Source code for ccpn.ui.gui.modules.IntegralTable

# Licence, Reference and Credits
__copyright__ = "Copyright (C) CCPN project ( 2014 - 2021"
__credits__ = ("Ed Brooksbank, Joanna Fox, Victoria A Higman, Luca Mureddu, Eliza Płoskoń",
               "Timothy J Ragan, Brian O Smith, Gary S Thompson & Geerten W Vuister")
__licence__ = ("CCPN licence. See")
__reference__ = ("Skinner, S.P., Fogh, R.H., Boucher, W., Ragan, T.J., Mureddu, L.G., & Vuister, G.W.",
                 "CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis",
                 "J.Biomol.Nmr (2016), 66, 111-124,")
# Last code modification
__modifiedBy__ = "$modifiedBy: Geerten Vuister $"
__dateModified__ = "$dateModified: 2021-12-23 15:18:25 +0000 (Thu, December 23, 2021) $"
__version__ = "$Revision: 3.0.4 $"
# Created
__author__ = "$Author: Luca Mureddu $"
__date__ = "$Date: 2017-04-07 10:28:42 +0000 (Fri, April 07, 2017) $"
# Start of code

from PyQt5 import QtWidgets
from ccpn.ui.gui.modules.CcpnModule import CcpnModule
from ccpn.ui.gui.widgets.Spacer import Spacer
from ccpn.ui.gui.widgets.GuiTable import GuiTable
from ccpn.ui.gui.widgets.Column import ColumnClass
from ccpn.core.lib.Notifiers import Notifier
from ccpn.ui.gui.widgets.PulldownListsForObjects import IntegralListPulldown
from ccpn.core.IntegralList import IntegralList
from ccpn.core.Integral import Integral
from ccpn.util.Logging import getLogger
from ccpn.core.lib.CallBack import CallBack

logger = getLogger()
ALL = '<all>'

[docs]class IntegralTableModule(CcpnModule): """ This class implements the module by wrapping a integralTable instance """ includeSettingsWidget = False maxSettingsState = 2 # states are defined as: 0: invisible, 1: both visible, 2: only settings visible settingsPosition = 'top' className = 'IntegralTableModule' _allowRename = True # we are subclassing this Module, hence some more arguments to the init def __init__(self, mainWindow=None, name='Integral Table', integralList=None, selectFirstItem=False): """ Initialise the Module widgets """ CcpnModule.__init__(self, mainWindow=mainWindow, name=name) # Derive application, project, and current from mainWindow self.mainWindow = mainWindow self.application = mainWindow.application self.project = mainWindow.application.project self.current = mainWindow.application.current self.integralTable = IntegralTable(parent=self.mainWidget, mainWindow=self.mainWindow, moduleParent=self, setLayout=True, grid=(0, 0)) if integralList is not None: self.selectIntegralList(integralList) elif selectFirstItem: self.integralTable.itWidget.selectFirstItem() # install the event filter to handle maximising from floated dock self.installMaximiseEventHandler(self._maximise, self._closeModule) def _maximise(self): """ Maximise the attached table """ self.integralTable._maximise()
[docs] def selectIntegralList(self, integralList=None): """ Manually select a IL from the pullDown """ self.integralTable._selectIntegralList(integralList)
def _closeModule(self): """ CCPN-INTERNAL: used to close the module """ self.integralTable._close() super()._closeModule()
[docs]class IntegralTable(GuiTable): """ Class to present a IntegralTable pulldown list, wrapped in a Widget """ className = 'IntegralTable' attributeName = 'integralLists' OBJECT = 'object' TABLE = 'table' @staticmethod def _setFigureOfMerit(obj, value): """ CCPN-INTERNAL: Set figureOfMerit from table Must be a floatRatio in range [0.0, 1.0] """ # ejb - why is it blanking a notification here? # NmrResidueTable._project.blankNotification() # clip and set the figure of merit obj.figureOfMerit = min(max(float(value), 0.0), 1.0) if value else None @staticmethod def _setBaseline(obj, value): """ CCPN-INTERNAL: Edit baseline of integral """ obj.baseline = float(value) if value else None def __init__(self, parent=None, mainWindow=None, moduleParent=None, integralList=None, **kwds): """ Initialise the widgets for the module. """ # Derive application, project, and current from mainWindow self.mainWindow = mainWindow if mainWindow: self.application = mainWindow.application self.project = mainWindow.application.project self.current = mainWindow.application.current else: self.application = None self.project = None self.current = None IntegralTable.project = self.project kwds['setLayout'] = True ## Assure we have a layout with the widget self.integralList = None # Initialise the scroll widget and common settings self._initTableCommonWidgets(parent, **kwds) figureOfMeritTipText = 'Figure of merit' commentsTipText = 'Textual notes about the integral' # create the column objects self.ITcolumns = ColumnClass([ ('#', lambda il: il.serial, '', None, None), ('Pid', lambda il:, 'Pid of integral', None, None), ('_object', lambda il: il, 'Object', None, None), ('Spectrum', lambda il:, 'Spectrum containing the Integral', None, None), ('IntegralList', lambda il: il.integralList.serial, 'IntegralList containing the Integral', None, None), ('Id', lambda il: il.serial, 'Integral serial', None, None), ('Value', lambda il: il.value, '', None, None), ('Lower Limit', lambda il: IntegralTable._getLowerLimit(il), '', None, None), ('Higher Limit', lambda il: IntegralTable._getHigherLimit(il), '', None, None), ('ValueError', lambda il: il.valueError, '', None, None), ('Bias', lambda il: il.bias, '', None, None), ('FigureOfMerit', lambda il: il.figureOfMerit, figureOfMeritTipText, lambda il, value: self._setFigureOfMerit(il, value), None), ('Baseline', lambda il: il.baseline, 'Baseline for the integral area', lambda il, value: self._setBaseline(il, value), None), ('Slopes', lambda il: il.slopes, '', None, None), # ('Annotation', lambda il: il.annotation, '', None, None), ('Comment', lambda il: self._getCommentText(il), commentsTipText, lambda il, value: self._setComment(il, value), None), ] ) # [Column(colName, func, tipText=tipText, setEditValue=editValue, format=columnFormat) # create the table; objects are added later via the displayTableForIntegrals method self.spacer = Spacer(self._widget, 5, 5, QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Fixed, grid=(0, 0), gridSpan=(1, 1)) self.itWidget = IntegralListPulldown(parent=self._widget, mainWindow=self.mainWindow, default=None, grid=(1, 0), gridSpan=(1, 1), minimumWidths=(0, 100), showSelectName=True, sizeAdjustPolicy=QtWidgets.QComboBox.AdjustToContents, callback=self._selectionPulldownCallback) self.spacer = Spacer(self._widget, 5, 5, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Fixed, grid=(2, 1), gridSpan=(1, 1)) self._widget.getLayout().setColumnStretch(1, 2) # initialise the currently attached dataFrame self._hiddenColumns = ['Pid', 'Spectrum', 'IntegralList', 'Id'] self.dataFrameObject = None # initialise the table super().__init__(parent=parent, mainWindow=self.mainWindow, dataFrameObject=None, setLayout=True, autoResize=True, selectionCallback=self._selectionCallback, actionCallback=self._actionCallback, multiSelect=True, grid=(3, 0), gridSpan=(1, 6)) self.moduleParent = moduleParent if integralList is not None: self._selectIntegralList(integralList) self.setTableNotifiers(tableClass=IntegralList, rowClass=Integral, cellClassNames=None, tableName='integralList', rowName='integral', changeFunc=self.displayTableForIntegralList, className=self.attributeName, updateFunc=self._update, tableSelection='integralList', pullDownWidget=self.ITcolumns, callBackClass=Integral, selectCurrentCallBack=self._selectOnTableCurrentIntegralsNotifierCallback, moduleParent=moduleParent) # Initialise the notifier for processing dropped items self._postInitTableCommonWidgets() def _processDroppedItems(self, data): """ CallBack for Drop events """ pids = data.get('pids', []) self._handleDroppedItems(pids, IntegralList, self.itWidget) def _selectIntegralList(self, integralList=None): """ Manually select a IntegralList from the pullDown """ if integralList is None: # logger.debug('select: No IntegralList selected') # raise ValueError('select: No IntegralList selected') self.itWidget.selectFirstItem() else: if not isinstance(integralList, IntegralList): getLogger().warning(f'select: Object {integralList} is not of type IntegralList') return else: for widgetObj in self.itWidget.textList: if == widgetObj: self.integralList = integralList def _getPullDownSelection(self): return self.itWidget.getText() def _selectPullDown(self, value):
[docs] def displayTableForIntegralList(self, integralList): """ Display the table for the IntegralList" """ self._update(integralList)
def _updateCallback(self, data): """ Notifier callback for updating the table """ thisIntegralList = getattr(data[Notifier.THEOBJECT], self.attributeName) # get the integralList if self.integralList in thisIntegralList: self.displayTableForIntegralList(self.integralList) else: self.clearTable() def _maximise(self): """ Redraw the table on a maximise event """ if self.integralList: self.displayTableForIntegralList(self.integralList) else: self.clear() def _update(self, integralList): """ Update the table """ self.populateTable(rowObjects=integralList.integrals, columnDefs=self.ITcolumns ) def _selectionCallback(self, data, *args): """ Set as current the selected integrals on the table """ integrals = data[CallBack.OBJECT] # self._clearRegions() if integrals is None: self.current.clearIntegrals() else: self.current.integrals = integrals def _actionCallback(self, data): """ Notifier DoubleClick action on item in table """ objs = data[CallBack.OBJECT] if not objs: return if isinstance(objs, (tuple, list)): integral = objs[0] else: integral = objs # self._showRegions() self._navigateToPosition() # logger.debug(str(NotImplemented)) def _selectionPulldownCallback(self, item): """ Notifier Callback for selecting integral from the pull down menu """ if item is not None: self.integralList = self.project.getByPid(item) if self.integralList is not None: self.displayTableForIntegralList(self.integralList) else: self.clearTable() def _selectOnTableCurrentIntegralsNotifierCallback(self, data): """ Callback from a notifier to select the current Integrals """ currentIntegrals = data['value'] self._selectOnTableCurrentIntegrals(currentIntegrals) def _selectOnTableCurrentIntegrals(self, currentIntegrals): """ Highlight current integrals on the opened integral table """ self.highlightObjects(currentIntegrals) def _navigateToPosition(self): """ If current strip contains the double clicked peak will navigateToPositionInStrip """ from ccpn.ui.gui.lib.StripLib import navigateToPositionInStrip, _getCurrentZoomRatio integral = self.current.integral if self.current.strip is not None: widths = None try: widths = _getCurrentZoomRatio(self.current.strip.viewRange()) if len(integral.limits) == 1: positions = integral.limits[0] navigateToPositionInStrip(strip=self.current.strip, positions=positions, widths=widths) except Exception as e: logger.warning('Impossible to navigate to peak position.', e) else: logger.warning('Impossible to navigate to peak position. Set a current strip first') @staticmethod def _getHigherLimit(integral): """ Returns HigherLimit """ # FIXME Wrapper? BUG if limits is None if integral is not None: if len(integral.limits) > 0: limits = integral.limits[0] if limits is not None: return float(max(limits)) @staticmethod def _getLowerLimit(integral): """ Returns Lower Limit """ if integral is not None: if len(integral.limits) > 0: limits = integral.limits[0] if limits: return float(min(limits)) def _close(self): """ Cleanup the notifiers when the window is closed """ super()._close()