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Commit abd3a5b6 authored by Jonathan Lambrechts's avatar Jonathan Lambrechts Committed by Valentin Vallaeys
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add slimPreEvaluatorGeoTIFF

parent cc23b84c
Pipeline #1218 passed with stage
in 36 minutes and 14 seconds
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benchmarks/bohai/mesh.py
View file @ abd3a5b6
......@@ -12,6 +12,7 @@ dist = slimPre.distance_shp(coast_shp, 1000, [1,2,20])
def fsize(x, y, z) :
d = R*dist.evaluate_geocentric(x,y,z)
h = bath.evaluate_geocentric(x,y,z)
if d < 1500 :
s0 = 750
elif d < 100000 :
......@@ -19,7 +20,9 @@ def fsize(x, y, z) :
s0 = 750*(1-f) + 20000 * f
else :
s0 = 20000
return s0/R
h = min(25,max(5, h))
s1 = 1000 * h**0.5
return min(s0, s1)/R
physicals = {1:"coast", 2:"coast", 10:"yellow_sea_north", 11:"yellow_sea_center", 12:"yellow_sea_south", 20:"yellow_river"}
......
benchmarks/bohai/prepro.py
View file @ abd3a5b6
......@@ -5,73 +5,44 @@ pre_data_dir_base = 'data_'+slimPre.partition_nb()+'/'
pre_data_dir = pre_data_dir_base+slimPre.partition_id()+'/'
slimPre.make_directory(pre_data_dir)
mesh_file_name = slimPre.fetch_ftp('slim_data/bohai/bohai_v1.msh')
initial_time = '2016-01-01 00:00:00'
final_time = '2016-01-05 00:00:00'
mesh_file_name = slimPre.partition_mesh(mesh_file_name, pre_data_dir+'mesh.msh')
mesh_file_name = slimPre.partition_mesh('bohai.msh', pre_data_dir+"mesh.msh")
mesh = slimPre.Mesh(mesh_file_name, mesh_proj='+proj=utm +ellps=WGS84 +zone=51')
region_global = slimPre.Region(mesh, '')
lonlat_global = slimPre.Coordinate_system(region_global, data_proj='+proj=latlong +ellps=WGS84')
### Bathymetry Process ###
print('Preprocessing Bathymetry')
from scipy.interpolate import griddata
bath_data_file_name = slimPre.fetch_ftp('slim_data/bohai/bohai_bath.xyz')
num_lines = sum(1 for line in open(bath_data_file_name)) -2
cloud = np.empty((num_lines,3))
fin = open(bath_data_file_name, 'r')
l = fin.readline()
l = fin.readline()
i = 0
while l != '' and l[0:9] != '<end_xyz>':
(x, y, b) = l.split(',')
cloud[i,:] = [float(x), float(y), float(b)]
l = fin.readline()
i = i+1
lonlat_coordinates = lonlat_global.coordinates * 180./np.pi
bath_linear = griddata(cloud[:,0:2], cloud[:,2], (lonlat_coordinates[:,0], lonlat_coordinates[:,1]), method='linear')
bath_nearest = griddata(cloud[:,0:2], cloud[:,2], (lonlat_coordinates[:,0], lonlat_coordinates[:,1]), method='nearest')
bath = np.where(np.isnan(bath_linear), bath_nearest, bath_linear)
bath = np.maximum(bath, 2.)
bath_tiff = slimPre.fetch_ftp('slim_data/bohai/bohai_bathymetry.tif')
bath = slimPre.geo_tiff(bath_tiff).evaluate_region(region_global)
slimPre.write_file(pre_data_dir+'bathymetry.nc', region=region_global, time=None, data=[('bathymetry', bath)])
slimPre.smooth_bathymetry(mesh, (pre_data_dir+'bathymetry.nc','bathymetry'), output_file_name=pre_data_dir_base+'bathymetry_smooth', coefficient=0.5)
### Coriolis Process ###
print('Preprocessing Coriolis')
lonlat_coordinates = lonlat_global.coordinates
corio = 2 * 7.292e-5 * np.sin(lonlat_coordinates[:,1])
lonlat = slimPre.Coordinate_system(region_global, data_proj='+proj=latlong +ellps=WGS84').coordinates
corio = 2 * 7.292e-5 * np.sin(lonlat[:,1])
slimPre.write_file(pre_data_dir+'coriolis.nc', region=region_global, time=None, data=[('coriolis', corio)])
### River Discharge Process ###
print('Preprocessing River Discharge')
t = [3600*j for j in range(300)]
time = slimPre.Time(time_vector=t, initial_time=initial_time)
discharge = np.ones(len(t)) * 1000
discharge[0] = 0
slimPre.write_file(pre_data_dir+'river_discharge.nc', region=None, time=time, data=[('river_discharge', discharge)])
### Open Sea Process ###
print('Preprocessing Open Sea Boundary')
time = slimPre.Time(initial_time=initial_time, final_time=final_time, time_step=900.)
