Content
Setup environment
ssh psana
cd <your-directory>
sit_setup
Save image in TIFF file
Configuration file
There are two versions of image saving modules ImgAlgos.ImgSaveInFile
(C++) and pyimgalgos.image_save_in_file (Python),
which create slightly different TIFF files.
Configuration file for Python module pyimgalgos.image_save_in_file
Content of the file psana-mecb3114-r0017-tiff.cfg
[psana] files = exp=mecb3114:run=17 #events = 5 #skip-events = 0 modules = ImgAlgos.AndorImageProducer \ pyimgalgos.image_save_in_file [ImgAlgos.AndorImageProducer] source = DetInfo(MecTargetChamber.0:Andor.1) key_in = key_out = andor_img outtype = asdata print_bits = 1 [pyimgalgos.image_save_in_file] source = DetInfo(MecTargetChamber.0:Andor.1) key_in = andor_img #ofname = andor.1.txt ofname = andor.1.tiff print_bits = 5
Configuration file for C++ module ImgAlgos.ImgSaveInFile
Module ImgAlgos.ImgSaveInFile can be added to the configuration file as:
modules = ImgAlgos.AndorImageProducer \ ... ImgAlgos.ImgSaveInFile ... [ImgAlgos.ImgSaveInFile] source = DetInfo(MecTargetChamber.0:Andor.1) key = andor_img saveAll = yes #ftype = tiff ftype = txt fname = andor print_bits = 3
Get TIFF files from data
Run psana with configuration file and optional experiment/run number structure exp=mecb3114:run=17
by the command:
psana -c psana-mecb3114-r0017-tiff.cfg exp=mecb3114:run=17
Tiff files will be produced with common prefix name andor.1
(which may contain path to the directory as well):
andor.1-mecb3114-r0017-ev000001.tiff andor.1-mecb3114-r0017-ev000002.tiff andor.1-mecb3114-r0017-ev000003.tiff
Andor calibrated image
Calibration constants
Dark run calibration can be done with procedure calibman (since ana-0.13.18). Files can be deployed in expected place, for example
/reg/d/psdm/SXR/sxrg3715/calib/Andor::CalibV1/SxrEndstation.0:Andor.2/pedestals/0-end.data
for types pedestals pixel_rms pixel_status
.
type common_mode
can be copied with parameters for mode 2 (see : Common mode correction algorithms ), for example
2 20 20 512 0 0 0 0 0 0 0 0 0 0 0 0
Get calibrated image
In psana Andor image can be retrieved from raw data to ndarray
using module ImgAlgos.AndorImageProducer.
Then it can be calibrated by the module
ImgAlgos.NDArrCalib
and further processed in python or saved as in the example.
Example of the configuration file psana-sxrg3715-r0046-andor-image.cfg
:
[psana] # Default calibration directory: # calib-dir = /reg/d/psdm/sxr/sxrg3715/calib calib-dir = /reg/neh/home1/dubrovin/LCLS/PSANA-V01/test-sxrg3715/calib files = exp=sxrg3715:run=46 #events = 5 #skip-events = 0 modules = ImgAlgos.AndorImageProducer:a2 \ ImgAlgos.NDArrCalib:a2 \ ImgAlgos.ImgSaveInFile:a2 [ImgAlgos.AndorImageProducer:a2] source = DetInfo(SxrEndstation.0:Andor.2) key_in = key_out = andor_img_raw #outtype = asdata outtype = float print_bits = 9 [ImgAlgos.NDArrCalib:a2] source = DetInfo(SxrEndstation.0:Andor.2) key_in = andor_img_raw key_out = andor_img_clb outtype = float do_peds = yes do_cmod = yes print_bits = 15 [ImgAlgos.ImgSaveInFile:a2] source = DetInfo(SxrEndstation.0:Andor.2) key = andor_img_clb saveAll = yes #ftype = tiff ftype = txt fname = andor-2-cm2 print_bits = 3
which can be executed by the command:
psana -c psana-sxrg3715-r0046-andor-image.cfg
Image examples
exp=xrg3715:run=46, SxrEndstation.0:Andor.2
Raw image full-size and zoomed
Image with subtracted pedestals
evaluated using the same run 46
Image with subtracted common mode
2 20 20 512 0 0 0 0 0 0 0 0 0 0 0 0
References
- Psana Module Examples
- Psana Module Catalog
- Calibration Management Tool
- Common mode correction algorithms