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)
76 version = zip_info['file-format-version']
78 for i in range(len([p for p in f.namelist()
79 if p.endswith('segment-header.properties')])):
80 segments.append(self._zip_segment(
81 f, path, info, zip_info, i, version))
82 if version not in ['0.%d' % i for i in range(13)]:
83 raise NotImplementedError(
84 'JPK file version %s not supported (yet).' % version)
85 curve_info = self._zip_translate_params(
86 zip_info, segments[0].info['raw info'], version)
87 for segment in segments: # HACK, should use curve-level spring constant
88 for key in ['spring constant (N/m)',
89 'z piezo sensitivity (m/V)']:
91 segment.info['spring constant (N/m)'] = \
92 curve_info['spring constant (N/m)']
94 return (segments, curve_info)
96 def _zip_info(self, zipfile):
97 with Closing(zipfile.open('header.properties')) as f:
98 info = self._parse_params(f.readlines())
101 def _zip_segment(self, zipfile, path, info, zip_info, index, version):
102 prop_file = zipfile.open(os.path.join(
103 'segments', str(index), 'segment-header.properties'))
104 prop = self._parse_params(prop_file.readlines())
106 expected_shape = (int(prop['force-segment-header']['num-points']),)
108 if 'list' not in prop['channels']:
109 prop['channels'] = {'list': prop['channels'].split()}
110 for chan in prop['channels']['list']:
111 chan_info = prop['channel'][chan]
112 channels.append(self._zip_channel(
113 zipfile, index, chan, chan_info))
114 if channels[-1].shape != expected_shape:
115 raise NotImplementedError(
116 'Channel %d:%s in %s has strange shape %s != %s'
117 % (index, chan, zipfile.path,
118 channels[-1].shape, expected_shape))
119 if len(channels) > 0:
120 shape = (len(channels[0]), len(channels))
121 dtype = channels[0].dtype
122 else: # no channels for this data block
124 dtype = numpy.float32
128 info=self._zip_translate_segment_params(prop))
129 for i,chan in enumerate(channels):
131 return self._zip_scale_segment(d, path, info, version)
133 def _zip_channel(self, zipfile, segment_index, channel_name, chan_info):
134 if chan_info['data']['type'] in ['constant-data', 'raster-data']:
135 return self._zip_calculate_channel(chan_info)
136 with Closing(zipfile.open(os.path.join(
137 'segments', str(segment_index),
138 chan_info['data']['file']['name']), 'r')) as f:
139 assert chan_info['data']['file']['format'] == 'raw', \
140 'Non-raw data format:\n%s' % pprint.pformat(chan_info)
141 dtype = self._zip_channel_dtype(chan_info)
142 data = numpy.frombuffer(
147 def _zip_calculate_channel(self, chan_info):
148 type_ = chan_info['data']['type']
149 n = int(chan_info['data']['num-points'])
150 if type_ == 'constant-data':
151 return float(chan_info['data']['value'])*numpy.ones(
154 elif type_ == 'raster-data':
155 start = float(chan_info['data']['start'])
156 step = float(chan_info['data']['step'])
159 stop=start + step*(n-0.5),
163 raise ValueError('Unrecognized data format "%s"' % type_)
165 def _zip_channel_dtype(self, chan_info):
166 type_ = chan_info['data']['type']
167 if type_ in ['float-data', 'float']:
168 dtype = numpy.dtype(numpy.float32)
169 elif type_ in ['integer-data', 'memory-integer-data']:
170 encoder = chan_info['data']['encoder']['type']
171 if encoder in ['signedinteger', 'signedinteger-limited']:
172 dtype = numpy.dtype(numpy.int32)
173 elif encoder in ['unsignedinteger', 'unsignedinteger-limited']:
174 dtype = numpy.dtype(numpy.uint32)
176 raise ValueError('Unrecognized encoder type "%s" for "%s" data'
178 elif type_ in ['short-data', 'short', 'memory-short-data']:
179 encoder = chan_info['data']['encoder']['type']
180 if encoder in ['signedshort', 'signedshort-limited']:
181 dtype = numpy.dtype(numpy.int16)
182 elif encoder in ['unsignedshort', 'unsignedshort-limited']:
183 dtype = numpy.dtype(numpy.uint16)
185 raise ValueError('Unrecognized encoder type "%s" for "%s" data'
188 raise ValueError('Unrecognized data format "%s"' % type_)
190 # '>' (big endian) byte order.
191 # From version 0.3 of JPKForceSpec.txt in the "Binary data" section:
192 # All forms of raw data are stored in chronological order
193 # (the order in which they were collected), and the
194 # individual values are stored in network byte order
195 # (big-endian). The data type used to store the data is
196 # specified by the "channel.*.data.type" property, and is
197 # either short (2 bytes per value), integer (4 bytes), or
198 # float (4 bytes, IEEE format).
