dtdisplay on-line help

File menu

The File menu is used to create new images, to open existing images and to load reflection lists that are displayed. New images that are created can also be saved to disk files. The commands in the file menu are New, Open, Save As, Image Template, Preferences, Print, Respond to updates and Exit.
New
The New command popups a menu with the following choices:
Image file...
When this is activated, a file selection dialog box appears. Select an image file from the list of files and then select OK. The file will be read in, automatically scaled to the color table and displayed.
Scan
This command is not yet implemented, therefore it is insensitive and cannot be selected.
Overlay
Overlay creates a new image by overlaying a series of images and displays the resulting image. The image can be saved to disk by selecting the File Save As... command. To use this command, first read in and display an image with either the File Open... or File New Image File... commands. Then select File New Overlay.... The (file selection dialog box appears. Enter the image filename template (include ? for replacable digits), sequence number start, the sequence number increment and the number of images to overlay, then select OK, overlay. The image filenames will be constructed from the template and a sequence number by replacing the question marks (?) in the template with the sequence number. For example, an image template ribosome.???? might represent the files ibosome.0001, ribosome.0002, etc.

When images are overlayed, the highest pixel value in any input image for a given position is placed in the created image. For example, if you have three 2x2 images with pixel values:

	1  2		2  3		4  3
	3  4		4  1		2  1
the overlay result image will be:
	4  3
	4  4
The overlay command is useful to create pseudo rotation images that span a larger volume of reciprocal space. If an error occurs while reading in an image, then the overlaying stops and the overlayed image in its current state is displayed.
Average
Average is similar to the overlay command and works the same way. Instead of selecting the highest pixel value for the output image, the average value is calculated. In addition, an image of standard deviations is calculated and written to the file named by the first image used in the averaging with the characters 'sd' appended.
Tile
Tile creates a new image by tiling a series of images and displays the resulting image. The image can be saved to disk by selecting the File Save As... command. To use this command, first read in and display an image with either the File Open... or File New Image File... commands. Then select File New Tile.... The (file selection dialog box appears. Enter the image filename template (include ? for replacable digits), sequence number start, the sequence number increment, the number of images to overlay and the image filename template, then select OK, tile. The image filenames will be constructed from the template and a sequence number by replacing the hash marks (?) in the template with the sequence number.

The tiled image has the same dimensions and data type as the input images. In order to achieve this, some pixels in the input images are skipped over. Zooming in on a displayed tiled image does not recover the pixels skipped over. The number of rows and columns in the output image is a function of the number of images. For example, if 4 images are tiled, then the tiled image will be 2x2. If 6 images are tile, then the tiled image will be 2 x 3 with gaps along each row. To avoid gaps, choose a number of images that is the square of an integer (namely, 4, 9, 16, 25, ...). Furthermore, the first image is placed at position (0, 0) while the next image is adjacent to the first image on the same row. Rows run along the FAST pixel direction while columns run down the SLOW pixel direction. In the display, the FAST and SLOW directions may have a non-standard orientation (see Orientation in section 3.1.2.1).

If an error occurs while reading in an image, then the tiling stops and the tiled image in its current state is displayed.

Statistics
When implemented, Statistics will create two new images from a series of images. The new images will contain the average and the standard deviation at each pixel position. This command is not yet implemented, therefore it is insensitive and cannot be selected.
Open...
The File Open... command selects an image file to display. When this is activated, the (file selection dialog box appears. Select an image file from the list and then select OK, open. The file will be read in, automatically scaled to the color table and displayed.
Save Image As...
This command saves the currently displayed image to a file. If there is no currently displayed image, then this command does nothing. A (file selection dialog box appears which allows you to enter a filename for the new image. If you select a filename that already exists, the old image will have a version number appended to it, so that the new file does not overwrite the old file.
Save Header As...
This command saves only the (possibly edited) header of the displayed image to a file. If there is no currently displayed image, then this command does nothing. A (file selection dialog box appears which allows you to enter a filename for the new header. If you select a filename that already exists, the old file will have a version number appended, so the new header will not overwrite the old file.
Image template...
This command lets you view and edit the current settings for the image filename template and sequence numbers. A (file selection dialog box appears. The settings in the dialog box come from the header of the last image read in or from the last time the image template dialog appeared. Remember that Overlay, Average, Tile and Statistics in the File New menu all use the image template dialog.
Read refln list...
The File Read refln list... command selects a reflection list to display. When this is activated, a file selection dialog box appears. Select a reflection list file from the list and then select OK. The file will be read in and displayed. If reflections are not displayed, check that Observed reflns is set in the View menu.

The properties of the reflection list display can be edited by selecting Edit reflection properties... in the Edit menu (see 3.1.2).

Write refln list...
The File Write refln list... command selects a reflection list file to write the reflection list to. When this is activated, a file selection dialog box appears. Select a reflection list file from the list and then select OK. The reflection list will be written to the selected file.
Respond to updates
This has options for dtintegrate, dtcollect and Others. If any of these are set, then dtdisplay listens and responds to updates from other X Window clients. Thus other clients, such as dtcollect and dtintegrate can request that dtdisplay read and display a new image or reflection list. The Others option applies to programs dtfind, dtrefine, and dtpredict. If a toggle button is not set, then dtdisplay ignores requests from those clients.
Exit
This command exits from dtdisplay.