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stack.py
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stack.py
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# -*- coding: utf-8 -*-
import geoarray as geo
import os
import mysat
lsat_path = '/dados/d3/rolf/LANDSAT_EVI_NDVI/'
modis_path = '/dados/d3/rolf/MODIS_MOD13Q1/'
def my_new_lsat_stack(bands, dtype, nodata, **metadata):
return geo.empty(width=320, height=268, bands=bands,
geotransform=(608775.00, 30.0, 0.0, -1324875.00, 0.0, -30.0),
proj_origin='+proj=utm +zone=21 +ellps=WGS84 +datum=WGS84 +units=m +no_defs',
nodata=nodata, dtype=dtype, **metadata)
def my_new_lsat_sensor_stack(lsat_rep_band, save_in_path):
def sensor_to_int(x):
return 5 if x == 'LT5' else 7 if x == 'LE7' else 8 if x == 'LC8' else 0
# sensor stack
sensor_band = lsat_rep_band.apply(source_int=(sensor_to_int, 'source'))
t = my_new_lsat_stack(bands=lsat_rep_band.rows, dtype='u1', nodata=0, SEMANTIC='5 LT5, 7 LE7, 8 LC8')
for i in range(lsat_rep_band.rows):
t[t, i] = sensor_band['source_int'][i]
geo.write(t, file_name=os.path.join(save_in_path, 'lsat_{0}.tif'.format('source')), overwrite=True)
def my_new_lsat_days_stack(lsat_rep_band, save_in_path):
# days after 1970-01-01 stack
t = my_new_lsat_stack(bands=lsat_rep_band.rows, dtype='u2', nodata=0, SEMANTIC='DAYS SINCE 1970-01-01')
for i in range(lsat_rep_band.rows):
t[t, i] = lsat_rep_band['datestamp'][i]
geo.write(t, file_name=os.path.join(save_in_path, 'lsat_{0}.tif'.format('days')), overwrite=True)
def make_stack_lsat_only(root, sensor=True, days=True, **bands):
repository = mysat.landsat(root)
repository = repository.order_by('date')
one_band = repository.where(repository.index_of('product', 'sr_ndvi'))
# sensor stack
if sensor:
my_new_lsat_sensor_stack(lsat_rep_band=one_band, save_in_path='/dados/d2/rolf')
print('{0}: {1} lsat_bands'.format('sensor', one_band.rows))
# days after 1970-01-01 stack
if days:
my_new_lsat_days_stack(lsat_rep_band=one_band, save_in_path='/dados/d2/rolf')
print('{0}: {1} lsat_bands'.format('days', one_band.rows))
# bands stack
for band_name, band in bands.items():
print('-----------------------------------')
one_band = repository.where(repository.index_of('product', band))
t = my_new_lsat_stack(bands=one_band.rows, dtype='i2', nodata=-9999, SEMANTIC=band_name)
for i in range(one_band.rows):
s = geo.read(one_band['file'][i], t.box, resample_alg=geo.GRIORA_NearestNeighbour)
t[s, i] = s[t, 0]
print('{0} band {1:02d}: {2}'.format(band_name, i, one_band['file'][i]))
if t is not None:
geo.write(t, file_name='/dados/d2/rolf/lsat_{0}.tif'.format(band_name), overwrite=True)
def brick_modis_only(root, sensor=True, days=True, **bands):
repository = mysat.mod13q1(root)
repository = repository.order_by('date')
one_band = repository.where(repository.index_of('product', '250m_16_days_NDVI'))
# sensor stack
if sensor:
my_new_lsat_sensor_stack(lsat_rep_band=one_band, save_in_path='/dados/d2/rolf')
print('{0}: {1} mod13q1_bands'.format('sensor', one_band.rows))
# days after 1970-01-01 stack
if days:
my_new_lsat_days_stack(lsat_rep_band=one_band, save_in_path='/dados/d2/rolf')
print('{0}: {1} mod13q1_bands'.format('days', one_band.rows))
# bands stack
for band_name, band in bands.items():
print('-----------------------------------')
one_band = repository.where(repository.index_of('product', band))
t = my_new_lsat_stack(bands=one_band.rows, dtype='i2', nodata=-9999, SEMANTIC=band_name)
for i in range(one_band.rows):
s = geo.read(one_band['file'][i], t.box, resample_alg=geo.GRIORA_NearestNeighbour)
t[s, i] = s[t, 0]
print('{0} band {1:02d}: {2}'.format(band_name, i, one_band['file'][i]))
if t is not None:
geo.write(t, file_name='/dados/d2/rolf/lsat_{0}.tif'.format(band_name), overwrite=True)
########
for band_name, bands in modis_bands.items():
print('-----------------------------------')
paths = []
dates = []
for band in bands:
files = [file for file in os.listdir(band[1]) if file.endswith(band[0] + '.tif')]
paths += [os.path.join(band[1], file) for file in files]
dates += [band[2](file) for file in files]
paths_dates = sorted(zip(paths, dates), key=lambda px: px[1])
