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Merge pull request #38 from agarny/cleaning-up
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Various cleaning ups of the user interface, as well as data/flatmap/scaffold viewer pages
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@shsa992
shsa992 committed Jul 26, 2019
2 parents 422f4e6 + 7ae4857 commit 662d1c9
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47 changes: 22 additions & 25 deletions source/DataViewer.rst
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.. |data-icon| image:: /_images/data_icon.png
.. |data-icon| image:: /_images/data_icon.png
:width: 10 %

|data-icon| Data Viewer
=======================
A module of the data portal designed for viewing and exporting Ephys and Genome data.
A module of the data portal designed for viewing and exporting Ephys and Genome data.

.. contents:: Contents:
:local:
Expand All @@ -14,25 +14,25 @@ A module of the data portal designed for viewing and exporting Ephys and Genome
Overview
********

This document describes how to use the data plotting viewer tool available on the SPARC Data Portal. Examples of this tool in action are available at: https://data-viewer-demo.netlify.com/
This document describes how to use the data plotting viewer tool available on the SPARC Data Portal. Examples of this tool in action are available at https://data-viewer-demo.netlify.com/.

This module has the ability to:
This module has the ability to:

- Plot Ephys CSV datasets on knowledgbase or Blackfynn.
- Plot Genome and other static CSV datasests.
- Navigate large datasets via the UI.
- Add and remove channels from plot and export.
- Export selected channels as CSV for use in Excel, or OpenCOR
- Plot electrophysiological CSV datasets in the knowledgbase or Blackfynn.
- Plot genome and other static CSV datasests.
- Navigate large datasets via the user interface.
- Add and remove channels from a plot and export them.
- Export selected channels as CSV for use in Excel or `OpenCOR <https://opencor.ws/>`_.

Viewer configuration
Viewer Configuration
********************

The viewer has two modes, for small and large datasests
The viewer has two modes, for small and large datasests.

Small Datasets
--------------

Used for smaller datasets and has more control over exports. (All checked channels will be exported)
This mode is used for smaller datasets and has more control over exports. (All checked channels will be exported.)

.. figure:: _images/exportmode.png
:figwidth: 95%
Expand All @@ -42,7 +42,7 @@ Used for smaller datasets and has more control over exports. (All checked channe
Large Datasets
--------------

Used to navigate larger datasets, it has search capability to plot desired channels
This mode is used to navigate larger datasets. It has search capability to plot the desired channels.

.. figure:: _images/viewmode.png
:figwidth: 95%
Expand All @@ -52,7 +52,7 @@ Used to navigate larger datasets, it has search capability to plot desired chann
Interactive Graphics Controls
*****************************

* Refine the view by draging over a region of interest
You can refine the view by draging over a region of interest.

.. figure:: _images/plot_refine.jpg
:figwidth: 95%
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:width: 90%
:align: center

* Add or remove data by clicking on it's label
You can also add or remove data by clicking on its label.

.. figure:: _images/select_channel.jpg
:figwidth: 45%
:width: 80%
:align: center

The table below describes the effect of different user actions in the flatmap being displayed in this flatmap viewer.
The table below describes the effect of different user actions in the flatmap being displayed.

======================= ==============
User action Result
Mouse action Result
======================= ==============
Left Zoom in via box selection
----------------------- --------------
Middle Zoom in via box selection
``left-click`` Zoom in via box selection
----------------------- --------------
Right None
``middle-click`` Zoom in via box selection
----------------------- --------------
Double click Reset View
``double-click`` Reset the view
======================= ==============


CSV (Comma-Separated Values) Exports
************************************

CSV files for use in Excel, OpenCOR, or your software of choice are available for export.
The selected data traces plotted will be exported into a version that is either CSV and/or OpenCOR compatible.
The selected data traces plotted are exported to a CSV file for use in Excel, OpenCOR or any CSV-capable software.

Export as CSV
-------------
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6 changes: 3 additions & 3 deletions source/FlatmapViewer.rst
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Expand Up @@ -5,7 +5,7 @@

.. |flatmap-icon| image:: /_images/flatmap_icon.png
:width: 10 %

|flatmap-icon| Flatmap Viewer
=============================

Expand Down Expand Up @@ -57,6 +57,6 @@ Node queries are made using the ``right-click`` context menu.
Map interaction
^^^^^^^^^^^^^^^

Besides zoom and pan, using standard mouse or touch-pad controls, a ``left-click`` will query for knowledge
Besides zoom and pan, using standard mouse or touchpad controls, a ``left-click`` will query for knowledge
about the current anatomical entity, and a ``right-click`` will show a context menu, allowing the different node
connectivity queries to be made.
connectivity queries to be made.
72 changes: 37 additions & 35 deletions source/ScaffoldViewer.rst
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Overview
********

