class DataFrameEditor(DockMixin, QWidget):
"""An editor for data frames"""
dock_cls = DataFrameDock
#: A signal that is emitted, if the table is cleared
cleared = QtCore.pyqtSignal()
#: A signal that is emitted when a cell has been changed. The argument
#: is a tuple of two integers and one float:
#: the row index, the column index and the new value
cell_edited = QtCore.pyqtSignal(int, int, object, object)
#: A signal that is emitted, if rows have been inserted into the dataframe.
#: The first value is the integer of the (original) position of the row,
#: the second one is the number of rows
rows_inserted = QtCore.pyqtSignal(int, int)
@property
def hidden(self):
return not self.table.filled
def __init__(self, *args, **kwargs):
super(DataFrameEditor, self).__init__(*args, **kwargs)
self.error_msg = PyErrorMessage(self)
# Label for displaying the DataFrame size
self.lbl_size = QLabel()
# A Checkbox for enabling and disabling the editability of the index
self.cb_index_editable = QCheckBox('Index editable')
# A checkbox for enabling and disabling the change of data types
self.cb_dtypes_changeable = QCheckBox('Datatypes changeable')
# A checkbox for enabling and disabling sorting
self.cb_enable_sort = QCheckBox('Enable sorting')
# A button to open a dataframe from the file
self.btn_open_df = QToolButton(parent=self)
self.btn_open_df.setIcon(QIcon(get_icon('run_arrow.png')))
self.btn_open_df.setToolTip('Open a DataFrame from your disk')
self.btn_from_console = LoadFromConsoleButton(pd.DataFrame)
self.btn_from_console.setToolTip('Show a DataFrame from the console')
# The table to display the DataFrame
self.table = DataFrameView(pd.DataFrame(), self)
# format line edit
self.format_editor = QLineEdit()
self.format_editor.setText(self.table.model()._format)
# format update button
self.btn_change_format = QPushButton('Update')
self.btn_change_format.setEnabled(False)
# table clearing button
self.btn_clear = QPushButton('Clear')
self.btn_clear.setToolTip(
'Clear the table and disconnect from the DataFrame')
# refresh button
self.btn_refresh = QToolButton()
self.btn_refresh.setIcon(QIcon(get_icon('refresh.png')))
self.btn_refresh.setToolTip('Refresh the table')
# close button
self.btn_close = QPushButton('Close')
self.btn_close.setToolTip('Close this widget permanentely')
# ---------------------------------------------------------------------
# ------------------------ layout --------------------------------
# ---------------------------------------------------------------------
vbox = QVBoxLayout()
self.top_hbox = hbox = QHBoxLayout()
hbox.addWidget(self.cb_index_editable)
hbox.addWidget(self.cb_dtypes_changeable)
hbox.addWidget(self.cb_enable_sort)
hbox.addWidget(self.lbl_size)
hbox.addStretch(0)
hbox.addWidget(self.btn_open_df)
hbox.addWidget(self.btn_from_console)
vbox.addLayout(hbox)
vbox.addWidget(self.table)
self.bottom_hbox = hbox = QHBoxLayout()
hbox.addWidget(self.format_editor)
hbox.addWidget(self.btn_change_format)
hbox.addStretch(0)
hbox.addWidget(self.btn_clear)
hbox.addWidget(self.btn_close)
hbox.addWidget(self.btn_refresh)
vbox.addLayout(hbox)
self.setLayout(vbox)
# ---------------------------------------------------------------------
# ------------------------ Connections --------------------------------
# ---------------------------------------------------------------------
self.cb_dtypes_changeable.stateChanged.connect(
self.set_dtypes_changeable)
self.cb_index_editable.stateChanged.connect(self.set_index_editable)
self.btn_from_console.object_loaded.connect(self._open_ds_from_console)
self.rows_inserted.connect(lambda i, n: self.set_lbl_size_text())
self.format_editor.textChanged.connect(self.toggle_fmt_button)
self.btn_change_format.clicked.connect(self.update_format)
self.btn_clear.clicked.connect(self.clear_table)
self.btn_close.clicked.connect(self.clear_table)
self.btn_close.clicked.connect(lambda: self.close())
self.btn_refresh.clicked.connect(self.table.reset_model)
self.btn_open_df.clicked.connect(self._open_dataframe)
self.table.set_index_action.triggered.connect(
self.update_index_editable)
self.table.append_index_action.triggered.connect(
self.update_index_editable)
self.cb_enable_sort.stateChanged.connect(
self.table.setSortingEnabled)
def update_index_editable(self):
model = self.table.model()
if len(model.df.index.names) > 1:
model.index_editable = False
self.cb_index_editable.setEnabled(False)
self.cb_index_editable.setChecked(model.index_editable)
def set_lbl_size_text(self, nrows=None, ncols=None):
"""Set the text of the :attr:`lbl_size` label to display the size"""
model = self.table.model()
nrows = nrows if nrows is not None else model.rowCount()
ncols = ncols if ncols is not None else model.columnCount()
if not nrows and not ncols:
self.lbl_size.setText('')
else:
self.lbl_size.setText('Rows: %i, Columns: %i' % (nrows, ncols))
def clear_table(self):
"""Clear the table and emit the :attr:`cleared` signal"""
df = pd.DataFrame()
self.set_df(df, show=False)
def _open_ds_from_console(self, oname, df):
self.set_df(df)
@docstrings.dedent
def set_df(self, df, *args, **kwargs):
"""
Fill the table from a :class:`~pandas.DataFrame`
Parameters
----------
%(DataFrameModel.parameters.no_parent)s
show: bool
If True (default), show and raise_ the editor
"""
show = kwargs.pop('show', True)
self.table.set_df(df, *args, **kwargs)
self.set_lbl_size_text(*df.shape)
model = self.table.model()
self.cb_dtypes_changeable.setChecked(model.dtypes_changeable)
if len(model.df.index.names) > 1:
model.index_editable = False
self.cb_index_editable.setEnabled(False)
else:
self.cb_index_editable.setEnabled(True)
self.cb_index_editable.setChecked(model.index_editable)
self.cleared.emit()
if show:
self.show_plugin()
self.dock.raise_()
def set_index_editable(self, state):
"""Set the :attr:`DataFrameModel.index_editable` attribute"""
self.table.model().index_editable = state == Qt.Checked
def set_dtypes_changeable(self, state):
"""Set the :attr:`DataFrameModel.dtypes_changeable` attribute"""
self.table.model().dtypes_changeable = state == Qt.Checked
def toggle_fmt_button(self, text):
try:
text % 1.1
except (TypeError, ValueError):
self.btn_change_format.setEnabled(False)
else:
self.btn_change_format.setEnabled(
text.strip() != self.table.model()._format)
def update_format(self):
"""Update the format of the table"""
self.table.model().set_format(self.format_editor.text().strip())
def to_dock(self, main, *args, **kwargs):
connect = self.dock is None
super(DataFrameEditor, self).to_dock(main, *args, **kwargs)
if connect:
self.dock.toggleViewAction().triggered.connect(self.maybe_tabify)
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 _open_dataframe(self):
self.open_dataframe()
def open_dataframe(self, fname=None, *args, **kwargs):
"""Opens a file dialog and the dataset that has been inserted"""
if fname is None:
fname = QFileDialog.getOpenFileName(
self, 'Open dataset', os.getcwd(),
'Comma separated files (*.csv);;'
'Excel files (*.xls *.xlsx);;'
'JSON files (*.json);;'
'All files (*)'
)
if with_qt5: # the filter is passed as well
fname = fname[0]
if isinstance(fname, pd.DataFrame):
self.set_df(fname)
elif not fname:
return
else:
ext = osp.splitext(fname)[1]
open_funcs = {
'.xls': pd.read_excel, '.xlsx': pd.read_excel,
'.json': pd.read_json,
'.tab': partial(pd.read_csv, delimiter='\t'),
'.dat': partial(pd.read_csv, delim_whitespace=True),
}
open_func = open_funcs.get(ext, pd.read_csv)
try:
df = open_func(fname)
except Exception:
self.error_msg.showTraceback(
'<b>Could not open DataFrame %s with %s</b>' % (
fname, open_func))
return
self.set_df(df)
def close(self, *args, **kwargs):
if self.dock is not None:
self.dock.close(*args, **kwargs) # removes the dock window
del self.dock
return super(DataFrameEditor, self).close(*args, **kwargs)
class StackedReader(DataReader, StraditizerControlBase):
"""A DataReader for stacked area plots
This reader only works within the straditizer GUI because the digitization
(see :meth:`digitize`) is interactive. The user has to manually distinguish
the stacked variables."""
