#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on May 13 2018
@author: kushal
Chatzigeorgiou Group
Sars International Centre for Marine Molecular Biology
GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007
"""
from ..core.common import ViewerUtils
from .pytemplates.roi_manager_pytemplate import *
from .roi_manager_modules import managers
from .roi_manager_modules.roi_types import *
from functools import partial
import traceback
import logging
logger = logging.getLogger()
[docs]class ModuleGUI(QtWidgets.QDockWidget):
"""The GUI front-end for the ROI Manager module"""
[docs] def __init__(self, parent, viewer_reference):
"""Instantiate attributes"""
self.vi = ViewerUtils(viewer_reference)
QtWidgets.QDockWidget.__init__(self, parent)
self.ui = Ui_DockWidget()
self.ui.setupUi(self)
self.manager = managers.ManagerManual(self, self.ui, self.vi) #: The back-end manager instance.
self.vi.viewer.workEnv.roi_manager = self.manager
self.vi.viewer.workEnv.rois = self.manager.roi_list
self.vi.viewer.ui.splitter.setEnabled(True)
action_add_ellipse_roi = QtWidgets.QWidgetAction(self)
action_add_ellipse_roi.setText('Add Ellipse ROI')
action_add_ellipse_roi.triggered.connect(partial(self.add_manual_roi, 'EllipseROI'))
self.btnAddROIMenu = QtWidgets.QMenu(self)
self.btnAddROIMenu.addAction(action_add_ellipse_roi)
self.ui.btnAddROI.clicked.connect(partial(self.add_manual_roi, 'PolyLineROI'))
self.ui.btnAddROI.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
self.ui.btnAddROI.customContextMenuRequested.connect(self.btnAddROI_context_menu_requested)
self.ui.btnSwitchToManualMode.clicked.connect(self.start_manual_mode)
action_delete_roi = QtWidgets.QWidgetAction(self)
action_delete_roi.setText('Delete')
action_delete_roi.triggered.connect(self.slot_delete_roi_menu)
self.list_widget_context_menu = QtWidgets.QMenu(self)
self.list_widget_context_menu.addAction(action_delete_roi)
self.ui.listWidgetROIs.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
self.ui.listWidgetROIs.customContextMenuRequested.connect(self._list_widget_context_menu_requested)
self.ui.listWidgetROIs.currentRowChanged.connect(self.request_zlevel)
self.ui.pushButtonImportFromImageJ.clicked.connect(self.import_from_imagej)
self.installEventFilter(self)
self.ui.lineEditROITag.sig_key_right.connect(self.play_forward)
self.ui.lineEditROITag.sig_key_left.connect(self.play_backward)
self.ui.lineEditROITag.sig_key_home.connect(self.img_seq_home)
self.ui.lineEditROITag.sig_key_end.connect(self.img_seq_end)
self.ui.horizontalSliderSpotSize.valueChanged.connect(self.set_spot_size)
for w in \
[
self.ui.radioButton_curve_data,
self.ui.radioButton_dfof,
self.ui.radioButton_spikes
]:
w.clicked.connect(self.set_curveplot_datatype)
[docs] def eventFilter(self, QObject, QEvent):
"""Set some keyboard shortcuts"""
if QEvent.type() == QEvent.KeyPress:
if len(self.manager.roi_list) < 1:
return super(ModuleGUI, self).eventFilter(QObject, QEvent)
max_ix = len(self.manager.roi_list) - 1
if QEvent.key() == QtCore.Qt.Key_PageUp:
ix = self.manager.roi_list.current_index
self.ui.listWidgetROIs.setCurrentRow(max(0, ix - 1))
elif QEvent.key() == QtCore.Qt.Key_PageDown:
ix = self.manager.roi_list.current_index
self.ui.listWidgetROIs.setCurrentRow(min(max_ix, ix + 1))
elif QEvent.key() == QtCore.Qt.Key_Right:
self.play_forward()
elif QEvent.key() == QtCore.Qt.Key_Left:
self.play_backward()
return super(ModuleGUI, self).eventFilter(QObject, QEvent)
def play_forward(self):
self.vi.viewer.play(500)
def play_backward(self):
self.vi.viewer.play(-500)
def img_seq_home(self):
self.vi.viewer.setCurrentIndex(0)
self.vi.viewer.play(0)
def img_seq_end(self):
self.vi.viewer.setCurrentIndex(self.vi.viewer.getProcessedImage().shape[0] - 1)
self.vi.viewer.play(0)
def _list_widget_context_menu_requested(self, p):
self.list_widget_context_menu.exec_(self.ui.listWidgetROIs.mapToGlobal(p))
def btnAddROI_context_menu_requested(self, p):
self.btnAddROIMenu.exec_(self.ui.btnAddROI.mapToGlobal(p))
[docs] def start_backend(self, type_str: str):
"""Choose backend, one of the Manager classes in the managers module."""
