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| Note |
|---|
In this example parameters were chosen in order to get a small number of "noisy" pixel just due to statistics. |
Typical image:
...
Plots for fraction of noisy pixels:
Plots for fraction of saturated pixels:
Masks: noisy, saturated, and combined:
Example for module ImgAlgos::ImgCalib
| Code Block | ||
|---|---|---|
| ||
[ImgAlgos.CameraImageProducer] source = DetInfo(:Opal1000) key_in = key_out = img subtract_offset = true print_bits = 1 [ImgAlgos.ImgCalib] source = DetInfo(:Opal1000) key_in = img key_out = calibrated fname_peds = <pedestal-file-name> fname_mask = <mask-file-name> fname_bkgd = fname_gain = print_bits = 31 |
Example of the mask file and resulting image:
Example for module ImgAlgos::ImgRadialCorrection
See Module ImgAlgos::ImgRadialCorrection
| Code Block | ||
|---|---|---|
| ||
[psana]
files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \
/reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-2>.xtc \
...
/reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc
skip-events = 500
events = 10
modules = cspad_mod.CsPadCalib \
# ImgAlgos.CSPadBkgdSubtract \
CSPadPixCoords.CSPadImageProducer \
ImgAlgos.ImgRadialCorrection \
ImgAlgos.ImgSaveInFile:1
[cspad_mod.CsPadCalib]
inputKey =
outputKey = calibrated
doPedestals = yes
doPixelStatus = no
doCommonMode = no
[ImgAlgos.CSPadBkgdSubtract]
source = DetInfo(CxiDs1.0:Cspad.0)
inputKey = calibrated
outputKey = bkgd_subtracted_arr
bkgd_fname = <the-file-name-with-background-array>
norm_sector = 0
print_bits = 0
[CSPadPixCoords.CSPadImageProducer]
calibDir = /reg/d/psdm/<instrument>/<experiment>/calib
typeGroupName = CsPad::CalibV1
source = CxiDs1.0:Cspad.0
key = calibrated
imgkey = current_img
#tiltIsApplied = true
[ImgAlgos.ImgRadialCorrection]
source = DetInfo(CxiDs1.0:Cspad.0)
inkey = current_img
outkey = r_cor_img
xcenter = 866
ycenter = 857
rmin = 100
rmax = 810
n_phi_bins = 60
event = 0
print_bits = 3
[ImgAlgos.ImgSaveInFile:1]
source = CxiDs1.0:Cspad.0
key = r_cor_img
fname = <file-name-for-image-array>
#saveAll = true
eventSave = 8
|
Note: the option of the background subtraction (ImgAlgos.CSPadBkgdSubtract) is commented out in this configuration file . In order to evoke this option, the comment sign (#) should be removed from the list of modules and the key=bkgd_subtracted_arr should be used in CSPadPixCoords.CSPadImageProducer.
Calibrated image and spectrum:
Calibrated and radial-corrected image, spectrum, and subtracted r-phi65 distribution for n_phi_bins=65:
Calibrated and radial-corrected image, spectrum, and subtracted r-phi12 distribution for n_phi_bins=12:
Example for module ImgAlgos::ImgPeakFinder
See Module ImgAlgos::ImgPeakFinder
Configuration file example:
| Code Block | ||
|---|---|---|
| ||
[psana]
files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \
/reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-2>.xtc \
...
/reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc
modules = ImgAlgos.ImgPeakFinder PrintSeparator
#skip-events = 500
events = 120
[ImgAlgos.ImgPeakFinder]
source = DetInfo(:Opal1000)
key =
peaksKey = peaks
threshold_low = 20
threshold_high = 50
sigma = 1.5
smear_radius = 2
peak_radius = 3
xmin = 200
xmax = 800
ymin = 100
ymax = 900
testEvent = 115
print_bits = 0
finderIsOn = true
|
This algorithm consumes ~15 ms/event on psana0101 for full Opal1000 (1024x1024) camera image.
Smearing algorithm use a "safety margin" which is currently set to 10 pixels (offset from each boarder of the full image size).
