[ccp4bb] image file extensions
Dear all, I'm trying to create some space on our server and want to compress all x-ray data files. I'm wondering what extensions I should search for. mccd and img come to mind easily. What other extensions are commonly used? Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] image file extensions
.osc 2011/2/9 Andreas Förster docandr...@gmail.com: Dear all, I'm trying to create some space on our server and want to compress all x-ray data files. I'm wondering what extensions I should search for. mccd and img come to mind easily. What other extensions are commonly used? Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] image file extensions
.ipf if you have files from (old) image plate detectors. clement Dear all, I'm trying to create some space on our server and want to compress all x-ray data files. I'm wondering what extensions I should search for. mccd and img come to mind easily. What other extensions are commonly used? Thanks. Andreas -- Andreas F#65533;ster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk Clement Angkawidjaja, Ph.D Specially appointed assistant professor Laboratory of Molecular Biotechnology (Kanaya Lab) Division of Advanced Science and Biotechnology Graduate School of Engineering, Osaka University 2-1 Yamadaoka, Suita-shi, Osaka 565-0871 Japan
[ccp4bb] image file extensions
Harry Powell had the most comprehensive answer, giving me the extensions that are used in mosflm: .img .mar* (i.e. .mar1600, .mar2300, etc) .mccd .osc .SFRM .sfrm .image .ipf .cbf In addition, finding files larger than a certain cutoff might do the trick too - especially if the objective is economizing disk space. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] image file extensions
Dear Andreas,
I had the same problem frequently and wrote a little python-script for
compressing our images on our server. It might help you and you can
easily modify the extension for which the script should search for...
Best Regards,
Georg
-- code starts below
#!/usr/bin/python
#
# script to compress all xray images (as specified in variables) downstream
# of a specfied directory using as many cores as available on the system
#
# requirement: python = 2.4, bzip2
# tested with systems: MacOS X (10.5.7), ubuntu 8.04.2 (LTS)
#
# USAGE AT YOUR OWN RISK
# georg.zoc...@gmx.de
#
#
# version 0.1
#
import os, sys, subprocess
# variables
# You can modify the data types here
imagetypes = [.ccd, .img, .cbf, mar2300]
# If you only want to get a file list without compressing anything
switch to 'on'
debug = 'off'
#
#
# do not modify anything below this line unless you know what you
are doing
images = []
usage =
\t usage: \t image_compressor directory \n
\t\t\t All image files downstream the specified directory will
'bzip2'-ed on several cores
\t\t\t USAGE AT YOUR OWN RISK\n
### check input
try :
sys.argv[1]
except:
print
print \t Please specify a directory to dive into...
print usage
sys.exit(0)
check = os.path.exists(sys.argv[1])
if check == True:
input = os.path.abspath(sys.argv[1])
if check == False:
print
print \t Specified directory not found...
print usage
sys.exit(0)
### functions
def __get_images():
Function to get all xray image files downstream of a specified
directory
return value is a list...
print \n\t generating file list
for dir, dirs, files in os.walk(sys.argv[1]):
for f in files:
if os.path.splitext(f)[1] in imagetypes :
images.append((os.path.join(dir, f)))
print \n\t\t\t...done
return images
def __get_ncpu():
Function to get the number of CPU-Cores on POSIX systems
try:
ncpu = int(os.sysconf('SC_NPROCESSORS_ONLN'))
if ncpu 0:
return ncpu
except (AttributeError,ValueError):
#pass
print \n\t System not POSIX compatible. Sys.exit...\n
sys.exit(0)
def run_bzip(ncpu, list):
dic = {}
j=0
list.sort()
while j = len(list):
for i in range(ncpu):
if j len(list):
break
if j = len(list):
print \t compressing image:, os.path.basename(list[j-1])
try:
if debug == off:
dic[i] = subprocess.Popen([rbzip2,-z9,
list[j]])
#for testing
if debug == on:
dic[i] = subprocess.Popen([rls,-l, list[j]])
except:
print
j+=1
dic[i].wait()
def main():
run_bzip(__get_ncpu(), __get_images())
### end functions
if __name__ =='__main__':
main()
code end above
Am 09.02.11 15:49, schrieb Andreas Förster:
Dear all,
I'm trying to create some space on our server and want to compress all
x-ray data files. I'm wondering what extensions I should search for.
mccd and img come to mind easily. What other extensions are commonly
used?
Thanks.
Andreas
--
Universität Tübingen
Interfakultäres Institut für Biochemie
Dr. Georg Zocher
Hoppe-Seyler-Str. 4
72076 Tuebingen
Germany
Fon: +49(0)-7071-2973374
Mail: georg.zoc...@uni-tuebingen.de
http://www.ifib.uni-tuebingen.de
Re: [ccp4bb] image file extensions
On 02/09/11 09:49, Andreas Förster wrote: Dear all, I'm trying to create some space on our server and want to compress all x-ray data files. I'm wondering what extensions I should search for. mccd and img come to mind easily. What other extensions are commonly used? Thanks. Andreas /bin/ls -lR | sort -nk5 | tail -40 will list the largest files in the directory tree. Those are probably the ones you need to compress. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] image file extensions
find . -name '*.osc' -or -name '*.img' -type f -size +3000 -print -exec
bzip2 '{}' \;
is a personal favorite, along those lines, with ample opportunities for
customization. (If the above command line wraps, it's all supposed to
be on one line)
Phil Jeffrey
Princeton
On 2/9/11 2:46 PM, David Schuller wrote:
/bin/ls -lR | sort -nk5 | tail -40
will list the largest files in the directory tree. Those are probably
the ones you need to compress.
