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netCDFController.py
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rCTRACKER ctracker3
netCDFController.py
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###########################################################################
# #
# Copyright 2017 Andrea Cimatoribus #
# EPFL ENAC IIE ECOL #
# GR A1 435 (Batiment GR) #
# Station 2 #
# CH-1015 Lausanne #
# Andrea.Cimatoribus@epfl.ch #
# #
# Alexandre Serex #
# alexandre.serex@epfl.ch #
# #
# This file is part of ctracker #
# #
# ctracker is free software: you can redistribute it and/or modify it #
# under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# (at your option) any later version. #
# #
# ctracker is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty #
# of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. #
# See the GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with ctracker. If not, see <http://www.gnu.org/licenses/>. #
# #
###########################################################################
import
numpy
as
np
from
netCDF4
import
Dataset
from
core.parameter
import
Parameter
from
tools.CFunctions
import
loc_time_fast
class
NetCDFController
(
Parameter
):
def
__init__
(
self
,
name
,
run
,
inout
,
ends
,
ntrackmax
,
gcmstart
,
complevel
,
chunk_id
,
chunk_time
,
*
args
,
**
kwargs
):
super
(
NetCDFController
,
self
)
.
__init__
(
name
,
*
args
,
**
kwargs
)
self
.
iendw
=
ends
[
0
]
self
.
iende
=
ends
[
1
]
self
.
jendn
=
ends
[
2
]
self
.
jends
=
ends
[
3
]
self
.
ntrackmax
=
ntrackmax
self
.
gcm_start
=
gcmstart
self
.
complevel
=
complevel
self
.
chunk_id
=
chunk_id
self
.
chunk_time
=
chunk_time
self
.
nc_time
=
np
.
array
([],
dtype
=
"float64"
)
self
.
run
=
self
.
nc_init_run
(
run
)
self
.
inout
=
self
.
nc_init_inout
(
inout
)
self
.
inputs
[
'default'
]
=
[
self
.
process_input
]
self
.
inputs
[
"sync"
]
=
[
self
.
sync
]
def
sync
(
self
):
self
.
run
.
sync
()
self
.
inout
.
sync
()
def
process_input
(
self
,
*
args
,
**
kwargs
):
self
.
nc_write_one_time
(
*
args
,
**
kwargs
)
def
nc_init_inout
(
self
,
nc_f
):
# store info on kill areas
nc_f
.
setncattr
(
"i_endw"
,
self
.
iendw
)
nc_f
.
setncattr
(
"i_ende"
,
self
.
iende
)
nc_f
.
setncattr
(
"j_endn"
,
self
.
jendn
)
nc_f
.
setncattr
(
"j_ends"
,
self
.
jends
)
# id
nc_f
.
createDimension
(
"pid"
,
size
=
self
.
ntrackmax
)
nc_f
.
createVariable
(
"pid"
,
"int32"
,
(
"pid"
,))
ncvar
=
nc_f
.
variables
[
"pid"
]
ncvar
[:]
=
np
.
arange
(
1
,
self
.
ntrackmax
+
1
)
ncvar
.
setncattr
(
"long_name"
,
"particle ID"
)
# exit code
nc_f
.
createVariable
(
"outc"
,
"i2"
,
(
"pid"
,))
ncvar
=
nc_f
.
variables
[
"outc"
]
ncvar
.
setncattr
(
"code -1"
,
"not released"
)
ncvar
.
setncattr
(
"code 0"
,
"still active"
)
ncvar
.
setncattr
(
"code 1"
,
"out of the horizontal domain"
)
ncvar
.
setncattr
(
"code 2"
,
"particle reached the surface"
)
ncvar
.
setncattr
(
"code 10+N"
,
"reached N-th kill region"
)
ncvar
[:]
=
-
1
# time of seeding
nc_f
.
createVariable
(
"t_ini"
,
"float64"
,
(
"pid"
,),
fill_value
=-
1.0
)
ncvar
=
nc_f
.
variables
[
"t_ini"
]
ncvar
.
setncattr
(
"units"
,
(
"seconds since
%s
"
%
self
.
gcm_start
.
astype
(
"datetime64[s]"
))
.
replace
(
"T"
,
" "
))
# end time
nc_f
.
createVariable
(
"t_end"
,
"float64"
,
(
"pid"
,),
fill_value
=-
1.0
)
ncvar
=
nc_f
.
variables
[
"t_end"
]
ncvar
.
setncattr
(
"units"
,
(
"seconds since
%s
"
%
self
.
gcm_start
.
astype
(
"datetime64[s]"
))
.
replace
(
"T"
,
" "
))
# i-position at seeding
nc_f
.
createVariable
(
"i_ini"
,
"float32"
,
(
"pid"
,),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
)
ncvar
=
nc_f
.
variables
[
"i_ini"
]
ncvar
.
