def test_extrapolate_rows(self):
lons = np.arange(10).reshape((2, 5), order="F")
lats = np.arange(10).reshape((2, 5), order="C")
lines = np.array([2, 7])
cols = np.array([2, 7, 12, 17, 22])
hlines = np.arange(10)
hcols = np.arange(24)
satint = SatelliteInterpolator((lons, lats), (lines, cols),
(hlines, hcols))
self.assertTrue(
np.allclose(
satint._extrapolate_rows(satint.tie_data[0]),
np.array([[
6381081.08333225, 6381639.66045187, 6372470.10269454,
6353590.21586788, 6325042.05851245
],
[
6370997., 6366146.21816553, 6351605.98629588,
6327412.61244969, 6293626.50067273
],
[
6345786.79166939, 6327412.61244969,
6299445.69529922, 6261968.60390423,
6215087.60607344
],
[
6335702.70833714, 6311919.17016336,
6278581.57890056, 6235791.00048604,
6183672.04823372
]])))
def navigate(self):
"""Return the longitudes and latitudes of the scene.
"""
tic = datetime.now()
lons40km = self._data["pos"][:, :, 1] * 1e-4
lats40km = self._data["pos"][:, :, 0] * 1e-4
try:
from geotiepoints import SatelliteInterpolator
except ImportError:
logger.warning("Could not interpolate lon/lats, "
"python-geotiepoints missing.")
self.lons, self.lats = lons40km, lats40km
else:
cols40km = np.arange(24, 2048, 40)
cols1km = np.arange(2048)
lines = lons40km.shape[0]
rows40km = np.arange(lines)
rows1km = np.arange(lines)
along_track_order = 1
cross_track_order = 3
satint = SatelliteInterpolator(
(lons40km, lats40km), (rows40km, cols40km), (rows1km, cols1km),
along_track_order, cross_track_order)
self.lons, self.lats = satint.interpolate()
logger.debug("Navigation time %s", str(datetime.now() - tic))
def test_fill_col_borders(self):
lons = np.arange(10).reshape((2, 5), order="F")
lats = np.arange(10).reshape((2, 5), order="C")
lines = np.array([2, 7])
cols = np.array([2, 7, 12, 17, 22])
hlines = np.arange(10)
hcols = np.arange(24)
satint = SatelliteInterpolator((lons, lats), (lines, cols),
(hlines, hcols))
satint._fill_col_borders()
self.assertTrue(
np.allclose(
satint.tie_data[0],
np.array([[
6372937.31273379, 6370997., 6366146.21816553,
6351605.98629588, 6327412.61244969, 6293626.50067273,
6286869.27831734
],
[
6353136.46335726, 6345786.79166939,
6327412.61244969, 6299445.69529922,
6261968.60390423, 6215087.60607344,
6205711.40650728
]])))
self.assertTrue(
np.allclose(satint.col_indices, np.array([0, 2, 7, 12, 17, 22,
23])))
def navigate(self):
"""Return the longitudes and latitudes of the scene.
"""
tic = datetime.now()
lons40km = self._data["pos"][:, :, 1] * 1e-4
lats40km = self._data["pos"][:, :, 0] * 1e-4
try:
from geotiepoints import SatelliteInterpolator
except ImportError:
logger.warning("Could not interpolate lon/lats, "
"python-geotiepoints missing.")
self.lons, self.lats = lons40km, lats40km
else:
cols40km = np.arange(24, 2048, 40)
cols1km = np.arange(2048)
lines = lons40km.shape[0]
rows40km = np.arange(lines)
rows1km = np.arange(lines)
along_track_order = 1
cross_track_order = 3
satint = SatelliteInterpolator(
(lons40km, lats40km), (rows40km, cols40km), (rows1km, cols1km),
along_track_order, cross_track_order)
self.lons, self.lats = satint.interpolate()
logger.debug("Navigation time %s", str(datetime.now() - tic))
def upsample_geolocation(self, dsid, info):
"""Upsample the geolocation (lon,lat) from the tiepoint grid."""
from geotiepoints import SatelliteInterpolator
# Read the fields needed:
col_indices = self.nc['nx_reduced'].values
row_indices = self.nc['ny_reduced'].values
lat_reduced = self.scale_dataset(dsid, self.nc['lat_reduced'], info)
lon_reduced = self.scale_dataset(dsid, self.nc['lon_reduced'], info)
shape = (self.nc['y'].shape[0], self.nc['x'].shape[0])
cols_full = np.arange(shape[1])
rows_full = np.arange(shape[0])
satint = SatelliteInterpolator(
(lon_reduced.values, lat_reduced.values),
(row_indices, col_indices), (rows_full, cols_full))
lons, lats = satint.interpolate()
self.cache['lon'] = xr.DataArray(lons,
attrs=lon_reduced.attrs,
dims=['y', 'x'])
self.cache['lat'] = xr.DataArray(lats,
attrs=lat_reduced.attrs,
dims=['y', 'x'])
return
def test_extrapolate_cols(self):
lons = np.arange(10).reshape((2, 5), order="F")
lats = np.arange(10).reshape((2, 5), order="C")
lines = np.array([2, 7])
cols = np.array([2, 7, 12, 17, 22])
hlines = np.arange(10)
hcols = np.arange(24)
satint = SatelliteInterpolator(
(lons, lats), (lines, cols), (hlines, hcols))
self.assertTrue(np.allclose(satint._extrapolate_cols(satint.tie_data[0]),
TIES_EXP2))
def test_fill_col_borders(self):
lons = np.arange(10).reshape((2, 5), order="F")
lats = np.arange(10).reshape((2, 5), order="C")
lines = np.array([2, 7])
cols = np.array([2, 7, 12, 17, 22])
hlines = np.arange(10)
hcols = np.arange(24)
satint = SatelliteInterpolator(
(lons, lats), (lines, cols), (hlines, hcols))
satint._fill_col_borders()
self.assertTrue(np.allclose(satint.tie_data[0], TIES_EXP3))
self.assertTrue(np.allclose(satint.col_indices,
np.array([0, 2, 7, 12, 17, 22, 23])))
def test_extrapolate_cols(self):
lons = np.arange(10).reshape((2, 5), order="F")
lats = np.arange(10).reshape((2, 5), order="C")
lines = np.array([2, 7])
cols = np.array([2, 7, 12, 17, 22])
hlines = np.arange(10)
hcols = np.arange(24)
satint = SatelliteInterpolator((lons, lats), (lines, cols), (hlines, hcols))
self.assertTrue(np.allclose(satint._extrapolate_cols(satint.tie_data[0]),
np.array([[ 6372937.31273379, 6370997. , 6366146.21816553,
6351605.98629588, 6327412.61244969, 6293626.50067273,
6286869.27831734],
[ 6353136.46335726, 6345786.79166939, 6327412.61244969,
6299445.69529922, 6261968.60390423, 6215087.60607344,
6205711.40650728]])))
def geo_interpolate(lons32km, lats32km):
from geotiepoints import SatelliteInterpolator
cols32km = np.arange(0, 2048, 32)
cols1km = np.arange(2048)
lines = lons32km.shape[0]
rows32km = np.arange(lines)
rows1km = np.arange(lines)
along_track_order = 1
cross_track_order = 3
satint = SatelliteInterpolator(
(lons32km, lats32km), (rows32km, cols32km), (rows1km, cols1km),
along_track_order, cross_track_order)
lons, lats = satint.interpolate()
return lons, lats
def geo_interpolate(lons32km, lats32km):
"""Interpolate geo data."""
cols32km = np.arange(0, 2048, 32)
cols1km = np.arange(2048)
lines = lons32km.shape[0]
rows32km = np.arange(lines)
rows1km = np.arange(lines)
along_track_order = 1
cross_track_order = 3
satint = SatelliteInterpolator((lons32km, lats32km), (rows32km, cols32km),
(rows1km, cols1km), along_track_order,
cross_track_order)
lons, lats = satint.interpolate()
return lons, lats
def navigate(self):
"""Get the longitudes and latitudes of the scene."""
lons40km = self._data["pos"][:, :, 1] * 1e-4
lats40km = self._data["pos"][:, :, 0] * 1e-4
try:
from geotiepoints import SatelliteInterpolator
except ImportError:
logger.warning("Could not interpolate lon/lats, "
"python-geotiepoints missing.")