#: The QTreeWidgetItem that holds the digitization widgets
digitize_child = None
#: A QPushButton to select the previous variable during the digitization
#: (see :meth:`decrease_current_col`)
btn_prev = None
#: A QPushButton to select the next variable during the digitization
#: (see :meth:`increase_current_col`)
btn_next = None
#: A QPushButton to select the features in the image for the current
#: variable (see :meth:`select_current_column`)
btn_edit = None
#: A QPushButton to add a new variable to the current ones
#: (see :meth:`select_and_add_current_column`)
btn_add = None
#: A QLabel to display the current column
lbl_col = None
strat_plot_identifier = 'stacked'
_current_col = 0
def digitize(self):
"""Digitize the data interactively
This method creates a new child item for the digitize button in the
straditizer control to manually distinguish the variables in the
stacked diagram."""
if getattr(self, 'straditizer_widgets', None) is None:
self.init_straditizercontrol(get_straditizer_widgets())
digitizer = self.straditizer_widgets.digitizer
digitizing = digitizer.btn_digitize.isChecked()
if digitizing and self.digitize_child is None:
raise ValueError("Apparently another digitization is in progress!")
elif not digitizing and self.digitize_child is None:
if len(self.columns) == 1 or self._current_col not in self.columns:
self._current_col = self.columns[0]
if len(self.columns) == 1:
super(StackedReader, self).digitize()
# start digitization
digitizer.btn_digitize.setCheckable(True)
digitizer.btn_digitize.setChecked(True)
self._init_digitize_child()
# Disable the changing of readers
digitizer.cb_readers.setEnabled(False)
digitizer.tree.expandItem(digitizer.digitize_item)
self.enable_or_disable_navigation_buttons()
self.reset_lbl_col()
elif not digitizing:
# stop digitization
digitizer.btn_digitize.setChecked(False)
digitizer.btn_digitize.setCheckable(False)
self._remove_digitze_child(digitizer)
digitizer.cb_readers.setEnabled(
digitizer.should_be_enabled(digitizer.cb_readers))
del self.straditizer_widgets
def _init_digitize_child(self):
self.lbl_col = QLabel('')
self.btn_prev = QPushButton('<')
self.btn_next = QPushButton('>')
self.btn_edit = QPushButton('Edit')
self.btn_add = QPushButton('+')
self.reset_lbl_col()
self.btn_box = w = QWidget()
vbox = QVBoxLayout()
vbox.addWidget(self.lbl_col)
hbox = QHBoxLayout()
hbox.addWidget(self.btn_prev)
hbox.addWidget(self.btn_next)
hbox.addWidget(self.btn_edit)
hbox.addWidget(self.btn_add)
vbox.addLayout(hbox)
w.setLayout(vbox)
self.digitize_child = QTreeWidgetItem(0)
self.straditizer_widgets.digitizer.digitize_item.addChild(
self.digitize_child)
self.straditizer_widgets.digitizer.tree.setItemWidget(
self.digitize_child, 0, w)
self.widgets2disable = [self.btn_prev, self.btn_next,
self.btn_edit, self.btn_add]
self.btn_next.clicked.connect(self.increase_current_col)
self.btn_prev.clicked.connect(self.decrease_current_col)
self.btn_edit.clicked.connect(self.select_current_column)
self.btn_add.clicked.connect(self.select_and_add_current_column)
def reset_lbl_col(self):
"""Reset the :attr:`lbl_col` to display the current column"""
self.lbl_col.setText('Part %i of %i' % (
self.columns.index(self._current_col) + 1, len(self.columns)))
def increase_current_col(self):
"""Take the next column as the current column"""
self._current_col = min(self.columns[-1], self._current_col + 1)
self.reset_lbl_col()
self.enable_or_disable_navigation_buttons()
def decrease_current_col(self):
"""Take the previous column as the current column"""
self._current_col = max(self.columns[0], self._current_col - 1)
self.reset_lbl_col()
self.enable_or_disable_navigation_buttons()
def _remove_digitze_child(self, digitizer):
digitizer.digitize_item.takeChild(
digitizer.digitize_item.indexOfChild(
self.digitize_child))
digitizer.btn_digitize.setChecked(False)
digitizer.btn_digitize.setCheckable(False)
for btn in self.widgets2disable:
btn.clicked.disconnect()
del (self.digitize_child, self.btn_prev, self.btn_next, self.btn_add,
self.btn_edit, self.lbl_col, self.btn_box)
self.widgets2disable.clear()
def enable_or_disable_navigation_buttons(self):
"""Enable or disable :attr:`btn_prev` and :attr:`btn_next`
Depending on the current column, we disable the navigation buttons
:attr:`btn_prev` and :attr:`btn_next`"""
disable_all = self.columns is None or len(self.columns) == 1
self.btn_prev.setEnabled(not disable_all and
self._current_col != self.columns[0])
self.btn_next.setEnabled(not disable_all and
self._current_col != self.columns[-1])
def select_and_add_current_column(self):
"""Select the features for a column and create it as a new one"""
return self._select_current_column(True)
def select_current_column(self):
"""Select the features of the current column"""
return self._select_current_column()
def _select_current_column(self, add_on_apply=False):
image = self.to_grey_pil(self.image).astype(int) + 1
start = self.start_of_current_col
end = start + self.full_df[self._current_col].values
all_end = start + self.full_df.loc[:, self._current_col:].values.sum(
axis=1)
x = np.meshgrid(*map(np.arange, image.shape[::-1]))[0]
image[(x < start[:, np.newaxis]) | (x > all_end[:, np.newaxis])] = 0
labels = skim.label(image, 8)
self.straditizer_widgets.selection_toolbar.data_obj = self
self.apply_button.clicked.connect(
self.add_col if add_on_apply else self.update_col)
self.apply_button.clicked.connect(self.update_plotted_full_df)
self.straditizer_widgets.selection_toolbar.start_selection(
labels, rgba=self.image_array(), remove_on_apply=False)
self.select_all_labels()
# set values outside the current column to 0
self._selection_arr[(x < start[:, np.newaxis]) |
(x >= end[:, np.newaxis])] = -1
self._select_img.set_array(self._selection_arr)
self.draw_figure()
@property
def start_of_current_col(self):
"""The first x-pixel of the current column"""
if self._current_col == self.columns[0]:
start = np.zeros(self.binary.shape[:1])
else:
idx = self.columns.index(self._current_col)
start = self.full_df.iloc[:, :idx].values.sum(axis=1)
start += self.column_starts[0]
return start
def update_plotted_full_df(self):
"""Update the plotted full_df if it is shown
See Also
--------
plot_full_df"""
pc = self.straditizer_widgets.plot_control.table
if pc.can_plot_full_df() and pc.get_full_df_lines():
pc.remove_full_df_plot()
pc.plot_full_df()
def update_col(self):
"""Update the current column based on the selection.
This method updates the end of the current column and adds or removes
the changes from the columns to the right."""