Some datasets in the SPARC knowledgebase search results are registered to an *anatomical scaffold*: a three dimensional model of the anatomy of interest.
This is indicated by the 3-D box icon shown at the top of this page. Clicking on the icon in search results opens a *Scaffold Viewer* tab in which the scaffold and embedded data can be viewed and interacted with in three dimensions.
Some datasets in the SPARC knowledgebase search results are registered to an *anatomical scaffold*: a 3D model of the anatomy of interest.
This is indicated by the 3D box icon shown at the top of this page.
To click on the icon in the search results opens a *Scaffold Viewer* tab in which the scaffold and embedded data can be viewed and interacted with in 3D.
The following image of the Scaffold Viewer tab shows a fitted rat stomach scaffold with neurite data from Powley *et al*.

.. figure:: _images/scaffold_viewer_tab.png
Expand All @@ -26,46 +27,47 @@ The following image of the Scaffold Viewer tab shows a fitted rat stomach scaffo
:align: center
:alt: Scaffold viewer tab

Interaction and viewing
Interaction and Viewing
***********************

Moving the mouse pointer over the scaffold or embedded data highlights and overlays a label for what is under it.
With an entity highlighted, clicking with the left button performs a search for the label terms in the SPARC knowledgebase.
The search can bring up related datasets for the study allowing further viewer tabs to be opened.

Interactively rotating, zooming and panning the view gives a greater understanding of the three dimensional structure.
Hold down one of the mouse/controller buttons and drag to change the view. The following table lists the controls.

========================= ==============
Mouse controller action Result
========================= ==============
Left button click Search knowledgebase for highlighted entity
------------------------- --------------
Left button drag Rotate
------------------------- --------------
Middle button drag, wheel Zoom
------------------------- --------------
Right button Pan
========================= ==============

On some systems, e.g. Mac, modifier keys Ctrl, Alt etc. may be used in place of different buttons.

Some Scaffold Views may contain time-varying or multi-state data.
In these cases a slider control is shown to change the time or state, and a play button enables animation between states.
These controls are shown in the above rat stomach Scaffold Viewer.

Viewer configuration
With an entity highlighted, to click the left button performs a search for the label terms in the SPARC knowledgebase.
The search can bring up related datasets for the study, allowing further viewer tabs to be opened.

Interactively rotating, zooming and panning the view gives a greater understanding of the 3D structure.
Hold down one of the mouse buttons and drag to change the view.
The following table lists the controls.

========================== ==============
Mouse action Result
========================== ==============
``left-click`` Search knowledgebase for highlighted entity
-------------------------- --------------
``Left-drag`` Rotate
-------------------------- --------------
``Middle-drag``, ``wheel`` Zoom
-------------------------- --------------
``right-click`` Pan
========================== ==============

On some systems, e.g. macOS, modifier keys ``Ctrl``, ``Alt``, etc. may be used in place of different buttons.

Some Scaffold views may contain time-varying or multi-state data.
In these cases, a slider control is shown to change the time or state, and a play button enables animation between states.
These controls are shown in the above rat stomach Scaffold viewer.

Viewer Configuration
********************

The |open-control| icon at the top-left corner of the window brings up a menu of additional viewing controls:

* :guilabel:`Reset View` - Restore the initial view of the scaffold to the default state.
* :guilabel:`View All` - Zoom in or out to see all of the scaffold in its current orientation.
* :guilabel:`Visibilty Controls` - Checkboxes controlling visibility of each entity.
Clicking on the |open-control| icon closes this menu.

* :guilabel:`View All` - Zoom in/out to see all of the scaffold in its current orientation.

* :guilabel:`Visibilty Controls` - Checkboxes controlling the visibility of each entity.

To click on the |open-control| icon closes this menu.

..
Examples
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5 changes: 4 additions & 1 deletion source/UserInterface.rst
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Expand Up @@ -8,7 +8,10 @@ Map visualization interface
:width: 90%
:align: center

The initial user interface for the map visualization interface. (A) shows the listing of exemplary use cases, selecting one will display further details and allow access to the appropriate viewers for that use case. (B) can be used to directly enter terms to query the knowledgebase for relevant data. (C) by default will show the human flatmap viewer but will have tabs added with the appropriate viewers as requested by the used.
The initial user interface for the map visualization interface.
(A) shows the listing of exemplary use cases, selecting one will display further details and allow access to the appropriate viewers for that use case.
(B) can be used to directly enter terms to query the knowledgebase for relevant data.
(C) will, by default, show the human flatmap viewer, but will have tabs added with the appropriate viewers, as requested by the user.

.. toctree::
:maxdepth: 1
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