199 return dtype.newbyteorder(byte_order)
201 def _zip_translate_params(self, params, chan_info, version):
204 #'time':self._time_from_TODO(raw_info[]),
206 if len(chan_info['channels']['list']) == 0:
208 force_unit = self._zip_unit(
209 chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['scaling'],
211 assert force_unit == 'N', force_unit
212 force_base = chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['base-calibration-slot']
213 assert force_base == 'distance', force_base
214 dist_unit = self._zip_unit(
215 chan_info['channel']['vDeflection']['conversion-set']['conversion']['distance']['scaling'],
217 assert dist_unit == 'm', dist_unit
218 distance_base = chan_info['channel']['vDeflection']['conversion-set']['conversion']['distance']['base-calibration-slot']
219 assert distance_base == 'volts', distance_base
220 base_conversion = chan_info['channel']['vDeflection']['conversion-set']['conversions']['base']
221 assert base_conversion == distance_base, base_conversion
222 distance_base_unit = self._zip_unit(
223 chan_info['channel']['vDeflection']['data'],
225 assert distance_base_unit == 'V', distance_base_unit
227 chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['scaling']['multiplier'])
229 chan_info['channel']['vDeflection']['conversion-set']['conversion']['distance']['scaling']['multiplier'])
230 info['spring constant (N/m)'] = force_mult
231 info['z piezo sensitivity (m/V)'] = sens_mult
234 def _zip_translate_segment_params(self, params):
237 'columns': list(params['channels']['list']),
238 'name': self._zip_segment_name(params),
242 def _zip_segment_name(self, params):
243 name = params['force-segment-header']['name']['name']
244 if name.endswith('-spm'):
245 name = name[:-len('-spm')]
248 elif name.startswith('pause-at-'):
252 def _zip_scale_segment(self, segment, path, info, version):
258 segment.info['raw data'] = data
261 channels = segment.info['raw info']['channels']['list']
262 for i,channel in enumerate(channels):
264 if channel == 'vDeflection':
265 conversion = 'distance'
266 segment = self._zip_scale_channel(
267 segment, channel, conversion=conversion,
268 path=path, info=info, version=version)
269 name,unit = split_data_label(segment.info['columns'][i])
270 if name == 'vDeflection':
271 assert unit == 'm', segment.info['columns'][i]
272 segment.info['columns'][i] = join_data_label('deflection', 'm')
273 # Invert because deflection voltage increases as the
274 # tip moves away from the surface, but it makes more
275 # sense to me to have it increase as it moves toward
276 # the surface (positive tension on the protein chain).
278 elif name == 'height':
279 assert unit == 'm', segment.info['columns'][i]
280 segment.info['columns'][i] = join_data_label('z piezo', 'm')
283 def _zip_scale_channel(self, segment, channel_name,
284 conversion=None, path=None, info={}, version=None):
285 channel = segment.info['raw info']['channels']['list'].index(
287 conversion_set = segment.info['raw info']['channel'][channel_name]['conversion-set']
288 if conversion == None:
289 conversion = conversion_set['conversions']['default']
290 if conversion == conversion_set['conversions']['base']:
291 segment.info['columns'][channel] = join_data_label(
294 segment.info['raw info']['channel'][channel_name]['data'],
297 conversion_info = conversion_set['conversion'][conversion]
298 if conversion_info['base-calibration-slot'] \
299 != conversion_set['conversions']['base']:
300 # Our conversion is stacked on a previous conversion. Do
301 # the previous conversion first.
302 segment = self._zip_scale_channel(
303 segment, channel_name,
304 conversion_info['base-calibration-slot'],
305 path=path, info=info, version=version)
306 if conversion_info['type'] == 'file':
307 # Michael Haggerty at JPK points out that the conversion
308 # information stored in the external file is reproduced in
309 # the force curve file. So there is no need to actually
310 # read `conversion_info['file']`. In fact, the data there
311 # may have changed with future calibrations, while the
312 # information stored directly in conversion_info retains
313 # the calibration information as it was when the experiment
315 pass # Fall through to 'simple' conversion processing.
317 assert conversion_info['type'] == 'simple', conversion_info['type']
318 assert conversion_info['scaling']['type'] == 'linear', \
319 conversion_info['scaling']['type']
320 assert conversion_info['scaling']['style'] == 'offsetmultiplier', \
321 conversion_info['scaling']['style']
322 multiplier = float(conversion_info['scaling']['multiplier'])
323 offset = float(conversion_info['scaling']['offset'])
324 unit = self._zip_unit(conversion_info['scaling'], version)
325 segment[:,channel] = segment[:,channel] * multiplier + offset
326 segment.info['columns'][channel] = join_data_label(channel_name, unit)
329 def _zip_unit(self, conversion_info, version):
330 if version in ['0.%d' % i for i in range(3)]:
331 return conversion_info['unit']
333 return conversion_info['unit']['unit']
335 def _parse_params(self, lines):
339 if line.startswith('#'):
342 # e.g.: force-segment-header.type=xy-position-segment-header
343 fields = line.split('=', 1)
344 assert len(fields) == 2, line
345 setting = fields[0].split('.')
346 sub_info = info # drill down, e.g. info['force-s..']['type']
347 for s in setting[:-1]:
348 if s not in sub_info:
350 sub_info = sub_info[s]
351 if setting[-1] == 'list': # split a space-delimited list
353 sub_info[setting[-1]] = fields[1].split(' ')
355 sub_info[setting[-1]] = []
357 sub_info[setting[-1]] = fields[1]
360 def _read_old(self, path, info):
361 raise NotImplementedError(
362 "Early JPK files (pre-zip) are not supported by Hooke. Please "
363 "use JPK's `out2jpk-force` script to convert your old files "
364 "to a more recent format before loading them with Hooke.")