current = self._current_col
start = self.start_of_current_col
selected = self.selected_part
end = (self.binary.shape[1] - selected[:, ::-1].argmax(axis=1) -
start)
not_selected = ~selected.any()
end[not_selected] = 0
diff_end = self.parent._full_df.loc[:, current] - end
self.parent._full_df.loc[:, current] = end
if current != self.columns[-1]:
self.parent._full_df.loc[:, current + 1] += diff_end
def get_binary_for_col(self, col):
s, e = self.column_bounds[self.columns.index(col)]
if self.parent._full_df is None:
return self.binary[:, s:e]
else:
vals = self.full_df.loc[:, col].values
ret = np.zeros((self.binary.shape[0], int(vals.max())))
dist = np.tile(np.arange(ret.shape[1])[np.newaxis], (len(ret), 1))
ret[dist <= vals[:, np.newaxis]] = 1
return ret
def add_col(self):
"""Create a column out of the current selection"""
def increase_col_nums(df):
df_cols = df.columns.values
df_cols[df_cols >= current] += 1
df.columns = df_cols
current = self._current_col
start = self.start_of_current_col
selected = self.selected_part
end = (self.binary.shape[1] - selected[:, ::-1].argmax(axis=1) -
start)
not_selected = ~selected.any()
end[not_selected] = 0
# ----- Update of reader column numbers -----
for reader in self.iter_all_readers:
for i, col in enumerate(reader.columns):
if col >= current:
reader.columns[i] += 1
self.columns.insert(self.columns.index(current + 1), current)
self.parent._column_starts = np.insert(
self.parent._column_starts, current, self._column_starts[current])
if self.parent._column_ends is not None:
self.parent._column_ends = np.insert(
self.parent._column_ends, current,
self.parent._column_ends[current])
# ----- Update of column numbers in dataframes -----
# increase column numbers in full_df
full_df = self.parent._full_df
increase_col_nums(full_df)
# increase column numbers in samples
samples = self.parent._sample_locs
if samples is not None:
increase_col_nums(samples)
# ----- Update of DataFrames -----
# update the current column in full_df and add the new one
full_df.loc[:, current + 1] -= end
full_df[current] = end
full_df.sort_index(axis=1, inplace=True)
# update the current column in samples and add the new one
if samples is not None:
new_samples = full_df.loc[samples.index, current]
samples.loc[:, current + 1] -= new_samples
samples[current] = new_samples
samples.sort_index(axis=1, inplace=True)
rough_locs = self.parent.rough_locs
if rough_locs is not None:
rough_locs[(current + 1, 'vmin')] = rough_locs[(current, 'vmin')]
rough_locs[(current + 1, 'vmax')] = rough_locs[(current, 'vmax')]
rough_locs.loc[:, current] = -1
rough_locs.sort_index(inplace=True, level=0)
self.reset_lbl_col()
self.enable_or_disable_navigation_buttons()
def plot_full_df(self, ax=None):
"""Plot the lines for the digitized diagram"""
vals = self.full_df.values
starts = self.column_starts
self.lines = lines = []
y = np.arange(np.shape(self.image)[0])
ax = ax or self.ax
if self.extent is not None:
y += self.extent[-1]
starts += self.extent[0]
x = np.zeros_like(vals[:, 0]) + starts[0]
for i in range(vals.shape[1]):
x += vals[:, i]
lines.extend(ax.plot(x.copy(), y, lw=2.0))
def plot_potential_samples(self, excluded=False, ax=None, plot_kws={},
*args, **kwargs):
"""Plot the ranges for potential samples"""
vals = self.full_df.values.copy()
starts = self.column_starts.copy()
self.sample_ranges = lines = []
y = np.arange(np.shape(self.image)[0])
ax = ax or self.ax
plot_kws = dict(plot_kws)
plot_kws.setdefault('marker', '+')
if self.extent is not None:
y += self.extent[-1]
starts = starts + self.extent[0]
x = np.zeros(vals.shape[0]) + starts[0]
for i, (col, arr) in enumerate(zip(self.columns, vals.T)):
all_indices, excluded_indices = self.find_potential_samples(
i, *args, **kwargs)
if excluded:
all_indices = excluded_indices
if not all_indices:
x += arr
continue
mask = np.ones(arr.size, dtype=bool)
for imin, imax in all_indices:
mask[imin:imax] = False
for imin, imax in all_indices:
lines.extend(ax.plot(
np.where(mask, np.nan, arr)[imin:imax] + x[imin:imax],
y[imin:imax], **plot_kws))
x += arr
def resize_axes(self, grouper, bounds):
"""Reimplemented to do nothing"""
xmin = bounds.min()
xmax = bounds.max()
grouper.plotters[0].update(xlim=(xmin, xmax))
return
class DataFrameEditor(DockMixin, QWidget):
"""An editor for data frames"""
dock_cls = DataFrameDock
#: A signal that is emitted, if the table is cleared
cleared = QtCore.pyqtSignal()
#: A signal that is emitted when a cell has been changed. The argument
#: is a tuple of two integers and one float:
#: the row index, the column index and the new value
cell_edited = QtCore.pyqtSignal(int, int, object, object)
#: A signal that is emitted, if rows have been inserted into the dataframe.
#: The first value is the integer of the (original) position of the row,
#: the second one is the number of rows
rows_inserted = QtCore.pyqtSignal(int, int)
@property
def hidden(self):
return not self.table.filled
def __init__(self, *args, **kwargs):
super(DataFrameEditor, self).__init__(*args, **kwargs)
self.error_msg = PyErrorMessage(self)
# Label for displaying the DataFrame size
self.lbl_size = QLabel()
# A Checkbox for enabling and disabling the editability of the index
self.cb_index_editable = QCheckBox('Index editable')
# A checkbox for enabling and disabling the change of data types
self.cb_dtypes_changeable = QCheckBox('Datatypes changeable')
# A checkbox for enabling and disabling sorting
self.cb_enable_sort = QCheckBox('Enable sorting')
# A button to open a dataframe from the file
self.btn_open_df = QToolButton(parent=self)
self.btn_open_df.setIcon(QIcon(get_icon('run_arrow.png')))
self.btn_open_df.setToolTip('Open a DataFrame from your disk')
self.btn_from_console = LoadFromConsoleButton(pd.DataFrame)
self.btn_from_console.setToolTip('Show a DataFrame from the console')
# The table to display the DataFrame
self.table = DataFrameView(pd.DataFrame(), self)
# format line edit
self.format_editor = QLineEdit()
self.format_editor.setText(self.table.model()._format)
# format update button
self.btn_change_format = QPushButton('Update')
self.btn_change_format.setEnabled(False)
# table clearing button
self.btn_clear = QPushButton('Clear')
self.btn_clear.setToolTip(
'Clear the table and disconnect from the DataFrame')
# refresh button
self.btn_refresh = QToolButton()
self.btn_refresh.setIcon(QIcon(get_icon('refresh.png')))
self.btn_refresh.setToolTip('Refresh the table')
# close button
self.btn_close = QPushButton('Close')
self.btn_close.setToolTip('Close this widget permanentely')
# ---------------------------------------------------------------------
# ------------------------ layout --------------------------------
# ---------------------------------------------------------------------
vbox = QVBoxLayout()
self.top_hbox = hbox = QHBoxLayout()
hbox.addWidget(self.cb_index_editable)
hbox.addWidget(self.cb_dtypes_changeable)
hbox.addWidget(self.cb_enable_sort)
hbox.addWidget(self.lbl_size)
hbox.addStretch(0)
hbox.addWidget(self.btn_open_df)
hbox.addWidget(self.btn_from_console)
vbox.addLayout(hbox)
vbox.addWidget(self.table)
self.bottom_hbox = hbox = QHBoxLayout()
hbox.addWidget(self.format_editor)
hbox.addWidget(self.btn_change_format)
hbox.addStretch(0)
hbox.addWidget(self.btn_clear)
hbox.addWidget(self.btn_close)
hbox.addWidget(self.btn_refresh)
vbox.addLayout(hbox)
self.setLayout(vbox)
# ---------------------------------------------------------------------
# ------------------------ Connections --------------------------------
# ---------------------------------------------------------------------
self.cb_dtypes_changeable.stateChanged.connect(
self.set_dtypes_changeable)
self.cb_index_editable.stateChanged.connect(self.set_index_editable)
self.btn_from_console.object_loaded.connect(self._open_ds_from_console)
self.rows_inserted.connect(lambda i, n: self.set_lbl_size_text())
self.format_editor.textChanged.connect(self.toggle_fmt_button)
self.btn_change_format.clicked.connect(self.update_format)