setncattr
(
"units"
,
"fractional cell_index"
)
# j-position at seeding
nc_f
.
createVariable
(
"j_ini"
,
"float32"
,
(
"pid"
,),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
)
ncvar
=
nc_f
.
variables
[
"j_ini"
]
ncvar
.
setncattr
(
"units"
,
"fractional cell_index"
)
# k-position at seeding
nc_f
.
createVariable
(
"k_ini"
,
"float32"
,
(
"pid"
,),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
)
ncvar
=
nc_f
.
variables
[
"k_ini"
]
ncvar
.
setncattr
(
"units"
,
"fractional cell_index"
)
# x-position at seeding
nc_f
.
createVariable
(
"x_ini"
,
"float32"
,
(
"pid"
,),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
)
ncvar
=
nc_f
.
variables
[
"x_ini"
]
ncvar
.
setncattr
(
"units"
,
"GCM grid units"
)
# y-position at seeding
nc_f
.
createVariable
(
"y_ini"
,
"float32"
,
(
"pid"
,),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
)
ncvar
=
nc_f
.
variables
[
"y_ini"
]
ncvar
.
setncattr
(
"units"
,
"GCM grid units"
)
# z-position at seeding
nc_f
.
createVariable
(
"z_ini"
,
"float32"
,
(
"pid"
,),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
)
ncvar
=
nc_f
.
variables
[
"z_ini"
]
ncvar
.
setncattr
(
"units"
,
"GCM grid units"
)
# i-position at exit
nc_f
.
createVariable
(
"i_end"
,
"float32"
,
(
"pid"
,),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
)
ncvar
=
nc_f
.
variables
[
"i_end"
]
ncvar
.
setncattr
(
"units"
,
"fractional cell_index"
)
# j-position at exit
nc_f
.
createVariable
(
"j_end"
,
"float32"
,
(
"pid"
,),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
)
ncvar
=
nc_f
.
variables
[
"j_end"
]
ncvar
.
setncattr
(
"units"
,
"fractional cell_index"
)
# k-position at exit
nc_f
.
createVariable
(
"k_end"
,
"float32"
,
(
"pid"
,),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
)
ncvar
=
nc_f
.
variables
[
"k_end"
]
ncvar
.
setncattr
(
"units"
,
"fractional cell_index"
)
# x-position at exit
nc_f
.
createVariable
(
"x_end"
,
"float32"
,
(
"pid"
,),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
)
ncvar
=
nc_f
.
variables
[
"x_end"
]
ncvar
.
setncattr
(
"units"
,
"GCM grid units"
)
# y-position at exit
nc_f
.
createVariable
(
"y_end"
,
"float32"
,
(
"pid"
,),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
)
ncvar
=
nc_f
.
variables
[
"y_end"
]
ncvar
.
setncattr
(
"units"
,
"GCM grid units"
)
# z-position at exit
nc_f
.
createVariable
(
"z_end"
,
"float32"
,
(
"pid"
,),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
)
ncvar
=
nc_f
.
variables
[
"z_end"
]
ncvar
.
setncattr
(
"units"
,
"GCM grid units"
)
return
nc_f
def
nc_init_run
(
self
,
nc_f
):
# id
nc_f
.
createDimension
(
"pid"
,
size
=
self
.
ntrackmax
)
nc_f
.
createVariable
(
"pid"
,
"int32"
,
(
"pid"
,))
ncvar
=
nc_f
.
variables
[
"pid"
]
ncvar
[:]
=
np
.
arange
(
1
,
self
.
ntrackmax
+
1
)
ncvar
.
setncattr
(
"long_name"
,
"particle ID"
)
# time
nc_f
.
createDimension
(
"time"
,
size
=
None
)
nc_f
.
createVariable
(
"time"
,
"float64"
,
(
"time"
,))
ncvar
=
nc_f
.
variables
[
"time"
]
ncvar
.
setncattr
(
"units"
,
(
"seconds since
%s
"
%
self
.
gcm_start
.
astype
(
"datetime64[s]"
))
.
replace
(
"T"
,
" "
))
# write times are highly dependent on the chunking in use
chunks
=
(
self
.
chunk_id
,
self
.
chunk_time
)
# itrack
nc_f
.
createVariable
(
"itrack"
,
"float32"
,
(
"pid"
,
"time"
),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
,
chunksizes
=
chunks
)
ncvar
=
nc_f
.
variables
[
"itrack"
]
ncvar
.
setncattr
(
"units"
,
"fractional cell_index"
)
# jtrack
nc_f
.
createVariable
(
"jtrack"
,
"float32"
,
(
"pid"
,
"time"
),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
,
chunksizes
=
chunks
)
ncvar
=
nc_f
.
variables
[
"jtrack"
]
ncvar
.
setncattr
(
"units"
,
"fractional cell_index"
)
# ktrack
nc_f
.