Image on different stages of this algorithm:
raw image,
image in the window with amplitudes above the threshold_low
- few peaks at the edges were discarded by the window limits,
- image still contains many 1-photon pixels, which need to be eliminated,
smeared image,
raw image with found peaks (marked by the red circles)
zoom of the previous plot.
Example for module ImgAlgos::ImgPeakFilter
...
Example for module ImgAlgos::ImgPeakFinderAB
See Module ImgAlgos::ImgPeakFinderAB
Configuration file example:
| Code Block | ||
|---|---|---|
| ||
[psana]
files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>.xtc
modules = ImgAlgos.CameraImageProducer \
ImgAlgos.ImgPeakFinderAB
events = 10
[ImgAlgos.CameraImageProducer]
source = DetInfo(:Opal1000)
key_in =
key_out = img
subtract_offset = true
print_bits = 1
[ImgAlgos.ImgPeakFinderAB]
source = DetInfo(:Opal1000)
key = img
key_peaks_out = peaks
#key_signal_out = signal-arr
#hot_pix_mask_inp_file = ana-misc-exp/mask.dat
#hot_pix_mask_out_file = noise-mask-out.dat
#frac_noisy_evts_file = noise-frac-out.dat
evt_file_out = tmp/img-
rmin = 10
dr = 1
SoNThr_noise = 3
SoNThr_signal = 3
frac_noisy_imgs = 0.9
peak_npix_min = 3
peak_npix_max = 100
peak_amp_tot_thr = 0.
peak_SoN_thr = 4.
event_npeak_min = 5
event_npeak_max = 1000
event_amp_tot_thr = 0.
nevents_mask_update = 0
nevents_mask_accum = 50
selection_mode = SELECTION_ON
out_file_bits = 15
print_bits = 513
|
...
Example for module ImgAlgos::ImgHitFinder
See Module ImgAlgos::ImgHitFinder
ImgHitFinder in regular mode needs in file with pedestals (offset) to correct the image and file with threshold.
In amo74213 run 93 these files can be obtained directly from data, discarding signal hits as outliers using
ImgAlgos.ImgAverage module as follows with configuration file:
| Code Block | ||
|---|---|---|
| ||
# File: psana-amo74213-r0093-opal-img-average.cfg
[psana]
#files = /reg/d/psdm/AMO/amo74213/xtc/e269-r0093-s05-c00.xtc
files = exp=amo74213:run=93:xtc
modules = ImgAlgos.CameraImageProducer \
ImgAlgos.ImgAverage
skip-events = 0
events = 1000
[ImgAlgos.CameraImageProducer]
source = DetInfo(:Opal1000)
key_in =
key_out = img
subtract_offset = true
print_bits = 1
[ImgAlgos.ImgAverage]
source = DetInfo(:Opal1000)
key = img
avefile = img-ave-for-peds
rmsfile = img-rms-for-thre
evts_stage1 = 100
evts_stage2 = 100
gate_width1 = 50
gate_width2 = 10
print_bits = 31
|
Run psana using command:
| Code Block | ||
|---|---|---|
| ||
psana -c psana-amo74213-r0093-opal-img-average.cfg |
At the end of this procedure two files will be created:
img-ave-for-peds-r0093.dat - may be used for pedestal subtraction:
img-rms-for-thre-r0093.dat - may be used multiplied by number of rms as a threshold:
The file with accumulated pixel hits can be obtained using configuration file:
| Code Block | ||
|---|---|---|
| ||
# File: psana-amo74213-r0093-opal-img-hit-finder.cfg
[psana]
#files = /reg/d/psdm/AMO/amo74213/xtc/e269-r0093-s05-c00.xtc
files = exp=amo74213:run=93:xtc
modules = ImgAlgos.CameraImageProducer \
ImgAlgos.ImgHitFinder \
ImgAlgos.ImgAverage
skip-events = 0
events = 1000
[ImgAlgos.CameraImageProducer]
source = DetInfo(:Opal1000)
key_in =
key_out = img
subtract_offset = true
print_bits = 1
[ImgAlgos.ImgHitFinder]
source = DetInfo(:Opal1000)
key_in = img
key_out = img_hits
