Commit 1f610840 authored by Somnath, Suhas's avatar Somnath, Suhas
Browse files

Upgraded example on microdata to a mini-tutorial

parent 0bf4572d
Writing to hdf5 using the Microdata objects
Tutorial 1.5: Writing to hdf5 using Microdata objects
**Chris R. Smith** --
License: MIT
This set of tutorials will serve as examples for developing end-to-end workflows for and using pycroscopy.
Classes for writing files
In order to deal with the numerous challenges in writing data in a consistent manner, especially during translation,
in the pycroscopy format, we developed two main classes: **MicroData** and **ioHDF5**.
The abstract class MicroData is extended by **MicroDataset** and **MicroDatagroup** which are skeletal counterparts
for the h5py.Dataset and h5py.Datagroup classes respectively. These classes allow programmers to quickly and simply
set up the tree structure that needs to be written to H5 files without having to worry about the low-level HDF5
constructs or defensive programming strategies necessary for writing the H5 files. Besides facilitating the
construction of a tree structure, each of the classes have a few features specific to pycroscopy to alleviate file
While we use **h5py** to read from pycroscopy files, the ioHDF5 class is used to write data to H5 files. ioHDF5
translates the tree structure described by a MicroDataGroup object and writes the contents to H5 files in a
standardized manner. As a wrapper around h5py, tt handles the low-level file I/O calls and includes defensive
programming strategies to minimize issues with writing to H5 files.
Why bother with Microdata and ioHDF5?
# Code source: Chris Smith --
# Liscense: MIT
* These classes simplify the process of writing to H5 files considerably. The programmer only needs to construct
the tree structure with simple python objects such as dictionaries for parameters, numpy datasets for storing data, etc.
* It is easy to corrupt H5 files. ioHDF5 uses defensive programming strategies to solve these problems.
Translation can be challenging in many cases:
* It may not be possible to read the entire data from the raw data file to memory as we did in the tutorial on
* ioHDF5 allows the general tree structure and the attributes to be written before the data is populated.
* Sometimes, the raw data files do not come with sufficient parameters that describe the size and shape of the data.
This makes it challenging to prepare the H5 file.
* ioHDF5 allows dataets to be dataFile I/O is expensive and we don't want to read the same raw data files multiple
import os
import numpy as np
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment