1 # Copyright (C) 2006-2010 Alberto Gomez-Casado
2 # Massimo Sandal <devicerandom@gmail.com>
3 # W. Trevor King <wking@drexel.edu>
5 # This file is part of Hooke.
7 # Hooke is free software: you can redistribute it and/or
8 # modify it under the terms of the GNU Lesser General Public
9 # License as published by the Free Software Foundation, either
10 # version 3 of the License, or (at your option) any later version.
12 # Hooke is distributed in the hope that it will be useful,
13 # but WITHOUT ANY WARRANTY; without even the implied warranty of
14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15 # GNU Lesser General Public License for more details.
17 # You should have received a copy of the GNU Lesser General Public
18 # License along with Hooke. If not, see
19 # <http://www.gnu.org/licenses/>.
21 """Driver for Veeco PicoForce force spectroscopy files.
30 from .. import curve as curve # this module defines data containers.
31 from .. import experiment as experiment # this module defines expt. types
32 from ..config import Setting # configurable setting class
33 from . import Driver as Driver # this is the Driver base class
36 __version__='0.0.0.20100516'
38 class PicoForceDriver (Driver):
39 """Handle Veeco Picoforce force spectroscopy files.
42 super(PicoForceDriver, self).__init__(name='picoforce')
44 def is_me(self, path):
49 return header[2:17] == 'Force file list'
52 info = self._read_header_path(path)
53 self._check_version(info)
54 data = self._read_data_path(path, info)
55 info['filetype'] = self.name
56 info['experiment'] = experiment.VelocityClamp
59 def _read_header_path(self, path):
60 """Read curve information from the PicoForce file at `path`.
62 See :meth:`._read_header_file`.
64 return self._read_header_file(file(path, 'rb'))
66 def _read_header_file(self, file):
67 r"""Read curve information from a PicoForce file.
69 Return a dict of dicts representing the information. If a
70 field is repeated multiple times, it's value is replaced by a
71 list of the values for each occurence.
78 >>> f = StringIO.StringIO('\r\n'.join([
79 ... '\*Force file list',
80 ... '\Version: 0x06120002',
81 ... '\Date: 04:42:34 PM Tue Sep 11 2007',
82 ... '\Start context: FOL2',
83 ... '\Data length: 40960',
85 ... '\*Equipment list',
86 ... '\Description: Extended PicoForce',
87 ... '\Controller: IIIA',
88 ... '\*Ciao force image list',
89 ... '\Data offset: 40960',
90 ... '\Data length: 8192',
91 ... '\*Ciao force image list',
92 ... '\Data offset: 49152',
93 ... '\Data length: 8192',
94 ... '\*Ciao force image list',
95 ... '\Data offset: 57344',
96 ... '\Data length: 8192',
98 >>> p = PicoForceDriver()
99 >>> d = p._read_header_file(f)
100 >>> pprint.pprint(d, width=60)
101 {'Ciao force image list': [{'Data length': '8192',
102 'Data offset': '40960'},
103 {'Data length': '8192',
104 'Data offset': '49152'},
105 {'Data length': '8192',
106 'Data offset': '57344'}],
107 'Equipment list': {'Controller': 'IIIA',
108 'Description': 'Extended PicoForce'},
109 'Force file list': {'Data length': '40960',
110 'Date': '04:42:34 PM Tue Sep 11 2007',
111 'Start context': 'FOL2',
113 'Version': '0x06120002'}}
119 if line.startswith('\*File list end'):
121 if line.startswith(r'\*'):
122 header_field = line[len(r'\*'):]
123 if header_field in info:
124 if isinstance(info[header_field], list):
125 info[header_field].append({}) # >=3rd appearance
126 else: # Second appearance
127 info[header_field] = [info[header_field], {}]
128 else: # First appearance
129 info[header_field] = {}
131 assert line.startswith('\\'), line
132 fields = line[len('\\'):].split(': ', 1)
134 if len(fields) == 1: # fields = [key]
136 else: # fields = [key, value]
138 if isinstance(info[header_field], list): # >=2nd header_field
139 target_dict = info[header_field][-1]
140 else: # first appearance of header_field
141 target_dict = info[header_field]
142 if key in target_dict and target_dict[key] != value:
143 raise NotImplementedError(
144 'Overwriting %s: %s -> %s'
145 % (key, target_dict[key], value))
146 target_dict[key] = value
149 def _check_version(self, info):
150 """Ensure the input file is a version we understand.
