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h5_to_csv.py
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h5_to_csv.py
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import h5py
import os
import csv
from threading import Thread
from points import points_h5
import random
def get_month(file=''):
date = list(file.split('_')[4])
m1 = date[4]
m2 = date[5]
return m1 + m2
def get_day(file=''):
date = list(file.split('_')[4])
m1 = date[6]
m2 = date[7]
return m1 + m2
added_latlng = {}
def exists(latLong, csv_des):
if latLong in added_latlng:
return added_latlng[latLong]
return -1
csv_dest = []
csv_columns = ['latitude', 'longitude']
for i in range(1, 13):
csv_columns.append('soil_moisture_'+str(i).zfill((2)))
csv_columns.append('surface_temperature_'+str(i).zfill((2)))
files = []
lens = [0, 31, 29, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31]
f_dest = 'S_DEST'
upper = [11.696331, -86.003182]
lower = [-55.715245, -19.998368]
# Compute indexes
indexes = []
h5f = h5py.File('smapl3/2016/01/SMAP_L3_SM_P_20160101_R16510_001.h5', 'r')
ds_lat = h5f['Soil_Moisture_Retrieval_Data_AM']['latitude']
ds_lng = h5f['Soil_Moisture_Retrieval_Data_AM']['longitude']
# print("Computing indexes")
# for i in range(0, 406):
# for j in range(0, 964):
# lat = ds_lat[i][j]
# lng = ds_lng[i][j]
# if str(lat) + ',' + str(lng) in points_h5:
# indexes.append((i, j))
# print("Computed indexes: " + str(len(indexes)))
# targets = (
# [{'f': 'SMAP_L3_SM_P_20160101_R16510_001.h5', 'm': '01', 'd': '01'}], [],)
targets = ([], [],)
# r = root, d = directories, f = files
for r, d, f in os.walk('smapl3/2017/01'):
for file in f:
if file.endswith('.h5'):
m = get_month(file)
d = get_day(file)
# if int(m) % 2 == 0:
# targets[0].append({'f': file, 'm': m, 'd': d})
targets[0].append({'f': file, 'm': m, 'd': d})
# else:
# targets[1].append({'f': file, 'm': m, 'd': d})
def crawl(files=[], csv_dest=[], t=''):
for data in files:
file = data['f']
m = data['m']
d = data['d']
h5f = h5py.File('smapl3/2017/' + m + '/' + file, 'r')
ds_sm = h5f['Soil_Moisture_Retrieval_Data_AM']['soil_moisture']
ds_st = h5f['Soil_Moisture_Retrieval_Data_AM']['surface_temperature']
ds_lat = h5f['Soil_Moisture_Retrieval_Data_AM']['latitude']
ds_lng = h5f['Soil_Moisture_Retrieval_Data_AM']['longitude']
indexes_indexes = list(range(len(indexes)))
random.shuffle(indexes_indexes)
soil_key = 'soil_moisture_' + m
tmp_key = 'surface_temperature_' + m
for i in range(0, 406):
for j in range(0, 964):
lat = ds_lat[i][j]
lng = ds_lng[i][j]
if lat < upper[0] and lat > lower[0] and lng > upper[1] and lng < lower[1]:
sm = ds_sm[i][j]
st = ds_st[i][j]
lat_lng_str = str(lat)+","+str(lng)
lat_str = str(lat)
lng_str = str(lng)
index = exists(lat_lng_str, csv_dest)
if index != -1:
# print(t + ": Exists " + lat_lng_str + " m:" + m)
if (soil_key) in csv_dest[index]:
csv_dest[index][soil_key] = (
csv_dest[index][soil_key][0] + sm, csv_dest[index][soil_key][1] + 1)
csv_dest[index][tmp_key] = (
csv_dest[index][tmp_key][0] + st, csv_dest[index][tmp_key][1] + 1)
else:
csv_dest[index][soil_key] = (sm, 1)
csv_dest[index][tmp_key] = (st, 1)
else:
print(t + ": Doesnt exists " +
lat_lng_str + " m:" + m + " d: " + d)
csv_dest.append({
'latitude': lat_str,
'longitude': lng_str,
soil_key: (sm, 1),
tmp_key: (st, 1),
})
added_latlng[lat_lng_str] = len(csv_dest) - 1
iindex = exists(lat_lng_str, csv_dest)
count = csv_dest[iindex][soil_key][1]
if csv_dest[iindex][soil_key][0] == -9999.0:
csv_dest[iindex][soil_key] = (0, count - 1)
if csv_dest[iindex][tmp_key][0] == -9999.0:
csv_dest[iindex][tmp_key] = (
0, csv_dest[iindex][tmp_key][1] - 1)
else:
csv_dest[iindex][tmp_key] = (
csv_dest[iindex][tmp_key][0] - 273.15, csv_dest[iindex][tmp_key][1])
if lens[int(m)] == count:
print(t + ": Done with " + m)
csv_dest[iindex][soil_key] = (
csv_dest[iindex][soil_key] / lens[int(m)], 99)
csv_dest[iindex][tmp_key] = (
csv_dest[iindex][tmp_key] / lens[int(m)], 99)
print(t + " done day: " + d)
h5f.close()
with open('names422017.csv', 'w', newline='') as csvfile:
writer = csv.DictWriter(csvfile, fieldnames=csv_columns)
writer.writeheader()
writer.writerows(csv_dest)
# threads = []
# for ii in range(len(targets)):
# # We start one thread per url present.
# data = targets[ii]
# process = Thread(target=crawl, args=[data, csv_dest, str(ii)])
# process.start()
# threads.append(process)
# for process in threads:
# process.join()
crawl(targets[0], csv_dest, '1')
currentPath = os.getcwd()
csv_file = currentPath + "/csv/Names23.csv"
with open('names422017.csv', 'w', newline='') as csvfile:
writer = csv.DictWriter(csvfile, fieldnames=csv_columns)
writer.writeheader()
writer.writerows(csv_dest)