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:

psana.Epix.Config10kaV1

  co.acqToAsicR0Delay                 co.asicMask                         co.calibPixelConfigArray            co.numberOfCalibrationRows          co.scopeEnable                       
  co.adcClkHalfT                      co.asicPixelConfigArray             co.calibrationRowCountPerASIC       co.numberOfColumns                  co.scopeTraceLength                  
  co.adcPipelineDelay                 co.asicPpbe                         co.carrierId0                       co.numberOfEnvironmentalRows        co.scopeTrigChan                     
  co.adcPipelineDelay0                co.asicPpbeControl                  co.carrierId1                       co.numberOfPixelsPerAsicRow         co.scopeTrigEdge                     
  co.adcPipelineDelay1                co.asicPpmat                        co.dacSetting                       co.numberOfReadableRows             co.scopeTrigHoldoff                  
  co.adcPipelineDelay2                co.asicPpmatControl                 co.digitalCardId0                   co.numberOfReadableRowsPerAsic      co.scopeTrigOffset                  
  co.adcPipelineDelay3                co.asicPPmatToReadout               co.digitalCardId1                   co.numberOfRows                     co.SyncDelay                        
  co.adcReadsPerPixel                 co.asicR0                           co.enableAutomaticRunTrigger        co.numberOfRowsPerAsic              co.SyncMode                         
  co.adcStreamMode                    co.asicR0ClkControl                 co.environmentalRowCountPerASIC     co.prepulseR0Delay                  co.SyncWidth                        
  co.analogCardId0                    co.asicR0Control                    co.epixRunTrigDelay                 co.prepulseR0En                     co.testPatternEnable                
  co.analogCardId1                    co.asicR0ToAsicAcq                  co.evrDaqCode                       co.prepulseR0Width                  co.TypeId                           
  co.asicAcq                          co.asicR0Width                      co.evrRunCode                       co.R0Mode                           co.usePgpEvr                        
  co.asicAcqControl                   co.asicRoClk                        co.evrRunTrigDelay                  co.scopeADCsameplesToSkip           co.Version                          
  co.asicAcqLToPPmatL                 co.asicRoClkHalfT                   co.numberOf125MhzTicksPerRunTrigger co.scopeADCThreshold                co.version                          
  co.asicAcqWidth                     co.asics                            co.numberOfAsics                    co.scopeArmMode                                                         
  co.asicGR                           co.asics_shape                      co.numberOfAsicsPerColumn           co.scopeChanAwaveformSelect                                             
  co.asicGRControl                    co.baseClockFrequency               co.numberOfAsicsPerRow              co.scopeChanBwaveformSelect

psana.Epix.Asic10kaConfigV1 as co.asic

            asic.atest              asic.FELmode            asic.RO_rst_en          asic.S2D_tcomp           
            asic.chipID             asic.Filter_DAC         asic.RowStart           asic.Sab_test            
            asic.ColumnStart        asic.Hrtest             asic.RowStop            asic.SLVDSbit            
            asic.ColumnStop         asic.is_en              asic.S2D                asic.tc                  
            asic.CompEn_lowBit      asic.Monost             asic.S2D0_DAC           asic.test                
            asic.CompEn_topTwoBits  asic.Monost_Pulser      asic.S2D0_GR            asic.testBE             
            asic.CompEnOn           asic.OCB                asic.S2D0_tcDAC         asic.testLVDTransmitter 
            asic.CompTH_DAC         asic.Pbit               asic.S2D1_DAC           asic.TPS_DAC            
            asic.DelCCKreg          asic.PixelCB            asic.S2D1_GR            asic.TPS_GR             
            asic.DelEXEC            asic.pixelDummy         asic.S2D1_tcDAC         asic.TPS_MUX            
            asic.DM1                asic.PP_OCB_S2D         asic.S2D2_DAC           asic.TPS_tcDAC          
            asic.DM1en              asic.Preamp             asic.S2D2_GR            asic.TPS_tcomp          
            asic.DM2                asic.Pulser             asic.S2D2_tcDAC         asic.trbit              
            asic.DM2en              asic.Pulser_DAC         asic.S2D3_DAC           asic.Vld1_b             
            asic.emph_bc            asic.PulserR            asic.S2D3_GR            asic.VREF_DAC           
            asic.emph_bd            asic.PulserSync         asic.S2D3_tcDAC         asic.VrefLow            
            asic.fastPP_enable      asic.RO_Monost          asic.S2D_DAC_Bias

