-# Copyright (C) 2008-2010 Massimo Sandal <devicerandom@gmail.com>
-# W. Trevor King <wking@drexel.edu>
+# Copyright (C) 2008-2012 Massimo Sandal <devicerandom@gmail.com>
+# W. Trevor King <wking@tremily.us>
#
# 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 JPK ForceRobot's velocity clamp data format.
from . import Driver as Driver
+def slash_join(*args):
+ r"""Join path components with forward slashes regardless of OS.
+
+ Notes
+ -----
+ From the `PKZIP Application Note`_, section J (Explanation of fields):
+
+ file name: (Variable)
+
+ ... All slashes should be forward slashes ``/`` as opposed to
+ backwards slashes ``\`` for compatibility with Amiga and UNIX
+ file systems etc. ...
+
+ .. _PKZIP Application Note:
+ http://www.pkware.com/documents/casestudies/APPNOTE.TXT
+
+ Examples
+ --------
+
+ >>> sep = os.path.sep
+ >>> os.path.sep = '/'
+ >>> print(slash_join('abc', 'def/ghi', 'jkl\\mno'))
+ abc/def/ghi/jkl\mno
+ >>> os.path.sep = '\\'
+ >>> print(slash_join('abc', 'def/ghi', 'jkl\\mno'))
+ abc/def/ghi/jkl\mno
+ >>> os.path.sep = sep
+
+ Note that when :const:`os.path.sep` is ``/`` (e.g. UNIX),
+ ``def/ghi`` is a compound segment, but when :const:`os.path.sep`
+ is ``\`` (e.g. Windows), ``def/ghi`` is a single segment.
+ """
+ sep = os.path.sep
+ try:
+ os.path.sep = '/'
+ return os.path.join(*args)
+ finally:
+ os.path.sep = sep
+
+
class JPKDriver (Driver):
"""Handle JPK ForceRobot's data format.
"""
with Closing(zipfile.ZipFile(path, 'r')) as f:
f.path = path
zip_info = self._zip_info(f)
+ version = zip_info['file-format-version']
+ if zip_info['jpk-data-file'] == 'jpk-data1D-file':
+ return self._zip_read_1d(
+ f, path, info, zip_info, version)
+ elif zip_info['jpk-data-file'] != 'spm-forcefile':
+ raise ValueError('unrecognized JPK file type "%s"'
+ % zip_info['jpk-data-file'])
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 ['0.3', '0.4', '0.5']:
+ segments.append(self._zip_segment(
+ f, path, info, zip_info, i, version))
+ if version not in ['0.%d' % i for i in range(13)]:
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)']
+ 'JPK file version %s not supported (yet).' % version)
+ curve_info = self._zip_translate_params(
+ zip_info, segments[0].info['raw info'], version)
+ for segment in segments: # HACK, should use curve-level spring constant
+ for key in ['spring constant (N/m)',
+ 'z piezo sensitivity (m/V)']:
+ if key in curve_info:
+ segment.info['spring constant (N/m)'] = \
+ curve_info['spring constant (N/m)']
+ names = [segment.info['name'] for segment in segments]
+ for name in set(names): # ensure unique names
+ count = names.count(name)
+ if count > 1:
+ i = 0
+ for j,n in enumerate(names):
+ if n == name:
+ segments[j].info['name'] += '-%d' % i
+ i += 1
return (segments, curve_info)
def _zip_info(self, zipfile):
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()
+ def _zip_segment(self, zipfile, path, info, zip_info, index, version):
+ with Closing(zipfile.open(slash_join(
+ 'segments', str(index), 'segment-header.properties'))
+ ) as f:
+ prop = self._parse_params(f.readlines())
expected_shape = (int(prop['force-segment-header']['num-points']),)
channels = []
+ if 'list' not in prop['channels']:
+ prop['channels'] = {'list': prop['channels'].split()}
for chan in prop['channels']['list']:
chan_info = prop['channel'][chan]
- channels.append(self._zip_channel(zipfile, index, chan, chan_info))
+ 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))
+ raise NotImplementedError(
+ 'channel %d:%s in %s has strange shape %s != %s'
+ % (index, chan, zipfile.path,
+ channels[-1].shape, expected_shape))
+ if len(channels) > 0:
+ shape = (len(channels[0]), len(channels))
+ dtype = channels[0].dtype
+ else: # no channels for this data block
+ shape = (0,0)
+ dtype = numpy.float32
d = curve.Data(
- shape=(len(channels[0]), len(channels)),
- dtype=channels[0].dtype,
+ shape=shape,
+ dtype=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)
+ return self._zip_scale_segment(d, path, info, version)
