def open_bh_sdt(fn, mode='r'):
"""
read Becker&Hickel SDT file into separate structures
any error here might result from the file being corrupt
"""
#b = file(fn, 'rb').read()
m = N.memmap(fn, mode=mode)
hdrEnd = dtype_bhfile_header.itemsize
lenDBhdr = dtype_BHFileBlockHeader.itemsize
hdr = N.rec.array(m[:hdrEnd], dtype=dtype_bhfile_header) [0]
#hdr = m[:hdrEnd].view(dtype_bhfile_header)
if hdr['header_valid'] != BH_HEADER_VALID:
print " * WARNING * SDT file file header not valid"
infoStart = hdr['info_offs']
infoEnd = infoStart + hdr['info_length']
info= m[infoStart:infoEnd]
info= info.view(N.dtype( (N.string_, len(info)) )) [0]
setupStart= hdr['setup_offs']
setupEnd = setupStart + hdr['setup_length']
setup = m[setupStart:setupEnd]
setup = setup.view(N.dtype( (N.string_, len(setup)) )) [0]
setupTxtEnd = N.char.find(setup, '*END') + len('*END')
setupTxt = setup[:setupTxtEnd]
# following bytes are: '\r\n\r\n.......'
# >>> U.hexdump(s.setup[s.setupTxtEnd:s.setupTxtEnd+21])
# 0000 0d 0a 0d 0a 42 49 4e 5f 50 41 52 41 5f 42 45 47 ....BIN_PARA_BEG
# 0010 49 4e 3a 00 0e IN:..
#setupBin =
nDBs = hdr['no_of_data_blocks']
if nDBs == 0x7fff:
nDBs = hdr['reserved1']
#if nDBs != 1:
# print " * WARNING * SDT file has more than one data block(nDBs=%s)"%(nDBs,)
nMDBs = hdr['no_of_meas_desc_blocks']
mdbStart = hdr['meas_desc_block_offs']
lenMDB = hdr['meas_desc_block_length']
numMDB = hdr['no_of_meas_desc_blocks']
dataMeasInfos = m[mdbStart:mdbStart+numMDB*lenMDB].view(dtype=dtype_MeasureInfo)
import weakref
dbHdr = []
dbData = []
db0Start = hdr['data_block_offs']
o = db0Start
for i in range(nDBs):
dbh = m[o:o+lenDBhdr].view(dtype=dtype_BHFileBlockHeader) [0]
dbHdr.append( dbh )
dbo = dbh['data_offs']
dbl = dbh['block_length']
#dbd = N.array(m[dbo:dbo+dbl], dtype=N.uint16)
#ValueError: setting an array element with a sequence.
dbd = m[dbo:dbo+dbl].view(dtype=N.uint16)
#dbd.SDT_DataHdr = dbh
#dbd.SDT_DataMeasInfo = weakref.proxy( measInfos[ dbh['meas_desc_block_no'] ] )
dbd = ndarray_inSdtFile(dbd,
dataHdr=dbh,
dataMeasInfo=dataMeasInfos[ dbh['meas_desc_block_no'] ]
)
nx = dbd.SDT_DataMeasInfo['image_x']
ny = dbd.SDT_DataMeasInfo['image_y']
if nx>0 and ny >0: # FLIM !!
dbd.shape = nx,ny,-1
dbd = dbd.T
dbData.append(dbd)
o = dbh['next_block_offs']
del dbh,dbd,dbo, dbl, nx, ny
del o, i, weakref
dataBlkHdrs = F.mockNDarray(*dbHdr)
dataBlks = F.mockNDarray(*dbData)
del dbHdr, dbData
#return U.localsAsOneObject()
#data = ndarray_inSdtFile(dbData[0], U.localsAsOneObject())
#data.SDT.data = weakref.proxy( self.) # remove circular reference
dataBlks.SDT = U.localsAsOneObject()
import weakref
dataBlks.SDT.dataBlks = weakref.proxy( dataBlks ) # remove circular reference
if len(dataBlks) == 1 and dataBlks[0].ndim>1:
# one FLIM data block
dataBlks[0].SDT = dataBlks.SDT.dataBlks
return dataBlks[0]
else:
return dataBlks
# reading Becker & Hickl SDT files
# from time resolved fluorescence spectroscopy
# and FLIM experiments
# ref SPC_data_file_structure.h
dtype_bhfile_header = N.dtype([
('revision', N.int16), #; // software revision number (lower 4 bits >= 10(decimal))
('info_offs', N.int32), #; // offset of the info part which contains general text
# // information (Title, date, time, contents etc.)
('info_length', N.int16),#; // length of the info part
('setup_offs', N.int32), #; // offset of the setup text data
# // (system parameters, display parameters, trace parameters etc.)
('setup_length', N.int16),#;// length of the setup data
('data_block_offs', N.int32),#; offset of the first data block
('no_of_data_blocks', N.int16),#;no_of_data_blocks valid only when in 0 .. 0x7ffe range,
#// if equal to 0x7fff the field 'reserved1' contains
#// valid no_of_data_blocks
('data_block_length', N.int32),#// length of the longest block in the file
('meas_desc_block_offs', N.int32),#; // offset to 1st. measurement description block
#// (system parameters connected to data blocks)
('no_of_meas_desc_blocks', N.int16),#; // number of measurement description blocks
('meas_desc_block_length', N.int16),#; // length of the measurement description blocks
('header_valid', N.uint16), #; // valid: 0x5555, not valid: 0x1111
('reserved1', N.uint32), #; // reserved1 now contains no_of_data_blocks
('reserved2', N.uint16),
('chksum', N.uint16), #; // checksum of file header
])
BH_HEADER_CHKSUM = 0x55aa
BH_HEADER_NOT_VALID = 0x1111
BH_HEADER_VALID = 0x5555
