New XTCAV Documentation

Introduction

The XTCAV (X-band Transverse deflecting mode CAVity) is a detector that is used to determine the x-ray power vs. time of each LCLS shot. It can also be used to give information about the relative energies and arrival times of x-ray pulses that are closely spaced in time (fs delays). Unfortunately, some data analysis is necessary to extract this "power profile" from the raw detector signal. This documentation will go through how to do this.

For most experiments, the analysis should be basically turn-key using the code we provide at LCLS. The "Quickstart" section should be enough if you just want to do that as fast as possible. Many experiments that rely heavily on the XTCAV, however, operate in unique electron-beam modes (multibunch, etc) that require more manual fine-tuning of the analysis. To support those cases, we go through a little of the theory behind the XTCAV & analysis routines used to extract the information of interest.

Some knowledge of the physical setup is necessary to understand any data processing results. The XTCAV works by sending the electron beam at the end of the LCLS (after the undulators, so after x-rays have been generated) through a transverse accelerator that "kicks" the electrons, causing the front (early) part of the beam to head one direction, and the back (late) to head the other way. Then, the beam is sent through a magnetic field, which bends it; electrons with high kinetic energy bend a little less than those with low KE. Here is a little schematic:

In this way, the electrons get sorted by both time and energy. The beam hits a fluorescent screen that is imaged by a camera – this image is the raw data we process. A typical XTCAV images looks like this, with "time" on the x-axis and "energy" on the y-axis:

You may notice there are vertical streaks in this image. Those streaks reflect the energy some electrons lost when they generated x-rays in the XFEL undulator! If we compare this image to a comparable image that did not generate x-rays ("lasing off" run, more on that later) then we can "reconstruct" the x-ray power as a function of time.

Contents

Quickstart

All XTCAV analysis is a three step process involving "dark", "lasing off", and "lasing on" runs. The first two are references; the last is how we commonly refer to runs that contain data of interest. Simple scripts are provided as part of the psana python environment for processing each.

Dark Runs

Dark runs are used to simply make pedestals for the XTCAV camera and other diagnostics. These runs without any electrons going through the accelerator. We take the average of a series of dark run images to get the general pixel values of the camera background. We can then subtract this "average image" from the lasing on and off runs to get a closer approximation of the actual energy of the electron bunches.

LCLS provides an "xtcavDark" script that automatically populates the experiment calib dir with dark images that are picked up in subsequent analysis. Just provide an experiment and run number, and optionally the maximum number of shots to process:

xtcavDark amox23616 104 --max_shots 400

Output

dark background reference
  Experiment: amox23616
  Run: 104
  Valid shots to process: 400
100.0 % done, 400 / 400
Maximum number of images processed

Lasing Off Runs

Lasing off runs provide a reference of what the electron beam would have looked like if it did not lose any energy to generate x-rays. To provide this reference, a "lasing off" run is generated that has electons but no x-rays. These electron bunches are captured on the XTCAV camera. The standard analysis clusters together these lasing off images into an (automatically or manually chosen) number of groups. Each cluster of lasing off images is averaged to reduce noise, and then compared to "lasing on" bunches (next step, below). Clustering and subsequent matching to lasing on bunches is done by comparing the electron current as a function of time (projection of the XTCAV image onto the x-axis, the time axis), which is physically expected to be invariant, whether lasing occurred or not.

A script to generate lasing off references is provided with an interface very similar to the one for dark runs. It has quite a few options and should handle nearly all use cases.

xtcavLasingOff amox23616 131 --max_shots 200

Output

Lasing off reference
	 Experiment: amox23616
	 Runs: 131
	 Number of bunches: 1
	 Valid shots to process: 200
	 Dark reference run: None
100.0 % done, 200 / 200
Averaging lasing off profiles into  12  groups.

Lasing On Runs

Runs with data of interest are commonly referred to as "lasing on". For each shot, we choose an aggregated lasing off profile with the most similar electron current. That reference is used to compute the energy that was lost to x-rays. There are two methods by which one can perform that calculation (physical details below): one can either compare the "energy loss" directly – ie subtract the mean electron energy in the lasing off run from the lasing on run -- or look at the increased energy spread in lasing on run vs. lasing off. Both are motivated by FEL theory.

We provide a third simple script that can be used to test these methods:

xtcavLasingOn amox23616 137 --max_shots 5

Output

Using file 104-end.data for dark reference
Using file 131-end.data for lasing off reference
Agreement: 91.4276%; Maximum power: 6.64857; GW Pulse Delay: 18.512 
Agreement: 91.1052%; Maximum power: 5.82139; GW Pulse Delay: 20.6758 
Agreement: 93.136%; Maximum power: 4.88641; GW Pulse Delay: 18.0389 
Agreement: 94.1173%; Maximum power: 6.76523; GW Pulse Delay: 16.2321 
Agreement: 92.9344%; Maximum power: 7.14828; GW Pulse Delay: 11.2065 

For real analysis, however, you likely want to incorporate some python code into whatever analysis masterpiece you are composing.

from xtcav2.LasingOnCharacterization import LasingOnCharacterization
XTCAVRetrieval = LasingOnCharacterization() 


for evt in ds.events():
	XTCAVRetrieval.processEvent(evt)
	t, power = XTCAVRetrieval.xRayPower()

Theory

Analysis Setup

Two things must be done before XTCAV analysis will function: a "dark run" must be analyzed to get the pedestal values for cameras, and a "no lasing" run must be analyzed to generate sets of "no lasing" images (the latter is quite a complex process). Note that for demonstration these first two scripts write constants to a "local" calibration directory called "calib". For a real-experiment you won't need these lines because you will have permission to write to your official experiment calibration-constants directory.