if hasattr(self, 'manager'):
del self.manager
if type_str == 'Manual':
self.start_manual_mode()
self.disable_curve_options(True)
self.ui.radioButton_curve_data.setChecked(True)
return
self.ui.btnAddROI.setDisabled(True) # only used for manual ROIs
self.disable_curve_options(False) # enable dfof and spike options
backend = f'Manager{type_str}'
manager = getattr(managers, backend)
self.manager = manager(self, self.ui, self.vi)
self.vi.viewer.workEnv.roi_manager = self.manager
self.ui.btnSwitchToManualMode.setEnabled(True)
self.ui.radioButton_curve_data.setChecked(True)
logger.info(f'ROI Manager backend set to: {backend}')
return self.manager
[docs] def start_manual_mode(self):
"""Start in manual mode. Creates a new back-end manager instance (Uses ManagerManual)"""
logger.info('ROI back-end set to: ManagerManual')
if hasattr(self, 'manager'):
del self.manager
self.manager = managers.ManagerManual(self, self.ui, self.vi)
self.ui.btnAddROI.setEnabled(True)
self.vi.viewer.workEnv.roi_manager = self.manager
self.ui.btnSwitchToManualMode.setDisabled(True)
def set_curveplot_datatype(self):
if self.ui.radioButton_curve_data.isChecked():
datatype = 'curve'
elif self.ui.radioButton_dfof.isChecked():
datatype = 'dfof'
elif self.ui.radioButton_spikes.isChecked():
datatype = 'spike'
if isinstance(self.manager, managers.ManagerVolMultiCNMFROI):
for roi in self.manager.roi_list:
roi.curve_data_type = datatype
if roi.visible:
roi.set_viewer_curveplot(datatype)
else:
for roi in self.manager.roi_list:
roi.set_viewer_curveplot(datatype)
def disable_curve_options(self, b):
self.ui.radioButton_curve_data.setDisabled(b)
self.ui.radioButton_dfof.setDisabled(b)
self.ui.radioButton_spikes.setDisabled(b)
[docs] def add_manual_roi(self, shape: str):
"""Add a manual ROI. Just calls ManagerManual.add_roi"""
if self.vi.viewer.workEnv.isEmpty:
QtWidgets.QMessageBox.warning(self,
'Empty Work Environment',
'You cannot add ROIs to an empty work environment')
return
self.manager.add_roi(shape)
def add_roi_tags_list_text(self):
pass
def show_all_rois(self):
pass
[docs] def package_for_project(self) -> dict:
"""
Gets all the ROI states so that they can be packaged along with
the rest of the work environment to be saved as a project Sample
"""
states = self.manager.get_all_states()
return states
[docs] def set_all_from_states(self, states: dict):
"""Set all the ROIs from a states dict. Instantiates the appropriate back-end Manager"""
if 'roi_type' not in states.keys():
raise TypeError('`roi_type` not specified in states dict')
roi_class = states["roi_type"]
if roi_class not in globals().keys():
raise TypeError(f'Specified ROI type <{roi_class}> not found in available ROI types.')
# All scatter types, CNMF(E), Suite2p, VolCNMF etc.
if issubclass(globals()[roi_class], ScatterROI):
self.start_backend(states['roi_type'])
self.manager.restore_from_states(states)
# Manual ROI classes
elif issubclass(globals()[roi_class], ManualROI):
self.start_manual_mode()
self.manager.restore_from_states(states)
[docs] def import_from_imagej(self):
"""Import ROIs from ImageJ zip file"""
path = QtWidgets.QFileDialog.getOpenFileName(None, 'Import ImageJ ROIs', '', '(*.zip)')
if path == '':
return
self.start_manual_mode()
try:
self.manager.import_from_imagej(path[0])
except:
QtWidgets.QMessageBox.warning(None, 'File open Error',
'Could not open the chosen file.\n'
'It might not be an ImageJ ROIs file' + traceback.format_exc())
def set_spot_size(self, size: int):
if hasattr(self.manager, 'set_spot_size'):
self.manager.set_spot_size(size)
def request_zlevel(self, roi_ix):
if not hasattr(self, 'manager'):
return
if not isinstance(self.manager, managers.ManagerVolROI):
return
roi = self.manager.roi_list[roi_ix]
if not roi.visible:
self.vi.viewer.ui.verticalSliderZLevel.setValue(roi.zcenter)