https://doi.org/10.5061/dryad.4b8gthtkq

In this dataset, we have incorporated the initial scattering patterns collected at beamline 8-ID-I (Advanced Photon Source, Argonne National Laboratory). The X-ray energy used for the measurements was 10.92 keV. The data was obtained through operando grazing incidence X-ray photon correlation spectroscopy (GIXPCS) using an optimized cone cell.

Contact Information

Name: R. Wu

Affiliations: Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA

ORCID ID: https://orcid.org/0000-0003-2666-6110

Email: ruiheng.wu@northwestern.edu

Description of the data and file structure

The dataset is available in either the original H5 file format or a supplementary type encapsulated within zip files. These zip files encompass both the H5 files and data subjected to primary treatment.

The experimental conditions are detailed within the filename. To illustrate with an example labeled "D224_Acid_PEDOT_Sample5_RbBr_step1_5_025C_att04_001.zip”, this dataset involves acid-treated PEDOT:PSS cycled in a 100mM RbBr solution at room temperature, using an attenuator identified as att4.

The datasets starting with the letter "E" also represent measurements conducted on acid-treated PEDOT:PSS. However, in this case, the cycling was performed in a 100mM NaCl solution.

The files and folders inside each zip file can be expressed by the following tree:

SuppMats_Data

|-- DXXX_SampleX_XXX_attX # Name of the example dataset

| |-- AVGN_DXXX_SampleX_XXX_attX # Scattering pattern extracted from h5 file and averaged over each N (noted in "AVGN") frames.

| |-- Cut_r2c2 # Local cut of the diffuse scattering part on the second row and the second column. The area was defined as: DiffScat_xstart=1298; DiffScat_xend=1552; DiffScat_ystart=262; DiffScat_yend=515;

| |-- Sum # A further sum of the cutted frames

| |-- Iteration # This folder saves the result after each iteration

| |-- FinalAlign # This folder saves the result after the final iteration, sometimes this folder will be empty

| |-- XXIteration.mat # These MAT format files save the final alignment result as pixel shift

| |-- Cut_r2c3 # Local cut of the diffuse scattering part on the second row and the second column. The area was defined as: DiffScat_xstart=1298; DiffScat_xend=1552; DiffScat_ystart=522; DiffScat_yend=775, the subfolders inside are the same as r2c2;

| |-- DXXX_SampleX_XXX_attX.batchinfo # Measurement information of the dataset

| |-- DXXX_SampleX_XXX_attX.hdf # head file for h5 file, no use for data treatment

| |-- DXXX_SampleX_XXX_attX.h5 # H5 file that can be treated with python or matlab code in the code pack

|-- DXXX_SampleX_XXX_attX # Name of another example dataset

|-- EXXX_SampleX_XXX_attX # Name of another example dataset, the letter "E" represent measurements conducted on acid-treated PEDOT:PSS in 100 mM NaCl

For the .mat files (XXIteration.mat), each file includes two arrays: "Shiftx" and "Shifty". Both of them are 1D array of pixel shift to the first frame.

For the .h5 files, the scattering pattern is in ['entry']['data']['data']. The file only have 'entry' category, under this is 'data' and 'instrument' (for instrumental information). Under the 'data', there is only another 'data' for data storage.

Sharing/Access information

The original data will also be posted on NU MRSEC DATA RETRIEVAL (NECTAR) later.

Code/Software

The Matlab and Python codes are provided in the associated Zenodo repository. For processing the original H5 files, it is recommended to utilize the attached code "XPCS alignment - multifolders.ipynb," which is included in the archive "Jupyter_notebook_for_alignment_and_fitting.zip." The Jupyter notebook is the preferred tool for alignment and fitting procedures.

For users preferring Matlab, the alignment code is available in the "Matlab_Code_Pack_20220504.zip" archive. The alignment process is executed by running the command lines within the "Intotal.m" file. Please note that this version is the older one, predating the code's rewriting in Python.

Following alignment, the final G-map is calculated and visualized using the command lines provided in the "Matlab_correlation.zip".

Moreover, the comprehensive data treatment, including self-dynamics model fitting and additional data verification tools such as variance and Poisson distribution checks, are compacted within the "Jupyter_notebook_for_alignment_and_fitting.zip" package.

Here is the information of the code included:

SuppMats_Software

|-- Jupyter notebook for alignment and fitting

| |-- Export APS Lambda 2M as TIFs v1.ipynb # Export the H5 file to tiff files

| |-- XPCS alignment - multifolders.ipynb # Further cut the tiff files and align the diffuse scattering region

| |-- XPCS alignment - skimage_224.ipynb # Align the diffuse scattering region using skimage package

| |-- variance-SI.ipynb # Variance check of the pattern

| |-- Poisson Distribution Cycle Multipic.ipynb # Poisson distribution check of the pattern

| |-- Fitting g2 - Multi (D224) - Averaged - Redope - Lim - Corrected - diag.ipynb # Self-dynamics model fitting using diagonal cut

| |-- Fitting g2 - Multi (D224) - Averaged - Redope - Lim - Corrected.ipynb # Self-dynamics model fitting using average cut

| |-- Figure 5 spinodal model_cubic_R_decay_plot.ipynb # Langevin model B diagram for Figure 5

| |-- XPCS Stack XXXXX.ipynb # Data visualization

|-- Matlab_correlation

| |-- g2Correlation_XXX.m # G map calculation

| |-- Plot_G2_Map - XXX.m # G map visualization

|-- Intotal.m # This is the Matlab command line to align the diffuse scattering region

|-- Code Pack 20220504 # This code pack will be called in "Intotal.m" for Matlab alignment