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Graphical User Interface » History » Version 10

Anchi Cheng, 05/07/2015 03:04 PM

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h1. Graphical User Interface
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h2. How to use this manual
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Many places in the manual, a specific section of a window for a node on a
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launcher/computer/instrument is mentioned. The first time they are mentioned, the full path
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is shown as
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computer/program window/node/subsection of the node to open the setting window/setting
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window/section in the window>
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It is assumed that the user knows how to follow this path to the specific section of the
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window by reading the following graphical user interface (GUI) manual and by a little of
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practice. A abbreviated path rather than the full path will be shown in the latter steps for
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the same node or application.
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h2. Leginon Window
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The window is divided into sections.
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* Status bar - Leginon status display such as completion of application
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loading.
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 !http://emg.nysbc.org/software/leginon/images/images/statusbar.png!
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* Main Menu - Submenus and options derived from Manager and Launcher
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 !http://emg.nysbc.org/software/leginon/images/images/mainmenu.png!
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* Node Selector - Selection for the node shown in the toolbar, message log, and node
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panel. It is also used to indicate warning by turning red for broken node.
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 !http://emg.nysbc.org/software/leginon/images/images/nodeselector.png!
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* Error indicator 
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 !http://emg.nysbc.org/software/leginon/images/icons/error.png! 
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 - This icon will appear next to a node (in the Node Selector) that has an error.
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* Message Log Information indicator 
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 !http://emg.nysbc.org/software/leginon/images/icons/info.png!
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 - This icon will appear next to a node (in the Node Selector) that has information in its message log.
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* User Input indicator 
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 !http://emg.nysbc.org/software/leginon/images/icons/userinput.png! 
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 - This icon will appear next to a node (in the Node Selector) that requires User input in order to continue processing.
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* Processing indicator 
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 !http://emg.nysbc.org/software/leginon/images/icons/processing/green0.png! 
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 - This icon will appear next to a node (in the Node Selector) that currently doing processing.
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h2. Node Panel
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* Node Panel - The main display/control panel for the node selected by the node
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selector.
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 !http://emg.nysbc.org/software/leginon/images/images/nodepanel2.png!
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* Toolbar - An area containing tools for general configuration and execution of the
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node as well as some tools for convenience specific for individual node.
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 !http://emg.nysbc.org/software/leginon/images/images/toolbar.png!
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* Message Log - Expandable/scrollable box showing logged information for the
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node.
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 !http://emg.nysbc.org/software/leginon/images/images/messagelog.png!
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h2. Parameter Entry
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* Free entry box- For typing in either text or numbers. If in a setting window, the
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altered entry is saved to the database when it is exited with "OK" or after
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"Apply"/"Test". Most numerical entry accepts floating point number in any python format.
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For example, 10.2 can also be entered as 1.02e+2.
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 !http://emg.nysbc.org/software/leginon/images/images/Entry_box.png!
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* Restricted-entry: The user can only select a valid entry from a list.
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 !http://emg.nysbc.org/software/leginon/images/images/Entry_box_restricted.png!
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* List box- This type of selection box select either an ordered sequence or a simple
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unordered list. If ordered, the items in the sequence can order with "up" and "down"
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tools.
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 !http://emg.nysbc.org/software/leginon/images/images/List_box.png!
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 * If ordered, the items in the sequence can be shifted around with "up" and "down"
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tools.
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 * Either free or restricted entry box is used for entering a new item to the list.
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"+" tool is used to add the entry to the list box. selecting an existing item and
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press "-" tool removes the item from the list.
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 * Multiple items can be selected by holding down the "ctrl" or "shift" key. The
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latter selects a range between the first and the new items.
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h2. Image Viewing
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* Display Panel - where the image is shown.
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* (pixel value button) 
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 !http://emg.nysbc.org/software/leginon/images/icons/value.png! 
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 - Pixel value display tool that shows the (x,y) coordinate the intensity value at the
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cursor. The coordinate origin is set at top-left corner.
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* (ruler button) 
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 !http://emg.nysbc.org/software/leginon/images/icons/ruler.png! 
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 - Ruler tool that displays the distance between a reference point and the current
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cursor position. Left click at any position inside the display panel defines the
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reference point.
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* (zoom button) 
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 !http://emg.nysbc.org/software/leginon/images/icons/zoom.png!
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 - Magnifying glass tool that zoom in (left click) or out (right click) at the location
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of the cursor.
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* (zoom selector list) 
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 !http://emg.nysbc.org/software/leginon/images/images/zoomselector.png! 
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 - Direct zoom factor selector.
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* (cross hair button) 
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 !http://emg.nysbc.org/software/leginon/images/images/bluech.png! 
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 - Cross hair reference tool displaying a blue cross hair centered at
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the center of the image for reference.
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* (display range selection/input) - Contrast and brightness adjustment of the image
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display. The default is mean +/- 5*standard deviation of image intensity. This can be
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modified by setting the minimum (top scroll bar or entry box) and the maximaum (bottom
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scroll bar or entry box) of the display range.
