def convertFile(pathToData,
outFile,
frameSize=[256, 256],
pixelsize=None,
complib='zlib',
complevel=9):
#seriesName = pathToData.split(os.sep)[-2]
#fnl = os.listdir(pathToData)
#fnl2 = [pathToData + f for f in fnl]
#f1 = read_kdf.ReadKdfData(pathToData).squeeze()
xSize, ySize = frameSize
f1 = open(pathToData, 'rb')
#detect file length
f1.seek(0, 2) #seek to end
fLength = f1.tell()
f1.seek(0) #back to begining
nFrames = fLength / (2 * xSize * ySize)
outF = tables.openFile(outFile, 'w')
filt = tables.Filters(complevel, complib, shuffle=True)
imageData = outF.createEArray(outF.root,
'ImageData',
tables.UInt16Atom(), (0, xSize, ySize),
filters=filt,
expectedrows=nFrames)
for i in range(nFrames):
d1 = numpy.fromfile(f1, '>u2', xSize * ySize) >> 4
imageData.append(d1.reshape(1, xSize, ySize))
if i % 100 == 0:
print(('%d of %d frames' % (i, nFrames)))
f1.close()
hdh = MetaData.HDFMDHandler(outF, MetaData.TIRFDefault)
if not pixelsize == None:
hdh.setEntry('voxelsize.x', pixelsize)
hdh.setEntry('voxelsize.y', pixelsize)
outEvents = outF.createTable(outF.root,
'Events',
SpoolEvent,
filters=tables.Filters(complevel=5,
shuffle=True))
outF.flush()
outF.close()
def convertFile(pathToData,
outFile,
pixelsize=None,
complib='zlib',
complevel=9):
#seriesName = pathToData.split(os.sep)[-2]
#fnl = os.listdir(pathToData)
#fnl2 = [pathToData + f for f in fnl]
f1 = read_kdf.ReadKdfData(pathToData).squeeze()
xSize, ySize = f1.shape[0:2]
outF = tables.openFile(outFile, 'w')
filt = tables.Filters(complevel, complib, shuffle=True)
imageData = outF.createEArray(outF.root,
'ImageData',
tables.UInt16Atom(), (0, xSize, ySize),
filters=filt,
expectedrows=f1.shape[2])
for i in range(f1.shape[2]):
imageData.append(f1[:, :, i].reshape(1, xSize, ySize))
hdh = MetaData.HDFMDHandler(outF, MetaData.PCODefault)
if not pixelsize == None:
hdh.setEntry('voxelsize.x', pixelsize)
hdh.setEntry('voxelsize.y', pixelsize)
outEvents = outF.createTable(outF.root,
'Events',
SpoolEvent,
filters=tables.Filters(complevel=5,
shuffle=True))
outF.flush()
outF.close()