152 Otherwise, raise `ValueError`.
154 version = info['Force file list'].get('Version', None)
155 if version not in ['0x06120002', '0x06130001', '0x07200000']:
156 raise NotImplementedError(
157 '%s file version %s not supported (yet!)\n%s'
158 % (self.name, version,
159 pprint.pformat(info['Force file list'])))
161 def _read_data_path(self, path, info):
162 """Read curve data from the PicoForce file at `path`.
164 See :meth:`._read_data_file`.
167 data = self._read_data_file(f, info)
171 def _read_data_file(self, file, info):
173 traces = self._extract_traces(buffer(file.read()), info)
174 self._validate_traces(
175 traces['Z sensor'], traces['Deflection'])
176 L = len(traces['Deflection'])
177 approach = self._extract_block(
178 info, traces['Z sensor'], traces['Deflection'], 0, L/2, 'approach')
179 retract = self._extract_block(
180 info, traces['Z sensor'], traces['Deflection'], L/2, L, 'retract')
181 data = [approach, retract]
184 def _extract_traces(self, buffer, info):
185 """Extract each of the three vector blocks in a PicoForce file.
187 The blocks are (in variable order):
189 * Z piezo sensor input
193 And their headers are marked with 'Ciao force image list'.
196 version = info['Force file list']['Version']
197 type_re = re.compile('S \[(\w*)\] "([\w\s.]*)"')
198 for image in info['Ciao force image list']:
199 offset = int(image['Data offset'])
200 length = int(image['Data length'])
201 sample_size = int(image['Bytes/pixel'])
203 raise NotImplementedError('Size: %s' % sample_size)
204 rows = length / sample_size
212 if version in ['0x06120002', '0x06130001']:
213 match = type_re.match(image['@4:Image Data'])
214 assert match != None, 'Bad regexp for %s, %s' \
215 % ('@4:Image Data', image['@4:Image Data'])
216 assert match.group(1).lower() == match.group(2).replace(' ','').lower(), \
217 'Name missmatch: "%s", "%s"' % (match.group(1), match.group(2))
218 tname = match.group(2)
220 assert version == '0x07200000', version
221 match = type_re.match(image['@4:Image Data'])
222 assert match != None, 'Bad regexp for %s, %s' \
223 % ('@4:Image Data', image['@4:Image Data'])
224 if match.group(1) == 'PulseFreq1':
225 assert match.group(2) == 'Freq. 1', match.group(2)
227 assert match.group(1).lower() == match.group(2).replace(' ','').lower(), \
228 'Name missmatch: "%s", "%s"' % (match.group(1), match.group(2))
229 tname = match.group(2)
230 if tname == 'Freq. 1': # Normalize trace names between versions
232 elif tname == 'Deflection Error':
235 #d.tofile('%s-2.dat' % tname, sep='\n')
236 tname = self._replace_name(tname, d, traces, info)
238 continue # Don't replace anything
240 #d.tofile('%s.dat' % tname, sep='\n')
245 def _validate_traces(self, z_piezo, deflection):
246 if len(z_piezo) != len(deflection):
247 raise ValueError('Trace length missmatch: %d != %d'
248 % (len(z_piezo), len(deflection)))
250 def _extract_block(self, info, z_piezo, deflection, start, stop, name):
252 shape=(stop-start, 2),
254 block[:,0] = z_piezo[start:stop]
255 block[:,1] = deflection[start:stop]
256 block.info = self._translate_block_info(
257 info, z_piezo.info, deflection.info, name)
258 block.info['columns'] = ['z piezo (m)', 'deflection (m)']
259 block = self._scale_block(block)
262 def _replace_name(self, trace_name, trace, traces, info):
263 """Determine if a duplicate trace name should replace an earlier trace.
