:topic: Custom Support Tools

*********************
CoNNECT Support Tools
*********************


Several custom support tools have been created to aid in the batch processing. These tools support parallel processing via HTCondor and SGE implemented in the custom batch processing 
described in the previous section.


.. note:: FIGURE TO BE INSERTED




.. _bids_python:

bids
====

.. note:: the functions of support_tools.bids do not support command line operation.

Python Implementation
---------------------

.. automodule:: support_tools.bids
    :members:


.. _condor_python:

condor
======

.. note:: the functions of support_tools.condor do not support command line operation.

Python Implementation
---------------------

.. automodule:: support_tools.condor
    :members:
    :special-members:


.. _convert_dicoms_python:

convert_dicoms.py
=================


.. autoprogram:: convert_dicoms:parser
    :prog: convert_dicoms.py


Python Implementation
---------------------

.. automodule:: support_tools.convert_dicoms
    :members:
    :special-members:


.. _copy_dirs_python:

copy_dirs.py
============

.. note:: the function of support_tools.copy_dirs does not support command line operation.

Python Implementation
---------------------

.. automodule:: support_tools.copy_dirs
    :members:
    :special-members:


.. _dti_flirt_python:

dti_flirt.py
============

.. autoprogram:: dti_flirt:parser
    :prog: dti_flirt.py

Python Implementation
---------------------

.. automodule:: support_tools.dti_flirt
    :members:
    :special-members:


.. _dti_preprocess_python:

dti_preprocess.py
=================

.. .. autoprogram:: support_tools.dti_preprocess:parser
    :prog: dti_preprocess.py

Python Implementation
---------------------

.. .. automodule:: support_tools.dti_preprocess
    :members:
    :special-members:


.. _evaluate_raw_file_transfer_python:

evaluate_raw_file_transfer.py
=============================

.. note:: the function of support_tools.evaluate_raw_file_transfer does not support command line operation.

Python Implementation
---------------------

.. automodule:: support_tools.evaluate_raw_file_transfer
    :members:
    :special-members:


.. _feat_full_firstlevel_python:

feat_full_firstlevel.py
=======================

.. .. autoprogram:: support_tools.feat_full_firstlevel:parser
    :prog: feat_full_firstlevel.py

Python Implementation
---------------------

.. automodule:: support_tools.feat_full_firstlevel
    :members:
    :special-members:


.. _feat_full_firstlevel_python:

flirt_pngappend.py
==================

.. note:: the function of support_tools.evaluate_raw_file_transfer does not support command line operation.

Python Implementation
---------------------

.. automodule:: support_tools.flirt_pngappend
    :members:
    :special-members:


.. _flirt_python:

flirt.py
========

.. .. autoprogram:: support_tools.flirt:parser
    :prog: flirt.py

Python Implementation
---------------------

.. automodule:: support_tools.flirt
    :members:
    :special-members:


.. _fsreconall_stage1_python:

fsreconall_stage1.py
====================

.. .. autoprogram:: support_tools.fsreconall_stage1:parser
    :prog: fsreconall_stage1.py

Python Implementation
---------------------

.. automodule:: support_tools.fsreconall_stage1
    :members:
    :special-members:


.. _fsreconall_stage2_python:

fsreconall_stage2.py
====================

.. .. autoprogram:: support_tools.fsreconall_stage2:parser
    :prog: fsreconall_stage2.py

Python Implementation
---------------------

.. automodule:: support_tools.fsreconall_stage2
    :members:
    :special-members:


.. _get_scan_id_python:

get_scan_id.py
==============

.. note:: the function of support_tools.get_scan_id does not support command line operation.

Python Implementation
---------------------

.. automodule:: support_tools.get_scan_id
    :members:
    :special-members:


.. _mysql_python:

mysql.py
========

.. note:: the functions of support_tools.mysql do not support command line operation.

Python Implementation
---------------------

.. automodule:: support_tools.mysql
    :members:
    :special-members:


.. _prepare_examcard_html_python:

prepare_examcard_html.py
========================

.. note:: the function of support_tools.prepare_examcard_html does not support command line operation.

Python Implementation
---------------------

.. automodule:: support_tools.prepare_examcard_html
    :members:
    :special-members:


.. _remove_dirs_python:

remove_dirs.py
==============

.. note:: the function of support_tools.remove_dirs does not support command line operation.

Python Implementation
---------------------

.. automodule:: support_tools.remove_dirs
    :members:
    :special-members:


.. _RestToolbox_python:

RestToolbox.py
==============

.. note:: the functions of support_tools.RestToolbox do not support command line operation.

Python Implementation
---------------------

.. automodule:: support_tools.RestToolbox
    :members:
    :special-members: