+ 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)