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See for details interface description in  CSPAD pixel coordinates and image producer in Python

2013-10-22 Brendan Murphy, amo74213

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Please let me know if you have more questions, I think that the results of this effort can be quite valuable to any LCLS users who use
the Acqiris.

A: Psana Module Catalog: Modules AcqirisArrProducer, AcqirisAverage, and AcqirisCalib.

See modules ImgAlgos::AcqirisArrProducer, AcqirisAverage, and AcqirisCalib in

• Psana Module Catalog - Old
• Psana Module Examples - Old

2012-10-17 Marcin Sikorski, xcs

Q: For 49 to 51 in xcs72913
Could you please help me with reading XPP Cspad's (both small and cspad 140) images in pyana? How to extract 2D image for every event() ? I tried to follow confluence page but I failed.
A: See description and examples of the package pyimgalgos:

• Psana Module Catalog
• Psana Module Examples

Until new release (> ana-0.10.2) is generated,
you will need to update this package in your release directory:

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Q: How to get images in tiff format
A: In Examples for meca6113.

2013-10-09 Cornelius Gati, MEC

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Q1: Need in psana modules:
1) Threshold peak finding algorithm: if pixel intensity exceeds threshold - set pixel to 1
2) Blob finding algorithm : find blobs and set central pixel to 1 or N (number of pixels in the blob)
A: Add psana module psana - Module CatalogCatalog#Module ImgAlgos::ImgHitFinder

2013-09-24 Cornelius Gati, MEC

Q1: How to start Matlab
A1: See: Computing (including Analysis)#Running the Analysis
For example:

ssh psananeh;
/reg/common/package/scripts/matlic;

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A: There is a couple of peak finding algorithms in psana:
Psana Module Catalog - OldOld#Module ImgAlgos::ImgPeakFinder
Psana Module Catalog - OldOld#Module ImgAlgos::ImgPeakFinderAB
Which one should be used depends on images in your experiment.
In order to advice anything else I need to know more about your analysis.

2013-09-19 Dieter Ries, works with ultracold neutrons.

Q: HDF5 Explorer - Old This looks like a very useful tool to me, but unfortunately I couldn't find any information on if hdf5explorer is available outside of SLAC Is it released to the public somewhere? If yes, where can I find it and under which license is it released?
A: to get entire LCLS software release use instructions in
PSDM software distribution

If you prefer to use HDF5 and directly access data, then look at some prescriptions in
How to access HDF5 data from Python

The right way to perform LCLS analysis is to use PSANA:
Psana User Manual - Old
or its interactive version:
Interactive PSANA Study
Tutorial
which currently allows to get data both in C++ and Python code.

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Q: How to get time synchronization between two arrays? Example in
How to access HDF5 data from PythonPython#Example 4: Time-based syncronization of two datasets always prints 'Missing of syncronization'.
A: This example assumes that both arrays should have the same times, but some of measurements may be missing.

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Q1: My module creates and writes to a .txt file. By default, this file is
located in the release directory; is it possible to specify a different location?
A1: use complete path, for example: /reg/neh/home/sbbrown/<further-path-to-your-subdirectory>/file.txt
Q2: How do I save a file to a local location.
A2: Use scp. Other options are described in Data exportation.

2013-07-30 Philip Hart

Q: How to calibrate pedestals of two (or more) cspad2x2 in pswana?
A: Psana Module Examples - OldOld#Example for module cspad_mod::CsPad2x2Pedestals

2013-07-16 Simon Lieu

Q: Could you please explain what EPICS and PV are?
EPICS - Experimental Physics and Industrial Control System
PV - Process Variables

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Q: How to generate CSPAD image from array, how to save image(s) in file etc.
Mariano works on specific analysis module which averages CSPAD array in bins, depending on external parameters. He wants to have arrays like
Nbins1750x1750 for data, background etc. The bin is defined by external variables.
A: Useful examples of code in Psana Module Catalog - Old: cspad_mod.CsPadCalib, ImgAlgos::ImgCalib, ImgAlgos::ImgSaveInFile, ImgAlgos::CSPadArrAverage, ImgAlgos::CSPadArrSaveInFile, ImgAlgos::CSPadMaskApply, ...

