XPCS Analysis 8-ID

This Wiki page is dedicated towards providing documentation on 8-ID XPCS Data Analysis and Visualization

Overview

The sections below provide description of Visualization of XPCS results followed by details on Data Reduction/Analysis of Raw Data to yield Correlation functions.

XPCS metadata and results are primarily saved into a HDF5 file format based on a Data Exchange format defined at the APS.

MetaData File (HDF5)

The concept is as follows: There are groups in the HDF5 file that are part of the Data Acquisition and these are categorized into the following:

/measurement

/measurement/instrument

/measurement/instrument/acquisition/

/measurement/instrument/detector/

/measurement/instrument/detector/roi/

/measurement/instrument/detector/kinetics/

/measurement/instrument/source_begin/

/measurement/sample/

The above groups each contain several HDF5 datasets or parameters which have a scalar, vector, ND arrays or string attributes. The above are present in every metadata HDF5 file associated with each data acquisition. This file is saved in the same directory/folder as the raw detector images file itself.

Analysis Parameters (XPCS Group)

When a data set is processed which primarily means some sort of a correlation analysis, then the parameters that are needed to analyze the data such as:

• user defined mask
• wave vector maps (called as qmaps) where each wave vector or an azimuthal angle is characterized by a unique integer in what is called as a digitized map
• look up table that links the integers in the qmaps to the q/phi values
• Start and end frame numbers to be processed which could be a subset of the frames collected
• More intricate (meaning ones that are not changed from their defaults often) analysis parameters such as the multitau delay level, striding and averaging frames prior to correlation
• location of the file in the local as well as in a remote file system
• A very critical field which defines where the output of the computation - the results - are saved in the HDF5 file.

The above parameters (data sets) are saved in the HDF5 file in a special group called "/xpcs". Often, a user analyzes a given data set more than once if not several times which could each be under different conditions such as varying one or more of the above analysis parameters. While there might be a short sighted convenience seen in keeping these different analysis into separate HDF5 files, the concept of maintaining groups in the same HDF5 file has a higher value as the user will readily know all the different analysis or processing that are done to a given data set.

Embracing that idea, the current implementation defines the first time analysis group as "/xpcs" and the output of this analysis is saved into a group that is defined under "/xpcs/output_data" which usually points to a group named "/exchange".

For every subsequent analysis that is performed, the XPCS group is called "/xpcs_N" where N=1,2,3,4,..... In the same way as described above, "/xpcs_N/output_data" points to "/exchange_N".

Result Structure (HDF5 EXCHANGE Group)

A visualization package is provided that is called "VIEW_XPCSGUI_RESULTS" which is maintained in the APS Internal Version Control repository Subversion.

• The package primarily comprises of a GUI called "viewresult" which has easy pre-defined plots for visualizing typical parameters such as the SAXS I(q), Average intensity variation with time, I(q,t) which shows the SAXS variation with time and most importantly the time correlation functions, g2, as a function of q and phi.
• Additionally, there are functions that are available to place the entire data structure into the Matlab workspace for processing that the user might want to do. The function is called as follows (as a default) with the HDF5 file as the only argument in which case it will open the default "/xpcs" group. Recently, a new function has been added called "select_xpcs_group" in which the user could specify a second argument called "first" or "last" which will then select the first which is "/xpcs" or the last which is "/xpcs_N" where N is the highest number found in that HDF5 file.

• viewresultinfo.result = loadhdf5result('FeO_20nm_film5_44p90mm_027_0001-0212.hdf');
• Alternatively, the user could call the above function in the following way in which case it would open "/xpcs_3" in the example below.

viewresultinfo.result = loadhdf5result('FeO_20nm_film5_44p90mm_027_0001-0212.hdf','/xpcs_3');

• A function called hdf5_find_group_suffix('FeO_20nm_film5_44p90mm_027_0001-0212.hdf','/xpcs') would return an integer N where N is the total number of "/xpcs" groups that are present in the HDF5 file.

Result Structure (.mat File)

While the above described HDF5 format offers several advantages and convenience, some times it is convenient to save the results into a native .mat file, which is the binary format of Matlab. (Note that as of R2016 or so, .mat is also internally a HDF5 file but the groups and data sets in such a file are not seen outside). The .mat file can be read using native Matlab funcion "load".

