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 modify it
8 # under the terms of the GNU Lesser General Public License as
9 # published by the Free Software Foundation, either version 3 of the
10 # License, or (at your option) any later version.
12 # Hooke is distributed in the hope that it will be useful, but WITHOUT
13 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
14 # or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General
15 # 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 . import Driver as Driver # this is the Driver base class
35 __version__='0.0.0.20100516'
37 class PicoForceDriver (Driver):
38 """Handle Veeco Picoforce force spectroscopy files.
41 super(PicoForceDriver, self).__init__(name='picoforce')
43 def is_me(self, path):
48 return header[2:17] == 'Force file list'
50 def read(self, path, info=None):
51 info = self._read_header_path(path)
52 self._check_version(info)
53 data = self._read_data_path(path, info)
54 info['filetype'] = self.name
55 info['experiment'] = experiment.VelocityClamp
58 def _read_header_path(self, path):
59 """Read curve information from the PicoForce file at `path`.
61 See :meth:`._read_header_file`.
63 return self._read_header_file(file(path, 'rb'))
65 def _read_header_file(self, file):
66 r"""Read curve information from a PicoForce file.
68 Return a dict of dicts representing the information. If a
69 field is repeated multiple times, it's value is replaced by a
70 list of the values for each occurence.
77 >>> f = StringIO.StringIO('\r\n'.join([
78 ... '\*Force file list',
79 ... '\Version: 0x06120002',
80 ... '\Date: 04:42:34 PM Tue Sep 11 2007',
81 ... '\Start context: FOL2',
82 ... '\Data length: 40960',
84 ... '\*Equipment list',
85 ... '\Description: Extended PicoForce',
86 ... '\Controller: IIIA',
87 ... '\*Ciao force image list',
88 ... '\Data offset: 40960',
89 ... '\Data length: 8192',
90 ... '\*Ciao force image list',
91 ... '\Data offset: 49152',
92 ... '\Data length: 8192',
93 ... '\*Ciao force image list',
94 ... '\Data offset: 57344',
95 ... '\Data length: 8192',
97 >>> p = PicoForceDriver()
98 >>> d = p._read_header_file(f)
99 >>> pprint.pprint(d, width=60)
100 {'Ciao force image list': [{'Data length': '8192',
101 'Data offset': '40960'},
102 {'Data length': '8192',
103 'Data offset': '49152'},
104 {'Data length': '8192',
105 'Data offset': '57344'}],
106 'Equipment list': {'Controller': 'IIIA',
107 'Description': 'Extended PicoForce'},
108 'Force file list': {'Data length': '40960',
109 'Date': '04:42:34 PM Tue Sep 11 2007',
110 'Start context': 'FOL2',
112 'Version': '0x06120002'}}
118 if line.startswith('\*File list end'):
120 if line.startswith(r'\*'):
121 header_field = line[len(r'\*'):]
122 if header_field in info:
123 if isinstance(info[header_field], list):
124 info[header_field].append({}) # >=3rd appearance
125 else: # Second appearance
126 info[header_field] = [info[header_field], {}]
127 else: # First appearance
128 info[header_field] = {}
130 assert line.startswith('\\'), line
131 fields = line[len('\\'):].split(': ', 1)
133 if len(fields) == 1: # fields = [key]
135 else: # fields = [key, value]
137 if isinstance(info[header_field], list): # >=2nd header_field
138 target_dict = info[header_field][-1]
139 else: # first appearance of header_field
140 target_dict = info[header_field]
141 if key in target_dict and target_dict[key] != value:
142 raise NotImplementedError(
143 'Overwriting %s: %s -> %s'
144 % (key, target_dict[key], value))
145 target_dict[key] = value
148 def _check_version(self, info):
149 """Ensure the input file is a version we understand.
151 Otherwise, raise `ValueError`.
153 version = info['Force file list'].get('Version', None)
154 if version not in ['0x06120002', '0x06130001', '0x07200000']:
155 raise NotImplementedError(
156 '%s file version %s not supported (yet!)\n%s'
157 % (self.name, version,
158 pprint.pformat(info['Force file list'])))
160 def _read_data_path(self, path, info):
161 """Read curve data from the PicoForce file at `path`.
