Batch script through Igor AFM data

gwiddion-batch.py

import glob, sys
try:
  import gwy
except:
  print "You need to install Gwyddion first"
  sys.exit(0)

# Script adapted from the Gwyddion documentation
# http://gwyddion.net/documentation/user-guide-en/pygwy.html

# Set up parameters for the 'align_rows' function.
settings = gwy.gwy_app_settings_get()
settings['/module/linematch/direction'] = int(gwy.ORIENTATION_HORIZONTAL)
settings['/module/linematch/do_extract'] = False
settings['/module/linematch/do_plot'] = False
settings['/module/linematch/method'] = 2

print 'Filename\tChannel\tRa\tRms\tSkewness\tKurtosis'

# expected PFM channels (we'll append the "Retrace" string later)
channels = [ 'Height', 'DACAmplitude', 'DACPhase', 'DACQFactor',
            'DACFrequency']

# Go through files matching the Igor patterns
for filename in glob.glob('*.ibw'):
    container = gwy.gwy_file_load(filename, gwy.RUN_NONINTERACTIVE)
    gwy.gwy_app_data_browser_add(container)

    # Find channel(s) called 'Height', expecting to find one.
    for channel in channels:
      ids = gwy.gwy_app_data_browser_find_data_by_title(container, channel + 'Retrace')
      if len(ids) == 1:
        i = ids[0]
        # Select the channel and run some functions.
        gwy.gwy_app_data_browser_select_data_field(container, i)
        gwy.gwy_process_func_run('align_rows', container, gwy.RUN_IMMEDIATE)
        gwy.gwy_process_func_run('flatten_base', container, gwy.RUN_IMMEDIATE)
        # Extract simple statistics and print them.
        data_field = container[gwy.gwy_app_get_data_key_for_id(i)]
        avg, ra, rms, skew, kurtosis = data_field.get_stats()
        print '%s\t%s\t%g\t%g\t%g\t%g' % (filename, channel, ra, rms, skew, kurtosis)
        # save a PNG
        slices = filename[:-4].split('_')
        if len(slices) < 3: continue

        # we have a good filename, so save the PNG
        pngFile = '%s_%s_%s_%s.png' % (slices[0], slices[1], channel, slices[2])
        gwy.gwy_file_save(container, pngFile, gwy.RUN_NONINTERACTIVE)
      else:
        sys.stderr.write('Expected one %s channel in %s but found %u.\n'
                         % (channel, filename, len(ids)))

    gwy.gwy_app_data_browser_remove(container)