--- /dev/null
+#!/usr/bin/python
+#
+# igorbinarywave provides pure Python interface between IGOR Binary
+# Wave files and Numpy arrays.
+#
+# Copyright 2010 W. Trevor King <wking@drexel.edu>
+
+# Based on WaveMetric's Technical Note 003, "Igor Binary Format"
+# ftp://ftp.wavemetrics.net/IgorPro/Technical_Notes/TN003.zip
+# From ftp://ftp.wavemetrics.net/IgorPro/Technical_Notes/TN000.txt
+# We place no restrictions on copying Technical Notes, with the
+# exception that you cannot resell them. So read, enjoy, and
+# share. We hope IGOR Technical Notes will provide you with lots of
+# valuable information while you are developing IGOR applications.
+
+import array
+import struct
+import sys
+import types
+
+import numpy
+
+
+__version__ = '0.1'
+
+
+class Field (object):
+ """Represent a Structure field.
+
+ See Also
+ --------
+ Structure
+ """
+ def __init__(self, format, name, default=None, help=None, count=1):
+ self.format = format # See the struct documentation
+ self.name = name
+ self.default = None
+ self.help = help
+ self.count = count
+ self.total_count = numpy.prod(count)
+
+class Structure (struct.Struct):
+ """Represent a C structure.
+
+ A convenient wrapper around struct.Struct that uses Fields and
+ adds dict-handling methods for transparent name assignment.
+
+ See Also
+ --------
+ Field
+
+ Examples
+ --------
+
+ Represent the C structure::
+
+ struct thing {
+ short version;
+ long size[3];
+ }
+
+ As
+
+ >>> from pprint import pprint
+ >>> thing = Structure(name='thing',
+ ... fields=[Field('h', 'version'), Field('l', 'size', count=3)])
+ >>> thing.set_byte_order('>')
+ >>> b = array.array('b', range(2+4*3))
+ >>> d = thing.unpack_dict_from(buffer=b)
+ >>> pprint(d)
+ {'size': array([ 33752069, 101124105, 168496141]), 'version': 1}
+ >>> [hex(x) for x in d['size']]
+ ['0x2030405L', '0x6070809L', '0xa0b0c0dL']
+
+ You can even get fancy with multi-dimensional arrays.
+
+ >>> thing = Structure(name='thing',
+ ... fields=[Field('h', 'version'), Field('l', 'size', count=(3,2))])
+ >>> thing.set_byte_order('>')
+ >>> b = array.array('b', range(2+4*3*2))
+ >>> d = thing.unpack_dict_from(buffer=b)
+ >>> d['size'].shape
+ (3, 2)
+ >>> pprint(d)
+ {'size': array([[ 33752069, 101124105],
+ [168496141, 235868177],
+ [303240213, 370612249]]),
+ 'version': 1}
+ """
+ def __init__(self, name, fields, byte_order='='):
+ # '=' for native byte order, standard size and alignment
+ # See http://docs.python.org/library/struct for details
+ self.name = name
+ self.fields = fields
+ self.set_byte_order(byte_order)
+
+ def __str__(self):
+ return self.name
+
+ def set_byte_order(self, byte_order):
+ """Allow changing the format byte_order on the fly.
+ """
+ if (hasattr(self, 'format') and self.format != None
+ and self.format.startswith(byte_order)):
+ return # no need to change anything
+ format = []
+ for field in self.fields:
+ format.extend([field.format]*field.total_count)
+ struct.Struct.__init__(self, format=byte_order+''.join(format).replace('P', 'L'))
+
+ def _flatten_args(self, args):
+ # handle Field.count > 0
+ flat_args = []
+ for a,f in zip(args, self.fields):
+ if f.total_count > 1:
+ flat_args.extend(a)
+ else:
+ flat_args.append(a)
+ return flat_args
+
+ def _unflatten_args(self, args):
+ # handle Field.count > 0
+ unflat_args = []
