<commit_before>Python API
==========

Functions
---------

.. autosummary::
   :template: function.rst
   :toctree: gen_api

   afqbrowser.mat2tables
   afqbrowser.assemble
   afqbrowser.run

JavaScript API
==============

3d-brain.js
-----------
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.waitForPlotLength                         |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.initAndAnimate                            |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.init                                      |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.onWindowResize                            |
|                                                      |
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|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.animate                                   |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.lightUpdate                               |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.highlightBundle                           |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.mouseoutBundle                            |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.mouseoverBundle                           |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
------------------------------------------------------+---------------------------------------------------------+

headings.js
-----------
+------------------------------------------------------+---------------------------------------------------------+
| afqb.global.updateHeadings                           |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+

save-settings.js
----------------
+------------------------------------------------------+---------------------------------------------------------+
| afqb.global.updateQueryString                        |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.global.initSettings                             |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.plots.restoreBrush                              |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.table.restoreRowSelection                       |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+

sortable-table.js
-----------------
+------------------------------------------------------+---------------------------------------------------------+
| afqb.table.buildTable                                |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.table.refreshTable                              |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.table.ascendingWithNull                         |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.table.descendingWithNull                        |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.table.rowSelect                                 |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| $(document).mousedown                                |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.table.tableMouseDown                            |
|                                                      |
|                                                      |
|                                                      |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+

tract-details.js
----------------
+------------------------------------------------------+---------------------------------------------------------+
| afqb.plots.buildFromNodes(error,useless,data)        | Container function which calls other plots functions    |
|                                                      | once nodes.csv data has been read.                      |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.plots.buildTractCheckboxes(error, data)         | Builds tract selection list in "Bundles" section. Reads |
|                                                      | unique tract IDs from nodes.csv and creates selectable  |
|                                                      | text for each tract.                                    |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.plots.buildPlotGui(error, data)                 | Builds control panel GUI for metric plots. Allows user  |
|                                                      | to select which metric to plot, error type (std err or  |
|                                                      | std dev) for shaded area, subject line opacity, and     |
|                                                      | whether or not brushing is allowed.                     |
|                                                      |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.plots.ready(error, data)                        | Generates initial 2D plots. Turns nodes.csv into nested |
|                                                      | json object. This object is used to determine x/y       |
|                                                      | range, plot subject lines, and calculate mean and       |
|                                                      | error for the default metric.                           |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.plots.changePlots(error, data)                  | Updates plots on sort or metric change. If data is      |
|                                                      | sorted, means are calculated for each group of subjects |
|                                                      | defined by the sort. If metric changes, axes and means  |
|                                                      | are updated accordingly. Calls afqb.plots.draw() and    |
|                                                      | afqb.plots.zoomAxis().                                  |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.plots.draw()                                    | Redraws subject and mean lines after new metric or      |
|                                                      | group selections. Calls afqb.plots.zoomAxis()           |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.plots.zoomAxis()                                | Updates y axis for proper zoom.                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |<commit_msg>Close tables so they render<commit_after>Python API
==========

Functions
---------

.. autosummary::
   :template: function.rst
   :toctree: gen_api

   afqbrowser.mat2tables
   afqbrowser.assemble
   afqbrowser.run

JavaScript API
==============

3d-brain.js
-----------
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.waitForPlotLength                         |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.initAndAnimate                            |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.init                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.onWindowResize                            |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.animate                                   |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.lightUpdate                               |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.highlightBundle                           |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.mouseoutBundle                            |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.three.mouseoverBundle                           |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+

headings.js
-----------
+------------------------------------------------------+---------------------------------------------------------+
| afqb.global.updateHeadings                           |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+

save-settings.js
----------------
+------------------------------------------------------+---------------------------------------------------------+
| afqb.global.updateQueryString                        |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.global.initSettings                             |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.plots.restoreBrush                              |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.table.restoreRowSelection                       |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+

sortable-table.js
-----------------
+------------------------------------------------------+---------------------------------------------------------+
| afqb.table.buildTable                                |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.table.refreshTable                              |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.table.ascendingWithNull                         |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.table.descendingWithNull                        |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.table.rowSelect                                 |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| $(document).mousedown                                |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.table.tableMouseDown                            |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+

tract-details.js
----------------
+------------------------------------------------------+---------------------------------------------------------+
| afqb.plots.buildFromNodes(error,useless,data)        | Container function which calls other plots functions    |
|                                                      | once nodes.csv data has been read.                      |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.plots.buildTractCheckboxes(error, data)         | Builds tract selection list in "Bundles" section. Reads |
|                                                      | unique tract IDs from nodes.csv and creates selectable  |
|                                                      | text for each tract.                                    |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.plots.buildPlotGui(error, data)                 | Builds control panel GUI for metric plots. Allows user  |
|                                                      | to select which metric to plot, error type (std err or  |
|                                                      | std dev) for shaded area, subject line opacity, and     |
|                                                      | whether or not brushing is allowed.                     |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.plots.ready(error, data)                        | Generates initial 2D plots. Turns nodes.csv into nested |
|                                                      | json object. This object is used to determine x/y       |
|                                                      | range, plot subject lines, and calculate mean and       |
|                                                      | error for the default metric.                           |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.plots.changePlots(error, data)                  | Updates plots on sort or metric change. If data is      |
|                                                      | sorted, means are calculated for each group of subjects |
|                                                      | defined by the sort. If metric changes, axes and means  |
|                                                      | are updated accordingly. Calls afqb.plots.draw() and    |
|                                                      | afqb.plots.zoomAxis().                                  |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.plots.draw()                                    | Redraws subject and mean lines after new metric or      |
|                                                      | group selections. Calls afqb.plots.zoomAxis()           |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
+------------------------------------------------------+---------------------------------------------------------+
| afqb.plots.zoomAxis()                                | Updates y axis for proper zoom.                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
|                                                      |                                                         |
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