self.lons, self.lats = lons40km, lats40km
else:
cols40km = np.arange(24, 2048, 40)
cols1km = np.arange(2048)
lines = lons40km.shape[0]
rows40km = np.arange(lines)
rows1km = np.arange(lines)
along_track_order = 1
cross_track_order = 3
satint = SatelliteInterpolator(
(lons40km, lats40km), (rows40km, cols40km), (rows1km, cols1km),
along_track_order, cross_track_order)
self.lons, self.lats = delayed(satint.interpolate, nout=2)()
self.lons = da.from_delayed(self.lons, (lines, 2048), lons40km.dtype)
self.lats = da.from_delayed(self.lats, (lines, 2048), lats40km.dtype)
def test_extrapolate_rows(self):
lons = np.arange(10).reshape((2, 5), order="F")
lats = np.arange(10).reshape((2, 5), order="C")
lines = np.array([2, 7])
cols = np.array([2, 7, 12, 17, 22])
hlines = np.arange(10)
hcols = np.arange(24)
satint = SatelliteInterpolator((lons, lats), (lines, cols), (hlines, hcols))
self.assertTrue(np.allclose(satint._extrapolate_rows(satint.tie_data[0]),
np.array([[ 6381081.08333225, 6381639.66045187, 6372470.10269454,
6353590.21586788, 6325042.05851245],
[ 6370997. , 6366146.21816553, 6351605.98629588,
6327412.61244969, 6293626.50067273],
[ 6345786.79166939, 6327412.61244969, 6299445.69529922,
6261968.60390423, 6215087.60607344],
[ 6335702.70833714, 6311919.17016336, 6278581.57890056,
6235791.00048604, 6183672.04823372]])))
def upsample_geolocation(self, dsid, info):
"""Upsample the geolocation (lon,lat) from the tiepoint grid"""
from geotiepoints import SatelliteInterpolator
# Read the fields needed:
col_indices = self.nc['nx_reduced'].values
row_indices = self.nc['ny_reduced'].values
lat_reduced = self.scale_dataset(dsid, self.nc['lat_reduced'], info)
lon_reduced = self.scale_dataset(dsid, self.nc['lon_reduced'], info)
shape = (self.nc['y'].shape[0], self.nc['x'].shape[0])
cols_full = np.arange(shape[1])
rows_full = np.arange(shape[0])
satint = SatelliteInterpolator((lon_reduced.values, lat_reduced.values),
(row_indices,
col_indices),
(rows_full, cols_full))
lons, lats = satint.interpolate()
self.cache['lon'] = xr.DataArray(lons, attrs=lon_reduced.attrs, dims=['y', 'x'])
self.cache['lat'] = xr.DataArray(lats, attrs=lat_reduced.attrs, dims=['y', 'x'])
return
def test_fillborders(self):
lons = np.arange(20).reshape((4, 5), order="F")
lats = np.arange(20).reshape((4, 5), order="C")
lines = np.array([2, 7, 12, 17])
cols = np.array([2, 7, 12, 17, 22])
hlines = np.arange(20)
hcols = np.arange(24)
satint = SatelliteInterpolator((lons, lats), (lines, cols), (hlines, hcols), chunk_size=10)
satint.fill_borders('x', 'y')
self.assertTrue(np.allclose(satint.tie_data[0],
np.array([[ 6384905.78040055, 6381081.08333225, 6371519.34066148,
6328950.00792935, 6253610.69157758, 6145946.19489936,
6124413.29556372],
[ 6377591.95940176, 6370997. , 6354509.6014956 ,
6305151.62592155, 6223234.99818839, 6109277.14889072,
6086485.57903118],
[ 6359307.40690478, 6345786.79166939, 6311985.2535809 ,
6245655.67090206, 6147295.76471541, 6017604.5338691 ,
5991666.28769983],
[ 6351993.58590599, 6335702.70833714, 6294975.51441502,
6221857.28889426, 6116920.07132621, 5980935.48786045,
5953738.5711673 ],
[ 6338032.26190294, 6320348.4990906 , 6276139.09205974,
6199670.56624433, 6091551.90273768, 5952590.38414781,
5924798.08042984],
[ 6290665.5946295 , 6270385.16249031, 6219684.08214232,
6137100.75832981, 6023313.2794414 , 5879194.72399075,
5850371.01290062],
[ 6172248.92644589, 6145476.82098957, 6078546.55734877,
5980676.23854351, 5852716.72120069, 5695705.57359808,
5664303.34407756],
[ 6124882.25917245, 6095513.48438928, 6022091.54743135,
5918106.430629 , 5784478.09790441, 5622309.91344102,
5589876.27654834]])))
self.assertTrue(np.allclose(satint.row_indices, np.array([ 0, 2, 7, 9, 10, 12, 17, 19])))
self.assertTrue(np.allclose(satint.col_indices, np.array([ 0, 2, 7, 12, 17, 22, 23])))
def test_fill_row_borders(self):
lons = np.arange(20).reshape((4, 5), order="F")
lats = np.arange(20).reshape((4, 5), order="C")
lines = np.array([2, 7, 12, 17])
cols = np.array([2, 7, 12, 17, 22])
hlines = np.arange(20)
hcols = np.arange(24)
satint = SatelliteInterpolator((lons, lats), (lines, cols), (hlines, hcols))
satint._fill_row_borders()
self.assertTrue(np.allclose(satint.tie_data[0],
np.array([[ 6381081.08333225, 6371519.34066148, 6328950.00792935,
6253610.69157758, 6145946.19489936],
[ 6370997. , 6354509.6014956 , 6305151.62592155,
6223234.99818839, 6109277.14889072],
[ 6345786.79166939, 6311985.2535809 , 6245655.67090206,
6147295.76471541, 6017604.5338691 ],
[ 6270385.16249031, 6219684.08214232, 6137100.75832981,
6023313.2794414 , 5879194.72399075],
[ 6145476.82098957, 6078546.55734877, 5980676.23854351,
5852716.72120069, 5695705.57359808],
[ 6095513.48438928, 6022091.54743135, 5918106.430629 ,
5784478.09790441, 5622309.91344102]])))
self.assertTrue(np.allclose(satint.row_indices,
np.array([ 0, 2, 7, 12, 17, 19])))
satint = SatelliteInterpolator((lons, lats), (lines, cols),
(hlines, hcols), chunk_size=10)
satint._fill_row_borders()
self.assertTrue(np.allclose(satint.tie_data[0],
np.array([[ 6381081.08333225, 6371519.34066148, 6328950.00792935,
6253610.69157758, 6145946.19489936],
[ 6370997. , 6354509.6014956 , 6305151.62592155,
6223234.99818839, 6109277.14889072],
[ 6345786.79166939, 6311985.2535809 , 6245655.67090206,
6147295.76471541, 6017604.5338691 ],
[ 6335702.70833714, 6294975.51441502, 6221857.28889426,
6116920.07132621, 5980935.48786045],
[ 6320348.4990906 , 6276139.09205974, 6199670.56624433,
6091551.90273768, 5952590.38414781],
[ 6270385.16249031, 6219684.08214232, 6137100.75832981,
6023313.2794414 , 5879194.72399075],
[ 6145476.82098957, 6078546.55734877, 5980676.23854351,
5852716.72120069, 5695705.57359808],
[ 6095513.48438928, 6022091.54743135, 5918106.430629 ,
5784478.09790441, 5622309.91344102]])))
self.assertTrue(np.allclose(satint.row_indices,
np.array([ 0, 2, 7, 9, 10, 12, 17, 19])))
def test_fill_row_borders(self):
lons = np.arange(20).reshape((4, 5), order="F")
lats = np.arange(20).reshape((4, 5), order="C")
lines = np.array([2, 7, 12, 17])
cols = np.array([2, 7, 12, 17, 22])
hlines = np.arange(20)
hcols = np.arange(24)
satint = SatelliteInterpolator((lons, lats), (lines, cols),
(hlines, hcols))
satint._fill_row_borders()
self.assertTrue(
np.allclose(
satint.tie_data[0],
np.array([[
6381081.08333225, 6371519.34066148, 6328950.00792935,
6253610.69157758, 6145946.19489936
],
[
6370997., 6354509.6014956, 6305151.62592155,
6223234.99818839, 6109277.14889072
],
[
6345786.79166939, 6311985.2535809,
6245655.67090206, 6147295.76471541,
6017604.5338691
],
[
6270385.16249031, 6219684.08214232,
6137100.75832981, 6023313.2794414,
5879194.72399075
],
[
6145476.82098957, 6078546.55734877,
5980676.23854351, 5852716.72120069,
5695705.57359808
],
[
6095513.48438928, 6022091.54743135,
5918106.430629, 5784478.09790441,
5622309.91344102
]])))
self.assertTrue(
np.allclose(satint.row_indices, np.array([0, 2, 7, 12, 17, 19])))
satint = SatelliteInterpolator((lons, lats), (lines, cols),
(hlines, hcols),
chunk_size=10)
satint._fill_row_borders()
self.assertTrue(
np.allclose(
satint.tie_data[0],
np.array(
[[
6381081.08333225, 6371519.34066148, 6328950.00792935,
6253610.69157758, 6145946.19489936
],
[
6370997., 6354509.6014956, 6305151.62592155,
6223234.99818839, 6109277.14889072
],
[
6345786.79166939, 6311985.2535809, 6245655.67090206,
6147295.76471541, 6017604.5338691
],
[
6335702.70833714, 6294975.51441502, 6221857.28889426,
6116920.07132621, 5980935.48786045
],
[
6320348.4990906, 6276139.09205974, 6199670.56624433,
6091551.90273768, 5952590.38414781
],
[
6270385.16249031, 6219684.08214232, 6137100.75832981,
6023313.2794414, 5879194.72399075
],
[
6145476.82098957, 6078546.55734877, 5980676.23854351,
5852716.72120069, 5695705.57359808
],
[
6095513.48438928, 6022091.54743135, 5918106.430629,
5784478.09790441, 5622309.91344102
]])))
self.assertTrue(
np.allclose(satint.row_indices,
np.array([0, 2, 7, 9, 10, 12, 17, 19])))
def get_lonlat_into(filename, out_lons, out_lats, out_mask):
"""Read lon,lat from hdf5 file"""
LOG.debug("Geo File = %s", filename)
shape = out_lons.shape
unzipped = unzip_file(filename)
if unzipped:
filename = unzipped
mda = HDF5MetaData(filename).read()
reduced_grid = False
h5f = h5py.File(filename, 'r')
if "column_indices" in h5f.keys():
col_indices = h5f["column_indices"][:]
if "row_indices" in h5f.keys():
row_indices = h5f["row_indices"][:]
if "nx_reduced" in h5f:
col_indices = h5f["nx_reduced"][:]
if "ny_reduced" in h5f:
row_indices = h5f["ny_reduced"][:]
for key in mda.get_data_keys():
if ((key.endswith("lat") or key.endswith("lon")) or
(key.endswith("lat_reduced") or key.endswith("lon_reduced"))):
lonlat = h5f[key]
fillvalue = lonlat.attrs["_FillValue"]
else:
continue
if key.endswith("lat"):
lonlat.read_direct(out_lats)
elif key.endswith("lon"):
lonlat.read_direct(out_lons)
elif key.endswith("lat_reduced"):
lat_reduced = lonlat[:]
reduced_grid = True
elif key.endswith("lon_reduced"):
lon_reduced = lonlat[:]
if reduced_grid:
from geotiepoints import SatelliteInterpolator
cols_full = np.arange(shape[1])
rows_full = np.arange(shape[0])
satint = SatelliteInterpolator((lon_reduced, lat_reduced),
(row_indices, col_indices),
(rows_full, cols_full))
out_lons[:], out_lats[:] = satint.interpolate()
new_mask = False
# FIXME: this is to mask out the npp bowtie deleted pixels...
if "NPP" in h5f.attrs['platform']:
new_mask = np.zeros((16, 3200), dtype=bool)
new_mask[0, :1008] = True
new_mask[1, :640] = True
new_mask[14, :640] = True
new_mask[15, :1008] = True
new_mask[14, 2560:] = True
new_mask[1, 2560:] = True
new_mask[0, 2192:] = True
new_mask[15, 2192:] = True
new_mask = np.tile(new_mask, (out_lons.shape[0] / 16, 1))
out_mask[:] = np.logical_or(
new_mask, np.logical_and(out_lats <= fillvalue, out_lons <= fillvalue))
h5f.close()
if unzipped:
os.remove(unzipped)
def get_lonlat_into(filename, out_lons, out_lats, out_mask):
"""Read lon,lat from hdf5 file"""
LOG.debug("Geo File = %s", filename)
shape = out_lons.shape
unzipped = unzip_file(filename)
if unzipped:
filename = unzipped
mda = HDF5MetaData(filename).read()
reduced_grid = False
h5f = h5py.File(filename, 'r')
if "column_indices" in h5f.keys():
col_indices = h5f["column_indices"][:]
if "row_indices" in h5f.keys():
row_indices = h5f["row_indices"][:]
if "nx_reduced" in h5f:
col_indices = h5f["nx_reduced"][:]
if "ny_reduced" in h5f:
row_indices = h5f["ny_reduced"][:]
for key in mda.get_data_keys():
if ((key.endswith("lat") or key.endswith("lon")) or
(key.endswith("lat_reduced") or key.endswith("lon_reduced"))):
lonlat = h5f[key]
fillvalue = lonlat.attrs["_FillValue"]
else:
continue
if key.endswith("lat"):
lonlat.read_direct(out_lats)
elif key.endswith("lon"):
lonlat.read_direct(out_lons)
elif key.endswith("lat_reduced"):
lat_reduced = lonlat[:]
reduced_grid = True
elif key.endswith("lon_reduced"):
lon_reduced = lonlat[:]
if reduced_grid:
from geotiepoints import SatelliteInterpolator
cols_full = np.arange(shape[1])
rows_full = np.arange(shape[0])
satint = SatelliteInterpolator((lon_reduced, lat_reduced),
(row_indices,
col_indices),
(rows_full, cols_full))
out_lons[:], out_lats[:] = satint.interpolate()
new_mask = False
# FIXME: this is to mask out the npp bowtie deleted pixels...
if "NPP" in h5f.attrs['platform']:
new_mask = np.zeros((16, 3200), dtype=bool)
new_mask[0, :1008] = True
new_mask[1, :640] = True
new_mask[14, :640] = True
new_mask[15, :1008] = True
new_mask[14, 2560:] = True
new_mask[1, 2560:] = True
new_mask[0, 2192:] = True
new_mask[15, 2192:] = True
new_mask = np.tile(new_mask, (out_lons.shape[0] / 16, 1))
out_mask[:] = np.logical_or(
new_mask, np.logical_and(out_lats <= fillvalue, out_lons <= fillvalue))
h5f.close()
if unzipped:
os.remove(unzipped)
def get_lonlat_into(filename, out_lons, out_lats, out_mask):
"""Read lon,lat from hdf5 file"""
LOG.debug("Geo File = %s", filename)
shape = out_lons.shape
unzipped = unzip_file(filename)
if unzipped:
filename = unzipped
mda = HDF5MetaData(filename).read()
reduced_grid = False
h5f = h5py.File(filename, 'r')
if "column_indices" in h5f.keys():
col_indices = h5f["column_indices"][:]
if "row_indices" in h5f.keys():
row_indices = h5f["row_indices"][:]
if "nx_reduced" in h5f:
col_indices = h5f["nx_reduced"][:]
if "ny_reduced" in h5f:
row_indices = h5f["ny_reduced"][:]
for key in mda.get_data_keys():
if ((key.endswith("lat") or key.endswith("lon")) or
(key.endswith("lat_reduced") or key.endswith("lon_reduced"))):
lonlat = h5f[key]
fillvalue = lonlat.attrs["_FillValue"]
else:
continue
if key.endswith("lat"):
lonlat.read_direct(out_lats)
elif key.endswith("lon"):
lonlat.read_direct(out_lons)
elif key.endswith("lat_reduced"):
lat_reduced = lonlat[:]
reduced_grid = True
elif key.endswith("lon_reduced"):
lon_reduced = lonlat[:]
if reduced_grid:
from geotiepoints import SatelliteInterpolator
cols_full = np.arange(shape[1])
rows_full = np.arange(shape[0])
satint = SatelliteInterpolator((lon_reduced, lat_reduced),
(row_indices,
col_indices),
(rows_full, cols_full))
out_lons[:], out_lats[:] = satint.interpolate()
new_mask = False
# FIXME: this is to mask out the npp bowtie deleted pixels...
if "NPP" in h5f.attrs['platform']:
if shape[1] == 3200: # M-bands:
new_mask = np.zeros((16, 3200), dtype=bool)
new_mask[0, :1008] = True
new_mask[1, :640] = True
new_mask[14, :640] = True
new_mask[15, :1008] = True
new_mask[14, 2560:] = True
new_mask[1, 2560:] = True
new_mask[0, 2192:] = True
new_mask[15, 2192:] = True
new_mask = np.tile(new_mask, (out_lons.shape[0] / 16, 1))
elif shape[1] == 6400: # I-bands:
LOG.info(
"PPS on I-band resolution. Mask out bow-tie deletion pixels")
LOG.warning("Not yet supported...")
