Set filetype and experiment fields in JPK driver.

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

diff --git a/hooke/driver/jpk.py b/hooke/driver/jpk.py
index ed7f6c4b4dae57bb62a1fe6641965530c53f23fe..1330713f4ac929eb60ef6605178b34bb0100e0a7 100644 (file)
--- a/hooke/driver/jpk.py
+++ b/hooke/driver/jpk.py
@@ -74,14 +74,21 @@ class JPKDriver (Driver):
             for i in range(len([p for p in f.namelist()
                                 if p.endswith('segment-header.properties')])):
                 segments.append(self._zip_segment(f, path, info, zip_info, i))
-            for name in ['approach', 'retract']:
-                if len([s for s in segments if s.info['name'] == name]) == 0:
-                    raise ValueError(
-                        'No segment for %s in %s, only %s'
-                        % (name, path, [s.info['name'] for s in segments]))
-            return (segments,
-                    self._zip_translate_params(zip_info,
-                                               segments[0].info['raw info']))
+        if zip_info['file-format-version'] not in ['0.5']:
+            raise NotImplementedError(
+                'JPK file version %s not supported (yet).'
+                % zip_info['file-format-version'])
+        for name in ['approach', 'retract']:
+            if len([s for s in segments if s.info['name'] == name]) == 0:
+                raise ValueError(
+                    'No segment for %s in %s, only %s'
+                    % (name, path, [s.info['name'] for s in segments]))
+        curve_info = self._zip_translate_params(zip_info,
+                                                segments[0].info['raw info'])
+        for segment in segments:
+            segment.info['spring constant (N/m)'] = \
+                curve_info['spring constant (N/m)']
+        return (segments, curve_info)
 
     def _zip_info(self, zipfile):
         with Closing(zipfile.open('header.properties')) as f:
@@ -137,8 +144,16 @@ class JPKDriver (Driver):
     def _zip_translate_params(self, params, chan_info):
         info = {
             'raw info':params,
+            'filetype':self.name,
             #'time':self._time_from_TODO(raw_info[]),
             }
+        # TODO: distinguish between force clamp and velocity clamp
+        # experiments.  Note that the JPK file format is flexible
+        # enough to support mixed experiments (i.e. both force clamp
+        # and velocity clamp segments in a single experiment), but I
+        # have no idea what sort of analysis such experiments would
+        # require ;).
+        info['experiment'] = experiment.VelocityClamp
         force_unit = chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['scaling']['unit']['unit']
         assert force_unit == 'N', force_unit
         force_base = chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['base-calibration-slot']
@@ -204,40 +219,17 @@ 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', \