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 T

x x 1 x pixel is masked

x x 0 1 pixel is under test

0 0 x x auto switch

0 1 x x force switch

1 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.

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

epix10ka data available on 2018-07-05

Command: find_detector_runs MFX epix10ka

    # mfxx32516: nruns 3-377, MfxEndstation.0:Epix10ka.0, MfxEndstation.0:Epix10ka.1
    # mfxx36916: runs 1-84,  MfxEndstation.0:Epix10ka.1

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

gain correction files

Camera1-AHL-H-Gain.txt
Camera1-AHL-L-Gain.txt
Camera1-AML-L-Gain.txt
Camera1-AML-M-Gain.txt
Camera1-FH-H-Gain.txt
Camera1-FL-L-Gain.txt
Camera1-FM-M-Gain.txt

Archived in /reg/g/psdm/detector/gains/epix10k/2018-06-04-Camera1/

Gain and offset Mean and RMS

          Gain             Offset
          Mean   RMS       Mean   RMS
-------------------------------------------------------
FL-L      1.28   0.06         0     ?
FM-M     42.43   2.00      2331   150
FH-H    128.49   6.17      2354   151
AML-L     1.26   0.06      2115   164
AML-M    42.52   1.92      2334   150
AHL-L     1.29   0.06      2119   190
AHL-H   128.72   6.03      2358   151
-------------------------------------------------------

Control bits table

cbits - pixel control bit array

    #--------------------------------
    #   data bit 14 is moved here 1/0 for H,M/L
    #  / trbit  1/0 for H/M
    # V / bit3  1/0 for F/A
    #  V / bit2 1/0 for H,M/L
    #   V / M  mask
    #    V / T  test       gain range index
    #     V /             /  in calib files
    #      V             V 
    # x111xx =28 -  FH_H 0 
    # x011xx =12 -  FM_M 1 
    # xx10xx = 8 -  FL_L 2
    # 0100xx =16 - AHL_H 3
    # 0000xx = 0 - AML_M 4
    # 1100xx =48 - AHL_L 5
    # 1000xx =32 - AML_L 6
    # 1101xx =49 - AHL_FL 7
    # 1001xx =33 - AML_FL 8
    #--------------------------------

		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

trbit=1/0 - H/M
data bit 14 = 0/1 - H,M/L
bit3 = 0/1 - Auto / Fixed
bit2 = ? 1 - Forced?

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 -h

command> epix10ka_pedestals_calibration -h

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/ - directory for particular panel includes its long id,

Sub-directories for each panel:

offset
pedestals
plots
work
gain # content will be provided by Philip

<dir-repo>/.aliases.txt - file with aliases for long panel ids,

<dir-repo>/panels/logs/ - directory for log files,

Panel calibration file name: epix10ka_0001_20180514120622_mfxx32516_r1021_pedestals_AHL-H.dat, where

epix10ka - detector type
0001 - panel id alias as specified in /reg/g/psdm/detector/gains/epix10k/panels/.aliases.txt
20180514120622 - run start time stamp in format '%Y%m%d%H%M%S'
mfxx32516_r1021 - experiment and run for production of this constants
pedestals - constants type
AHL-H - gain range (mode)

File with already processed arrays is saved as

<dir-repo>/<panel-id>/work/epix10ka_0001_20180514120622_mfxx32516_r1021_sp02-df.npz

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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EPIX10KA