self.btn_clear.clicked.connect(self.clear_table)
self.btn_close.clicked.connect(self.clear_table)
self.btn_close.clicked.connect(lambda: self.close())
self.btn_refresh.clicked.connect(self.table.reset_model)
self.btn_open_df.clicked.connect(self._open_dataframe)
self.table.set_index_action.triggered.connect(
self.update_index_editable)
self.table.append_index_action.triggered.connect(
self.update_index_editable)
self.cb_enable_sort.stateChanged.connect(
self.table.setSortingEnabled)
def update_index_editable(self):
model = self.table.model()
if len(model.df.index.names) > 1:
model.index_editable = False
self.cb_index_editable.setEnabled(False)
self.cb_index_editable.setChecked(model.index_editable)
def set_lbl_size_text(self, nrows=None, ncols=None):
"""Set the text of the :attr:`lbl_size` label to display the size"""
model = self.table.model()
nrows = nrows if nrows is not None else model.rowCount()
ncols = ncols if ncols is not None else model.columnCount()
if not nrows and not ncols:
self.lbl_size.setText('')
else:
self.lbl_size.setText('Rows: %i, Columns: %i' % (nrows, ncols))
def clear_table(self):
"""Clear the table and emit the :attr:`cleared` signal"""
df = pd.DataFrame()
self.set_df(df, show=False)
def _open_ds_from_console(self, oname, df):
self.set_df(df)
@docstrings.dedent
def set_df(self, df, *args, **kwargs):
"""
Fill the table from a :class:`~pandas.DataFrame`
Parameters
----------
%(DataFrameModel.parameters.no_parent)s
show: bool
If True (default), show and raise_ the editor
"""
show = kwargs.pop('show', True)
self.table.set_df(df, *args, **kwargs)
self.set_lbl_size_text(*df.shape)
model = self.table.model()
self.cb_dtypes_changeable.setChecked(model.dtypes_changeable)
if len(model.df.index.names) > 1:
model.index_editable = False
self.cb_index_editable.setEnabled(False)
else:
self.cb_index_editable.setEnabled(True)
self.cb_index_editable.setChecked(model.index_editable)
self.cleared.emit()
if show:
self.show_plugin()
self.dock.raise_()
def set_index_editable(self, state):
"""Set the :attr:`DataFrameModel.index_editable` attribute"""
self.table.model().index_editable = state == Qt.Checked
def set_dtypes_changeable(self, state):
"""Set the :attr:`DataFrameModel.dtypes_changeable` attribute"""
self.table.model().dtypes_changeable = state == Qt.Checked
def toggle_fmt_button(self, text):
try:
text % 1.1
except (TypeError, ValueError):
self.btn_change_format.setEnabled(False)
else:
self.btn_change_format.setEnabled(
text.strip() != self.table.model()._format)
def update_format(self):
"""Update the format of the table"""
self.table.model().set_format(self.format_editor.text().strip())
def to_dock(self, main, *args, **kwargs):
connect = self.dock is None
super(DataFrameEditor, self).to_dock(main, *args, **kwargs)
if connect:
self.dock.toggleViewAction().triggered.connect(self.maybe_tabify)
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 _open_dataframe(self):
self.open_dataframe()
def open_dataframe(self, fname=None, *args, **kwargs):
"""Opens a file dialog and the dataset that has been inserted"""
if fname is None:
fname = QFileDialog.getOpenFileName(
self, 'Open dataset', os.getcwd(),
'Comma separated files (*.csv);;'
'Excel files (*.xls *.xlsx);;'
'JSON files (*.json);;'
'All files (*)'
)
if with_qt5: # the filter is passed as well
fname = fname[0]
if isinstance(fname, pd.DataFrame):
self.set_df(fname)
elif not fname:
return
else:
ext = osp.splitext(fname)[1]
open_funcs = {
'.xls': pd.read_excel, '.xlsx': pd.read_excel,
'.json': pd.read_json,
'.tab': partial(pd.read_csv, delimiter='\t'),
'.dat': partial(pd.read_csv, delim_whitespace=True),
}
open_func = open_funcs.get(ext, pd.read_csv)
try:
df = open_func(fname)
except Exception:
self.error_msg.showTraceback(
'<b>Could not open DataFrame %s with %s</b>' % (
fname, open_func))
return
self.set_df(df)
def close(self, *args, **kwargs):
if self.dock is not None:
self.dock.close(*args, **kwargs) # removes the dock window
del self.dock
return super(DataFrameEditor, self).close(*args, **kwargs)
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()
class DependenciesDialog(QDialog):
"""A dialog for displaying the dependencies"""
#: description label
label = None
#: the QVBoxLayout containing all the widgets
vbox = None
#: The :class:`DependenciesTree` that contains the package infos
tree = None
#: The QPushButton used for copying selected packages to the clipboard
bt_copy = None
#: A simple info label for info messages
info_label = None
#: A QTimer that clears the :attr:`info_label` after some time
timer = None
@docstrings.dedent
def __init__(self, versions, *args, **kwargs):
"""
Parameters
----------
%(DependenciesTree.parameters)s
"""
super(DependenciesDialog, self).__init__(*args, **kwargs)
self.setWindowTitle('Dependencies')
self.versions = versions
self.vbox = layout = QVBoxLayout()
self.label = QLabel("""
psyplot and the plugins depend on several python libraries. The
tree widget below lists the versions of the plugins and the
requirements. You can select the items in the tree and copy them to
clipboard.""", parent=self)
layout.addWidget(self.label)
self.tree = DependenciesTree(versions, parent=self)
self.tree.setSelectionMode(QAbstractItemView.MultiSelection)
layout.addWidget(self.tree)
# copy button
self.bt_copy = QPushButton('Copy selection to clipboard')
self.bt_copy.setToolTip(
'Copy the selected packages in the above table to the clipboard.')
self.bt_copy.clicked.connect(lambda: self.copy_selected())
self.bbox = QDialogButtonBox(QDialogButtonBox.Ok)
self.bbox.accepted.connect(self.accept)
hbox = QHBoxLayout()
hbox.addWidget(self.bt_copy)
hbox.addStretch(1)
hbox.addWidget(self.bbox)
layout.addLayout(hbox)
#: A label for simple status update
self.info_label = QLabel('', self)
layout.addWidget(self.info_label)
self.timer = QtCore.QTimer(self)
self.timer.timeout.connect(self.clear_label)
self.setLayout(layout)
def copy_selected(self, label=None):
"""Copy the selected versions and items to the clipboard"""
d = {}
items = self.tree.selectedItems()
if not items:
QMessageBox.warning(self, "No packages selected!",
"Please select packages in the tree!")
return
for item in items:
d[item.text(0)] = item.text(1)
if label is None:
label = QApplication.clipboard()
label.setText("\n".join(
'%s: %s' % t for t in d.items()))
self.info_label.setText('Packages copied to clipboard.')
self.timer.start(3000)
def clear_label(self):
"""Clear the info label"""
self.info_label.setText('')
class SelectionToolbar(QToolBar, StraditizerControlBase):
"""A toolbar for selecting features in the straditizer and data image
The current data object is set in the :attr:`combo` and can be accessed
through the :attr:`data_obj` attribute. It's either the straditizer or the
data_reader that is accessed"""
_idPress = None
_idRelease = None
#: A signal that is emitted when something is selected
selected = QtCore.pyqtSignal()
set_cursor_id = None
reset_cursor_id = None
#: The QCombobox that defines the data object to be used
combo = None
@property
def ax(self):
"""The :class:`matplotlib.axes.Axes` of the :attr:`data_obj`"""
return self.data_obj.ax
@property
def data(self):
"""The np.ndarray of the :attr:`data_obj` image"""
text = self.combo.currentText()
if text == 'Reader':
return self.straditizer.data_reader.binary
elif text == 'Reader - Greyscale':
return self.straditizer.data_reader.to_grey_pil(
self.straditizer.data_reader.image)
else:
from straditize.binary import DataReader
return DataReader.to_grey_pil(self.straditizer.image)
@property
def data_obj(self):
"""The data object as set in the :attr:`combo`.
Either a :class:`~straditize.straditizer.Straditizer` or a
:class:`straditize.binary.DataReader` instance. """
text = self.combo.currentText()
if text in ['Reader', 'Reader - Greyscale']:
return self.straditizer.data_reader
else:
return self.straditizer
@data_obj.setter
def data_obj(self, value):
"""The data object as set in the :attr:`combo`.
