pfile-tools 0.1.0

UNKNOWN

h1. pfile-tools: GE P-File Utilities

This package provides a library refrence to GE's proprietary P-file format for their MR scanners. This is not a translation of their copyrighted header files, but a re-implementation. It's designed to let you catalog and anonymize your raw data, and hopefully provide enough information to run your own reconstruction.

In addition to the library, pfile-tools provides small scripts to display pfile header values and do an anomymization.

h2. Status

Header support is limited to stuff we've needed in-house or stuff that's really obvious. If you need something added, let me know.

Also, we currently only support reading revision 20 of the files. I suspect that it'll also effectively work on other revisions (particularly 22), but I don't know for sure which. Let me know!

h2. Installation

For now, it's:

<pre>
$ git clone https://github.com/njvack/pfile-tools.git
$ cd pfile-tools
$ python setup.py install
</pre>

Installation via easy_install and pip is coming.

h2. API Usage

<pre>
>>> from pfile_tools import headers
>>> pfile = headers.Pfile.from_file('/path/to/PXXXX.7')
>>> print(pfile.revision)
20
>>> print(pfile.header.exam_number)
5313
>>> print(pfile.header.exam_datetime)
datetime(2012, 3, 6, 10, 47, 42)
</pre>

Pfile.header is a Python "ctypes Structure":http://docs.python.org/library/ctypes.html#ctypes.Structure.

h2. dump_pfile_header

Does what it says on the tin -- dumps a p-file's header to standard out, in a delimited (by default, tab-delimited) format.

<pre>
Usage: dump_pfile_header [OPTIONS] pfile

Dumps header information from a GE P-file

Options:
-h, --help show this help message and exit
-r REVISION, --revision=REVISION
Force a header revision (available: 20)
--offsets Show offsets to data elements
--sizes Show data element sizes
--show-padding Print unknown 'padding' elements
--separator=SEPARATOR
Output field separator (default: \t)
</pre>

h2. anonymize_pfile

Strips personally-identifying information from a p-file.

<pre>
Usage: anonymize_pfile.py [OPTIONS] pfile pfile_out

Removes personally-identifying information from a GE P-file

Options:
-h, --help show this help message and exit
-r REVISION, --revision=REVISION
Force a header revision (available: 20)
--inplace Edit file in-place. Ignores pfile_out.
-v, --verbose Print lots of extra debugging.

Anonymization options:
--name=yes/no Set patient name to 'ANONYMIZED' (yes)
--id=yes/no Set patient ID to 'ANONYMIZED' (yes)
--dateofbirth=yes/no
Set date of birth to '' (yes)
--age=yes/no Set age to 0 (yes)
--weight=yes/no Set weight to 0 (yes)
--sex=yes/no Set sex to 0 (yes)
</pre>

h2. License

pfile_tools is provided under the short-and-sweet BSD license. See LICENSE.txt for more information.