runXS.py Starter Guide

Here’s a step-by-step guide to running and customizing the runXS.py script from SciAnalysis on your own Windows machine:

✅ 1. Set the SciAnalysis Path

At the top of the script, you’ll see:

SciAnalysis_PATH='/home/kyager/current/code/SciAnalysis/main/'
SciAnalysis_PATH in sys.path or sys.path.append(SciAnalysis_PATH)

🛠️ Change this to your actual SciAnalysis folder path. For example, if you cloned the repo to your Desktop:

SciAnalysis_PATH = 'C:\\Users\\YourName\\Desktop\\SciAnalysis\\SciAnalysis'

Make sure to:

Use double backslashes \ or a raw string r'C:\path'
Point to the SciAnalysis subfolder containing XSAnalysis/ and tools.py

📁2. Set the Mask Path

The mask is often used for excluding detector artifacts or bad pixels.

in CaliWS.yaml, Look for lines like:

mask_dir: "/nsls2/data/cms/legacy/xf11bm/software/SciAnalysis//SciAnalysis/XSAnalysis/masks/"
# mask_file: "Dectris/Pilatus800k_gaps-mask.png"
mask_file: "Dectris/Pilatus800k_vertical_gaps-mask.png"
custom_mask: "./Pilatus800_current-mask.png"

🛠️ Un-comment and change this to your actual mask file path (Example):

mask_dir = 'C:\\Users\\YourName\\Your_SciAnalysis_Path\\mask\\'

If you don’t have a mask, you can either:

Generate one from a white and black image.
Comment it out and proceed (some protocols will still work without a mask).

🧪3. Customize Input and Output Paths

Later in the script (typically inside a loop or batch block), define:

input_dir = '/path/to/data/'
output_dir = '/path/to/output/'

🛠️ Replace these with actual folder paths:

input_dir = 'C:\\Users\\YourName\\Desktop\\data\\'
output_dir = 'C:\\Users\\YourName\\Desktop\\results\\'

Ensure:

Data files (e.g., .tif, .h5, etc.) are present in input_dir
output_dir exists or will be created

🧬4. Customize or Add Protocols

SciAnalysis lets you define custom protocols by subclassing existing ones:

Example from the script:

protocols = [
    Protocols.sector_average(name='vertical', angle=0, dangle=20, ylog=True, plot_range=[0, 3.5, None, None],  gridlines=True, save_results = [ 'txt', 'plots' ]) ,
    Protocols.sector_average(name='horizontal', angle=90, dangle=20, ylog=True, plot_range=[0, 3.5, None, None],  gridlines=True, save_results = [ 'txt', 'plots' ]) ,
    Protocols.linecut_angle(q0=2.10, dq=0.05*2, name='linecut_angle_peak3',show_region='save') ,

    ]

You can:

Modify protocols to change parameters, saving behavior, or others

⚙️5. Batch Processing Configuration

Locate the file name selector like:

#pattern = '*flaton*'
#pattern = 'Ag*'
pattern = '*'
#pattern = '*71857*'

The pattern variable determines which files in your input_dir are processed:

'*' — Process all files.
'Ag*' — Process files starting with “Ag”.
'flaton' — Process files containing “flaton” anywhere in the filename.
'71857' — Process files with “71857” in the name.

✅ You can uncomment and customize any one of these lines to suit your data selection.

Locate batch processor like:

# Run
########################################
print('Processing {} infiles...'.format(len(infiles)))
process.run(infiles, protocols, output_dir=output_dir, force=True)

force=True forces re-processing of all input files:
- Even if results already exist (e.g., .xml, .png, .dat files), they will be overwritten.
- Useful when you’ve changed protocols, masks, or input parameters and want to regenerate outputs.
If you want to skip already-processed files, change to: force = False

🚀

6. Run the Script

Open Anaconda Prompt or Command Prompt, navigate to the script folder:

cd C:\Users\YourName\Desktop\SciAnalysis\examples
python runXS.py

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