fname_peds = img-ave-for-peds-r0093.dat
fname_mask =
fname_gain =
fname_thre = img-rms-for-thre-r0093.dat
masked_value = 0
thre_mode = 3
#thre_mode = 2
thre_param = 5
thre_below_value = 0
thre_above_value = 1
win_row_min = 10
win_row_max = 1000
win_col_min = 10
win_col_max = 1000
print_bits = 39
[ImgAlgos.ImgAverage]
source = DetInfo(:Opal1000)
key = img_hits
sumfile = img-sum-result
print_bits = 25
|
and run it by the command:
| Code Block | ||
|---|---|---|
| ||
psana -c psana-amo74213-r0093-opal-img-hit-finder.cfg |
Which creates the file: img-sum-result-r0093.dat for thre_mode = 2 and thre_mode = 3, respectively:
Example for module ImgAlgos::ImgSpectra
See Module ImgAlgos::ImgSpectra
Configuration file for psana:
| Code Block | ||
|---|---|---|
| ||
[psana]
files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>.xtc
modules = ImgAlgos.CameraImageProducer \
ImgAlgos.ImgSpectra \
ImgAlgos.ImgSaveInFile:2
# ImgAlgos.ImgSaveInFile
# psana_examples.DumpOpal1k \
events = 100
[ImgAlgos.CameraImageProducer]
source = DetInfo(:Opal1000)
key_in =
key_out = img
subtract_offset = true
print_bits = 1
[ImgAlgos.ImgSpectra]
source = DetInfo(:Opal1000)
key_in = img
key_out = spectra
sig_band_rowc = 512.
ref_band_rowc = 552.
sig_band_tilt = 0.
ref_band_tilt = 0.
sig_band_width = 10
ref_band_width = 10
print_bits = 3
[ImgAlgos.ImgSpectraProc]
source = DetInfo(:Opal1000)
key_in = spectra
print_bits = 15
[ImgAlgos.ImgSaveInFile:2]
source = DetInfo(:Opal1000)
key = spectra
fname = spec-xppi0412
saveAll = true
[ImgAlgos.ImgSaveInFile]
source = DetInfo(:Opal1000)
key = img
fname = img-xppi0412
saveAll = true
|
This script can be used in order to produce text files with image and spectral array:
or graphics for several images:
Example for module ImgAlgos::ImgSpectraProc
See Module ImgAlgos::ImgSpectraProc
Configuration file for psana:
| Code Block | ||
|---|---|---|
| ||
[ImgAlgos.ImgSpectraProc] source = DetInfo(:Opal1000) key_in = spectra print_bits = 15 |
For each event it prints something similar to:
| Code Block | ||
|---|---|---|
| ||
[info:ImgAlgos.ImgSpectraProc] Spectral array shape =3, 1024 [info:ImgAlgos.ImgSpectraProc] Image spectra for run=0060 Evt=000100 Column: 0 100 200 300 400 500 600 700 800 900 1000 Signal: 1211 4062 11150 17070 16406 12949 7991 5168 3968 3542 3811 Refer.: 933 3485 10425 17128 17791 13522 8315 5000 3390 2967 3193 Diff. : 0.259 0.153 0.067 -0.003 -0.081 -0.043 -0.040 0.033 0.157 0.177 0.176 [info:ImgAlgos.ImgSpectraProc] Run=0060 Evt=000100 Time=20120507-125420.982421325 done... |
...
| Code Block | ||
|---|---|---|
| ||
modules = ... ImgAlgos.ImgSaveInFile:1 ... [ImgAlgos.ImgSaveInFile:1] source = DetInfo(:Opal1000) # or CxiDs1.0:Cspad.0 key = img fname = my-img #ftype = txt #ftype = bin #ftype = png ftype = tiff #eventSave = 5 saveAll = true |
See Module ImgAlgos::ImgSaveInFile
Example for module ImgPeakFinder and ImgPeakFilter for CSPad
Module ImgAlgos::ImgPeakFinder works on image. In order to apply this algorithm to CSPad the image should be produced. In next example the image is produced using consequtive modules cspad_mod.CsPadCalib, ImgAlgos.CSPadMaskApply, and CSPadPixCoords.CSPadImageProducer:
| Code Block | ||
|---|---|---|
| ||
[psana]
files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \
...
/reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc
events = 1000
experiment = cxii0212
calib-dir = ana-cxii0212/calib
modules = cspad_mod.CsPadCalib \
ImgAlgos.CSPadMaskApply \
CSPadPixCoords.CSPadImageProducer \
ImgAlgos.ImgPeakFinder \
ImgAlgos.ImgPeakFilter \
ImgAlgos.ImgSaveInFile:1
[cspad_mod.CsPadCalib]
inputKey =
outputKey = calibrated
doPedestals = yes
doPixelStatus = no
doCommonMode = yes
[ImgAlgos.CSPadMaskApply]
source = DetInfo(CxiDs1.0:Cspad.0)
inkey = calibrated
outkey = masked_arr
mask_fname = <your-local-directory>/<mask-file-name>.dat
masked_amp = 0
print_bits = 5
mask_control_bits = 15
[CSPadPixCoords.CSPadImageProducer]
calibDir = /reg/d/psdm/<instrument>/<experiment>/calib
typeGroupName = CsPad::CalibV1
source = CxiDs1.0:Cspad.0
key = masked_arr
imgkey = img
print_bits = 0
#tiltIsApplied = true
[ImgAlgos.ImgPeakFinder]
source = DetInfo(CxiDs1.0:Cspad.0)
key = img
peaksKey = peaks
threshold_low = 2
threshold_high = 5
sigma = 1.5
smear_radius = 5
peak_radius = 7
xmin = 20
xmax = 1700
ymin = 20
ymax = 1700
#testEvent = 5
print_bits = 3
#finderIsOn = true
[ImgAlgos.ImgPeakFilter]
source = DetInfo(CxiDs1.0:Cspad.0)
key = peaks
threshold_peak = 5
threshold_total= 0
n_peaks_min = 10
print_bits = 11
fname = cspad-img
selection_mode = SELECTION_ON
[ImgAlgos.ImgSaveInFile:1]
source = CxiDs1.0:Cspad.0
key = img
fname = cspad-img
#eventSave = 1
saveAll = true
|
Example for module ImgAlgos::CSPadArrAverage
See Module ImgAlgos::CSPadArrAverage
Configuration file example for evaluation of pedestals:
| Code Block | ||
|---|---|---|
| ||
[psana] modules = ImgAlgos.CSPadArrAverage files = <path-to-the-dark-run-file>.xtc [ImgAlgos.CSPadArrAverage] source = DetInfo(CxiDs1.0:Cspad.0) key = avefile = cspad-pedestals-ave.dat rmsfile = cspad-pedestals-rms.dat print_bits = 15 evts_stage1 = 100 evts_stage2 = 100 gate_width1 = 100 gate_width2 = 10 |
Configuration file example for evaluation of background:
| Code Block | ||
|---|---|---|
| ||
[psana] files = <path-to-the-background-run-file>.xtc modules = cspad_mod.CsPadCalib ImgAlgos.CSPadArrAverage skip-events = 500 events = 1000000 [cspad_mod.CsPadCalib] inputKey = outputKey = calibrated doPedestals = yes doPixelStatus = no doCommonMode = no [ImgAlgos.CSPadArrAverage] source = DetInfo(CxiDs1.0:Cspad.0) key = calibrated avefile = cspad-background-ave.dat rmsfile = cspad-background-rms.dat print_bits = 15 |
Images of the CSPad arrays for averaged and rms values, respectively, in one of the CXI runs:
Example for module ImgAlgos::CSPadBkgdSubtract
See Module ImgAlgos::CSPadBkgdSubtract
| Code Block | ||
|---|---|---|
| ||
[psana]
files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \
/reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-2>.xtc \
...
/reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc
skip-events = 500
events = 10
modules = cspad_mod.CsPadCalib ImgAlgos.CSPadBkgdSubtract
[cspad_mod.CsPadCalib]
inputKey =
outputKey = calibrated
doPedestals = yes
doPixelStatus = no
doCommonMode = no
[ImgAlgos.CSPadBkgdSubtract]
source = DetInfo(CxiDs1.0:Cspad.0)
inputKey = calibrated
outputKey = bkgd_subtracted
bkgd_fname = <the-file-name-with-background-array>
norm_sector = 0
print_bits = 3
|
The file with the background array, bkgd_fname, was obtained by averaging 1000 events using module CSPadArrAverage. Subtraction is done with normalization for norm_sector=0.
Event image and pixel amplitude spectrum before and after the background subtraction are shown in plots:
Other event with better subtracted background:
Example for Module ImgAlgos::CSPadMaskApply
See Module ImgAlgos::CSPadMaskApply
The array for mask contains zeros and ones for masked and passed pixels, respectively, and has a shape of full-size CSPad array 4*8*185388.
For example, it can be generated by the command
| Code Block | ||
|---|---|---|
| ||
./MakePixelMask.py <input-background-cspad-arr-file-name> <threshold> <output-file-name> |
for the averaged background amplitude array <input-background-cspad-arr-file-name> abtained as a result of ImgAlgos::CSPadArrAverage module.
Plots show the averaged background, and the mask arrays generated from this background for three thresholds 10, 20, and 30 EDU:
The best results in filtering can be achieved in combination of modiles:
| Code Block | ||
|---|---|---|
| ||
modules = cspad_mod.CsPadCalib \
ImgAlgos.CSPadBkgdSubtract \
ImgAlgos.CSPadMaskApply \
...
[cspad_mod.CsPadCalib]
inputKey =
outputKey = calibrated_arr
doPedestals = yes
doPixelStatus = no
doCommonMode = no
[ImgAlgos.CSPadBkgdSubtract]
source = DetInfo(CxiDs1.0:Cspad.0)
inputKey = calibrated_arr
outputKey = bkgd_subtracted_arr
bkgd_fname = ana-cxi49012/cspad-cxi49012-r0025-background-ave.dat
norm_sector = 0
print_bits = 0
[ImgAlgos.CSPadMaskApply]
source = DetInfo(CxiDs1.0:Cspad.0)
inkey = bkgd_subtracted_arr
outkey = masked_arr
mask_fname = ana-cxi49012/cspad-cxi49012-r0025-mask-40.dat
masked_amp = 0
print_bits = 3
mask_control_bits = 1
|
where
cspad_mod.CsPadCalib - subtracts the pedestals from raw CSPad data,
ImgAlgos.CSPadBkgdSubtract - subtracts the background,
ImgAlgos.CSPadMaskApply - apply the mask.
In the test with images for background represented by the water and solvent rings this filter provides the background suppression factor about 100.
The background images that still pass this filter have significantly larger intensity with respect to averaged background:
Input parameter mask_control_bits allows to control masking regions of 2x1. For example, if all edges need to be masked, then use mask_control_bits = 15, which gives image array like:
where red regions/lines of pixels of amplitude=8 are masked.