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('>'))
+ if chan_info['data']['type'] in ['constant-data', 'raster-data']:
+ return self._zip_calculate_channel(chan_info)
+ with Closing(zipfile.open(slash_join(
+ 'segments', str(segment_index),
+ chan_info['data']['file']['name']), 'r')) as f:
+ assert chan_info['data']['file']['format'] == 'raw', \
+ 'non-raw data format:\n%s' % pprint.pformat(chan_info)
+ dtype = self._zip_channel_dtype(chan_info)
+ data = numpy.frombuffer(
+ buffer(f.read()),
+ dtype=dtype,)
+ if dtype.kind in ['i', 'u']:
+ data = self._zip_channel_decode(data, chan_info)
+ return data
+
+ def _zip_calculate_channel(self, chan_info):
+ type_ = chan_info['data']['type']
+ n = int(chan_info['data']['num-points'])
+ if type_ == 'constant-data':
+ return float(chan_info['data']['value'])*numpy.ones(
+ shape=(n,),
+ dtype=numpy.float32)
+ elif type_ == 'raster-data':
+ start = float(chan_info['data']['start'])
+ step = float(chan_info['data']['step'])
+ return numpy.arange(
+ start=start,
+ stop=start + step*(n-0.5),
+ step=step,
+ dtype=numpy.float32)
+ else:
+ raise ValueError('unrecognized data format "%s"' % type_)
+
+ def _zip_channel_dtype(self, chan_info):
+ type_ = chan_info['data']['type']
+ if type_ in ['float-data', 'float']:
+ dtype = numpy.dtype(numpy.float32)
+ elif type_ in ['integer-data', 'memory-integer-data']:
+ encoder = chan_info['data']['encoder']['type']
+ if encoder in ['signedinteger', 'signedinteger-limited']:
+ dtype = numpy.dtype(numpy.int32)
+ elif encoder in ['unsignedinteger', 'unsignedinteger-limited']:
+ dtype = numpy.dtype(numpy.uint32)
+ else:
+ raise ValueError('unrecognized encoder type "%s" for "%s" data'
+ % (encoder, type_))
+ elif type_ in ['short-data', 'short', 'memory-short-data']:
+ encoder = chan_info['data']['encoder']['type']
+ if encoder in ['signedshort', 'signedshort-limited']:
+ dtype = numpy.dtype(numpy.int16)
+ elif encoder in ['unsignedshort', 'unsignedshort-limited']:
+ dtype = numpy.dtype(numpy.uint16)
+ else:
+ raise ValueError('unrecognized encoder type "%s" for "%s" data'
+ % (encoder, type_))
+ else:
+ raise ValueError('unrecognized data format "%s"' % type_)
+ byte_order = '>'
# '>' (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
# 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
+ return dtype.newbyteorder(byte_order)
- def _zip_translate_params(self, params, chan_info):
+ def _zip_channel_decode(self, data, encoder_info):
+ return self._zip_apply_channel_scaling(
+ data, encoder_info['data']['encoder'])
+
+ def _zip_translate_params(self, params, chan_info, version):
info = {
'raw info':params,
#'time':self._time_from_TODO(raw_info[]),
}
- force_unit = chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['scaling']['unit']['unit']
+ if len(chan_info['channels']['list']) == 0:
+ return info
+ force_unit = self._zip_unit(
+ chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['scaling'],
+ version)
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']
+ dist_unit = self._zip_unit(
+ chan_info['channel']['vDeflection']['conversion-set']['conversion']['distance']['scaling'],
+ version)
assert dist_unit == 'm', dist_unit
+ distance_base = chan_info['channel']['vDeflection']['conversion-set']['conversion']['distance']['base-calibration-slot']
+ assert distance_base == 'volts', distance_base
+ base_conversion = chan_info['channel']['vDeflection']['conversion-set']['conversions']['base']
+ assert base_conversion == distance_base, base_conversion
+ if 'encoder' in chan_info['channel']['vDeflection']['data']:
+ distance_base_unit = self._zip_unit(
+ chan_info['channel']['vDeflection']['data']['encoder']['scaling'],
+ version)
+ else:
+ distance_base_unit = self._zip_unit(
+ chan_info['channel']['vDeflection']['data'],
+ version)
+ assert distance_base_unit == 'V', distance_base_unit
force_mult = float(
chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['scaling']['multiplier'])
+ sens_mult = float(
+ chan_info['channel']['vDeflection']['conversion-set']['conversion']['distance']['scaling']['multiplier'])
