How-browse-dowloaded-Nexus-files | WikiSoleil | Acces-experimental-data |
Downloadfor other NeXus tools and utilities, see : http://www.nexusformat.org/
Usage
$ nxextractor
INFO app:Found default configuration file: /usr/Local/configFiles/GD/RecordingConfigurations/common/nxextract.conf The line show us the tool has found the file 'nxextract.conf'. This file contains configuration parameters of the tool and should be edited by power users only, it content is explained in a dedicated page.
Optionstemplatenxextractor is invoked using a template which describe the expected extraction/output. A output consist of one or several ASCII or binary files.
There are two ways of choosing a template:
The second method uses the configuration file (nxextract.conf) to find the template trough a set of directory paths. If the template is not found by this method, you should use the first.
listTo retreive the list of available templates (through the configuration file nxextract.conf), use the --list option alone, like in this example:
$ nxextractor --list
INFO app:Found default configuration file: /usr/Local/configFiles/GD/RecordingConfigurations/common/nxextract.conf scan_1D_images_bmp_raw scan The --list option has returned two names: scan_1D_images_bmp_raw and scan. On this server one can use the short way to invoke these templates. DefineThis option allow the declaration of a symbol and a associated value. This symbol value is used by the template. Thus, its usage depends of the template.
By convention, the symbol dir is used in all the templates: it define the output directory path: $nxextractor -t my_template -D dir=/output/path ...
NOTE: Do not forget the space between --Define (or -D) and the name of the symbol ! However, the usage of this option and the dir symbol is not mandatory. This is the case (at SOLEIL) if the configuration file nxextract.conf contains a set of rules defining the right output path into the storage facility according to the location of the input nexus files. configurationAllow the user to manually provide the full path of a configuration file to use:
$nxextractor -c /path/to/my/configuration/file ...
silentTurn-off thelog messages (warning, info) mode & ownershipThese options are available only when running nxextractor on linux systems under 'root' account. It allows to automatically sets the rights and ownership of extracted files.
An example: How to extract data from NeXus files stored a project directoryThis example are working on every SOLEIL beamlines. srv2$ su - 'my_project'
Lets suppose the data were acquired using the ScanServer, so the template to use is 'scan'. $nxextractor -t scan /nfs/ruche-{beamline}/{beamline}-users/my_project/{NeXus files directory}/
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How-browse-dowloaded-Nexus-files | WikiSoleil | Acces-experimental-data |