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autocal: Automatically calibrate a KappaCCD

The "autocal" program can be used to go through all the necessary steps of a KappaCCD calibration in an automated way. On a partly calibrated system, only the steps necessary to complete the calibration will be performed.

For a description of all the steps in the calibration see the manuals of the individual calibration tools and the description of the step-wise calibration procedure

The program will progress without asking any questions for as long as it can. When human interaction is required, it will start an irritating beeping sequence until the issue is resolved. If the program is not absolutely sure that everything went 100% OK, it will ask you to consult an expert. In most of these cases nothing serious will be wrong, but it is in any case very valuable to send such messages to collect@bruker-axs.nl such that we can check, and possibly improve the calibration software to handle your case more smoothly.

If everything proceeds successfully, the complete calibration from scratch can be performed in 24 hours. To reach this, the calibration process should be started in the morning. The last human interaction (a sample change) should be required approximately 6 hours after the start.

The goal of the autocal program is to perform only those calibrations that have not been performed before. This means that:

If you want to re-calibrate you need to remove the outdated calibration file(s) before running autocal.
If the "autocal" run is interrupted, you can simply restart it from the same directory, and it will restart more-or-less where it left off.

Prerequisites

For running autocal, one needs:

An AMBI testcrystal as delivered with the KappaCCD
Two calibration directories: "/usr/local/hklint" and "/usr/local/calibration" both containing a subdirectory with a name equal to the detector id of your KappaCCD (e.g. /usr/local/calibration/9602). These "detector id" directories must be writeable by the user running the autocal program. (you can run commands like:
```
chown -R ccd.ccd /usr/local/calibration
chown -R ccd.ccd /usr/local/hklint
```
to [temporarily] change the ownership of the calibration files, rather than running the whole calibration as root).
For a normal KappaCCD, about 650MB disk space (the exact amount depends a bit on the circumstances).

If the machine has never been calibrated for collect/evalccd before, (machines coming from the factory before January 2000 were not calibrated for collect/evalccd) one additionally needs:

The fluorescent Y2O3 powder sample delivered with the KappaCCD
The ability to move theta from +51 degrees to -20 degrees (better -30). This must be enabled by setting the theta limits, and you must verify that the machine can make these moves without colliding with any physical barrier!.
The original grid image from the calibration CD (either grid.kcd or FLM-4-1.SPE will do).

Usage

The program is invoked by the command line:

  autocal [options]

Options are:

noambi: Inhibit the measurement and integration of a standard AMBI data set to verify the calibration.
ambi: Enable the measurement and integration of a standard AMBI data set to verify the calibration. This is the default.
denzo: Generate calibration files in a form suitable for the HKL2000 system as well. This is the default.
nodenzo: Do not generate calibration files in a form suitable for the HKL2000 system.
factory: Generate some extra images only needed in a factory calibration. This is the default on machines named "nows65".
nofactory: Do not generate extra images only needed in a factory calibration. This is the default on machines not named "nows65".
mkdir: With this option, autocal will not perform any calibration measurements but only check whether the calibration directories exist, and if not, create them. The program will then show the names of these directories and exit.

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