#
# This file is part of Hooke.
#
-# Hooke is free software: you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public
-# License as published by the Free Software Foundation, either
-# version 3 of the License, or (at your option) any later version.
+# Hooke is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Lesser General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
#
-# Hooke is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU Lesser General Public License for more details.
+# Hooke is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General
+# Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with Hooke. If not, see
# <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
-class Closing (object):
- """Add .__enter__() .__exit__() for `with` statements.
-
- See :pep:`343`.
- """
- def __init__(self, obj):
- self.obj = obj
-
- def __enter__(self):
- return self.obj
-
- def __exit__(self, *exc_info):
- try:
- close_it = self.obj.close
- except AttributeError:
- pass
- else:
- close_it()
-
-
class JPKDriver (Driver):
"""Handle JPK ForceRobot's data format.
"""
super(JPKDriver, self).__init__(name='jpk')
def is_me(self, path):
+ if os.path.isdir(path):
+ return False
if zipfile.is_zipfile(path): # JPK file versions since at least 0.5
with Closing(zipfile.ZipFile(path, 'r')) as f:
if 'header.properties' not in f.namelist():
headlines = []
for i in range(3):
headlines.append(f.readline())
- if headlines[0].startswith('# xPosition') \
- and headlines[1].startswith('# yPosition'):
- return True
+ if headlines[0].startswith('# xPosition') \
+ and headlines[1].startswith('# yPosition'):
+ return True
return False
def read(self, path, info=None):
with Closing(zipfile.ZipFile(path, 'r')) as f:
f.path = path
zip_info = self._zip_info(f)
+ version = zip_info['file-format-version']
segments = []
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']))
+ segments.append(self._zip_segment(
+ f, path, info, zip_info, i, version))
+ if version not in ['0.%d' % i for i in range(13)]:
+ raise NotImplementedError(
+ 'JPK file version %s not supported (yet).' % version)
+ curve_info = self._zip_translate_params(
+ zip_info, segments[0].info['raw info'], version)
+ for segment in segments: # HACK, should use curve-level spring constant
+ for key in ['spring constant (N/m)',
+ 'z piezo sensitivity (m/V)']:
+ if key in curve_info:
+ 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:
info = self._parse_params(f.readlines())
return info
- def _zip_segment(self, zipfile, path, info, zip_info, index):
+ def _zip_segment(self, zipfile, path, info, zip_info, index, version):
prop_file = zipfile.open(os.path.join(
'segments', str(index), 'segment-header.properties'))
prop = self._parse_params(prop_file.readlines())
prop_file.close()
expected_shape = (int(prop['force-segment-header']['num-points']),)
channels = []
+ if 'list' not in prop['channels']:
+ prop['channels'] = {'list': prop['channels'].split()}
for chan in prop['channels']['list']:
chan_info = prop['channel'][chan]
- channels.append(self._zip_channel(zipfile, index, chan, chan_info))
+ channels.append(self._zip_channel(
+ zipfile, index, chan, chan_info))
if channels[-1].shape != expected_shape:
- raise NotImplementedError(
- 'Channel %d:%s in %s has strange shape %s != %s'
- % (index, chan, zipfile.path,
- channels[-1].shape, expected_shape))
+ raise NotImplementedError(
+ 'Channel %d:%s in %s has strange shape %s != %s'
+ % (index, chan, zipfile.path,
+ channels[-1].shape, expected_shape))
+ if len(channels) > 0:
+ shape = (len(channels[0]), len(channels))
+ dtype = channels[0].dtype
+ else: # no channels for this data block
+ shape = (0,0)
+ dtype = numpy.float32
d = curve.Data(
- shape=(len(channels[0]), len(channels)),
- dtype=channels[0].dtype,
+ shape=shape,
+ dtype=dtype,
info=self._zip_translate_segment_params(prop))
for i,chan in enumerate(channels):
d[:,i] = chan
- return self._zip_scale_segment(d, path, info)
+ return self._zip_scale_segment(d, path, info, version)
def _zip_channel(self, zipfile, segment_index, channel_name, chan_info):
- f = zipfile.open(os.path.join(
- 'segments', str(segment_index),
- chan_info['data']['file']['name']), 'r')
- assert chan_info['data']['file']['format'] == 'raw', \
- 'Non-raw data format:\n%s' % pprint.pformat(chan_info)
- assert chan_info['data']['type'] == 'float-data', \
- 'Non-float data format:\n%s' % pprint.pformat(chan_info)
- data = numpy.frombuffer(
- buffer(f.read()),
- dtype=numpy.dtype(numpy.float32).newbyteorder('>'),
- # Is JPK data always big endian? I can't find a config
- # setting. The ForceRobot brochure
- # http://www.jpk.com/forcerobot300-1.download.6d694150f14773dc76bc0c3a8a6dd0e8.pdf
- # lists a PowerPC chip on page 4, under Control
- # electronics, and PPCs are usually big endian.