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 !http://emg.nysbc.org/software/leginon/images/images/contrbright.png!
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* Image Stats Panel
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 !http://emg.nysbc.org/software/leginon/images/images/imstatpanel.png!
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* Image/Target/Marker Control Panel - where the image and targets to be displayed in
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the display panel are determined. Targets are indicated by short cross symbols or other
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shapes of different colors. The items shown with a screen icon are of image type. Items
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of image type can be displayed alone while markers will show only when one of the items
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of image type is also displayed.
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 !http://emg.nysbc.org/software/leginon/images/images/imcontrolpanel.png!
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 * (status indicator)
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  !http://emg.nysbc.org/software/leginon/images/icons/green.png! !http://emg.nysbc.org/software/leginon/images/icons/red.png!
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  - This can be either green or red. During a step-by-step testing of parameters,
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green indicates that the step has been tested and you can proceed to the next
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testing step. Skiping to a step below a red-indicated step will cause an
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error.
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 * (image display tool) 
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  !http://emg.nysbc.org/software/leginon/images/icons/display.png! 
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  - Display selection. Only one of the image type can be displayed at
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one time.
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 * (target/marker display tool) 
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  !http://emg.nysbc.org/software/leginon/images/images/target_display.png! 
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  - Display target or marker selection. Pressed down (as shown for
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the green target) is active. More than one type of markers can be displayed on
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layers above the image. If the markers are overlapped, the marker last to be
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activated for display is at the top.
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 * (marker tool) 
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  !http://emg.nysbc.org/software/leginon/images/icons/arrow.png! 
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  - Marker input selection. Certain markers can be manually edited.
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In general, these are targets for further acquisition. In such case, the marker
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selection tool can be activated by left clicking the icon. Once activated, left
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click in the display panel adds the marker to the image and right click removes the
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marker pointed to.
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 * (settings) 
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  !http://emg.nysbc.org/software/leginon/images/icons/settings.png! 
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  - Settings are available for certain items in the image control
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panel, mainly steps in automatic hole finding. Left click opens the setting window
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and the behavior of the setting window is similar to others of the same type.
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h2. Tool Bar
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Tool bar of the node contains tools for setting and execution of the node functions. In
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addition, some tools are available as pop-up for convenience. The general rule for the flow
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of setting up and execution is to go from left to right up to the execution tool (execution
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icon).
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!http://emg.nysbc.org/software/leginon/images/images/toolbar.png!
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h2. Settings Window
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Settings windows are opened by left clicking its button 
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!http://emg.nysbc.org/software/leginon/images/icons/settings.png!
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in the toolbar. Note that only one setting swindow can be opened at a time and that all
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functions in the main leginon window is inactivated when a settings window is open even if
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the leginon window is the focus. The content of the settings window depends on the purpose
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of the settings. The general controls are described here:
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 * Test: found in settings of image processing steps. When clicked, the current setting
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in the window is saved to database and applied to the current input and the results
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saved as its output. If the item output is displayed in the node display panel, the
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content will be changed accordingly.
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  !http://emg.nysbc.org/software/leginon/images/images/test.png!
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 * Apply: save the modified setting to database for future execution but not the
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current test input. It is activated only if the modification of the input is completed,
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normally by pressing the Enter key on the keyboard. Since current GUI does not allow
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changes to the main window to be made while setting window is on, Using button is not
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necessary since "OK" button will save the settings anyway.
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  !http://emg.nysbc.org/software/leginon/images/images/apply.png!
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 * Cancel: close the setting window and revert the setting to the last saved values.
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This means you can not cancel setting modification if you have "test"ed or "apply"ed the
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settings.
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  !http://emg.nysbc.org/software/leginon/images/images/cancel.png!
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 * OK or Done: close the setting window and save all modified settings to the
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database.
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  !http://emg.nysbc.org/software/leginon/images/images/ok.png!
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h2. Execution tools
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Found in the node toolbar. They may take on different meanings for different node
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classes. The general ones are described here:
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 * (Execute/Submit button) 
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  !http://emg.nysbc.org/software/leginon/images/icons/play.png!
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  : Perform one of the four possible functions if available and active for a node:
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   # When the application is in standby, it executes, sometimes with setting up the
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main function of the node.
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   # When the application is running automatically, it indicates that the node is in
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use.
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   # When the application is paused for user input, it submit the user approved
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inputs and continue on the flow.
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   # When the application is paused by the "pause" tool in the same node, it removes
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the pause flag and continue on the application flow.
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 * (Pause button) 
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  !http://emg.nysbc.org/software/leginon/images/icons/pause.png! 
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  : Pause data processing flow when the current input in a queue list is done.
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 * (Abort button) 
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  !http://emg.nysbc.org/software/leginon/images/icons/stop.png!
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  : Abort all data processing of the whole list in the queue.
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[[Terminology|< Terminology]] | [[Minimum Requirements and current NRAMM setup|Minimum Requirements and current NRAMM setup >]]
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