Based on e-mail exchange between Mikhail, Gabriel, Jack, Faisal, Philip.
For composite detectors see EPIX10KA2M and EPIX10KAQUAD
Pictures from Gabriel's presentation
Chris Kenney:
- sensor regular pixel size 100x100 µm²,
- shown on plot gap pixels 100x225 µm² and four central pixels 225x225 µm².
- See plot for composite detectors in EPIX10KA2M and EPIX10KAQUAD
Configuration objects for epix10ka
Python psana has currently defined a few configuration objects for epix10ka:
Gain coding
Data gain bits assignment
2018-02-23 Gabriel:
Each pixel value is represented over 16 bits; the lowest 14 bits (0 to 13) encode the 14-bit ADC value, and bit 14 encodes the gain mode as either High (bit14==1) or Medium/Low (bit14==0) !!! THIS IS WRONG. SHOULD BE bit14==1/0 for L/H,M !!!. The choice between Medium and Low is determined globally for the ASIC by the asic.trbit.
Gain modes (Fixed High/Medium, Fixed Low, Auto High/Medium to Low, Forced High/Medium to Low, Masked) are determined per pixel; this information is required for reconstruction and is presumably saved in the metadata (the various modes have somewhat different pedestals, for example).
In practice the whole pixel matrix is most likely to be programmed with the same pattern, i.e., gain mode. While we had a philosophical discussion on using bit 15 for providing more info, due to the asynchronous way the pixel configuration mask is programmed, there is a lot of potential for confusion, so now bit 15 is not used.
2018-02-26 Faisal:
1) Just to elaborate a bit more, trbit is not part of the pixel config. It is part of the ASIC config just like atest, CompEn, etc. Your statement is correct it is defined per ASIC not camera.
2) Configuration array can also be found under psana.Epix.Config10kaV1 …. asicPixelConfigArray. Please see https://github.com/slaclab/cac/blob/master/psana/epix10ka/dump_config.py
Bit coding is as follows: MSB to LSB
Pixel Mask
ga g M Tx x 1 x pixel is maskedx x 0 1 pixel is under test0 0 x x auto switch0 1 x x force switch1 0 x x low gain (fixed)1 1 x x high gain (fixed)For example
0x0 for all pixel is auto switch. If tr=1, then auto switch high to low, if tr=0 then auto switch medium to low. Please note trbit is not part of the pixel config.
0xC is fixed high gain if tr=1, fixed medium if tr=0.
0x8 is fixed low gain. tr=1. tr=0 is not to be used here.
If you want to mask a pixel AND it with 0x2
If you want to test a pixel e.g. run the internal pusler then AND its config with 0x1.
2020-06-30 Dan and Maciej about forced gain modes
Calibration rows
Each ASIC has (176+2 rows x 192 columns), the last two rows are the calibration rows. These rows are not connected to the sensor and are constructed without a pixel/sensor interface. They will be powered just like any other pixel in the ASIC, therefore, they see similar voltages, noise, etc just like other pixels.
# psana returns 4 rows: r0, r1, r2, r3
wirebonds#|||||||||##¯¯¯¯|¯¯¯¯## A2 | A1 ##----|----## A3 | A0 ##____|____##|||||||||# wirebonds# r0 is row 176 in ASIC0 and ASIC3
# r1 is row 176 in ASIC1 and ASIC2
# r2 is row 177 (last) in ASIC0 and ASIC3
# r3 is row 177 (last) in ASIC1 and ASIC2
# when pixel (ga,g ,M,T) is xx0x then 176 is baseline and 177 is pixel max
# when pxiel (ga,g ,M,T) is xx1x then 176 is pixel max and 177 is baseline
Calibration files for dark
2018-02-28 Philip:
"force switch" mode: the camera starts high then goes low - this simulates switching.
This mode should be used for calibration of pedestals for switched mode.
I think by the way that we need to have two pedestal files in standard running:
H/M (dark)
H/M->L (forced)
In the case where we run the array in H/M/L without auto-ranging, we can
just populate the relevant pedestals.
