io.net_cdf_io Module

This module contains fileIO operations and file conversion for the image processing tool kit in the NSLS-II data analysis software package. The functions included in this module focus on reading and writing netCDF files. This is the file format used by Mark Rivers for x-ray computed microtomography data collected at Argonne National Laboratory, Sector 13BMD, GSECars.

skbeam.io.net_cdf_io.load_netCDF(file_name)

This function loads the specified netCDF file format data set (e.g.*.volume APS-Sector 13 GSECARS extension) file into a numpy array for further analysis.

Required Dependencies:

netcdf4Python/numpy interface to the netCDF ver. 4 library

Package name: netcdf4-python Install from: https://github.com/Unidata/netcdf4-python

numpy

Cython – optional

HDF5 C library version 1.8.8 or higher

Install from: ftp://ftp.hdfgroup.org/HDF5/current/src Be sure to build with ‘–enable-hl –enable-shared’.

netCDF-4 C library

Install from:

ftp://ftp.unidata.ucar.edu/pub/netcdf. Version 4.1.1 or higher

Be sure to build with ‘–enable-netcdf-4 –enable-shared’, and set CPPFLAGS=”-I $HDF5_DIR/include” and LDFLAGS=”-L $HDF5_DIR/lib”, where $HDF5_DIR is the directory where HDF5 was installed. If you want OPeNDAP support, add ‘–enable-dap’. If you want HDF4 SD support, add ‘–enable-hdf4’ and add the location of the HDF4 headers and library to CPPFLAGS and LDFLAGS.

Parameters

file_namestring

Complete path to the file to be loaded into memory

Returns

md_dictdict

Dictionary containing all metadata contained in the netCDF file. This metadata contains data collection, and experiment information as well as values and variables pertinent to the image data.

datandarray

ndarray containing the image data contained in the netCDF file. The image data is scaled using the scale factor defined in the netCDF metadata, if a scale factor was recorded during data acquisition or reconstruction. If a scale factor is not present, then a default value of 1.0 is used.