Merge remote-tracking branch 'origin/jay/UIRefactor' into

jay/reflectivity

Conflicts:
	org.eclipse.ice.feature/feature.xml
	org.eclipse.ice.repository/ice.product
Signed-off-by: Jay Jay Billings <billingsjj@ornl.gov>

docs/visualization/.gitignore

+/documen.synctex.gz
+/tmp/
+/bin/

docs/visualization/.project

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docs/visualization/MeshEditorTutorial.tex

+%%This is a very basic article template.
+%%There is just one section and two subsections.
+\documentclass{article}
+\usepackage{graphicx}
+
+\setlength{\parskip}{1em}
+
+\begin{document}
+
+
+\section{Editing Meshes}
+
+This document is designed to outline the basic user controls of the Mesh Editor plugin in ICE.
+
+\subsection{Getting Started}
+
+Once ICE is installed on your system, there are no addional dependencies or
+preparation required to use the Mesh Editor.
+
+\subsubsection{Opening a Mesh Editor}
+
+To open a Mesh Editor in ICE, you have four options:
+ 
+
+\begin{center}
+\includegraphics[height=5cm]{images/CreateNewMeshOptions.jpg}
+\end{center}
+
+The UI elements which can be used to open a Mesh Editor are
+highlighted. Instruction for how to use each one, from top to bottom, left to
+right, are given below.
+
+ 
+1) Click the File menu, then New, then Create Item Wizard.
+
+ 
+2) Click the New Item Button and select Create Item Wizard.
+
+
+3) Click the Mesh Editor button.
+
+
+4) In the ICE Perspective, click the Create an Item button, select Mesh Editor,
+and click OK.
+
+\section{Working With the Mesh Editor}
+
+The mesh editor will initially open to an empty grid, as shown below. There is
+currently no way to import pre-existing meshes from another source directly
+into the Mesh Editor.
+
+\begin{center}
+\includegraphics[width=12cm]{images/EmptyMeshEditor.jpg}
+\end{center}
+
+\subsection{Navigation}
+
+Meshes are constructed on the background grid. Gridlines are spaced one unit
+apart from each other. The origin is the initial center of the screen, with the
+x axis in red and the y axis in green coming out from it in the positive x and y
+directions, respectively. 
+
+\subsubsection{Camera Controls}
+
+The camera is controlled with keyboard and mouse commands. The W, A, S, and D
+keys are used to move the camera around the editor's area, while scrolling the
+mouse wheel is used to zoom the camera in and out. 
+
+If the controls are not working, ensure that the Mesh Editor has focus by
+clicking inside of it.
+
+\begin{center}
+    \begin{tabular}{| l | l |}
+    \hline
+    \multicolumn{2}{|c|}{\textbf{Camera Controls}} \\
+  	\hline
+    \textbf{Action} & \textbf{Key(s)} \\ \hline
+    Scroll Up & W \\ \hline
+    Scroll Down & S \\ \hline
+    Scroll Left & A \\ \hline
+    Scroll Right & D \\ \hline
+    Zoom In & Scroll mouse wheel up \\ \hline
+    Zoom out & Scroll mouse wheel down \\
+    \hline
+    \end{tabular}
+\end{center}
+
+\subsection{Adding Elements}
+
+2D meshes are constructed in the editor by specifying one quadtrilatiral at a
+time. To add a new polygon, the Mesh Editor must be in Add Elements Mode. This
+is the editor's default setting, and it can later be reset by clicking the Mode
+button in the top left corner. 
+
+\begin{center}
+\includegraphics[width=12cm]{images/MeshEditorAddMode}
+\end{center}
+
+\subsubsection{Placing Vertices}
+
+In Add Elements Mode, clicking anywhere on the grid will place a new vertex at
+that location. These new, temporary vertices and the edges between them will be
+colored in green, to show that the polygon in still under construction.
+
+Alternatively, you may select a vertex not already in the new polygon. This
+allows you to reuse vertices and/or edges already present in the mesh to form
