pycroscopy 0.0a19

A suite of Python libraries for high performance scientific computing of microscopy data.

See <https://pycroscopy.github.io/pycroscopy/> for more info.

0. Description

A python package for image processing and scientific analysis of imaging modalities such as multi-frequency scanning probe microscopy, scanning tunneling spectroscopy, x-ray diffraction microscopy, and transmission electron microscopy. Classes implemented here are ported to a high performance computing platform at Oak Ridge National Laboratory (ORNL).

1. Package Structure

The package structure is simple, with 4 main modules:

1. io: Input/Output from custom & proprietary microscope formats to HDF5.

2. processing: Multivariate Statistics, Machine Learning, and Filtering.

3. analysis: Model-dependent analysis of image information.

4. viz: Visualization and interactive slicing of high-dimensional data by lightweight Qt viewers.

Once a user converts their microscope’s data format into an HDF5 format, by simply extending some of the classes in io, the user gains access to the rest of the utilities present in pycroscopy.*.

2. Installation

Pycroscopy requires the installation of the base python libraries, a C compiler, and preferrably - a development environment such as Spyder from Continuum or PyCharm.

1. Install Anaconda 2.5.0 Python 2.7 64-bit:

   1. Mac users: <https://repo.continuum.io/archive/Anaconda2-2.5.0-MacOSX-x86_64.pkg>

   2. Windows users: <https://repo.continuum.io/archive/Anaconda2-2.5.0-Windows-x86_64.exe>

   3. Linux users: <https://repo.continuum.io/archive/Anaconda2-2.5.0-Linux-x86_64.sh>

2. Install a C compiler - Windows users ONLY:

   If you are running on a Windows machine, you will need to load a C compiler, which is required to build certain packages in python including one for parallel processing. Mac Users can skip this step as OS X natively comes with a C compiler.

   1. Install Microsoft Visual C++ 2008 SP1 Redistributable Package (x64) from <http://www.microsoft.com/en-us/download/confirmation.aspx?id=2092>

  b. Install Microsoft Visual C++ for Python from <http://aka.ms/vcpython27>

3. Install multiprocess for parallel computation tasks

   Open a terminal (mac / linux) or command prompt (windows) and type:

   pip install multiprocess

4. Install pycroscopy:

   Open a terminal (mac / linux) or command prompt (windows) and type:

   pip install pycroscopy

5. Enjoy pycroscopy!