Leginon

h1. Graphical User Interface

h2. How to use this manual

Many places in the manual, a specific section of a window for a node on a

launcher/computer/instrument is mentioned. The first time they are mentioned, the full path

is shown as

computer/program window/node/subsection of the node to open the setting window/setting

window/section in the window>

It is assumed that the user knows how to follow this path to the specific section of the

window by reading the following graphical user interface (GUI) manual and by a little of

practice. A abbreviated path rather than the full path will be shown in the latter steps for

the same node or application.

h2. Leginon Window

The window is divided into sections.

* Status bar - Leginon status display such as completion of application

loading.

!http://emg.nysbc.org/software/leginon/images/images/statusbar.png!

* Main Menu - Submenus and options derived from Manager and Launcher

!http://emg.nysbc.org/software/leginon/images/images/mainmenu.png!

* Node Selector - Selection for the node shown in the toolbar, message log, and node

panel. It is also used to indicate warning by turning red for broken node.

!http://emg.nysbc.org/software/leginon/images/images/nodeselector.png!

* Error indicator !http://emg.nysbc.org/software/leginon/images/icons/error.png! - This icon will appear next to a node (in the Node Selector) that has an

error.

* Message Log Information indicator !http://emg.nysbc.org/software/leginon/images/icons/info.png!

- This icon will appear next to a node (in the Node Selector) that has information in

its message log.

* User Input indicator !http://emg.nysbc.org/software/leginon/images/icons/userinput.png! - This icon will appear next to a node (in the Node Selector) that

requires User input in order to continue processing.

* Processing indicator !http://emg.nysbc.org/software/leginon/images/icons/processing/green0.png! - This icon will appear next to a node (in the Node Selector) that

currently doing processing.

h2. Node Panel

* Node Panel - The main display/control panel for the node selected by the node

selector.

!http://emg.nysbc.org/software/leginon/images/images/nodepanel2.png!

* Toolbar - An area containing tools for general configuration and execution of the

node as well as some tools for convenience specific for individual node.

!http://emg.nysbc.org/software/leginon/images/images/toolbar.png!

* Message Log - Expandable/scrollable box showing logged information for the

node.

!http://emg.nysbc.org/software/leginon/images/images/messagelog.png!

h2. Parameter Entry

* Free entry box- For typing in either text or numbers. If in a setting window, the

altered entry is saved to the database when it is exited with "OK" or after

"Apply"/"Test". Most numerical entry accepts floating point number in any python format.

For example, 10.2 can also be entered as 1.02e+2.

!http://emg.nysbc.org/software/leginon/images/images/Entry_box.png!

* Restricted-entry: The user can only select a valid entry from a list.

!http://emg.nysbc.org/software/leginon/images/images/Entry_box_restricted.png!

* List box- This type of selection box select either an ordered sequence or a simple

unordered list. If ordered, the items in the sequence can order with "up" and "down"

tools.

!http://emg.nysbc.org/software/leginon/images/images/List_box.png!

* If ordered, the items in the sequence can be shifted around with "up" and "down"

tools.

* Either free or restricted entry box is used for entering a new item to the list.

"+" tool is used to add the entry to the list box. selecting an existing item and

press "-" tool removes the item from the list.

* Multiple items can be selected by holding down the "ctrl" or "shift" key. The

latter selects a range between the first and the new items.

h2. Image Viewing

* Display Panel - where the image is shown.

* (pixel value button) !http://emg.nysbc.org/software/leginon/images/icons/value.png! - Pixel value display tool that shows the (x,y) coordinate the intensity value at the

cursor. The coordinate origin is set at top-left corner.

* (ruler button) !http://emg.nysbc.org/software/leginon/images/icons/ruler.png! - Ruler tool that displays the distance between a reference point and the current

cursor position. Left click at any position inside the display panel defines the

reference point.

* (zoom button) !http://emg.nysbc.org/software/leginon/images/icons/zoom.png!

- Magnifying glass tool that zoom in (left click) or out (right click) at the location

of the cursor.

* (zoom selector list) !http://emg.nysbc.org/software/leginon/images/images/zoomselector.png! - Direct zoom factor selector.

* (cross hair button) !http://emg.nysbc.org/software/leginon/images/images/bluech.png! - Cross hair reference tool displaying a blue cross hair centered at

the center of the image for reference.

* (display range selection/input) - Contrast and brightness adjustment of the image

display. The default is mean +/- 5*standard deviation of image intensity. This can be

modified by setting the minimum (top scroll bar or entry box) and the maximaum (bottom

scroll bar or entry box) of the display range.