Example for module ImgAlgos::CSPadArrNoise
See Module ImgAlgos::CSPadArrNoise
| Code Block | ||
|---|---|---|
| ||
[psana]
modules = cspad_mod.CsPadCalib ImgAlgos.CSPadArrNoise
files = /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s00-c00.xtc \
/reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s01-c00.xtc \
/reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s02-c00.xtc \
/reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s03-c00.xtc \
/reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s04-c00.xtc \
/reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s05-c00.xtc
#skip-events = 1000
events = 10
[cspad_mod.CsPadCalib]
inputKey =
outputKey = calibrated
doPedestals = yes
doPixelStatus = no
doCommonMode = no
[ImgAlgos.CSPadArrNoise]
source = DetInfo(CxiDs1.0:Cspad.0)
key = calibrated
statusfile = ana-cxi49012/cspad-cxi49012-r0020-noise-status.dat
maskfile = ana-cxi49012/cspad-cxi49012-r0200-noise-mask.dat
print_bits = 255
rmin = 3
dr = 1
SoNThr = 3
frac_noisy_imgs = 0.15
|
Index map in median algorithm for rmin=3, dr=1:
| Code Block | ||
|---|---|---|
| ||
CSPadArrNoise::printMatrixOfIndexesForMedian(): 0 0 0 0 1 0 0 0 0 0 0 1 1 1 1 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 1 0 1 1 0 0 + 0 0 1 1 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 1 0 0 0 1 1 1 1 1 0 0 0 0 0 0 1 0 0 0 0 |
Pixel status (fraction of events where S/N > SoNThr):
For cspad-cxi49012-r0020 with parameters from confguration file (frac_noisy_imgs=0.15) we get, depending on number of events:
Nnoisy, Ntotal, Nnoisy/Ntotal pixels =94585 2296960 0.041 for 10 events
Nnoisy, Ntotal, Nnoisy/Ntotal pixels =2112 2296960 0.00092 for 100 events
Pixel mask for noisy pixels with |S/N| > SoNThr:
Example for Module ImgAlgos::CSPadArrPeakFinder
See Module ImgAlgos::CSPadArrPeakFinder
| Code Block | ||
|---|---|---|
| ||
[psana]
files = \
/reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s00-c00.xtc \
/reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s01-c00.xtc \
/reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s02-c00.xtc \
/reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s03-c00.xtc \
# /reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s04-c00.xtc \ suddenly it became unavailable...
/reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s05-c00.xtc
#skip-events = 1000
#events = 200
modules = cspad_mod.CsPadCalib \
ImgAlgos.CSPadMaskApply \
ImgAlgos.CSPadArrPeakFinder
[cspad_mod.CsPadCalib]
inputKey =
outputKey = calibrated
doPedestals = yes
doPixelStatus = no
doCommonMode = no
[ImgAlgos.CSPadMaskApply]
source = DetInfo(CxiDs1.0:Cspad.0)
inkey = calibrated
outkey = masked_arr
mask_fname = ana-cxi49012/cspad-cxi49012-r0150-mask-badregs.dat
#mask_fname = ana-cxi49012/cspad-cxi49012-r0150-mask-bkgd.dat
#mask_fname = ana-cxi49012/cspad-cxi49012-r0150-mask-rects.dat
masked_amp = 8
print_bits = 1
mask_control_bits = 15
[ImgAlgos.CSPadArrPeakFinder]
source = DetInfo(CxiDs1.0:Cspad.0)
key = masked_arr
key_peaks_out = peaks
hot_pix_mask_inp_file = ana-cxi49012/cspad-cxi49012-r0150-noise-mask.dat
hot_pix_mask_out_file = ana-cxi49012/cspad-cxi49012-r0150-noise-mask-out.dat
frac_noisy_evts_file = ana-cxi49012/cspad-cxi49012-r0150-noise-frac.dat
evt_file_out = tmp/cspad-ev-
rmin = 3
dr = 1
SoNThr = 3
frac_noisy_imgs = 0.1
peak_npix_min = 4
peak_npix_max = 25
peak_amp_tot_thr = 100.
event_npeak_min = 10
event_amp_tot_thr = 1000.
nevents_mask_update = 100
nevents_mask_accum = 50
selection_mode = SELECTION_ON
out_file_bits = 15
print_bits = 512
|
Results:
| Code Block | ||
|---|---|---|
| ||
[info:TimeInterval::startTime] Start time: 2012-06-12 15:32:02 [info:ImgAlgos.CSPadArrPeakFinder] N processed events = 1000 N selected = 55 Fraction of selected = 0.055 [info:ImgAlgos.CSPadArrPeakFinder] N processed events = 2000 N selected = 62 Fraction of selected = 0.031 [info:ImgAlgos.CSPadArrPeakFinder] N processed events = 3000 N selected = 81 Fraction of selected = 0.027 [info:ImgAlgos.CSPadArrPeakFinder] N processed events = 4000 N selected = 95 Fraction of selected = 0.02375 [info:ImgAlgos.CSPadArrPeakFinder] N processed events = 5000 N selected = 150 Fraction of selected = 0.03 [info:ImgAlgos.CSPadArrPeakFinder] N processed events = 6000 N selected = 265 Fraction of selected = 0.0441667 [info:ImgAlgos.CSPadArrPeakFinder] N processed events = 7000 N selected = 404 Fraction of selected = 0.0577143 [info:ImgAlgos.CSPadArrPeakFinder] ===== JOB SUMMARY ===== [info:TimeInterval::stopTime] Time to process 7945 events is 3747.48 sec, or 0.471678 sec/event |
Selected events
ev-007713:
ev-008944:
Example for module ImgAlgos::CSPadArrPeakAnalysis
See Module ImgAlgos::CSPadArrPeakAnalysis
Example of the psana configuration file:
