Remote data services

Archiving and retrieving data

Archiving data

The raw data (projection images, log files) from your beamtime will be archived to the PSI Petabyte tape archive by your local contact according to the PSI data policy. If you also want to archive reconstructed data, please get in contact with your local contact to discuss the available options and workflows (which are still under development).

Retrieving data from the archive

Datasets from the archive can be retrieved by any user with a valid external PSI account that has access to the corresponding p-group.

There are several methods to retrieve the data. The easiest to use is the following procedure (see also the following screen shots):

1. Log in to discovery.psi.ch with your external PSI account
2. Accept the updated terms, if necessary
3. Locate the profile badge at the top right corner of the page, click it and select "Datasets"
4. Now you should be presented a list of datasets you have access to. Use the filter options on the left side to narrow down the list. Note that the text search does not work very well...
5. Select the "Retrievable" filter above the list of datasets. Now only those data sets are displayed which can be retrieved from the archive.
6. Select all of the datasets you want to retrieve by checking the corresponding selection box.
7. Push the "Retrieve" link at the top right of the dataset list.
8. In the pop up dialog "Retrieve to", select the option "PSI-Ra". This will directly transfer your datasets into the "retrieved" folder inside your p-group directory (e.g.: /das/work/p12/p12345/retrieve).
9. You will be notified by email once the transfer is complete.

Running reconstructions on Ra

The procedure to reconstruct "standard" TOMCAT tomography data on Ra is essentially identical to running the reconstructions at the beamline during your experimental campaign. Follow these steps and instructions to get started.

Using the Fiji Reconstruction Manager

1. Open the Fiji software: From the start menu (the Egyptian eye symbol in the lower left corner of the screen) select TOMCAT > Fiji (TOMCAT)
2. In Fiji, open the Reco manager plugin: Plugins > TOMCAT > Reco Manager (latest, etc)
3. Click "Select a Dataset" and navigate to the location of the raw data (usually in the read-only eAccount, see above for details on the file locations for your data).
4. Proceed with the reconstruction just like you did when using the same interface at the beamline.
5. The results of the reconstruction will be automatically saved in the pGroup directory associated with the eAccount to which the raw data belongs.

Checking the status of the cluster queue

The cluster job scheduling system used on Ra is SLURM. The easiest way to check the status of the cluster queues is by using the Sview program. Launch the program by selecting the sview entry in the Ra start menu in the lower left corner:

The Sview program will list all running jobs in all queues. Through the menu, you can filter this list to only show a particular set of jobs, for example, just those that were launched by yourself. Right clicking on a job opens a context menu from which you are able to pause or cancel a job, etc.

As an alternative to the Sview GUI, you can use the following commands in a terminal to monitor the queue and manipulate individual jobs:

See the currently scheduled, running, and possibly stuck jobs in the queue:

This gives you the full list of all currently running and scheduled jobs by all users. To restrict the list to your own jobs, specify the user argument (-u). Additionally, you can use the watch command to automatically update the display every few seconds:

Delete a job from the queue:

where <Job-ID> is the number shown when calling the squeue command. For example:

Note that depending on how many users are using the cluster, it can happen that your reconstruction jobs are stuck in the queue for some time before they are being executed. Remember that this is a shared resource.

Common reconstruction problems and some solutions

Fiji does not display images anymore

When working on the Ra cluster, from time to time it happens that Fiji is not displaying any images anymore, but instead presents the user with a gray window where the image should be. In this case, please try to restart Fiji. In very rare cases, it might also be necessary to completely log out of your Ra session (using the "Logout..." command from the main desktop menu in the lower left corner of the screen) and to reconnect to it.

Wrong center of rotation

For most data sets, the reconstruction software should automatically detect the appropriate location of the rotation center for the reconstruction. However, occasionally this automatic determination fails, and phase reconstructions are particularly prone to this problem, but also data sets with an inherently low image contrast.

A wrong value for the rotation center has usually a quite obvious effect on the reconstructed image in that is produces "half-moon" or "C"-shaped features, pointing either to the left or to the right of the image throughout the whole image plane, as shown in the image below.

These artefacts can be fixed by manually adjusting the value used for the rotation center. The direction of the half-circle features indicates whether the center needs to be made higher or lower, as shown in the graphic below. The required change in the center value with respect to the current value is equal to the radius of the half-circle feature detected in the image.

Setting the minimun and maximum intensity values for the reconstruction

The reconstructed images diplayed by the reconstruction manager are 32-bit floating point numbers. These are almost always converted to 8 or 16 bit integer value tif files for the final reconstructed data sets. However, the conversion from floating point to integer numbers needs to be explicitly specified. That is, we need to determine which floating point number corresponds to a value of 0 in the final data sets (lowest intensity value or lower histogram edge), and which float corresponds to a value of 255 or 65535 for 8-bit and 16-bit data, respectively (highest intensity value or upper histogram edge). Running a histogram command on the reconstructed slice (Ctrl-h in Fiji) can help to determine a sensible set of values. Make sure you test these values on a few different slices at different heights through the sample to make sure the values are valid for the whole 3D data set.

Python Error when reconstructing: "RuntimeError: Bad magic number in .pyc file"

The cause for this error is usually that a local conda installation in your account is interfering with the python installation of the pipleline. Make sure that any locally installed conda instances DO NOT activate themselves automatically at login, but rather activate them only as needed. Run the reconstruction pipeline from a terminal in which the local conda environment has not been activated.

"ImportError: No module named h5py" when running reconstructions via the script

The h5py library cannot be found, most likely because the TOMCAT python environment has not yet been activated in the terminal where you are running the reconstruction script. Make sure to activate the TOMCAT conda environment prior to using the reconstruction script (see below: https://www.psi.ch/de/sls/tomcat/computing-infrastructure#configuring-python).