+part of your new polygon.
+
+\begin{figure}
+\begin{center}
+\includegraphics[width=12cm]{images/MeshEditorReuseEdge}
+\caption{One of the edges from the trapezoid is being combined with a new edge
+in the creation of the current polygon.}
+\end{center}
+\end{figure}
+
+Once the fourth vertex has been specified, the polygon will change to purple to
+show that it has been completed. At any time before this, you can press the Esc
+button to cancel the new polygon, removing it from the editor and allowing you
+to start the process over. 
+
+\subsection{Editing Elements}
+
+To edit an already present element of the mesh, you must switch to Edit Elements
+Mode. The Mode button in the upper left corner alows you to switch between
+modes, as shown below.
+
+\begin{center}
+\includegraphics[width=12cm]{images/MeshEditorEditMode}
+\end{center}
+
+A vertex can be selected by either clicking it in the Mesh Editor, or by
+selecting it from the tree in the ICE Perspective's Mesh Elements View. Holding
+down shift while clicking will allow multiple vertices to be selected at once,
+while holding down control during a click will toggle a vertex's state either
+into or out of the selection. Selected elements are displayed in blue.
+The current selection can be cleared by pressing the Esc button.
+
+\begin{center}
+\includegraphics[width=12cm]{images/MeshEditorSelection}
+\end{center}
+
+Click on a selected vertex and drag it to change its location. The clicked
+vertex will stay beneath your mouse cursor, while all other selected vertices
+will be moved as well, keeping their relative position to the dragged vertex.
+White circles are displayed to show each vertex's new location. Pressing Escape
+during the drag will deselect the vertices and cancel the movement.
+
+\begin{figure}
+\begin{center}
+\includegraphics[width=12cm]{images/MeshEditorDragVertex}
+\caption{Two vertices are selected. When the bottom vertex is moved left, the
+top vertex is moved left by an equal amount.}
+\end{center}
+\end{figure}
+
+\begin{center}
+    \begin{tabular}{| l | l |}
+    \hline
+    \multicolumn{2}{|c|}{\textbf{Edit Mode Controls}} \\
+  	\hline
+    \textbf{Action} & \textbf{Key(s)} \\ \hline
+    Select vertex & Left click \\ \hline
+    Add to selection & Shift + left click \\ \hline
+    Toggle (Add/Remove) Selection & Ctrl + left click \\ \hline
+    Move selected vertices & Left click on vertex and drag mouse \\ \hline
+    Clear selection/Cancel move & Escape \\ 
+    \hline
+    \end{tabular}
+\end{center}
+
+Alternatively, you can edit a vertex more precisely by setting its exact
+coordinates. First, select it in the Mesh Elements view, then open the
+Properties View. The vertex's x and y coordinates will be displayed in editable
+text boxes.
+
+\begin{center}
+\includegraphics[width=12cm]{images/VertexPropertiesView}
+\end{center}
+
+Selecting a polygon in the same way, then opening the tab for one of its edges
+in the Properties View, will display the edge's boundary conditions for that
+polygon. These are editable, just like the vertices are.
+
+\begin{center}
+\includegraphics[width=12cm]{images/EdgeBoundaryConditions}
+\end{center}
+
+\subsection{Deleting Elements}
+
+Polygons in the mesh can be deleted. All four vertices for the polygon must be
+selected, then press the Delete button on the toolbar. Vertices and edges which
+are still part of other, undeleted, polygons will remain, but all others will be
+removed from the editor.
+
+\subsection{Additional Controls}
+
+The Toggle Axis button on the toolbar allows will add/remove the axes from the
+editor. 
+
+\begin{center}
+\includegraphics[width=12cm]{images/MeshEditorToggleAxis}
+\end{center}
+
+\end{document}