t = mygdal.create(px_size=320, py_size=268, bands=len(paths_dates),
proj='+proj=utm +zone=21 +ellps=WGS84 +datum=WGS84 +units=m +no_defs',
nodata=-3000,
gdal_dtype=mygdal.GDT_Int16,
geotransform=(608775.00, 30.0, 0.0, -1324875.00, 0.0, -30.0))
for i in range(len(paths_dates)):
s = mygdal.open_file(filename=paths_dates[i][0])
print('{0} band {1:02d}: {2}'.format(band_name, i, paths_dates[i][0]))
s.copy_to(target=t, to_bands=i, resample_alg=mygdal.GRA_NearestNeighbour)
t.save_as('/dados/d2/rolf/modis_{0}.tif'.format(band_name), overwrite=True)
make_stack_lsat_only(root=lsat_path, sensor=True, days=True, ndvi='sr_ndvi', evi='sr_evi')
#
# def brick_lsat_modis():
# all_bands = {'ndvi': [('NDVI', modis_path, modis_extr_date, modis_extr_sensor),
# ('sr_ndvi', lsat_path, lsat_extr_date, lsat_extr_sensor)],
# 'evi': [('EVI', modis_path, modis_extr_date, modis_extr_sensor),
# ('sr_evi', lsat_path, lsat_extr_date, lsat_extr_sensor)]}
# paths = []
# dates = []
# sensor = []
# for band in all_bands['ndvi']:
# files = [file for file in os.listdir(band[1]) if file.endswith(band[0] + '.tif')]
# paths += [os.path.join(band[1], file) for file in files]
# dates += [band[2](file) for file in files]
# sensor += [file[0:3] for file in files]
#
# paths_dates = sorted(zip(paths, dates, sensor), key=lambda px: px[1])
#
# # sensor stack
# t = mygdal.create(px_size=320, py_size=268, bands=len(paths_dates),
# proj='+proj=utm +zone=21 +ellps=WGS84 +datum=WGS84 +units=m +no_defs',
# gdal_dtype=mygdal.GDT_Byte,
# geotransform=(608775.00, 30.0, 0.0, -1324875.00, 0.0, -30.0))
# for i in range(len(paths_dates)):
# if paths_dates[i][2] == 'LT5':
# t.bands[i].fill(5)
# elif paths_dates[i][2] == 'LE7':
# t.bands[i].fill(7)
# elif paths_dates[i][2] == 'LC8':
# t.bands[i].fill(8)
# elif paths_dates[i][2] == 'MOD':
# t.bands[i].fill(113)
# t.save_as('/dados/d2/rolf/lsat_modis_{0}.tif'.format('sensor'), overwrite=True)
# print('{0}: {1} lsat_bands'.format('sensor', len(paths_dates)))
#
# # days after 1970-01-01 stack
# t = mygdal.create(px_size=320, py_size=268, bands=len(paths_dates),
# proj='+proj=utm +zone=21 +ellps=WGS84 +datum=WGS84 +units=m +no_defs',
# gdal_dtype=mygdal.GDT_UInt16,
# geotransform=(608775.00, 30.0, 0.0, -1324875.00, 0.0, -30.0))
# for i in range(len(paths_dates)):
# if paths_dates[i][2] != 'MOD':
# year = '{0}-01-01'.format(paths_dates[i][1][0:4])
# days = int(paths_dates[i][1][4:7])
# days_after_1970 = mynumpy.datetime64_to_timestamp(numpy.datetime64(year, 'D') +
# numpy.timedelta64(days, 'D')) / 86400
# t.bands[i].fill(days_after_1970)
# else:
# year = '{0}-01-01'.format(paths_dates[i][1][0:4])
# s = mygdal.open_file(paths_dates[i][0][:len(modis_path) + 55] + 'composite_day_of_the_year.tif')
# s.copy_to(target=t, to_bands=i, resample_alg=mygdal.GRA_NearestNeighbour)
# days = t.bands[i].array.astype('timedelta64[D]')
# days_after_1970 = mynumpy.datetime64_to_timestamp(numpy.datetime64(year, 'D') + days - 1) / 86400
# t.bands[i][:] = days_after_1970
# t.set_metadata({'Semantic': 'days since 1970-01-01'})
# t.save_as('/dados/d2/rolf/lsat_modis_{0}.tif'.format('days'), overwrite=True)
# print('{0}: {1} lsat_bands'.format('days', len(paths_dates)))
#
# for band_name, bands in all_bands.items():
# print('-----------------------------------')
# paths = []
# dates = []
# for band in bands:
# files = [file for file in os.listdir(band[1]) if file.endswith(band[0] + '.tif')]
# paths += [os.path.join(band[1], file) for file in files]
# dates += [band[2](file) for file in files]
# paths_dates = sorted(zip(paths, dates), key=lambda px: px[1])
#
# t = mygdal.create(px_size=320, py_size=268, bands=len(paths_dates),
# proj='+proj=utm +zone=21 +ellps=WGS84 +datum=WGS84 +units=m +no_defs',
# nodata=-9999,
# gdal_dtype=mygdal.GDT_Int16,
# geotransform=(608775.00, 30.0, 0.0, -1324875.00, 0.0, -30.0))
#
# for i in range(len(paths_dates)):
# s = mygdal.open_file(filename=paths_dates[i][0])
# print('{0} band {1:02d}: {2}'.format(band_name, i, paths_dates[i][0]))
# s.copy_to(t, to_bands=i)
# t.save_as('/dados/d2/rolf/lsat_modis_{0}.tif'.format(band_name), overwrite=True)
#
#