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# Scripts Reference

Command-line scripts are available, for Ptychography, CDI and holo-tomography.

## Ptychography scripts

These are instructions to run the command-line scripts for ptychography analysis such as pynx-ptycho-cxi, pynx-ptycho-id01, pynx-ptycho-id13, pynx-ptycho-id16a, etc…

pynx-ptycho-cxi

  Documentation for the pynx-ptycho-cxi command-line script to reconstruct ptychography datasets using the CXI file format

pynx-ptycho-simulation

  Documentation for the pynx-ptycho-simulation command-line script to reconstruct simulated ptychography datasets-mostly for testing & development.

pynx-ptycho-id01

  Documentation for the pynx-ptycho-id01 command-line script to reconstruct ptychography datasets from the ID01 ESRF beamline.

pynx-ptycho-id13

  Documentation for the pynx-ptycho-id13 command-line script to reconstruct ptychography datasets from the ID13 ESRF beamline.

pynx-ptycho-id16a

  Documentation for the pynx-ptycho-id16a command-line script to reconstruct far-field ptychography datasets from the ID16A ESRF beamline.

pynx-ptycho-id16a-nf

  Documentation for the pynx-ptycho-id16a-nf command-line script to reconstruct near-field ptychography datasets from the ID16A ESRF beamline.

pynx-ptycho-hermes

  Documentation for the pynx-ptycho-hermes command-line script to reconstruct ptychography datasets from the Hermès Soleil beamline.

## Coherent Diffraction Imaging scripts

These are instructions to run the command-line scripts: pynx-cdi-id01 and pynx-cdi-id10. They can also be used for generic data not from these beamlines.

Most of the parameters are identical, with a some changes in the default parameters according to each (small-angle or Bragg CDI).

### pynx-cdi-id01:

pynx-cdi-id01

  Documentation for the pynx-cdi-id01 command-line script to reconstruct objects from a CDI dataset, with defaults parameters for the Bragg CDI case.

### pynx-cdi-id10:

pynx-cdi-id10

  Documentation for the pynx-cdi-id10 command-line script to reconstruct objects from a CDI dataset, with defaults parameters for the small-angle case (with a beamstop).

## CDI-regrid

pynx-cdi-regrid

  Documentation for pynx-cdi-regrid to prepare 3D small-angle cdi CXI file from multiple projections.

## Holo-tomography scripts

### pynx-holotomo-id16b:

pynx-holotomo-id16b

  Documentation for the pynx-holotomo-id16b command-line script to reconstruct objects from an ID16B holo-tomography dataset.