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import h5py
import sys
import numpy as np
import os
def create_virtual_file( vsource, pro_indxs, datasource_shape, mydtype, filename ):
layout = h5py.VirtualLayout(shape= tuple([ len( pro_indxs ) ]+ list(datasource_shape)[1:]), dtype=mydtype)
for n in range( len( pro_indxs ) ):
layout[n] = vsource[ pro_indxs[n] ]
with h5py.File(filename, "w", libver="latest") as f:
f.create_virtual_dataset("data", layout=layout, fillvalue=-5)
fn = sys.argv[1]
dn = sys.argv[2]
rep = sys.argv[3]
pyhst2_input = """
"""
entry = h5py.File(fn,"r")[dn]
pro_indxs = []
ff_indxs = []
ff_poss = []
bck_indxs = []
keys = entry["instrument/detector"]["image_key"]
old_ff_pos = -1
ffblock = None
ipro = 0
for i,k in enumerate(list(keys)):
if k== 2:
bck_indxs.append(i)
if k== 0:
pro_indxs.append(i)
ipro += 1
if k==1:
if ipro== old_ff_pos:
ffblock.append(i)
else:
ffblock = []
ff_indxs.append( ffblock )
ff_poss.append(ipro )
old_ff_pos = ipro
datasource_shape = entry["instrument/detector/data"] .shape
mydtype = entry["instrument/detector/data"].dtype
vsource = h5py.VirtualSource(fn, dn+"/instrument/detector/data", shape= datasource_shape )
filename = os.path.join(rep,"pyhst2_projs.h5")
create_virtual_file( vsource, pro_indxs, datasource_shape, mydtype, filename )
pyhst2_input += """
FILE_PREFIX={}
PROJ_DS_NAME = "data"
""".format( os.path.join(rep,"pyhst2_projs.h5") )
if len(bck_indxs):
filename = os.path.join(rep,"pyhst2_background.h5")
create_virtual_file( vsource, bck_indxs, datasource_shape, mydtype, filename )
pyhst2_input += """
BACKGROUND_FILE={}
BACKGROUND_DS_NAME = "data"
""".format( os.path.join(rep,"pyhst2_projs.h5") )
s_files="""["""
s_intervals="""["""
if len(ff_indxs):
for ffblock, pos in zip(ff_indxs, ff_pos ) :
s_intervals += """ {} ,""".format(pos)
fname = "pyhst2_ff%05d.h5"%ff_pos
fname = os.path.join(rep, fname)
s_files+=""" "{}",""".format(fname=
create_virtual_file( vsource, ffblock, datasource_shape, mydtype, fname ) )
pyhst2_input += """
FF_PREFIX={ffprefix}]
FF_DS_NAME = "data"
FF_INTERVALS={intervals}]
""".format( ffprefix=s_files[:-1] , intervals=s_intervals[:-1] )
print (pyhst2_input)
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