Workflows

The following notebooks provide a brief introduction to a couple of topics regarding the data structure and packages used during reconstruction when using mumott. This includes the alignment package (from Mads and partly modified by Christian) as well as the mumott reconstruction package (Leonard)n”, In general, these tools should allow users at a beamline to work with SAXS based tomographic data as well as scanning SAXS imaging.

Contents

• Introduction to Jupyter notebooks
• Plotting Template
  • Step 0 - Import packages & libraries
  • Step 1 - Load relevant parameters for the scans
  • Step 2 - Loading of metadata and first visualization of scans
  • Step 3 - Check data from full dataset - normalized transmission signal (0…1)
  • Step 4 - Explore the scattering data & choose regions of interest
  • Step 5 - Export args into external file
  • Step 6. Radiation damage check
  • Step 7 Visualizing full dataset for colorful images
• 0 - Plotting Template cSAXS
  • Step 1 - Initiate tomo-scan parameters
  • Step 2 - Loading metadata
  • Step 3 - Choose q ranges
  • Step 4 - save args to file
  • Step 5 - visualize full dataset, check radiation damage
• 0 - Plotting Template formax
  • Step 1 - Initiate tomo-scan parameters
  • Step 2 - Loading metadata
  • Step 3 - Choose q ranges
  • Step 4 - save args to file
  • Step 5 - visualize full dataset, check radiation damage
• 0 - Plotting Template PX
  • Step 1 - Initiate tomo-scan parameters
  • Step 2 - Loading metadata
  • Step 3 - Choose q ranges
  • Step 4 - save args to file
  • Step 5 - visualize full dataset, check radiation damage
• 1a-Alignment_template_absorption
  • Step 1 - Load args from file
  • Step 2 - Visualizes absorption data
  • Step 3 - Make tomogram for 0 tilt (FBP projections)
  • Step 4 - full dataset
  • Step 5 - SIRT reconstructions
  • Step 6 - Save alignment parameters
• 1b-Alignment_template_scattering
  • Step 1 - Load args from previous step.
  • Step 2 - Visualize absorption data
  • Step 3 - Make tomogram for 0 tilt (FBP projections)
  • Step 4 - full dataset
  • Step 5 - SIRT reconstructions
  • Step 6 - Save alignment parameters
• 2-Export Template for single q bin
  • Step 1 - Load args first template
  • Step 2 - Choose q range for reconstructions
  • Step 3 - Load scattering data
  • Step 4 Import alignment and export data for Mumott
• 2-ExportQRES Template for multiple q bins all together
  • Step 1 - Load args from previous step.
  • Step 2 - Choose number of q bins
  • Step 3 - Load scattering data
  • Step 4 Import alignment and export data
• 3-Reconstruct_template (no regularization) | mumott v 0.2.1
  • Step 1 - Set environment parameters for Mumott
  • Step 2 - Load data
  • Step 3 - Visualize transformed data and check projections
  • Step 4 - Start optimization
  • Step 5 - Save output to file
• 3-Reconstruct_template with regularization | mumott v 0.2.1
  • Step 1 - Set environment parameters for Mumott
  • Step 2 - Load data
  • Step 3 - Visualize transformed data and check projections
  • Step 4 - Start optimization with optimization loop
  • Step 5 - Pick regularization parameter for reconstruction
  • Step 6 - Save output to file
• 3-Reconstruct_template, q resolved | mumott v 0.2.1
  • Step 1 - Set environment parameters for Mumott
  • Step 2 - Load data
  • Step 3 - Loop reconstructions over q
• 4-Investigate_recon_template | mumott v 0.2.1
  • Case 1 - Only one 1 bin
  • Case 2 - Q resolved data