- # http://en.wikipedia.org/wiki/PowerPC#Endian_modes
- )
- f.close()
+ if chan_info['data']['type'] in ['constant-data', 'raster-data']:
+ return self._zip_calculate_channel(chan_info)
+ with Closing(zipfile.open(os.path.join(
+ 'segments', str(segment_index),
+ chan_info['data']['file']['name']), 'r')) as f:
+ assert chan_info['data']['file']['format'] == 'raw', \
+ 'Non-raw data format:\n%s' % pprint.pformat(chan_info)
+ dtype = self._zip_channel_dtype(chan_info)
+ data = numpy.frombuffer(
+ buffer(f.read()),
+ dtype=dtype,)
return data
- def _zip_translate_params(self, params, chan_info):
+ def _zip_calculate_channel(self, chan_info):
+ type_ = chan_info['data']['type']
+ n = int(chan_info['data']['num-points'])
+ if type_ == 'constant-data':
+ return float(chan_info['data']['value'])*numpy.ones(
+ shape=(n,),
+ dtype=numpy.float32)
+ elif type_ == 'raster-data':
+ start = float(chan_info['data']['start'])
+ step = float(chan_info['data']['step'])
+ return numpy.arange(
+ start=start,
+ stop=start + step*(n-0.5),
+ step=step,
+ dtype=numpy.float32)
+ else:
+ raise ValueError('Unrecognized data format "%s"' % type_)
+
+ def _zip_channel_dtype(self, chan_info):
+ type_ = chan_info['data']['type']
+ if type_ in ['float-data', 'float']:
+ dtype = numpy.dtype(numpy.float32)
+ elif type_ in ['integer-data', 'memory-integer-data']:
+ encoder = chan_info['data']['encoder']['type']
+ if encoder in ['signedinteger', 'signedinteger-limited']:
+ dtype = numpy.dtype(numpy.int32)
+ elif encoder in ['unsignedinteger', 'unsignedinteger-limited']:
+ dtype = numpy.dtype(numpy.uint32)
+ else:
+ raise ValueError('Unrecognized encoder type "%s" for "%s" data'
+ % (encoder, type_))
+ elif type_ in ['short-data', 'short', 'memory-short-data']:
+ encoder = chan_info['data']['encoder']['type']
+ if encoder in ['signedshort', 'signedshort-limited']:
+ dtype = numpy.dtype(numpy.int16)
+ elif encoder in ['unsignedshort', 'unsignedshort-limited']:
+ dtype = numpy.dtype(numpy.uint16)
+ else:
+ raise ValueError('Unrecognized encoder type "%s" for "%s" data'
+ % (encoder, type_))
+ else:
+ raise ValueError('Unrecognized data format "%s"' % type_)
+ byte_order = '>'
+ # '>' (big endian) byte order.
+ # From version 0.3 of JPKForceSpec.txt in the "Binary data" section:
+ # All forms of raw data are stored in chronological order
+ # (the order in which they were collected), and the
+ # individual values are stored in network byte order
+ # (big-endian). The data type used to store the data is
+ # specified by the "channel.*.data.type" property, and is
+ # either short (2 bytes per value), integer (4 bytes), or
+ # float (4 bytes, IEEE format).
