-import string
-from .. import curve as lhc
-
-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 jpkDriver(lhc.Driver):
-
- def __init__(self, filename):
- self.filename=filename #self.filename can always be useful, and should be defined
- self.filedata = open(filename,'r') #We open the file
- self.filelines=self.filedata.readlines()
- self.filedata.close()
- '''These are two strings that can be used by Hooke commands/plugins to understand what they are looking at. They have no other
- meaning. They have to be somehow defined however - commands often look for those variables.
-
- self.filetype should contain the name of the exact filetype defined by the driver (so that filetype-specific commands can know
- if they're dealing with the correct filetype)
- self.experiment should contain instead the type of data involved (for example, various drivers can be used for force-clamp experiments,
- but hooke commands could like to know if we're looking at force clamp data, regardless of their origin, and not other
- kinds of data)
-
- Of course, all other variables you like can be defined in the class.
- '''
- self.filetype = 'jpk'
- self.experiment = 'smfs'
-
-
-
- def __del__(self):
- self.filedata.close()
-
- def is_me(self):
- '''
- we define our magic heuristic for jpk files
- '''
- myfile=file(self.filename)
- headerlines=myfile.readlines()[0:3]
- myfile.close()
- if headerlines[0][0:11]=='# xPosition' and headerlines[1][0:11]=='# yPosition':
- return True
- else:
+# 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/>.
+
+"""Driver for JPK ForceRobot's velocity clamp data format.
+"""
+
+import os.path
+import pprint
+import zipfile
+
+import numpy
+
+from .. import curve as curve
+from .. import experiment as experiment
+from ..util.util import Closing as Closing
+from ..util.si import join_data_label, split_data_label
+from . import Driver as Driver
+
+
+class JPKDriver (Driver):
+ """Handle JPK ForceRobot's data format.
+ """
+ def __init__(self):
+ super(JPKDriver, self).__init__(name='jpk')
+
+ def is_me(self, path):
+ if os.path.isdir(path):
return False
-
- def close_all(self):
- self.filedata.close()
-
- def _read_data_segment(self):
- #routine that actually reads the data
-
- height_ms=[]
- height_m=[]
- height=[]
- v_deflection=[]
- h_deflection=[]
-
- self.springconstant=0 #if we don't meet any spring constant, use deflection...
-
- for line in self.filelines:
- #we meet the segment defining the order of data columns
-
- if line[0:9]=='# columns':
- splitline=line.split()[2:]
- height_ms_index=splitline.index('smoothedStrainGaugeHeight')
- height_m_index=splitline.index('strainGaugeHeight')
- height_index=splitline.index('height')
- v_deflection_index=splitline.index('vDeflection')
- #h_deflection=splitline.index('hDeflection')
-
- if line[0:16]=='# springConstant':
- self.springconstant=float(line.split()[2])
-
- if line[0] != '#' and len(line.split())>1:
- dataline=line.split()
- height_ms.append(float(dataline[height_ms_index]))
- height_m.append(float(dataline[height_m_index]))
- height.append(float(dataline[height_index]))
- v_deflection.append(float(dataline[v_deflection_index]))
- #h_deflection.append(float(dataline[h_deflection_index]))
-
- if self.springconstant != 0:
- force=[item*self.springconstant for item in v_deflection]
- else: #we have measured no spring constant :(
- force=v_deflection
-
- height_ms=DataChunk([item*-1 for item in height_ms])
- height_m=DataChunk([item*-1 for item in height_m])
- height=DataChunk([item*-1 for item in height])
- deflection=DataChunk(v_deflection)
- force=DataChunk(force)
-
- return height_ms,height_m,height,deflection,force
-
- def deflection(self):
- height_ms,height_m,height,deflection,force=self._read_data_segment()
- deflection_ext=deflection.ext()
- deflection_ret=deflection.ret()
- deflection_ret.reverse()
- return deflection_ext,deflection_ret
-
- def default_plots(self):
-
- height_ms,height_m,height,deflection,force=self._read_data_segment()
-
- height_ms_ext=height_ms.ext()
- height_ms_ret=height_ms.ret()
- force_ext=force.ext()
- force_ret=force.ret()
- #reverse the return data, to make it coherent with hooke standard
- height_ms_ret.reverse()
- force_ret.reverse()
-
- main_plot=lhc.PlotObject()
- main_plot.add_set(height_ms_ext,force_ext)
- main_plot.add_set(height_ms_ret,force_ret)
-
-
-
- if self.springconstant != 0:
- main_plot.units=['meters','force']
+ if zipfile.is_zipfile(path): # JPK file versions since at least 0.5
+ with Closing(zipfile.ZipFile(path, 'r')) as f:
+ if 'header.properties' not in f.namelist():
+ return False
+ with Closing(f.open('header.properties')) as h:
+ if 'jpk-data-file' in h.read():
+ return True
else:
- main_plot.units=['meters','meters']
-
- main_plot.normalize_vectors()
-
- main_plot.destination=0
- main_plot.title=self.filename
-
- return [main_plot]
+ with Closing(open(path, 'r')) as f:
+ headlines = []
+ for i in range(3):
+ headlines.append(f.readline())
+ if headlines[0].startswith('# xPosition') \
+ and headlines[1].startswith('# yPosition'):
+ return True
+ return False
+
+ def read(self, path, info=None):
+ if info == None:
+ info = {}
+ if zipfile.is_zipfile(path): # JPK file versions since at least 0.5
+ return self._read_zip(path, info)
+ else:
+ return self._read_old(path, info)
+
+ def _read_zip(self, path, info):
+ with Closing(zipfile.ZipFile(path, 'r')) as f:
+ f.path = path
+ zip_info = self._zip_info(f)
+ segments = []
+ for i in range(len([p for p in f.namelist()
+ if p.endswith('segment-header.properties')])):
+ segments.append(self._zip_segment(f, path, info, zip_info, i))
+ if zip_info['file-format-version'] not in ['0.5']:
+ raise NotImplementedError(
+ 'JPK file version %s not supported (yet).'