265 Return the target trace name if it should be replaced by the
266 new trace, or `None` if the new trace should be dropped.
269 #target = traces[trace_name]
271 ## Compare the info dictionaries for each trace
272 #ik = set(trace.info.keys())
273 #ok = set(traces[trace_name].info.keys())
274 #if ik != ok: # Ensure we have the same set of keys for both traces
275 # msg.append('extra keys: %s, missing keys %s' % (ik-ok, ok-ik))
277 # # List keys we *require* to change between traces
278 # variable_keys = ['Data offset', 'X data type'] # TODO: What is X data type?
279 # for key in trace.info.keys():
280 # if key in variable_keys:
281 # if target.info[key] == trace.info[key]:
282 # msg.append('constant %s (%s == %s)'
283 # % (key, target.info[key], trace.info[key]))
285 # if target.info[key] != trace.info[key]:
286 # msg.append('variable %s (%s != %s)'
287 # % (key, target.info[key], trace.info[key]))
289 #if not (traces[trace_name] == trace).all():
290 # msg.append('data difference')
292 # raise NotImplementedError(
293 # 'Missmatched duplicate traces for %s: %s'
294 # % (trace_name, ', '.join(msg)))
296 log = logging.getLogger('hooke')
297 for name,t in traces.items():
298 if (t == trace).all():
299 log.debug('replace %s with %s-2' % (name, trace_name))
300 return name # Replace this identical dataset.
301 log.debug('store %s-2 as Other' % (trace_name))
305 def _translate_block_info(self, info, z_piezo_info, deflection_info, name):
306 version = info['Force file list']['Version']
310 'raw z piezo info': z_piezo_info,
311 'raw deflection info': deflection_info,
312 'spring constant (N/m)': float(z_piezo_info['Spring Constant']),
315 t = info['Force file list']['Date'] # 04:42:34 PM Tue Sep 11 2007
316 ret['time'] = time.strptime(t, '%I:%M:%S %p %a %b %d %Y')
318 volt_re = re.compile(
319 'V \[Sens. ([\w\s.]*)\] \(([.0-9]*) V/LSB\) (-?[.0-9]*) V')
321 'V \[Sens. ([\w\s.]*)\] \(([.0-9]*) kHz/LSB\) (-?[.0-9]*) kHz')
322 if version in ['0x06120002', '0x06130001']:
323 match = volt_re.match(z_piezo_info['@4:Z scale'])
324 assert match != None, 'Bad regexp for %s, %s' \
325 % ('@4:Z scale', z_piezo_info['@4:Z scale'])
326 assert match.group(1) == 'ZSensorSens', z_piezo_info['@4:Z scale']
328 assert version == '0x07200000', version
329 match = hz_re.match(z_piezo_info['@4:Z scale'])
330 assert match != None, 'Bad regexp for %s, %s' \
331 % ('@4:Z scale', z_piezo_info['@4:Z scale'])
332 assert match.group(1) == 'Freq. 1', z_piezo_info['@4:Z scale']
333 ret['z piezo sensitivity (V/bit)'] = float(match.group(2))
334 ret['z piezo range (V)'] = float(match.group(3))
335 ret['z piezo offset (V)'] = 0.0
336 # offset assumed if raw data is signed...
338 match = volt_re.match(deflection_info['@4:Z scale'])
339 assert match != None, 'Bad regexp for %s, %s' \
340 % ('@4:Z scale', deflection_info['@4:Z scale'])
341 assert match.group(1) == 'DeflSens', z_piezo_info['@4:Z scale']
342 ret['deflection sensitivity (V/bit)'] = float(match.group(2))
343 ret['deflection range (V)'] = float(match.group(3))
344 ret['deflection offset (V)'] = 0.0
345 # offset assumed if raw data is signed...
