1 # Copyright (C) 2008-2010 Massimo Sandal <devicerandom@gmail.com>
2 # W. Trevor King <wking@drexel.edu>
4 # This file is part of Hooke.
6 # Hooke is free software: you can redistribute it and/or modify it
7 # under the terms of the GNU Lesser General Public License as
8 # published by the Free Software Foundation, either version 3 of the
9 # License, or (at your option) any later version.
11 # Hooke is distributed in the hope that it will be useful, but WITHOUT
12 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
13 # or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General
14 # Public License for more details.
16 # You should have received a copy of the GNU Lesser General Public
17 # License along with Hooke. If not, see
18 # <http://www.gnu.org/licenses/>.
20 """Driver for JPK ForceRobot's velocity clamp data format.
22 This driver is based on JPK's :file:`JPKForceSpec.txt` version 0.12.
23 The specs are freely available from JPK, just email support@jpk.com.
32 from .. import curve as curve
33 from ..util.util import Closing as Closing
34 from ..util.si import join_data_label, split_data_label
35 from . import Driver as Driver
38 class JPKDriver (Driver):
39 """Handle JPK ForceRobot's data format.
42 super(JPKDriver, self).__init__(name='jpk')
44 def is_me(self, path):
45 if os.path.isdir(path):
47 if zipfile.is_zipfile(path): # JPK file versions since at least 0.5
48 with Closing(zipfile.ZipFile(path, 'r')) as f:
49 if 'header.properties' not in f.namelist():
51 with Closing(f.open('header.properties')) as h:
52 if 'jpk-data-file' in h.read():
55 with Closing(open(path, 'r')) as f:
58 headlines.append(f.readline())
59 if headlines[0].startswith('# xPosition') \
60 and headlines[1].startswith('# yPosition'):
64 def read(self, path, info=None):
67 if zipfile.is_zipfile(path): # JPK file versions since at least 0.5
68 return self._read_zip(path, info)
70 return self._read_old(path, info)
72 def _read_zip(self, path, info):
73 with Closing(zipfile.ZipFile(path, 'r')) as f:
75 zip_info = self._zip_info(f)
77 for i in range(len([p for p in f.namelist()
78 if p.endswith('segment-header.properties')])):
79 segments.append(self._zip_segment(f, path, info, zip_info, i))
80 if zip_info['file-format-version'] not in ['0.%d' % i
82 raise NotImplementedError(
83 'JPK file version %s not supported (yet).'
84 % zip_info['file-format-version'])
85 curve_info = self._zip_translate_params(zip_info,
86 segments[0].info['raw info'])
87 for segment in segments: # HACK, should use curve-level spring constant
88 segment.info['spring constant (N/m)'] = \
89 curve_info['spring constant (N/m)']
90 return (segments, curve_info)
92 def _zip_info(self, zipfile):
93 with Closing(zipfile.open('header.properties')) as f:
94 info = self._parse_params(f.readlines())
97 def _zip_segment(self, zipfile, path, info, zip_info, index):
98 prop_file = zipfile.open(os.path.join(
99 'segments', str(index), 'segment-header.properties'))
100 prop = self._parse_params(prop_file.readlines())
102 expected_shape = (int(prop['force-segment-header']['num-points']),)
104 if 'list' not in prop['channels']:
105 prop['channels'] = {'list': prop['channels'].split()}
106 for chan in prop['channels']['list']:
107 chan_info = prop['channel'][chan]
108 channels.append(self._zip_channel(
109 zipfile, index, chan, chan_info))
110 if channels[-1].shape != expected_shape:
111 raise NotImplementedError(
112 'Channel %d:%s in %s has strange shape %s != %s'
113 % (index, chan, zipfile.path,
114 channels[-1].shape, expected_shape))
115 if len(channels) > 0:
116 shape = (len(channels[0]), len(channels))
117 dtype = channels[0].dtype
118 else: # no channels for this data block
120 dtype = numpy.float32
124 info=self._zip_translate_segment_params(prop))
125 for i,chan in enumerate(channels):
127 return self._zip_scale_segment(d, path, info)
129 def _zip_channel(self, zipfile, segment_index, channel_name, chan_info):
130 f = zipfile.open(os.path.join(
131 'segments', str(segment_index),
132 chan_info['data']['file']['name']), 'r')
133 assert chan_info['data']['file']['format'] == 'raw', \
134 'Non-raw data format:\n%s' % pprint.pformat(chan_info)
135 assert chan_info['data']['type'] == 'float-data', \
136 'Non-float data format:\n%s' % pprint.pformat(chan_info)
137 data = numpy.frombuffer(
139 dtype=numpy.dtype(numpy.float32).newbyteorder('>'))
140 # '>' (big endian) byte order.
141 # From version 0.3 of JPKForceSpec.txt in the "Binary data" section:
142 # All forms of raw data are stored in chronological order
143 # (the order in which they were collected), and the
144 # individual values are stored in network byte order
145 # (big-endian). The data type used to store the data is
146 # specified by the "channel.*.data.type" property, and is
147 # either short (2 bytes per value), integer (4 bytes), or
148 # float (4 bytes, IEEE format).
