openNCEM Documentation
======================

A collection of packages and tools for electron microscopy data analysis supported by the National Center for Electron Microscopy facility of the Molecular Foundry.

Installation
------------

We recommend installing the ``ncempy`` package from PyPi:

.. code-block:: bash

    >> pip install ncempy

If you wish to install the optional EDSTomo module then run:

.. code-block:: bash

    pip install 'ncempy[edstomo]'

Components
----------

The openNCEM collection comes with different components. The general functionality is condensed in libraries/packages, distinguished by programming language or framework. Tools are provided, addressing particular problems or tasks, leveraging the functionality provided in the libraries/packages.

.. toctree::
   :maxdepth: 2

    ncempy - openNCEM's python package<ncempy>
    tools - wrapping the provided functionality into useful tools<tools>

Examples
--------
Simple file reading
^^^^^^^^^^^^^^^^^^^
For simple file loading use the convenient `read` function.

Here is an example of loading a Digital Micrograph file. It returns the data and the metadata in
an easily human readable form. 

.. code-block:: python
   
   >>> import ncempy.io as nio
   >>> dmData = nio.read('path/to/file/data.dm3')
   >>> print(dmData['data'].shape) # the shape of the data
   >>> print(dmData['pixelSize']) # print the pixel size

For developers
^^^^^^^^^^^^^^
Developers will want access to the entire internal structure of the file.
Then you need to instantiate the class, parse the header and then access its contents

Here is how to open a DM file and have access to the internal file parameters

.. code-block:: python

   >>> import ncempy.io as nio
   >>> with nio.dm.fileDM('/path/to/file/data.dm3') as dm0:
   >>>     dmData = dm0.getDataset(0) #the full first data set
   >>>     dmSlice = dm0.getSlice(0, 1) #the second image of the first data set; equal to dmData[1,:,:] from the line above
   >>>     print(dm0.metaData) # all of the interesting metadata for this data set (pixel size, accelerating voltage, etc.)
   >>>     print(dm0.allTags) # all of the tags in the file including tags specific to the Digital Micrpograph software program

License
-------

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.


    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.


    You should have received a copy of the GNU General Public License
    along with this program.  If not, see https://www.gnu.org/licenses/.