections: list of QPushButtons
Buttons that should be clicked when the info button is clicked"""
button = InfoButton(self, fname=fname, rst=rst, name=name)
self.tree.setItemWidget(child, 1, button)
for btn in connections:
btn.clicked.connect(button.click)
return button
def raise_figures(self):
"""Raise the figures of the current straditizer in the GUI"""
from psyplot_gui.main import mainwindow
if mainwindow.figures and self.straditizer:
dock = self.straditizer.ax.figure.canvas.manager.window
dock.widget().show_plugin()
dock.raise_()
if self.straditizer.magni is not None:
dock = self.straditizer.magni.ax.figure.canvas.manager.window
dock.widget().show_plugin()
dock.raise_()
def set_current_stradi(self, i):
"""Set the i-th straditizer to the current one"""
if not self._straditizers:
return
self.straditizer = self._straditizers[i]
self.menu_actions.set_stradi_in_console()
block = self.stradi_combo.blockSignals(True)
self.stradi_combo.setCurrentIndex(i)
self.stradi_combo.blockSignals(block)
self.raise_figures()
self.refresh()
self.autosaved.clear()
def _close_stradi(self, stradi):
"""Close the given straditizer and all it's figures"""
is_current = stradi is self.straditizer
if is_current:
self.selection_toolbar.disconnect()
stradi.close()
try:
i = self._straditizers.index(stradi)
except ValueError:
pass
else:
del self._straditizers[i]
self.stradi_combo.removeItem(i)
if is_current and self._straditizers:
self.stradi_combo.setCurrentIndex(0)
elif not self._straditizers:
self.straditizer = None
self.refresh()
self.digitizer.digitize_item.takeChildren()
self.digitizer.btn_digitize.setChecked(False)
self.digitizer.btn_digitize.setCheckable(False)
self.digitizer.toggle_txt_tolerance('')
def close_straditizer(self):
"""Close the current straditizer"""
self._close_stradi(self.straditizer)
def close_all_straditizers(self):
"""Close all straditizers"""
self.selection_toolbar.disconnect()
for stradi in self._straditizers:
stradi.close()
self._straditizers.clear()
self.straditizer = None
self.stradi_combo.clear()
self.digitizer.digitize_item.takeChildren()
self.digitizer.btn_digitize.setChecked(False)
self.digitizer.btn_digitize.setCheckable(False)
self.digitizer.toggle_txt_tolerance('')
self.refresh()
def add_straditizer(self, stradi):
"""Add a straditizer to the list of open straditizers"""
if stradi and stradi not in self._straditizers:
self._straditizers.append(stradi)
self.stradi_combo.addItem(' ')
self.set_current_stradi(len(self._straditizers) - 1)
def reset_control(self):
"""Reset the GUI of straditize"""
if getattr(self.selection_toolbar, '_pattern_selection', None):
self.selection_toolbar._pattern_selection.remove_plugin()
del self.selection_toolbar._pattern_selection
if getattr(self.digitizer, '_samples_editor', None):
self.digitizer._close_samples_fig()
tb = self.selection_toolbar
tb.set_label_wand_mode()
tb.set_rect_select_mode()
tb.new_select_action.setChecked(True)
tb.select_action.setChecked(False)
tb.wand_action.setChecked(False)
self.disable_apply_button()
self.close_all_straditizers()
self.colnames_manager.reset_control()
def autosave(self):
"""Autosave the current straditizer"""
self.autosaved = [self.straditizer.to_dataset().copy(True)] + \
self.autosaved[:4]
def reload_autosaved(self):
"""Reload the autosaved straditizer and close the old one"""
from straditize.straditizer import Straditizer
if not self.autosaved:
return
answer = QMessageBox.question(
self, 'Reload autosave',
'Shall I reload the last autosaved stage? This will close the '
'current figures.')
