<commit_before>Scitran Data |travis_badge|
===========================

.. |travis_badge| image:: https://travis-ci.org/scitran/data.svg?branch=ksh-dataio
    :target: https://travis-ci.org/scitran/data

**TODO** put some sort of warning that upgrading from this package BREAKS WORLDS, and does
not replace nimsdata, rather scitran.data will install along side.

Data handling utilities.

Provides class and functions for parsing, identifying and writing scientific datasets. Currently,
medical images (such as various flavors of MRI, dicoms, niftis, and some raw-files) are supported.

Also provides base classes that can be used to extend this package to cover additional data-domains.

Note that these utilites also have command-line interfaces, so you don't need a full NIMS
instance to use them. E.g., you can run our image reconstruction pipeline.


How to use the documentation
----------------------------
Documentation is available as docstrings provided within the code, and
`additional narrative documentation <https://scitran.github.io/data>`_.


Dependencies
------------

development version is currently using the following:

================ ====================
package          version
================ ====================
Pillow           2.6.1
numpy            1.9.0
nibabel          1.4.0dev
pydicom          0.9.9
dcmstack         0.7.0dev
================ ====================


installation on fresh ubuntu 14.04
----------------------------------
- install dependencies, **had to chmod o+w /var/local to allow regular user to write; not ideal**<commit_msg>update readme to add pytz to list of dependencies<commit_after>Scitran Data |travis_badge|
===========================

.. |travis_badge| image:: https://travis-ci.org/scitran/data.svg?branch=ksh-dataio
    :target: https://travis-ci.org/scitran/data

**TODO** put some sort of warning that upgrading from this package BREAKS WORLDS, and does
not replace nimsdata, rather scitran.data will install along side.

Data handling utilities.

Provides class and functions for parsing, identifying and writing scientific datasets. Currently,
medical images (such as various flavors of MRI, dicoms, niftis, and some raw-files) are supported.

Also provides base classes that can be used to extend this package to cover additional data-domains.

Note that these utilites also have command-line interfaces, so you don't need a full NIMS
instance to use them. E.g., you can run our image reconstruction pipeline.


How to use the documentation
----------------------------
Documentation is available as docstrings provided within the code, and
`additional narrative documentation <https://scitran.github.io/data>`_.


Dependencies
------------

development version is currently using the following:

================ ====================
package          version
================ ====================
Pillow           2.6.1
numpy            1.9.0
nibabel          1.4.0dev
pydicom          0.9.9
dcmstack         0.7.0dev
pytz             2014.10
================ ====================


installation on fresh ubuntu 14.04
----------------------------------
- install dependencies, **had to chmod o+w /var/local to allow regular user to write; not ideal**
{'fraction_non_alphanumeric': 0.18821705426356589, 'fraction_numerical': 0.013643410852713178, 'mean_word_length': 3.2005208333333335, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 6, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5640171', 'n_tokens_mistral': 879, 'n_tokens_neox': 823, 'n_words': 337}