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

"""Module Documentation here

"""
#=========================================================================================
# Licence, Reference and Credits
#=========================================================================================
__copyright__ = "Copyright (C) CCPN project (https://www.ccpn.ac.uk) 2014 - 2022"
__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 https://ccpn.ac.uk/software/licensing/")
__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, http://doi.org/10.1007/s10858-016-0060-y")
#=========================================================================================
# Last code modification
#=========================================================================================
__modifiedBy__ = "$modifiedBy: Luca Mureddu $"
__dateModified__ = "$dateModified: 2022-03-04 18:50:46 +0000 (Fri, March 04, 2022) $"
__version__ = "$Revision: 3.1.0 $"
#=========================================================================================
# Created
#=========================================================================================
__author__ = "$Author: CCPN $"
__date__ = "$Date: 2017-04-07 10:28:41 +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.Label import Label
from ccpn.ui.gui.widgets.PulldownList import PulldownList
from ccpn.ui.gui.widgets.PulldownListsForObjects import PeakListPulldown
from ccpn.ui.gui.widgets.GuiTable import GuiTable
from ccpn.ui.gui.widgets.Column import ColumnClass
from ccpn.ui.gui.widgets.Spacer import Spacer
from ccpn.ui.gui.lib.GuiStripContextMenus import _selectedPeaksMenuItem, _addMenuItems, \
    _getNdPeakMenuItems, _setEnabledAllItems
from ccpn.core.PeakList import PeakList
from ccpn.core.Peak import Peak
from ccpn.core.NmrAtom import NmrAtom
from ccpn.core.lib.CallBack import CallBack
from ccpn.core.lib.peakUtils import getPeakPosition, getPeakAnnotation, getPeakLinewidth
from ccpn.util.Logging import getLogger


logger = getLogger()

UNITS = ['ppm', 'Hz', 'point']


[docs]class PeakTableModule(CcpnModule): """ This class implements the module by wrapping a PeakListTable instance """ includeSettingsWidget = False maxSettingsState = 2 settingsPosition = 'top' className = 'PeakTableModule' _allowRename = True def __init__(self, mainWindow=None, name='Peak Table', peakList=None, selectFirstItem=False): super().__init__(mainWindow=mainWindow, name=name) # Derive application, project, and current from mainWindow self.mainWindow = mainWindow self.application = mainWindow.application self.project = mainWindow.project self.current = mainWindow.application.current # mainWidget self.peakListTable = PeakListTableWidget(parent=self.mainWidget, mainWindow=self.mainWindow, moduleParent=self, setLayout=True, grid=(0, 0)) if peakList is not None: self.selectPeakList(peakList) elif selectFirstItem: self.peakListTable.pLwidget.selectFirstItem() self.installMaximiseEventHandler(self._maximise, self._closeModule) @property def _dataFrame(self): if self.peakListTable._dataFrameObject: return self.peakListTable._dataFrameObject.dataFrame def _maximise(self): """ Maximise the attached table """ self.peakListTable._maximise()
[docs] def selectPeakList(self, peakList=None): """ Manually select a peakList from the pullDown """ self.peakListTable._selectPeakList(peakList)
def _closeModule(self): """Re-implementation of closeModule function from CcpnModule to unregister notification """ self.peakListTable._close() super()._closeModule()
