4D Tutorial Files instructions
 

Two hdf5 files are provided for your examples that are used by the six jupyter notebooks written as examples:

1. App5_Batch_Converter.ipynb: converts app5 files (produced by exporting from NanoMEGAS TopSpin precession diffraction software) into hdf5 files.  It can do a single file or a whole directory of files, it just looks through the directory list and attempts to convert everything with the right names.
2. VirtualDarkField.ipynb: demonstrates various approaches in Virtual Imaging with single apertures and arrays of apertures.
3. StrainMapping.ipynb: demonstrates strain mapping on an epitaxial thin film system.
4. Scan1_ACOM_auto.ipynb: performs automated crystal orientation mapping on a dataset from two-phase alpha-beta titanium.  It exports the results as two .ang files.  These are basically tagged lists of Euler angles for every pixel in the scan.
5. CombineMapsByComparingCI.ipynb: is a quick script that loads and compares the two .ang files and for each pixel (i.e. line in the file, which is just a plain text list, separated by line breaks) works out which of the two phases has the best correlation to the diffraction pattern (i.e. highest Correlation Index) and writes that as the equivalent line in a new .ang file that covers both phases and only reports best fit for each pixel.
6. Scan1_orix_13_10.ipynb: is a notebook for then performing visualisation and calculation on the resulting orientation (Euler Angle) data.

NB: the required libraries to be installed should be listed in the first code cell of each notebook and if you need to install new things or a specific version, please do so.  The use of environments in your python installation is advised to ensure that you do not mess up an existing python installation through conflicts between different libraries.  There are a number of approaches, including conda, which is very straightforward for a personal installation on a single computer, and others which may be preferable to a system administrator on a multiuser server.

NB2: Whilst the majority of packages should install on any system, the ACOM notebook needs the pymatgen library as a dependency of that module of py4DSTEM as written.  I have found this difficult to install on a Mac, but no problem on Linux.  There is a workaround for this, using manual definitions in crystallography instead of the automated ones that pymatgen makes easy.

NB3: If you have further questions after installing and trying things, contact
ian.maclaren@glasgow.ac.uk

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