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1. Set up your release work directory:
   You should always run this code from your own release working directory.
   See the Account Setup section to set up the analysis environment. Set up your release working directory from pslogin:

   Code Block
   none none
   [user@pslogin ~] newrel ana-current myrelease [user@pslogin ~] cd myrelease [user@pslogin myrelease] sit_setup

   
   
2. Add the package:
   This step is optional. Since release ana-0.3.7, xtcexplorer has been built into the release so you can skip to (3).
   Checking out a local copy is beneficial, though! That will enable you to edit the source files and customise the analysis.
   
   You need an afs token to check out the package, so if you didn't already you need to run 'kinit' first:

   Code Block
   none none
   [user@pslogin myrelease] kinit Password for user@SLAC.STANFORD.EDU:

   Now you're ready to check out the package and "compile" (to avoid a bug in the current release, use V00-01-14):

   Code Block
   none none
   [user@pslogin myrelease] addpkg XtcExplorer V00-01-14 [user@pslogin myrelease] scons

   Note! You can also do 'addpkg XtcExplorer VXX-XX-XX' to get a specific version of the package, or to get the most recent one, do 'addpkg XtcExplorer HEAD', but be aware that it may look different from described here, and might have fresh bugs as well as new features.
   
   
3. Run the program:
   Launch the GUI with the command 'xtcexplorer' and optionally give the input xtc files that you want to read
   as arguments. You can also browse to find files after launching the browser.
   
   To have access to the xtc files, you need to login to psana for this:

   Code Block
   [user@psanaXXX myrelease] sit_setup [user@psanaXXX myrelease] xtcexplorer /reg/d/psdm/CXI/cxi22010/xtc/e60-r0465-s0*

Description of the GUIs

The following documentation describes version 0.1.15 (or "tag" V00-01-15"). For earlier versions, see earlier versions of this confluence page (go to "Tools" -> "Page history").

LCLS Xtc Explorer

xtcexplorer will launch the main GUI. At startup, it has two sections:

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XtcExplorer/src/pyana_bld.py          # display of Beam-line data
XtcExplorer/src/pyana_epics.py        # display of Epics PV data
XtcExplorer/src/pyana_scan.py         # display of motor scan data
XtcExplorer/src/pyana_encoder.py      # display of encoder data
XtcExplorer/src/pyana_ipimb.py        # display of diode data from IPIMB and PIM
XtcExplorer/src/pyana_waveform.py     # display of waveform data
XtcExplorer/src/pyana_cspadimage.py        # display of CsPadcamera image data
XtcExplorer/src/pyana_imageplotter.py      # a plotter #module displayto ofcontrol camerathe imageevent data
XtcExplorer/src/pyana_plotter.py      # a plotter module to control the event display
display

Additional helper classes and functions are defined in

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 do_ebeam           = False       #  Plot data from EBeam object
 do_gasdetector     = False       #  Plot data from GasDetector
 do_phasecavity     = False       #  Plot data from PhaseCavity
 do_ipimb           = False       #  Plot data from SharedIpimb  (No longer used, see pyana_ipimb)

Example of how to run this pyana module by itself, i.e. no GUI, processing 300 shots and using an xtcexplorer-generated config file:

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  sources           =             # string, space-separated list of addresses (Detector-Id|Device-ID)

Image Removed

  quantities        =             # string containing quantities to plot. "average stack single"

Image Added

Example how to run this pyana Example how to run this pyana module by itself, i.e. no GUI, processing 300 events and using an xtcexplorer-generated config file:

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pyana -n 300 -c xb_pyana_5299.cfg -m XtcExplorer.pyana_waveform <xtc files>

pyana_

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image

This module will take care of displaying all camera images, including CsPad images.
Additionally, it can

• filter images above a threshold value
• filter images with ROI above a threshold value
• apply algorithms to an image (e.g. rotation, shift, etc)
• Sum&average images above threshold, and images below threshold
• Load dark image from a file for background subtraction
• Save the average image(s) or selected single-shot images (up to a maximum) to file (numpy binary file)

CsPad data is reconstructed in pyana_cspad.py.

• If a threshold is provided, shots above threshold will be displayed / stored, and shots below
  threshold will be added to sum of darks for averaging.
• If a dark file is provided, background subtraction is done before filtering. If not, the below-threshold
  average can be used for background subtraction
• The plot configuration depends on whether threshold and dark subtraction is used. Intensity projections
  are also added to the plot, can be turned off (in the code).
• In Interactive mode (see pyana_plotter), you can click on the image to some interaction with the plot is possible:
  • change intensity range (color range)
  : Left
  • by left-
  click
  • clicking to set low limit, right-
  click
  • clicking to set high limit, middle-click to reset to full scale.
  • change threshold value and region of interest if a ROI was defined: Click on the rectangle, enter new values when prompted in terminal window
  • switch to SlideShow mode when you are content with the display: Middle-click on the canvas and enter new display mode value
  .You can save the average image(s) or the selected single-shot images to file (numpy binary file)
  • (2 for SlideShow).

Options must be specified in a configuration file. Only the img_ sources parameter is required.

  img_sources       =             # string, Address of Detector-Id|Device-ID
  dark_img_file inputdark    =             # filename of a binary numpy (.npy) with dark image for subtraction
  out_avg_file  threshold    =        # Threshold information, format: 'value # name (base) of output file for average image (numpy array)
  out_shot_file     (xmin:xmax,ymin:xmax) type'     
  algorithms   =        # algorithms to be applied #to name (base) of numpy array file for selected single-shot eventsthe image, e.g.: 'rotate:30' to rotate 30 degrees
  plot_vrange       =             # range (format vmin:vmax) of values for plotting (pixel intensity)
  thresholdshow_projections =    # bool, include projections =onto x,y axes, or not.   
  outputfile   =        # thresholdbase intensityname andfor thresholdoutput area. Format: value (xlow:xhigh,ylow:yhigh)
file. 
  n_hdf5       =        # temporarily unsupported. 
  max_save     = 0      # if larger than zero, will save event images in separate files, up to maximum. 

Example of how to run this pyana module by itself, i.e. no GUI, processing 10 events and using an xtcexplorer-generated config file:

pyana -n 10 -c xb_pyana_5299.cfg -m XtcExplorer.pyana_cspad -m XtcExplorer.pyana_plotter <xtc files>

pyana_image.py

This module processes generic camera frames, e.g from Pulnix TM6740 device. It allows any number of images, given as a space-separated list of addresses in the configuration file.

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Example of how to run this pyana module by itself, i.e. no GUI, processing 10 events and using an xtcexplorer-generated config file:

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sources     # list of IPIMB addresses
variables quantities  # keywords defining what to plot. The following keywords are defined:
            #   fex:pos        plot position based on sum and difference of the 4 diodes
            #   fex:sum        plot sum of signal from all 4 diodes
            #   fex:channels   plot all 4 channels (fex value)
            #   fex:chX        plot fex value from channel X, X=0,1,2,3
            #   raw:chX        plot raw value from channel X, X=0,1,2,3
            #   raw:chXvolt    plot raw voltage from channel X, X=0,1,2,3

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