new_mask = np.zeros((32, 6400), dtype=bool)
new_mask[0:2, :2016] = True
new_mask[0:2, 4384:] = True
new_mask[2:4, :1280] = True
new_mask[2:4, 5120:] = True
new_mask[28:30, :1280] = True
new_mask[28:30, 5120:] = True
new_mask[30:32, :2016] = True
new_mask[30:32, 4384:] = True
new_mask = np.tile(new_mask, (out_lons.shape[0] / 32, 1))
else:
LOG.error("VIIRS shape not supported. " +
"No handling of bow-tie deletion pixels: shape = ", str(shape))
out_mask[:] = np.logical_or(
new_mask, np.logical_and(out_lats == fillvalue, out_lons == fillvalue))
# new_mask, np.logical_and(out_lats <= fillvalue, out_lons <= fillvalue))
h5f.close()
if unzipped:
os.remove(unzipped)
def get_lonlat_into(filename, out_lons, out_lats, out_mask):
"""Read lon,lat from hdf5 file"""
LOG.debug("Geo File = %s", filename)
shape = out_lons.shape
unzipped = unzip_file(filename)
if unzipped:
filename = unzipped
mda = HDF5MetaData(filename).read()
reduced_grid = False
h5f = h5py.File(filename, 'r')
if "column_indices" in h5f.keys():
col_indices = h5f["column_indices"][:]
if "row_indices" in h5f.keys():
row_indices = h5f["row_indices"][:]
if "nx_reduced" in h5f:
col_indices = h5f["nx_reduced"][:]
if "ny_reduced" in h5f:
row_indices = h5f["ny_reduced"][:]
for key in mda.get_data_keys():
if ((key.endswith("lat") or key.endswith("lon")) or
(key.endswith("lat_reduced") or key.endswith("lon_reduced"))):
lonlat = h5f[key]
fillvalue = lonlat.attrs["_FillValue"]
else:
continue
if key.endswith("lat"):
lonlat.read_direct(out_lats)
elif key.endswith("lon"):
lonlat.read_direct(out_lons)
elif key.endswith("lat_reduced"):
lat_reduced = lonlat[:]
reduced_grid = True
elif key.endswith("lon_reduced"):
lon_reduced = lonlat[:]
if reduced_grid:
from geotiepoints import SatelliteInterpolator
cols_full = np.arange(shape[1])
rows_full = np.arange(shape[0])
satint = SatelliteInterpolator((lon_reduced, lat_reduced),
(row_indices, col_indices),
(rows_full, cols_full))
out_lons[:], out_lats[:] = satint.interpolate()
new_mask = False
# FIXME: this is to mask out the npp bowtie deleted pixels...
# if "NPP" in h5f.attrs['platform']:
if h5f.attrs['platform'] in VIIRS_PLATFORMS:
if shape[1] == 3200: # M-bands:
new_mask = np.zeros((16, 3200), dtype=bool)
new_mask[0, :1008] = True
new_mask[1, :640] = True
new_mask[14, :640] = True
new_mask[15, :1008] = True
new_mask[14, 2560:] = True
new_mask[1, 2560:] = True
new_mask[0, 2192:] = True
new_mask[15, 2192:] = True
new_mask = np.tile(new_mask, (out_lons.shape[0] / 16, 1))
elif shape[1] == 6400: # I-bands:
LOG.info(
"PPS on I-band resolution. Mask out bow-tie deletion pixels")
LOG.warning("Not yet supported...")
new_mask = np.zeros((32, 6400), dtype=bool)
new_mask[0:2, :2016] = True
new_mask[0:2, 4384:] = True
new_mask[2:4, :1280] = True
new_mask[2:4, 5120:] = True
new_mask[28:30, :1280] = True
new_mask[28:30, 5120:] = True
new_mask[30:32, :2016] = True
new_mask[30:32, 4384:] = True
new_mask = np.tile(new_mask, (out_lons.shape[0] / 32, 1))
else:
LOG.error(
"VIIRS shape not supported. " +
"No handling of bow-tie deletion pixels: shape = ", str(shape))
out_mask[:] = np.logical_or(
new_mask, np.logical_and(out_lats == fillvalue, out_lons == fillvalue))
# new_mask, np.logical_and(out_lats <= fillvalue, out_lons <= fillvalue))
h5f.close()
if unzipped:
os.remove(unzipped)
def load(self, satscene, *args, **kwargs):
"""Read data from file and load it into *satscene*.
"""
lonlat_is_loaded = False
geofilename = kwargs.get('geofilename')
prodfilename = kwargs.get('filename')
products = []
if "CTTH" in satscene.channels_to_load:
products.append("ctth")
if "CT" in satscene.channels_to_load:
products.append("cloudtype")
if "CMA" in satscene.channels_to_load:
products.append("cloudmask")
if "PC" in satscene.channels_to_load:
products.append("precipclouds")
if "CPP" in satscene.channels_to_load:
products.append("cpp")
if len(products) == 0:
return
try:
area_name = satscene.area_id or satscene.area.area_id
except AttributeError:
area_name = "satproj_?????_?????"
# Looking for geolocation file
conf = ConfigParser()
conf.read(os.path.join(CONFIG_PATH, satscene.fullname + ".cfg"))
try:
geodir = conf.get(satscene.instrument_name + "-level3",
"cloud_product_geodir",
vars=os.environ)
except NoOptionError:
LOG.warning("No option 'geodir' in level3 section")
geodir = None
if not geofilename and geodir:
# Load geo file from config file:
try:
if not satscene.orbit:
orbit = ""
else:
orbit = satscene.orbit
geoname_tmpl = conf.get(satscene.instrument_name + "-level3",
"cloud_product_geofilename",
raw=True,
vars=os.environ)
filename_tmpl = (satscene.time_slot.strftime(geoname_tmpl)
% {"orbit": str(orbit).zfill(5) or "*",
"area": area_name,
"satellite": satscene.satname + satscene.number})
file_list = glob.glob(os.path.join(geodir, filename_tmpl))
if len(file_list) > 1:
LOG.warning("More than 1 file matching for geoloaction: "
+ str(file_list))
elif len(file_list) == 0:
LOG.warning(
"No geolocation file matching!: "
+ os.path.join(geodir, filename_tmpl))
else:
geofilename = file_list[0]
except NoOptionError:
geofilename = None
# Reading the products
classes = {"ctth": CloudTopTemperatureHeight,
"cloudtype": CloudType,
"cloudmask": CloudMask,
"precipclouds": PrecipitationClouds,
"cpp": CloudPhysicalProperties
}
nodata_mask = False
area = None
lons = None
lats = None
chn = None
shape = None
read_external_geo = {}
for product in products:
LOG.debug("Loading " + product)
if isinstance(prodfilename, (list, tuple, set)):
for fname in prodfilename:
kwargs['filename'] = fname
self.load(satscene, *args, **kwargs)
return
elif (prodfilename and
os.path.basename(prodfilename).startswith('S_NWC')):
if os.path.basename(prodfilename).split("_")[2] == NEW_PRODNAMES[product]:
filename = prodfilename
else:
continue
else:
filename = conf.get(satscene.instrument_name + "-level3",
"cloud_product_filename",
raw=True,
vars=os.environ)
directory = conf.get(satscene.instrument_name + "-level3",
"cloud_product_dir",
vars=os.environ)
pathname_tmpl = os.path.join(directory, filename)
LOG.debug("Path = " + str(pathname_tmpl))
if not satscene.orbit:
orbit = ""
else:
orbit = satscene.orbit
filename_tmpl = (satscene.time_slot.strftime(pathname_tmpl)
% {"orbit": str(orbit).zfill(5) or "*",
"area": area_name,
"satellite": satscene.satname + satscene.number,
"product": product})
file_list = glob.glob(filename_tmpl)
if len(file_list) == 0:
product_name = NEW_PRODNAMES.get(product, product)
LOG.info("No " + str(product) +
" product in old format matching")
filename_tmpl = (satscene.time_slot.strftime(pathname_tmpl)
% {"orbit": str(orbit).zfill(5) or "*",
"area": area_name,
"satellite": satscene.satname + satscene.number,
"product": product_name})
file_list = glob.glob(filename_tmpl)
if len(file_list) > 1:
LOG.warning("More than 1 file matching for " + product + "! "
+ str(file_list))
continue
elif len(file_list) == 0:
LOG.warning(
"No " + product + " matching!: " + filename_tmpl)
continue
else:
filename = file_list[0]
chn = classes[product]()
chn.read(filename, lonlat_is_loaded == False)
satscene.channels.append(chn)
# Check if geolocation is loaded:
if not chn.area:
read_external_geo[product] = chn
shape = chn.shape
# Check if some 'channel'/product needs geolocation. If some product does
# not have geolocation, get it from the geofilename:
if not read_external_geo:
LOG.info("Loading PPS parameters done.")
