output issue

aredakau

Hello Bence and Joe,

I have created a DRS file to process Rb/Sr data but the output are coming opposite. For example, the actual Raw Data labelled as corrected data and vice versa. Could you please check the code for me and see where is the error?

Thanks for your help in advance

`from iolite import QtGui
from time import sleep
import numpy as np

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"]
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("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)

# 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)


Rb85 = data.timeSeries("Rb85_CPS").data()
Sr87 = data.timeSeries("Sr87_CPS").data()
Sr86 = data.timeSeries("Sr86_CPS").data()

Rb87=Rb85*0.38562
Rb87_Sr86_Raw =  Rb87 / Sr86 *  mask
Sr87_Sr86_Raw =  Sr87 / Sr86 *  mask

data.createTimeSeries("Rb87_CPS", data.Output, indexChannel.time(), Rb87)
data.createTimeSeries("Rb87_Sr86_Raw", data.Output, indexChannel.time(),Rb87_Sr86_Raw)
data.createTimeSeries("Sr87_Sr86_Raw", data.Output, indexChannel.time(),Sr87_Sr86_Raw)

#std correction
StdSpline_Rb87_Sr86 = data.spline(rmName, "Rb87_Sr86_Raw").data()
StdValue_Rb87_Sr86 = data.referenceMaterialData(rmName)["87Rb/86Sr"].value()
print("StdSpline_Rb87_Sr86 mean = %f"%StdSpline_Rb87_Sr86.mean())
print("StdValue_Rb87_Sr86 = %f"%StdValue_Rb87_Sr86)
StdCorr_Rb87_Sr86 = (Rb87_Sr86_Raw)* StdValue_Rb87_Sr86 / StdSpline_Rb87_Sr86

data.createTimeSeries("StdCorr_Rb87_Sr86", data.Output, indexChannel.time(), StdCorr_Rb87_Sr86)



StdSpline_Sr87_Sr86 = data.spline(rmName, "Sr87_Sr86_Raw").data()
StdValue_Sr87_Sr86 = data.referenceMaterialData(rmName)["87Sr/86Sr"].value()
print("StdSpline_Sr87_Sr86 mean = %f"%StdSpline_Sr87_Sr86.mean())
print("StdValue_Sr87_Sr86 = %f"%StdValue_Sr87_Sr86)
StdCorr_Sr87_Sr86 = (Sr87_Sr86_Raw)* StdValue_Sr87_Sr86 / StdSpline_Sr87_Sr86

data.createTimeSeries("StdCorr_Sr87_Sr86", data.Output, indexChannel.time(), StdCorr_Sr87_Sr86)

if propErrors:
	groups = [s for s in data.selectionGroupList() if s.type != data.Baseline]
	data.propagateErrors(groups, [data.timeSeries("StdCorr_Rb87_Sr86")], data.timeSeries("Rb87_Sr86_Raw"), rmName)
	data.propagateErrors(groups, [data.timeSeries("StdCorr_Sr87_Sr86")], data.timeSeries("Sr87_Sr86_Raw"), rmName)


drs.message("Finished!")
drs.progress(100)
drs.finished()

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","Sr86")
drs.setSetting("ReferenceMaterial", "M_MicaMG")
drs.setSetting("MaskChannel", "Sr86")
drs.setSetting("MaskCutoff", 0.1)
drs.setSetting("MaskTrim", 0.0)
drs.setSetting("PropagateError", True)

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)))

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)

Joe

It isn't immediately obvious to me. Would you be able to share some files for testing? Data file +/- laser log +/- appropriate reference material files. If yes, please email them to joe at iolite-software.com.

Very happy to see someone having a go at their own DRS!

aredakau

Hi Joe,

Thanks for your help in advance.

I have sent some ICP files + DRS + reference material to your email.

Ahmad

aredakau

Hi Joe,

Please discard my enquiry. Nothing wrong with the code. I have made mistake in data processing outside iolite, and I thought the issue was in my coding.

Regards,
Ahmad

VitorBarrote

Hey guys,

How could I add to this DRS a semi-quant calculation of Sr and Rb concentrations?

Thanks

Joe

Hi Vitor,

Calculating a semi-quant channel verbosely would look something like:

Sr_in_RM = data.referenceMaterialData('NameOfRM')['Sr'].value()
Sr_RM_spline = data.spline('NameOfRM', 'Sr87_CPS').data()
Sr_CPS = data.timeSeries('Sr87_CPS').data()
Sr_ppm = (Sr_in_RM/Sr_RM_spline)*Sr_CPS
data.createTimeSeries('Sr87_sq_ppm', data.Output, None, Sr_ppm)

Where NameOfRM is replaced with the name of whichever RM you're using, and it is assumed that baseline subtracted channels have already been calculated. Swap out the Sr and 87 for Rb and 85 and you've got Rb too.

All the best,

VitorBarrote

Thanks Joe!