+ % zip_info['file-format-version'])
+ for name in ['approach', 'retract']:
+ if len([s for s in segments if s.info['name'] == name]) == 0:
+ raise ValueError(
+ 'No segment for %s in %s, only %s'
+ % (name, path, [s.info['name'] for s in segments]))
+ curve_info = self._zip_translate_params(zip_info,
+ segments[0].info['raw info'])
+ for segment in segments:
+ segment.info['spring constant (N/m)'] = \
+ curve_info['spring constant (N/m)']
+ return (segments, curve_info)
+
+ def _zip_info(self, zipfile):
+ with Closing(zipfile.open('header.properties')) as f:
+ info = self._parse_params(f.readlines())
+ return info
+
+ def _zip_segment(self, zipfile, path, info, zip_info, index):
+ prop_file = zipfile.open(os.path.join(
+ 'segments', str(index), 'segment-header.properties'))
+ prop = self._parse_params(prop_file.readlines())
+ prop_file.close()
+ expected_shape = (int(prop['force-segment-header']['num-points']),)
+ channels = []
+ for chan in prop['channels']['list']:
+ chan_info = prop['channel'][chan]
+ channels.append(self._zip_channel(zipfile, index, chan, chan_info))
+ if channels[-1].shape != expected_shape:
+ raise NotImplementedError(
+ 'Channel %d:%s in %s has strange shape %s != %s'
+ % (index, chan, zipfile.path,
+ channels[-1].shape, expected_shape))
+ d = curve.Data(
+ shape=(len(channels[0]), len(channels)),
+ dtype=channels[0].dtype,
+ info=self._zip_translate_segment_params(prop))
+ for i,chan in enumerate(channels):
+ d[:,i] = chan
+ return self._zip_scale_segment(d, path, info)
+
+ def _zip_channel(self, zipfile, segment_index, channel_name, chan_info):
+ f = zipfile.open(os.path.join(
+ 'segments', str(segment_index),
+ chan_info['data']['file']['name']), 'r')
+ assert chan_info['data']['file']['format'] == 'raw', \
+ 'Non-raw data format:\n%s' % pprint.pformat(chan_info)
+ assert chan_info['data']['type'] == 'float-data', \
+ 'Non-float data format:\n%s' % pprint.pformat(chan_info)
+ data = numpy.frombuffer(
+ buffer(f.read()),
+ dtype=numpy.dtype(numpy.float32).newbyteorder('>'))
+ # '>' (big endian) byte order.
+ # From version 0.3 of JPKForceSpec.txt in the "Binary data" section:
+ # All forms of raw data are stored in chronological order
+ # (the order in which they were collected), and the
+ # individual values are stored in network byte order
+ # (big-endian). The data type used to store the data is
+ # specified by the "channel.*.data.type" property, and is
+ # either short (2 bytes per value), integer (4 bytes), or
+ # float (4 bytes, IEEE format).
+ f.close()
+ return data
+
+ def _zip_translate_params(self, params, chan_info):
+ info = {
+ 'raw info':params,
+ 'filetype':self.name,
+ #'time':self._time_from_TODO(raw_info[]),
+ }
+ # TODO: distinguish between force clamp and velocity clamp
+ # experiments. Note that the JPK file format is flexible
+ # enough to support mixed experiments (i.e. both force clamp
+ # and velocity clamp segments in a single experiment), but I
+ # have no idea what sort of analysis such experiments would
+ # require ;).
