Scripts: compress.py

#
# Copy a series of map files to a single Chimera map (HDF5) file.
# Use compression and optionally crop and threshold and change the value type
# for each map.
#
#   runscript compress.py *.mrc out.cmap 14,213,0,511,539,144 150 int16 1.5,1.5,2.4
#
# The arguments are input map files, output map name, subregion bounds
# (xmin,ymin,zmin,xmax,ymax,zmax), threshold, new value type, and grid spacing.
# Arguments subregion, threshold, new value type, grid spacing can be
# specified as the string none or omitted.
#
# This was written to compress map time series for Bessel beam cell motion
# data from Lillian Fritz-Laylin.
#
def compress_maps(input_files, output_file, subregion = None, threshold = None,
                  value_type = None, grid_spacing = None):
  for i,p in enumerate(input_files):
    run('open %s' % p)
    m = 0         # Model id number
    if not subregion is None:
      run('vop scale #%d subregion %s' % (m, subregion))
      m += 1
    if not threshold is None:
      run('vop threshold #%d min %s' % (m, threshold))
      m += 1
    if not value_type is None:
      run('vop scale #%d valueType %s' % (m, value_type))
      m += 1
    if not grid_spacing is None:
      run('volume #%d voxelSize %s' % (m, grid_spacing))
    mp = chimera.openModels.list(id = m)[0]
    mp.data.name = '%04d' % i
    run('volume #%d save %s saveFormat cmap compress true append true'
      % (m, output_file))
    run('close all')

def run(command):
  from chimera import replyobj, runCommand
  replyobj.status(command)
  replyobj.info(command + '\n')
  runCommand(command)

  
if not 'arguments' in locals() or len(arguments) < 2 or len(arguments) > 6:
  import Commands
  raise Commands.CommandError('Require 2 to 6 arguments: runscript compress.py '
                              '<input-files> <output-file> <subregion> '
                              '<threshold> <value-type> <grid-spacing>')

import glob
input_files = glob.glob(arguments[0])
input_files.sort()
args = tuple((None if a == 'none' else a) for a in arguments[1:])
compress_maps(input_files, *args)