dtprocess on-line help

Getting Started

Running dtprocess

After dtprocess has been installed and placed in your PATH, just enter dtprocess along with an optional header or image filename to run it. Messages are written to the Output text area and to stdout and stderr as required. The syntax for running dtprocess is simply:

dtprocess [header_file]

Remember, the d*TREK header filename after the dtprocess command is optional.

The main controls of dtprocess are a Flow Chart of steps, 2 Lists, and a Menu area. Select a flow chart button to display a different menu. Each menu has controls (e.g. text fields) to enter specific options and a 'Run' button. Users interact with each menu in the same way:

Select a header from the top list.
Select one or more image files or reflection list files from the bottom list.
Set any control values in the menu.
Select the 'Run' button.

In most cases, dtprocess performs the first two steps for you. Also, sensible default values can be saved to a file, so the third step may be trivial or unnecessary. Even the last step is performed automatically in Auto run next mode.

Mode: manual or automatic?

Select the flow chart mode with the option menu above the flow chart.

In Manual mode, you must select a flow chart button to view a new menu.

In Auto show next mode, when you activate or 'run' the function of the menu successfully, the next item in the flow chart is automatically selected and the new menu displayed.

In Auto run next mode, the new menu is also automatically run. This mode is best suited when you have preset all the control (widget) values ahead of time -- either manually or by reading in a header file.

In Auto strategy mode, you find spots, index, refine, predict and determine a data collection strategy. This is the best mode to use first.

If any errors occur in an auto mode, the mode reverts to manual mode.

Flow chart and Menus

Along the left edge of the dtprocess window is a flow chart of the steps required to process a scan of images. When you select a button in the flow chart, the button turns yellow and a new menu appears on the right. In general, you will want to follow the order suggested by the flow chart, but this is not required. The flow chart buttons in order are:

Setup calibration and scan info.
Find spots for autoindexing and refinement.
Index spots to get the initial crystal unit cell and crystal orientation.
Refine crystal, detector and source properties.
Predict reflections.
Orient: Determine crystal goniometer angles to achieve a specific crystal orientation.
Strategy: Determine a suitable scan rotation for data collection.
Integrate a scan of images to get h, k, l, Intensities and SigmaI.
Merge reflection list files.
Scale/Average a reflection list that has multiple batches.

For processing a previously collected scan of images, the Orient and Strategy steps are skipped.

Lists: headers, images, reflnlists

Two lists are displayed on the right of the Flow Chart. The top list is always a list of header files. The bottom list depends on the which step in the Flow Chart is active, but is either a list of images or a list of reflnlist files. The lists show files without their directory specification.

To update any list or change the directory or filter specification just select File from the menubar then Header template..., Image file template..., or Reflnlist...to pop-up a dialog box where you can make your change(s).

Output files

The d*TREK suite of programs all function in the same way. Inputs are a header file with the current experimental values, one or more image or reflnlist files and some control values. Outputs are a header file with modified values and/or new reflnlist files. The output files are generated by the programs that dtprocess activates. d*TREK programs also implement a simple file versioning system, so that no file is implicitly overwritten.

When a menu is 'run', the menu is replaced with the log file for that run. When a run is finished, you may dismiss the log file simply by pressing the Dismiss button.

You may use View / Log file... to view log files after they are dismissed.

You may purge many of the output files by selecting Utils Purge from the menubar.