1 # Copyright (C) 2010 W. Trevor King <wking@drexel.edu>
3 # This file is part of Hooke.
5 # Hooke is free software: you can redistribute it and/or modify it
6 # under the terms of the GNU Lesser General Public License as
7 # published by the Free Software Foundation, either version 3 of the
8 # License, or (at your option) any later version.
10 # Hooke is distributed in the hope that it will be useful, but WITHOUT
11 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
12 # or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General
13 # Public License for more details.
15 # You should have received a copy of the GNU Lesser General Public
16 # License along with Hooke. If not, see
17 # <http://www.gnu.org/licenses/>.
19 """Driver for W. Trevor King's velocity clamp data format.
21 See my related projects:
23 * http://www.physics.drexel.edu/~wking/code/git/git.php?p=unfold_protein.git
24 * http://www.physics.drexel.edu/~wking/code/git/git.php?p=calibrate_cantilever.git
25 * http://www.physics.drexel.edu/~wking/code/git/git.php?p=data_logger.git
26 * http://www.physics.drexel.edu/~wking/code/git/git.php?p=piezo.git
27 * http://www.physics.drexel.edu/~wking/code/git/git.php?p=pycomedi.git
29 And the deprecated projects (which Hooke replaces):
31 * http://www.physics.drexel.edu/~wking/code/git/git.php?p=scale_unfold.git
32 * http://www.physics.drexel.edu/~wking/code/git/git.php?p=sawmodel.git
44 from .. import curve as curve
45 from .. import experiment as experiment
46 from ..config import Setting
47 from . import Driver as Driver
50 import calibcant.config
51 calibcant_dir = calibcant.config.LOG_DIR
61 class WTKDriver (Driver):
62 """Handle W. Trevor King's data_logger data format.
65 super(WTKDriver, self).__init__(name='wtk')
67 def default_settings(self):
69 Setting(section=self.setting_section, help=self.__doc__),
70 Setting(section=self.setting_section,
71 option='cantilever calibration directory',
72 value=calibcant_dir, type='path',
73 help='Set the directory where cantilever calibration data is stored'),
76 def is_me(self, path):
77 if os.path.isdir(path):
79 if not path.endswith('_unfold'):
81 for p in self._paths(path):
82 if not os.path.isfile(p):
86 def read(self, path, info=None):
87 approach_path,retract_path,param_path = self._paths(path)
89 unlabeled_approach_data = numpy.loadtxt(
90 approach_path, dtype=numpy.uint16)
91 unlabeled_retract_data = numpy.loadtxt(
92 retract_path, dtype=numpy.uint16)
93 params = self._read_params(param_path)
94 params = self._translate_params(params)
96 # move data into Data blocks.
97 approach = self._scale_block(
98 unlabeled_approach_data, params, 'approach')
99 retract = self._scale_block(
100 unlabeled_retract_data, params, 'retract')
101 info = {'filetype':self.name, 'experiment':experiment.VelocityClamp()}
102 return ([approach, retract], info)
104 def _paths(self, path):
105 return (path+'_approach', path, path+'_param')
107 def _read_params(self, param_path):
109 for line in file(param_path):
110 ldata = [x.strip() for x in line.split(':', 1)]
111 if ldata[0] == 'Data fields':
112 params['columns'] = ldata[1].split()
113 elif len(ldata) == 2:
114 argwords = ldata[1].split()
115 if ldata[0] == 'Time' or len(argwords) != 1:
116 params[ldata[0]] = ldata[1]
117 else: # single word probably a number
118 params[ldata[0]] = float(ldata[1])
120 pass # ignore comment lines
123 def _translate_params(self, params):
124 ret = {'raw info':params,}
126 t = params['Time'] # 20100504135849
127 ret['time'] = self._time_from_localtime_string(t)
129 assert params['columns'] == ['Z_piezo_out', 'Deflection_in', 'Z_piezo_in'], \
130 'Unexpected columns: %s' % ret['columns']
131 ret['columns'] = ['z piezo (m)', 'deflection (m)', ]
133 calibcant_file = self._find_previous_cantilever_calibration_file(
135 calibcant_info = self._read_cantilever_calibration_file(calibcant_file)
136 ret['raw spring constant'] = calibcant_info
137 ret['spring constant (N/m)'] = calibcant_info['Cantilever k (N/m)']
138 ret['deflection sensitivity (m/V)'] = \
139 1.0/numpy.sqrt(calibcant_info['photoSensitivity**2 (V/nm)**2']) * 1e-9
141 # (32768 bits = 2**15 bits = 10 Volts)
142 ret['deflection sensitivity (V/bit)'] = 1.0/3276.8
143 ret['deflection range (V)'] = 20.0
144 ret['deflection offset (V)'] = 10.0 # assumes raw data is unsigned
146 ret['z piezo sensitivity (V/bit)'] = 1.0/3276.8 # output volts / bit
147 ret['z piezo range (V)'] = 20.0 # output volts
148 ret['z piezo offset (V)'] = 10.0 # output volts, assumes unsigned
149 ret['z piezo gain'] = \
150 params['Z piezo gain (Vp/Vo)'] # piezo volts / output volt
151 ret['z piezo sensitivity (m/V)'] = \
152 params['Z piezo sensitivity (nm/Vp)'] * 1e-9 # m / piezo volts
156 def _scale_block(self, data, info, name):
157 """Convert the block from its native format to a `numpy.float`
161 shape=(data.shape[0], 2),
163 info=copy.deepcopy(info)
165 ret.info['name'] = name
166 ret.info['raw data'] = data # store the raw data
167 ret.info['columns'] = ['z piezo (m)', 'deflection (m)']
170 # approach data does not have a Z_piezo_in column as of unfold v0.0.