+ i = 0
+ for f in self.fields:
+ if f.total_count > 1:
+ data = numpy.array(args[i:i+f.total_count])
+ data = data.reshape(f.count)
+ unflat_args.append(data)
+ else:
+ unflat_args.append(args[i])
+ i += f.total_count
+ return unflat_args
+
+ def pack(self, *args):
+ return struct.Struct.pack(self, *self._flatten_args(args))
+
+ def pack_into(self, buffer, offset, *args):
+ return struct.Struct.pack_into(self, buffer, offset,
+ *self._flatten_args(args))
+
+ def _clean_dict(self, dict):
+ for f in self.fields:
+ if f.name not in dict:
+ if f.default != None:
+ dict[f.name] = f.default
+ else:
+ raise ValueError('%s field not set for %s'
+ % f.name, self.__class__.__name__)
+ return dict
+
+ def pack_dict(self, dict):
+ dict = self._clean_dict(dict)
+ return self.pack(*[dict[f.name] for f in self.fields])
+
+ def pack_dict_into(self, buffer, offset, dict={}):
+ dict = self._clean_dict(dict)
+ return self.pack_into(buffer, offset,
+ *[dict[f.name] for f in self.fields])
+
+ def unpack(self, string):
+ return self._unflatten_args(struct.Struct.unpack(self, string))
+
+ def unpack_from(self, buffer, offset=0):
+ return self._unflatten_args(
+ struct.Struct.unpack_from(self, buffer, offset))
+
+ def unpack_dict(self, string):
+ return dict(zip([f.name for f in self.fields],
+ self.unpack(string)))
+
+ def unpack_dict_from(self, buffer, offset=0):
+ return dict(zip([f.name for f in self.fields],
+ self.unpack_from(buffer, offset)))
+
+
+# Numpy doesn't support complex integers by default, see
+# http://mail.python.org/pipermail/python-dev/2002-April/022408.html
+# http://mail.scipy.org/pipermail/numpy-discussion/2007-October/029447.html
+# So we roll our own types. See
+# http://docs.scipy.org/doc/numpy/user/basics.rec.html
+# http://docs.scipy.org/doc/numpy/reference/generated/numpy.dtype.html
+complexInt8 = numpy.dtype([('real', numpy.int8), ('imag', numpy.int8)])
+complexInt16 = numpy.dtype([('real', numpy.int16), ('imag', numpy.int16)])
+complexInt32 = numpy.dtype([('real', numpy.int32), ('imag', numpy.int32)])
+complexUInt8 = numpy.dtype([('real', numpy.uint8), ('imag', numpy.uint8)])
+complexUInt16 = numpy.dtype([('real', numpy.uint16), ('imag', numpy.uint16)])
+complexUInt32 = numpy.dtype([('real', numpy.uint32), ('imag', numpy.uint32)])
+
+
+# Begin IGOR constants and typedefs from IgorBin.h
+
+# From IgorMath.h
+TYPE_TABLE = { # (key: integer flag, value: numpy dtype)
+ 0:None, # Text wave, not handled in ReadWave.c
+ 1:numpy.complex, # NT_CMPLX, makes number complex.
+ 2:numpy.float32, # NT_FP32, 32 bit fp numbers.
+ 3:numpy.complex64,
+ 4:numpy.float64, # NT_FP64, 64 bit fp numbers.
+ 5:numpy.complex128,
+ 8:numpy.int8, # NT_I8, 8 bit signed integer. Requires Igor Pro
+ # 2.0 or later.
+ 9:complexInt8,
+ 0x10:numpy.int16,# NT_I16, 16 bit integer numbers. Requires Igor
+ # Pro 2.0 or later.
+ 0x11:complexInt16,
+ 0x20:numpy.int32,# NT_I32, 32 bit integer numbers. Requires Igor
+ # Pro 2.0 or later.
+ 0x21:complexInt32,
+# 0x40:None, # NT_UNSIGNED, Makes above signed integers
+# # unsigned. Requires Igor Pro 3.0 or later.
+ 0x48:numpy.uint8,
+ 0x49:complexUInt8,
+ 0x50:numpy.uint16,
+ 0x51:complexUInt16,
+ 0x60:numpy.uint32,
+ 0x61:complexUInt32,
+}
+
+# From wave.h
+MAXDIMS = 4
+
+# From binary.h
+BinHeaderCommon = Structure( # WTK: this one is mine.