H/M (dark)
H/M->L (forced)
In the case where we run the array in H/M/L without auto-ranging, we can
just populate the relevant pedestals.
2018-02-28 Angelo:
The force switch mode should be ignored. It is a debugging mode that should not be used for calibration.
Gabriel can explain how to do the calibration if needed
Raw data
dataset exp=mfxx32516:run=377
calibDir: /reg/d/psdm/MFX/mfxx32516/calib
det.source : Source("MfxEndstation.0:Epix10ka.0")
shape of ndarray: (352, 384)
Gain correction files
On 2018-06-20 Gabriel generated gain and offset files in
Archived in /reg/g/psdm/detector/gains/epix10k/2018-06-04-Camera1/
Control bits table
| Data | config | asicPixelConfigArray | |||||
|---|---|---|---|---|---|---|---|
| Index | Gain mode | bit14 | trbit | bit3: ga | bit2: g | bit1: Mask | bit0: Test |
| 0 | FH_H | x | 1 | 1 | 1 | ||
| 1 | FM_M | x | 0 | 1 | 1 | ||
| 2 | FL_L | x | x | 1 | 0 | ||
| 3 | AHL_H | 0 | 1 | 0 | 0 | ||
| 4 | AML_M | 0 | 0 | 0 | 0 | ||
| 5 | AHL_L | 1 | 1 | 0 | 0 | ||
| 6 | AML_L | 1 | 0 | 0 | 0 | ||
| 7 | AHL Forced L | 1 | 1 | 0 | 1 | ||
| 8 | AML Forced L | 1 | 0 | 0 | 1 | ||
| pixel control bit array | 1<<5 =32 | 1<<4 =16 | 1<<3 =8 | 1<<2 =4 | Not used | Not used | |
Gain correction formula
corrected = (raw - pedestals)/gain
Common mode correction
Added on 2020-06-04.
The value (raw - pedestals) can be corrected for common mode effect.
First image below shows one epix10ka segment non-corrected image of shape (352, 384). Vertical stripes presumably arising from this hardware effect.
The same median algorithm is applied as for Jungfrau, but separately for up- and down- part of the segment with parameters
cmpars=(<algorithm-id>, <mode>, <maximal-correction>), where
- algorithm-id is not used
- mode=0 - no correction, bit1=1 - in rows (is not useful for epix10ka), bit2=1 - in columns (the best for epix10ka)
- maximal-correction - maximal allowed correction in ADU
NOTE: currently mask on gain mode is not applied - all pixels are used to evaluate and correct for offset.
Examples of the command to get corrected image:
nda_cdata = det.calib(evt, cmpars=None) # default - cm pars from calib directory/system
nda_cdata = det.calib(evt, cmpars=(0, 0, 100)) # use cmpars, do not apply cm correction
nda_cdata = det.calib(evt, cmpars=(0, 2, 100)) # use cmpars, apply cm correction in columns
Images before and after common mode correction:
Meeting with Gabriel
On 2018-07-06 15:13 meeting with Gabriel.
Summary:
- control bit table is correct
- formula should include pedestals in stead of offset
- pedestals need to be generated and saved as txt file of shape (7, 1, 352, 384) under calib directory, for example:
/reg/d/psdm/MFX/mfxx32516/calib/Epix10ka::CalibV1/MfxEndstation.0:Epix10ka.0/pedestals/0-end.data - Gabriel on pedestal calibration:
- offsets and gain are calibrated not very often (say, once per month...)
- pedestals should be calibrated pretty often (once per hour...)
- pedestal calibration is implemented in AMI, using offsets,
- script works on dark runs accumulated for 5 gain modes
- + 2 gain modes are evaluated using combination of other 2 and offsets
- pedestal calibration procedure needs to be completed.
Calibration Details
See this page: https://confluence.slac.stanford.edu/display/ppareg/ePix10K+Calibration
Per panel calibration constants
Algorithm for xtc data with charge injection processing is developed by Gabriel and is wrapped in psana environment as CLI
Detector/app/epix10ka_offset_calibration
Similarly, dark run processing script is
Detector/app/epix10ka_pedestals_calibration
These commands will be available in releases > ana-1.3.58. See description using option "-h", e.g.
command> epix10ka_offset_calibration
command> epix10ka_pedestals_calibration
File naming convention in panel calibration repository
/reg/g/psdm/detector/gains/epix10k/panels/ - default repository <dir-repo>, can be re-directed for test by option "-o <dir-name>".