Either a :class:`~straditize.straditizer.Straditizer` or a
:class:`straditize.binary.DataReader` instance. """
if self.straditizer is None:
return
if isinstance(value, six.string_types):
possible_values = {
self.combo.itemText(i) for i in range(self.combo.count())}
if value not in possible_values:
raise ValueError(
'Do not understand %r! Please use one of %r' % (
value, possible_values))
else:
self.combo.setCurrentText(value)
else:
if value is self.straditizer:
self.combo.setCurrentText('Straditizer')
elif value and value is self.straditizer.data_reader:
self.combo.setCurrentText('Reader')
else:
raise ValueError('Do not understand %r! Please either use '
'the Straditizer or DataReader instance!' % (
value, ))
@property
def fig(self):
"""The :class:`~matplotlib.figure.Figure` of the :attr:`data_obj`"""
try:
return self.ax.figure
except AttributeError:
return None
@property
def canvas(self):
"""The canvas of the :attr:`data_obj`"""
try:
return self.fig.canvas
except AttributeError:
return None
@property
def toolbar(self):
"""The toolbar of the :attr:`canvas`"""
return self.canvas.toolbar
@property
def select_action(self):
"""The rectangle selection tool"""
return self._actions['select']
@property
def wand_action(self):
"""The wand selection tool"""
return self._actions['wand_select']
@property
def new_select_action(self):
"""The action to make new selection with one of the selection tools"""
return self._type_actions['new_select']
@property
def add_select_action(self):
"""The action to add to the current selection with the selection tools
"""
return self._type_actions['add_select']
@property
def remove_select_action(self):
"""
An action to remove from the current selection with the selection tools
"""
return self._type_actions['remove_select']
@property
def select_all_action(self):
"""An action to select all features in the :attr:`data`"""
return self._actions['select_all']
@property
def expand_select_action(self):
"""An action to expand the current selection to the full feature"""
return self._actions['expand_select']
@property
def invert_select_action(self):
"""An action to invert the current selection"""
return self._actions['invert_select']
@property
def clear_select_action(self):
"""An action to clear the current selection"""
return self._actions['clear_select']
@property
def select_right_action(self):
"""An action to select everything in the data column to the right"""
return self._actions['select_right']
@property
def select_pattern_action(self):
"""An action to start a pattern selection"""
return self._actions['select_pattern']
@property
def widgets2disable(self):
if not self._actions:
return []
elif self._selecting:
return [self.combo]
else:
return list(chain([self.combo],
self._actions.values(),
self._appearance_actions.values()))
@property
def labels(self):
"""The labeled data that is displayed"""
if self.data_obj._selection_arr is not None:
return self.data_obj._selection_arr
text = self.combo.currentText()
if text == 'Reader':
return self.straditizer.data_reader.labels.copy()
elif text == 'Reader - Greyscale':
return self.straditizer.data_reader.color_labels()
else:
return self.straditizer.get_labels()
@property
def rect_callbacks(self):
"""The functions to call after the rectangle selection.
If not set manually, it is the :meth:`select_rect` method. Note that
this is cleared at every call of the :meth:`end_selection`.
Callables in this list must accept two arguments ``(slx, sly)``:
the first one is the x-slice, and the second one the y-slice. They both
correspond to the :attr:`data` attribute."""
return self._rect_callbacks or [self.select_rect]
@rect_callbacks.setter
def rect_callbacks(self, value):
"""The functions to call after the rectangle selection.
If not set manually, it is the :meth:`select_rect` method. Note that
this is cleared at every call of the :meth:`end_selection`.
Callables in this list must accept two arguments ``(slx, sly)``:
the first one is the x-slice, and the second one the y-slice. They both
correspond to the :attr:`data` attribute."""
self._rect_callbacks = value
@property
def poly_callbacks(self):
"""The functions to call after the polygon selection
If not set manually, it is the :meth:`select_poly` method. Note that
this is cleared at every call of the :meth:`end_selection`.
Callables in this list must accept one argument, a ``np.ndarray``
of shape ``(N, 2)``. This array defines the ``N`` x- and y-coordinates
of the points of the polygon"""
return self._poly_callbacks or [self.select_poly]
@poly_callbacks.setter
def poly_callbacks(self, value):
"""The functions to call after the polygon selection.
If not set manually, it is the :meth:`poly_callbacks` method. Note that
this is cleared at every call of the :meth:`end_selection`.
Callables in this list must accept one argument, a ``np.ndarray``
of shape ``(N, 2)``. This array defines the ``N`` x- and y-coordinates
of the points of the polygon"""
self._poly_callbacks = value
#: A :class:`PointOrRectangleSelector` to select features in the image
selector = None
_pattern_selection = None
def __init__(self, straditizer_widgets, *args, **kwargs):
super(SelectionToolbar, self).__init__(*args, **kwargs)
self._actions = {}
self._wand_actions = {}
self._pattern_actions = {}
self._select_actions = {}
self._appearance_actions = {}
# Boolean that is True if we are in a selection process
self._selecting = False
self.init_straditizercontrol(straditizer_widgets)
self._ids_select = []
self._rect_callbacks = []
self._poly_callbacks = []
self._selection_mode = None
self._lastCursor = None
self.create_actions()
self._changed_selection = False
self._connected = []
self._action_clicked = None
self.wand_type = 'labels'
self.select_type = 'rect'
self.pattern_type = 'binary'
self.auto_expand = False
def create_actions(self):
"""Define the actions for the toolbar and set everything up"""
# Reader toolbar
self.combo = QComboBox()
self.combo.setSizeAdjustPolicy(QComboBox.AdjustToContents)
self.addWidget(self.combo)
select_group = QActionGroup(self)
# select action
self._actions['select'] = a = self.addAction(
QIcon(get_icon('select.png')), 'select', self.toggle_selection)
a.setToolTip('Select pixels within a rectangle')
a.setCheckable(True)
select_group.addAction(a)
# select menu
select_menu = QMenu(self)
self._select_actions['rect_select'] = menu_a = select_menu.addAction(
QIcon(get_icon('select.png')), 'rectangle',
self.set_rect_select_mode)
menu_a.setToolTip('Select a rectangle')
a.setToolTip(menu_a.toolTip())
self._select_actions['poly_select'] = menu_a = select_menu.addAction(
QIcon(get_icon('poly_select.png')), 'polygon',
self.set_poly_select_mode)
menu_a.setToolTip('Select a rectangle')
a.setToolTip(menu_a.toolTip())
a.setMenu(select_menu)
# wand_select action
self._actions['wand_select'] = a = self.addAction(
QIcon(get_icon('wand_select.png')), 'select',
self.toggle_selection)
a.setCheckable(True)
select_group.addAction(a)
# wand menu
tool_menu = QMenu(self)
self._wand_actions['wand_select'] = menu_a = tool_menu.addAction(
QIcon(get_icon('wand_select.png')), 'wand',
self.set_label_wand_mode)
menu_a.setToolTip('Select labels within a rectangle')
a.setToolTip(menu_a.toolTip())
self._wand_actions['color_select'] = menu_a = tool_menu.addAction(
QIcon(get_icon('color_select.png')), 'color wand',
self.set_color_wand_mode)
menu_a.setToolTip('Select colors')
self._wand_actions['row_select'] = menu_a = tool_menu.addAction(
QIcon(get_icon('row_select.png')), 'row selection',
self.set_row_wand_mode)
menu_a.setToolTip('Select pixel rows')
self._wand_actions['col_select'] = menu_a = tool_menu.addAction(
QIcon(get_icon('col_select.png')), 'column selection',
self.set_col_wand_mode)
menu_a.setToolTip('Select pixel columns')
a.setMenu(tool_menu)
# color_wand widgets
self.distance_slider = slider = QSlider(Qt.Horizontal)
slider.setMinimum(0)
slider.setMaximum(255)
slider.setValue(30)
slider.setSingleStep(1)
self.lbl_slider = QLabel('30')
slider.valueChanged.connect(lambda i: self.lbl_slider.setText(str(i)))
slider.setMaximumWidth(self.combo.sizeHint().width())
self.cb_whole_fig = QCheckBox('Whole plot')
self.cb_whole_fig.setToolTip('Select the colors on the entire plot')
self.cb_use_alpha = QCheckBox('Use alpha')
self.cb_use_alpha.setToolTip('Use the alpha channel, i.e. the '
'transparency of the RGBA image.')
