old_contents: """
    RUNSCRIPT to rebin raw images of q-calibration series along
    the energy axis.
  
    USAGE
      Set infile names, binning and run
      $ python run_image_preprocess.py 
  
    Copyright (c) 2013, rhambach. 
      This file is part of the TEMareels package and released
      under the MIT-Licence. See LICENCE file for details.
       
  """
  
  # use TEMareels package specified in _set_pkgdir (overrides PYTHONPATH)
  import _set_pkgdir
  import glob;
  import numpy as np
  import scipy.signal as sig
  from TEMareels.tools.img_filter import binning
  from TEMareels.tools import tvips
  import TEMareels.tools.tifffile as tiff
  
  # define infile name and binning along y-direction (E-axis)
  pattern = "/path/to/q_calibration/img%d.tif";
  files   = [pattern%i for i in range(344,345)]
  ybin    = 64;
    
  for filename in files:
  
    image = tvips.load_TVIPS(filename)     # img[iy,ix]
    #image = tiff.imread(filename).astype(np.float64);
    if ~np.allclose(image.shape, (4096,4096)): 
      raise IOError("Unexpected image size in file '%s'"%filename); 
    medimg= sig.medfilt2d(image,kernel_size=3); # filtering 
    binimg= binning(medimg,ybin);          # binning along y
    #binimg = binning(binimg.T,32).T;      # binning along x
  
    outfile = filename.split(".tif")[0]+"_filt_bin%d.tif"%ybin;
    tiff.imsave(outfile,image.astype(np.float32));
  
  
  
  
  
  
  
new_contents: """
    RUNSCRIPT to rebin raw images of q-calibration series along
    the energy axis.
  
    USAGE
      Set infile names, binning and run
      $ python run_image_preprocess.py 
  
    Copyright (c) 2013, rhambach. 
      This file is part of the TEMareels package and released
      under the MIT-Licence. See LICENCE file for details.
       
  """
  
  # use TEMareels package specified in _set_pkgdir (overrides PYTHONPATH)
  import _set_pkgdir
  import glob;
  import numpy as np
  import scipy.signal as sig
  from TEMareels.tools.img_filter import binning
  from TEMareels.tools import tvips
  import TEMareels.tools.tifffile as tiff
  
  # define infile name and binning along y-direction (E-axis)
  pattern = "/path/to/q_calibration/img%d.tif";
  files   = [pattern%i for i in range(344,345)]
  ybin    = 64;
    
  for filename in files:
  
    image = tvips.load_TVIPS(filename)     # img[iy,ix]
    #image = tiff.imread(filename).astype(np.float64);
    if ~np.allclose(image.shape, (4096,4096)): 
      raise IOError("Unexpected image size in file '%s'"%filename); 
    medimg= sig.medfilt2d(image,kernel_size=3); # filtering 
    binimg= binning(medimg,ybin);          # binning along y
    #binimg = binning(binimg.T,32).T;      # binning along x
  
    outfile = filename.split(".tif")[0]+"_filt_bin%d.tif"%ybin;
    tiff.imsave(outfile,binimg.astype(np.float32));
  
  
  
  
  
  
  
subject: Update Qcal_image_preprocess.py