• load SPS64_140k_200nm_154C_F2_TimeSeries_avg.mat

OR

• load('SPS64_140k_200nm_154C_F2_TimeSeries_avg.mat')

will load the parameters saved in the .mat file into the workspace.

Summary of Result Structure

Irrespective of the results being saved in HDF5 or .mat format, the respective functions (loadhdf5result and load) described above offers the exact same result structure in the work space so that the rest of the code (plotting, fitting, visualization) are agnostic to the format. The standard name for the structure in the workspace, when the functions are called as described above (especially for the HDF5, note viewresultinfo.result). This is a structure in Matlab which is a way to store several parameters comprising of numerics and strings in a hierarchical manner.

How to process the Result Structure?

Below, a typical result structure is shown under two different scenarios.The variables are given names that are some what self-explanatory but not obviously always. The general format for the different parameters involving q/phi are (#q x #phi x #dt). In cases where there is only one phi partition, it will look like (#q x 1 x #dt). These two cases are shown below along with a description to the right of what the parameter means to a user.

Files NOT containing azimuthal (phi) bins viewresultinfo.result ans =

           hdf5_filename: {'XR6_25p0C_Sq1_001_0001-0074.hdf'}
   result_group_location: {'/exchange'}
         xpcs_group_name: {'/xpcs'}
                staticQs: {[90x1 double]} %%list of q-values in the static partition
               dynamicQs: {[18x1 double]} %%list of q-values in the dynamic partition
              staticPHIs: {[90x1 double]} %%list of PHI-values in the static partition
             dynamicPHIs: {[18x1 double]} %%list of PHI-values in the dynamic partition
                     aIt: {[1300x1340 double]} %%2-d image of average intensity over all frames
          totalIntensity: {[64x1 double]} %%total intensity, one data point per frame (per kinetics slice for kinetics mode)
              timeStamps: {[64x1 double]} %%time stamp for each frame
            framespacing: {[1.289641633866325e+00]} %% constant spacing in time (sec) between frames
      StdDevframespacing: {[1.222323102678448e-02]} %%standard deviation in the time spacing (in sec)
                   delay: {[19x1 double]} %%time delay (sec) for the g2 plots
            darkAverages: {[NaN]} %%does not exist
              darkStdDev: {[NaN]} %%does not exist
                   Iqphi: {[90x1 double]} %%I(q) - time averaged
                  Iqphit: {[90x1x10 double]} %%I(q) with time - stability plot
                   g2avg: {[18x1x19 double]} %% measured g2 vs delay time (num of dyn qs x num dyn phis x number of delay)

% matlab syntax: squeeze(viewresultinfo.result.g2avg{1}(1,1,:))

               g2avgErr: {[18x1x19 double]} %%g2 error bars
                   %%%FIT1 is simple exp
               g2avgFIT1: {[18x1x19 double]} %%simple exp fitted values of g2
                 tauFIT1: {[18x1 double]} %%tau values at each dynamic q for simple exp
              tauErrFIT1: {[18x1 double]}%%tau error values at each dynamic q for simple exp
            baselineFIT1: {[18x1 double]} %%baseline values at each dynamic q for simple exp
         baselineErrFIT1: {[18x1 double]} %%baseline error values at each dynamic q for simple exp
            contrastFIT1: {[18x1 double]} %%contrast values at each dynamic q for simple exp
         contrastErrFIT1: {[18x1 double]} %%contrast error values at each dynamic q for simple exp
                %%%FIT2 is stretched exp          
               g2avgFIT2: {[18x1x19 double]} %%stretched exp fitted values of g2
                 tauFIT2: {[18x1 double]} %%tau values at each dynamic q for stretched exp
              tauErrFIT2: {[18x1 double]} %%tau error values at each dynamic q for stretched exp
            baselineFIT2: {[18x1 double]} %%baseline values at each dynamic q for stretched exp
         baselineErrFIT2: {[18x1 double]} %%baseline error values at each dynamic q for stretched exp
            contrastFIT2: {[18x1 double]} %%contrast values at each dynamic q for stretched exp
         contrastErrFIT2: {[18x1 double]} %%contrast error values at each dynamic q for stretched exp
            exponentFIT2: {[18x1 double]} %%exponent values at each dynamic q for stretched exp
         exponentErrFIT2: {[18x1 double]} %%exponent error values at each dynamic q for stretched exp