self.color_wand_actions = [
self.addWidget(slider), self.addWidget(self.lbl_slider),
self.addWidget(self.cb_whole_fig),
self.addWidget(self.cb_use_alpha)]
self.set_label_wand_mode()
self.addSeparator()
type_group = QActionGroup(self)
self._type_actions = {}
# new selection action
self._type_actions['new_select'] = a = self.addAction(
QIcon(get_icon('new_selection.png')), 'Create a new selection')
a.setToolTip('Select pixels within a rectangle and ignore the current '
'selection')
a.setCheckable(True)
type_group.addAction(a)
# add to selection action
self._type_actions['add_select'] = a = self.addAction(
QIcon(get_icon('add_select.png')), 'Add to selection')
a.setToolTip('Select pixels within a rectangle and add them to the '
'current selection')
a.setCheckable(True)
type_group.addAction(a)
# remove action
self._type_actions['remove_select'] = a = self.addAction(
QIcon(get_icon('remove_select.png')), 'Remove from selection')
a.setToolTip('Select pixels within a rectangle and remove them from '
'the current selection')
a.setCheckable(True)
type_group.addAction(a)
# info button
self.addSeparator()
self.info_button = InfoButton(self, 'selection_toolbar.rst')
self.addWidget(self.info_button)
# selection appearence options
self.addSeparator()
self.sl_alpha = slider = QSlider(Qt.Horizontal)
self._appearance_actions['alpha'] = self.addWidget(slider)
slider.setMinimum(0)
slider.setMaximum(100)
slider.setValue(100)
slider.setSingleStep(1)
self.lbl_alpha_slider = QLabel('100 %')
slider.valueChanged.connect(
lambda i: self.lbl_alpha_slider.setText(str(i) + ' %'))
slider.valueChanged.connect(self.update_alpha)
slider.setMaximumWidth(self.combo.sizeHint().width())
# Select all and invert selection buttons
self.addSeparator()
self._actions['select_all'] = a = self.addAction(
QIcon(get_icon('select_all.png')), 'all', self.select_all)
a.setToolTip('Select all labels')
self._actions['expand_select'] = a = self.addAction(
QIcon(get_icon('expand_select.png')), 'expand',
self.expand_selection)
a.setToolTip('Expand the selected areas to select the entire feature')
self._actions['invert_select'] = a = self.addAction(
QIcon(get_icon('invert_select.png')), 'invert',
self.invert_selection)
a.setToolTip('Invert selection')
self._actions['clear_select'] = a = self.addAction(
QIcon(get_icon('clear_select.png')), 'clear',
self.clear_selection)
a.setToolTip('Clear selection')
self._actions['select_right'] = a = self.addAction(
QIcon(get_icon('select_right.png')), 'right',
self.select_everything_to_the_right)
a.setToolTip('Select everything to the right of each column')
self._actions['select_pattern'] = a = self.addAction(
QIcon(get_icon('pattern.png')), 'pattern',
self.start_pattern_selection)
a.setCheckable(True)
a.setToolTip(
'Select a binary pattern/hatch within the current selection')
# wand menu
pattern_menu = QMenu(self)
self._pattern_actions['binary'] = menu_a = pattern_menu.addAction(
QIcon(get_icon('pattern.png')), 'Binary',
self.set_binary_pattern_mode)
menu_a.setToolTip(
'Select a binary pattern/hatch within the current selection')
a.setToolTip(menu_a.toolTip())
self._pattern_actions['grey'] = menu_a = pattern_menu.addAction(
QIcon(get_icon('pattern_grey.png')), 'Greyscale',
self.set_grey_pattern_mode)
menu_a.setToolTip(
'Select a pattern/hatch within the current selection based on '
'grey scale colors')
a.setMenu(pattern_menu)
self.new_select_action.setChecked(True)
for a in self._type_actions.values():
a.toggled.connect(self.add_or_remove_pattern)
self.refresh()
def should_be_enabled(self, w):
if self.straditizer is None:
return False
elif (self._actions and
w in [self.remove_select_action, self.invert_select_action,
self.clear_select_action, self.expand_select_action,
self.select_right_action] and
not self._selecting):
return False
elif w in self._appearance_actions.values() and not self._selecting:
return False
elif (self.combo and not self.combo.currentText().startswith('Reader')
and w is self.select_right_action):
return False
return True
def disable_actions(self):
if self._changed_selection:
return
for a in self._actions.values():
if a.isChecked():
a.setChecked(False)
self.toggle_selection()
else:
a.setChecked(False)
def select_all(self):
"""Select all features in the image
See Also
--------
straditize.label_selection.LabelSelection.select_all_labels"""
obj = self.data_obj
if obj._selection_arr is None:
rgba = obj.image_array() if hasattr(obj, 'image_array') else None
self.start_selection(self.labels, rgba=rgba)
obj.select_all_labels()
self.canvas.draw()
def invert_selection(self):
"""Invert the current selection"""
obj = self.data_obj
if obj._selection_arr is None:
rgba = obj.image_array() if hasattr(obj, 'image_array') else None
self.start_selection(self.labels, rgba=rgba)
if (obj._selection_arr != obj._orig_selection_arr).any():
selection = obj.selected_part
# clear the current selection
obj._selection_arr[:] = np.where(
obj._selection_arr.astype(bool) & (~selection),
obj._orig_selection_arr.max() + 1, obj._orig_selection_arr)
obj._select_img.set_array(obj._selection_arr)
obj.unselect_all_labels()
else:
obj.select_all_other_labels()
self.canvas.draw()
def clear_selection(self):
"""Clear the current selection"""
obj = self.data_obj
if obj._selection_arr is None:
return
obj._selection_arr[:] = obj._orig_selection_arr.copy()
obj._select_img.set_array(obj._selection_arr)
obj.unselect_all_labels()
self.canvas.draw()
def expand_selection(self):
"""Expand the selected areas to select the full labels"""
obj = self.data_obj
if obj._selection_arr is None:
return
arr = obj._orig_selection_arr.copy()
selected_labels = np.unique(arr[obj.selected_part])
obj._selection_arr = arr
obj._select_img.set_array(arr)
obj.unselect_all_labels()
obj.select_labels(selected_labels)
self.canvas.draw()
def update_alpha(self, i):
"""Set the transparency of the selection image
Parameters
----------
i: int
The transparency between 0 and 100"""
self.data_obj._select_img.set_alpha(i / 100.)
self.data_obj._update_magni_img()
self.canvas.draw()
def select_everything_to_the_right(self):
"""Selects everything to the right of the current selection"""
reader = self.data_obj
if reader._selection_arr is None:
return
bounds = reader.column_bounds
selection = reader.selected_part
new_select = np.zeros_like(selection)
for start, end in bounds:
can_be_selected = reader._selection_arr[:, start:end].astype(bool)
end = start + can_be_selected.shape[1]
last_in_row = selection[:, start:end].argmax(axis=-1).reshape(
(-1, 1))
dist2start = np.tile(np.arange(end - start)[np.newaxis],
(len(selection), 1))
can_be_selected[dist2start <= last_in_row] = False
can_be_selected[~np.tile(last_in_row.astype(bool),
(1, end - start))] = False
new_select[:, start:end] = can_be_selected
max_label = reader._orig_selection_arr.max()
reader._selection_arr[new_select] = max_label + 1
reader._select_img.set_array(reader._selection_arr)
reader._update_magni_img()
self.canvas.draw()
def start_pattern_selection(self):
"""Open the pattern selection dialog
This method will enable the pattern selection by starting a
:class:`straditize.widgets.pattern_selection.PatternSelectionWidget`"""
from straditize.widgets.pattern_selection import PatternSelectionWidget
if self.select_pattern_action.isChecked():
from straditize.binary import DataReader
from psyplot_gui.main import mainwindow
obj = self.data_obj
if obj._selection_arr is None:
if hasattr(obj, 'image_array'):
rgba = obj.image_array()
else:
rgba = None
self.start_selection(self.labels, rgba=rgba)
self.select_all()
if not obj.selected_part.any():
self.select_pattern_action.setChecked(False)
raise ValueError(
"No data in the image is selected. Please select the "
"coarse region in which the pattern should be searched.")
