-# Copyright (C) 2008-2010 A. Seeholzer
-# Alberto Gomez-Casado
-# Richard Naud <richard.naud@epfl.ch>
+# Copyright (C) 2008-2012 A. Seeholzer
+# Alberto Gomez-Casado <a.gomezcasado@tnw.utwente.nl>
+# Richard Naud
# Rolf Schmidt <rschmidt@alcor.concordia.ca>
# W. Trevor King <wking@drexel.edu>
#
# This file is part of Hooke.
#
-# Hooke is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as
-# published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
+# Hooke is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
#
-# Hooke is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General
-# Public License for more details.
+# Hooke is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
#
-# You should have received a copy of the GNU Lesser General Public
-# License along with Hooke. If not, see
-# <http://www.gnu.org/licenses/>.
+# You should have received a copy of the GNU Lesser General Public License
+# along with Hooke. If not, see <http://www.gnu.org/licenses/>.
"""Driver for MFP-3D files.
"""
import copy
+import os.path
import pprint
import numpy
from .. import curve as curve
-from .. import experiment as experiment
-from ..config import Setting
+from ..util.igorbinarywave import loadibw
from . import Driver as Driver
-from .igorbinarywave import loadibw
__version__='0.0.0.20100604'
def is_me(self, path):
"""Look for identifying fields in the IBW note.
"""
+ if os.path.isdir(path):
+ return False
if not path.endswith('.ibw'):
return False
targets = ['Version:', 'XOPVersion:', 'ForceNote:']
def read(self, path, info=None):
data,bin_info,wave_info = loadibw(path)
- approach,retract = self._translate_ibw(data, bin_info, wave_info)
-
- info = {'filetype':self.name, 'experiment':experiment.VelocityClamp}
- return ([approach, retract], info)
+ blocks,info = self._translate_ibw(data, bin_info, wave_info)
+ return (blocks, info)
def _translate_ibw(self, data, bin_info, wave_info):
if bin_info['version'] != 5:
value = None
note[key] = value
bin_info['note'] = note
+
+ # Ensure a valid MFP3D file version.
if note['VerDate'] not in ['80501.041', '80501.0207']:
raise Exception(note['VerDate'])
raise NotImplementedError(
'%s file version %s not supported (yet!)\n%s'
% (self.name, note['VerDate'], pprint.pformat(note)))
+ # Parse known parameters into standard Hooke format.
info = {
'raw info':{'bin':bin_info,
'wave':wave_info},
- 'time':wave_info['creationDate'],
- 'spring constant (N/m)':note['SpringConstant'],
+ 'time':note['Seconds'],
+ 'spring constant (N/m)':float(note['SpringConstant']),
+ 'temperature (K)':self._temperature(note),
}
- # MFP3D's native data dimensions match Hooke's (<point>, <column>) layout.
- approach = self._scale_block(data[:wave_info['npnts']/2,:], info, 'approach')
- retract = self._scale_block(data[wave_info['npnts']/2:,:], info, 'retract')
- return (approach, retract)
- def _scale_block(self, data, info, name):
+ # Extract data blocks
+ blocks = []
+ indexes = [int(i) for i in note['Indexes'].split(',')]
+ assert indexes[0] == 0, indexes
+ for i,start in enumerate(indexes[:-1]):
+ stop = indexes[i+1]
+ blocks.append(self._scale_block(data[start:stop+1,:], info, i))
+
+ return (blocks, info)
+
+ def _scale_block(self, data, info, index):
"""Convert the block from its native format to a `numpy.float`
array in SI units.
"""
+ # MFP3D's native data dimensions match Hooke's (<point>, <column>) layout.
shape = 3
# raw column indices
columns = info['raw info']['bin']['dimLabels'][1]
dtype=numpy.float,
info=copy.deepcopy(info)
)
+
+ version = info['raw info']['bin']['note']['VerDate']
+ if version == '80501.041':
+ name = ['approach', 'retract', 'pause'][index]
+ elif version == '80501.0207':
+ name = ['approach', 'pause', 'retract'][index]
+ else:
+ raise NotImplementedError()
ret.info['name'] = name
ret.info['raw data'] = data # store the raw data
ret[:,t_scol] = data[:,t_rcol]
return ret
+
+ def _temperature(self, note):
+ # I'm not sure which field we should be using here. Options are:
+ # StartHeadTemp
+ # StartScannerTemp
+ # StartBioHeaterTemp
+ # EndScannerTemp
+ # EndHeadTemp
+ # I imagine the 'Start*Temp' fields were measured at
+ # 'StartTempSeconds' at the beginning of a series of curves,
+ # while our particular curve was initiated at 'Seconds'.
+ # python -c "from hooke.hooke import Hooke;
+ # h=Hooke();
+ # h.run_command('load playlist',
+ # {'input':'test/data/vclamp_mfp3d/playlist'});
+ # x = [(int(c.info['raw info']['bin']['note']['Seconds'])
+ # - int(c.info['raw info']['bin']['note']['StartTempSeconds']))
+ # for c in h.playlists.current().items()];
+ # print 'average', float(sum(x))/len(x);
+ # print 'range', min(x), max(x);
+ # print x"
+ # For the Line*Point*.ibw series, the difference increases slowly
+ # 46, 46, 47, 47, 48, 49, 49, 50, 50, 51, 51, 52, 52, 53, 53, 54,...
+ # However, for the Image*.ibw series, the difference increase
+ # is much faster:
+ # 21, 38, 145, 150, 171, 181
+ # This makes the 'Start*Temp' fields less and less relevant as
+ # the experiment continues. Still, I suppose it's better than
+ # nothing.
+ #
+ # The 'Thermal' fields seem to be related to cantilever calibration.
+ celsius = unicode(note['StartHeadTemp'], 'latin-1')
+ if celsius.endswith(u' \u00b0C'):
+ number = celsius.split(None, 1)[0]
+ return float(number) + 273.15 # Convert to Kelvin.
+ else:
+ raise NotImplementedError(
+ 'unkown temperature format: %s' % repr(celsius))
projects / hooke.git / blobdiff