Wait for Drift Setup Dialog

This dialog allows you to set parameters for the Wait for Drift task, which measures drift repeatedly until it reaches a criterion level or a time limit is reached.  These parameters are used by the DriftWaitTask script command unless they are overridden by non-zero entries to the command.  The successive drift measurements are shown in the status bar.  When measuring with Focus or Trial images, the drift is also printed to the log if the Verbose option is on in the Tasks menu.  When measuring with autofocus runs, the drift and elapsed time are included in each autofocus report in the log.

The top part of the dialog is always present.  The bottom part has options specific to tilt series that are stored in the tilt series parameters.  It appears only when this dialog is opened from the Tilt Series Setup dialog or when a tilt series is stopped.

Parameters Controlling the Drift Task

Images to measure drift between

Use these radio buttons to select what kind of images to use for measuring drift.  The choices are:

For the autofocus option, the program will take 3 Focus images for 'drift protection' regardless of the setting of the option for this in the Focus menu.

Change Trial parameters

Select this option to use a specified exposure time and binning whenever using Trial images.  Use the text box to set the Trial exposure and the spin button to set the Binning.  Longer exposure time will improve the signal-to-noise ratio and lower binning may improve the accuracy of correlations somewhat, both of which should improve the accuracy of the measurement.

This option applies only to Trial images under the assumption that Focus parameters should already be set to give a good signal-to-noise ratio for measurement of small shifts.  Aside from the exposure and binning, the accuracy of measurements with Focus images should be improved with full-field rather than subarea images.

Time span of drift measurements

Enter the time interval between the two images being correlated to measure drift in the text box.

When autofocusing, a delay will be imposed between the images of the autofocus run to make the time between the first and third images as long as this interval.   This makes the defocus measurement more vulnerable to a decay in the drift rate within the autofocus run because some of the shift due to drift will be attributed to defocus instead.  For example, if the beam-tilt-induced shift is 10 pixels and drift decays from 5 pixels between the first two images to 3 pixels between the second pair, then the beam-tilt-induced shift will be estimated at 11, off by 10%.  Intervals long enough to increase the autofocus time substantially should be used only when the shifts induced by the beam tilt are much bigger than the shift attributable to drift, such as with a relatively large defocus, very high magnification, or high beam tilt.  Use Report Shift & Drift or Report On Existing, or autofocus with Verbose on in the Focus/Tune menu to assess the relative size of these shifts.

The actual time span of the drift measurement may be longer than this interval if the basic acquisition time is more than the interval when using Trial or Focus images, or more than half the interval when using autofocus runs.

Drift rate to reach

Enter the criterion (target) drift rate in the text box, in the units show after the box (nm versus Angstroms).

Maximum time to wait

Enter the maximum total time to wait for the drift to reach the target rate.

Skip if immediately previous autofocus had drift below X

This option allows the routine to test whether an autofocus just prior to running the drift waiting a drift rate low enough so that further testing can be skipped.  Because the drift measurement from this autofocus is inherently less accurate if it is made over a smaller time interval than is specified here, it is usually advisable to use a smaller drift value here than the final drift rate that you want to reach.

Generate error if target drift rate is not reached

Select this option to have the program put up a message box and issue a general stop command to anything else running when the target drift rate is not achieved after the maximum wait time has elapsed.  With the option off, the program will print a failure message to the log and scripts can test for success with the 'GetLastTaskDrift' command.

Correct drift with image shift

Select this option to have image shift applied to correct for the drift between each pair of successive images.  When measuring with autofocus, only the drift between the first and third image of an autofocus run is corrected, not the drift between the third image of one run and the first of the next run.

Show Angstroms/sec instead of nm/sec

This option is here because nm/sec, used elsewhere in the program, becomes awkward at low drift rates.

Parameters Controlling When to Wait in Tilt Series

Waiting for drift is a time-consuming step and the controls here provide different ways to restrict when it is run.  It may be possible to tell that an option is appropriate from the drift rates in tilt series where the step is run at every tilt.  In other cases, it might be necessary to evaluate the quality of the final result in order to determine whether an option is an acceptable way to save time.

Tilt series angular restrictions

Select Run at any angle to wait for drift regardless of tilt angle in a tilt series, Run only above to wait only above the angle given in the text box, or Run only below to wait only below the angle in its respective text box.  Waiting for drift only above an angle would be appropriate for situations where drift is much higher at high tilt (such as with side-entry holders) and not a concern at lower angles (e.g., if frame alignment handles the drift adequately).  Waiting only below an angle might be appropriate if the higher tilt images contribute little of the high-frequency information that is impaired by drift.

Dose-symmetric series: Run only at tilt reversals

Select this option to wait for drift only after the tilt direction changes in dose-symmetric series, or more specifically, to skip waiting after tilting between adjacent angles on the same side of the series.  This option would be appropriate if drift is found to be low after such tilt changes.

Dose-symmetric series: Ignore angular restrictions

Select this option to wait for drift regardless of tilt angle in a dose-symmetric series, even if a restriction is selected with the radio buttons above.  This option allows you to set up a different behavior for dose-symmetric and other tilt series without having to revisit this dialog and change the angular restriction choice.

Suppose the option Run only below is selected with an angle X.  This matrix shows when the task will be run in a dose-symmetric series for the different combinations:

  Only at Reversals OFF Only at Reversals ON
Ignore restrictions OFF At all angles below X At reversals below X
Ignore restrictions ON At all angles At all reversals