163 See :meth:`._read_data_file`.
166 data = self._read_data_file(f, info)
170 def _read_data_file(self, file, info):
172 traces = self._extract_traces(buffer(file.read()), info)
173 self._validate_traces(
174 traces['Z sensor'], traces['Deflection'])
175 L = len(traces['Deflection'])
176 approach = self._extract_block(
177 info, traces['Z sensor'], traces['Deflection'], 0, L/2, 'approach')
178 retract = self._extract_block(
179 info, traces['Z sensor'], traces['Deflection'], L/2, L, 'retract')
180 data = [approach, retract]
183 def _extract_traces(self, buffer, info):
184 """Extract each of the three vector blocks in a PicoForce file.
186 The blocks are (in variable order):
188 * Z piezo sensor input
192 And their headers are marked with 'Ciao force image list'.
195 version = info['Force file list']['Version']
196 type_re = re.compile('S \[(\w*)\] "([\w\s.]*)"')
197 for image in info['Ciao force image list']:
198 offset = int(image['Data offset'])
199 length = int(image['Data length'])
200 sample_size = int(image['Bytes/pixel'])
202 raise NotImplementedError('Size: %s' % sample_size)
203 rows = length / sample_size
211 if version in ['0x06120002', '0x06130001']:
212 match = type_re.match(image['@4:Image Data'])
213 assert match != None, 'Bad regexp for %s, %s' \
214 % ('@4:Image Data', image['@4:Image Data'])
215 if version == '0x06130001' and match.group(1) == 'ZLowVoltage':
216 assert match.group(2) == 'Low Voltage Z', \
217 'Name missmatch: "%s", "%s"' % (match.group(1), match.group(2))
219 assert match.group(1).lower() == match.group(2).replace(' ','').lower(), \
220 'Name missmatch: "%s", "%s"' % (match.group(1), match.group(2))
221 tname = match.group(2)
223 assert version == '0x07200000', version
224 match = type_re.match(image['@4:Image Data'])
225 assert match != None, 'Bad regexp for %s, %s' \
226 % ('@4:Image Data', image['@4:Image Data'])
227 if match.group(1) == 'PulseFreq1':
228 assert match.group(2) == 'Freq. 1', match.group(2)
230 assert match.group(1).lower() == match.group(2).replace(' ','').lower(), \
231 'Name missmatch: "%s", "%s"' % (match.group(1), match.group(2))
232 tname = match.group(2)
233 if tname == 'Freq. 1': # Normalize trace names between versions
235 elif tname == 'Deflection Error':
238 #d.tofile('%s-2.dat' % tname, sep='\n')
239 tname = self._replace_name(tname, d, traces, info)
241 continue # Don't replace anything
243 #d.tofile('%s.dat' % tname, sep='\n')
248 def _validate_traces(self, z_piezo, deflection):
249 if len(z_piezo) != len(deflection):
250 raise ValueError('Trace length missmatch: %d != %d'
251 % (len(z_piezo), len(deflection)))
253 def _extract_block(self, info, z_piezo, deflection, start, stop, name):
255 shape=(stop-start, 2),
257 block[:,0] = z_piezo[start:stop]
258 block[:,1] = deflection[start:stop]
259 block.info = self._translate_block_info(
260 info, z_piezo.info, deflection.info, name)
261 block.info['columns'] = ['z piezo (m)', 'deflection (m)']
262 block = self._scale_block(block)
265 def _replace_name(self, trace_name, trace, traces, info):
266 """Determine if a duplicate trace name should replace an earlier trace.
268 Return the target trace name if it should be replaced by the
269 new trace, or `None` if the new trace should be dropped.
272 #target = traces[trace_name]
274 ## Compare the info dictionaries for each trace
275 #ik = set(trace.info.keys())
276 #ok = set(traces[trace_name].info.keys())
277 #if ik != ok: # Ensure we have the same set of keys for both traces
278 # msg.append('extra keys: %s, missing keys %s' % (ik-ok, ok-ik))
280 # # List keys we *require* to change between traces
281 # variable_keys = ['Data offset', 'X data type'] # TODO: What is X data type?
