1 # Copyright (C) 2008-2010 A. Seeholzer
3 # Richard Naud <richard.naud@epfl.ch>
4 # Rolf Schmidt <rschmidt@alcor.concordia.ca>
5 # W. Trevor King <wking@drexel.edu>
7 # This file is part of Hooke.
9 # Hooke is free software: you can redistribute it and/or modify it
10 # under the terms of the GNU Lesser General Public License as
11 # published by the Free Software Foundation, either version 3 of the
12 # License, or (at your option) any later version.
14 # Hooke is distributed in the hope that it will be useful, but WITHOUT
15 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
16 # or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General
17 # Public License for more details.
19 # You should have received a copy of the GNU Lesser General Public
20 # License along with Hooke. If not, see
21 # <http://www.gnu.org/licenses/>.
23 """Driver for MFP-3D files.
25 This driver reads IGOR binary waves.
28 Matlab version: Richard Naud August 2008 (http://lcn.epfl.ch/~naud/)
29 Python port: A. Seeholzer October 2008
30 Hooke submission: Rolf Schmidt, Alberto Gomez-Casado 2009
39 from .. import curve as curve
40 from .. import experiment as experiment
41 from . import Driver as Driver
42 from .igorbinarywave import loadibw
45 __version__='0.0.0.20100604'
48 class MFP3DDriver (Driver):
49 """Handle Asylum Research's MFP3D data format.
52 super(MFP3DDriver, self).__init__(name='mfp3d')
54 def is_me(self, path):
55 """Look for identifying fields in the IBW note.
57 if os.path.isdir(path):
59 if not path.endswith('.ibw'):
61 targets = ['Version:', 'XOPVersion:', 'ForceNote:']
62 found = [False]*len(targets)
63 for line in open(path, 'rU'):
64 for i,ft in enumerate(zip(found, targets)):
66 if f == False and line.startswith(t):
68 if min(found) == True:
72 def read(self, path, info=None):
73 data,bin_info,wave_info = loadibw(path)
74 blocks,info = self._translate_ibw(data, bin_info, wave_info)
75 info['filetype'] = self.name
76 info['experiment'] = experiment.VelocityClamp
79 def _translate_ibw(self, data, bin_info, wave_info):
80 if bin_info['version'] != 5:
81 raise NotImplementedError('IBW version %d (< 5) not supported'
82 % bin_info['version'])
83 # We need version 5 for multidimensional arrays.
85 # Parse the note into a dictionary
87 for line in bin_info['note'].split('\r'):
88 fields = [x.strip() for x in line.split(':', 1)]
95 bin_info['note'] = note
97 # Ensure a valid MFP3D file version.
98 if note['VerDate'] not in ['80501.041', '80501.0207']:
99 raise Exception(note['VerDate'])
100 raise NotImplementedError(
101 '%s file version %s not supported (yet!)\n%s'
102 % (self.name, note['VerDate'], pprint.pformat(note)))
104 # Parse known parameters into standard Hooke format.
106 'raw info':{'bin':bin_info,
108 'time':note['Seconds'],
109 'spring constant (N/m)':float(note['SpringConstant']),
110 'temperature (K)':self._temperature(note),
113 # Extract data blocks
115 indexes = [int(i) for i in note['Indexes'].split(',')]
116 assert indexes[0] == 0, indexes
117 for i,start in enumerate(indexes[:-1]):
119 blocks.append(self._scale_block(data[start:stop+1,:], info, i))
121 return (blocks, info)
123 def _scale_block(self, data, info, index):
124 """Convert the block from its native format to a `numpy.float`
127 # MFP3D's native data dimensions match Hooke's (<point>, <column>) layout.
130 columns = info['raw info']['bin']['dimLabels'][1]
131 # Depending on your MFP3D version:
132 # VerDate 80501.0207: ['Raw', 'Defl', 'LVDT', 'Time']
133 # VerDate 80501.041: ['Raw', 'Defl', 'LVDT']
134 if 'Time' in columns:
139 shape=(data.shape[0], n_col),
141 info=copy.deepcopy(info)
144 version = info['raw info']['bin']['note']['VerDate']
145 if version == '80501.041':
146 name = ['approach', 'retract', 'pause'][index]
147 elif version == '80501.0207':
148 name = ['approach', 'pause', 'retract'][index]
150 raise NotImplementedError()
151 ret.info['name'] = name
152 ret.info['raw data'] = data # store the raw data
154 z_rcol = columns.index('LVDT')
155 d_rcol = columns.index('Defl')
157 # scaled column indices
158 ret.info['columns'] = ['z piezo (m)', 'deflection (m)']
159 z_scol = ret.info['columns'].index('z piezo (m)')
160 d_scol = ret.info['columns'].index('deflection (m)')
162 # Leading '-' because increasing voltage extends the piezo,
163 # moving the tip towards the surface (positive indentation),
164 # but it makes more sense to me to have it increase away from
165 # the surface (positive separation).
166 ret[:,z_scol] = -data[:,z_rcol].astype(ret.dtype)
168 # Leading '-' because deflection voltage increases as the tip
169 # moves away from the surface, but it makes more sense to me
170 # to have it increase as it moves toward the surface (positive
171 # tension on the protein chain).
172 ret[:,d_scol] = -data[:,d_rcol]
174 if 'Time' in columns:
175 ret.info['columns'].append('time (s)')
176 t_rcol = columns.index('Time')
177 t_scol = ret.info['columns'].index('time (s)')
178 ret[:,t_scol] = data[:,t_rcol]
182 def _temperature(self, note):
183 # I'm not sure which field we should be using here. Options are:
189 # I imagine the 'Start*Temp' fields were measured at
190 # 'StartTempSeconds' at the beginning of a series of curves,
191 # while our particular curve was initiated at 'Seconds'.
192 # python -c "from hooke.hooke import Hooke;
194 # h.run_command('load playlist',
195 # {'input':'test/data/vclamp_mfp3d/playlist'});
196 # x = [(int(c.info['raw info']['bin']['note']['Seconds'])
197 # - int(c.info['raw info']['bin']['note']['StartTempSeconds']))
198 # for c in h.playlists.current().items()];
199 # print 'average', float(sum(x))/len(x);
200 # print 'range', min(x), max(x);
202 # For the Line*Point*.ibw series, the difference increases slowly
203 # 46, 46, 47, 47, 48, 49, 49, 50, 50, 51, 51, 52, 52, 53, 53, 54,...
204 # However, for the Image*.ibw series, the difference increase
206 # 21, 38, 145, 150, 171, 181
207 # This makes the 'Start*Temp' fields less and less relevant as
208 # the experiment continues. Still, I suppose it's better than
211 # The 'Thermal' fields seem to be related to cantilever calibration.
212 celsius = unicode(note['StartHeadTemp'], 'latin-1')
213 if celsius.endswith(u' \u00b0C'):
214 number = celsius.split(None, 1)[0]
215 return float(number) + 273.15 # Convert to Kelvin.
217 raise NotImplementedError(
218 'unkown temperature format: %s' % repr(celsius))