#=========================================================================================
# 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 $"
__dateModified__ = "$dateModified: 2021-06-04 19:38:32 +0100 (Fri, June 04, 2021) $"
__version__ = "$Revision: 3.0.4 $"
#=========================================================================================
# Created
#=========================================================================================
__author__ = "$Author: Luca Mureddu $"
__date__ = "$Date: 2017-05-28 10:28:42 +0000 (Sun, May 28, 2017) $"
#=========================================================================================
# 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.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 = 'Annotate Peaks'
AnnotationLabel = 'Annotation'
FromSubstanceName = 'Use_linked_Substance_Name'
FromSpectrumName = 'Use_Spectrum_Name'
AnnotationOptions = [FromSubstanceName, FromSpectrumName]
DefaultPeakListIndice = -1
########################################################################################################################
########################################## ALGORITHM ########################################################
########################################################################################################################
def _getAnnotation(spectrum, _kwargs):
useSpectrumName = _kwargs.get(AnnotationLabel) == FromSpectrumName
useSubstanceName = _kwargs.get(AnnotationLabel) == FromSubstanceName
annotation = ''
if useSpectrumName:
annotation = spectrum.name
if useSubstanceName:
substances = spectrum.referenceSubstances
if len(substances) > 1:
getLogger().warning('Multiple substances for Spectrum: %s. Skipped.' % spectrum.name)
annotation = spectrum.name
if len(substances) == 1:
annotation = substances[0].name
return annotation
########################################################################################################################
########################################## GUI PIPE #############################################################
########################################################################################################################
[docs]class SetPeakAnnotationsFromSpectrumGuiPipe(GuiPipe):
pipeName = PipeName
def __init__(self, name=pipeName, parent=None, project=None, **kw):
super(SetPeakAnnotationsFromSpectrumGuiPipe, self)
GuiPipe.__init__(self, parent=parent, name=name, project=project, **kw)
self.parent = parent
row = 0
self.snapPeaksLabel = Label(self.pipeFrame, AnnotationLabel, grid=(row, 0))
setattr(self, AnnotationLabel, RadioButtons(self.pipeFrame,
texts=AnnotationOptions, selectedInd=0,
direction='v',
callback=None, grid=(row, 1)))
########################################################################################################################
########################################## PIPE #############################################################
########################################################################################################################
[docs]class SetPeakAnnotationsFromSpectrumPipe(SpectraPipe):
"""
Annotate peaks in the input spectra using available options:
- parent spectrum Name
- reference Substance name linked to the parent spectrum
- others to be implemented ( such as a free entry Regex text )
"""
guiPipe = SetPeakAnnotationsFromSpectrumGuiPipe
pipeName = PipeName
pipeCategory = PIPE_SCREEN
_kwargs = {
AnnotationLabel: FromSubstanceName,
}
[docs] def runPipe(self, spectra):
'''
:param spectra: inputData
:return: spectra
'''
if not spectra:
getLogger().warning('Spectra not present. Add spectra first')
return spectra
with undoBlockWithoutSideBar():
if self.project is not None:
# pks = [pk for sp in spectra for pk in sp.peakLists[DefaultPeakListIndice].peaks]
# list(map(lambda pk: setattr(pk, 'annotation', _getAnnotation(pk.spectrum, self._kwargs)), pks))
for sp in spectra:
for pk in sp.peakLists[DefaultPeakListIndice].peaks:
pk.annotation = _getAnnotation(sp, self._kwargs)
return spectra
SetPeakAnnotationsFromSpectrumPipe.register() # Registers the pipe in the pipeline