347 nm_sens_re = re.compile('V ([.0-9]*) nm/V')
348 match = nm_sens_re.match(info['Scanner list']['@Sens. Zsens'])
349 assert match != None, 'Bad regexp for %s/%s, %s' \
350 % ('Scanner list', '@Sens. Zsens', info['Scanner list']['@4:Z scale'])
351 ret['z piezo sensitivity (m/V)'] = float(match.group(1))*1e-9
353 match = nm_sens_re.match(info['Ciao scan list']['@Sens. DeflSens'])
354 assert match != None, 'Bad regexp for %s/%s, %s' \
355 % ('Ciao scan list', '@Sens. DeflSens', info['Ciao scan list']['@Sens. DeflSens'])
356 ret['deflection sensitivity (m/V)'] = float(match.group(1))*1e-9
358 match = volt_re.match(info['Ciao force list']['@Z scan start'])
359 assert match != None, 'Bad regexp for %s/%s, %s' \
360 % ('Ciao force list', '@Z scan start', info['Ciao force list']['@Z scan start'])
361 ret['z piezo scan (V/bit)'] = float(match.group(2))
362 ret['z piezo scan start (V)'] = float(match.group(3))
364 match = volt_re.match(info['Ciao force list']['@Z scan size'])
365 assert match != None, 'Bad regexp for %s/%s, %s' \
366 % ('Ciao force list', '@Z scan size', info['Ciao force list']['@Z scan size'])
367 ret['z piezo scan size (V)'] = float(match.group(3))
369 const_re = re.compile('C \[([:\w\s]*)\] ([.0-9]*)')
370 match = const_re.match(z_piezo_info['@Z magnify'])
371 assert match != None, 'Bad regexp for %s, %s' \
372 % ('@Z magnify', info['@Z magnify'])
373 assert match.group(1) == '4:Z scale', match.group(1)
374 ret['z piezo gain'] = float(match.group(2))
376 if version in ['0x06120002', '0x06130001']:
377 match = volt_re.match(z_piezo_info['@4:Z scale'])
378 assert match != None, 'Bad regexp for %s, %s' \
379 % ('@4:Z scale', info['@4:Z scale'])
380 assert match.group(1) == 'ZSensorSens', match.group(1)
381 ret['z piezo sensitivity (V/bit)'] = float(match.group(2))
382 ret['z piezo range (V)'] = float(match.group(3))
384 assert version == '0x07200000', version
387 match = volt_re.match(z_piezo_info['@4:Ramp size'])
388 assert match != None, 'Bad regexp for %s, %s' \
389 % ('@4:Ramp size', info['@4:Ramp size'])
390 assert match.group(1) == 'Zsens', match.group(1)
391 ret['z piezo ramp size (V/bit)'] = float(match.group(2))
392 ret['z piezo ramp size (V)'] = float(match.group(3))
394 match = volt_re.match(z_piezo_info['@4:Ramp offset'])
395 assert match != None, 'Bad regexp for %s, %s' \
396 % ('@4:Ramp offset', info['@4:Ramp offset'])
397 assert match.group(1) == 'Zsens', match.group(1)
398 ret['z piezo ramp offset (V/bit)'] = float(match.group(2))
399 ret['z piezo ramp offset (V)'] = float(match.group(3))
406 def _scale_block(self, data):
407 """Convert the block from its native format to a `numpy.float`
416 ret.info['raw data'] = data # store the raw data
417 data.info = {} # break circular reference info <-> data
419 z_col = info['columns'].index('z piezo (m)')
420 d_col = info['columns'].index('deflection (m)')
422 # Leading '-' because Veeco's z increases towards the surface
423 # (positive indentation), but it makes more sense to me to
424 # have it increase away from the surface (positive
427 (data[:,z_col].astype(ret.dtype)
428 * info['z piezo sensitivity (V/bit)']
429 - info['z piezo offset (V)'])
430 * info['z piezo gain']
431 * info['z piezo sensitivity (m/V)']
434 # Leading '-' because deflection voltage increases as the tip
435 # moves away from the surface, but it makes more sense to me
436 # to have it increase as it moves toward the surface (positive
437 # tension on the protein chain).
440 * info['deflection sensitivity (V/bit)']
441 - info['deflection offset (V)'])
442 * info['deflection sensitivity (m/V)']