return
# Load geolocation
interpolate = False
if geofilename:
geodict = get_lonlat(geofilename)
lons, lats = geodict['lon'], geodict['lat']
if lons.shape != shape or lats.shape != shape:
interpolate = True
row_indices = geodict['row_indices']
column_indices = geodict['col_indices']
lonlat_is_loaded = True
else:
LOG.warning("No Geo file specified: " +
"Geolocation will be loaded from product")
if lonlat_is_loaded:
if interpolate:
from geotiepoints import SatelliteInterpolator
cols_full = np.arange(shape[1])
rows_full = np.arange(shape[0])
satint = SatelliteInterpolator((lons, lats),
(row_indices,
column_indices),
(rows_full, cols_full))
# satint.fill_borders("y", "x")
lons, lats = satint.interpolate()
try:
from pyresample import geometry
lons = np.ma.masked_array(lons, nodata_mask)
lats = np.ma.masked_array(lats, nodata_mask)
area = geometry.SwathDefinition(lons=lons,
lats=lats)
except ImportError:
area = None
for chn in read_external_geo.values():
if area:
chn.area = area
else:
chn.lat = lats
chn.lon = lons
LOG.info("Loading PPS parameters done.")
return
tie_lats = params['tiepoints']['lats']
tie_cols = params['tiepoints']['cols']
tie_rows = params['tiepoints']['rows']
# From tie_cols and tie_rows, generate a gegulaer grid
#fine_rows = np.arange(0, 3085, 257)
#fine_cols = np.arange(0, 6313, 332)
fine_rows = np.arange(0, 15436, 250)
fine_cols = np.arange(0, 31561, 250)
#print params
#fine_cols = np.arange(0, data.shape[1])
#fine_rows = np.arange(0, data.shape[0])
interpolator = SatelliteInterpolator(
(tie_lons, tie_lats), (tie_rows, tie_cols), (fine_rows, fine_cols), 1,
3)
#np.save('tie_lons.npy', tie_lons)
#np.save('tie_lats.npy', tie_lats)
#np.save('tie_cols.npy', tie_cols)
#np.save('tie_rows.npy', tie_rows)
#np.save('fine_cols.npy', fine_cols)
#np.save('fine_rows.npy', fine_rows)
lons, lats = interpolator.interpolate()
print 'RESULT :'
print lons
print lats
np.save('result_lons.npy', lons)
np.save('result_lats.npy', lats)
#print 'DATA'
#print data.shape
def load(self, satscene, *args, **kwargs):
"""Read data from file and load it into *satscene*.
"""
lonlat_is_loaded = False
geofilename = kwargs.get('geofilename')
prodfilename = kwargs.get('filename')
products = []
if "CTTH" in satscene.channels_to_load:
products.append("ctth")
if "CT" in satscene.channels_to_load:
products.append("cloudtype")
if "CMA" in satscene.channels_to_load:
products.append("cloudmask")
if "PC" in satscene.channels_to_load:
products.append("precipclouds")
if "CPP" in satscene.channels_to_load:
products.append("cpp")
if len(products) == 0:
return
try:
area_name = satscene.area_id or satscene.area.area_id
except AttributeError:
area_name = "satproj_?????_?????"
# Looking for geolocation file
conf = ConfigParser()
conf.read(os.path.join(CONFIG_PATH, satscene.fullname + ".cfg"))
try:
geodir = conf.get(satscene.instrument_name + "-level3",
"cloud_product_geodir",
vars=os.environ)
except NoOptionError:
LOG.warning("No option 'geodir' in level3 section")
geodir = None
if not geofilename and geodir:
# Load geo file from config file:
try:
if not satscene.orbit:
orbit = ""
else:
orbit = satscene.orbit
geoname_tmpl = conf.get(satscene.instrument_name + "-level3",
"cloud_product_geofilename",
raw=True,
vars=os.environ)
filename_tmpl = (satscene.time_slot.strftime(geoname_tmpl)
% {"orbit": str(orbit).zfill(5) or "*",
"area": area_name,
"satellite": satscene.satname + satscene.number})
file_list = glob.glob(os.path.join(geodir, filename_tmpl))
if len(file_list) > 1:
LOG.warning("More than 1 file matching for geoloaction: "
+ str(file_list))
elif len(file_list) == 0:
LOG.warning(
"No geolocation file matching!: " + filename_tmpl)
else:
geofilename = file_list[0]
except NoOptionError:
geofilename = None
# Reading the products
classes = {"ctth": CloudTopTemperatureHeight,
"cloudtype": CloudType,
"cloudmask": CloudMask,
"precipclouds": PrecipitationClouds,
"cpp": CloudPhysicalProperties
}
nodata_mask = False
area = None
lons = None
lats = None
chn = None
shape = None
read_external_geo = {}
for product in products:
LOG.debug("Loading " + product)
if isinstance(prodfilename, (list, tuple, set)):
for fname in prodfilename:
kwargs['filename'] = fname
self.load(satscene, *args, **kwargs)
return
elif (prodfilename and
os.path.basename(prodfilename).startswith('S_NWC')):
if os.path.basename(prodfilename).split("_")[2] == NEW_PRODNAMES[product]:
filename = prodfilename
else:
continue
else:
filename = conf.get(satscene.instrument_name + "-level3",
"cloud_product_filename",
raw=True,
vars=os.environ)
directory = conf.get(satscene.instrument_name + "-level3",
"cloud_product_dir",
vars=os.environ)
pathname_tmpl = os.path.join(directory, filename)
LOG.debug("Path = " + str(pathname_tmpl))
if not satscene.orbit:
orbit = ""
else:
orbit = satscene.orbit
filename_tmpl = (satscene.time_slot.strftime(pathname_tmpl)
% {"orbit": str(orbit).zfill(5) or "*",
"area": area_name,
"satellite": satscene.satname + satscene.number,
"product": product})
file_list = glob.glob(filename_tmpl)
if len(file_list) == 0:
product_name = NEW_PRODNAMES.get(product, product)
LOG.info("No " + str(product) +
" product in old format matching")
filename_tmpl = (satscene.time_slot.strftime(pathname_tmpl)
% {"orbit": str(orbit).zfill(5) or "*",
"area": area_name,
"satellite": satscene.satname + satscene.number,
"product": product_name})
file_list = glob.glob(filename_tmpl)
if len(file_list) > 1:
LOG.warning("More than 1 file matching for " + product + "! "
+ str(file_list))
continue
elif len(file_list) == 0:
LOG.warning(
"No " + product + " matching!: " + filename_tmpl)
continue
else:
filename = file_list[0]
chn = classes[product]()
chn.read(filename, lonlat_is_loaded == False)
satscene.channels.append(chn)
# Check if geolocation is loaded:
if not chn.area:
read_external_geo[product] = chn
shape = chn.shape
# Check if some 'channel'/product needs geolocation. If some product does
# not have geolocation, get it from the geofilename:
if not read_external_geo:
LOG.info("Loading PPS parameters done.")