[docs]class PeakListTableWidget(GuiTable): """ Class to present a peakList Table """ className = 'PeakListTable' attributeName = 'peakLists' positionsUnit = UNITS[0] #default @staticmethod def _setFigureOfMerit(obj, value): """ CCPN-INTERNAL: Set figureOfMerit from table Must be a floatRatio in range [0.0, 1.0] """ # clip and set the figure of merit obj.figureOfMerit = min(max(float(value), 0.0), 1.0) if value else None def __init__(self, parent=None, mainWindow=None, moduleParent=None, peakList=None, multiSelect=True, actionCallback=None, selectionCallback=None, **kwds): """ Initialise the table """ # 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 PeakListTableWidget.project = self.project self.settingWidgets = None self._selectedPeakList = None kwds['setLayout'] = True # Assure we have a layout with the widget # Initialise the scroll widget and common settings self._initTableCommonWidgets(parent, **kwds) row = 0 self.spacer = Spacer(self._widget, 5, 5, QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Fixed, grid=(row, 0), gridSpan=(1, 1)) row += 1 gridHPos = 0 self.pLwidget = PeakListPulldown(parent=self._widget, mainWindow=self.mainWindow, grid=(row, gridHPos), gridSpan=(1, 1), showSelectName=True, minimumWidths=(0, 100), sizeAdjustPolicy=QtWidgets.QComboBox.AdjustToContents, callback=self._pulldownPLcallback) # create widgets for selection of position units gridHPos += 1 self.posUnitPulldownLabel = Label(parent=self._widget, text=' Position Unit', grid=(row, gridHPos)) gridHPos += 1 self.posUnitPulldown = PulldownList(parent=self._widget, texts=UNITS, callback=self._pulldownUnitsCallback, grid=(row, gridHPos), objectName='posUnits_PT') row += 1 self.spacer = Spacer(self._widget, 5, 5, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Fixed, grid=(row, gridHPos + 1), gridSpan=(1, 1)) self._widget.getLayout().setColumnStretch(gridHPos + 1, 2) self._hiddenColumns = ['Pid', 'Spectrum', 'PeakList', 'Id', 'HeightError', 'VolumeError'] self.dataFrameObject = None selectionCallback = self._selectionCallback if selectionCallback is None else selectionCallback actionCallback = self._actionCallback if actionCallback is None else actionCallback super().__init__(parent=parent, mainWindow=self.mainWindow, dataFrameObject=None, setLayout=True, autoResize=True, multiSelect=multiSelect, actionCallback=actionCallback, selectionCallback=selectionCallback, grid=(3, 0), gridSpan=(1, 6)) self.moduleParent = moduleParent # populate the table if there are peakLists in the project if peakList is not None: self._selectPeakList(peakList) self.setTableNotifiers(tableClass=PeakList, rowClass=Peak, cellClassNames=(NmrAtom, 'assignedPeaks'), tableName='peakList', rowName='peak', changeFunc=self._updateAllModule, className=self.attributeName, updateFunc=self._updateAllModule, tableSelection='_selectedPeakList', pullDownWidget=self.pLwidget, callBackClass=Peak, selectCurrentCallBack=self._selectOnTableCurrentPeaksNotifierCallback, moduleParent=moduleParent) # Initialise the notifier for processing dropped items self._postInitTableCommonWidgets() def _setContextMenu(self, enableExport=True, enableDelete=True): """Subclass guiTable to add new items to context menu """ super()._setContextMenu(enableExport=enableExport, enableDelete=enableDelete) _actions = self.tableMenu.actions() if _actions: # _topMenuItem = _actions[0] # _topSeparator = self.tableMenu.insertSeparator(_topMenuItem) # self._copyPeakMenuAction = self.tableMenu.addAction('Copy Peaks...', self._copyPeaks) # # move new actions to the top of the list # self.tableMenu.insertAction(_topSeparator, self._copyPeakMenuAction) # add the selected peaks menu to the bottom self.tableMenu.addSeparator() _peakItem = _selectedPeaksMenuItem(None) _addMenuItems(self, self.tableMenu, [_peakItem]) # _selectedPeaksMenu submenu - add to Strip._selectedPeaksMenu items = _getNdPeakMenuItems(menuId='Main') # attach to the _selectedPeaksMenu submenu _addMenuItems(self, self._selectedPeaksMenu, items) def _raiseTableContextMenu(self, pos): """Raise the right-mouse menu """ # Enable/disable menu items as required self._navigateToPeakMenuMain.setEnabled(False) _setEnabledAllItems(self._selectedPeaksMenu, True if self.current.peaks else False) super(PeakListTableWidget, self)._raiseTableContextMenu(pos) def _processDroppedItems(self, data): """CallBack for Drop events """ pids = data.get('pids', []) self._handleDroppedItems(pids, PeakList, self.pLwidget) def _getTableColumns(self, peakList): """Add default columns plus the ones according with peakList.spectrum dimension format of column = ( Header Name, value, tipText, editOption) editOption allows the user to modify the value content by doubleclick """ columnDefs = [] # Serial column columnDefs.append(('#', 'serial', 'Peak serial number', None, None)) columnDefs.append(('Pid', lambda pk: pk.pid, 'Pid of the Peak', None, None)) columnDefs.append(('_object', lambda pk: pk, 'Object', None, None)) columnDefs.append(('Spectrum', lambda pk: pk.peakList.spectrum.id, 'Spectrum containing the Peak', None, None)) columnDefs.append(('PeakList', lambda pk: pk.peakList.serial, 'PeakList containing the Peak', None, None)) columnDefs.append(('Id', lambda pk: pk.serial, 'Peak serial', None, None)) # Assignment column for i in range(peakList.spectrum.dimensionCount): assignTipText = 'NmrAtom assignments of peak in dimension %s' % str(i + 1) columnDefs.append( ('Assign F%s' % str(i + 1), lambda pk, dim=i: getPeakAnnotation(pk, dim), assignTipText, None, None) ) # # Expanded Assignment columns # for i in range(peakList.spectrum.dimensionCount): # assignTipText = 'NmrAtom assignments of peak in dimension %s' % str(i + 1) # columnDefs.append(('Assign F%s' % str(i + 1), lambda pk, dim=i: self._getNmrChain(pk, dim), assignTipText, None, None)) # columnDefs.append(('Assign F%s' % str(i + 1), lambda pk, dim=i: self._getSequenceCode(pk, dim), assignTipText, None, None)) # columnDefs.append(('Assign F%s' % str(i + 1), lambda pk, dim=i: self._getResidueType(pk, dim), assignTipText, None, None)) # columnDefs.append(('Assign F%s' % str(i + 1), lambda pk, dim=i: self._getAtomType(pk, dim), assignTipText, None, None)) # Peak positions column for i in range(peakList.spectrum.dimensionCount): positionTipText = 'Peak position in dimension %s' % str(i + 1) columnDefs.append( ('Pos F%s' % str(i + 1), lambda pk, dim=i, unit=self.positionsUnit: getPeakPosition(pk, dim, unit), positionTipText, None, '%0.3f') ) # linewidth column TODO remove hardcoded Hz unit for i in range(peakList.spectrum.dimensionCount): linewidthTipTexts = 'Peak line width %s' % str(i + 1) columnDefs.append( ('LW F%s (Hz)' % str(i + 1), lambda pk, dim=i: getPeakLinewidth(pk, dim), linewidthTipTexts, None, '%0.3f') ) # height column heightTipText = 'Magnitude of spectrum intensity at peak center (interpolated), unless user edited' columnDefs.append(('Height', lambda pk: pk.height if pk.height else 'None', heightTipText, None, None)) columnDefs.append(('HeightError', lambda pk: pk.heightError, 'Error of the height', None, None)) columnDefs.append(('S/N', lambda pk: pk.signalToNoiseRatio, 'Signal to Noise Ratio', None, None)) # volume column volumeTipText = 'Integral of spectrum intensity around peak location, according to chosen volume method' columnDefs.append(('Volume', lambda pk: pk.volume if pk.volume else 'None', volumeTipText, None, None)) columnDefs.append(('VolumeError', lambda pk: pk.volumeError, 'Error of the volume', None, None)) # ClusterId column clusterIdTipText = 'The peak clusterId. ClusterIds are used for grouping peaks in fitting routines.' columnDefs.append(('ClusterId', lambda pk: pk.clusterId if pk.clusterId else 'None', clusterIdTipText, lambda pk, value: self._setClusterId(pk, value), None)) # figureOfMerit column figureOfMeritTipText = 'Figure of merit' columnDefs.append(('Merit', lambda pk: pk.figureOfMerit, figureOfMeritTipText, lambda pk, value: self._setFigureOfMerit(pk, value), None) ) # annotation column annotationTipText = 'Any other peak label (excluded assignments)' columnDefs.append(('Annotation', lambda pk: self._getAnnotation(pk), annotationTipText, lambda pk, value: self._setAnnotation(pk, value), None)) # comment column commentsTipText = 'Textual notes about the peak' columnDefs.append(('Comment', lambda pk: self._getCommentText(pk), commentsTipText, lambda pk, value: self._setComment(pk, value), None) ) return ColumnClass(columnDefs) #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # Updates #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ def _maximise(self): """Refresh the table on a maximise event """ self._updateTable() def _updateAllModule(self, data=None): """Updates the table and the settings widgets """ self._updateTable() def _updateTable(self, useSelectedPeakList=True, peaks=None, peakList=None): """Display the peaks on the table for the selected PeakList. Obviously, If the peak has not been previously deleted and flagged isDeleted """ self._selectedPeakList = self.project.getByPid(self.pLwidget.getText()) if useSelectedPeakList: if self._selectedPeakList: self.populateTable(rowObjects=self._selectedPeakList.peaks, columnDefs=self._getTableColumns(self._selectedPeakList), selectedObjects=self.current.peaks) else: self.clear() else: if peaks: if peakList: self.populateTable(rowObjects=peaks, columnDefs=self._getTableColumns(peakList), selectedObjects=self.current.peaks) else: self.clear() def _selectPeakList(self, peakList=None): """Manually select a PeakList from the pullDown """ if peakList is None: # logger.warning('select: No PeakList selected') # raise ValueError('select: No PeakList selected') self.pLwidget.selectFirstItem() else: if not isinstance(peakList, PeakList): logger.warning('select: Object is not of type PeakList') raise TypeError('select: Object is not of type PeakList') else: for widgetObj in self.pLwidget.textList: if peakList.pid == widgetObj: self._selectedPeakList = peakList self.pLwidget.select(self._selectedPeakList.pid) #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # Widgets callbacks #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ def _getPullDownSelection(self): return self.pLwidget.getText() def _actionCallback(self, data, *args): """If current strip contains the double clicked peak will navigateToPositionInStrip """ from ccpn.ui.gui.lib.StripLib import navigateToPositionInStrip, _getCurrentZoomRatio # multiselection table will return a list of objects objs = data[CallBack.OBJECT] if not objs: return if isinstance(objs, (tuple, list)): peak = objs[0] else: peak = objs if self.current.strip is not None: validPeakListViews = [pp.peakList for pp in self.current.strip.peakListViews if isinstance(pp.peakList, PeakList)] if peak and peak.peakList in validPeakListViews: widths = None if peak.peakList.spectrum.dimensionCount <= 2: widths = _getCurrentZoomRatio(self.current.strip.viewRange()) navigateToPositionInStrip(strip=self.current.strip, positions=peak.position, axisCodes=peak.axisCodes, widths=widths) else: logger.warning('Impossible to navigate to peak position. Set a current strip first') def _selectionCallback(self, data, *args): """ set as current the selected peaks on the table """ peaks = data[CallBack.OBJECT] if peaks is None: self.current.clearPeaks() else: self.current.peaks = peaks def _pulldownUnitsCallback(self, unit): # update the table with new units self._setPositionUnit(unit) self._updateAllModule() def _pulldownPLcallback(self, data): self._updateAllModule() def _copyPeaks(self): from ccpn.ui.gui.popups.CopyPeaksPopup import CopyPeaks popup = CopyPeaks(parent=self.mainWindow, mainWindow=self.mainWindow) self._selectedPeakList = self.project.getByPid(self.pLwidget.getText()) if self._selectedPeakList is not None: spectrum = self._selectedPeakList.spectrum popup._selectSpectrum(spectrum) popup._selectPeaks(self.current.peaks) popup.exec_() def _selectOnTableCurrentPeaksNotifierCallback(self, data): """ Callback from a notifier to highlight the peaks on the peak table :param data: """ currentPeaks = data['value'] self._selectOnTableCurrentPeaks(currentPeaks) def _selectOnTableCurrentPeaks(self, currentPeaks): """ Highlight the list of peaks on the table :param currentPeaks: """ self.highlightObjects(currentPeaks) def _setPositionUnit(self, value): if value in UNITS: self.positionsUnit = value