+ return dtype.newbyteorder(byte_order)
+
+ def _zip_translate_params(self, params, chan_info, version):
info = {
'raw info':params,
#'time':self._time_from_TODO(raw_info[]),
}
- force_unit = chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['scaling']['unit']['unit']
+ if len(chan_info['channels']['list']) == 0:
+ return info
+ force_unit = self._zip_unit(
+ chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['scaling'],
+ version)
assert force_unit == 'N', force_unit
force_base = chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['base-calibration-slot']
assert force_base == 'distance', force_base
- dist_unit = chan_info['channel']['vDeflection']['conversion-set']['conversion']['distance']['scaling']['unit']['unit']
+ dist_unit = self._zip_unit(
+ chan_info['channel']['vDeflection']['conversion-set']['conversion']['distance']['scaling'],
+ version)
assert dist_unit == 'm', dist_unit
+ distance_base = chan_info['channel']['vDeflection']['conversion-set']['conversion']['distance']['base-calibration-slot']
+ assert distance_base == 'volts', distance_base
+ base_conversion = chan_info['channel']['vDeflection']['conversion-set']['conversions']['base']
+ assert base_conversion == distance_base, base_conversion
+ distance_base_unit = self._zip_unit(
+ chan_info['channel']['vDeflection']['data'],
+ version)
+ assert distance_base_unit == 'V', distance_base_unit
force_mult = float(
chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['scaling']['multiplier'])
+ sens_mult = float(
+ chan_info['channel']['vDeflection']['conversion-set']['conversion']['distance']['scaling']['multiplier'])
info['spring constant (N/m)'] = force_mult
+ info['z piezo sensitivity (m/V)'] = sens_mult
return info
def _zip_translate_segment_params(self, params):
info = {
- 'raw info':params,
- 'columns':list(params['channels']['list']),
- 'name':params['force-segment-header']['name']['name'],
+ 'raw info': params,
+ 'columns': list(params['channels']['list']),
+ 'name': self._zip_segment_name(params),
}
- if info['name'] in ['extend-spm', 'retract-spm', 'pause-at-end-spm']:
- info['name'] = info['name'][:-len('-spm')]
- if info['name'] == 'extend':
- info['name'] = 'approach'
- else:
- raise NotImplementedError(
- 'Unrecognized segment type %s' % info['name'])
return info
- def _zip_scale_segment(self, segment, path, info):
+ def _zip_segment_name(self, params):
+ name = params['force-segment-header']['name']['name']
+ if name.endswith('-spm'):
+ name = name[:-len('-spm')]
+ if name == 'extend':
+ name = 'approach'
+ elif name.startswith('pause-at-'):
+ name = 'pause'
+ return name
+
+ def _zip_scale_segment(self, segment, path, info, version):
data = curve.Data(
shape=segment.shape,
dtype=segment.dtype,
# 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, version=version)
+ 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={}, version=None):
+ 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']:
+ segment.info['columns'][channel] = join_data_label(
+ channel_name,
+ self._zip_unit(
+ segment.info['raw info']['channel'][channel_name]['data'],
+ version))
+ 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'],
- info, path)
+ segment, channel_name,
+ conversion_info['base-calibration-slot'],
+ path=path, info=info, version=version)
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', \
conversion_info['scaling']['style']
multiplier = float(conversion_info['scaling']['multiplier'])
offset = float(conversion_info['scaling']['offset'])
- unit = conversion_info['scaling']['unit']['unit']
+ unit = self._zip_unit(conversion_info['scaling'], version)
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 _zip_unit(self, conversion_info, version):
+ if version in ['0.%d' % i for i in range(3)]:
+ return conversion_info['unit']
+ else:
+ return conversion_info['unit']['unit']
+
def _parse_params(self, lines):
info = {}
for line in lines:
sub_info[s] = {}
sub_info = sub_info[s]
if setting[-1] == 'list': # split a space-delimited list
- sub_info[setting[-1]] = fields[1].split(' ')
+ if fields[1]:
+ sub_info[setting[-1]] = fields[1].split(' ')
+ else:
+ sub_info[setting[-1]] = []
else:
sub_info[setting[-1]] = fields[1]
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)
-
-# LocalWords: JPK ForceRobot's
+ 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