!http://emg.nysbc.org/software/leginon/images/images/contrbright.png!

* Image Stats Panel

!http://emg.nysbc.org/software/leginon/images/images/imstatpanel.png!

* Image/Target/Marker Control Panel - where the image and targets to be displayed in

the display panel are determined. Targets are indicated by short cross symbols or other

shapes of different colors. The items shown with a screen icon are of image type. Items

of image type can be displayed alone while markers will show only when one of the items

of image type is also displayed.

!http://emg.nysbc.org/software/leginon/images/images/imcontrolpanel.png!

* (status indicator)

<inlinegraphic

fileref="http://emg.nysbc.org/software/leginon/images/icons/green.png"

format="PNG"/>

<inlinegraphic

fileref="http://emg.nysbc.org/software/leginon/images/icons/red.png"

format="PNG"/>

- This can be either green or red. During a step-by-step testing of parameters,

green indicates that the step has been tested and you can proceed to the next

testing step. Skiping to a step below a red-indicated step will cause an

error.

* (image display tool) !http://emg.nysbc.org/software/leginon/images/icons/display.png! - Display selection. Only one of the image type can be displayed at

one time.

* (target/marker display tool) !http://emg.nysbc.org/software/leginon/images/images/target_display.png! - Display target or marker selection. Pressed down (as shown for

the green target) is active. More than one type of markers can be displayed on

layers above the image. If the markers are overlapped, the marker last to be

activated for display is at the top.

* (marker tool) !http://emg.nysbc.org/software/leginon/images/icons/arrow.png! - Marker input selection. Certain markers can be manually edited.

In general, these are targets for further acquisition. In such case, the marker

selection tool can be activated by left clicking the icon. Once activated, left

click in the display panel adds the marker to the image and right click removes the

marker pointed to.

* (settings) !http://emg.nysbc.org/software/leginon/images/icons/settings.png! - Settings are available for certain items in the image control

panel, mainly steps in automatic hole finding. Left click opens the setting window

and the behavior of the setting window is similar to others of the same type.

h2. Tool Bar

Tool bar of the node contains tools for setting and execution of the node functions. In

addition, some tools are available as pop-up for convenience. The general rule for the flow

of setting up and execution is to go from left to right up to the execution tool (execution

icon).

!http://emg.nysbc.org/software/leginon/images/images/toolbar.png!

h2. Settings Window

Settings windows are opened by left clicking its button !http://emg.nysbc.org/software/leginon/images/icons/settings.png!

in the toolbar. Note that only one setting swindow can be opened at a time and that all

functions in the main leginon window is inactivated when a settings window is open even if

the leginon window is the focus. The content of the settings window depends on the purpose

of the settings. The general controls are described here:

* Test: found in settings of image processing steps. When clicked, the current setting

in the window is saved to database and applied to the current input and the results

saved as its output. If the item output is displayed in the node display panel, the

content will be changed accordingly.

!http://emg.nysbc.org/software/leginon/images/images/test.png!

* Apply: save the modified setting to database for future execution but not the

current test input. It is activated only if the modification of the input is completed,

normally by pressing the Enter key on the keyboard. Since current GUI does not allow

changes to the main window to be made while setting window is on, Using button is not

necessary since "OK" button will save the settings anyway.

!http://emg.nysbc.org/software/leginon/images/images/apply.png!

* Cancel: close the setting window and revert the setting to the last saved values.

This means you can not cancel setting modification if you have "test"ed or "apply"ed the

settings.

!http://emg.nysbc.org/software/leginon/images/images/cancel.png!

* OK or Done: close the setting window and save all modified settings to the

database.

!http://emg.nysbc.org/software/leginon/images/images/ok.png!

h2. Execution tools

Found in the node toolbar. They may take on different meanings for different node

classes. The general ones are described here:

* (Execute/Submit button) !http://emg.nysbc.org/software/leginon/images/icons/play.png!

: Perform one of the four possible functions if available and active for a node:

* When the application is in standby, it executes, sometimes with setting up the

main function of the node.

* When the application is running automatically, it indicates that the node is in

use.

* When the application is paused for user input, it submit the user approved

inputs and continue on the flow.

* When the application is paused by the "pause" tool in the same node, it removes

the pause flag and continue on the application flow.

* (Pause button) !http://emg.nysbc.org/software/leginon/images/icons/pause.png! : Pause data processing flow when the current input in a queue list is done.

* (Abort button) !http://emg.nysbc.org/software/leginon/images/icons/stop.png!

: Abort all data processing of the whole list in the queue.