if answer == QMessageBox.Yes:
self.close_straditizer()
stradi = Straditizer.from_dataset(self.autosaved.pop(0))
self.menu_actions.finish_loading(stradi)
def __init__(self, parent, fmto, artist=None, base=None):
"""
Parameters
----------
%(FontWeightWidget.parameters)s
"""
QWidget.__init__(self, parent)
hbox = QHBoxLayout()
if artist is not None:
self.current_font = self.artist_to_qfont(artist)
self.current_color = QtGui.QColor.fromRgbF(
*mcol.to_rgba(artist.get_color()))
else:
self.current_color = QtGui.QColor(Qt.black)
self.fmto_name = fmto.name or fmto.key
# choose font button
button = QPushButton('Choose font')
button.clicked.connect(partial(self.choose_font, None))
hbox.addWidget(button)
# font size spin box
self.spin_box = spin_box = QSpinBox(self)
spin_box.setRange(1, 1e9)
if artist is not None:
spin_box.setValue(int(artist.get_size()))
spin_box.valueChanged.connect(self.modify_size)
hbox.addWidget(spin_box)
# font color button
self.btn_font_color = button = QToolButton(self)
button.setIcon(QIcon(get_icon('font_color.png')))
button.clicked.connect(partial(self.choose_color, None))
hbox.addWidget(button)
# bold button
self.btn_bold = button = QToolButton(self)
button.setIcon(QIcon(get_icon('bold.png')))
button.clicked.connect(self.toggle_bold)
button.setCheckable(True)
if artist is not None:
button.setChecked(self.current_font.weight() > 50)
hbox.addWidget(button)
# italic button
self.btn_italic = button = QToolButton(self)
button.setIcon(QIcon(get_icon('italic.png')))
button.clicked.connect(self.toggle_italic)
button.setCheckable(True)
if artist is not None:
button.setChecked(self.current_font.italic())
hbox.addWidget(button)
if base is not None:
# add a button to change to the base formatoption
fmtos = [
base,
getattr(fmto.plotter, base.key + 'size', None),
getattr(fmto.plotter, base.key + 'weight', None),
]
fmtos = list(filter(None, fmtos))
hbox.addWidget(Switch2FmtButton(parent, *fmtos))
self.setLayout(hbox)
class PatternSelectionWidget(QWidget, DockMixin):
"""A wdiget to select patterns in the image
This widget consist of an :class:`EmbededMplCanvas` to display the template
for the pattern and uses the :func:`skimage.feature.match_template`
function to identify it in the :attr:`arr`
See Also
--------
straditize.widget.selection_toolbar.SelectionToolbar.start_pattern_selection
"""
#: The template to look for in the :attr:`arr`
template = None
#: The selector to select the template in the original image
selector = None
#: The extents of the :attr:`template` in the original image
template_extents = None
#: The matplotlib artist of the :attr:`template` in the
#: :attr:`template_fig`
template_im = None
#: The :class:`EmbededMplCanvas` to display the :attr:`template`
template_fig = None
axes = None
#: A QSlider to set the threshold for the template correlation
sl_thresh = None
_corr_plot = None
key_press_cid = None
def __init__(self, arr, data_obj, remove_selection=False, *args, **kwargs):
"""
Parameters
----------
arr: np.ndarray of shape ``(Ny, Nx)``
The labeled selection array
data_obj: straditize.label_selection.LabelSelection
The data object whose image shall be selected
remove_selection: bool
If True, remove the selection on apply
"""
super(PatternSelectionWidget, self).__init__(*args, **kwargs)
self.arr = arr
self.data_obj = data_obj
self.remove_selection = remove_selection
self.template = None
# the figure to show the template
self.template_fig = EmbededMplCanvas()
# the button to select the template
self.btn_select_template = QPushButton('Select a template')
self.btn_select_template.setCheckable(True)
# the checkbox to allow fractions of the template
self.fraction_box = QGroupBox('Template fractions')
self.fraction_box.setCheckable(True)
self.fraction_box.setChecked(False)
self.fraction_box.setEnabled(False)
self.sl_fraction = QSlider(Qt.Horizontal)
self.lbl_fraction = QLabel('0.75')
self.sl_fraction.setValue(75)
# the slider to select the increments of the fractions
self.sl_increments = QSlider(Qt.Horizontal)
self.sl_increments.setValue(3)
self.sl_increments.setMinimum(1)
self.lbl_increments = QLabel('3')
# the button to perform the correlation
self.btn_correlate = QPushButton('Find template')
self.btn_correlate.setEnabled(False)
# the button to plot the correlation
self.btn_plot_corr = QPushButton('Plot correlation')