docs/visualization/OutputVisualizationTutorial.tex

+\documentclass{article}
+\usepackage{graphicx}
+\usepackage{hyperref}
+\usepackage{url}
+
+\setlength{\parskip}{1em}
+
+\begin{document}
+
+
+\title{Visualizing Output}
+
+Currently, ICE features two plugins for visualizing and plotting simulation
+output data:
+
+\textbf{VisIt Tools} - An interactive 3D visualization tool for rendering
+meshes, scalar plots, contour plots, and more. 
+
+\textbf{CSV Plotting Tools} - A customizable, 2D data plotting utility for data 
+from .csv files.
+
+\section{Installation and Configuration}
+
+The CSV Plotting Tools require no additional software or preparation before use.
+The VisIt Tools need both an instance of VisIt and a connection between ICE and
+the VisIt session.
+
+\subsection{VisIt Installation} 
+
+Before preparing ICE,
+\href{https://wci.llnl.gov/simulation/computer-codes/visit/}{VisIt}, developed
+by Lawrence Livermore National Laboratory, must be downloaded. This must be
+version 2.8.2 or higher, and does not need to be on the same machine that ICE is
+installed on, as ICE is capable of launching a VisIt session on a remote machine. Make
+note of the folder where you installed VisIt for use in the next step.
+
+\subsection{Configuring the VisIt Connection}
+
+Once VisIt is installed, ICE must connect to a VisIt session in order to provide
+data visualization. There are two different parts of ICE which connect with
+VisIt, both providing slightly different functionalities. These are the Plot
+Editor, which is slightly more user friendly, and the Visualization Perspective,
+which allows for arbitrary Python commands to be sent to the VisIt client. 
+
+\subsubsection{Connecting for the Plot Editor} 
+
+This process will set up a default connection to VisIt in the ICE Preferences
+page, and so only needs to be performed once. After creating the connection, ICE
+will launch and connect with VisIt each time it is started.
+
+To set the connection, select Window $\rightarrow$ Preferences in ICE's
+toolbar. (If you are using Mac OSx, this will instead be located at Eclipse
+$\rightarrow$ Preferences.) Then select Visualization $\rightarrow$ VisIt in the
+tree of the Preferences page.
+
+\begin{center}
+\includegraphics[width=12cm]{images/VisItPreferencePage_ICE}
+\end{center}
+
+Press the new row button, the button with a "+" symbol in the upper right,
+highlighted in the image above. You can then click on each of the cells of the
+new row to edit them. The default values automatically supplied by ICE should
+be fine for most users. However, two fields may need to be changed:
+
+\textbf{Host:} The default value of "localhost" is for connections to local
+installations of VisIt on your computer. If you want to launch a remote VisIt
+connection, you must change this to the hostname of the machine to connect to.
+
+\textbf{Path:} You need to put the full path to the VisIt folder here. The path
+should end with the folder containing the VisIt executable. For example, if
+VisIt.exe is in a folder called VisIt 2.9.1, the the path should end in
+\textbackslash{}VisIt 2.9.1\textbackslash , not \textbackslash{}VisIt
+2.9.1\textbackslash VisIt.exe.
+
+Once finished, press Apply, then OK. ICE will then open VisIt and connect to it.
+
+\subsubsection{Connecting for the Visualization Perspective} 
+
+First, open the Visualization perspective. On the main menu bar at the top of
+the window, click Window $\rightarrow$ Perspective $\rightarrow$ Open
+Perspective $\rightarrow$ Other\ldots, select Visualization in the dialog that pops up and click OK.
+Alternatively, you can also access the same pop-up dialog by clicking the Open Perspective button in
+the main toolbar in the upper right-hand corner of the ICE workbench. 
+
+\begin{center}
+\includegraphics{images/ICE_OpenPerspective}
+\end{center}
+
+Now click the Launch VisIt button in the menu bar.
+
+\begin{center}
+\includegraphics{images/ICE_VisItLaunchButton}
+\end{center}
+
+This will open a dialog offering you three options for connecting to VisIt.
+
+\begin{center}
+\includegraphics[width=12cm]{images/ICE_VisItLaunchOptions}
+\end{center}
+
+\textbf{1) Launch VisIt locally -} If you installed VisIt on your local machine,
+use the Browse button to direct ICE to your local installation directory. Using this
+method of connecting will launch a new VisIt session. Optionally, you can also
+set a port number (default 9600) and--if you want to share your VisIt session
+with another user--a password.
+
+\textbf{2) Launch VisIt remotely -} If you installed VisIt on a remote machine,
+specify the hostname and full path to the VisIt installation directory. Using this
+method of connecting will launch a new VisIt session. Optionally, you can
+specify a port number (default 9600) and--if you want to share your VisIt
+session with another user--a password. If you need or want to use an external
+gateway or proxy to access the remote VisIt installation, you may specify its
+URL and port number as well.
+
+\textbf{3) Connect to VisIt -} If you would like to connect to a session of VisIt
+already running somewhere else, specify the hostname, port number, and password set on
+the VisIt session; you will need to obtain this information from the person who
+initially launched the VisIt session. If you need or want to use an external
+gateway or proxy to access the remote VisIt installation, you may specify its
+URL and port number as well.
+
+If you've forgotten where VisIt is installed on Windows, find a shortcut to
+VisIt either on your desktop or in the start menu. Right-click the shortcut and
+open its Properties. The path to the VisIt executable's directoy will be shown
+next to Target.
+
+Regardless of which method you choose to connect to VisIt, enter a Connection
+name at the bottom of the pop-up dialog. 
+
+If you are connecting to an existing session, specify a Window ID between 1 and
+16. Which Window ID you use depends on how you would like to connect to VisIt.
+If multiple users connect using the same Window ID, they will all see and be
+able to interact with the same VisIt view. However, if you would like multiple
+users to each have their own unique session each with its own controls, assign a
+unique Window ID to each user. The VisIt installation can support up to 16
+unique window IDs at a time.
+
+Once you are done, click the Finish button at the bottom, and ICE should begin
+connecting to VisIt.
+
+\section{VisIt}
+
+\subsection{Opening a VisIt File}
+
+\subsubsection{Opening a Plot Editor} 
+
+To open a plot editor, first the file must be placed in the Project Explorer.
+This view lists files imported into ICE. To access the Project Explorer, use the
+the main menu bar at the top of the window and navigate to Window $\rightarrow$
+Show View $\rightarrow$ Project Explorer. 
+
+By default, the Project Explorer should automatically import the
+ICEFiles/default and ICEFiles/itemDB folders. If it does not, or it you want to
+import a different folder into ICE, right click in the Project Explorer and
+select Import... from the context menu. Then select General $\rightarrow$ File
+System from the tree and press the Next button. You can then select directories
+and/or files to import into the Project Explorer and which folder they should be
+imported under, as seen below.
+
+\begin{center}
+\includegraphics[width=12cm]{images/ImportFileDialog}
+\end{center}
+
+Once a file is in the Project Explorer, you can simply double click on it to 
+open it in VisIt.
+
+\subsubsection{Opening in the Visualization Perspective}
+
+\begin{center}
+\includegraphics[width=12cm]{images/VisualizationPerspectiveOverview}
+\end{center}
+
+To open a file in the Visualization Perspective, it must first be imported into
+the Visualization File Viewer, located in the upper left of the screen. To do
+this, click the Open a File button, with a green plus sign icon. This will open
+a dialog to let you select a local file to import.
+
+\begin{center}
+\includegraphics[width=12cm]{images/VisualizationAddFile}
+\end{center}
+
+Currently, ICE can only open files in VisIt on the same machine as that VisIt
+session is running. If you are connected to a remote VisIt installation, you
+will instead need to click the arrow beside the Open a File button and select
+``Add a remote file'' from the drop down menu. This will open a dialog box to
+browse the file system of the remote machine VisIt is hosted on, which can be
+used to select a file as normal.
+
+\begin{center}
+\includegraphics[width=12cm]{images/VisualizationAddPlots}
+\end{center}
+
+Once your file is in the Visualization File Viewer, you will need to create a
+plot from it. To do this, select the file and then click the Add a Plot to the
+List button located in the VisIt Plot Viewer on the left of the screen. A window
+will open, prompting you to select which plots from the file you would like
+to view. After you have made your selection and hit OK, these plots will be
+placed in the VisIt Plot Viewer.
+
+\begin{center}
+\includegraphics[width=12cm]{images/VisualizationSelectPlots}
+\end{center}
+
+Finally, you may double click a plot in the VisIt Plot Viewer to open that plot
+in VisIt. 
+
+\subsection{Using VisIt}
+
+Both methods of accessing VisIt allow the user to rotate the model by clicking
+and dragging inside the display area or zoom it by scrolling the mouse wheel.
+Other commands require slightly different actions between the two. 
+
+\subsubsection{Selecting the Plot}
+
+In the Plot Editor, pressing the Select Series\ldots button will open a dialog
+which lists the various plots in the opened file. Simply select one and click OK
+to open it. 
+
+\begin{center}
+\includegraphics[width=12cm]{images/PlotEditorSelectSeriesButton}
+\end{center}
+
+In the Visualization Perspective, the opened plots will be listed in the VisIt
+Plot Viewer. Double click on one to open it.
+
+\subsubsection{Setting the Plot Representation}
+
+VisIt is capable of displaying plots in several different representations, such
+as pseudocolor, contour, or volume.
+
+To switch between these in the Plot Editor, right click inside the display area
+and select one of the listed options under the Representation category in the
