This is a personal unofficial repository of Cheetah. The official Website is http://www.desy.de/~barty/cheetah/, and the repository is https://github.com/antonbarty/cheetah/.
Here, features specific for SACLA are being developed. When matured, they will hopefully be merged to the official distribution.
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saveSACLA option
This is a multi-event HDF5 similar to CXIDB format but more primitive. The biggest difference is that we do not use 3D or 4D arrays to store multiple images. Instead, we make a group tag-XXXXX for each frame.
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SACLA API integration (cheetah-sacla-api2)
This is similar to cheetah-sacla, but reads images from SACLA Data Access User API (Joti et al., 2015, J. Synchrotron Radiat.) instead of a HDF5 file created by DataConvert3/4. It also supports filtering by low-level filter (LLF) and photodiode values (for time-resolved experiments).
cheetah-sacla-api is obsolete, only for backward-compatibility (to access old datasets).
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SACLA online API integration (cheetah-sacla-online)
This is intended for online realtime image filtering. Under development.
The original README follows.
To build cheetah you need cmake (and optionally ccmake).
If you're on psexport you can just do:
$ export PATH=~filipe/cmake/bin:${PATH}
Otherwise just ask your sysadmin to install it.
If your HDF5 is not installed in a standard location set the HDF5_ROOT environment variable to point to it, e.g.:
$ export HDF5_ROOT=${HOME}/local
You also need to have LCLS's ana available somewhere. If you're building at CFEL, LCLS or Uppsala this should already be available.
If not you can try to use the scripts/download_psana.py to download it but you will likely have to do modifications. The best is probably to ask LCLS about getting a portable version of ana.
Now that you have cmake we can start the build:
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Create and go into a build directory:
$ mkdir build $ cd build -
Run ccmake and point it to the base directory
$ ccmake .. -
You will see something like:
ANA_ARCH x86_64-rhel6-gcc44-opt
ANA_RELEASE /opt/psana/g/psdm/portable/sw/releases/ana-current
ANA_SIT_DATA /opt/psana/g/psdm/portable/sw/releases/ana-current/../../../data
BUILD_CHEETAH_ANA_MOD ON
BUILD_CHEETAH_MYANA OFF
BUILD_PSANA ON
CMAKE_BUILD_TYPE
CMAKE_CXX_COMPILER /usr/bin/c++
CMAKE_C_COMPILER /usr/bin/cc
CMAKE_INSTALL_PREFIX /usr/local
HDF5_C_INCLUDE_DIR /opt/include
HDF5_hdf5_LIBRARY_RELEASE /opt/lib64/libhdf5.so
RPATH_ON_INSTALLED_BINS ON
ANA_ARCH: ana architecture to be used
Press [enter] to edit option CMake Version 2.8.10.2
Press [c] to configure
Press [h] for help Press [q] to quit without generating
Press [t] to toggle advanced mode (Currently Off)
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It's possible that you have to specify
ANA_RELEASEmanually. It should point to the ana-current directory, for example on psexport it is/reg/g/psdm/sw/releases/ana-current/ -
You can also specify the
CMAKE_INSTALL_PREFIX. I set mine to~/usr -
Press "c" to configure.
ANA_ARCH x86_64-rhel6-gcc44-opt
ANA_RELEASE /opt/psana/g/psdm/portable/sw/releases/ana-current
ANA_SIT_DATA /opt/psana/g/psdm/portable/sw/releases/ana-current/../../../data
BUILD_CHEETAH_ANA_MOD ON
BUILD_CHEETAH_MYANA OFF
BUILD_PSANA ON
CMAKE_BUILD_TYPE
CMAKE_CXX_COMPILER /usr/bin/c++
CMAKE_C_COMPILER /usr/bin/cc
CMAKE_INSTALL_PREFIX /home/filipe/usr
HDF5_C_INCLUDE_DIR /opt/include
HDF5_hdf5_LIBRARY_RELEASE /opt/lib64/libhdf5.so
RPATH_ON_INSTALLED_BINS ON
ANA_ARCH: ana architecture to be used
Press [enter] to edit option CMake Version 2.8.10.2
Press [c] to configure Press [g] to generate and exit
Press [h] for help Press [q] to quit without generating
Press [t] to toggle advanced mode (Currently Off)
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If everything went well you should see a screen just like the one above and be able to press "g" to generate the Makefiles.
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When you press "g" ccmake will generate the necessary Makefiles and exit.
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Now just run make. This will build things and place the result in the build directory.
$ make -
If you want to install just do.
$ make install
- If you do not care for
LD_LIBRARY_PATHsandRPATHsyou can safely skip this section and everything should work as expected. Otherwise read on!
Cheetah uses as the main backend psana. psana looks up and loads shared libraries at runtime according to the psana.cfg configuration files. If it cannot find the library specified it will exit with an error. The loaded dynamic libraries will themselves load other libraries, for example libcheetah_ana_mod loads libcheetah such that you end up with the following chain:
psana->libcheetah_ana_mod->libcheetah->libhdf5(among others)
This can often cause headaches for the user if the libraries are not in
standard locations (which they usually are not). One solution is to set
the LD_LIBRARY_PATH variable to include the directory of all the
necessary libraries. Another option is to set the RPATH on the programs
and libraries which tells them where to look for libraries. The RPATH
takes precedence over the LD_LIBRARY_PATH and because it's hardwired
is less flexible.
When building cheetah all binaries inside the build directory will
have the RPATH set to the location using during the linking stage. This
means that you should be able to run them directly from the build
directory without the need to set any LD_LIBRARY_PATH.
When you do make install the binaries are moved to their install
directory and the RPATH is can be removed from the binaries. This
means that on the one hand you now can control where they load the libraries from
using the LD_LIBRARY_PATH, but on the other hand they will likely not
find the required libraries if you do not specify any LD_LIBRARY_PATH.
If you wish to remove the RPATH from the installed binaries and you
know what you're doing set RPATH_ON_INSTALLED_BINS to FALSE in
ccmake.