+ name='BinHeaderCommon',
+ fields=[
+ Field('h', 'version', help='Version number for backwards compatibility.'),
+ ])
+
+BinHeader1 = Structure(
+ name='BinHeader1',
+ fields=[
+ Field('h', 'version', help='Version number for backwards compatibility.'),
+ Field('l', 'wfmSize', help='The size of the WaveHeader2 data structure plus the wave data plus 16 bytes of padding.'),
+ Field('h', 'checksum', help='Checksum over this header and the wave header.'),
+ ])
+
+BinHeader2 = Structure(
+ name='BinHeader2',
+ fields=[
+ Field('h', 'version', help='Version number for backwards compatibility.'),
+ Field('l', 'wfmSize', help='The size of the WaveHeader2 data structure plus the wave data plus 16 bytes of padding.'),
+ Field('l', 'noteSize', help='The size of the note text.'),
+ Field('l', 'pictSize', default=0, help='Reserved. Write zero. Ignore on read.'),
+ Field('h', 'checksum', help='Checksum over this header and the wave header.'),
+ ])
+
+BinHeader3 = Structure(
+ name='BinHeader3',
+ fields=[
+ Field('h', 'version', help='Version number for backwards compatibility.'),
+ Field('h', 'wfmSize', help='The size of the WaveHeader2 data structure plus the wave data plus 16 bytes of padding.'),
+ Field('l', 'noteSize', help='The size of the note text.'),
+ Field('l', 'formulaSize', help='The size of the dependency formula, if any.'),
+ Field('l', 'pictSize', default=0, help='Reserved. Write zero. Ignore on read.'),
+ Field('h', 'checksum', help='Checksum over this header and the wave header.'),
+ ])
+
+BinHeader5 = Structure(
+ name='BinHeader5',
+ fields=[
+ Field('h', 'version', help='Version number for backwards compatibility.'),
+ Field('h', 'checksum', help='Checksum over this header and the wave header.'),
+ Field('l', 'wfmSize', help='The size of the WaveHeader5 data structure plus the wave data.'),
+ Field('l', 'formulaSize', help='The size of the dependency formula, if any.'),
+ Field('l', 'noteSize', help='The size of the note text.'),
+ Field('l', 'dataEUnitsSize', help='The size of optional extended data units.'),
+ Field('l', 'dimEUnitsSize', help='The size of optional extended dimension units.', count=MAXDIMS),
+ Field('l', 'dimLabelsSize', help='The size of optional dimension labels.', count=MAXDIMS),
+ Field('l', 'sIndicesSize', help='The size of string indicies if this is a text wave.'),
+ Field('l', 'optionsSize1', default=0, help='Reserved. Write zero. Ignore on read.'),
+ Field('l', 'optionsSize2', default=0, help='Reserved. Write zero. Ignore on read.'),
+ ])
+
+
+# From wave.h
+MAX_WAVE_NAME2 = 18 # Maximum length of wave name in version 1 and 2
+ # files. Does not include the trailing null.
+MAX_WAVE_NAME5 = 31 # Maximum length of wave name in version 5
+ # files. Does not include the trailing null.
+MAX_UNIT_CHARS = 3
+
+# Header to an array of waveform data.
+
+WaveHeader2 = Structure(
+ name='WaveHeader2',
+ fields=[
+ Field('h', 'type', help='See types (e.g. NT_FP64) above. Zero for text waves.'),
+ Field('P', 'next', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('c', 'bname', help='Name of wave plus trailing null.', count=MAX_WAVE_NAME2+2),
+ Field('h', 'whVersion', default=0, help='Write 0. Ignore on read.'),
+ Field('h', 'srcFldr', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('P', 'fileName', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('c', 'dataUnits', default=0, help='Natural data units go here - null if none.', count=MAX_UNIT_CHARS+1),
+ Field('c', 'xUnits', default=0, help='Natural x-axis units go here - null if none.', count=MAX_UNIT_CHARS+1),
+ Field('l', 'npnts', help='Number of data points in wave.'),
+ Field('h', 'aModified', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('d', 'hsA', help='X value for point p = hsA*p + hsB'),
+ Field('d', 'hsB', help='X value for point p = hsA*p + hsB'),
+ Field('h', 'wModified', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('h', 'swModified', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('h', 'fsValid', help='True if full scale values have meaning.'),
+ Field('d', 'topFullScale', help='The min full scale value for wave.'), # sic, 'min' should probably be 'max'
+ Field('d', 'botFullScale', help='The min full scale value for wave.'),
+ Field('c', 'useBits', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('c', 'kindBits', default=0, help='Reserved. Write zero. Ignore on read.'),
+ Field('P', 'formula', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('l', 'depID', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('L', 'creationDate', help='DateTime of creation. Not used in version 1 files.'),
+ Field('c', 'wUnused', default=0, help='Reserved. Write zero. Ignore on read.', count=2),
