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#!python
import sys, os
import numpy, h5py
class Converter(object):
def __init__(self, infile):
self.infile = infile
info = infile + ".info"
if os.path.exists(info):
self.info = self.read_info(info)
else:
self.info = {}
def read_info(self, infofile):
"""
Read an info file containing data
@param infofile: filename of .info
@return: dict with parameters
"""
dico = {}
with open(infofile) as f:
for line in f:
words = [i.strip() for i in line.split("=")]
if len(words) == 2:
if words[1].isdigit():
dico[words[0]] = int(words[ 1])
else:
try:
dico[words[0]] = float(words[ 1])
except ValueError:
dico[words[0]] = words[ 1]
return dico
def save(self, outfile, path="data"):
sys.stdout.write("Converting volume to HDF5. Frame 0000")
dtype = numpy.float32
h5 = h5py.File(outfile)
if path in h5:
del h5[path]
shape = [self.info[i] for i in ('NUM_Z', 'NUM_Y', "NUM_X")]
chunks = (1, self.info['NUM_Y'], self.info["NUM_X"])
ds = h5.create_dataset(path, shape=shape, dtype=dtype, chunks=chunks)
block_size = self.info['NUM_Y'] * self.info["NUM_X"] * numpy.float32(1).itemsize
with open(self.infile) as ff:
for i in range(self.info['NUM_Z']):
block = ff.read(block_size)
data = numpy.fromstring(block, dtype=dtype)
data.shape = self.info['NUM_Y'], self.info["NUM_X"]
ds[i, :, :] = data
sys.stdout.write("\b"*4 + "%04i" % (i + 1))
print(" Done")
def main():
path = "data"
if len(sys.argv) == 2:
infile = sys.argv[1]
outfile = os.path.splitext(infile)[0] + ".h5"
elif len(sys.argv) == 3:
infile = sys.argv[1]
outfile = sys.argv[2]
elif len(sys.argv) == 4:
infile = sys.argv[1]
outfile = sys.argv[2]
path = sys.argv[3]
else:
print(__doc__)
sys.exit(-1)
conv = Converter(infile)
conv.save(outfile, path)
if __name__ == "__main__":
main()
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