#=========================================================================================
# Licence, Reference and Credits
#=========================================================================================
__copyright__ = "Copyright (C) CCPN project (http://www.ccpn.ac.uk) 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 http://www.ccpn.ac.uk/v3-software/downloads/license")
__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: Ed Brooksbank $"
__dateModified__ = "$Date: 2021-05-19 16:26:00 +0100 (Wed, May 19, 2021) $"
__dateModified__ = "$dateModified: 2021-06-04 19:38:32 +0100 (Fri, June 04, 2021) $"
__version__ = "$Revision: 3.0.4 $"
#=========================================================================================
# Created
#=========================================================================================
__author__ = "$Author: Luca Mureddu $"
__date__ = "$Date: 2021-05-19 16:26:00 +0100 (Wed, May 19, 2021) $"
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# Start of code
#=========================================================================================
#### GUI IMPORTS
from ccpn.AnalysisScreen.gui.widgets import HitFinderWidgets as hw
from ccpn.ui.gui.widgets.PipelineWidgets import GuiPipe
from ccpn.ui.gui.widgets.Label import Label
from ccpn.ui.gui.widgets.CheckBox import CheckBox
from ccpn.ui.gui.widgets.DoubleSpinbox import DoubleSpinbox, ScientificDoubleSpinBox
from ccpn.ui.gui.widgets.RadioButtons import RadioButtons
#### NON GUI IMPORTS
from ccpn.framework.lib.pipeline.PipeBase import SpectraPipe, PIPE_SCREEN
from ccpn.core.lib.peakUtils import snap1DPeaksToExtrema
from ccpn.AnalysisScreen.lib.experimentAnalysis.Common import _getReferencesFromSample
from ccpn.util.Logging import getLogger
from ccpn.core.lib.ContextManagers import undoBlock, notificationEchoBlocking, \
undoBlockWithoutSideBar, undoStackBlocking
########################################################################################################################
### Attributes:
### Used in setting the dictionary keys on _kwargs either in GuiPipe and Pipe
########################################################################################################################
PipeName = 'Propagate Peaks From References'
Propagate_ToSG = 'Propagate_To'
PeakListLabel = 'PeakList'
Last = 'Last'
New = 'New'
PlistOptions = [Last, New]
SnapNewPeak = 'Snap_Peaks'
Tolerance = 'Max_snap_distance_(ppm)'
SGVarNames = [Propagate_ToSG]
defaultPeakListIndice = -1
DefaultSnap = True
DefaultTolerance = 0.1 #ppm
########################################################################################################################
########################################## ALGORITHM ########################################################
########################################################################################################################
########################################################################################################################
########################################## GUI PIPE #############################################################
########################################################################################################################
[docs]class PropagatePeaksFromReferencesGuiPipe(GuiPipe):
pipeName = PipeName
def __init__(self, name=pipeName, parent=None, project=None, **kw):
super(PropagatePeaksFromReferencesGuiPipe, self)
GuiPipe.__init__(self, parent=parent, name=name, project=project, **kw)
self.parent = parent
row = 0
hw._addSGpulldowns(self, row, SGVarNames)
row += len(SGVarNames)
self.snapPeaksLabel = Label(self.pipeFrame, PeakListLabel, grid=(row, 0))
setattr(self, PeakListLabel, RadioButtons(self.pipeFrame,
texts=PlistOptions, selectedInd=0,
direction='v',
callback=None, grid=(row, 1)))
row += 1
self.snapPeaksLabel = Label(self.pipeFrame, SnapNewPeak, grid=(row, 0))
setattr(self, SnapNewPeak, CheckBox(self.pipeFrame, checked=DefaultSnap, callback=None, grid=(row, 1)))
row += 1
self.ToleranceLabel = Label(self.pipeFrame, text=Tolerance, grid=(row, 0))
setattr(self, Tolerance, ScientificDoubleSpinBox(self.pipeFrame, value=DefaultTolerance, min=0.0001,
step=0.01, decimals=3, grid=(row, 1)))
self._updateWidgets()
def _updateWidgets(self):
self._setSpectrumGroupPullDowns(SGVarNames)
########################################################################################################################
########################################## PIPE #############################################################
########################################################################################################################
[docs]class PropagatePeaksFromReferencesPipe(SpectraPipe):
"""
Apply phasing to all the spectra in the pipeline
"""
guiPipe = PropagatePeaksFromReferencesGuiPipe
pipeName = PipeName
pipeCategory = PIPE_SCREEN
_kwargs = {
Propagate_ToSG: 'ControlSpectrumGroup.pid', #this will be replaced by the SG pid in the gui
SnapNewPeak: DefaultSnap,
Tolerance : DefaultSnap,
PeakListLabel : Last,
}
[docs] def runPipe(self, spectra):
'''
:param spectra: inputData
:return: spectra
'''
# self.project.blankNotification()
propagate_ToSG = self._getSpectrumGroup(self._kwargs[Propagate_ToSG])
createNewPL = True if self._kwargs[PeakListLabel] == New else False
with undoBlockWithoutSideBar():
if self.project is not None:
if propagate_ToSG is not None:
for controlSpectrum in propagate_ToSG.spectra:
allPeaks = []
references = _getReferencesFromSample(controlSpectrum)
for spectrum in references:
allPeaks += spectrum.peakLists[-1].peaks
# create a newPeakList where to paste the references peaks
if createNewPL:
pl= controlSpectrum.newPeakList()
else:
pl = controlSpectrum.peakLists[-1] or controlSpectrum.newPeakList() # New PL if None avail
for peak in allPeaks:
peak.copyTo(pl)
if self._kwargs[SnapNewPeak]:
snap1DPeaksToExtrema(allPeaks, self._kwargs[Tolerance])
return spectra
else:
getLogger().warning('Spectra not present. Add spectra first')
return spectra
PropagatePeaksFromReferencesPipe.register() # Registers the pipe in the pipeline