Synchronizing individual laser log samples

Joe

Discussion for note.

geologyhero

Hi Joe, thanks for writing up that script. I suffer with constant bad sync between laser and mass spec.
Is there any easy way to know if it did something to the aligning of the laser log?
https://photos.app.goo.gl/FJpxBZiWdB1fDKvR8
Should there be changes in the seconds if it did something?

Joe

From the bit of the output I can see, it appears to not have adjusted any of the laser log samples. In order for that script to work, you should have the log and data approximately synced to start and it just does small adjustments (< 10 seconds) then for each sample (i.e. without moving the whole log relative to the data). If you share a data file and log combo that is giving you a hard time (send it to the support email), I’ll have a look and see what works best.

All the best,

Joe

Thank you for sending the files. I've had a look and have come up with a solution, I think.

The reason your data and log don't sync very well is that the laser seems to ablate much longer than data are actually recorded. A screenshot illlustrating this is below:
sync
I'm not sure if that is on purpose or not? It seems a bit strange to me...

Anyways, this creates two problems that the local sync script does not anticipate:
1) There is a 'not a number' (nan) in the data used for local sync because this value is inserted between data files in the time series. This can easily be fixed by replacing the nan by a number, e.g.

da = np.nan_to_num(da, nan=np.nanmean(tb.dataForSelection(sel)))

Adding this one line would cause the sync to actually do something rather than return no offset for all samples, but there is another problem...
2) Because the laser log square wave and the total beam signal are not the same duration, the sync offset will depend entirely on the background surrounding your data. If the noise is higher before ablation begins, it'll 'sync' too early. One way we can solve this problem is by adjusting the signal so it is higher at the end, e.g.

da *= np.linspace(1, 2, len(da))

With these two changes, I see much improved syncronization. There are a still a couple cases where large spikes just before ablation began cause it to sync to that, but for the most part it looks very good.

Here is the complete modified code:

import numpy as np

tb = data.timeSeries('TotalBeam')
sg = data.createSelectionGroup('LocalAdjustTemp', data.Sample)
ts = np.median(np.diff(tb.time()))
n = int(round(10/ts)) # 10 = number of seconds to search around log sample

for i, lls in enumerate(data.laserLogSamples()):
    sel = data.createSelection(sg, lls.startTime(), lls.endTime(), 'Temp')
    si = tb.selectionIndices(sel)
    try:
        da = tb.data()[si[0]-n:si[-1]+n] # Take n points before or after sample
        da = np.nan_to_num(da, nan=np.nanmean(tb.dataForSelection(sel)))
        da *= np.linspace(1, 2, len(da))
        lla = np.pad(np.ones(si[-1] - si[0]), (n, n), 'constant', constant_values=(0, 0))
        offset = data.timeOffset(np.arange(len(da)), da, np.arange(len(lla)), lla)
    except Exception as e:
        print('problem for %i, %s'%(i, e))
        continue

    print('%i = %i, %f s, len(da) = %i, len(lla) = %i'%(i, offset, offset*ts, len(da), len(lla)))
    lls.setStartTime(lls.startTime().addMSecs(offset*ts*1000))
    lls.setEndTime(lls.endTime().addMSecs(offset*ts*1000))

data.removeSelectionGroup('LocalAdjustTemp')

All the best,

geologyhero

Thanks Joe for having a look at it and coming up with a solution. The people who set up the method on the ICP-MS have not used the laser log, which is probably why they did not care if the laser time and analysis time matched. I will change the method so we also measure some blank time after the analysis.