TXM user guide: Reconstruction

General information

The TXM reconstruction process requires 3 steps:

1. Pre-processing to create data compatible with the generic reconstruction process
2. Center-finding
3. Final reconstruction

All the required scripts should be located in:

/dls/i13/data/YYYY/mgXXXXX-X/processing/recoTXM

with the year and beamtime ID, respectively.

Load the Hamilton and Python 3.7 modules. All required modules can be loaded with the following command after navigating into the recoTXM directory:

cd /dls/i13/data/YYYY/mgXXXXX-X/processing/recoTXM/
source loadPython

Pre-processing

The pre-processing script

./TXMclusterPreprocessing.sh -scan XXXX

will start the required process on the cluster. The script will perform some required steps (logfile processing, dark & flat correction) and also some registration steps as required. These are defined in 

pythonTXMpreprocessing.py

and should only be changed after consultation with your local contact.

The status of the process can be checked with a:

watch qstat

Center-finding

The center-finding for scan number YYYY is started with

python pythonTXMrecCenter.py -txm -cor XXX YYYY

XXX is the search center and the default range is 10 pixels (plus/minus) with a spacing of 1 pixel. These parameters can be adjusted with the -range and -dx keywords.

The slice can be selected with the -slice keyword and a new sinogram creation can be forced with -redo. An example with all parameters is:

python pythonTXMrecCenter.py -txm -cor 500 -range 10 -dx 1 -slice 505 -redo 1016

Final reconstruction

The final reconstruction is launched with the center of rotation and scan number as parameters:

 ./TXMclusterReco.sh -cor XXX -scan YYYY