Direkt zum Inhalt
  • Paul Scherrer Institut PSI
  • PSI Research, Labs & User Services

Digital User Office

  • Digital User Office
  • DE
  • EN
  • FR
Paul Scherrer Institut (PSI)
Suche
Paul Scherrer Institut (PSI)

Hauptnavigation

  • Research at PSIÖffnen dieses Hauptmenu Punktes
    • Research Initiatives
    • Ethics and Research integrity
    • Scientific Highlights
    • Scientific Events
    • Scientific Career
    • PSI-FELLOW
    • PSI Data Policy
  • Research Divisions and LabsÖffnen dieses Hauptmenu Punktes
    • Overview
    • Research with Neutrons and Muons
    • Photon Science
    • Energy and Environment
    • Nuclear Energy and Safety
    • Biology and Chemistry
    • Scientific Computing, Theory and Data
    • Large Research Facilities
  • Facilities and InstrumentsÖffnen dieses Hauptmenu Punktes
    • Overview
    • Large Research Facilities
    • Facilities
    • PSI Facility Newsletter
  • PSI User ServicesÖffnen dieses Hauptmenu Punktes
    • User Office
    • Methods at the PSI User Facilities
    • Proposals for beam time
    • Proposal Deadlines
    • Data Analysis Service (PSD)
    • EU support programmes
  • New ProjectsÖffnen dieses Hauptmenu Punktes
    • SLS 2.0
    • IMPACT
  • DE
  • EN
  • FR

Digital User Office (mobile)

  • Digital User Office

Sie befinden sich hier:

  1. PSI Home
  2. Labs & User Services
  3. PSD
  4. SLS
  5. CSAXS
  6. User Information
  7. Software

Sekundäre Navigation

CSAXS

  • Status
  • User Information Ausgeklappter Submenü Punkt
    • Application for beamtime
    • Operation Schedule
    • Manuals
    • Software
    • Infrastructure
  • People
  • Beamline Layout
    • Source
    • Optics
  • Endstations
  • Research
  • Publications
  • Scientific Highlights
  • Contacts

Info message

Dieser Inhalt ist nicht auf Deutsch verfügbar.

Your local contact will provide you with the latest version of our cxs_software package upon the start of your beamtime, or you can request them earlier from your local contact. These macros provide the functionality for reading and displaying the detector frames and for example for azimuthal integration. A zip-file with these macros can be downloaded here as well. The macros are provided as-is without any guarantees or liability on our part. An introduction to some of the packages is available in the cSAXS notes (see under manuals). Besides the basic codes below you can find other packages for example to analyze and visualize orientation and degree of orientation of scanning SAXS, reconstruct and visualize SAS tensor tomography, and ptychography reconstruction code. The codes are provided "as they are" and without any guarantee of results, performance, or support. The user of the codes should always take responsibility to ensure the correctness of the results.

Note: If these codes, or subfunctions or parts of it, is used for research in a publication or if it is fully or partially rewritten for another computing language the authors and institution should be acknowledged in written form in the publication. For example "Data processing was carried out using the "cSAXS matlab package" developed by the CXS group, Paul Scherrer Institut, Switzerland." Variations on this text can be incorporated, upon discussion with the CXS group, if needed to more specifically reflect the use of the package, or function, for the published work. A publication that focuses on describing features, or parameters, that are already existing in the code should be first discussed with the authors.

Data format - NeXus H5

Data and metadata is provided in one H5 file per scan. We organize the H5 file contents following NeXus guidelines and in particular following NXsas as much as it is practical.

The files can be explored and contents read with standard tools such as h5py. We also provide routines in Matlab to read it. In particular within the base package below we have the function io.nexus_read

% read the whole file contents
        nxs = io.nexus_read('~/Data10/data/S00000-00999/S00250/e16812_1_00250.h5');  
% let the function try to find the file, read whole file contents
        nxs = io.nexus_read('~/Data10', 'scanNr', 250, 'filter', '/');
% load only spec data
        nxs = io.nexus_read('~/Data10', 'scanNr', 250, 'filter', 'spec');
% load only pilatus_1 data
        nxs = io.nexus_read('~/Data10', 'scanNr', 250, 'filter', 'pilatus_1');
% load all detectors
        nxs = io.nexus_read('~/Data10', 'scanNr', 250, 'filter', 'detectors');

The following show 1) a sketch with beamline components and the corresponding H5 groups, and 2) the organization of the H5 groups.

Beamline sketch and NeXus file groups
NeXus Layout

cSAXS beamline software packages

Base package

Basic functionalities for file reading and radial integration and plotting. Also provides a lot of functions used in the other packages.