return
# Load geolocation
interpolate = False
if geofilename:
geodict = get_lonlat(geofilename)
lons, lats = geodict['lon'], geodict['lat']
if lons.shape != shape or lats.shape != shape:
interpolate = True
row_indices = geodict['row_indices']
column_indices = geodict['col_indices']
lonlat_is_loaded = True
else:
LOG.warning("No Geo file specified: " +
"Geolocation will be loaded from product")
if lonlat_is_loaded:
if interpolate:
from geotiepoints import SatelliteInterpolator
cols_full = np.arange(shape[1])
rows_full = np.arange(shape[0])
satint = SatelliteInterpolator((lons, lats),
(row_indices,
column_indices),
(rows_full, cols_full))
#satint.fill_borders("y", "x")
lons, lats = satint.interpolate()
try:
from pyresample import geometry
lons = np.ma.masked_array(lons, nodata_mask)
lats = np.ma.masked_array(lats, nodata_mask)
area = geometry.SwathDefinition(lons=lons,
lats=lats)
except ImportError:
area = None
for chn in read_external_geo.values():
if area:
chn.area = area
else:
chn.lat = lats
chn.lon = lons
LOG.info("Loading PPS parameters done.")
return
def read(self, filename, load_lonlat=True):
"""Read product in hdf format from *filename*
"""
LOG.debug("Filename: %s" % filename)
is_temp = False
if not h5py.is_hdf5(filename):
# Try see if it is bzipped:
import bz2
bz2file = bz2.BZ2File(filename)
import tempfile
tmpfilename = tempfile.mktemp()
try:
ofpt = open(tmpfilename, 'wb')
ofpt.write(bz2file.read())
ofpt.close()
is_temp = True
except IOError:
import traceback
traceback.print_exc()
raise IOError("Failed to read the file %s" % filename)
filename = tmpfilename
if not h5py.is_hdf5(filename):
if is_temp:
os.remove(filename)
raise IOError("File is not a hdf5 file!" % filename)
h5f = h5py.File(filename, "r")
# Read the global attributes
self._md = dict(h5f.attrs)
self._md["satellite"] = h5f.attrs['satellite_id']
self._md["orbit"] = h5f.attrs['orbit_number']
self._md["time_slot"] = (timedelta(seconds=long(h5f.attrs['sec_1970']))
+ datetime(1970, 1, 1, 0, 0))
# Read the data and attributes
# This covers only one level of data. This could be made recursive.
for key, dataset in h5f.iteritems():
setattr(self, key, InfoObject())
getattr(self, key).info = dict(dataset.attrs)
for skey, value in dataset.attrs.iteritems():
if isinstance(value, h5py.h5r.Reference):
self._refs[(key, skey)] = h5f[value].name.split("/")[1]
if type(dataset.id) is h5py.h5g.GroupID:
LOG.warning("Format reader does not support groups")
continue
try:
getattr(self, key).data = dataset[:]
is_palette = (dataset.attrs.get("CLASS", None) == "PALETTE")
if(len(dataset.shape) > 1 and
not is_palette and
key not in ["lon", "lat",
"row_indices", "column_indices"]):
self._projectables.append(key)
if self.shape is None:
self.shape = dataset.shape
elif self.shape != dataset.shape:
raise ValueError("Different variable shapes !")
else:
self._keys.append(key)
except TypeError:
setattr(self, key, np.dtype(dataset))
self._keys.append(key)
h5f.close()
if is_temp:
os.remove(filename)
if not load_lonlat:
return
# Setup geolocation
# We need a no-data mask from one of the projectables to
# mask out bow-tie deletion pixels from the geolocation array
# So far only relevant for VIIRS.
# Preferably the lon-lat data in the PPS VIIRS geolocation
# file should already be masked.
# The no-data values in the products are not only where geo-location is absent
# Only the Cloud Type can be used as a proxy so far.
# Adam Dybbroe, 2012-08-31
nodata_mask = False # np.ma.masked_equal(np.ones(self.shape), 0).mask
for key in self._projectables:
projectable = getattr(self, key)
if key in ['cloudtype']:
nodata_array = np.ma.array(projectable.data)
nodata_mask = np.ma.masked_equal(nodata_array, 0).mask
break
try:
from pyresample import geometry
except ImportError:
return
tiepoint_grid = False
if hasattr(self, "row_indices") and hasattr(self, "column_indices"):
column_indices = self.column_indices.data
row_indices = self.row_indices.data
tiepoint_grid = True
interpolate = False
if hasattr(self, "lon") and hasattr(self, "lat"):
if 'intercept' in self.lon.info:
offset_lon = self.lon.info["intercept"]
elif 'offset' in self.lon.info:
offset_lon = self.lon.info["offset"]
if 'gain' in self.lon.info:
gain_lon = self.lon.info["gain"]
lons = self.lon.data * gain_lon + offset_lon
if 'intercept' in self.lat.info:
offset_lat = self.lat.info["intercept"]
elif 'offset' in self.lat.info:
offset_lat = self.lat.info["offset"]
if 'gain' in self.lat.info:
gain_lat = self.lat.info["gain"]
lats = self.lat.data * gain_lat + offset_lat
if lons.shape != self.shape or lats.shape != self.shape:
# Data on tiepoint grid:
interpolate = True
if not tiepoint_grid:
errmsg = ("Interpolation needed but insufficient" +
"information on the tiepoint grid")
raise IOError(errmsg)
else:
# Geolocation available on the full grid:
# We neeed to mask out nodata (VIIRS Bow-tie deletion...)
# We do it for all instruments, checking only against the
# nodata
lons = np.ma.masked_array(lons, nodata_mask)
lats = np.ma.masked_array(lats, nodata_mask)
self.area = geometry.SwathDefinition(lons=lons, lats=lats)
elif hasattr(self, "region") and self.region.data["area_extent"].any():
region = self.region.data
proj_dict = dict([elt.split('=')
for elt in region["pcs_def"].split(',')])
self.area = geometry.AreaDefinition(region["id"],
region["name"],
region["proj_id"],
proj_dict,
region["xsize"],
region["ysize"],
region["area_extent"])
if interpolate:
from geotiepoints import SatelliteInterpolator
cols_full = np.arange(self.shape[1])
rows_full = np.arange(self.shape[0])
satint = SatelliteInterpolator((lons, lats),
(row_indices,
column_indices),
(rows_full, cols_full))
#satint.fill_borders("y", "x")
lons, lats = satint.interpolate()
self.area = geometry.SwathDefinition(lons=lons, lats=lats)
def load(scene, geofilename=None, **kwargs):
del kwargs
import glob
lonlat_is_loaded = False
products = []
if "CTTH" in scene.channels_to_load:
products.append("CTTH")
if "CloudType" in scene.channels_to_load:
products.append("CT")
if "CMa" in scene.channels_to_load:
products.append("CMA")
if "PC" in scene.channels_to_load:
products.append("PC")
if "CPP" in scene.channels_to_load:
products.append("CPP")
if len(products) == 0:
return
try:
area_name = scene.area_id or scene.area.area_id
except AttributeError:
area_name = "satproj_?????_?????"