152 def _zip_translate_params(self, params, chan_info):
155 #'time':self._time_from_TODO(raw_info[]),
157 force_unit = chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['scaling']['unit']['unit']
158 assert force_unit == 'N', force_unit
159 force_base = chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['base-calibration-slot']
160 assert force_base == 'distance', force_base
161 dist_unit = chan_info['channel']['vDeflection']['conversion-set']['conversion']['distance']['scaling']['unit']['unit']
162 assert dist_unit == 'm', dist_unit
163 distance_base = chan_info['channel']['vDeflection']['conversion-set']['conversion']['distance']['base-calibration-slot']
164 assert distance_base == 'volts', distance_base
165 # Assume volts unit is V, but it is not specified in the JPK
168 chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['scaling']['multiplier'])
170 chan_info['channel']['vDeflection']['conversion-set']['conversion']['distance']['scaling']['multiplier'])
171 info['spring constant (N/m)'] = force_mult
172 info['z piezo sensitivity (m/V)'] = sens_mult
175 def _zip_translate_segment_params(self, params):
178 'columns':list(params['channels']['list']),
179 'name':params['force-segment-header']['name']['name'],
181 if info['name'] in ['extend-spm', 'retract-spm', 'pause-at-end-spm']:
182 info['name'] = info['name'][:-len('-spm')]
183 if info['name'] == 'extend':
184 info['name'] = 'approach'
186 raise NotImplementedError(
187 'Unrecognized segment type %s' % info['name'])
190 def _zip_scale_segment(self, segment, path, info):
196 segment.info['raw data'] = data
199 channels = segment.info['raw info']['channels']['list']
200 for i,channel in enumerate(channels):
202 if channel == 'vDeflection':
203 conversion = 'distance'
204 segment = self._zip_scale_channel(
205 segment, channel, conversion=conversion, path=path, info=info)
206 name,unit = split_data_label(segment.info['columns'][i])
207 if name == 'vDeflection':
208 assert unit == 'm', segment.info['columns'][i]
209 segment.info['columns'][i] = join_data_label('deflection', 'm')
210 # Invert because deflection voltage increases as the
211 # tip moves away from the surface, but it makes more
212 # sense to me to have it increase as it moves toward
213 # the surface (positive tension on the protein chain).
215 elif name == 'height':
216 assert unit == 'm', segment.info['columns'][i]
217 segment.info['columns'][i] = join_data_label('z piezo', 'm')
220 def _zip_scale_channel(self, segment, channel_name, conversion=None,
222 channel = segment.info['raw info']['channels']['list'].index(
224 conversion_set = segment.info['raw info']['channel'][channel_name]['conversion-set']
225 if conversion == None:
226 conversion = conversion_set['conversions']['default']
227 if conversion == conversion_set['conversions']['base']:
228 # Our conversion is the base data.
229 if conversion != 'volts':
230 raise NotImplementedError(
231 'unknown units for base channel: %s' % conversion)
232 segment.info['columns'][channel] = join_data_label(
235 conversion_info = conversion_set['conversion'][conversion]
236 if conversion_info['base-calibration-slot'] \
237 != conversion_set['conversions']['base']:
238 # Our conversion is stacked on a previous conversion. Do
239 # the previous conversion first.
240 segment = self._zip_scale_channel(
241 segment, channel_name,
242 conversion_info['base-calibration-slot'],
243 path=path, info=info)
244 if conversion_info['type'] == 'file':
245 # Michael Haggerty at JPK points out that the conversion
246 # information stored in the external file is reproduced in
247 # the force curve file. So there is no need to actually
248 # read `conversion_info['file']`. In fact, the data there
249 # may have changed with future calibrations, while the
250 # information stored directly in conversion_info retains
251 # the calibration information as it was when the experiment
253 pass # Fall through to 'simple' conversion processing.
255 assert conversion_info['type'] == 'simple', conversion_info['type']
256 assert conversion_info['scaling']['type'] == 'linear', \
257 conversion_info['scaling']['type']
258 assert conversion_info['scaling']['style'] == 'offsetmultiplier', \
259 conversion_info['scaling']['style']
260 multiplier = float(conversion_info['scaling']['multiplier'])
261 offset = float(conversion_info['scaling']['offset'])
262 unit = conversion_info['scaling']['unit']['unit']
263 segment[:,channel] = segment[:,channel] * multiplier + offset
264 segment.info['columns'][channel] = join_data_label(channel_name, unit)
267 def _parse_params(self, lines):
271 if line.startswith('#'):
274 # e.g.: force-segment-header.type=xy-position-segment-header
275 fields = line.split('=', 1)
276 assert len(fields) == 2, line
277 setting = fields[0].split('.')
278 sub_info = info # drill down, e.g. info['force-s..']['type']
279 for s in setting[:-1]:
280 if s not in sub_info:
282 sub_info = sub_info[s]
283 if setting[-1] == 'list': # split a space-delimited list
284 sub_info[setting[-1]] = fields[1].split(' ')
286 sub_info[setting[-1]] = fields[1]
289 def _read_old(self, path, info):
290 raise NotImplementedError(
291 "Early JPK files (pre-zip) are not supported by Hooke. Please "
292 "use JPK's `out2jpk-force` script to convert your old files "
293 "to a more recent format before loading them with Hooke.")