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Q: How to save something in root-style ntuples?
A: ROOT as a histogramming package for psana
Psana User Manual - OldOld#Histogramming Service

2013-05-05 Henrik Till Lemke, xpp

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Q: How to get TIFF images of CSPad2x2 ?
A: Use example to produce text image. Then use script ConvertTextImageToTiff.py to convert TXT to TIFF format.
If you need to subtract pedestals use Psana Module Catalog - OldOld#Module cspad_mod.CsPadCalib.

2013-02-20 Marc Messerschmidt, cxi

Q: could you check and maybe update the CSpad geometry files using powder
diffraction from cxi80410/run1458?
The pattern should look like the following:
A: Use constants from 2013-01-31 CSPad CxiDs1 alignment

2013-02-19 Marc Messerschmidt, cxi

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Q: I'm having trouble viewing our experiment's hdf5 files with hdfview. It
looks like the hdf5 libraries have something wrong, as the option to use
such files is greyed out. I get an error stating that my experiment's
files are not a compatible version.
The version of hdfview I'm using is located at
/reg/neh/operator/xppopr/hdfview/hdfview and an example file
is /reg/d/psdm/xpp/xpp56012/hdf5/xpp56012-r0186.h5.

A: Try HDF5 Explorer - Old

2013-02-13 Mtg with cxi guys.

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Portability:
There is a document explaining of how you can import/install the LCLS offline packages on your own computer: PSDM software distribution

Extensibility:
This option existed for a long time, though it was not documented anywhere. So, I have composed a new confluence page devoted to this issue: Users' Software Repository
You are encouraged to work on shareable code. All necessary infrastructure exists, though it was not actively used so far...

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Software visibility is a good idea for well collaborating team.
This is not a case for LCLS user groups; due to competition most of groups do not want to share their tools. So, central framework code is completely
visible. Users' code is your own business. But, as I said, infrastructure is available for a long time. It's almost the first time when someone express some
interest to this infrastructure... In particular, for CSPad we have developed a bunch of general purpose modules: Psana Module Catalog - Old
If you have more ideas or need help, please let us know.
In particular, I will be willing to (help) write modules for polarization, solid angle correction, and more detailed gain correction.

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Non-linear gain correction:
I discussed this issue with Philip Hart. It exists as a good idea, but calibration, maintenance, and parametrization issues are not well elaborated.
In your case I would suggest to use the flat field calibration with intensity equivalent to your rings and apply psana module cspad_mod.CsPadCalib: Psana Module Catalog - OldOld#Module cspadmod.CsPadCalib

2013-02-10 Chun Hong Yoon, cxi43312

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A:Example which you need is in Psana Module Examples - OldOld#Examplefor Package CSPadPixCoords.
See description of psana modules in Psana Module Catalog - Old.

2013-01-31 Henrik Till Lemke, xpp

Q: Is there a way to receive x,y pixel coordinates for each pixel in a 32,185,388 matrix from just the calibration input, so independent of the calibration saved in a particular experiment folder and defining a particular run?
A: Add module CSPadPixCoordsWODB.py in PyCSPadImage package:
CSPad image producer in Python (DEPRICATED)

2013-01-31 Derek Anthony Mendez Jr, cxi64813

Q: Need in help in alignment of cspad ds1 for /reg/d/psdm/cxi/cxi64813/xtc/e243-r0058-s00-c00.xtc
A: Done:

• CSPAD Alignment
• 2013-01-31 CSPad CxiDs1 alignment

2013-01-24 Henrik Till Lemke, xpp

Q: The XPP cspad is being rearranged today and we'll have a new geometry. Would you be able to produce an input for your software until end tomorrow? I guess the metrology measurement will become available late afternoon today.

