IMCA-CAT News

JDirector 2.2.1_imca41 has been released. This update adds support for entering X-ray beam attenuation as transmission and other improvements.

• Added support for entering X-ray beam transmission instead of attenuation for users who would prefer to think in terms of transmission. This applies to the scan editor, the manual diffraction centering configuration, and the job sample table.
• Fixed the job sample table to use correct detector distance limits. Previously, the limits were hard-coded which was wrong. Now the limits are obtained from the instrument server.
• Improved log messages. This involved fixing a case where an undefined value was printed as null, where extraneous trailing punctuation was used, and where an exception trace was unnecessarily printed for a diffraction center that terminated due to a low-score cutoff.

JDirector 2.2.1_imca36 has been released. This update adds support for saving ancillary files with data in auto-mode and other improvements.

• In auto-mode, instead of saving camera snapshots from the centering and before and after steps directly in the sample directory, they are now saved in a "camera" subdirectory. This makes the sample directory less cluttered and more uniform.
• Added support for saving ancillary files ("camera", "diff-center", etc.) with the data in auto-mode. This behavior is off by default but can be enabled via an option in the Job Control options pane. This is useful for mail-in when collecting for more than one user and want the ancillary files to be saved with the data. In this mode of operation, the recipe usually contains a path not relative to the sample image directory (i.e. user-defined absolute path or relative to the working directory) and using escape characters. This can also be used if a user wants to collect their data to a different location than the default one produced by auto-mode.
• In auto-mode, for the ancillary "camera" and "diff-center" subdirectories, if they already exist, they will now be renamed out of the way first. They are renamed to a name ending in ".old" or ".oldN" where N is an integer >= 2. This makes the latest camera and diffraction center images always appear in the "camera" and "diff-center" subdirectories. The previous behavior for "camera" was to just overwrite the images. (The "camera" subdirectory did not exist previously; it is new in this release.) The previous behavior for "diff-center" was to create a new "diff-centerN" directory where N was an integer >= 2 if "diff-center" already existed. With that approach, the path to the latest diffraction center images was not stable.
• Disabled mediaLib in order to prevent the message "Could not load mediaLib accelerator wrapper classes. Continuing in pure Java mode." from being written to the standard error stream the first time one did something involving reading an X-ray diffraction image (e.g. loading an image into the Image Viewer view).

Aaproc 0.1.1 has been released. This update ensures that a log of the autoPROC process program's output to the standard output stream is captured in a log file.

• Fixed an issue where the log file of the autoPROC process program's output to its standard output stream was not being saved. When invoked in a terminal, process creates a log file (e.g. process.20140910_131055.log) of what it writes to its standard output stream. But when invoked as a subprocess of the aap program, it does not create this log file. Now aap creates this log file for process to achieve the expected behavior.

Aaproc 0.1.0 has been released. This is the first release made available to all users.

Aaproc (Auto Auto-Process) is a suite of programs for automatically auto-processing X-ray crystallography datasets. It includes a program, aap, for finding datasets on the file system and auto-processing them using external programs (e.g. autoPROC). The aap program writes a summary of dataset processing to a file named aap-result.html in the current working directory.

Aaproc is installed on the processing server (i.e. plankton). If we typically want to auto-process every dataset as it is collected at IMCA-CAT, Aaproc might be useful to us. An easy way to use it is to collect all datasets to their own directories somewhere below a particular directory tree. Let's say we collect all datasets under /depot17id/luke/20140725. Now simply do the following at a command shell:

$ cd /depot17id/luke/20140725 $ aap

The aap program will run indefinitely, detecting datasets as they are collected, will attempt to auto-process the datasets using autoPROC, and will write a processing summary to /depot17id/luke/20140725/aap-result.html as it goes. This will work equally well for data collected in manual or auto mode.

Documentation is available in the form of Unix manual pages. We can view the aap program manual by typing the following at a shell:

$ man aap

Similarly, we can view the aaproc.conf configuration file manual by typing the following at a shell:

$ man aaproc.conf

JDirector 2.2.1_imca35 has been released. This update fixes a bug in auto-mode abort handling and improves the speed and quality of auto-mode diffraction centering.

• Fixed a bug in auto-mode where pressing the Abort button at the bottom right of the JDirector window would not abort the currently running auto-mode jobs.
• Reclassified some auto-mode diffraction center log errors as warnings so that an error dialog is not displayed. The most common case where this is helpful is when an auto-mode diffraction center fails because the minimum score threshold is not achieved. Instead of an error dialog popping up, the error will just appear in the sample's status field.
• Reduced width of second diffraction center raster from three cells to one cell. This will avoid the possibility of the second raster walking away from the optimal Z center found by the first raster, and it will speed up diffraction centering on average because it will now rasterize just one column of cells as opposed to the usual three.

on 17 July we noticed that the detector distance is refining 20mm further than the distance set in the image header. There was a control system problem on 16 July that likely caused this problem.

This has been resolved and the correct distance should now be written to the image header.

If you have any questions or concerns about this, please contact the staff.

In the interest of improving communication between support staff and users, we have a new e-mail address that will go to all the IMCA-CAT support staff.

Please use ONE of the following addresses:

support at imca.aps.anl.gov

or...

imca-support at anl.gov

JDirector 2.2.1_imca31 has been released. This update fixes a bug in auto mode diffraction centering and improves auto mode diffraction centering.

• Fixed a bug in auto mode diffraction centering where it would abort after running for exactly 10 minutes even if it had already finished diffraction centering and was just finishing synchronizing the XYZ stage and Phi axis positions.
• For auto mode diffraction centering, a loop-find will now always be executed even if the "use stored center" option is checked.
• For auto mode diffraction centering, reduce the maximum raster size from 50x50 cells to a smaller staff-configured size. This aims to avoid really big rasters that take a long time to scan.

JDirector 2.2.1_imca30.1 has been released. This update fixes a bug in the image viewer.

• Fixed a bug in the image viewer that could lead to excessive CPU utilization and a freeze when inverting the color of an image multiple times from the Contrast Adjustment tool.

JDirector 2.2.1_imca29 has been released. This update adds support for assigning a username to a puck.

• Added support for assigning a username to a puck and for a corresponding '%u' substitution character expansion in scan template paths and manual diffraction centering paths. (This is useful for staff for mail-in data collection.)