DRIVER_MODULES = [
# ('csvdriver', True),
# ('hdf5', True),
-# ('hemingclamp', True),
+ ('hemingway', True),
('jpk', True),
# ('mcs', True),
# ('mfp1dexport', True),
+++ /dev/null
-# Copyright (C) 2008-2010 Massimo Sandal <devicerandom@gmail.com>
-# 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 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/>.
-
-"""Library for interpreting Hemingway force spectroscopy files.
-"""
-__version__='2007_02_15_devel'
-
-__changelog__='''
-2007_02_15: fixed time counter with my counter
-2007_02_07: Initial implementation
-'''
-import string
-from .. import curve as lhc
-
-class DataChunk(list):
- '''Dummy class to provide ext and ret methods to the data list.
- In this case ext and self can be equal.
- '''
-
- def ext(self):
- return self
-
- def ret(self):
- return self
-
-class hemingclampDriver(lhc.Driver):
-
- def __init__(self, filename):
-
- self.filedata = open(filename,'r')
- self.data = self.filedata.readlines()[6:]
- self.filedata.close()
-
- self.filetype = 'hemingclamp'
- self.experiment = 'clamp'
-
- self.filename=filename
-
- def __del__(self):
- self.filedata.close()
-
- def is_me(self):
- '''
- we define our magic heuristic for HemingClamp files
- '''
- myfile=file(self.filename)
- headerlines=myfile.readlines()[0:3]
- myfile.close()
- if headerlines[0][0:10]=='#Hemingway' and headerlines[1][0:19]=='#Experiment: FClamp':
- return True
- else:
- return False
-
- def _getdata_all(self):
- time = []
- phase = []
- zpiezo = []
- defl = []
- imposed = []
- trim_indexes = []
- trim_counter = 0.0
-
- for i in self.data:
- temp = string.split(i)
- #time.append(float(temp[0])*(1.0e-3)) # This is managed differently now, since each data point = 1ms: see below
- phase.append(float(temp[1])*(1.0e-7)) # The nonsensical (e-7) multiplier is just there to make phase data nicely plottable along other data
- zpiezo.append(float(temp[2])*(1.0e-9))
- defl.append(float(temp[3])*(1.0e-9))
- imposed.append(float(temp[4])*(1.0e-9))
-
- for x in range (0,len(phase)):
- if phase[x] != trim_counter:
- trim_indexes.append(x)
- trim_counter = phase[x]
-
- #we rebuild the time counter assuming 1 point = 1 millisecond
- c=0.0
- for z in zpiezo:
- time.append(c)
- c+=(1.0e-3)
-
- return time,phase,zpiezo,defl,imposed,trim_indexes
-
- def time(self):
- return DataChunk(self._getdata_all()[0])
-
- def phase(self):
- return DataChunk(self._getdata_all()[1])
-
- def zpiezo(self):
- return DataChunk(self._getdata_all()[2])
-
- def deflection(self):
- return DataChunk(self._getdata_all()[3])
-
- def imposed(self):
- return DataChunk(self._getdata_all()[4])
-
- def trimindexes(self):
- return DataChunk(self._getdata_all()[5])
-
- def close_all(self):
- '''
- Explicitly closes all files
- '''
- self.filedata.close()
-
- def default_plots(self):
- main_plot=lhc.PlotObject()
- defl_plot=lhc.PlotObject()
-
- time=self.time()
- phase=self.phase()
- zpiezo=self.zpiezo()
- deflection=self.deflection()
- imposed=self.imposed()
-
- main_plot.vectors=[[time,zpiezo],[time,phase]]
- main_plot.units=['seconds','meters']
- main_plot.destination=0
- main_plot.title=self.filename
-
- defl_plot.vectors=[[time,deflection],[time,imposed]]
- defl_plot.units=['seconds','Newtons']
- defl_plot.destination=1
-
- return [main_plot, defl_plot]
-
--- /dev/null
+# Copyright (C) 2008-2010 Massimo Sandal <devicerandom@gmail.com>
+# 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 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/>.
+
+"""Library for interpreting Hemingway force spectroscopy files.
+"""
+
+import numpy
+
+from .. import curve as curve
+from .. import experiment as experiment
+from ..config import Setting
+from ..util.util import Closing as Closing
+from . import Driver as Driver
+
+
+class HemingwayDriver (Driver):
+ """Handle Hemingway force spectroscopy files.
+ """
+ def __init__(self):
+ super(HemingwayDriver, self).__init__(name='hemingway')
+
+ def is_me(self, path):
+ headlines = []
+ with Closing(file(path, 'r')) as f:
+ for i in range(2):
+ headlines.append(f.readline())
+ return (headlines[0].startswith('#Hemingway')
+ and headlines[1].startswith('#Experiment: FClamp'))
+
+ def read(self, path, info=None):
+ file_info = {}
+ with Closing(file(path, 'r')) as f:
+ while True:
+ line = f.readline().strip()
+ if line == '#END':
+ break
+ fields = line.split(':', 1)
+ if len(fields) == 2:
+ file_info[fields[0]] = fields[1]
+ data = numpy.genfromtxt(f, dtype=numpy.float)
+ ret = curve.Data(
+ shape=data.shape,
+ dtype=data.dtype,
+ buffer=data,
+ info=file_info,
+ )
+ ret.info['columns'] = [
+ 'time (s)', # first data column in file just increasing index
+ 'phase (m?rad)',
+ 'z piezo (m)',
+ 'deflection (N)',
+ 'imposed (N)',
+ ]
+ # assume 1 ms timestep
+ ret[:,0] = numpy.arange(0, 1e-3*data.shape[0], 1e-3, dtype=ret.dtype)
+
+ file_info['filetype'] = self.name
+ file_info['experiment'] = experiment.ForceClamp
+ return ([ret,], file_info)
--- /dev/null
+# Copyright (C) 2010 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 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/>.
+
+"""
+>>> import os.path
+>>> from hooke.hooke import Hooke, HookeRunner
+>>> h = Hooke()
+>>> r = HookeRunner()
+>>> playlist = os.path.join('test', 'data', 'fclamp_hemingway', 'playlist')
+>>> h = r.run_lines(h, ['load_playlist ' + playlist]) # doctest: +ELLIPSIS
+<FilePlaylist playlist.hkp>
+Success
+<BLANKLINE>
+>>> h = r.run_lines(h, ['curve_info']) # doctest: +ELLIPSIS, +REPORT_UDIFF
+name: 20080428_a53t-0-0-10.dat
+path: test/data/fclamp_hemingway/20080428_a53t-0-0-10.dat
+experiment: <class 'hooke.experiment.ForceClamp'>
+driver: <hooke.driver.hemingway.HemingwayDriver object at 0x...>
+filetype: hemingway
+note:
+blocks: 1
+block sizes: [(14798, 5)]
+Success
+<BLANKLINE>
+"""
projects / hooke.git / commitdiff