Shape Overlay Based Detector Geometry Calibration

This repository provides a tool to calibrate AGIPD detector geometry information

The tool can be seen as an alternative to the calibration mode of CrysFEL's hdfsee. The calibration can either be based on a starting geometry that needs to be refined or a completely new geometry. In the latter case the initial conditions for the geometry are defined so that all modules are 29px apart from each other.

The geometry calibration is supported by two modes of graphical user interfaces. A Qt-based and a jupyter notebook based interface.

Using the Qt-Gui

It is recommended to use this Gui application through the pre-installed path on the on- and offline cluster.

source /gpfs/exfel/sw/software/modules
module load xfel

The following optional arguments can be set via the command line:

Argument		Description
-h, --help
-nb, --notebook		Do not start gui, create a notebook
-no_kernel		Do not try to attempt creating a xfel notebook kernel
-nb_folder	nb_folder	Set default directory to save notebooks
-nb_file	nb_file	Set file name of the notbook
-r, --run	run_dir	The path name to a exp folder
-g, --geometry	geomfile	Path to geometry file
-c, --clen	clen	Detector distance [m]
-e, --energy	energy	Photon energy [ev]
-l, --level	min max	Display range for plotting

If no run directory, using -r/--run, option has been preselected a directory can to be set by clicking the Run-dir button. Train id's can be selected after a run has been selected. The user can either choose to display images by pulses or if the signal is to week/noisy by applying a Maximum or Mean across the entire train to all images. To do so the user can just select the Max or Mean button instead of the default Sel #. After an image number / function has been selected the image can be assembled using the Assemble button. Optionally a pre-defined geometry file can be loaded using the Load button.

After the image is displayed quadrants can be selected by clicking on them. They can be moved by using the Ctrl+arrow-up/down/left/right key combination. Circles that can help to align quadrants are added by the Draw Helper Objects button. The radii of the circles an be adjusted using the radius spin box in the top left.

Once the quadrants have been positioned a geometry file can be saved by using the Save button.

Calibration Using Jupyter

The -nb, --notebook flag creates a jupyter notebook uses the home direcory.

Setup

Using Maxwell Cluster (recommended)

It is recommended to use the already setup application available in xfel's anaconda3 distirbution. All packages should be available via the xfel module. At the moment the module has to be activated by

$: module load exfel exfel_anaconda3
$: geoAssembler

Using pip

The software is can be installed by pip:

$: pip install .
$: geoAssembler

Dependencies

If the user doesn't want or cannot use the xfel module and wants to install the tool the following python packages should be available:

• numpy
• cfelpyutils
• pyqtgraph
• matplotlib
• ipywidgets
• pyqt5
• pyFAI

Testing:

Testing the implementation is done py pytest. To apply the test suite run

$: pytest -v geoAssembler/tests