Maxwell : hdfview

HDFView is a visual tool for browsing and editing HDF4 and HDF5 files. Using HDFView, you can

• view a file hierarchy in a tree structure
• create new files, add or delete groups and datasets
• view and modify the content of a dataset
• add, delete and modify attributes

Using  HDFview

Either invoke hdfview directly or expand the PATH using the xray module. The xray module also sets the environment for CCP4 and other MX-related packages which might or might not be desirable.

[@max-wgs001] module load xray
[@max-wgs001] which hdfview # version 2.x of hdview
/opt/xray/bin/hdfview 
[@max-wgs001] which hdfview3 # version 3.0 of hdview; at this date still in beta. 
/opt/xray/bin/hdfview3
 

Note: In case of trouble with data from Dectris Eiger

Dectris Eiger detectors are creating HDF5 data files which are compressed using lz4 compression scheme. Hence, this data can only be read with addinional external filter plugins installed and a system variable named HDF5_PLUGIN_PATH pointing to its location set. lz4 filter plugin is installed on maxwell servers, but depending on the users shell, it may happen that this variable is not defined by default. Then the user has to set/define it by him/herself (for the recommended bash shell it should be defined by default, for (t)csh this is not the case).
In case you encounter a problem reading such files, please check whether the variable is set and define it if needed before calling e.g. hdfview (same holds when using python/h5py).

## to figure out your shell
[@max-<snip>]$ echo $SHELL
/bin/tcsh
## to check if environment variable is defined (returns nothing if undefined)
[@max-<snip>]$ printenv | grep -i hdf5_p

## set/define the variable (for (t)csh)
[@max-<snip>]$ setenv HDF5_PLUGIN_PATH  "/usr/lib64/hdf5/plugins"

## or for zsh
export HDF5_PLUGIN_PATH=/usr/lib64/hdf5/plugins

## (opt.) check again
[@max-<snip>]$ printenv | grep -i hdf5_p
HDF5_PLUGIN_PATH=/usr/lib64/hdf5/plugins

The procedure given above should work for both versions made available via "module load xray", i.e. the then availble calls hdfview or hdfview3.

Alternatively, you may change to bash shell by typing 'bash' in the current terminal window or (maybe better) to ask your system administrators to set bash shell as default for your account.