+++ /dev/null
-# Copyright (C) 2006-2010 Alberto Gomez-Casado
-# 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 Picoforce force spectroscopy files.
-
-An alternave implementation of :mod:`hooke.driver.picoforce`.
-"""
-
-import re, struct
-from scipy import arange
-
-from .. import curve as lhc
-
-__version__='0.0.0.20081706'
-
-
-
-class DataChunk(list):
- #Dummy class to provide ext and ret methods to the data list.
-
- def ext(self):
- halflen=(len(self)/2)
- return self[0:halflen]
-
- def ret(self):
- halflen=(len(self)/2)
- return self[halflen:]
-
-class picoforcealtDriver(lhc.Driver):
-
- #Construction and other special methods
-
- def __init__(self,filename):
- '''
- constructor method
- '''
-
- self.textfile=file(filename)
- self.binfile=file(filename,'rb')
-
- #The 0,1,2 data chunks are:
- #0: D (vs T)
- #1: Z (vs T)
- #2: D (vs Z)
-
- self.forcechunk=0
- self.distancechunk=1
- #TODO eliminate the need to set chunk numbers
-
- self.filepath=filename
- self.debug=True
-
- self.filetype='picoforce'
- self.experiment='smfs'
-
-
-
- def _get_samples_line(self):
- '''
- Gets the samples per line parameters in the file, to understand trigger behaviour.
- '''
- self.textfile.seek(0)
-
- samps_expr=re.compile(".*Samps")
-
- samps_values=[]
- for line in self.textfile.readlines():
- if samps_expr.match(line):
- try:
- samps=int(line.split()[2]) #the third word splitted is the offset (in bytes)
- samps_values.append(samps)
- except:
- pass
-
- #We raise a flag for the fact we meet an offset, otherwise we would take spurious data length arguments.
-
- return int(samps_values[0])
-
- def _get_chunk_coordinates(self):
- '''
- This method gets the coordinates (offset and length) of a data chunk in our
- Picoforce file.
-
- It returns a list containing two tuples:
- the first element of each tuple is the data_offset, the second is the corresponding
- data size.
-
- In near future probably each chunk will get its own data structure, with
- offset, size, type, etc.
- '''
- self.textfile.seek(0)
-
- offset_expr=re.compile(".*Data offset")
- length_expr=re.compile(".*Data length")
-
- data_offsets=[]
- data_sizes=[]
- flag_offset=0
-
- for line in self.textfile.readlines():
-
- if offset_expr.match(line):
- offset=int(line.split()[2]) #the third word splitted is the offset (in bytes)
- data_offsets.append(offset)
- #We raise a flag for the fact we meet an offset, otherwise we would take spurious data length arguments.
- flag_offset=1
-
- #same for the data length
- if length_expr.match(line) and flag_offset:
- size=int(line.split()[2])
- data_sizes.append(size)
- #Put down the offset flag until the next offset is met.
- flag_offset=0
-
- return zip(data_offsets,data_sizes)
-
- def _get_data_chunk(self,whichchunk):
- '''
- reads a data chunk and converts it in 16bit signed int.
- '''
- offset,size=self._get_chunk_coordinates()[whichchunk]
-
-
- self.binfile.seek(offset)
- raw_chunk=self.binfile.read(size)
-
- my_chunk=[]
- for data_position in range(0,len(raw_chunk),2):
- data_unit_bytes=raw_chunk[data_position:data_position+2]
- #The unpack function converts 2-bytes in a signed int ('h').
