2cbf

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Revision as of 14:35, 22 April 2021 by Kay (talk | contribs) (convert many frames)
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2cbf is part of the XDS distribution. It converts any image file format that is known to XDS to a miniCBF file. This program is also used by XDSGUI.

Single-line example (bash shell):

for i in ../images/*img ; do echo $i; echo $i `basename $i`.cbf | 2cbf ; done

This converts all .img files in ../images to miniCBF files with the extension .img.cbf in the current directory.

To have control over the number of digits encoding the frame number, one can use bash's printf command. Example:

#!/bin/bash
for j in $(seq 1 120); do
  echo Data_02_$(printf "%04d" "$j").sfrm 
done

To convert frames stored in Dectris-format .h5 files, one should replace "master" with a 6-digit framenumber, and use the LIB= keyword:

echo collect_01_000001.h5 collect_1.cbf LIB=/usr/local/lib64/dectris-neggia.so | 2cbf

It should work without LIB=, but then H5ToXds is required.

To convert a full data set, use e.g.:

#!/bin/bash
for j in $(seq 1 100); do
  echo x1_1_$(printf "%06d" "$j").h5 x1_1_$(printf "%04d" "$j").cbf LIB=/usr/local/bin/linux_bin/dectris-neggia.so | 2cbf
done

or just use GlobalPhasing's hdf2mini-cbf :

hdf2mini-cbf x1_1_master.h5 -linkrange 1 100

which seems to convert batches of 100 frames - don't know how to restrict it to convert only frames 1 to 100. The advantage of hdf2mini-cbf is that it writes a proper mini-CBF header which is suitable for MOSFLM or DIALS.