A: Done:

• CSPAD Alignment
• 2013-01-24 CSPad XPP alignment

2013-01-22 Derek Anthony Mendez Jr, cxi64813

Q: I was told to speak to you about the built-in CSPAD calibrations (centering, quad shifting, etc) implemented in psana. I would like to speak with you for maybe ten minutes
about how they work.
A: BEside our conversation, look at

• CSPadPixCoords::CSPadImageProducer
• CSPAD Geometry Software (depricated)
• CSPAD Alignment

2012-12-11 Ferguson, Kenneth Ramon, cxii0312

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• names of datasets with spaces: these names were saved correctly in hdf5expconfig file, but only the part of the name by the 1st space was retreaved for the next session;
• names of datasets were saved in hdf5expconfig file, but were not available for another hdf5 file. Apply try-except protection.
• in GUIWhatToDisplay the self.indTabOpen was not necessarily initialized.
  These bugs are fixed since release ana-0.7.2.
  How to get updated package is explained in
  HDF5 Explorer - OldOld#HDF5Explorer How to run this program

2012-11-08 Marc Messerschmidt, cxi

Q: CSPad2x2 pedestals are not calculated with CSPadArrAverage module.
A: CSPad2x2 is not implemented in CSPadArrAverage module.
Use module CsPad2x2Pedestals: Psana Module Catalog - OldOld#Module cspadmod.CsPad2x2Pedestals

2012-10-17 David McGonegle, MEC

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cd <your-favorite-directory>
sit_setup
psana -m cspad_mod.CsPadPedestals <dark-image-files.xtc>

Please see for details:
Psana Module Catalog - OldOld#Module cspad_mod.CsPadPedestals

2012-09-15 Marc Messerschmidt, cxi

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A: In order to help access data, two psana modules were implemented:

• ImgAlgos::ImgSpectra
• ImgAlgos::ImgSpectraProc

2012-09-12 Sebastian Carron (at Wed. grp mtg.)

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A: There are a few other options to get CSPad pixel coordinates;

• try psana with package CSPadPixCoords,
• if you prefer python code, try package PyCSPadImage.

2012-07-23 Wenkai Zhang, xpp50312

Q: How to get corrected (pedestals, common mode, gain, peakfinder) image for CSPad2x2?
A: Use psana, see example in Example of psana analysis for CSPad2x2.

2012-07-06 Chun Hong Yoon, cxi43312

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• Psana::PNCCD::FramesV1
• Psana::PNCCD::FullFrameV1
  Example in $SIT_RELDIR/ana-0.5.8/psana_examples/src/DumpPnccd.cpp is also updated.
  See also Module ImgAlgos::PnccdImageProducer

2012-07-02 Johan Hattne, CXI

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Q: How to get CSPad2x2 data in psana module and save it as an array
A: Implemented new module: CSPadPixCoords::CSPad2x2ImageProducer. See description and example:
Module CSPadPixCoords::CSPad2x2ImageProducer,
Example for Module CSPadPixCoords::CSPad2x2ImageProducer

2012-06-29 Daniel Flath, XCS

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Q: How to write CSPad image in file (tiff, binary, or text)?
A: Use psana modules and configuration file as explained in Psana Module Examples - OldOld#Example for Package CSPadPixCoords

2012-04-05 Andreas Schropp, MEC

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In responce I produced the description of the available package CSPad image producer in Python (DEPRICATED).

2011-10-10 Stefan Hau-Riege and Jan Feldkamp, cxi37411

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Experiment uses 2 CSPads. Need to be supported in HDF5Explorer.

HDF5Explorer is updated for multi-CSPad data.

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CSPad alignment and stimulated developement of the image producer as a psana module CSPAD Geometry Software (depricated)

2011-03-08 Adrian Mancuso, cxi80410

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