Introduction

NOTE: this software is for experiments in LCLS1-style hutches (XPP,XCS,MFX,CXI,MEC).  LCLS2-style hutches (TMO, RIX, UED) use LCLS2-style software found here: LCLS-II Data Acquisition and Analysis.

This site documents the usage of "psana python", which is software that can be used to analyze LCLS data.  Using relatively simple python code, it is possible to analyze LCLS data in parallel on hundreds of CPU cores, both offline and in real-time while data is being taken. NOTE: the graphical LCLS analysis tool AMI is used for many routine real-time monitoring plots.  psana-python is typically used for real-time analysis that cannot be done in AMI and for offline analysis.

This video (53 minutes, made on Dec. 15, 2022) can also be used as an introduction to LCLS data analysis:

Getting Started

Before getting started, please consider if the LCLS supported frameworks will work for you. Due to the complexity of our systems and the changing nature of our hardware and setup, there some non-negligible overhead in writing your own analysis code at the psana-level.

• One choice is a crystallography pipeline as Cheetah or CCTBX. LCLS staff can help you to make connections with experts and support the necessary facility setup. 
• A second, often used model is to use the small data & cube/binning setup described here: smalldata_tools: Analysis tools for aligned data
  • This code wraps the psana code described below and saved hdf5 files that can be further analyzed as the user group desires.

To get started with a simple 17-line introductory script, and see a list of psana features click here.  This link also shows you how to login to the analysis computers.

After that, we believe the best way for new users to learn is by running the many small "building block" examples here.

Other Useful Links

• Get a computer 

  Link in New Window
  PCDS:Accounts PCDS:Accounts linkText account href PCDS:Accounts

  at LCLS

• Learn how to use the batch system to run analysis jobs.

• Locate the 

  Link in New Window
  linkText data of your experiment href PCDS:Managing Files

• Look through our 

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  PCDS:Data Retention Policy PCDS:Data Retention Policy linkText Data Retention Policies href PCDS:Data Retention Policy

• The LCLS real-time online graphical analysis tool 

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  linkText AMI href PCDS:AMI Online Monitoring

• How to get remote computer graphics working (e.g. on your laptop) 

  Link in New Window
  linkText Remote Visualization href PCDS:Remote Visualization

How To Get Help with Analysis Tools

Send your questions to: pcds-help@slac.stanford.edu with relevant information (e.g. scripts, and other files involved in any failure you see). One of our experts will contact you. If it is the middle of the night and your experiment is having significant difficulty your hutch-scientist point-of-contact knows how to reach us by phone, 24/7.

Once in a while we also send updates on new features to our mailing list.  This is a low-traffic list (i.e. no spam).  You can subscribe by sending email to listserv@slac.stanford.edu with the following line in the body of the message:

subscribe pcds-ana-users-l

How to Use This Site

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Recommended Next Topics

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Foreword

This site presents a complete documentation for the data analysis tools and methods which are presently supported at LCLS. If this is the first time you're visiting this page then we advise that you read the rest of this page to learn how to get most (and do it quicker) out of the information which we've prepared for you here.

The first tip is on how to find the information you need. This is what we suggest:

• note the document tree on the left side bar of the Portal. The tree is designed to help you find your way to the right document. If you

  won

  don't see the tree then it's most likely turned off.

  That' easy to fix - just

  To fix this, look on the top-right side of this page and

  notice

  click on a little icon (left

  to

  of the 'Search' box) which will toggle the visibility of the side bar.

• most pages in this site list topics to review next, as well as additional related topics
• feel free to use

  if you know what you're looking for use search on the sidebar just above the tree.

  Please do so only if you know what you're looking for. In other cases a better approach would be to

  One can also use the tree structure to get yourself familiar with the general structure of the documentation.

  This may make your search more efficient.

• some pages on this site will redirect you (if needed) to other Confluence 'spaces' (sites). Note that the 'Search' will not propagate to those other spaces

  for those who're impatient enough to "get the right answer" quicker we have also prepared the usual HOWTO which is found in the very end of the document tree

  .

  If you think there is something important missing on the HOWTO list then let us know please. You may contact us as explained at the bottom of this page.

Steps to follow to begin using our software

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Where to look for help with the Analysis tools

We advise sending your questions to our "hot line" e-mail: pcds-help@slac.stanford.edu. One of our experts will contact you.

In case if you run into some problem with our software then it would be helpful if you provided the following information:

• on which machine you're seeing the problem
• which software are you using
• which data (files, etc.) you're trying to read, or where you're writing your results (intermediate files, etc.)

How to contact us for comments, suggestions on this documentation

We try do our best in keeping documents on this Portal complete and current. If you notice any errors, or if you think we should add something to the Portal then you have two options:

• contact us by sending a message to: pcds-help@slac.stanford.edu
• or leave a comment right at the page which you think needs to be corrected or improved