if self.pattern_type == 'binary':
arr = DataReader.to_binary_pil(obj.image)
else:
arr = DataReader.to_grey_pil(obj.image)
self._pattern_selection = w = PatternSelectionWidget(
arr, obj)
w.to_dock(mainwindow, 'Pattern selection')
w.btn_close.clicked.connect(self.uncheck_pattern_selection)
w.btn_cancel.clicked.connect(self.uncheck_pattern_selection)
self.disable_actions()
pattern_action = self.select_pattern_action
for a in self._actions.values():
a.setEnabled(False)
pattern_action.setEnabled(True)
pattern_action.setChecked(True)
w.show_plugin()
w.maybe_tabify()
w.raise_()
elif self._pattern_selection is not None:
self._pattern_selection.cancel()
self._pattern_selection.close()
self.uncheck_pattern_selection()
del self._pattern_selection
def uncheck_pattern_selection(self):
"""Disable the pattern selection"""
self.select_pattern_action.setChecked(False)
del self._pattern_selection
for a in self._actions.values():
a.setEnabled(self.should_be_enabled(a))
def add_or_remove_pattern(self):
"""Enable the removing or adding of the pattern selection"""
if getattr(self, '_pattern_selection', None) is None:
return
current = self._pattern_selection.remove_selection
new = self.remove_select_action.isChecked()
if new is not current:
self._pattern_selection.remove_selection = new
if self._pattern_selection.btn_select.isChecked():
self._pattern_selection.modify_selection(
self._pattern_selection.sl_thresh.value())
def set_rect_select_mode(self):
"""Set the current wand tool to the color wand"""
self.select_type = 'rect'
self.select_action.setIcon(QIcon(get_icon('select.png')))
self._action_clicked = None
self.toggle_selection()
def set_poly_select_mode(self):
"""Set the current wand tool to the color wand"""
self.select_type = 'poly'
self.select_action.setIcon(QIcon(get_icon('poly_select.png')))
self._action_clicked = None
self.toggle_selection()
def set_label_wand_mode(self):
"""Set the current wand tool to the color wand"""
self.wand_type = 'labels'
self.wand_action.setIcon(QIcon(get_icon('wand_select.png')))
for a in self.color_wand_actions:
a.setVisible(False)
self._action_clicked = None
self.toggle_selection()
def set_color_wand_mode(self):
"""Set the current wand tool to the color wand"""
self.wand_type = 'color'
self.wand_action.setIcon(QIcon(get_icon('color_select.png')))
for a in self.color_wand_actions:
a.setVisible(True)
self._action_clicked = None
self.toggle_selection()
def set_row_wand_mode(self):
"""Set the current wand tool to the color wand"""
self.wand_type = 'rows'
self.wand_action.setIcon(QIcon(get_icon('row_select.png')))
for a in self.color_wand_actions:
a.setVisible(False)
self._action_clicked = None
self.toggle_selection()
def set_col_wand_mode(self):
"""Set the current wand tool to the color wand"""
self.wand_type = 'cols'
self.wand_action.setIcon(QIcon(get_icon('col_select.png')))
for a in self.color_wand_actions:
a.setVisible(False)
self._action_clicked = None
self.toggle_selection()
def set_binary_pattern_mode(self):
"""Set the current pattern mode to the binary pattern"""
self.pattern_type = 'binary'
self.select_pattern_action.setIcon(QIcon(get_icon('pattern.png')))
def set_grey_pattern_mode(self):
"""Set the current pattern mode to the binary pattern"""
self.pattern_type = 'grey'
self.select_pattern_action.setIcon(QIcon(get_icon('pattern_grey.png')))
def disconnect(self):
if self.set_cursor_id is not None:
if self.canvas is None:
self.canvas.mpl_disconnect(self.set_cursor_id)
self.canvas.mpl_disconnect(self.reset_cursor_id)
self.set_cursor_id = None
self.reset_cursor_id = None
if self.selector is not None:
self.selector.disconnect_events()
self.selector = None
def toggle_selection(self):
"""Activate selection mode"""
if self.canvas is None:
return
self.disconnect()
key = next((key for key, a in self._actions.items() if a.isChecked()),
None)
if key is None or key == self._action_clicked:
self._action_clicked = None
if key is not None:
self._actions[key].setChecked(False)
else:
if self.wand_action.isChecked() and self.wand_type == 'color':
self.selector = PointOrRectangleSelector(
self.ax, self.on_rect_select, rectprops=dict(fc='none'),
lineprops=dict(c='none'), useblit=True)
elif self.select_action.isChecked() and self.select_type == 'poly':
self.selector = mwid.LassoSelector(
self.ax, self.on_poly_select)
else:
self.selector = PointOrRectangleSelector(
self.ax, self.on_rect_select, useblit=True)
self.set_cursor_id = self.canvas.mpl_connect(
'axes_enter_event', self._on_axes_enter)
self.reset_cursor_id = self.canvas.mpl_connect(
'axes_leave_event', self._on_axes_leave)
self._action_clicked = next(key for key, a in self._actions.items()
if a.isChecked())
self.toolbar.set_message(self.toolbar.mode)
def enable_or_disable_widgets(self, b):
super(SelectionToolbar, self).enable_or_disable_widgets(b)
if not b:
for w in [self.clear_select_action, self.invert_select_action,
self.expand_select_action]:
w.setEnabled(self.should_be_enabled(w))
if self._actions and not self.select_action.isEnabled():
for a in self._actions.values():
if a.isChecked():
a.setChecked(False)
self.toggle_selection()
def refresh(self):
super(SelectionToolbar, self).refresh()
combo = self.combo
if self.straditizer is None:
combo.clear()
else:
if not combo.count():
combo.addItem('Straditizer')
if self.straditizer.data_reader is not None:
if not any(combo.itemText(i) == 'Reader'
for i in range(combo.count())):
combo.addItem('Reader')
combo.addItem('Reader - Greyscale')
else:
for i in range(combo.count()):
if combo.itemText(i).startswith('Reader'):
combo.removeItem(i)
def _on_axes_enter(self, event):
ax = self.ax
if ax is None:
return
if (event.inaxes is ax and self.toolbar._active == '' and
self.selector is not None):
if self._lastCursor != cursors.SELECT_REGION:
self.toolbar.set_cursor(cursors.SELECT_REGION)
self._lastCursor = cursors.SELECT_REGION
def _on_axes_leave(self, event):
ax = self.ax
if ax is None:
return
if (event.inaxes is ax and self.toolbar._active == '' and
self.selector is not None):
if self._lastCursor != cursors.POINTER:
self.toolbar.set_cursor(cursors.POINTER)
self._lastCursor = cursors.POINTER
def end_selection(self):
"""Finish the selection and disconnect everything"""
if getattr(self, '_pattern_selection', None) is not None:
self._pattern_selection.close()
del self._pattern_selection
self._selecting = False
self._action_clicked = None
self.toggle_selection()
self.auto_expand = False
self._labels = None
self._rect_callbacks.clear()
self._poly_callbacks.clear()
self._wand_actions['color_select'].setEnabled(True)
def get_xy_slice(self, lastx, lasty, x, y):
"""Transform x- and y-coordinates to :class:`slice` objects
Parameters
----------
lastx: int
The initial x-coordinate
lasty: int
The initial y-coordinate
x: int
The final x-coordinate
y: int
The final y-coordinate
Returns
-------
slice
The ``slice(lastx, x)``
slice
The ``slice(lasty, y)``"""
all_x = np.floor(np.sort([lastx, x])).astype(int)
all_y = np.floor(np.sort([lasty, y])).astype(int)
extent = getattr(self.data_obj, 'extent', None)
if extent is not None:
all_x -= np.ceil(extent[0]).astype(int)
all_y -= np.ceil(min(extent[2:])).astype(int)
if self.wand_action.isChecked() and self.wand_type == 'color':
all_x[0] = all_x[1]
all_y[0] = all_y[1]
all_x[all_x < 0] = 0
all_y[all_y < 0] = 0
all_x[1] += 1
all_y[1] += 1
return slice(*all_x), slice(*all_y)
def on_rect_select(self, e0, e1):
"""Call the :attr:`rect_callbacks` after a rectangle selection
Parameters
----------
e0: matplotlib.backend_bases.Event
The initial event
e1: matplotlib.backend_bases.Event
The final event"""
slx, sly = self.get_xy_slice(e0.xdata, e0.ydata, e1.xdata, e1.ydata)
for func in self.rect_callbacks:
func(slx, sly)
def select_rect(self, slx, sly):
"""Select the data defined by a rectangle
Parameters
----------
slx: slice
The x-slice of the rectangle
sly: slice
The y-slice of the rectangle
See Also
--------
rect_callbacks"""
obj = self.data_obj
if obj._selection_arr is None:
arr = self.labels
rgba = obj.image_array() if hasattr(obj, 'image_array') else None
self.start_selection(arr, rgba=rgba)
expand = False
if self.select_action.isChecked():
arr = self._select_rectangle(slx, sly)
expand = True
elif self.wand_type == 'labels':
arr = self._select_labels(slx, sly)
elif self.wand_type == 'rows':
arr = self._select_rows(slx, sly)
elif self.wand_type == 'cols':
