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add code un read_blk.py
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added code to re-organize data (more compatiable with neo imagesequence)
change some loop into comprehension, and made some change for code indentation
added some comment
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@teogale
teogale committed Aug 22, 2019
1 parent 9267c58 commit e7afea9
Showing 1 changed file with 70 additions and 123 deletions.
193 changes: 70 additions & 123 deletions neo/rawio/read_blk.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,115 +32,60 @@ def read_header(file_name):

file = open(file_name,"rb")

i = [['file_size', 'int32',1],
['checksum_header', 'int32',1],
['check_data','int32',1],
['lenheader','int32',1],
['versionid','float32',1],
['filetype','int32',1],
['filesubtype','int32',1],
['datatype','int32',1],
['sizeof','int32',1],
['framewidth','int32',1],
['frameheight','int32',1],
['nframesperstim','int32',1],
['nstimuli','int32',1],
['initialxbinfactor','int32',1],
['initialybinfactor','int32',1],
['xbinfactor','int32',1],
['ybinfactor','int32',1],
['username','uint8',32],
['recordingdate','uint8',16],
['x1roi','int32',1],
['y1roi','int32',1],
['x2roi','int32',1],
['y2roi','int32',1],
['stimoffs','int32',1],
['stimsize','int32',1],
['frameoffs','int32',1],
['framesize','int32',1],
['refoffs','int32',1],
['refsize','int32',1],
['refwidth','int32',1],
['refheight','int32',1],
['wichblocks','uint16',16],
['whichframe','uint16',16],
['loclip','int32',1],
['hiclip','int32',1],
['lopass','int32',1],
['hipass','int32',1],
['operationsperformed','uint8',64],
['magnifiaction','float32',1],
['gain','uint16',1],
['wavelength','uint16',1],
['exposuretime','int32',1],
['nrepetitions','int32',1],
['acquisitiondelay','int32',1],
['interstiminterval','int32',1],
['creationdate','uint8',16],
['datafilename','uint8',64],
['orareserved','uint8',256]
]
i = [
['file_size', 'int32',1],['checksum_header', 'int32',1],['check_data','int32',1],
['lenheader','int32',1],['versionid','float32',1],['filetype','int32',1],['filesubtype','int32',1],
['datatype','int32',1],['sizeof','int32',1],['framewidth','int32',1],['frameheight','int32',1],
['nframesperstim','int32',1],['nstimuli','int32',1],['initialxbinfactor','int32',1],['initialybinfactor','int32',1],
['xbinfactor','int32',1],['ybinfactor','int32',1],['username','uint8',32],['recordingdate','uint8',16],
['x1roi','int32',1],['y1roi','int32',1],['x2roi','int32',1],['y2roi','int32',1],['stimoffs','int32',1],
['stimsize','int32',1],['frameoffs','int32',1],['framesize','int32',1],['refoffs','int32',1],
['refsize','int32',1],['refwidth','int32',1],['refheight','int32',1],['wichblocks','uint16',16],
['whichframe','uint16',16],['loclip','int32',1],['hiclip','int32',1],['lopass','int32',1],
['hipass','int32',1],['operationsperformed','uint8',64],['magnifiaction','float32',1],
['gain','uint16',1],['wavelength','uint16',1],['exposuretime','int32',1],['nrepetitions','int32',1],
['acquisitiondelay','int32',1],['interstiminterval','int32',1],['creationdate','uint8',16],
['datafilename','uint8',64],['orareserved','uint8',256]
]

dic = {}
for x in i:
dic = read(name=x[0],type=x[1], nb=x[2],dictionary=dic,file=file)

if dic['filesubtype']==13:

# later
i = [["includerefframe","int32",1],
i = [
["includerefframe","int32",1],
["temp","uint8",128],
# p.listofstimuli=temp(1:max(find(temp~=0)))'; % up to first non-zero stimulus
["ntrials","int32",1],
["scalefactors","int32",1],
["cameragain","short",1],
["ampgain","short",1],
["samplingrate","short",1],
["average","short",1],
["exposuretime","short",1],
["samplingaverage","short",1],
["presentaverage","short",1],
["framesperstim","short",1],
["trialsperblock","short",1],
["sizeofanalogbufferinframes","short",1],
["cameratrials","short",1],
["filler","uint8",106],
["dyedaqreserved","uint8",106]
["ntrials","int32",1],["scalefactors","int32",1],["cameragain","short",1],
["ampgain","short",1],["samplingrate","short",1],["average","short",1],
["exposuretime","short",1],["samplingaverage","short",1],["presentaverage","short",1],
["framesperstim","short",1],["trialsperblock","short",1],["sizeofanalogbufferinframes","short",1],
["cameratrials","short",1],["filler","uint8",106],["dyedaqreserved","uint8",106]
]

for x in i:
dic = read(name=x[0],type=x[1], nb=x[2],dictionary=dic,file=file)