+ Field('L', 'modDate', help='DateTime of last modification.'),
+ Field('P', 'waveNoteH', help='Used in memory only. Write zero. Ignore on read.'),
+ Field('f', 'wData', help='The start of the array of waveform data.', count=4),
+ ])
+
+WaveHeader5 = Structure(
+ name='WaveHeader5',
+ fields=[
+ Field('P', 'next', help='link to next wave in linked list.'),
+ Field('L', 'creationDate', help='DateTime of creation.'),
+ Field('L', 'modDate', help='DateTime of last modification.'),
+ Field('l', 'npnts', help='Total number of points (multiply dimensions up to first zero).'),
+ Field('h', 'type', help='See types (e.g. NT_FP64) above. Zero for text waves.'),
+ Field('h', 'dLock', default=0, help='Reserved. Write zero. Ignore on read.'),
+ Field('c', 'whpad1', default=0, help='Reserved. Write zero. Ignore on read.', count=6),
+ Field('h', 'whVersion', default=1, help='Write 1. Ignore on read.'),
+ Field('c', 'bname', help='Name of wave plus trailing null.', count=MAX_WAVE_NAME5+1),
+ Field('l', 'whpad2', default=0, help='Reserved. Write zero. Ignore on read.'),
+ Field('P', 'dFolder', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ # Dimensioning info. [0] == rows, [1] == cols etc
+ Field('l', 'nDim', help='Number of of items in a dimension -- 0 means no data.', count=MAXDIMS),
+ Field('d', 'sfA', help='Index value for element e of dimension d = sfA[d]*e + sfB[d].', count=MAXDIMS),
+ Field('d', 'sfB', help='Index value for element e of dimension d = sfA[d]*e + sfB[d].', count=MAXDIMS),
+ # SI units
+ Field('c', 'dataUnits', default=0, help='Natural data units go here - null if none.', count=MAX_UNIT_CHARS+1),
+ Field('c', 'dimUnits', default=0, help='Natural dimension units go here - null if none.', count=(MAXDIMS, MAX_UNIT_CHARS+1)),
+ Field('h', 'fsValid', help='TRUE if full scale values have meaning.'),
+ Field('h', 'whpad3', default=0, help='Reserved. Write zero. Ignore on read.'),
+ Field('d', 'topFullScale', help='The max and max full scale value for wave'), # sic, probably "max and min"
+ Field('d', 'botFullScale', help='The max and max full scale value for wave.'), # sic, probably "max and min"
+ Field('P', 'dataEUnits', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('P', 'dimEUnits', default=0, help='Used in memory only. Write zero. Ignore on read.', count=MAXDIMS),
+ Field('P', 'dimLabels', default=0, help='Used in memory only. Write zero. Ignore on read.', count=MAXDIMS),
+ Field('P', 'waveNoteH', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('l', 'whUnused', default=0, help='Reserved. Write zero. Ignore on read.', count=16),
+ # The following stuff is considered private to Igor.
+ Field('h', 'aModified', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('h', 'wModified', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('h', 'swModified', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('c', 'useBits', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('c', 'kindBits', default=0, help='Reserved. Write zero. Ignore on read.'),
+ Field('P', 'formula', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('l', 'depID', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('h', 'whpad4', default=0, help='Reserved. Write zero. Ignore on read.'),
+ Field('h', 'srcFldr', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('P', 'fileName', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('P', 'sIndices', default=0, help='Used in memory only. Write zero. Ignore on read.'),
+ Field('f', 'wData', help='The start of the array of data. Must be 64 bit aligned.', count=1),
+ ])
+
+# End IGOR constants and typedefs from IgorBin.h
+
+# Begin functions from ReadWave.c
+
+def need_to_reorder_bytes(version):
+ # If the low order byte of the version field of the BinHeader
+ # structure is zero then the file is from a platform that uses
+ # different byte-ordering and therefore all data will need to be
+ # reordered.
+ return version & 0xFF == 0
+
+def byte_order(needToReorderBytes):
+ little_endian = sys.byteorder == 'little'
+ if needToReorderBytes:
+ little_endian = not little_endian
+ if little_endian:
+ return '<' # little-endian
+ return '>' # big-endian
+
+def version_structs(version, byte_order):
+ if version == 1:
+ bin = BinHeader1
+ wave = WaveHeader2
+ elif version == 2:
+ bin = BinHeader2
+ wave = WaveHeader2
+ elif version == 3:
+ bin = BinHeader3
+ wave = WaveHeader2
+ elif version == 5:
+ bin = BinHeader5
+ wave = WaveHeader5
+ else:
+ raise ValueError('This does not appear to be a valid Igor binary wave file. The version field = %d.\n', version);
+ checkSumSize = bin.size + wave.size
+ if version == 5:
+ checkSumSize -= 4 # Version 5 checksum does not include the wData field.
