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combine_2d_list.py
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combine_2d_list.py
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# *************************************************************************
#
# Combine 2D data into 1 HDF5 file
# for binned data
#
# *************************************************************************
# usage python combine_2d_list.py DIRNAME OUT_ROOT
# output = OUT_ROOT-xx.h5
# *************************************************************************
#
# (ver 2.0 -- here we handle binned data)
#
# *************************************************************************
#
# FST, (c) 2019 Regents of The University of California
#
# *************************************************************************
import sys
sys.path.append('/Users/franktsung/Documents/codes/python-tsung/')
sys.path.append('/Volumes/Lacie-5TB/codes/pyVisOS/')
import osh5io
import osh5def
import osh5vis
import osh5utils
from h5_utilities import *
import matplotlib.pyplot as plt
import sys
import getopt
import glob
import numpy as np
argc=len(sys.argv)
if(argc < 3):
print('Usage: python combine_2d_list.py DIRNAME OUT_ROOT')
sys.exit()
dirname=sys.argv[1]
outfilename = sys.argv[2]
filelist=sorted(glob.glob(dirname+'/*.h5'))
total_time=len(filelist)
my_share = total_time
i_begin=0
i_end = total_time
if i_end > 1000: i_end = 999
h5_filename=filelist[1]
h5_data=osh5io.read_h5(h5_filename)
list_length=len(h5_data)
array_dims=h5_data[0].shape
nx=array_dims[0]
ny=array_dims[1]
time_step=h5_data[0].run_attrs['TIME'][0]
# h5_output=hdf_data()
# h5_output.shape=[total_time,ny]
print('nx='+repr(nx))
print('time_step='+repr(time_step))
print('total_time='+repr(total_time))
#
xaxis=h5_data[0].axes[1]
taxis=osh5def.DataAxis(0, time_step * (total_time -1), total_time,
attrs={'NAME':'t', 'LONG_NAME':'time', 'UNITS':'1 / \omega_p'})
data_attrs=h5_data[0].data_attrs
h5_output= np.zeros((list_length,total_time,ny))
# h5_output.axes=[data_basic_axis(0,h5_data[0].axes[0].min,h5_data[0].axes[0].max,ny),
# data_basic_axis(1,0.0,(time_step*total_time-1),total_time)]
# run_attrs = h5_output.run_attrs
run_attrs = {'XMAX' : np.array( [ time_step * (total_time-1),xaxis.max] ) ,
'XMIN' : np.array( [0, xaxis.min, 0] ) }
file_number=0
for file_number in range(i_begin,i_end):
h5_filename=filelist[file_number]
if (file_number % 10 == 0 ):
print(h5_filename)
h5_data=osh5io.read_h5(h5_filename)
for i in range(list_length):
temp=np.average((h5_data[i]),axis=0)
h5_output[i,file_number,1:ny]=temp[1:ny]
# file_number+=1
print('before write')
for i in range(list_length):
list_filename="%s-%02d.h5" %(outfilename,i)
print(list_filename)
b=osh5def.H5Data(h5_output[i,:,:], timestamp='x', data_attrs=data_attrs,run_attrs=run_attrs, axes=[taxis, xaxis])
osh5io.write_h5(b,filename=list_filename)
print('after write')
# print('Before barrier'+repr(rank))