| Code Block | ||
|---|---|---|
| ||
modules = cspad_mod.CsPadCalib \
ImgAlgos.CSPadMaskApply \
ImgAlgos.CSPadArrPeakFinder \
ImgAlgos.CSPadArrPeakAnalysis
# ...configuration parameters of other modules...
[ImgAlgos.CSPadArrPeakAnalysis]
source = DetInfo(CxiDs1.0:Cspad.0)
key = peaks
print_bits = 7
fname_root = file.root
|
After execution in psana the file.root containing histogram(s) and ntuple(s) will be produced. Then, auxiliary script in root, running by the commend
root -q -f proc.C
produces the plots with histograms:
Example for TimeStampFilter and XtcOutputModule
This example demonstrates how to run psana with the time stamp filter and event writer in xtc file.
Both modules are available in psana library and they need only to be described in the configuration file. For example, the configuration file tstamp-filter-and-event-writer.cfg may looks like:
| Code Block | ||
|---|---|---|
| ||
[psana]
files = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s00-c00.xtc \
/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s01-c00.xtc \
/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s02-c00.xtc \
/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s03-c00.xtc \
/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s04-c00.xtc \
/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s05-c00.xtc
skip-events = 10
events = 100
modules = ImgAlgos.TimeStampFilter PSXtcOutput.XtcOutputModule
[PSXtcOutput.XtcOutputModule]
dirName = ./test_out
[ImgAlgos.TimeStampFilter]
tsinterval = 2012-02-02 18:17:00.409143728 / 2012-02-02 18:17:00.525853474
filterIsOn = true
print_bits = 11
|
Command to run psana is:
psana -c ./tstamp-filter-and-event-writer.cfg
For this configuration file psana will skip 10 events and loop over the next 100 events from the /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s0*-c00.xtc files and run consecutively modules = ImgAlgos.TimeStampFilter PSXtcOutput.XtcOutputModule. Parameters of these modules are described in the bottom part of the configuration file. Module TimeStampFilter passes events from the specified time interval and prints some useful information. Module XtcOutputModule will write passed events in the file with auto-generated name ./test_out/e158-r0021.xtcf.
See also: Module ImgAlgos::TimeStampFilter and PSXtcOutput::PSXtcOutput
Examples for Package pyimgalgos
Package pyimgalgos contains python modules which work with both frameworks pyana and psana.
Configuration file for pyana and/or psana should have relevant sections with parameters for [pyana] and/or [psana]. Alean section is ignored in each framework at run time. This is the only difference between two frameworks in the configuration file. All module descriptions are the same for two frameworks, as shown in examples below.
See description of modules in Package pyimgalgos.