arr = self._select_cols(slx, sly)
else:
arr = self._select_colors(slx, sly)
expand = True
if arr is not None:
obj._selection_arr = arr
obj._select_img.set_array(arr)
obj._update_magni_img()
if expand and self.auto_expand:
self.expand_selection()
else:
self.canvas.draw()
def on_poly_select(self, points):
"""Call the :attr:`poly_callbacks` after a polygon selection
Parameters
----------
e0: matplotlib.backend_bases.Event
The initial event
e1: matplotlib.backend_bases.Event
The final event"""
for func in self.poly_callbacks:
func(points)
def select_poly(self, points):
"""Select the data defined by a polygon
Parameters
----------
points: np.ndarray of shape (N, 2)
The x- and y-coordinates of the vertices of the polygon
See Also
--------
poly_callbacks"""
obj = self.data_obj
if obj._selection_arr is None:
rgba = obj.image_array() if hasattr(obj, 'image_array') else None
self.start_selection(self.labels, rgba=rgba)
arr = self.labels
mpath = mplp.Path(points)
x = np.arange(obj._selection_arr.shape[1], dtype=int)
y = np.arange(obj._selection_arr.shape[0], dtype=int)
extent = getattr(obj, 'extent', None)
if extent is not None:
x += np.ceil(extent[0]).astype(int)
y += np.ceil(min(extent[2:])).astype(int)
pointsx, pointsy = np.array(points).T
x0, x1 = x.searchsorted([pointsx.min(), pointsx.max()])
y0, y1 = y.searchsorted([pointsy.min(), pointsy.max()])
X, Y = np.meshgrid(x[x0:x1], y[y0:y1])
points = np.array((X.flatten(), Y.flatten())).T
mask = np.zeros_like(obj._selection_arr, dtype=bool)
mask[y0:y1, x0:x1] = (
mpath.contains_points(points).reshape(X.shape) &
obj._selection_arr[y0:y1, x0:x1].astype(bool))
if self.remove_select_action.isChecked():
arr[mask] = -1
else:
if self.new_select_action.isChecked():
arr = obj._orig_selection_arr.copy()
obj._select_img.set_cmap(obj._select_cmap)
obj._select_img.set_norm(obj._select_norm)
arr[mask] = arr.max() + 1
obj._selection_arr = arr
obj._select_img.set_array(arr)
obj._update_magni_img()
if self.auto_expand:
self.expand_selection()
else:
self.canvas.draw()
def _select_rectangle(self, slx, sly):
"""Select a rectangle within the array"""
obj = self.data_obj
arr = self.labels
data_mask = obj._selection_arr.astype(bool)
if self.remove_select_action.isChecked():
arr[sly, slx][data_mask[sly, slx]] = -1
else:
if self.new_select_action.isChecked():
arr = obj._orig_selection_arr.copy()
obj._select_img.set_cmap(obj._select_cmap)
obj._select_img.set_norm(obj._select_norm)
arr[sly, slx][data_mask[sly, slx]] = arr.max() + 1
return arr
def _select_labels(self, slx, sly):
"""Select the unique labels in the array"""
obj = self.data_obj
arr = self.labels
data_mask = obj._selection_arr.astype(bool)
current_selected = obj.selected_labels
new_selected = np.unique(
arr[sly, slx][data_mask[sly, slx]])
valid_labels = np.unique(
obj._orig_selection_arr[sly, slx][data_mask[sly, slx]])
valid_labels = valid_labels[valid_labels > 0]
if not len(valid_labels):
return
if new_selected[0] == -1 or new_selected[-1] > obj._select_nlabels:
mask = np.isin(obj._orig_selection_arr, valid_labels)
current_selected = np.unique(
np.r_[current_selected,
obj._orig_selection_arr[sly, slx][
arr[sly, slx] > obj._select_nlabels]])
arr[mask] = obj._orig_selection_arr[mask]
curr = set(current_selected)
valid = set(valid_labels)
if self.remove_select_action.isChecked():
new = curr - valid
elif self.add_select_action.isChecked():
new = curr | valid
else:
new = valid
arr = obj._orig_selection_arr.copy()
obj.select_labels(np.array(sorted(new)))
return arr
def _select_rows(self, slx, sly):
"""Select the pixel rows defined by `sly`
Parameters
----------
slx: slice
The x-slice (is ignored)
sly: slice
The y-slice defining the rows to select"""
obj = self.data_obj
arr = self.labels
rows = np.arange(arr.shape[0])[sly]
if self.remove_select_action.isChecked():
arr[rows, :] = np.where(arr[rows, :], -1, 0)
else:
if self.new_select_action.isChecked():
arr = obj._orig_selection_arr.copy()
obj._select_img.set_cmap(obj._select_cmap)
obj._select_img.set_norm(obj._select_norm)
arr[rows, :] = np.where(arr[rows, :], arr.max() + 1, 0)
return arr
def _select_cols(self, slx, sly):
"""Select the pixel columns defined by `slx`
Parameters
----------
slx: slice
The x-slice defining the columns to select
sly: slice
The y-slice (is ignored)"""
obj = self.data_obj
arr = self.labels
cols = np.arange(arr.shape[1])[slx]
if self.remove_select_action.isChecked():
arr[:, cols] = np.where(arr[:, cols], -1, 0)
else:
if self.new_select_action.isChecked():
arr = obj._orig_selection_arr.copy()
obj._select_img.set_cmap(obj._select_cmap)
obj._select_img.set_norm(obj._select_norm)
arr[:, cols] = np.where(arr[:, cols], arr.max() + 1, 0)
return arr
def _select_colors(self, slx, sly):
"""Select the array based on the colors"""
if self.cb_use_alpha.isChecked():
rgba = self._rgba
n = 4
else:
rgba = self._rgba[..., :-1]
n = 3
rgba = rgba.astype(int)
# get the unique colors
colors = list(
map(np.array, set(map(tuple, rgba[sly, slx].reshape((-1, n))))))
obj = self.data_obj
arr = self.labels
mask = np.zeros_like(arr, dtype=bool)
max_dist = self.distance_slider.value()
data_mask = obj._selection_arr.astype(bool)
for c in colors:
mask[np.all(np.abs(rgba - c.reshape((1, 1, -1))) <= max_dist,
axis=-1)] = True
if not self.cb_whole_fig.isChecked():
import skimage.morphology as skim
all_labels = skim.label(mask, 8, return_num=False)
selected_labels = np.unique(all_labels[sly, slx])
mask[~np.isin(all_labels, selected_labels)] = False
if self.remove_select_action.isChecked():
arr[mask & data_mask] = -1
else:
if self.new_select_action.isChecked():
arr = obj._orig_selection_arr.copy()
obj._select_img.set_cmap(obj._select_cmap)
obj._select_img.set_norm(obj._select_norm)
arr[mask & data_mask] = arr.max() + 1
return arr
def _remove_selected_labels(self):
self.data_obj.remove_selected_labels(disable=True)
def _disable_selection(self):
return self.data_obj.disable_label_selection()
def start_selection(self, arr=None, rgba=None,
rect_callbacks=None, poly_callbacks=None,
apply_funcs=(), cancel_funcs=(), remove_on_apply=True):
"""Start the selection in the current :attr:`data_obj`
Parameters
----------
arr: np.ndarray
The labeled selection array that is used. If specified, the
:meth:`~straditize.label_selection.enable_label_selection` method
is called of the :attr:`data_obj` with the given `arr`. If this
parameter is ``None``, then we expect that this method has already
been called
rgba: np.ndarray
The RGBA image that shall be used for the color selection
(see the :meth:`set_color_wand_mode`)
rect_callbacks: list
A list of callbacks that shall be called after a rectangle
selection has been made by the user (see :attr:`rect_callbacks`)
poly_callbacks: list
A list of callbacks that shall be called after a polygon
selection has been made by the user (see :attr:`poly_callbacks`)
apply_funcs: list
A list of callables that shall be connected to the
:attr:`~straditize.widgets.StraditizerWidgets.apply_button`
cancel_funcs: list
A list of callables that shall be connected to the
:attr:`~straditize.widgets.StraditizerWidgets.cancel_button`
remove_on_apply: bool
If True and the
:attr:`~straditize.widgets.StraditizerWidgets.apply_button` is
clicked, the selected labels will be removed."""
obj = self.data_obj
if arr is not None:
obj.enable_label_selection(
arr, arr.max(), set_picker=False,
zorder=obj.plot_im.zorder + 0.1,
extent=obj.plot_im.get_extent())
self._selecting = True
self._rgba = rgba
if rgba is None:
self.set_label_wand_mode()
self._wand_actions['color_select'].setEnabled(False)
else:
self._wand_actions['color_select'].setEnabled(True)
self.connect2apply(
(self._remove_selected_labels if remove_on_apply else
self._disable_selection),
obj.remove_small_selection_ellipses, obj.draw_figure,
self.end_selection, *apply_funcs)
self.connect2cancel(self._disable_selection,
obj.remove_small_selection_ellipses,
obj.draw_figure,
self.end_selection, *cancel_funcs)
if self.should_be_enabled(self._appearance_actions['alpha']):
self.update_alpha(self.sl_alpha.value())
for w in chain(self._actions.values(),
self._appearance_actions.values()):
w.setEnabled(self.should_be_enabled(w))
if remove_on_apply:
self.straditizer_widgets.apply_button.setText('Remove')
if rect_callbacks is not None:
self._rect_callbacks = rect_callbacks[:]
if poly_callbacks is not None:
self._poly_callbacks = poly_callbacks[:]
del obj