Difference between revisions of "2cbf"

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(improve example)
Line 5: Line 5:
 
This converts all .img files in ../images to miniCBF files with the extension .img.cbf in the current directory.
 
This converts all .img files in ../images to miniCBF files with the extension .img.cbf in the current directory.
  
For 2cbf to work with the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#LIB= LIB=] option, it is mandatory to have a filename like test_123456.xy, i.e. with a 6-digit number and a 2-letter extension. If you want to use LIB= and your filenames do not follow this pattern, just symlink them, and construct the symlinks accordingly: e.g.
+
To have control over the number of digits encoding the frame number, one can use bash's printf command. Example:
 
<pre>
 
<pre>
 
#!/bin/bash
 
#!/bin/bash
# purpose: create symlinks for xds_par
 
# usage: mklinks
 
 
 
for j in $(seq 1 120); do
 
for j in $(seq 1 120); do
   ln -sfn Data_02_$(printf "%04d" "$j").sfrm Data_02_$(printf "%06d" "$j").sf
+
   echo Data_02_$(printf "%04d" "$j").sfrm  
 
done
 
done
 
echo ready
 
 
</pre>
 
</pre>
  
If you don't do this, you'll get an error message like
+
To convert frames stored in Dectris-format .h5 files, one should replace "master" with a 6-digit framenumber, and use the [https://xds.mr.mpg.de/html_doc/xds_parameters.html#LIB= LIB=] keyword:
<pre>
+
  echo collect_01_000001.h5 collect_1.cbf LIB=/usr/local/lib64/dectris-neggia.so | 2cbf
forrtl: severe (59): list-directed I/O syntax error, unit -5, file Internal List-Directed Read
 
Image              PC                Routine            Line        Source           
 
2cbf              000000000041DCDC  Unknown              Unknown  Unknown
 
2cbf              00000000004476AA  Unknown              Unknown  Unknown
 
2cbf              0000000000445C2B  Unknown              Unknown Unknown
 
2cbf              00000000004059B8  getfrm_                  1713  MAIN_2CBF.f90
 
2cbf              0000000000404C6A  MAIN__                    58  MAIN_2CBF.f90
 
2cbf              0000000000402ADE  Unknown              Unknown  Unknown
 
libc-2.17.so       00007FB47339BB35  __libc_start_main    Unknown  Unknown
 
2cbf               00000000004029E9  Unknown              Unknown  Unknown
 
</pre>
 

Revision as of 19:08, 21 March 2021

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