282 # for key in trace.info.keys():
283 # if key in variable_keys:
284 # if target.info[key] == trace.info[key]:
285 # msg.append('constant %s (%s == %s)'
286 # % (key, target.info[key], trace.info[key]))
288 # if target.info[key] != trace.info[key]:
289 # msg.append('variable %s (%s != %s)'
290 # % (key, target.info[key], trace.info[key]))
292 #if not (traces[trace_name] == trace).all():
293 # msg.append('data difference')
295 # raise NotImplementedError(
296 # 'Missmatched duplicate traces for %s: %s'
297 # % (trace_name, ', '.join(msg)))
299 log = logging.getLogger('hooke')
300 for name,t in traces.items():
301 if (t == trace).all():
302 log.debug('replace %s with %s-2' % (name, trace_name))
303 return name # Replace this identical dataset.
304 log.debug('store %s-2 as Other' % (trace_name))
308 def _translate_block_info(self, info, z_piezo_info, deflection_info, name):
309 version = info['Force file list']['Version']
313 'raw z piezo info': z_piezo_info,
314 'raw deflection info': deflection_info,
315 'spring constant (N/m)': float(z_piezo_info['Spring Constant']),
318 t = info['Force file list']['Date'] # 04:42:34 PM Tue Sep 11 2007
319 ret['time'] = time.strptime(t, '%I:%M:%S %p %a %b %d %Y')
321 volt_re = re.compile(
322 'V \[Sens. ([\w\s.]*)\] \(([.0-9]*) V/LSB\) (-?[.0-9]*) V')
324 'V \[Sens. ([\w\s.]*)\] \(([.0-9]*) kHz/LSB\) (-?[.0-9]*) kHz')
325 if version in ['0x06120002', '0x06130001']:
326 match = volt_re.match(z_piezo_info['@4:Z scale'])
327 assert match != None, 'Bad regexp for %s, %s' \
328 % ('@4:Z scale', z_piezo_info['@4:Z scale'])
329 assert match.group(1) == 'ZSensorSens', z_piezo_info['@4:Z scale']
331 assert version == '0x07200000', version
332 match = hz_re.match(z_piezo_info['@4:Z scale'])
333 assert match != None, 'Bad regexp for %s, %s' \
334 % ('@4:Z scale', z_piezo_info['@4:Z scale'])
335 assert match.group(1) == 'Freq. 1', z_piezo_info['@4:Z scale']
336 ret['z piezo sensitivity (V/bit)'] = float(match.group(2))
337 ret['z piezo range (V)'] = float(match.group(3))
338 ret['z piezo offset (V)'] = 0.0
339 # offset assumed if raw data is signed...
341 match = volt_re.match(deflection_info['@4:Z scale'])
342 assert match != None, 'Bad regexp for %s, %s' \
343 % ('@4:Z scale', deflection_info['@4:Z scale'])
344 assert match.group(1) == 'DeflSens', z_piezo_info['@4:Z scale']
345 ret['deflection sensitivity (V/bit)'] = float(match.group(2))
346 ret['deflection range (V)'] = float(match.group(3))
347 ret['deflection offset (V)'] = 0.0
348 # offset assumed if raw data is signed...
