2cbf: Difference between revisions

2cbf (view source)

Revision as of 15:35, 22 April 2021

301 bytes removed , 22 April 2021

convert many frames

Kay

Bureaucrats

2,684

edits

@@ Line 1: / Line 1: @@
 [http://xds.mpimf-heidelberg.mpg.de/html_doc/2cbf_program.html 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]].
-Example (bash shell):
+Single-line example (bash shell):
-  for i in ../img/*img ; do echo $i; echo $i $i.cbf | 2cbf ; done
+  for i in ../images/*img ; do echo $i; echo $i `basename $i`.cbf | 2cbf ; done
-This converts all .img files in ../img to miniCBF files with the extension .img.cbf .
+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>
 #!/bin/bash
-# purpose: create symlinks for xds_par
-# usage: mklinks
 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
+</pre>
-echo ready
+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
+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
-If you don't do this, you'll get an error message like
+or just use GlobalPhasing's hdf2mini-cbf :
-<pre>
+  hdf2mini-cbf x1_1_master.h5 -linkrange 1 100
-forrtl: severe (59): list-directed I/O syntax error, unit -5, file Internal List-Directed Read
+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.
-Image              PC                Routine            Line        Source
-cbf               000000000041DCDC  Unknown               Unknown  Unknown
-cbf               00000000004476AA  Unknown               Unknown  Unknown
-cbf               0000000000445C2B  Unknown               Unknown  Unknown
-cbf               00000000004059B8  getfrm_                  1713  MAIN_2CBF.f90
-cbf               0000000000404C6A  MAIN__                     58  MAIN_2CBF.f90
-cbf               0000000000402ADE  Unknown               Unknown  Unknown
-libc-2.17.so       00007FB47339BB35  __libc_start_main     Unknown  Unknown
-cbf               00000000004029E9  Unknown               Unknown  Unknown
-</pre>