self.btn_plot_corr.setCheckable(True)
self.btn_plot_corr.setEnabled(False)
# slider for subselection
self.btn_select = QPushButton('Select pattern')
self.sl_thresh = QSlider(Qt.Horizontal)
self.lbl_thresh = QLabel('0.5')
self.btn_select.setCheckable(True)
self.btn_select.setEnabled(False)
self.sl_thresh.setValue(75)
self.sl_thresh.setVisible(False)
self.lbl_thresh.setVisible(False)
# cancel and close button
self.btn_cancel = QPushButton('Cancel')
self.btn_close = QPushButton('Apply')
self.btn_close.setEnabled(False)
vbox = QVBoxLayout()
vbox.addWidget(self.template_fig)
hbox = QHBoxLayout()
hbox.addStretch(0)
hbox.addWidget(self.btn_select_template)
vbox.addLayout(hbox)
fraction_layout = QGridLayout()
fraction_layout.addWidget(QLabel('Fraction'), 0, 0)
fraction_layout.addWidget(self.sl_fraction, 0, 1)
fraction_layout.addWidget(self.lbl_fraction, 0, 2)
fraction_layout.addWidget(QLabel('Increments'), 1, 0)
fraction_layout.addWidget(self.sl_increments, 1, 1)
fraction_layout.addWidget(self.lbl_increments, 1, 2)
self.fraction_box.setLayout(fraction_layout)
vbox.addWidget(self.fraction_box)
vbox.addWidget(self.btn_correlate)
vbox.addWidget(self.btn_plot_corr)
vbox.addWidget(self.btn_select)
thresh_box = QHBoxLayout()
thresh_box.addWidget(self.sl_thresh)
thresh_box.addWidget(self.lbl_thresh)
vbox.addLayout(thresh_box)
hbox = QHBoxLayout()
hbox.addWidget(self.btn_cancel)
hbox.addWidget(self.btn_close)
vbox.addLayout(hbox)
self.setLayout(vbox)
self.btn_select_template.clicked.connect(
self.toggle_template_selection)
self.sl_fraction.valueChanged.connect(
lambda i: self.lbl_fraction.setText(str(i / 100.)))
self.sl_increments.valueChanged.connect(
lambda i: self.lbl_increments.setText(str(i)))
self.btn_correlate.clicked.connect(self.start_correlation)
self.btn_plot_corr.clicked.connect(self.toggle_correlation_plot)
self.sl_thresh.valueChanged.connect(
lambda i: self.lbl_thresh.setText(str((i - 50) / 50.)))
self.sl_thresh.valueChanged.connect(self.modify_selection)
self.btn_select.clicked.connect(self.toggle_selection)
self.btn_cancel.clicked.connect(self.cancel)
self.btn_close.clicked.connect(self.close)
def toggle_template_selection(self):
"""Enable or disable the template selection"""
if (not self.btn_select_template.isChecked()
and self.selector is not None):
self.selector.set_active(False)
for a in self.selector.artists:
a.set_visible(False)
self.btn_select_template.setText('Select a template')
elif self.selector is not None and self.template_im is not None:
self.selector.set_active(True)
for a in self.selector.artists:
a.set_visible(True)
self.btn_select_template.setText('Apply')
else:
self.selector = RectangleSelector(self.data_obj.ax,
self.update_image,
interactive=True)
if self.template_extents is not None:
self.selector.draw_shape(self.template_extents)
self.key_press_cid = self.data_obj.ax.figure.canvas.mpl_connect(
'key_press_event', self.update_image)
self.btn_select_template.setText('Cancel')
self.data_obj.draw_figure()
if self.template is not None:
self.fraction_box.setEnabled(True)
self.sl_increments.setMaximum(min(self.template.shape[:2]))
self.btn_correlate.setEnabled(True)
def update_image(self, *args, **kwargs):
"""Update the template image based on the :attr:`selector` extents"""
if self.template_im is not None:
self.template_im.remove()
del self.template_im
elif self.axes is None:
self.axes = self.template_fig.figure.add_subplot(111)
self.template_fig.figure.subplots_adjust(bottom=0.3)
if not self.selector.artists[0].get_visible():
self.template_extents = None
self.template = None
self.btn_select_template.setText('Cancel')
else:
self.template_extents = np.round(self.selector.extents).astype(int)
x, y = self.template_extents.reshape((2, 2))
if getattr(self.data_obj, 'extent', None) is not None:
extent = self.data_obj.extent
x -= int(min(extent[:2]))
y -= int(min(extent[2:]))
slx = slice(*sorted(x))
sly = slice(*sorted(y))
self.template = template = self.arr[sly, slx]
if template.ndim == 3:
self.template_im = self.axes.imshow(template)
else:
self.template_im = self.axes.imshow(template, cmap='binary')
self.btn_select_template.setText('Apply')
self.template_fig.draw()
def start_correlation(self):
"""Look for the correlations of template and source"""
if self.fraction_box.isChecked():
self._fraction = self.sl_fraction.value() / 100.