<dir-repo>/3791847426-0170080513-1879048214-0191557724-0003673288-2996154369-0218103833/,
Sub-directories for each panel:
offsetpedestalsplotsworkgain# content will be provided by Philip
<dir-repo>/.aliases.txt
<dir-repo>/panels/logs/
Panel calibration file name: epix10ka_0001_20180514120622_mfxx32516_r1021_pedestals_AHL-H.dat, where
epix10ka - detector type0001- panel id alias as specified in/reg/g/psdm/detector/gains/epix10k/panels/.aliases.txt20180514120622- run start time stamp in format '%Y%m%d%H%M%S'mfxx32516_r1021- experiment and run for production of this constantspedestals- constants typeAHL-H- gain range (mode)
File with already processed arrays is saved as
<dir-repo>
with extra fields in name sp02 for charge injection spacing number of pixels.
Constants merging for multi-panel detectors
command> epix10ka_deploy_constants -h
shows description of command line options. This command with sufficient number of parameters (at least experiment, run, and detector name)
- combines gain mode and panel calibration files in arrays of shape (7, <number-of-panels>, 352, 384)
- deploys calibration files in the calib directory, e.g.
/reg/d/psdm/MFX/mfxx32516/calib/Epix10ka::CalibV1/MfxEndstation.0:Epix10ka.0/pixel_gain/0-end.data
/reg/d/psdm/MFX/mfxx32516/calib/Epix10ka::CalibV1/MfxEndstation.0:Epix10ka.0/pedestals/0-end.data
Pedestal Deployment Meeting Notes (8/2/18)
- script that is use to drive the daq with hutch python: /reg/g/pcds/pyps/mfx/dev/mfx/experiments/mfxls3416.py
- for epix, 5 gain ranges (3 fixed, 2 auto) generate 7 pedestals
- maybe have "all range" option, and fast "selected ranges" option.
- maybe "all range" at beginning of expt, but "selected ranges" during expt.
- jason thinks medium/low is the default
- in the "selected ranges" mode makepeds will reuse the current numbers for ranges that weren't selected.
- multi-panel epix10k should be the same as jungfrau (might need to massage
- the daq appropriately)
- mikhail/gabriel: data processing call in makepeds script
- silke/jason/dan: hutch python, makepeds wrapper
- /reg/g/pcds/engineering_tools/R1.2.9/scripts/makepeds calls makepeds_psana calls mikhail's stuff (jungfrau_ndarr_dark_proc)
List of known detectors on 2018-11-12
command> find_detector_names
#== type 0022 epix10ka
'DetLab.0:Epix10ka.0': 'epix10ka_0000',\
'MecTargetChamber.0:Epix10ka.0': 'epix10ka_0001',\
'MecTargetChamber.0:Epix10ka.1': 'epix10ka_0002',\
'MfxEndstation.0:Epix10ka.0': 'epix10ka_0003',\
'MfxEndstation.0:Epix10ka.1': 'epix10ka_0004',\
'MfxEndstation.0:Epix10ka.2': 'epix10ka_0005',\
Composite detectors
EPIX10KA2M and EPIX10KAQUAD - composite detectors made of epix10ka panels.
References
- https://github.com/slaclab/cac/tree/master/psana/epix10ka - scripts from Faisal
- https://pswww.slac.stanford.edu/apps/portal/index.php?exper_id=1107 - under Workflow -> Batch Processing - batch processing
- /reg/d/psdm/MFX/mfxx32516/results/abunimeh/2 - experimental and jupyter notebook scripts
- ePix10K Calibration, by Gabriel Blaj
- EPIX10KA2M and EPIX10KAQUAD
- Jungfrau and Epix10ka Calibration
- 2021-09-28 learn about existence of presentation 2019-10-02-ePix10K-500um-Sensor-Geometry.pdf
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