Example of configuration file for CSPAD
File py-xcs72913-r0049-cspad.cfg:
| Code Block | ||
|---|---|---|
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# Run this script: # psana -c py-xcs72913-r0049-cspad.cfg # pyana -c py-xcs72913-r0049-cspad.cfg # # Useful commands: # psana -m EventKeys -n 5 /reg/d/psdm/xcs/xcs72913/xtc/e265-r0049-* # psana -m psana_examples.dump_cspad -n 5 exp=xcs72913:run=49 # pyana -m pyana_examples.dump_cspad -n 5 /reg/d/psdm/xcs/xcs72913/xtc/e265-r0049-* [pyana] files = /reg/d/psdm/xcs/xcs72913/xtc/e265-r0049-s00-c00.xtc /reg/d/psdm/xcs/xcs72913/xtc/e265-r0049-s04-c00.xtc /reg/d/psdm/xcs/xcs72913/xtc/e265-r0049-s05-c00.xtc num-events = 5 #skip-events = 0 #num-cpu = 1 verbose = 1 ; logging output: 0-nothing?, 1+INFO, 2+DEBUG, ... modules = pyimgalgos.tahometer pyimgalgos.cspad_arr_producer pyimgalgos.cspad_image_producer pyimgalgos.image_save_in_file [psana] files = exp=xcs72913:run=49 events = 5 #skip-events = 0 modules = pyimgalgos.tahometer pyimgalgos.cspad_arr_producer pyimgalgos.cspad_image_producer pyimgalgos.image_save_in_file verbose = 1 [pyimgalgos.tahometer] dn = 10 print_bits = 255 [pyimgalgos.cspad_arr_producer] #source = -|Cspad-* source = XcsEndstation-0|Cspad-0 data_type = double #data_type = float #data_type = unsigned #data_type = uint16 val_miss = 0 key_out = cspad_array print_bits = 1 [pyimgalgos.cspad_image_producer] calib_dir = /reg/d/psdm/xcs/xcs72913/calib/CsPad::CalibV1/XcsEndstation.0:Cspad.0/ key_in = cspad_array key_out = cspad_image print_bits = 1 # Supported output file formats tiff, gif, png, eps, jpg, jpeg, txt, npy(default), npz [pyimgalgos.image_save_in_file] key_in = cspad_image ofname = img-for-cspad.txt print_bits = 255 |
To run this script use command
psana -c py-xcs72913-r0049-cspad.cfg
or
pyana -c py-xcs72913-r0049-cspad.cfg
Example of configuration file for CSPAD2x2
File py-meca6113-r0028-cspad2x2.cfg
| Code Block | ||
|---|---|---|
| ||
# Run this script: # psana -c py-meca6113-r0028-cspad2x2.cfg # pyana -c py-meca6113-r0028-cspad2x2.cfg # # Useful commands: # psana -m EventKeys -n 5 /reg/d/psdm/mec/meca6113/xtc/e332-r0028-s03-c00.xtc # psana -m psana_examples.dump_cspad -n 5 exp=meca6113:run=28 # pyana -m pyana_examples.dump_cspad -n 5 /reg/d/psdm/mec/meca6113/xtc/e332-r0028-s03-c00.xtc [pyana] files = /reg/d/psdm/mec/meca6113/xtc/e332-r0028-s03-c00.xtc num-events = 5 #skip-events = 0 #num-cpu = 1 verbose = 0 ; logging output: 0-nothing?, 1+INFO, 2+DEBUG, ... modules = pyimgalgos.tahometer pyimgalgos.cspad_arr_producer pyimgalgos.cspad_image_producer pyimgalgos.image_save_in_file [psana] files = exp=meca6113:run=28 events = 5 #skip-events = 0 modules = pyimgalgos.tahometer pyimgalgos.cspad_arr_producer pyimgalgos.cspad_image_producer pyimgalgos.image_save_in_file [pyimgalgos.tahometer] dn = 10 print_bits = 255 [pyimgalgos.cspad_arr_producer] #source = -|Cspad-* source = MecTargetChamber-0|Cspad2x2-3 #data_type = double data_type = float #data_type = unsigned #data_type = uint16 #data_type = uint32 val_miss = 0 key_out = cspad2x2_array print_bits = 255 [pyimgalgos.cspad_image_producer] calib_dir = /reg/d/psdm/mec/meca6113/calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.3/ key_in = cspad2x2_array key_out = cspad2x2_image print_bits = 1 # Supported output file formats tiff, gif, png, eps, jpg, jpeg, txt, npy(default), npz [pyimgalgos.image_save_in_file] key_in = cspad2x2_image ofname = img-for-cspad2x2.tiff print_bits = 255 |
To run this script use command
psana -c py-meca6113-r0028-cspad2x2.cfg
or
pyana -c py-meca6113-r0028-cspad2x2.cfg
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