171 z_rcol = info['raw info']['columns'].index('Z_piezo_out')
172 d_rcol = info['raw info']['columns'].index('Deflection_in')
174 # scaled column indices
175 z_scol = ret.info['columns'].index('z piezo (m)')
176 d_scol = ret.info['columns'].index('deflection (m)')
178 # Leading '-' because increasing voltage extends the piezo,
179 # moving the tip towards the surface (positive indentation),
180 # but it makes more sense to me to have it increase away from
181 # the surface (positive separation).
183 (data[:,z_rcol].astype(ret.dtype)
184 * info['z piezo sensitivity (V/bit)']
185 - info['z piezo offset (V)'])
186 * info['z piezo gain']
187 * info['z piezo sensitivity (m/V)']
190 # Leading '-' because deflection voltage increases as the tip
191 # moves away from the surface, but it makes more sense to me
192 # to have it increase as it moves toward the surface (positive
193 # tension on the protein chain).
196 * info['deflection sensitivity (V/bit)']
197 - info['deflection offset (V)'])
198 * info['deflection sensitivity (m/V)']
203 def _list_re_search(self, list, regexp):
204 "Return list entries matching re"
205 reg = re.compile(regexp)
212 def _list_cantilever_calibration_files(self, timestamp=None, basedir=None):
213 if timestamp == None:
214 timestamp = time.time()
216 basedir = self.config['cantilever calibration directory']
217 YYYYMMDD = time.strftime("%Y%m%d", time.localtime(timestamp))
218 dir = os.path.join(data_logger.normalize_logdir(basedir), YYYYMMDD)
219 if not os.path.exists(dir):
221 all_calibfiles = os.listdir(dir) # everything in the directory
222 #regexp = "%s.*_analysis_text " % (YYYYMMDD)
223 regexp = ".*_analysis_text"
224 calibfiles = self._list_re_search(all_calibfiles, regexp)
225 paths = [os.path.join(dir, cf) for cf in calibfiles]
228 def _calibfile_timestamp(self, path):
229 filename = os.path.basename(path)
230 YYYYMMDDHHMMSS = filename[0:14]
231 return self._time_from_localtime_string(YYYYMMDDHHMMSS)
233 def _find_previous_cantilever_calibration_file(
234 self, timestamp=None, basedir=None, previous_days=1):
236 If timestamp == None, uses current time.
237 Warning : brittle! depends on the default data_logger.py save filesystem.
238 Renaming files or moving directories will break me.
240 #if FORCED_CANTILEVER_CALIBRATION_FILE != None:
241 # return FORCED_CANTILEVER_CALIBRATION_FILE
243 for i in range(previous_days+1):
244 calibfiles.extend(self._list_cantilever_calibration_files(
245 timestamp-24*3600*i,basedir=basedir))
246 assert len(calibfiles) > 0 , \
247 "No calibration files in that day range in directory '%s'" % basedir
249 for i in range(len(calibfiles)):
250 if self._calibfile_timestamp(calibfiles[i]) > timestamp:
255 def _read_cantilever_calibration_file(self, filename):
256 ret = {'file': filename}
257 line_re = re.compile('(.*) *: (.*) [+]/- (.*) \((.*)\)\n')
258 for line in file(filename):
259 match = line_re.match(line)
262 'Invalid cantilever calibration line in %s: %s'
264 key,value,std_dev,rel_err = [
265 x.strip() for x in match.group(*range(1,5))]
266 if key == 'Variable (units)':
267 continue # ignore the header line
269 std_dev = float(std_dev)
270 # Handle older calibcant output.
272 key = 'Cantilever k (N/m)'
273 elif key == 'a**2 (V/nm)**2':
274 key = 'photoSensitivity**2 (V/nm)**2'
276 ret[key + ' (std. dev.)'] = std_dev
279 def _time_from_localtime_string(self, timestring, format="%Y%m%d%H%M%S"):
281 >>> print time.tzname
284 >>> d._time_from_localtime_string("19700101", format="%Y%m%d")/3600.0
286 >>> d._time_from_localtime_string("20081231", format="%Y%m%d")
288 >>> d._time_from_localtime_string("20090101", format="%Y%m%d")
291 timestruct = time.strptime(timestring, format)
292 timestamp = calendar.timegm(timestruct)
293 # Date strings are in localtime, so what we really want is
294 # .timelocale, but that doesn't exist. Workaround to convert
296 timestamp += time.timezone # assume no Daylight Savings Time (DST)
297 if bool(time.localtime(timestamp).tm_isdst) == True:
298 timestamp -= time.timezone - time.altzone # correct if DST
299 assert time.strftime(format, time.localtime(timestamp)) == timestring, "error in time_from_localtime_string, %s != %s" % (time.strftime(format, time.localtime(timestamp)), timestring)