else:
i = [["inclidesreframe","int32",1],
["listofstimuli","uint8",256],
["nvideoframesperdataframe","int32",1],
["ntrials","int32",1],
["scalefactor","int32",1],
["meanampgain","float32",1],
["meanampdc","float32",1],
["vdaqreserved","uint8",256]
i = [
["inclidesreframe","int32",1],["listofstimuli","uint8",256],["nvideoframesperdataframe","int32",1],
["ntrials","int32",1],["scalefactor","int32",1],["meanampgain","float32",1],
["meanampdc","float32",1],["vdaqreserved","uint8",256]
]

for x in i:
dic = read(name=x[0],type=x[1], nb=x[2],dictionary=dic,file=file)

i = [["user","uint8",256],
["comment","uint8",256],
["refscalefactor","int32",1]
]

i = [["user","uint8",256],["comment","uint8",256],["refscalefactor","int32",1]]
for x in i:
dic = read(name=x[0],type=x[1], nb=x[2],dictionary=dic,file=file)
dic["actuallength"] = os.stat(file_name).st_size

file.close()

return dic

def load(*arg):

# file_name can be a string or a list

# file(s) name(s) can be one (or multiple string)

flag = ''
doarray = False
type_out = ''
Expand All @@ -161,19 +106,15 @@ def load(*arg):
gain = header['meanampgain']
dc = header['meanampdc']
scalefactor = header['scalefactor']

# [["dtype","nbytes","datatype","type_out"],[...]]
l = [[11,1,"uchar","unint8"],[12,2,"ushort","uint16"],
[13,4,"ulong","uint32"],[14,4,"float","single"]]
for i in l:
if dtype==i[0]:
nbytes = i[1]
datatype = i[2]
type_out = i[3]

nbytes,datatype,type_out = i[1],i[2],i[3]
if framesize!=ni*nj*nbytes:
framesize = ni*nj*nbytes

if (filesize-lenh)>(framesize*nfr*nstim):
nfr2 = nfr+1
includesrefframe = True
Expand All @@ -190,7 +131,6 @@ def load(*arg):

nbin = int(nblocks/flag)


if not conds:
conds =[i for i in range(1,nstim+1)]

Expand All @@ -199,33 +139,22 @@ def load(*arg):
if doarray:
data = numpy.zeros((ni,nj,nfr,ncond,nbin,type_out))
else:
data = [ [[] for x in range(ncond)] for i in range(nbin)]
for k in range(nbin):
for i in range(ncond):
data[k][i]=numpy.zeros((ni,nj,nfr),type_out)

data = [ [[numpy.zeros((ni,nj,nfr),type_out)] for x in range(ncond)] for i in range(nbin)]
for k in range(1,nbin+1):
bin = numpy.arange(math.floor((k-1/nbin*nblocks)+1),math.floor((k/nbin*nblocks)+1))
sbin = bin.size

for j in range(1,sbin+1):

file =open(arg[(bin[j-1]-1)],'rb')
for i in range(1,ncond+1):

framestart = conds[i-1]*nfr2-nfr
offset = framestart * ni * nj * nbytes + lenh
file.seek(offset,0)

a = []
for m in range(ni*nj*nfr):
a.append((int.from_bytes(file.read(nbytes),byteorder=sys.byteorder,signed=False)))
a = [int.from_bytes(file.read(nbytes),byteorder=sys.byteorder,signed=True) for m in range(ni*nj*nfr)]

a = numpy.array(a,dtype=type_out,order='F')
a = numpy.reshape(a,(ni*nj,nfr),order='F')
a = numpy.reshape(numpy.array(a,dtype=type_out,order='F'),(ni*nj,nfr),order='F')
# ligne 196 from matlab
a = numpy.reshape(a,(ni,nj,nfr),order='F')

# missing condition
"""
if includesrefframe:
Expand All @@ -242,32 +171,50 @@ def load(*arg):
"""
if sbin == 1:
if doarray:
# not usefull
# not tested
data[:][:][:][i-1][k-1] = a
# ni,nj,nfr,ncond,nbin,type_out
#data[:][:][:][i-1][k-1] = a
pass
else:
#work
print(k,"k",i,"i")
data[k-1][i-1] = a
else:
#not tested
if doarray:
data[:][:][:][i-1][k-1] = data[:][:][:][i-1][k-1] + a/sbin
# not useful
#data[:][:][:][i-1][k-1] = data[:][:][:][i-1][k-1] + a/sbin
pass
else:
data[k-1][i-1] = data[k-1][i-1] + a/sbin
###############################"""^^^^^^"""
file.close()

return data













### data format [block][stim][width][height][frame]]
### data structure should be [block][stim][frame][width][height] in order to be easy to use with neo
### each file is a block
### each stim could be a segment
### then an image sequence [frame][width][height]
### image need to be rotated

# changing order of data for compatibility
# [block][stim][width][height][frame]]
# to
# [block][stim][frame][width][height]

for block in range(len(data)):
for stim in range(len(data[block])):
a = []
for frame in range(header['nframesperstim']):
a.append([])
for width in range(len(data[block][stim])):
a[frame].append([])
for height in range(len(data[block][stim][width])):
a[frame][width].append(data[block][stim][width][height][frame])
# rotation of data to be the same as thomas deneux screenshot
# for
a[frame] = numpy.rot90(numpy.fliplr(a[frame]))
data[block][stim] = a

return data,header

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