+ info['experiment'] = experiment.VelocityClamp
+ force_unit = chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['scaling']['unit']['unit']
+ assert force_unit == 'N', force_unit
+ force_base = chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['base-calibration-slot']
+ assert force_base == 'distance', force_base
+ dist_unit = chan_info['channel']['vDeflection']['conversion-set']['conversion']['distance']['scaling']['unit']['unit']
+ assert dist_unit == 'm', dist_unit
+ force_mult = float(
+ chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['scaling']['multiplier'])
+ info['spring constant (N/m)'] = force_mult
+ return info
+
+ def _zip_translate_segment_params(self, params):
+ info = {
+ 'raw info':params,
+ 'columns':list(params['channels']['list']),
+ 'name':params['force-segment-header']['name']['name'],
+ }
+ if info['name'] in ['extend-spm', 'retract-spm', 'pause-at-end-spm']:
+ info['name'] = info['name'][:-len('-spm')]
+ if info['name'] == 'extend':
+ info['name'] = 'approach'
+ else:
+ raise NotImplementedError(
+ 'Unrecognized segment type %s' % info['name'])
+ return info
+
+ def _zip_scale_segment(self, segment, path, info):
+ data = curve.Data(
+ shape=segment.shape,
+ dtype=segment.dtype,
+ info={})
+ data[:,:] = segment
+ segment.info['raw data'] = data
+
+ # raw column indices
+ channels = segment.info['raw info']['channels']['list']
+ for i,channel in enumerate(channels):
+ conversion = None
+ if channel == 'vDeflection':
+ conversion = 'distance'
+ segment = self._zip_scale_channel(
+ segment, channel, conversion=conversion, path=path, info=info)
+ name,unit = split_data_label(segment.info['columns'][i])
+ if name == 'vDeflection':
+ assert unit == 'm', segment.info['columns'][i]
+ segment.info['columns'][i] = join_data_label('deflection', 'm')
+ elif name == 'height':
+ assert unit == 'm', segment.info['columns'][i]
+ segment.info['columns'][i] = join_data_label('z piezo', 'm')
+ return segment
+
+ def _zip_scale_channel(self, segment, channel_name, conversion=None,
+ path=None, info={}):
+ channel = segment.info['raw info']['channels']['list'].index(
+ channel_name)
+ conversion_set = segment.info['raw info']['channel'][channel_name]['conversion-set']
+ if conversion == None:
+ conversion = conversion_set['conversions']['default']
+ if conversion == conversion_set['conversions']['base']:
+ # Our conversion is the base data.
+ if conversion != 'volts':
+ raise NotImplementedError(
+ 'unknown units for base channel: %s' % conversion)
+ segment.info['columns'][channel] = join_data_label(
+ channel_name, 'V')
+ return segment
+ conversion_info = conversion_set['conversion'][conversion]
+ if conversion_info['base-calibration-slot'] \
+ != conversion_set['conversions']['base']:
+ # Our conversion is stacked on a previous conversion. Do
+ # the previous conversion first.
+ segment = self._zip_scale_channel(
+ segment, channel_name,
+ conversion_info['base-calibration-slot'],
+ path=path, info=info)
+ if conversion_info['type'] == 'file':
+ # Michael Haggerty at JPK points out that the conversion
+ # information stored in the external file is reproduced in
+ # the force curve file. So there is no need to actually
+ # read `conversion_info['file']`. In fact, the data there
+ # may have changed with future calibrations, while the
+ # information stored directly in conversion_info retains
+ # the calibration information as it was when the experiment
+ # was performed.
+ pass # Fall through to 'simple' conversion processing.
+ else:
+ assert conversion_info['type'] == 'simple', conversion_info['type']
+ assert conversion_info['scaling']['type'] == 'linear', \
+ conversion_info['scaling']['type']
+ assert conversion_info['scaling']['style'] == 'offsetmultiplier', \
+ conversion_info['scaling']['style']
+ multiplier = float(conversion_info['scaling']['multiplier'])
+ offset = float(conversion_info['scaling']['offset'])
+ unit = conversion_info['scaling']['unit']['unit']
+ segment[:,channel] = segment[:,channel] * multiplier + offset
+ segment.info['columns'][channel] = join_data_label(channel_name, unit)
+ return segment
+
+ def _parse_params(self, lines):
+ info = {}
+ for line in lines:
+ line = line.strip()
+ if line.startswith('#'):
+ continue
+ else:
+ # e.g.: force-segment-header.type=xy-position-segment-header
+ fields = line.split('=', 1)
+ assert len(fields) == 2, line
+ setting = fields[0].split('.')
+ sub_info = info # drill down, e.g. info['force-s..']['type']
+ for s in setting[:-1]:
+ if s not in sub_info:
+ sub_info[s] = {}
+ sub_info = sub_info[s]
+ if setting[-1] == 'list': # split a space-delimited list
+ sub_info[setting[-1]] = fields[1].split(' ')
+ else:
+ sub_info[setting[-1]] = fields[1]
+ return info
+
+ def _read_old(self, path, info):
+ raise NotImplementedError('No old-style JPK files were available for testing, please send us yours: %s' % path)
projects / hooke.git / blobdiff