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Files containing azimuthal (phi) bins viewresultinfo.result ans =

           hdf5_filename: {'FeO_20nm_film5_44p90mm_027_0001-0212.hdf'}
   result_group_location: {'/exchange'}
         xpcs_group_name: {'/xpcs'}
                staticQs: {[72x60 double]}
               dynamicQs: {[24x1 double]}
              staticPHIs: {[72x60 double]}
             dynamicPHIs: {[24x1 double]}
                     aIt: {[1300x1340 double]} %%2-d image of average intensity over all frames
          totalIntensity: {[202x1 double]} %%total intensity, one data point per frame (per kinetics slice for kinetics mode)
              timeStamps: {[202x1 double]} %%time stamp for each frame
            framespacing: {[3.132541805357482e+00]} %% constant spacing in time (sec) between frames
      StdDevframespacing: {[1.387878691212486e-02]} %%standard deviation in the time spacing (in sec)
                   delay: {[25x1 double]} %%time delay (sec) for the g2 plots
            darkAverages: {[NaN]} %%does not exist
              darkStdDev: {[NaN]} %%does not exist
                   Iqphi: {[72x60 double]} %%I(q) - time averaged
                  Iqphit: {[72x60x10 double]} %%I(q) with time - stability plot
                   g2avg: {[24x1x25 double]} %% measured g2 vs delay time (num of dyn qs x num dyn phis x number of delay)
                                         %%%squeeze(viewresultinfo.result.g2avg{1}(1,1,:))

% matlab syntax: squeeze(viewresultinfo.result.g2avg{1}(1,1,:))

                g2avgErr: {[24x1x25 double]} %%g2 error bars
                       %%%FIT1 is simple exp
               g2avgFIT1: {[24x1x25 double]} %%simple exp fitted values of g2
                 tauFIT1: {[24x1 double]} %%tau values at each dynamic q for simple exp
              tauErrFIT1: {[24x1 double]} %%tau error values at each dynamic q for simple exp
            baselineFIT1: {[24x1 double]} %%baseline values at each dynamic q for simple exp
         baselineErrFIT1: {[24x1 double]} %%baseline error values at each dynamic q for simple exp
            contrastFIT1: {[24x1 double]} %%contrast values at each dynamic q for simple exp
         contrastErrFIT1: {[24x1 double]} %%contrast error values at each dynamic q for simple exp
                       %%%FIT2 is stretched exp
               g2avgFIT2: {[24x1x25 double]} %%stretched exp fitted values of g2
                 tauFIT2: {[24x1 double]} %%tau values at each dynamic q for stretched exp
              tauErrFIT2: {[24x1 double]} %%tau error values at each dynamic q for stretched exp
            baselineFIT2: {[24x1 double]} %%baseline values at each dynamic q for stretched exp
         baselineErrFIT2: {[24x1 double]} %%baseline error values at each dynamic q for stretched exp
            contrastFIT2: {[24x1 double]} %%contrast values at each dynamic q for stretched exp
         contrastErrFIT2: {[24x1 double]} %%contrast error values at each dynamic q for stretched exp
            exponentFIT2: {[24x1 double]} %%exponent values at each dynamic q for stretched exp
         exponentErrFIT2: {[24x1 double]} %%exponent error values at each dynamic q for stretched exp

1. dadga
2. agdga
3. test
4. help

Beamline Summary

Date	Start Time	Duration	Task	Status
12/7	1:00 PM	1 Day	cadmus	DONE
12/14	1:00 PM	1 Day	echo	DONE
12/21	1:00 PM	1 Day	overhead comfort displays	DONE
12/22	1:00 PM	1 Day	demeter	DONE
1/3	1:00 PM	1 Day	phoenix	DONE
Run 2017-1 (or April/May shutdown)	TBD	TBD	other MCR systems as approved by AOP	DONE

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