GC Image Users' Guide

Graphics

GC Image supports drawing and editing of graphical elements, including points, polylines, rectangles, and polygons. The Image Viewer palette contains a button to set the cursor mode to graphics mode and there is a pull-down graphics mode selector. The selectable graphics cursor modes are: There is also a palette button to delete one or more selected graphic objects, a menu item for selecting all graphic objects, and menu items for importing and exporting files that describe graphic objects. The Configure -> Configure Settings interface allows the user to set visibility options and set default colors for graphic objects.

Draw Point

Create a point graphic by first setting the graphics mode to Draw Point. In this mode, click the left mouse-button to set the location of the point. After the point graphic is drawn, the graphics mode reverts to Select Graphic mode and the newly created point graphic is selected. Selected points are outlined graphically, as illustrated in Figure 1.
Figure 1: A selected point graphic.

Draw Polyline

Create a polyline graphic by first setting the graphics mode to Draw Polyline. In this mode, move the cursor to the starting point of the polyline and click the left mouse-button. Then, similarly move to each successive point of the polyline and click the left mouse-button. At the ending point of the polyline, double-click the left mouse-button. After the polyline is drawn, the graphics cursor mode reverts to Select Graphic mode and the newly created polyline graphic is selected. The knots of selected polylines are highlighted graphically, as illustrated in Figure 2.
Figure 2: A selected polyline graphic.

Draw Rectangle

Create a rectangle graphic by first setting the graphics mode to Draw Rectangle. In this mode, click the left mouse-button to set one corner of the rectangular sub-region, drag the cursor to the opposite corner of the rectangular sub-region, and release the mouse button. After the rectangle is drawn, the graphics cursor mode reverts to Select Graphic mode and the newly created rectangle graphic is selected. The corners of selected rectangles are highlighted graphically, as illustrated in Figure 3.
Figure 3: A selected rectangle graphic.

Draw Polygon

Create a polygon graphic by first setting the graphics mode to Draw Polygon. In this mode, click the left mouse-button to set one vertex of the polygon, repeatedly move the mouse to subsequent vertices and click the left mouse-button, and double-click the left mouse-button at the final vertex. After the polygon is drawn, the graphics cursor mode reverts to Select Graphic mode and the newly created polygon graphic is selected. The vertices of selected polygons are highlighted graphically, as illustrated in Figure 4.
Figure 4: A selected polygon graphic.

Selecting Graphics

In graphics cursor mode, the default mode is Select Graphic. In this mode, when the cursor is positioned over an existing graphic (a point, polyline, rectangle, or polygon) and the left mouse-button is clicked, the indicated graphic is selected. When selected, a graphic is highlighted with handles at the knots (e.g., vertices of polygons).

Multiple graphics can be selected with successive control-clicks with the left mouse-button. Control-click with the left mouse button on a selected graphic will remove it from the selection set. All graphics can be selected by choosing "Edit -> Select All" (or using the <Ctl>-A keys) in graphics mode.

Editing Graphics and Graphics Metadata

In Select Graphic mode, one or more selected graphics can be moved (i.e., translated) by click-and-drag with the left mouse-button, beginning in the interior of a selected graphic. In Select Graphic mode, a vertex of a selected graphic can be moved (independent of other vertices) by click-and-drag with the left mouse-button, beginning on the knot around the vertex.

In Edit Vertices mode, a vertex can be added to or deleted from a selected polyline or polygon. In this mode, clicking on a knot around a vertex will delete it (unless it is one of only two vertices in the object) and clicking on a segment will add a vertex in the middle of the segment.

In graphics mode, when one graphic is selected, clicking the right mouse-button brings up a graphic metadata popup, in which metadata, including the name of the graphic, a description, area flag, inclusion flag, text object flag, and color, can be assigned. Figure 5 illustrates the Graphic Metadata dialog.
Figure 5: The Graphic Metadata dialog.

The Area Flag indicates that this graphic is marked as an area and values are generated for this graphic. The data will now be reported under the Area section of the blob table. It also allows the user to view this data by selecting the Area Properties tab. The values are calculated from all pixels contained by the graphic. Figure 6 illustrates the Area Properties dialog.
Figure 6: The Area Properties dialog.

The Include Flag for a graphic is used in generating reports, indicating that the blob peaks defined by the graphic are reported as a set. As described in Peak Detection and Analysis, a polygon or rectangle graphic can be used to indicate a set of blobs whose peaks are intersected or contained in the graphic and which satisfy the CLIC expression of the graphic. (CLIC expressions, described in Chemical Identification , impose rule-based constraints on set inclusion.)

The Exclude Flag for a graphic is used in generating reports, indicating that blobs with peaks contained in a polygon or rectangle or blobs intersected by a point or polyline are excluded from reporting (e.g., in the total response of all blobs). Use of the include and exclude flags for graphics is described more fully in Peak Detection and Analysis and Reports .

The Add Text Object indicates that a text label with the name of the graphic is present. See Text and Chemical Structure Annotations for a description of text objects in GC Image.

The Set Color setting can be used to override the default color of the graphic. (The default color is set according to the inclusion class: included, excluded, or unflagged.) First, check the Set Color flag and then click the Color button to invoke the color chooser. As described in Peak Detection and Analysis, the color also can be applied to the blob set defined by the graphic, using the Color Blobs setting.

In graphics mode, when multiple graphics are selected, clicking the right mouse-button brings up a popup for shared metadata. Figure 7 illustrates the Graphics Metadata dialog for multiple graphics.
Figure 7: The Graphics Metadata dialog for multiple graphics.

Deleting Graphics

To delete a graphic(s), first enter graphic mode, then select the graphic(s) to be deleted, and then click the Delete Object button on the palette. If multiple graphics are selected, all selected graphics are deleted. The delete key may also be used.

Exporting and Importing Graphics

To export all graphic objects, text annotations, and chemical structure annotations from the current image, select File -> Export Graphics Table from the menu, then indicate the folder and filename in the popup dialog.

To import a set of graphic objects and annotations previously exported to a file, select File -> Import Graphics Table from the menu. Then, in the popup dialog, whether the imported graphics are to be appended to or replace any existing graphics and the file from which the graphics are to be imported.

Graphics Configuration

To configure the default settings for graphics, select Configure -> Configure Settings from the menu and open the Graphics Display tab, as illustrated in Figure 8, which allows the following settings to be changed:
Figure 8: Graphics Display configuration.

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GC Image™ Users' Guide © 2001–2007 by GC Image, LLC, and the University of Nebraska.