  • cSAXS base package

Scanning SAXS package

Analysis and plotting of scanning SAXS, main orientation of scattering, degree of orientation. Please cite Bunk et. al. New J. Phys. 11, 123016 (2009). Uses the base package above.

  • cSAXS scanning SAXS package

SASTT package

Reconstruction of small-angle scattering tensor tomography (SASTT), which provides information about 3D anisotropic nanostructure within a bulk sample. For the method with spherical harmonics model cite Liebi et. al. Nature 527, 349 (2015) and Liebi et. al. Acta Cryst. A74, 12 (2018). For the IRTT method cite Gao et. al. Acta Cryst. A75, 223 (2019). Uses the base and scanning SAXS packages above.

  • cSAXS SASTT package

Tomography package

Beamline codes for alignment of projections and reconstruction for tomography and laminography. Projection alignment methods by 3D consistency with deep sub-pixel accuracy are included. If used cite Odstrčil et al. Opt. Express 25, 36637 (2019). Uses the base package above.

  • cSAXS tomography package

PtychoShelves

A versatile high-level framework for high-performance analysis of ptychographic data. This package is used for preparation and reconstruction of data from cSAXS as well as other beamlines and synchrotrons. It allows for modular use of several data inputs and reconstruction algorithms. Includes Matlab prototype codes as well as highly optimized C code both for CPU and GPU. If used cite Wakonig et al. J. Appl. Cryst. 53, 574-586 (2020). Uses the base package above.

  • PtychoShelves
  • Documentation
  • License
PtychoShelves

Other open source codes

LSQ-ML - Iterative least-squares maximum-likelihood ptychography solver

This source code provides an implementation of the LSQ-ML method described in Opt. Express 26, 3108 (2018) in a simple Matlab-based framework. The reference implementation includes an artificial data generator and implementations of the ePIE, ePIE-OPRP and difference-map codes that were used in the article. Note that this is not the cSAXS ptychography package (which is planned to be published here at a later date), but rather a simplified version intended to showcase the LSQ-ML algorithm.
The code is using Matlab-based GPU acceleration, however seamless fallback CPU option is available as well.

  • LSQ-ML (License)

Alignment methods for nanotomography with deep sub-pixel accuracy

This repository contains codes for alignment of projections and reconstruction for tomography and laminography. Alignment methods by 3D consistency with deep sub-pixel accuracy are included. Additionally we include artificial, i.e. simulated, and experimental examples. If used cite Odstrčil et. al. Opt. Express 25, 36637 (2019).

  • Alignment of projections (Zenodo repository)

Mit Sidebar

Further information
  • Organize your journey
  • Before Arrival
  • How to get to PSI?
  • Your Stay At PSI
  • Safety
  • Safety Instructions

User Contact Points at PSI

PSI User Office
DUO Login

How to apply?

A short description of the procedures relevant to proposals at the PSI user facilities.

Call for Proposals

PX Beamlines: Call is open for proposals
More Information

All other Beamlines
08 February 2020: Call is open for proposals
More Information

EU Support for SLS-non-PX-users

Effective March 1, 2012 the funding for travel support and daily allowances will be only available through a application at BioStruct-X.
Find the complete information on the
EU Access Programmes Webpage


PSI Joint Users Association

Association representing the interests of PSI user community
top

Fussbereich

Paul Scherrer Institut

Forschungsstrasse 111
5232 Villigen PSI
Schweiz

Telefon: +41 56 310 21 11
Telefax: +41 56 310 21 99

Der Weg zu uns
Kontakt

Besucherzentrum psi forum
Schülerlabor iLab
Zentrum für Protonentherapie
PSI Bildungszentrum
PSI Guest House (in english)
PSI Gastronomie
psi forum-Shop

 

Service & Support

  • Telefonbuch
  • User Office
  • Accelerator Status
  • Publikationen des PSI
  • Lieferanten
  • E-Rechnung
  • Computing
  • Sicherheit

Karriere

  • Arbeiten am PSI
  • Stellenangebote
  • Aus- und Weiterbildung
  • Career Center
  • Berufsbildung
  • PSI Bildungszentrum

Für die Medien

  • Das PSI in Kürze
  • Zahlen und Fakten
  • Mediacorner
  • Medienmitteilungen
  • Social Media

Folgen Sie uns: Twitter (deutsch) LinkedIn Youtube Facebook Instagram Issuu RSS

Footer legal

  • Impressum
  • Nutzungsbedingungen
  • Editoren-Login