350 nm_sens_re = re.compile('V ([.0-9]*) nm/V')
351 if version in ['0x06120002', '0x06130001']:
352 match = nm_sens_re.match(info['Ciao scan list']['@Sens. ZSensorSens'])
353 assert match != None, 'Bad regexp for %s/%s, %s' \
354 % ('Ciao scan list', '@Sens. ZSensorSens',
355 info['Ciao scan list']['@Sens. ZSensorSens'])
357 assert version == '0x07200000', version
358 match = nm_sens_re.match(info['Ciao scan list']['@Sens. ZsensSens'])
359 assert match != None, 'Bad regexp for %s/%s, %s' \
360 % ('Ciao scan list', '@Sens. ZsensSens',
361 info['Ciao scan list']['@Sens. ZsensSens'])
362 ret['z piezo sensitivity (m/V)'] = float(match.group(1))*1e-9
364 match = nm_sens_re.match(info['Ciao scan list']['@Sens. DeflSens'])
365 assert match != None, 'Bad regexp for %s/%s, %s' \
366 % ('Ciao scan list', '@Sens. DeflSens', info['Ciao scan list']['@Sens. DeflSens'])
367 ret['deflection sensitivity (m/V)'] = float(match.group(1))*1e-9
369 match = volt_re.match(info['Ciao force list']['@Z scan start'])
370 assert match != None, 'Bad regexp for %s/%s, %s' \
371 % ('Ciao force list', '@Z scan start', info['Ciao force list']['@Z scan start'])
372 ret['z piezo scan (V/bit)'] = float(match.group(2))
373 ret['z piezo scan start (V)'] = float(match.group(3))
375 match = volt_re.match(info['Ciao force list']['@Z scan size'])
376 assert match != None, 'Bad regexp for %s/%s, %s' \
377 % ('Ciao force list', '@Z scan size', info['Ciao force list']['@Z scan size'])
378 ret['z piezo scan size (V)'] = float(match.group(3))
380 const_re = re.compile('C \[([:\w\s]*)\] ([.0-9]*)')
381 match = const_re.match(z_piezo_info['@Z magnify'])
382 assert match != None, 'Bad regexp for %s, %s' \
383 % ('@Z magnify', info['@Z magnify'])
384 assert match.group(1) == '4:Z scale', match.group(1)
385 ret['z piezo gain'] = float(match.group(2))
387 if version in ['0x06120002', '0x06130001']:
388 match = volt_re.match(z_piezo_info['@4:Z scale'])
389 assert match != None, 'Bad regexp for %s, %s' \
390 % ('@4:Z scale', info['@4:Z scale'])
391 assert match.group(1) == 'ZSensorSens', match.group(1)
392 ret['z piezo sensitivity (V/bit)'] = float(match.group(2))
393 ret['z piezo range (V)'] = float(match.group(3))
395 assert version == '0x07200000', version
398 match = volt_re.match(z_piezo_info['@4:Ramp size'])
399 assert match != None, 'Bad regexp for %s, %s' \
400 % ('@4:Ramp size', info['@4:Ramp size'])
401 assert match.group(1) == 'Zsens', match.group(1)
402 ret['z piezo ramp size (V/bit)'] = float(match.group(2))
403 ret['z piezo ramp size (V)'] = float(match.group(3))
405 match = volt_re.match(z_piezo_info['@4:Ramp offset'])
406 assert match != None, 'Bad regexp for %s, %s' \
407 % ('@4:Ramp offset', info['@4:Ramp offset'])
408 assert match.group(1) == 'Zsens', match.group(1)
409 ret['z piezo ramp offset (V/bit)'] = float(match.group(2))
410 ret['z piezo ramp offset (V)'] = float(match.group(3))
417 def _scale_block(self, data):
418 """Convert the block from its native format to a `numpy.float`
427 ret.info['raw data'] = data # store the raw data
428 data.info = {} # break circular reference info <-> data
430 z_col = info['columns'].index('z piezo (m)')
431 d_col = info['columns'].index('deflection (m)')
433 # Leading '-' because Veeco's z increases towards the surface
434 # (positive indentation), but it makes more sense to me to
435 # have it increase away from the surface (positive
438 (data[:,z_col].astype(ret.dtype)
439 * info['z piezo sensitivity (V/bit)']
440 - info['z piezo offset (V)'])
441 * info['z piezo gain']
442 * info['z piezo sensitivity (m/V)']
445 # Leading '-' because deflection voltage increases as the tip
446 # moves away from the surface, but it makes more sense to me
447 # to have it increase as it moves toward the surface (positive
448 # tension on the protein chain).
451 * info['deflection sensitivity (V/bit)']
452 - info['deflection offset (V)'])
453 * info['deflection sensitivity (m/V)']