img2nx

Synopsis

Moves data from individual image files to a singel image stack in a NeXus file.

img2nx [OPTIONS] [DETECTOR FILES]

Description

img2nx stores the data stored in an individual image files to an image stack within a NeXus file. The program assues that the group where the data should be stored exists (you have to create a basic NeXus-file first). However, concerning the data field two modes of operation can be distinguished

• the datafield in the target path exists: in this case the program checks if the first image the user wants to append fits into the stack and aborts if this is not the case
• the data-field does not exist: in this case a new field will be created which can store the data from the first image in the stack provided by the user.

The detector files can be provided either by individually listing them as command line arguments to img2nx or by using the special syntax based on C format strings. Consider the following series of image files

$ls
img_0001.tif
img_0002.tif
img_0003.tif
.
.
.
img_1000.tif

These files could be addressed using a syntax like this img_%04i.tif:1:1000.

img2nx provides extensive logging information which, in case of an unexpected program termination, can be used to continue a run to finish the original job.

Options

-h, --help	show a brief overview on program useage and options
-t, --target	the NeXus path to the field where the data should be stored
-d, --deflate	if set to a value between 1 and 9 deflate compression will be used on a newly created dataset. Obviously this only works if the dataset is created by img2nx.
-d, --log-file	a file where all the log messages from the program will be stored. In addition to this output will also be written to standard error
-q, --quiet	no output to standard error. This is particularly usefull when img2nx is used along with the -l option where the logging output is anyhow written to a file on disk.

Examples

In the first case we have a bunch of TIF images which should be stored in the stack

$ls
img_0001.tif
img_0002.tif
img_0003.tif
.
.
.
img_1000.tif

To store them in the detector group of a NeXus file we can use

$img2nx -tdata.nx://:NXentry/:NXinstrument/:NXdetector/data img_%04i.tif:1:1000

If the field data in the detector group of the file already exists the data from the image files will be appended, if the field does not exist it will be created according to the data stored in the first image.

If we want to do the same job for instance for a batch queue we rather want no logging output on the command line but rather store this information into a file. This can be achieved with

$TARGET_PATH=data.nx://:NXentry/:NXinstrument/:NXdetector/data
$img2nx -q -lsample.log -t$TARGET_PATH img_%04i.tif:1:1000

The -q option stops logging information to be propagated to the standard error channel of the console while the -l option determines the file where the logging information shall be stored.

Return value

The program returns 0 in the case of success, 1 otherwise.