conf = ConfigParser.ConfigParser()
conf.read(os.path.join(CONFIG_PATH, scene.fullname+".cfg"))
directory = conf.get(scene.instrument_name+"-level3", "dir")
try:
geodir = conf.get(scene.instrument_name+"-level3", "geodir")
except NoOptionError:
LOG.warning("No option 'geodir' in level3 section")
geodir = None
filename = conf.get(scene.instrument_name+"-level3", "filename",
raw=True)
pathname_tmpl = os.path.join(directory, filename)
if not geofilename and geodir:
# Load geo file from config file:
try:
if not scene.orbit:
orbit = ""
else:
orbit = scene.orbit
geoname_tmpl = conf.get(scene.instrument_name+"-level3",
"geofilename", raw=True)
filename_tmpl = (scene.time_slot.strftime(geoname_tmpl)
%{"orbit": orbit.zfill(5) or "*",
"area": area_name,
"satellite": scene.satname + scene.number})
file_list = glob.glob(os.path.join(geodir, filename_tmpl))
if len(file_list) > 1:
LOG.warning("More than 1 file matching for geoloaction: "
+ str(file_list))
elif len(file_list) == 0:
LOG.warning("No geolocation file matching!: " + filename_tmpl)
else:
geofilename = file_list[0]
except NoOptionError:
geofilename = None
classes = {"CTTH": CloudTopTemperatureHeight,
"CT": CloudType,
"CMA": CloudMask,
"PC": PrecipitationClouds,
"CPP": CloudPhysicalProperties
}
nodata_mask = False
chn = None
for product in products:
LOG.debug("Loading " + product)
if not scene.orbit:
orbit = ""
else:
orbit = scene.orbit
filename_tmpl = (scene.time_slot.strftime(pathname_tmpl)
%{"orbit": orbit.zfill(5) or "*",
"area": area_name,
"satellite": scene.satname + scene.number,
"product": product})
file_list = glob.glob(filename_tmpl)
if len(file_list) > 1:
LOG.warning("More than 1 file matching for " + product + "! "
+ str(file_list))
continue
elif len(file_list) == 0:
LOG.warning("No " + product + " matching!: " + filename_tmpl)
continue
else:
filename = file_list[0]
chn = classes[product]()
chn.read(filename, lonlat_is_loaded==False)
scene.channels.append(chn)
# Setup geolocation
# We need a no-data mask from one of the projectables to
# mask out bow-tie deletion pixels from the geolocation array
# So far only relevant for VIIRS.
# Preferably the lon-lat data in the PPS VIIRS geolocation
# file should already be masked.
# The no-data values in the products are not only where geo-location is absent
# Only the Cloud Type can be used as a proxy so far.
# Adam Dybbroe, 2012-08-31
if hasattr(chn, '_projectables'):
for key in chn._projectables:
projectable = getattr(chn, key)
if key in ['ct']:
nodata_array = np.ma.array(projectable.data)
nodata_mask = np.ma.masked_equal(\
nodata_array, projectable.info["_FillValue"]).mask
break
else:
LOG.warning("Channel has no '_projectables' member." +
" No nodata-mask set...")
if chn is None:
return
# Is this safe!? AD 2012-08-25
shape = chn.shape
interpolate = False
if geofilename:
geodict = get_lonlat(geofilename)
lons, lats = geodict['lon'], geodict['lat']
if lons.shape != shape or lats.shape != shape:
interpolate = True
row_indices = geodict['row_indices']
column_indices = geodict['column_indices']
lonlat_is_loaded = True
else:
LOG.warning("No Geo file specified: " +
"Geolocation will be loaded from product")
if lonlat_is_loaded:
if interpolate:
from geotiepoints import SatelliteInterpolator
cols_full = np.arange(shape[1])
rows_full = np.arange(shape[0])
satint = SatelliteInterpolator((lons, lats),
(row_indices,
column_indices),
(rows_full, cols_full))
#satint.fill_borders("y", "x")
lons, lats = satint.interpolate()
try:
from pyresample import geometry
lons = np.ma.masked_array(lons, nodata_mask)
lats = np.ma.masked_array(lats, nodata_mask)
scene.area = geometry.SwathDefinition(lons=lons,
lats=lats)
except ImportError:
scene.area = None
scene.lat = lats
scene.lon = lons
LOG.info("Loading PPS parameters done.")
def test_fillborders(self):
lons = np.arange(20).reshape((4, 5), order="F")
lats = np.arange(20).reshape((4, 5), order="C")
lines = np.array([2, 7, 12, 17])
cols = np.array([2, 7, 12, 17, 22])
hlines = np.arange(20)
hcols = np.arange(24)
satint = SatelliteInterpolator((lons, lats), (lines, cols),
(hlines, hcols),
chunk_size=10)
satint.fill_borders('x', 'y')
self.assertTrue(
np.allclose(
satint.tie_data[0],
np.array(
[[
6384905.78040055, 6381081.08333225, 6371519.34066148,
6328950.00792935, 6253610.69157758, 6145946.19489936,
6124413.29556372
],
[
6377591.95940176, 6370997., 6354509.6014956,
6305151.62592155, 6223234.99818839, 6109277.14889072,
6086485.57903118
],
[
6359307.40690478, 6345786.79166939, 6311985.2535809,
6245655.67090206, 6147295.76471541, 6017604.5338691,
5991666.28769983
],
[
6351993.58590599, 6335702.70833714, 6294975.51441502,
6221857.28889426, 6116920.07132621, 5980935.48786045,
5953738.5711673
],
[
6338032.26190294, 6320348.4990906, 6276139.09205974,
6199670.56624433, 6091551.90273768, 5952590.38414781,
5924798.08042984
],
[
6290665.5946295, 6270385.16249031, 6219684.08214232,
6137100.75832981, 6023313.2794414, 5879194.72399075,
5850371.01290062
],
[
6172248.92644589, 6145476.82098957, 6078546.55734877,
5980676.23854351, 5852716.72120069, 5695705.57359808,
5664303.34407756
],
[
6124882.25917245, 6095513.48438928, 6022091.54743135,
5918106.430629, 5784478.09790441, 5622309.91344102,
5589876.27654834
]])))
self.assertTrue(
np.allclose(satint.row_indices,
np.array([0, 2, 7, 9, 10, 12, 17, 19])))
self.assertTrue(
np.allclose(satint.col_indices, np.array([0, 2, 7, 12, 17, 22,
23])))
def load(scene, geofilename=None, **kwargs):
del kwargs
import glob
lonlat_is_loaded = False
products = []
if "CTTH" in scene.channels_to_load:
products.append("ctth")
if "CloudType" in scene.channels_to_load:
products.append("cloudtype")
if "CMa" in scene.channels_to_load:
products.append("cloudmask")
if "PC" in scene.channels_to_load:
products.append("precipclouds")
if "CPP" in scene.channels_to_load:
products.append("cpp")
if len(products) == 0:
return
try:
area_name = scene.area_id or scene.area.area_id
except AttributeError:
area_name = "satproj_?????_?????"
conf = ConfigParser.ConfigParser()
conf.read(os.path.join(CONFIG_PATH, scene.fullname + ".cfg"))
directory = conf.get(scene.instrument_name + "-level3", "dir")
try:
geodir = conf.get(scene.instrument_name + "-level3", "geodir")
except NoOptionError:
LOG.warning("No option 'geodir' in level3 section")
geodir = None
filename = conf.get(scene.instrument_name + "-level3", "filename",
raw=True)
pathname_tmpl = os.path.join(directory, filename)
if not geofilename and geodir:
# Load geo file from config file:
try:
if not scene.orbit:
orbit = ""
else:
orbit = scene.orbit
geoname_tmpl = conf.get(scene.instrument_name + "-level3",
"geofilename", raw=True)
filename_tmpl = (scene.time_slot.strftime(geoname_tmpl)
% {"orbit": orbit.zfill(5) or "*",
"area": area_name,
"satellite": scene.satname + scene.number})
file_list = glob.glob(os.path.join(geodir, filename_tmpl))
if len(file_list) > 1:
LOG.warning("More than 1 file matching for geoloaction: "
+ str(file_list))
elif len(file_list) == 0:
LOG.warning("No geolocation file matching!: " + filename_tmpl)
else:
geofilename = file_list[0]
except NoOptionError:
geofilename = None
classes = {"ctth": CloudTopTemperatureHeight,
"cloudtype": CloudType,
"cloudmask": CloudMask,
"precipclouds": PrecipitationClouds,
"cpp": CloudPhysicalProperties
}
nodata_mask = False
chn = None
for product in products:
LOG.debug("Loading " + product)
if not scene.orbit:
orbit = ""
else:
orbit = scene.orbit
filename_tmpl = (scene.time_slot.strftime(pathname_tmpl)
% {"orbit": orbit.zfill(5) or "*",
"area": area_name,
"satellite": scene.satname + scene.number,
"product": product})
file_list = glob.glob(filename_tmpl)
if len(file_list) > 1:
LOG.warning("More than 1 file matching for " + product + "! "
+ str(file_list))
continue
elif len(file_list) == 0:
LOG.warning("No " + product + " matching!: " + filename_tmpl)
continue
else:
filename = file_list[0]
chn = classes[product]()
chn.read(filename, lonlat_is_loaded == False)
scene.channels.append(chn)
# Setup geolocation
# We need a no-data mask from one of the projectables to
# mask out bow-tie deletion pixels from the geolocation array
# So far only relevant for VIIRS.
# Preferably the lon-lat data in the PPS VIIRS geolocation
# file should already be masked.
# The no-data values in the products are not only where geo-location is absent
# Only the Cloud Type can be used as a proxy so far.
# Adam Dybbroe, 2012-08-31
if hasattr(chn, '_projectables'):
for key in chn._projectables:
projectable = getattr(chn, key)
if key in ['cloudtype']:
nodata_array = np.ma.array(projectable.data)
nodata_mask = np.ma.masked_equal(nodata_array, 0).mask
break
else:
LOG.warning("Channel has no '_projectables' member." +
" No nodata-mask set...")