+ bin.set_byte_order(byte_order)
+ wave.set_byte_order(byte_order)
+ return (bin, wave, checkSumSize)
+
+def checksum(buffer, byte_order, oldcksum, numbytes):
+ x = numpy.ndarray(
+ (numbytes/2,), # 2 bytes to a short -- ignore trailing odd byte
+ dtype=numpy.dtype(byte_order+'h'),
+ buffer=buffer)
+ oldcksum += x.sum()
+ if oldcksum > 2**31: # fake the C implementation's int rollover
+ oldcksum %= 2**32
+ if oldcksum > 2**31:
+ oldcksum -= 2**31
+ return oldcksum & 0xffff
+
+# Translated from ReadWave()
+def loadibw(filename):
+ if hasattr(filename, 'read'):
+ f = filename # filename is actually a stream object
+ else:
+ f = open(filename, 'rb')
+ try:
+ b = buffer(f.read(BinHeaderCommon.size))
+ version = BinHeaderCommon.unpack_dict_from(b)['version']
+ needToReorderBytes = need_to_reorder_bytes(version)
+ byteOrder = byte_order(needToReorderBytes)
+
+ if needToReorderBytes:
+ BinHeaderCommon.set_byte_order(byteOrder)
+ version = BinHeaderCommon.unpack_dict_from(b)['version']
+ bin_struct,wave_struct,checkSumSize = version_structs(version, byteOrder)
+
+ b = buffer(b + f.read(bin_struct.size + wave_struct.size - BinHeaderCommon.size))
+ c = checksum(b, byteOrder, 0, checkSumSize)
+ if c != 0:
+ raise ValueError('Error in checksum - should be 0, is %d. This does not appear to be a valid Igor binary wave file.' % c)
+ bin_info = bin_struct.unpack_dict_from(b)
+ wave_info = wave_struct.unpack_dict_from(b, offset=bin_struct.size)
+ if wave_info['type'] == 0:
+ raise NotImplementedError('Text wave')
+ if version in [1,2,3]:
+ tail = 16 # 16 = size of wData field in WaveHeader2 structure
+ waveDataSize = bin_info['wfmSize'] - wave_struct.size
+ # = bin_info['wfmSize']-16 - (wave_struct.size - tail)
+ else:
+ assert version == 5, version
+ tail = 4 # 4 = size of wData field in WaveHeader5 structure
+ waveDataSize = bin_info['wfmSize'] - (wave_struct.size - tail)
+ # dtype() wrapping to avoid numpy.generic and
+ # getset_descriptor issues with the builtin Numpy types
+ # (e.g. int32). It has no effect on our local complex
+ # integers.
+ t = numpy.dtype(TYPE_TABLE[wave_info['type']])
+ assert waveDataSize == wave_info['npnts'] * t.itemsize, \
+ ('%d, %d, %d, %s' % (waveDataSize, wave_info['npnts'], t.itemsize, t))
+ tail_data = array.array('f', b[-tail:])
+ data_b = buffer(buffer(tail_data) + f.read(waveDataSize-tail))
+ data = numpy.ndarray(
+ wave_info['npnts'],
+ dtype=t.newbyteorder(byteOrder),
+ buffer=data_b
+ )
+ finally:
+ if not hasattr(filename, 'read'):
+ f.close()
+
+ return data, bin_info, wave_info
+
+
+def saveibw(filename):
+ raise NotImplementedError
+
+
+if __name__ == '__main__':
+ """IBW -> ASCII conversion
+ """
+ import optparse
+ import sys
+
+ p = optparse.OptionParser(version=__version__)
+
+ p.add_option('-f', '--infile', dest='infile', metavar='FILE',
+ default='-', help='Input IGOR Binary Wave (.ibw) file.')
+ p.add_option('-o', '--outfile', dest='outfile', metavar='FILE',
+ default='-', help='File for ASCII output.')
+ p.add_option('-v', '--verbose', dest='verbose', default=0,
+ action='count', help='Increment verbosity')
+ p.add_option('-t', '--test', dest='test', default=False,
+ action='store_true', help='Run internal tests and exit.')
+
+ options,args = p.parse_args()
+
+ if options.test == True:
+ import doctest
+ num_failures,num_tests = doctest.testmod(verbose=options.verbose)
+ sys.exit(min(num_failures, 127))
+
+ if len(args) > 0 and options.infile == None:
+ options.infile = args[0]
+ if options.infile == '-':
+ options.infile = sys.stdin
+ if options.outfile == '-':
+ options.outfile = sys.stdout
+
+ data,bin_info,wave_info = loadibw(options.infile)
+ numpy.savetxt(options.outfile, data, fmt='%g', delimiter='\n')
+ if options.verbose > 0:
+ import pprint
+ pprint.pprint(bin_info)
+ pprint.pprint(wave_info)
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