increments = self.sl_increments.value()
else:
self._fraction = 0
increments = 1
corr = self.correlate_template(self.arr, self.template, self._fraction,
increments)
if corr is not None:
self._correlation = corr
enable = self._correlation is not None
self.btn_plot_corr.setEnabled(enable)
self.btn_select.setEnabled(enable)
def toggle_selection(self):
"""Modifiy the selection (or not) based on the template correlation"""
obj = self.data_obj
if self.btn_select.isChecked():
self._orig_selection_arr = obj._selection_arr.copy()
self._selected_labels = obj.selected_labels
self._select_cmap = obj._select_cmap
self._select_norm = obj._select_norm
self.btn_select.setText('Reset')
self.btn_close.setEnabled(True)
obj.unselect_all_labels()
self.sl_thresh.setVisible(True)
self.lbl_thresh.setVisible(True)
self.modify_selection(self.sl_thresh.value())
else:
if obj._selection_arr is not None:
obj._selection_arr[:] = self._orig_selection_arr
obj._select_img.set_array(self._orig_selection_arr)
obj.select_labels(self._selected_labels)
obj._update_magni_img()
del self._orig_selection_arr, self._selected_labels
self.btn_select.setText('Select pattern')
self.btn_close.setEnabled(False)
self.sl_thresh.setVisible(False)
self.lbl_thresh.setVisible(False)
obj.draw_figure()
def modify_selection(self, i):
"""Modify the selection based on the correlation threshold
Parameters
----------
i: int
An integer between 0 and 100, the value of the :attr:`sl_thresh`
slider"""
if not self.btn_select.isChecked():
return
obj = self.data_obj
val = (i - 50.) / 50.
# select the values above 50
if not self.remove_selection:
# clear the selection
obj._selection_arr[:] = obj._orig_selection_arr.copy()
select_val = obj._selection_arr.max() + 1
obj._selection_arr[self._correlation >= val] = select_val
else:
obj._selection_arr[:] = self._orig_selection_arr.copy()
obj._selection_arr[self._correlation >= val] = -1
obj._select_img.set_array(obj._selection_arr)
obj._update_magni_img()
obj.draw_figure()
def correlate_template(self,
arr,
template,
fraction=False,
increment=1,
report=True):
"""Correlate a template with the `arr`
This method uses the :func:`skimage.feature.match_template` function
to find the given `template` in the source array `arr`.
Parameters
----------
arr: np.ndarray of shape ``(Ny,Nx)``
The labeled selection array (see :attr:`arr`), the source of the
given `template`
template: np.ndarray of shape ``(nx, ny)``
The template from ``arr`` that shall be searched
fraction: float
If not null, we will look through the given fraction of the
template to look for partial matches as well
increment: int
The increment of the loop with the `fraction`.
report: bool
If True and `fraction` is not null, a QProgressDialog is opened
to inform the user about the progress"""
from skimage.feature import match_template
mask = self.data_obj.selected_part
x = mask.any(axis=0)
if not x.any():
raise ValueError("No data selected!")
