ImageTracker operates on stacks of individual image files—a set of images constitutes a video. ImageTracker can read many types of images, including TIFF, PNG, JPG, MHA, and VTK. Currently, ImageTracker does not support Metamorph stacks, video files (e.g. AVI, WMV), or raw camera files. Software such as ImageJ, supplied by the National Institutes of Health (NIH), can be used to convert images from many file formats into a format ImageTracker can read.
A.3.1
Loading Images
ImageTracker can have one active image stack and one active vector stack loaded at a time. To load an image stack, select the Images tab from the data control panel and select the Image Files item from the filter list at the top. An Image Files control panel appears below the filter list, as seen in Figure A.2. Below the filter list is a list of file names that will be loaded into ImageTracker. Modify this file list by using one of the buttons at the bottom of the list.
Example Select a single image, and let ImageTracker find files in the same directory with the same naming convention. This is the easiest and most common way to specify a series of files.
Figure A.2: The Image Files control panel specifies which image files are loaded in ImageTracker.
Selection Select multiple files to add to the file list. The file names will be sorted alphabetically as they are added. A maximum of around 1000 file names can be selected at one time.
Pattern Specify a file series naming convention pattern by selecting a root directory, file prefix, number format, file extension, and numeric range. Press the Enter key as you modify each field in the pattern specification dialog to update the example name displayed below. (This option is seldom used, but is appropriate for loading a subset of a large sequence of files.)
Remove Remove any selected file names from the list.
When the list of file names is complete, click the Apply button to load the named files into ImageTracker. The first image in the list will be displayed in the image panel. The Apply button should be pressed whenever any changes are made to the Image File
control panel to have those changes reflected in ImageTracker.
A.3.2
Image Controls
In the main ImageTracker window, images loaded in the Image Files panel are displayed in the main image display panel on the right, as shown in Figure A.1. Controls below the image display panel adjust the index of the frame that is displayed. Move the slider to scan through the loaded images. To jump to a specific frame, enter the frame index in the text box and press Enter. A set of buttons to the right of the slider enables playing, rewinding, pausing, single frame advance and rewind, and skipping to either end of the image sequence.
Images and vector visualizations are displayed simultaneously. The frame index range is based on the larger of the number of loaded images and loaded vector images. If the two sequences are of different sizes, the visualization from the shorter sequence will no longer update once the frame index exceeds the length of that sequence.
The display properties of the image display panel can be adjusted by selecting View →Window/Contrast from the ImageTracker menu. This dialog controls only the display of images and does not change the actual intensity values. The Maximum and Minimum sliders change the intensity values displayed in the image panel. The Range combo box controls the range of values displayed on the intensity sliders. The Auto button automatically adjusts the maximum and minimum display values to the maximum and minimum intensity values in the currently displayed image. You may need to adjust the display contrast when switching between different types of images (e.g. changing from 8-bit to 16-bit images).
To change the magnification of the current image, right click on the image, and drag the mouse up or down. To move the current image, center click on the image and drag the mouse in the desired direction. To rotate an image, left click on the image and drag the mouse.
Image size and intensity statistics for the currently displayed image can be shown by selecting View → Image Info from the menu. This will display the Logger window with the most recent message containing the image information. Note that a log level of Info or lower needs to be selected in order for the image information to be displayed.
A.3.3
Loading Vector Images
A vector image is an image in which every pixel contains vector information instead of intensity information. For example, the output of an optical flow computation is a vector image where vectors explain the motion of intensities between images.
Vector data is loaded in a similar way to image data. Click on the Vectors tab of the data control panel to bring up the Vector Files control panel. A list of vector image files can be modified in the same way as the list of image files on the Images tab. The Visualization control panel below the vector file list provides options for how to display the vector image data.
Vector images can be displayed with two different visualizations: Glyph and Height Map. The Method combo box in the vector visualization control panel selects between these two options. Controls below this combo box enable modifying aspects of the visualization.
If the controls for the current visualization are not visible (this sometimes happens when the vector images are automatically loaded as the result of a processing task), press the Apply button below the vector files list. This will update the visualization control panel.
The Glyph visualization displays regularly-spaced vector glyphs across a vector field, as seen in Figure A.3a. Each glyph is scaled according to the vector magnitude and ori- ented according to the vector direction. The vector visualization control enables rescal- ing glyphssetting the scaling to 1.0 will match the glyph lengths to the underlying vector magnitudes. Drawing a glyph at every pixel location would clutter the visualization; the
(a) (b)
Figure A.3: Vector file visualization in ImageTracker. a) Vector glyph visualization and (b) vector height map visualization.
Mask Ratio slider adjusts the spacing between adjacent glyphs. Some spacings produce distracting patterns of glyph placement. Adjusting the Mask Ratio up or down by a few values will usually correct this.
Height map visualization maps the magnitude of the vector image to the height of a surface, as seen in Figure A.3b. It may be helpful to rotate the image plane to better view the surface when using this visualization. The Color Map combo box controls the colormap used to paint the surface, where color is a redundant encoding of vector magnitude. The Scale Factor slider controls the scaling of the height map. The Magnitude Function combo box selects between height mapping the vector magnitude or a single vector component.
A.3.4
Saving Visualizations
To save a visualization displayed by ImageTracker, select File→Save View Images. This will bring up a dialog that enables selecting an output directory, file naming convention, and the range of frames to save. The images saved will be exactly what is displayed in the ImageTracker image panel. To save the result of applying a set of filters, see Section A.4.
It is important to not let any other window obscure the ImageTracker image display panel when saving visualizations. Doing so will corrupt the saved images, as the un- derlying image capture procedure copies data from the screen buffer. The frame index slider provides progress information and a message will be displayed when ImageTracker has finished saving the visualizations.
Due to an error in the VTK class that handles image capture, if a set of visualizations is saved, the image display panel is resized, and then another set of visualizations is saved, ImageTracker will crash.