baseline subtract

aredakau

Hello all,

I need help regarding baseline subtract. I have no experience with Python, but I am trying to create a DRS that can calculate isotopic ratios. To do that I used some function from the templates in github which work very well. However, I am facing an issue with the baseline subtract as baseline comes very large which makes inspecting the selection of the ratios very difficult. I know that fixing the Cutoff Threshold could help with this but I have no idea what is the appropriate function that can used to do that.

Here is the lines that I am trying to use for baseline

`def runDRS():

drs.message("Starting baseline subtract DRS...")
drs.progress(0)

# Get settings
settings = drs.settings()
print(settings)   

indexChannel = data.timeSeries(settings["IndexChannel"])
rmName = settings["ReferenceMaterial"]
maskChannel = data.timeSeries(settings["MaskChannel"])
cutoff = settings["MaskCutoff"]
threshold = setting["MaskThreshold"] #trying to add 'maskthershold'
trim = settings["MaskTrim"]
propErrors = settings["PropagateError"]

# Create debug messages for the settings being used
IoLog.debug("indexChannelName = %s" % indexChannel.name)
IoLog.debug("maskChannelName = %s" % maskChannel.name)
IoLog.debug("maskCutoff = %f" % cutoff)
Iolog.debug("maskthreshold= %f" %threshold)  #trying to add 'maskthershold'
IoLog.debug("maskTrim = %f" % trim)

# Setup index time
drs.message("Setting up index time...")
drs.progress(5)
drs.setIndexChannel(indexChannel)

# Setup the mask
drs.message("Making mask...")
drs.progress(10)
mask = drs.createMaskFromCutoff(maskChannel, cutoff, trim) 
#I thins this above line need to be changed but what is the correct function?

# Interp onto index time and baseline subtract
drs.message("Interpolating onto index time and baseline subtracting...")
drs.progress(25)

allInputChannels = data.timeSeriesList(data.Input)

for counter, channel in enumerate(allInputChannels):
	drs.message("Baseline subtracting %s" % channel.name)
	drs.progress(25 + 50*counter/len(allInputChannels))
	sleep(0.5) # Sleeping only so that the progress can be observed

	drs.baselineSubtract(data.selectionGroup("Baseline"), [allInputChannels[counter]], mask, 25, 100)`

Also, here is the settingsWidget() part

`def settingsWidget():

widget = QtGui.QWidget()
formLayout = QtGui.QFormLayout()
widget.setLayout(formLayout)

timeSeriesNames = data.timeSeriesNames(data.Input)
defaultChannelName = ""
if timeSeriesNames:
	defaultChannelName = timeSeriesNames[0]

rmNames = data.selectionGroupNames(data.ReferenceMaterial)

drs.setSetting("IndexChannel",defaultChannelName)
drs.setSetting("ReferenceMaterial", "M_MicaMG")
drs.setSetting("MaskChannel", defaultChannelName)
drs.setSetting("MaskCutoff", 100000.0)
drs.setSetting("MaskThreshold", 1000) #trying to add MaskThreshold
drs.setSetting("MaskTrim", 0.0)
drs.setSetting("PropagateError", False)

settings = drs.settings()

indexComboBox = QtGui.QComboBox(widget)
indexComboBox.addItems(data.timeSeriesNames(data.Input))
indexComboBox.setCurrentText(settings["IndexChannel"])
indexComboBox.currentTextChanged.connect(lambda t: drs.setSetting("IndexChannel", t))

rmComboBox = QtGui.QComboBox(widget)
rmComboBox.addItems(rmNames)
rmComboBox.setCurrentText(settings["ReferenceMaterial"])
rmComboBox.currentTextChanged.connect(lambda t: drs.setSetting("ReferenceMaterial", t))


maskComboBox = QtGui.QComboBox(widget)
maskComboBox.addItems(data.timeSeriesNames(data.Input))
maskComboBox.setCurrentText(settings["MaskChannel"])
maskComboBox.currentTextChanged.connect(lambda t: drs.setSetting("MaskChannel", t))

maskLineEdit = QtGui.QLineEdit(widget)
maskLineEdit.setText(settings["MaskCutoff"])
maskLineEdit.textChanged.connect(lambda t: drs.setSetting("MaskCutoff", float(t)))

maskLineEdit = QtGui.QLineEdit(widget) # Is this part correct?
maskLineEdit.setText(settings["MaskThreshold"])
maskLineEdit.textChanged.connect(lambda t: drs.setSetting("MaskThreshold", float(t)))

maskTrimLineEdit = QtGui.QLineEdit(widget)
maskTrimLineEdit.setText(settings["MaskTrim"])
maskTrimLineEdit.textChanged.connect(lambda t: drs.setSetting("MaskTrim", float(t)))

propCheckBox = QtGui.QCheckBox(widget)
propCheckBox.setChecked(settings["PropagateError"])
propCheckBox.toggled.connect(lambda t: drs.setSetting("PropagateError", bool(t)))

formLayout.addRow("Index channel", indexComboBox)
formLayout.addRow("Reference material", rmComboBox) 
formLayout.addRow("Mask channel", maskComboBox)
formLayout.addRow("Mask cutoff", maskLineEdit)
formLayout.addRow("Mask trim", maskTrimLineEdit)
formLayout.addRow("PropagateError", propCheckBox)

drs.setSettingsWidget(widget)`

Thanks for you help in advanced

Regards,
Ahmad

Bence

Hi Ahmad,

It looks like you've made good progress.

If you're having issues seeing your ratios correctly because the ratios in your baselines have a very large amount of variation, you can mask out these areas. To do this, just multiply your channels by the mask array. Here's a made up example just to show how to mask channels:

Hf177 = data.timeSeries("Hf177_CPS").data()
Hf178 = data.timeSeries("Hf178_CPS").data()

Hf177_Hf178 = Hf177 / Hf178 * mask

Multiplying by the mask will blank out all values where the mask does not equal 1. For example if your mask threshold is set to 1000, any time the index channel drops below 1000, the mask will be blank.

The key line is

mask = drs.createMaskFromCutoff(maskChannel, cutoff, trim)

Where maskChannel is less than cutoff, the mask will be blank. Here is the link to the documentation: https://iolite.xyz/docs/api/api.html#iolite.DRSPyInterface.createMaskFromCutoff

I noticed that you also have a mask threshold value... it doesn't appear to be used in the code. Is that correct? If you really wanted to have both (not that I'd recommend it), you could just change the mask line above to use your threshold variable.

I hope that helps.

Cheers,
Bence

aredakau

Hi Bence,

Thanks for your quick replay, that was very helpful. It works well now.

Thank you very much

Cheers,
Ahmad