createVariable
(
"ktrack"
,
"float32"
,
(
"pid"
,
"time"
),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
,
chunksizes
=
chunks
)
ncvar
=
nc_f
.
variables
[
"ktrack"
]
ncvar
.
setncattr
(
"units"
,
"fractional cell_index"
)
# xtrack
nc_f
.
createVariable
(
"xtrack"
,
"float32"
,
(
"pid"
,
"time"
),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
,
chunksizes
=
chunks
)
ncvar
=
nc_f
.
variables
[
"xtrack"
]
ncvar
.
setncattr
(
"units"
,
"GCM grid units"
)
# ytrack
nc_f
.
createVariable
(
"ytrack"
,
"float32"
,
(
"pid"
,
"time"
),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
,
chunksizes
=
chunks
)
ncvar
=
nc_f
.
variables
[
"ytrack"
]
ncvar
.
setncattr
(
"units"
,
"GCM grid units"
)
# ztrack
nc_f
.
createVariable
(
"ztrack"
,
"float32"
,
(
"pid"
,
"time"
),
zlib
=
True
,
complevel
=
self
.
complevel
,
shuffle
=
True
,
chunksizes
=
chunks
)
ncvar
=
nc_f
.
variables
[
"ztrack"
]
ncvar
.
setncattr
(
"units"
,
"GCM grid units"
)
nc_f
.
sync
()
return
nc_f
def
nc_write_one_time
(
self
,
*
args
,
file
=
"run"
,
outc
=
None
,
init
=
False
):
# The particle ids start from 1, python index from 0
time
,
ids
,
ijk
,
xyz
=
args
[
0
]
ids
-=
1
nc_f
=
self
.
run
if
file
==
"inout"
:
nc_f
=
self
.
inout
if
init
:
nc_f
=
self
.
inout
nc_f
.
variables
[
"t_ini"
][
ids
]
=
time
nc_f
.
variables
[
"outc"
][
ids
]
=
0
nc_f
.
variables
[
"i_ini"
][
ids
]
=
ijk
[:,
0
]
nc_f
.
variables
[
"j_ini"
][
ids
]
=
ijk
[:,
1
]
nc_f
.
variables
[
"k_ini"
][
ids
]
=
ijk
[:,
2
]
nc_f
.
variables
[
"x_ini"
][
ids
]
=
xyz
[:,
0
]
nc_f
.
variables
[
"y_ini"
][
ids
]
=
xyz
[:,
1
]
nc_f
.
variables
[
"z_ini"
][
ids
]
=
xyz
[:,
2
]
elif
np
.
any
(
outc
>
0
):
# particles exit
nonzerooc
=
outc
>
0
nc_f
.
variables
[
"t_end"
][
ids
[
nonzerooc
]]
=
time
nc_f
.
variables
[
"outc"
][
ids
[
nonzerooc
]]
=
outc
[
nonzerooc
]
nc_f
.
variables
[
"i_end"
][
ids
]
=
ijk
[:,
0
]
nc_f
.
variables
[
"j_end"
][
ids
]
=
ijk
[:,
1
]
nc_f
.
variables
[
"k_end"
][
ids
]
=
ijk
[:,
2
]
nc_f
.
variables
[
"x_end"
][
ids
]
=
xyz
[:,
0
]
nc_f
.
variables
[
"y_end"
][
ids
]
=
xyz
[:,
1
]
nc_f
.
variables
[
"z_end"
][
ids
]
=
xyz
[:,
2
]
else
:
tind
=
self
.
loc_time
(
nc_f
,
time
)
nc_f
.
variables
[
"itrack"
][
ids
,
tind
]
=
ijk
[:,
0
]
nc_f
.
variables
[
"jtrack"
][
ids
,
tind
]
=
ijk
[:,
1
]
nc_f
.
variables
[
"ktrack"
][
ids
,
tind
]
=
ijk
[:,
2
]
nc_f
.
variables
[
"xtrack"
][
ids
,
tind
]
=
xyz
[:,
0
]
nc_f
.
variables
[
"ytrack"
][
ids
,
tind
]
=
xyz
[:,
1
]
nc_f
.
variables
[
"ztrack"
][
ids
,
tind
]
=
xyz
[:,
2
]
def
loc_time
(
self
,
nc_f
,
time
):
ind
=
loc_time_fast
(
self
.
nc_time
,
self
.
nc_time
.
size
,
time
,
False
)
if
ind
>=
0
:
return
ind
else
:
# We did not find the time we are looking for,
# so we add it to the time axis
# both in memory and on disk
self
.
nc_time
=
np
.
append
(
self
.
nc_time
,
time
)
ind
=
self
.
nc_time
.
size
-
1
nc_f
.
variables
[
"time"
][
ind
]
=
time
return
ind
def
dataset
(
file
,
*
args
,
**
kwargs
):
return
Dataset
(
file
,
*
args
,
**
kwargs
)
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