Use 'simple' conversion handler to process 'file'-type JPK conversions.

[hooke.git] / hooke / driver / jpk.py

diff --git a/hooke/driver/jpk.py b/hooke/driver/jpk.py
index bc13761b8c5d2da637b95d9d4a53311ebdb1b5d7..30fabdf0c0817a162687fcc32e3489b5110f249b 100644 (file)
--- a/hooke/driver/jpk.py
+++ b/hooke/driver/jpk.py
@@ -208,40 +208,17 @@ class JPKDriver (Driver):
             # the previous conversion first.
             segment = self._zip_scale_channel(
                 segment, channel, conversion_info['base-calibration-slot'],
-                info, path)
+                path=path, info=info)
         if conversion_info['type'] == 'file':
-            key = ('%s_%s_to_%s_calibration_file'
-                   % (channel_name,
-                      conversion_info['base-calibration-slot'],
-                      conversion))
-            calib_path = conversion_info['file']
-            if key in info:
-                calib_path = os.path.join(os.path.dirname(path), info[key])
-                self.logger().debug(
-                    'Overriding %s -> %s calibration for %s channel: %s'
-                    % (conversion_info['base-calibration-slot'],
-                       conversion, channel_name, calib_path))
-            if os.path.exists(calib_path):
-                with file(calib_path, 'r') as f:
-                    lines = [x.strip() for x in f.readlines()]
-                    f.close()
-                calib = {  # I've emailed JPK to confirm this file format.
-                    'title':lines[0],
-                    'multiplier':float(lines[1]),
-                    'offset':float(lines[2]),
-                    'unit':lines[3],
-                    'note':'\n'.join(lines[4:]),
-                    }
-                segment[:,channel] = (segment[:,channel] * calib['multiplier']
-                                      + calib['offset'])
-                segment.info['columns'][channel] = (
-                    '%s (%s)' % (channel_name, calib['unit']))
-                return segment
-            else:
-                self.logger().warn(
-                    'Skipping %s -> %s calibration for %s channel.  Calibration file %s not found'
-                    % (conversion_info['base-calibration-slot'],
-                       conversion, channel_name, calib_path))
+            # Michael Haggerty at JPK points out that the conversion
+            # information stored in the external file is reproduced in
+            # the force curve file.  So there is no need to actually
+            # read `conversion_info['file']`.  In fact, the data there
+            # may have changed with future calibrations, while the
+            # information stored directly in conversion_info retains
+            # the calibration information as it was when the experiment
+            # was performed.
+            pass  # Fall through to 'simple' conversion processing.
         else:
             assert conversion_info['type'] == 'simple', conversion_info['type']
         assert conversion_info['scaling']['type'] == 'linear', \