From: W. Trevor King Date: Mon, 20 Aug 2012 18:09:06 +0000 (-0400) Subject: Replace hooke.util.igorbinarywave with external igor package. X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=9c4404f39b567c19d65e5ed819cc0742e1d98cad;p=hooke.git Replace hooke.util.igorbinarywave with external igor package. http://pypi.python.org/pypi/igor Now that This way we share a more general package instead of rolling our own. Most of the changes to the mfp3d driver are due to the fact that the igor package reads the IBW into a single dict (vs. three dicts for igorbinarywave), and some of the keys have changed. The dimension labels have also changed a bit, since ...['wave']['labels'][1] is ['', 'Raw', 'Defl', 'LVDT'] instead of the old ['Raw', 'Defl', 'LVDT'] The blank label is for labeling all the columns. From WaveMetrics' TN003: A 3 point 1D wave has 4 dimension labels. The first dimension label is the label for the dimension as a whole. The next three dimension labels are the labels for rows 0, 1, and 2. So the labels are: ['', 'Raw', 'Defl', 'LVDT'] ^ ^ ^ ^-- column 2 | | `-- column 1 | `-- column 0 `-- columns as a whole --- diff --git a/hooke/driver/mfp3d.py b/hooke/driver/mfp3d.py index cddbf04..700df4d 100644 --- a/hooke/driver/mfp3d.py +++ b/hooke/driver/mfp3d.py @@ -34,9 +34,9 @@ import os.path import pprint import numpy +from igor.binarywave import load as _loadibw from .. import curve as curve -from ..util.igorbinarywave import loadibw from . import Driver as Driver @@ -68,19 +68,19 @@ class MFP3DDriver (Driver): return False def read(self, path, info=None): - data,bin_info,wave_info = loadibw(path) - blocks,info = self._translate_ibw(data, bin_info, wave_info) + data = _loadibw(path) + blocks,info = self._translate_ibw(data) return (blocks, info) - def _translate_ibw(self, data, bin_info, wave_info): - if bin_info['version'] != 5: - raise NotImplementedError('IBW version %d (< 5) not supported' - % bin_info['version']) + def _translate_ibw(self, data): + if data['version'] != 5: + raise NotImplementedError( + 'IBW version {} (< 5) not supported'.format(data['version'])) # We need version 5 for multidimensional arrays. # Parse the note into a dictionary note = {} - for line in bin_info['note'].split('\r'): + for line in data['wave']['note'].split('\r'): fields = [x.strip() for x in line.split(':', 1)] key = fields[0] if len(fields) == 2: @@ -88,7 +88,7 @@ class MFP3DDriver (Driver): else: value = None note[key] = value - bin_info['note'] = note + data['wave']['note'] = note # Ensure a valid MFP3D file version. if note['VerDate'] not in ['80501.041', '80501.0207']: @@ -99,8 +99,7 @@ class MFP3DDriver (Driver): # Parse known parameters into standard Hooke format. info = { - 'raw info':{'bin':bin_info, - 'wave':wave_info}, + 'raw info':data, 'time':note['Seconds'], 'spring constant (N/m)':float(note['SpringConstant']), 'temperature (K)':self._temperature(note), @@ -112,7 +111,9 @@ class MFP3DDriver (Driver): assert indexes[0] == 0, indexes for i,start in enumerate(indexes[:-1]): stop = indexes[i+1] - blocks.append(self._scale_block(data[start:stop+1,:], info, i)) + blocks.append( + self._scale_block( + data['wave']['wData'][start:stop+1,:], info, i)) return (blocks, info) @@ -123,7 +124,7 @@ class MFP3DDriver (Driver): # MFP3D's native data dimensions match Hooke's (, ) layout. shape = 3 # raw column indices - columns = info['raw info']['bin']['dimLabels'][1] + columns = info['raw info']['wave']['labels'][1][1:] # Depending on your MFP3D version: # VerDate 80501.0207: ['Raw', 'Defl', 'LVDT', 'Time'] # VerDate 80501.041: ['Raw', 'Defl', 'LVDT'] @@ -137,7 +138,7 @@ class MFP3DDriver (Driver): info=copy.deepcopy(info) ) - version = info['raw info']['bin']['note']['VerDate'] + version = info['raw info']['wave']['note']['VerDate'] if version == '80501.041': name = ['approach', 'retract', 'pause'][index] elif version == '80501.0207': @@ -189,8 +190,8 @@ class MFP3DDriver (Driver): # h=Hooke(); # h.run_command('load playlist', # {'input':'test/data/vclamp_mfp3d/playlist'}); - # x = [(int(c.info['raw info']['bin']['note']['Seconds']) - # - int(c.info['raw info']['bin']['note']['StartTempSeconds'])) + # x = [(int(c.info['raw info']['wave']['note']['Seconds']) + # - int(c.info['raw info']['wave']['note']['StartTempSeconds'])) # for c in h.playlists.current().items()]; # print 'average', float(sum(x))/len(x); # print 'range', min(x), max(x); diff --git a/hooke/util/igorbinarywave.py b/hooke/util/igorbinarywave.py deleted file mode 100644 index 3715c39..0000000 --- a/hooke/util/igorbinarywave.py +++ /dev/null @@ -1,612 +0,0 @@ -#!