info['spring constant (N/m)'] = force_mult
+ info['z piezo sensitivity (m/V)'] = sens_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'],
+ 'raw info': params,
+ 'columns': list(params['channels']['list']),
+ 'name': self._zip_segment_name(params),
}
- 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):
+ def _zip_segment_name(self, params):
+ name = params['force-segment-header']['name']['name']
+ if name.endswith('-spm'):
+ name = name[:-len('-spm')]
+ if name == 'extend':
+ name = 'approach'
+ elif name.startswith('pause-at-'):
+ name = 'pause'
+ return name
+
+ def _zip_scale_segment(self, segment, path, info, version):
data = curve.Data(
shape=segment.shape,
dtype=segment.dtype,
if channel == 'vDeflection':
conversion = 'distance'
segment = self._zip_scale_channel(
- segment, channel, conversion=conversion, path=path, info=info)
+ segment, channel, conversion=conversion,
+ path=path, info=info, version=version)
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('z piezo', 'm')
return segment
- def _zip_scale_channel(self, segment, channel_name, conversion=None,
- path=None, info={}):
+ def _zip_scale_channel(self, segment, channel_name,
+ conversion=None, path=None, info={}, version=None):
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')
+ channel_name,
+ self._zip_unit(
+ segment.info['raw info']['channel'][channel_name]['data'],
+ version))
return segment
conversion_info = conversion_set['conversion'][conversion]
if conversion_info['base-calibration-slot'] \
segment = self._zip_scale_channel(
segment, channel_name,
conversion_info['base-calibration-slot'],
- path=path, info=info)
+ path=path, info=info, version=version)
if conversion_info['type'] == 'file':
# Michael Haggerty at JPK points out that the conversion
# information stored in the external file is reproduced in
pass # Fall through to 'simple' conversion processing.
else:
assert conversion_info['type'] == 'simple', conversion_info['type']
+ segment[:,channel] = self._zip_apply_channel_scaling(
+ segment[:,channel], conversion_info)
+ unit = self._zip_unit(conversion_info['scaling'], version)
+ segment.info['columns'][channel] = join_data_label(channel_name, unit)
+ return segment
+
+ def _zip_apply_channel_scaling(self, channel_data, conversion_info):
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
+ return channel_data * multiplier + offset
+
+ def _zip_unit(self, conversion_info, version):
+ if version in ['0.%d' % i for i in range(3)]:
+ return conversion_info['unit']
+ else:
+ return conversion_info['unit']['unit']
def _parse_params(self, lines):
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(' ')
+ if fields[1]:
+ sub_info[setting[-1]] = fields[1].split(' ')
+ else:
+ sub_info[setting[-1]] = []
else:
sub_info[setting[-1]] = fields[1]
return info
+ def _zip_read_1d(self, zipfile, path, info, zip_info, version):
+ expected_shape = (int(zip_info['data']['num-points']),)
+ if zip_info['data']['type'] in ['constant-data', 'raster-data']:
+ return self._zip_calculate_channel(zip_info)
+ with Closing(zipfile.open(
+ zip_info['data']['file']['name'], 'r')) as f:
+ assert zip_info['data']['file']['format'] == 'raw', \
+ 'non-raw data format:\n%s' % pprint.pformat(chan_info)
+ dtype = self._zip_channel_dtype(zip_info)
+ data = numpy.frombuffer(
+ buffer(f.read()),
+ dtype=dtype,)
+ if dtype.kind in ['i', 'u']:
+ data = self._zip_channel_decode(data, zip_info)
+ if data.shape != expected_shape:
+ raise NotImplementedError(
+ 'channel %s has strange shape %s != %s'
+ % (path, data.shape, expected_shape))
+ d = curve.Data(
+ shape=data.shape,
+ dtype=data.dtype,
+ info=zip_info)
+ d[:] = data
+ return d
+
def _read_old(self, path, info):
raise NotImplementedError(
"Early JPK files (pre-zip) are not supported by Hooke. Please "
"use JPK's `out2jpk-force` script to convert your old files "
- "to a more recent format before loading them with Hooke.")
+ "(%s) to a more recent format before loading them with Hooke."
+ % path)