dtcollect on-line help

Scan Dialog

Scan...

The Scan dialog window provides a way to create, edit, save, read and collect sophisticated data collection scans. The Scan dialog as shown in Figure 4 is displayed when Scan... is selected from the Collect menu in the main window. The Scan dialog has a menubar, a table of scans, output areas to show the status of the scan and image currently being collected, and at the bottom buttons to start, pause and abort a scan.

dtcollect Scan dialog, narrow view.

File: The File menu has options to read and write scan information and to close or exit from the Scan dialog. Scan information is saved in the header of an image file. The header of human-readable ASCII characters consists of keyword=values(s) attributes. The keywords used for scans are described in the Appendix A. For now, the first scan in an image header has keywords that all start with the sequence SCAN_. More than one scan can exist in the image header. Subsequent scans usually have scan keywords prefixed with a short string such as S1_, S2_ , ... to give a new keyword. For example, a header with two scans would have (among others) the keywords:
SCAN_ROTATION S1_SCAN_ROTATION
Open...: This pop-ups the scan file selection dialog where you select the image or scan file (they have the same format) to read scan information from. If you select a file, it is read and if there are no errors and it contains scan information, then the scan(s) in the file is (are) inserted into the scan table ON TOP OF the currently selected scan. Only the currently selected scan is overwritten. In order to read in a scan file and avoid replacing the currently selected scan, first use the Edit Insert menu item to insert a new scan which then can overwritten.
Save: This saves the scan to the file that was last read in. The file is OVERWRITTEN with the new information without prompting you, so be careful.
Save as...: This pop-ups the scan file selection dialog where you select the scan file to save scan information to. The file is created if it does not exist, it is OVERWRITTEN if it does exist.
Close: This closes the Scan dialog window. It does not abort or stop any scans in progess.

Edit

The Edit menu allows some simple editing of entire scans within the scan table. You may Cut, Copy, Paste, Insert and Delete an entire row of scan information. These operations all use the currently selected scan in the scan table. To select a scan, simply click on any value in the scan or on the scan's radiobox diamond on the left of the scan table. The currently selected scan is shown by the radio box diamond on the far left and by a label above the scan table.

Cut: Cut the selected scan and remove it from the table. Save it in a buffer.
Copy: Copy the selected scan into a buffer, leaving the original scan in the table.
Paste: Paste the cut or copied scan replacing the currently selected scan.
Insert: Insert a new scan after the currently selected scan. To insert a new scan at the beginning of the scan table, insert two scans, cut the first scan in the table and finally paste it over second inserted scan.
Delete: This is like Cut, except the deleted scan is not saved in a buffer and is lost.

View

The View menu allows some simple changes to the display of the scan table. You can increase or decrease the number of scans visible without scrolling in the scan table. You can also widen or narrow the window size. To a certain extent, the view properties change automatically in reaction to cutting and inserting scans.

Enlarge: Enlarge the scrolled window that contains the scan table by one scan row. No more than 10 rows can be visible at a time.
Shrink: Shrink the scrolled window that contains the scan table by one scan row. At least one row will remain visible at all times.
Narrow: Narrow the window, so that only the most common scan properties are visible. The other properties can be viewed by scrolling with the horizontal scrollbar. This can also be achieved by resizing the window with the controls provided by the window manager or by selecting the small arrow button above the scan table.
Widen: Widen the window, so that all the scan properties are visible. This can also be achieved by resizing the window with the controls provided by the window manager or by selecting the small arrow button above the scan table.

Scan table

The scan table consists of a series of scans arranged vertically with the individual properties of the scan arranged horizontally. The scan table has scrollbars on the top and the left side so that you can scroll to view hidden areas of the table. Below the actual scans are controls to change or effect the values in the currently selected scan row. To select a scan, simply click on any value in the scan or on the scan’s radiobox diamond on the left of the scan table. The currently selected scan is shown by highlighting and by a label above the scan table and to the right of the menu bar.

dtcollect Scan dialog, wide view.

To change a field in the scan table, simply select the field with the mouse or by tabbing to it and enter the new value(s). The currently selected field is highlighted. You may also use shift+ to go to the previous field with the keyboard. Values are updated whenever you leave the field by pressing , or using a mouse click. If a field is blank or begins with an equal sign , then the correspoding value from the previous scan is placed in the field. That is, every field has a default value whether you can see it or not. As long as the first scan has values, then all the scans have values. With this feature, you can insert new scans and change only the values that are different from the previous scan. This makes it very easy to created sophisticated scan tables with minimal input.