/usr/bin/python -# -# Copyright (C) 2010-2012 W. Trevor King -# -# 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 . - -"""igorbinarywave provides pure Python interface between IGOR Binary -Wave files and Numpy arrays. - -This is basically a stand-alone package that we bundle into Hooke for -convenience. It is used by the mfp*d drivers, whose data is saved in -IBW files. -""" - -# 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, strict=True): - 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)) - if version == 5: - shape = [n for n in wave_info['nDim'] if n > 0] - else: - shape = (wave_info['npnts'],) - data = numpy.ndarray( - shape=shape, - dtype=t.newbyteorder(byteOrder), - buffer=data_b, - order='F', - ) - - if version == 1: - pass # No post-data information - elif version == 2: - # Post-data info: - # * 16 bytes of padding - # * Optional wave note data - pad_b = buffer(f.read(16)) # skip the padding - if max(pad_b) != 0: - if strict: - assert max(pad_b) == 0, pad_b - else: - print sys.stderr, 'warning: post-data padding not zero: %s.' % pad_b - bin_info['note'] = str(f.read(bin_info['noteSize'])).strip() - elif version == 3: - # Post-data info: - # * 16 bytes of padding - # * Optional wave note data - # * Optional wave dependency formula - """Excerpted from TN003: - - A wave has a dependency formula if it has been bound by a - statement such as "wave0 := sin(x)". In this example, the - dependency formula is "sin(x)". The formula is stored with - no trailing null byte. - """ - pad_b = buffer(f.read(16)) # skip the padding - if max(pad_b) != 0: - if strict: - assert max(pad_b) == 0, pad_b - else: - print sys.stderr, 'warning: post-data padding not zero: %s.' % pad_b - bin_info['note'] = str(f.read(bin_info['noteSize'])).strip() - bin_info['formula'] = str(f.read(bin_info['formulaSize'])).strip() - elif version == 5: - # Post-data info: - # * Optional wave dependency formula - # * Optional wave note data - # * Optional extended data units data - # * Optional extended dimension units data - # * Optional dimension label data - # * String indices used for text waves only - """Excerpted from TN003: - - dataUnits - Present in versions 1, 2, 3, 5. The dataUnits - field stores the units for the data represented by the - wave. It is a C string terminated with a null - character. This field supports units of 0 to 3 bytes. In - version 1, 2 and 3 files, longer units can not be - represented. In version 5 files, longer units can be - stored using the optional extended data units section of - the file. - - xUnits - Present in versions 1, 2, 3. The xUnits field - stores the X units for a wave. It is a C string - terminated with a null character. This field supports - units of 0 to 3 bytes. In version 1, 2 and 3 files, - longer units can not be represented. - - dimUnits - Present in version 5 only. This field is an - array of 4 strings, one for each possible wave - dimension. Each string supports units of 0 to 3 - bytes. Longer units can be stored using the optional - extended dimension units section of the file. - """ - bin_info['formula'] = str(f.read(bin_info['formulaSize'])).strip() - bin_info['note'] = str(f.read(bin_info['noteSize'])).strip() - bin_info['dataEUnits'] = str(f.read(bin_info['dataEUnitsSize'])).strip() - bin_info['dimEUnits'] = [ - str(f.read(size)).strip() for size in bin_info['dimEUnitsSize']] - bin_info['dimLabels'] = [] - for size in bin_info['dimLabelsSize']: - labels = str(f.read(size)).split(chr(0)) # split null-delimited strings - bin_info['dimLabels'].append([L for L in labels if len(L) > 0]) - if wave_info['type'] == 0: # text wave - bin_info['sIndices'] = f.read(bin_info['sIndicesSize']) - - 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('-n', '--not-strict', dest='strict', default=True, - action='store_false', help='Attempt to parse invalid IBW files.') - 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, strict=options.strict) - numpy.savetxt(options.outfile, data, fmt='%g', delimiter='\t') - if options.verbose > 0: - import pprint - pprint.pprint(bin_info) - pprint.pprint(wave_info)