O'Grady, Paul Christopher Fri 2/24/2017 12:16 PM To: Liang, Mengning; Cc: Dubrovin, Mikhail; Suggested Meetings Hi Meng, I talked with Mikhail about the fiber-diffraction “sprint” to get results for Germany that you have strong confidence in. We’ll come by your office around 4 today to launch. We’ll also touch base Monday, Tuesday, Wednesday, Thursday next week at 3pm to make sure we’re headed in the right direction. Those are allowed to be brief (more important to do real work). chris |
O'Grady, Paul Christopher Fri 2/24/2017 5:06 PM To: Liang, Mengning <mliang@slac.stanford.edu>; Dubrovin, Mikhail <dubrovin@slac.stanford.edu>; meng provides "100 events” (good and bad) in run 169 meng provides her current psocake-peak-params meng provides problematic l=0,l=1 indexing output, mikhail fixes code mikhail: move to psocake-consistent parameters to make life easier for meng mikhail: do fraser_xyz and fraser have same conventions and yield same results? mikhail: peak-fit needs to output qh and qv for the *peak* (not lattice) for images that don't index for the 100 bad events mikhail: check after event-selection most things should fit (70-80%) and most should index mikhail: as a longer-term target modify the pipeline so that meng can look at outputs at various stages more easily all: tweak peak-finding parameters for the 100 events all: ask chuck what should we use for background |
Liang, Mengning Mon 2/27/2017 3:14 PM To: Dubrovin, Mikhail; Cc: O'Grady, Paul Christopher; Peakfinding parameters : For arc: peaks_arc = alg_arc.peak_finder_v1(nda, thr_low=40, thr_high=160, radius=8, dr=0.5) For equator: peaks_equ = alg_equ.peak_finder_v4(nda, thr_low=60, thr_high=100, rank=4, r0=4, dr=0.5) ----------------------------------------------------------------------------- Peak selection: For arc: alg_arc = PyAlgos(windows=winds_arc, mask=mask_arc, pbits=0) alg_arc.set_peak_selection_pars(npix_min=20, npix_max=150, amax_thr=100, atot_thr=2000, son_min=5) For equator: alg_equ = PyAlgos(windows=winds_equ, mask=mask_equ, pbits=0) alg_equ.set_peak_selection_pars(npix_min=5, npix_max=150, amax_thr=100, atot_thr=600, son_min=4) |
O'Grady, Paul Christopher Mon 2/27/2017 3:46 PM Adding notes from today: for peak-finding we will standardize on: - median filter. - peakfinderv4 good events should have 2-4 equatorial peaks, 0-2 arc peaks, OR 2 arc peaks and 1-3 eq peaks 80% of the good events should be found, with tuned peak-finding and the above event-selection criteria switch to mode 5 common-mode (unbonded pixels) meng file with equatorial peaks incorrectly indexed as l=1: ~mliang/analysis/rel-cxif5315/work1/index3d/test1/peak-idx-cxif5315-r0169-2017-01-23T10:39:03.txt |
Liang, Mengning Mon 2/27/2017 3:48 PM To: Dubrovin, Mikhail; Cc: O'Grady, Paul Christopher; Here is a list of good events (psocake event numbers) They will have 2-4 peaks in the equatorial region or 2 peaks in the arc region + 1-4 peaks in the equatorial region. Thanks, Meng |
2017-02-27-cxif5315-r0169-good-events.txt
2017-02-27-cxif5315-r0169-bad-events.txt
alg_arc = PyAlgos(windows=winds_arc, mask=mask_arc, pbits=2) alg_arc.set_peak_selection_pars(npix_min=20, npix_max=1000, amax_thr=0, atot_thr=2000, son_min=5) alg_equ = PyAlgos(windows=winds_equ, mask=mask_equ, pbits=0) alg_equ.set_peak_selection_pars(npix_min=5, npix_max=1000, amax_thr=0, atot_thr=600, son_min=5) for i, evt in enumerate(ds.events()) : nda_data = det.calib(evt, cmpars=(5,50)) if nda_data is not None : nda = np.array(nda_data, dtype=np.float32, copy=True) if BKG_MODE == BKG_MODE_NORMAL : nda = subtract_bkgd(nda, nda_bkgd, mask=nda_smask, winds=winds_bkgd, pbits=0) peaks_arc = alg_arc.peak_finder_v4r2(nda, thr_low=40, thr_high=160, rank=8, r0=10, dr=2) peaks_equ = alg_equ.peak_finder_v4r2(nda, thr_low=60, thr_high=100, rank=4, r0=6, dr=2) |
sit_setup ~yoon82/ana2 # some problem fixed in this local release psocake -e cxif5315 -r 169 -d CxiDs2.0:Cspad.0 -n 468 -o psocake python cxif5315/proc-cxif5315-r0169-data-pfvn-2017-02-27.py |
Conclusion: within mask-permitted region analysis script finds the same peaks as psocake |
r0=6 dr=2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 1 1 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 1 1 0 0 0 0 0 + 0 0 0 0 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 Number of pixels to estimate background = 88 r0=10 dr=2 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 Number of pixels to estimate background = 136 |
Liang, Mengning Tue 2/28/2017 4:09 PM To: Dubrovin, Mikhail; 148 – double hit in equator – 3 peaks 162 – no peaks 525 – double hit in equator - 6 peaks 1456 – should find multiple arc peaks 1521 – double hit equator – 4 total peaks 2551 – no peaks I could not find parameters to find the right peaks in these events – can see by eye where the peaks are. Thanks, Meng |
2017-03-01 Images for 6 events selected by Meng
cxif5315/proc-cxif5315-r0169-data-pfvn-2017-02-27.py
filter is separated from peak processing peaks as cxif5315/filter-peaks-2017-03-07.py
almost done with cxif5315/fit-peaks-2017-03-08.py -p
cd ~/LCLS/rel-mengning sit_setup |
cxif5315/proc-cxif5315-r0169-data-pfvn-2017-02-27.py -h # help cxif5315/proc-cxif5315-r0169-data-pfvn-2017-02-27.py -n 20 -m 10 -i # plot images cxif5315/proc-cxif5315-r0169-data-pfvn-2017-02-27.py # run over all events and find peaks |
With peak-finder have generated files with peaks. Now filter tham.
cxif5315/filter-peaks-2017-03-07.py -h cxif5315/filter-peaks-2017-03-07.py -i work/xpfv4r2-cxif5315-r0169-2017-03-03-e085409.txt -p # -p - plot histograms cxif5315/filter-peaks-2017-03-07.py -i work/xpfv4r2-cxif5315-r0169-2017-03-03-bad100.txt cxif5315/filter-peaks-2017-03-07.py -i work/xpfv4r2-cxif5315-r0169-2017-03-03-good100.txt cxif5315/filter-peaks-2017-03-07.py -i work/xpfv4r2-cxif5315-r0169-2017-03-03-esix.txt |
less ./results/peaks.txt less ./results/peaks-filtered-log.txt |
cxif5315/proc-cxif5315-r0169-data-pfvn-2017-02-27.py -m 525 -n 1 -i |
Meng's events (148, 162, 525, 1456, 1521, 2551)
148 – double hit in equator – 3 peaks 162 – no peaks 525 – double hit in equator - 6 peaks 1456 – should find multiple arc peaks 1521 – double hit equator – 4 total peaks 2551 – no peaks |
- ask Kurtik about smoothing and other event processing stages - median background ? - class0 background - no equ peaks, no arc peaks, water ring yrs - radial background - fudge factor on existing subtraction - learm more about pattern_sim from Chuck |