- #we use output[0] because unpack returns a 1-value tuple, and we want the number only
- data_unit=struct.unpack('h',data_unit_bytes)[0]
- my_chunk.append(data_unit)
-
- return DataChunk(my_chunk)
-
- def _force(self):
- #returns force vector
- Kspring=self.get_spring_constant()
- return DataChunk([(meter*Kspring) for meter in self._deflection()])
-
- def _deflection(self):
- #for internal use (feeds _force)
- voltrange=1
- z_scale=self._get_Z_scale()
- deflsensitivity=self.get_deflection_sensitivity()
- volts=[((float(lsb))*voltrange*z_scale) for lsb in self.data_chunks[self.forcechunk]]
- deflect=[volt*deflsensitivity for volt in volts]
-
- return deflect
-
-
- def _Z(self):
- #returns distance vector (calculated instead than from data chunk)
- rampsize=self._get_rampsize()
- sampsline=self._get_samples_line()
- senszscan=self._get_Z_scan_sens()
-
- xstep=senszscan*rampsize/sampsline*10**(-9)
-
- xext=arange(sampsline*xstep,0,-xstep)
- xret=arange(sampsline*xstep,0,-xstep)
-
- return DataChunk(xext.tolist()+xret.tolist())
-
- def _get_Z_scale(self):
- self.textfile.seek(0)
- expr=re.compile(".*@4:Z scale")
-
- for line in self.textfile.readlines():
- if expr.match(line):
- zscale=float((line.split()[5]).strip("() []"))
- break
- return zscale
-
- def _get_rampsize(self):
- self.textfile.seek(0)
- expr=re.compile(".*@4:Ramp size:")
-
- for line in self.textfile.readlines():
- if expr.match(line):
- zsens=float((line.split()[7]).strip("() []"))
- break
- return zsens
-
- def _get_Z_scan_sens(self):
- self.textfile.seek(0)
- expr=re.compile(".*@Sens. Zsens")
-
- for line in self.textfile.readlines():
- if expr.match(line):
- zsens=float((line.split()[3]).strip("() []"))
- break
- return zsens
-
-
-
- def get_deflection_sensitivity(self):
- '''
- gets deflection sensitivity
- '''
- self.textfile.seek(0)
-
- def_sensitivity_expr=re.compile(".*@Sens. DeflSens")
-
- for line in self.textfile.readlines():
- if def_sensitivity_expr.match(line):
- def_sensitivity=float(line.split()[3])
- break
- #return it in SI units (that is: m/V, not nm/V)
- return def_sensitivity*(10**(-9))
-
- def get_spring_constant(self):
- '''
- gets spring constant.
- We actually find *three* spring constant values, one for each data chunk (F/t, Z/t, F/z).
- They are normally all equal, but we retain all three for future...
- '''
- self.textfile.seek(0)
-
- springconstant_expr=re.compile(".*Spring Constant")
-
- constants=[]
-
- for line in self.textfile.readlines():
- if springconstant_expr.match(line):
- constants.append(float(line.split()[2]))
-
- return constants[0]
-
- def is_me(self):
- '''
- self-identification of file type magic
- '''
- curve_file=file(self.filepath)
- header=curve_file.read(30)
- curve_file.close()
-
- if header[2:17] == 'Force file list': #header of a picoforce file
- #here DONT translate chunk
- self.data_chunks=[self._get_data_chunk(num) for num in [0,1,2]]
- return True
- else:
- return False
-
- def close_all(self):
- '''
- Explicitly closes all files
- '''
- self.textfile.close()
- self.binfile.close()
-
- def default_plots(self):
- '''
- creates the default PlotObject
- '''
- force=self._force()
- zdomain=self._Z()
- samples=self._get_samples_line()
- main_plot=lhc.PlotObject()
- main_plot.vectors=[[zdomain.ext()[0:samples], force.ext()[0:samples]],[zdomain.ret()[0:samples], force.ret()[0:samples]]]
- main_plot.normalize_vectors()
- main_plot.units=['meters','newton']
- main_plot.destination=0
- main_plot.title=self.filepath
-
-
- return [main_plot]
-
- def deflection(self):
- #interface for correct plotmanip and others
- deflectionchunk=DataChunk(self._deflection())
- return deflectionchunk.ext(),deflectionchunk.ret()
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