Sample of dark run analysis:

# these first two lines for example purposes only, to allow user to write
# calibration information to local directory called "calib"
# should be deleted for real analysis.
import psana
psana.setOption('psana.calib-dir','calib')
from xtcav.DarkBackgroundReference import *

DarkBackgroundReference(experiment='xpptut15', 
	run_number='300',   # run number within experiment
	max_shots=1000,		# maximum number of shots to process
	validity_range=(300,302))  # range of runs for which this dark run should be used

Sample of "no-lasing" reference generating script:

# these two lines for example purposes only, to allow user to write
# calibration information to local directory called "calib"
# should be deleted for real analysis.
import psana
psana.setOption('psana.calib-dir','calib')
from xtcav.LasingOffReference import *
LasingOffReference(
	experiment='xpptut15',
	run_number='301',
	max_shots=200,
	num_bunches=1,
	validity_range=(301,)) #only give first run number to have the validity range be open-ended ("end")

This script can be easily run in parallel by submitting a parallel MPI job to the batch system as described here. Once the dark/lasing-off analysis has been completed, users can analyze the lasing-on events using a standard psana-python script similar to the one below.

Example Analysis Script

This script assumes that dark/lasing-off data has been analyzed (see above).   Unlike the previous two scripts it reads dark/lasing-off constants from the official calibration-directory.  

from psana import *
import matplotlib.pyplot as plt
from xtcav.LasingOnCharacterization import *
experiment = 'xpptut15'
run = '302'
mode = 'smd'
ds = psana.DataSource("exp=%s:run=%s:%s" % (experiment, run, mode))
ngood = 0
XTCAVRetrieval=LasingOnCharacterization() 
for evt in ds.events():
    if not XTCAVRetrieval.processEvent(evt):
        continue # continue to next image if analysis fails for some reason
    # time and power are lists, with each entry corresponding to
    # a bunch number.  The number of bunches is set by the GLOC.nb
    # parameter in the lasing-off analysis.  In general, one should
    # also cut on the "agreement" value, which measures the agreement
    # between the first and second moment analysis (larger is better).
    time, power = XTCAVRetrieval.xRayPower(method='RMS')  
    agreement = XTCAVRetrieval.reconstructionAgreement()
    ngood += 1
    print 'Agreement: %g%% ' % (agreement*100)
    plt.plot(time[0],power[0])
    plt.xlabel('Time (fs)')
    plt.ylabel('Lasing Power (GW)')
    plt.title('Agreement %4.2f'%agreement)
    plt.show()
    if ngood > 1: 
        break

Notes: The LasingOnCharacerization module uses the detector interface to find the datasource being used. The program will fail if you try to process events without first setting a datasource. If you are analyzing an older experiment, you may find that psana does not support the 'smd' mode. Instead, use the 'idx' mode.

One caveat: this data shows "horns" at the beginning and the end of the bunch which confuse the algorithm (the accelerator often behaves in this manner).  Only the middle peak in the plotted spectrum is the relevant lasing peak.

Some tips for lasing-on analysis:

• The second-moment analysis (energy spread method) of the XTCAV image generally provides a better estimate of the true power profile of the XTCAV image. It is recommended that you use method='RMS' when calling xRayPower(), as demonstrated above.
• Ignore shots where the X-ray intensity is low, but cutting on the FEEGasDetector value to select stronger shots

Examining The "Ingredients" of the XTCAV Analysis

This is a utility that can help users understand why XTCAV results look the way they do.   Run it like this:

 xtcavDisplay exp=xpptut15:run=302

It produces plots that look like this:

These plots show the following quantities for both lasing-on shot that is being analyzed and the lasing-off shot that it is being compared to (which is selected as the one having the closest current-profile):

• Current
• Energy computed using the first-moment ("Delta") method
• Energy computed using the second-moment ("Sigma") method
• Power

Close the existing plot window to show the plots for the next event.  

XTCAV Analysis Parameters

-experiment: Name of XTCAV experiment (i.e. 'xpptut15')

-run_number: Run number within experiment. Can be in string or integer format.

-num_bunches: Number of bunches: typically 1, but can be 2+ for some LCLS experiments. For analysis of a lasing on run, this must be the same as the number of bunches in the reference lasing off run that you're using.