if chn is None:
return
# Is this safe!? AD 2012-08-25
shape = chn.shape
interpolate = False
if geofilename:
geodict = get_lonlat(geofilename)
lons, lats = geodict['lon'], geodict['lat']
if lons.shape != shape or lats.shape != shape:
interpolate = True
row_indices = geodict['row_indices']
column_indices = geodict['column_indices']
lonlat_is_loaded = True
else:
LOG.warning("No Geo file specified: " +
"Geolocation will be loaded from product")
if lonlat_is_loaded:
if interpolate:
from geotiepoints import SatelliteInterpolator
cols_full = np.arange(shape[1])
rows_full = np.arange(shape[0])
satint = SatelliteInterpolator((lons, lats),
(row_indices,
column_indices),
(rows_full, cols_full))
#satint.fill_borders("y", "x")
lons, lats = satint.interpolate()
try:
from pyresample import geometry
lons = np.ma.masked_array(lons, nodata_mask)
lats = np.ma.masked_array(lats, nodata_mask)
scene.area = geometry.SwathDefinition(lons=lons,
lats=lats)
except ImportError:
scene.area = None
scene.lat = lats
scene.lon = lons
LOG.info("Loading PPS parameters done.")
def read(self, filename, load_lonlat=True):
"""Read product in hdf format from *filename*
"""
LOG.debug("Filename: %s" % filename)
is_temp = False
if not h5py.is_hdf5(filename):
# Try see if it is bzipped:
import bz2
bz2file = bz2.BZ2File(filename)
import tempfile
tmpfilename = tempfile.mktemp()
try:
ofpt = open(tmpfilename, 'wb')
ofpt.write(bz2file.read())
ofpt.close()
is_temp = True
except IOError:
import traceback
traceback.print_exc()
raise IOError("Failed to read the file %s" % filename)
filename = tmpfilename
if not h5py.is_hdf5(filename):
if is_temp:
os.remove(filename)
raise IOError("File is not a hdf5 file!" % filename)
h5f = h5py.File(filename, "r")
# Read the global attributes
self._md = dict(h5f.attrs)
self._md["satellite"] = h5f.attrs['platform']
self._md["orbit"] = h5f.attrs['orbit_number']
self._md["time_slot"] = (timedelta(seconds=long(h5f.attrs['sec_1970']))
+ datetime(1970, 1, 1, 0, 0))
# Read the data and attributes
# This covers only one level of data. This could be made recursive.
for key, dataset in h5f.iteritems():
setattr(self, key, InfoObject())
getattr(self, key).info = dict(dataset.attrs)
for skey, value in dataset.attrs.iteritems():
if isinstance(value, h5py.h5r.Reference):
self._refs[(key, skey)] = h5f[value].name.split("/")[1]
if type(dataset.id) is h5py.h5g.GroupID:
LOG.warning("Format reader does not support groups")
continue
try:
getattr(self, key).data = dataset[:]
is_palette = (dataset.attrs.get("CLASS", None) == "PALETTE")
if(len(dataset.shape) > 1 and
not is_palette and
key not in ["lon", "lat",
"row_indices", "column_indices"]):
self._projectables.append(key)
if self.shape is None:
self.shape = dataset.shape
elif self.shape != dataset.shape:
raise ValueError("Different variable shapes !")
else:
self._keys.append(key)
except TypeError:
setattr(self, key, np.dtype(dataset))
self._keys.append(key)
h5f.close()
if is_temp:
os.remove(filename)
if not load_lonlat:
return
# Setup geolocation
# We need a no-data mask from one of the projectables to
# mask out bow-tie deletion pixels from the geolocation array
# So far only relevant for VIIRS.
# Preferably the lon-lat data in the PPS VIIRS geolocation
# file should already be masked.
# The no-data values in the products are not only where geo-location is absent
# Only the Cloud Type can be used as a proxy so far.
# Adam Dybbroe, 2012-08-31
nodata_mask = False #np.ma.masked_equal(np.ones(self.shape), 0).mask
for key in self._projectables:
projectable = getattr(self, key)
if key in ['cloudtype']:
nodata_array = np.ma.array(projectable.data)
nodata_mask = np.ma.masked_equal(nodata_array, 0).mask
break
try:
from pyresample import geometry
except ImportError:
return
tiepoint_grid = False
if hasattr(self, "row_indices") and hasattr(self, "column_indices"):
column_indices = self.column_indices.data
row_indices = self.row_indices.data
tiepoint_grid = True
interpolate = False
if hasattr(self, "lon") and hasattr(self, "lat"):
if 'intercept' in self.lon.info:
offset_lon = self.lon.info["intercept"]
elif 'offset' in self.lon.info:
offset_lon = self.lon.info["offset"]
if 'gain' in self.lon.info:
gain_lon = self.lon.info["gain"]
lons = self.lon.data * gain_lon + offset_lon
if 'intercept' in self.lat.info:
offset_lat = self.lat.info["intercept"]
elif 'offset' in self.lat.info:
offset_lat = self.lat.info["offset"]
if 'gain' in self.lat.info:
gain_lat = self.lat.info["gain"]
lats = self.lat.data * gain_lat + offset_lat
if lons.shape != self.shape or lats.shape != self.shape:
# Data on tiepoint grid:
interpolate = True
if not tiepoint_grid:
errmsg = ("Interpolation needed but insufficient" +
"information on the tiepoint grid")
raise IOError(errmsg)
else:
# Geolocation available on the full grid:
# We neeed to mask out nodata (VIIRS Bow-tie deletion...)
# We do it for all instruments, checking only against the nodata
lons = np.ma.masked_array(lons, nodata_mask)
lats = np.ma.masked_array(lats, nodata_mask)
self.area = geometry.SwathDefinition(lons=lons, lats=lats)
elif hasattr(self, "region") and self.region.data["area_extent"].any():
region = self.region.data
proj_dict = dict([elt.split('=')
for elt in region["pcs_def"].split(',')])
self.area = geometry.AreaDefinition(region["id"],
region["name"],
region["proj_id"],
proj_dict,
region["xsize"],
region["ysize"],
region["area_extent"])
if interpolate:
from geotiepoints import SatelliteInterpolator
cols_full = np.arange(self.shape[1])
rows_full = np.arange(self.shape[0])
satint = SatelliteInterpolator((lons, lats),
(row_indices,
column_indices),
(rows_full, cols_full))
#satint.fill_borders("y", "x")
lons, lats = satint.interpolate()
self.area = geometry.SwathDefinition(lons=lons, lats=lats)
tie_cols = params['tiepoints']['cols']
tie_rows = params['tiepoints']['rows']
# From tie_cols and tie_rows, generate a gegulaer grid
#fine_rows = np.arange(0, 3085, 257)
#fine_cols = np.arange(0, 6313, 332)
fine_rows = np.arange(0, 15436, 250)
fine_cols = np.arange(0, 31561, 250)
#print params
#fine_cols = np.arange(0, data.shape[1])
#fine_rows = np.arange(0, data.shape[0])
interpolator = SatelliteInterpolator((tie_lons, tie_lats),
(tie_rows, tie_cols),
(fine_rows, fine_cols),
1, 3)
#np.save('tie_lons.npy', tie_lons)
#np.save('tie_lats.npy', tie_lats)
#np.save('tie_cols.npy', tie_cols)
#np.save('tie_rows.npy', tie_rows)
#np.save('fine_cols.npy', fine_cols)
#np.save('fine_rows.npy', fine_rows)
lons, lats = interpolator.interpolate()
print 'RESULT :'
print lons
print lats
np.save('result_lons.npy', lons)
np.save('result_lats.npy', lats)
#print 'DATA'
#print data.shape