with Closing(zipfile.ZipFile(path, 'r')) as f:
f.path = path
zip_info = self._zip_info(f)
+ version = zip_info['file-format-version']
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.%d' % i
- for i in range(12)]:
+ segments.append(self._zip_segment(
+ f, path, info, zip_info, i, version))
+ if version not in ['0.%d' % i for i in range(12)]:
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:
+ '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
segment.info['spring constant (N/m)'] = \
curve_info['spring constant (N/m)']
return (segments, curve_info)
info = self._parse_params(f.readlines())
return info
- def _zip_segment(self, zipfile, path, info, zip_info, index):
+ def _zip_segment(self, zipfile, path, info, zip_info, index, version):
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 = []
+ 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(os.path.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,)
+ 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_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']
+ force_unit = self._zip_segment_conversion_unit(
+ chan_info['channel']['vDeflection']['conversion-set']['conversion']['force'],
+ 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_segment_conversion_unit(
+ chan_info['channel']['vDeflection']['conversion-set']['conversion']['distance'],
+ 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
+ # Assume volts unit is V, but it is not specified in the JPK
+ # file format.
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']
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
conversion_info['scaling']['style']
multiplier = float(conversion_info['scaling']['multiplier'])
offset = float(conversion_info['scaling']['offset'])
- unit = conversion_info['scaling']['unit']['unit']
+ unit = self._zip_segment_conversion_unit(conversion_info, version)
segment[:,channel] = segment[:,channel] * multiplier + offset
segment.info['columns'][channel] = join_data_label(channel_name, unit)
return segment
+ def _zip_segment_conversion_unit(self, conversion_info, version):
+ if version in ['0.%d' % i for i in range(3)]:
+ return conversion_info['scaling']['unit']
+ else:
+ return conversion_info['scaling']['unit']['unit']
+
def _parse_params(self, lines):
info = {}
for line in lines:
projects / hooke.git / blobdiff