Below each field in a scan row is discussed. The convenience control below the scan table that effects the field is discussed at the same time.

Shutter

This gives the shutter status for the images in the scan. It can be Open, Closed or anything else. If it is neither Open nor Closed, then the scan is skipped when collecting scans. This is useful to skip scans. The control below this field is a radiobox with the Open and Closed choices.

Rel rot start

The relative rotation angle starting position in degrees. The actual hard- ware value depends on the crystal goniometer Relative Zero Position values and which axis is designated the rotation axis. The crystal goniometer moves to the Relative Zero Position plus this value at the start of a scan. The scrollbar below goes from -360 to 360 degrees in 1 degree increments and 10 degree page increments. Use the text field to enter values that are not integers.

Rel rot end

The relative rotation angle ending position in degrees. Remember that this is relative to the crystal goniometer Relative Zero Position.

Rot incr

Rotation angle increment per images in degrees. Each image exposure will be this many degrees wide. The scrollbar goes from 0 to 5.00 in steps of 0.05 degrees.

Time

The exposure time per image in seconds. The scrollbar has a maximum of 3600 seconds, so enter exposure times longer than this directly in the text field.

Axis

Select either the Phi or Omega axis or enter any axis you wish. Be aware that names other than Phi or Omega may not be supported on your diffractometer.

Template

Seq Start

Seq Incr

These together describe a way to give potentially unique names to the images of a scan. The template is a filename with question marks that will be replaced with the image sequence number. The first sequence number is given by Sequence Start, and the next by Sequence Start + Sequence Increment and so on. The image sequence number is used to fill in the question marks in the template. Examples:

image.????, 1, 1 gives: image.0001, image.0002, ... rib4???.osc, 0, 2 gives: rib4000.osc, rib4002.osc, ... test???.???, 2000, -1 gives: test002.000, test001.999, ... test???.???, -2000, 1 gives: test-02.000, test-01.999, ...

Note that Sequence Start and Sequence Increment are integers. The control below this pops up an image file select dialog. Please note that changing any of these fields affects only the image file names. It does not change the rotation angle start, end or the number of images in a scan.

The default values for these fields are copied from the main window File Image template... command.

Relative zero position

These values describe the crystal goniometer and the detector goniometer positions when the rotation angle is at 0.0 (which may or may not be between the Rel rot start and Rel rot end angles). If the Rel start angle is 0.0, then these values are the position of the crystal goniometer and detector at the start of the scan. The angles are in degrees and distances in millimeters. The first detector goniometer value MUST BE the sample to detector distance. The number of angles and distances to enter depends on the diffractometer. The control below pop-ups a menu to enter these values into separate fields. The default Relative Zero Position is the current crystal and detector goniometer positions found on the main window, if the current text field is empty when the Scan dialog window is popped up.

Wavelength

Enter the desired source wavelength in Angstroms or eV. Any value above 100 will be treated as eV, while values below this are assumed to be Angstroms. The control below pop-ups the wavelength chooser. The wavelength selected by the chooser will be placed in the scan. The source will be moved to this wavelength at the beginning of a scan (if possible). There are options to flag the source device controller to optimize the source intensity after the wavelength change and to scan the wavelength near the chosen one to select either peak or inflection points in the scan. This may be useful for multiwavelength anomalous diffraction (MAD) experiments. The default value of the wavlelength is the wavelength found in the main window, if the current text field is empty when the Scan dialog window is popped up.

Num osc

The number of oscillations made per image. Zero oscillations means a simple rotation is made.

Dark intvl

Enter the dark current image update interval. This applies only to CCD and TV detectors. Dark images will be re-collected at the image interval entered here.

Scan, Pause, Abort

The Scan button starts the actual data acquisition. All the scans in the table are collected. If there is an error in any scan, then data collection stops. The scan may be aborted outright or paused after the current image completes by selecting the Abort or Pause buttons. If paused, the Pause button changes to Resume which can then be selected to resume a scan.

When a scan is active, the main window controls are colored, labelled and updated as described for the Expose button. The Scan dialog gives the progress of the scan and information about the current image.

As each image is created it is displayed in the image display area of the main window. You can interact with the image with the mouse as described in section 3.4.