+context menu.
+
+The Visualization Perspective features a drop down menu at the top of the VisIt
+Plot Viewer which allows for switching between the available representations. 
+
+\begin{center}
+\includegraphics[width=12cm]{images/VisItRepresentationDropDown}
+\end{center}
+
+\subsubsection{Animation and Time Data}
+
+The Plot Editor features a time slider widget at the bottom of the screen. 
+
+\begin{center}
+\includegraphics[width=12cm]{images/TimeSliderWidget}
+\end{center}
+
+The controls, in order of left to right, are:
+
+1) Return to the previous time step.
+
+2) Automatically play the plot as an animation by displaying the time steps
+sequentially. 
+
+3) Advance to the next time step. 
+
+4) Opens an options menu that allows the user to set the playback speed, toggle
+whether the animation should loop when it reaches the end, and set the plot to
+the first or last time step.
+
+5) A display for the current time step. It can be edited to set the plot to an
+arbitrary time step. 
+
+6) A slider that shows the current time step's position on the timeline. The
+slider can be dragged around the timeline, setting the plot's time step
+accordingly.
+
+In the Visualization Perspective, the Visit Plot Viewer has a similiar set of
+controls.
+
+\begin{center}
+\includegraphics[width=12cm]{images/VizPerspectiveTimeControls}
+\end{center}
+
+The buttons, in order of left to right, are:
+
+1) Return to the previous time step.
+
+2) Automatically play the plot as an animation backwards, going through the time
+steps in reverse order.
+
+3) Pause the animation.
+
+4) Automatically play the plot as an animation by displaying the time steps
+sequentially.
+
+5) Advance to the next time step. 
+
+\subsubsection{Sending VisIt Python Commands}
+
+This functionality is only available in the Visualization Perspective.
+
+\begin{center}
+\includegraphics[width=12cm]{images/PythonScriptButton}
+\end{center}
+
+The Execute Python Script button in the upper right of the VisIt Plot Viewer
+will open a new window with a Python shell. Commands entered into this shell
+will be sent to the instance of VisIt. 
+
+Python code can be written into the shell directly, but the Load from File
+button will import an existing .py script into the console. Once done, hit the
+Execute button to send the python command(s) to VisIt.
+
+Writing Python scripts for VisIt is beyond the scope of this tutorial. However,
+you are welcome to refer to the
+\href{https://wci.llnl.gov/simulation/computer-codes/visit/manuals}{VisIt Python
+Interface Manual} provided by the VisIt development team at Lawrence Livermore
+National Laboratory.
+
+\section{CSV Plot Viewer}
+
+ICE offers functionality for the viewing of CSV files. 
+
+\subsection{Opening a CSV File}
+
+CSV files are opened in Plot Editors through the Project Explorer. Open the
+Project Explorer with Window $\rightarrow$ Show View $\rightarrow$ Project
+Explorer and import the file by right clicking and selecting import. Once the
+file is in the Project Explorer, double click to open it.
+
+ICE expects CSV files to be in an [m x n] format, with no row holding empty
+values. The first row in the file will be used to name a series, with the series
+data being specified by the column of values beneath it.
+
+\subsection{Using the CSV Plot Viewer}
+
+\begin{center}
+\includegraphics[width=12cm]{images/CSVPlotViewer}
+\end{center}
+
+\subsubsection{Controlling the Graphics}
+
+The row of buttons at the top of the viewer provide basic graph editing
+capabilities.
+
+The first button allows the user to edit a variety of basic graph attributes,
+such as font, axis titles and scales, line colors, etc.
+
+The next two buttons allow for the addition and removal of annotations for
+specific data points. 
+
+The central grouping of buttons allow the user to zoom and pan the camera in a
+variety of ways. 
+
+The two yellow arrow buttons will undo/redo changes made to the graph.
+
+The final button will export a screenshot of the graph.
+
+\subsubsection{Setting the Independent Series}
+
+By default, the first column in the file will serve as the independent series
+setting the graph's x axis. By right clicking the Plot Viewer and selecting Set
+Independent Series\ldots you can replace it with any other series in the file.
+
+\subsubsection{Setting the Dependent Series}
+
+When first opened, only the series defined by the second column in the file will
+be displayed. There are several ways to change this. 
+
+The Select Series\ldots button in the upper lefthand corer will display a list
+of all the series in the file. Selecting one and pressing OK will graph that
+series and removing all others.
+
+Right clicking and choosing Select series\ldots from the context menu will open
+a dialog in which any of the series will be selected. All selected series will
+be graphed at once, with deselected series removed.
+
+ 
+
+Finally, the Remove all series option in the context menu will completely clear
+the graph.
+
+\section{MOOSE Embedded Visualization}
+
+MOOSE Workflow Items allow for easy visualization of their associated files,