# <http://www.gnu.org/licenses/>.
"""Driver for JPK ForceRobot's velocity clamp data format.
+
+This driver is based on JPK's :file:`JPKForceSpec.txt` version 0.12.
+The specs are freely available from JPK, just email support@jpk.com.
"""
import os.path
import numpy
from .. import curve as curve
-from .. import experiment as experiment
from ..util.util import Closing as Closing
+from ..util.si import join_data_label, split_data_label
from . import Driver as 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))
- if zip_info['file-format-version'] not in ['0.5']:
+ if zip_info['file-format-version'] not in ['0.%d' % i
+ for i in range(12)]:
raise NotImplementedError(
'JPK file version %s not supported (yet).'
% zip_info['file-format-version'])
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']
# raw column indices
channels = segment.info['raw info']['channels']['list']
- z_col = channels.index('height')
- d_col = channels.index('vDeflection')
-
- segment = self._zip_scale_channel(
- segment, z_col, 'calibrated', path, info)
- segment = self._zip_scale_channel(
- segment, d_col, 'distance', path, info)
-
- assert segment.info['columns'][z_col] == 'height (m)', \
- segment.info['columns'][z_col]
- assert segment.info['columns'][d_col] == 'vDeflection (m)', \
- segment.info['columns'][d_col]
-
- # scaled column indices same as raw column indices,
- # because columns is a copy of channels.list
- segment.info['columns'][z_col] = 'z piezo (m)'
- segment.info['columns'][d_col] = 'deflection (m)'
+ for i,channel in enumerate(channels):
+ conversion = None
+ if channel == 'vDeflection':
+ conversion = 'distance'
+ segment = self._zip_scale_channel(
+ segment, channel, conversion=conversion, path=path, info=info)
+ name,unit = split_data_label(segment.info['columns'][i])
+ if name == 'vDeflection':
+ assert unit == 'm', segment.info['columns'][i]
+ segment.info['columns'][i] = join_data_label('deflection', 'm')
+ # Invert because deflection voltage increases as the
+ # tip moves away from the surface, but it makes more
+ # sense to me to have it increase as it moves toward
+ # the surface (positive tension on the protein chain).
+ segment[:,i] *= -1
+ elif name == 'height':
+ assert unit == 'm', segment.info['columns'][i]
+ segment.info['columns'][i] = join_data_label('z piezo', 'm')
return segment
- def _zip_scale_channel(self, segment, channel, conversion, path, info):
- channel_name = segment.info['raw info']['channels']['list'][channel]
+ def _zip_scale_channel(self, segment, channel_name, conversion=None,
+ path=None, info={}):
+ channel = segment.info['raw info']['channels']['list'].index(
+ channel_name)
conversion_set = segment.info['raw info']['channel'][channel_name]['conversion-set']
+ if conversion == None:
+ conversion = conversion_set['conversions']['default']
+ if conversion == conversion_set['conversions']['base']:
+ # Our conversion is the base data.
+ if conversion != 'volts':
+ raise NotImplementedError(
+ 'unknown units for base channel: %s' % conversion)
+ segment.info['columns'][channel] = join_data_label(
+ channel_name, 'V')
+ return segment
conversion_info = conversion_set['conversion'][conversion]
if conversion_info['base-calibration-slot'] \
!= conversion_set['conversions']['base']:
# Our conversion is stacked on a previous conversion. Do
# the previous conversion first.
segment = self._zip_scale_channel(
- segment, channel, conversion_info['base-calibration-slot'],
+ segment, channel_name,
+ conversion_info['base-calibration-slot'],
path=path, info=info)
if conversion_info['type'] == 'file':
# Michael Haggerty at JPK points out that the conversion
offset = float(conversion_info['scaling']['offset'])
unit = conversion_info['scaling']['unit']['unit']
segment[:,channel] = segment[:,channel] * multiplier + offset
- segment.info['columns'][channel] = '%s (%s)' % (channel_name, unit)
+ segment.info['columns'][channel] = join_data_label(channel_name, unit)
return segment
def _parse_params(self, lines):
return info
def _read_old(self, path, info):
- raise NotImplementedError('No old-style JPK files were available for testing, please send us yours: %s' % path)
+ raise NotImplementedError(
+ "Early JPK files (pre-zip) are not supported by Hooke. Please "
+ "use JPK's `out2jpk-force` script to convert your old files "
+ "to a more recent format before loading them with Hooke.")
projects / hooke.git / blobdiff