y = mask.any(axis=1)
xmin = x.argmax()
xmax = len(x) - x[::-1].argmax()
ymin = y.argmax()
ymax = len(y) - y[::-1].argmax()
if arr.ndim == 3:
mask = np.tile(mask[..., np.newaxis], (1, 1, arr.shape[-1]))
src = np.where(mask[ymin:ymax, xmin:xmax], arr[ymin:ymax, xmin:xmax],
0)
sny, snx = src.shape
if not fraction:
corr = match_template(src, template)
full_shape = np.array(corr.shape)
else: # loop through the template to allow partial hatches
shp = np.array(template.shape, dtype=int)[:2]
ny, nx = shp
fshp = np.round(fraction * shp).astype(int)
fny, fnx = fshp
it = list(
product(range(0, fny, increment), range(0, fnx, increment)))
ntot = len(it)
full_shape = fshp - shp + src.shape
corr = np.zeros(full_shape, dtype=float)
if report:
txt = 'Searching template...'
dialog = QProgressDialog(txt, 'Cancel', 0, ntot)
dialog.setWindowModality(Qt.WindowModal)
t0 = dt.datetime.now()
for k, (i, j) in enumerate(it):
if report:
dialog.setValue(k)
if k and not k % 10:
passed = (dt.datetime.now() - t0).total_seconds()
dialog.setLabelText(txt + ' %1.0f seconds remaning' %
((passed * (ntot / k - 1.))))
if report and dialog.wasCanceled():
return
else:
y_end, x_start = fshp - (i, j) - 1
sly = slice(y_end, full_shape[0])
slx = slice(0, -x_start or full_shape[1])
corr[sly, slx] = np.maximum(
corr[sly, slx],
match_template(src, template[:-i or ny, j:]))
ret = np.zeros_like(arr, dtype=corr.dtype)
dny, dnx = src.shape - full_shape
for i, j in product(range(dny + 1), range(dnx + 1)):
ret[ymin + i:ymax - dny + i, xmin + j:xmax - dnx + j] = np.maximum(
ret[ymin + i:ymax - dny + i, xmin + j:xmax - dnx + j], corr)
return np.where(mask, ret, 0)
def toggle_correlation_plot(self):
"""Toggle the correlation plot between :attr:`template` and :attr:`arr`
"""
obj = self.data_obj
if self._corr_plot is None:
self._corr_plot = obj.ax.imshow(
self._correlation,
extent=obj._select_img.get_extent(),
zorder=obj._select_img.zorder + 0.1)
self._corr_cbar = obj.ax.figure.colorbar(self._corr_plot,
orientation='vertical')
self._corr_cbar.set_label('Correlation')
else:
for a in [self._corr_cbar, self._corr_plot]:
try:
a.remove()
except ValueError:
pass
del self._corr_plot, self._corr_cbar
obj.draw_figure()
def to_dock(self,
main,
title=None,
position=None,
docktype='df',
*args,
**kwargs):
if position is None:
position = main.dockWidgetArea(main.help_explorer.dock)
connect = self.dock is None
ret = super(PatternSelectionWidget, self).to_dock(main,
title,
position,
docktype=docktype,
*args,
**kwargs)
if connect:
self.dock.toggleViewAction().triggered.connect(self.maybe_tabify)
return ret
def maybe_tabify(self):
main = self.dock.parent()
if self.is_shown and main.dockWidgetArea(
main.help_explorer.dock) == main.dockWidgetArea(self.dock):
main.tabifyDockWidget(main.help_explorer.dock, self.dock)
def cancel(self):
if self.btn_select.isChecked():
self.btn_select.setChecked(False)
self.toggle_selection()
self.close()
def close(self):
from psyplot_gui.main import mainwindow
if self.selector is not None:
self.selector.disconnect_events()
for a in self.selector.artists:
try:
a.remove()
except ValueError:
pass
self.data_obj.draw_figure()
del self.selector
if self._corr_plot is not None:
self.toggle_correlation_plot()
if self.key_press_cid is not None:
self.data_obj.ax.figure.canvas.mpl_disconnect(self.key_press_cid)
for attr in ['data_obj', 'arr', 'template', 'key_press_cid']:
try:
delattr(self, attr)
except AttributeError:
pass
mainwindow.removeDockWidget(self.dock)
return super(PatternSelectionWidget, self).close()