-max_shots: number of images to process for dark background or lasing off reference generation. In principle the bigger the better, but around 1000 should work fine. If you select a bigger number for dark background generation, then you should get a more representative average of the background noise.  If you select a bigger number for lasing off reference generation, you will get more references. This will take longer to process but you'll have a better chance of finding a well matched profile when processing lasing on shots. 

-num_groups: The number of groups into which lasing off profiles are clustered. Setting this number to 1 would average all of the lasing off profiles in the run together while setting this number to 'maxshots' would not average your profiles at all. Averaging profiles helps to remove some of the noise you might find in an individual profile but may also make comparisons less accurate. Our experiments have found that setting this parameter to maxshots/3 (which should theoretically lead to groups of ~3) works best.

-dark_reference_path/lasingoff_reference_path: File paths for the generated dark and lasing off references you want to use. If none given, the most recent generated reference file (with the run being processed included in the 'validity_range') will be chosen. You can set the `dark_reference_path` when initializing both the LasingOnCharacterization and the LasingOffReference. You can set the `lasingoff_reference_path` when initializing the LasingOnCharacterization.

-roi_expand (default 1): Ratio by which to expand the image from the max and min of the region of interest. This should not affect any analysis but will affect the returned image. Do not set to <1! Call the method 'processedXTCAVImage'. If the image does not look clipped, the parameters are fine.

-roi_fraction (default 0.001): fraction of pixels that must be non-zero in roi(s) of image for analysis.  If you find that all of your images are registering as 'empty', try decreasing this parameter.

-snr_filter (default 10): Number of sigmas for the noise threshold. This is an important parameter. If you find that all of your images are registering as 'empty', try decreasing this parameter. If you find that your images contain a lot of noise, try increasing this parameter. This parameter is particularly important for 2+ bunch data. Since it sets a threshold based on the noise in an image, zeroing out pixels below that threshold, it is the factor that can separate the two island in case of two bunches. For two bunch data, you may need to tweak this parameter until the two bunches are separated for most of the shots. Bottom line:

• For single bunch: As low as possible while still removing the noise (i.e.) not getting noise current profiles.
• For double bunch: As low as possible while separating the two bunches. Call the 'processedXTCAVImage' method again, and look at the size of axis 0: this will be the number of bunches detected. You can probably write a program to automatize the determination of this parameter, until you get lets say a 95% of two bunch detection.

-validity_range (default `(current_run_number - end)`): The range of run numbers for which the reference run you are creating is valid. Parameter can be set in initialization of both the DarkBackground and the LasingOffReference. See example above. Note: Hopefully this is obvious, but if you set the validity range to (574,578) then the reference run will not be used for run 579 unless the reference path is explicitly given.

-start_image (default 0): Image within the run to start building the reference from. Can be set for `DarkBackgroundReference` and `LasingOffReference`.

-island_split_method: (default value: 'scipylabel') Only necessary when analyzing data with more than 1 bunch. Several image processing algorithms have been created to separate bunches that appear on the same image.  See here for some algorithm details.

• 'scipyLabel' calls the scipy label function to label contiguous regions.  this is fast, but requires a region of no signal (after de-noising) between the regions.
• 'autothreshold' tries to separate the islands by automatically finding thresholds that separate them.  this is the recommended mode for multi-bunch operation.
• 'contourLabel' tries to adjust a threshold until two large groups are found, grouping together pixels using an opencv contour method.  there are two parameters ('ratio1/ratio2') that are settable for the contour method that determine

Differences from Previous XTCAV code

• Changes to the user interface:
  • All parameters should be set during the initialization of `DarkBackgroundReference`, `LasingOffReference`, and `LasingOnCharacterization`.
  • There is no longer a `.Generate()` call. A reference will be created upon initialization of the `DarkBackgroundReference` and `LasingOffReference` classes. The reference will be saved to the psana data directory (default location unless the `calibration_path` parameter is set). If you would like to access the generated reference profiles, you can either load them from the saved file or access the member variable `averaged_profiles` within the `LasingOffReference` class.
  • Some parameters, such as roi_waist_threshold, have been deprecated. The current code automatically chooses this value for you based on the `snr_filter` (see documentation above). Other parameter names have changed so that naming convention is consistent across the entire xtcav package (again, see documentation above). 
• Changes to analysis:
  • Improved profile clustering algorithm
  • Image is no longer median filtered before analysis
  • Power profile for lasing off image is not averaged between RMS and COM methods
• Other changes include: improved code readability, integration with psana detector interface, and speed up in processing time.

Detector Resolution

(From Tim Maxwell)

Time resolution is around 1.1 fs RMS for soft x-rays, 2.5 fs fwhm (in quadrature, of course). So actually pulse length is probably 4.3 - 9.7 fs FWHM.

This also doesn't include the "slippage resolution." That is, if they're using the full undulator, then by the end the x-rays can have slipped out of the electron slice by ~3 fs for soft x-rays. Obviously not a small number if trying to make 5 fs pulses. They've been advised to not use the full undulator when shorter pulses are more important than number of photons.