# Yellow Sea North
region = slimPre.Region(mesh, physical_tags=['yellow_sea_north'])
(ssh, ssu, ssv) = slimPre.tpxo_tide(region, time)
flow = slimPre.residual_flow(region, 0.1*1e6, pre_data_dir_base+'bathymetry_smooth/bathymetry_smooth.idx')
ssu += flow[None,:,0]
ssv += flow[None,:,1]
slimPre.write_file(pre_data_dir+'yellow_sea_north.nc', region=region, time=time, data=[('h', ssh), ('u', ssu), ('v', ssv)])
# Yellow Sea Center
......@@ -79,17 +50,13 @@ region = slimPre.Region(mesh, physical_tags=['yellow_sea_center'])
(ssh, ssu, ssv) = slimPre.tpxo_tide(region, time)
slimPre.write_file(pre_data_dir+'yellow_sea_center.nc', region=region, time=time, data=[('h', ssh), ('u', ssu), ('v', ssv)])
# Yellow Sea South
region = slimPre.Region(mesh, physical_tags=['yellow_sea_south'])
(ssh, ssu, ssv) = slimPre.tpxo_tide(region, time)
flow = slimPre.residual_flow(region, -0.1*1e6, pre_data_dir_base+'bathymetry_smooth/bathymetry_smooth.idx')
ssu += flow[None,:,0]
ssv += flow[None,:,1]
slimPre.write_file(pre_data_dir+'yellow_sea_south.nc', region=region, time=time, data=[('h', ssh), ('u', ssu), ('v', ssv)])
print( 'Preprocessing done ' )
print('Preprocessing done')
slimPre.exit(0)
dgpy/scripts/slimPre.py
View file @ abd3a5b6
......@@ -1009,3 +1009,13 @@ class distance_shp(slim_private.pre_evaluator) :
if there is 'entity' field of integer associated with the shp features, this argument can be used to keep only the features with given values of 'entity'
"""
super(distance_shp, self).__init__(dgpy.slimPreEvaluatorDistanceSHP(shp_filename, dmax, tags))
class geo_tiff(slim_private.pre_evaluator) :
""" extract data from a geo TIFF file """
def __init__(self, tiff_filename) :
"""
arguments:
* filename : string
path to the geo TIFF file
"""
super(geo_tiff, self).__init__(dgpy.slimPreEvaluatorGeoTIFF(tiff_filename))
modules/slimFunction/CMakeLists.txt
View file @ abd3a5b6
......@@ -13,6 +13,7 @@ set(SRC
unrefMesher.cpp
slimPreEvaluator.cpp
slimPreEvaluatorDistanceSHP.cpp
slimPreEvaluatorGeoTIFF.cpp
)
set(LIBS "")
......@@ -50,6 +51,7 @@ if(ENABLE_FES)
endif(ENABLE_FES)
option(ENABLE_PROJ "Enable PROJ" ON)
option(ENABLE_GEOTIFF "Enable GEOTIFF (requires ENABLE_PROJ)" ON)
option(ENABLE_UNREF "Enable UNREF mesh generator (requires ENABLE_PROJ)" ON)
option(ENABLE_FLANN "Enable flann to compute distance from coastlines (requires ENABLE_PROJ and ENABLE_UNREF)" ON)
if(ENABLE_PROJ)
......@@ -105,6 +107,25 @@ if(ENABLE_PROJ)
set(HAVE_FLANN ON)
list(APPEND EXTERNAL_MODULE_DEPS libproj)
endif (ENABLE_FLANN)
if (ENABLE_GEOTIFF)
find_package(TIFF REQUIRED)
ExternalProject_Add(geotiff
URL http://download.osgeo.org/geotiff/libgeotiff/libgeotiff-1.4.2.tar.gz
URL_MD5 96ab80e0d4eff7820579957245d844f8
PREFIX libgeotiff
INSTALL_COMMAND ""
CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE} -DWITH_UTILITIES=NO -DCMAKE_C_FLAGS=-fPIC -DGEOTIFF_CSV_DATA_DIR=${CMAKE_CURRENT_BINARY_DIR}/libgeotiff/src/geotiff/csv
BINARY_DIR libgeotiff/build
)
include_directories(${CMAKE_CURRENT_BINARY_DIR}/libgeotiff/src/geotiff)
include_directories(${CMAKE_CURRENT_BINARY_DIR}/libgeotiff/src/geotiff/libxtiff)
include_directories(${CMAKE_CURRENT_BINARY_DIR}/libgeotiff/build)
list(APPEND LIBS ${CMAKE_CURRENT_BINARY_DIR}/libgeotiff/build/lib/libgeotiff.a ${CMAKE_CURRENT_BINARY_DIR}/libgeotiff/build/lib/libxtiff.a)
include_directories(${TIFF_INCLUDE_DIRS})
list(APPEND LIBS ${TIFF_LIBRARY})
list(APPEND EXTERNAL_MODULE_DEPS geotiff)
set(HAVE_GEOTIFF ON)
endif(ENABLE_GEOTIFF)
endif(ENABLE_PROJ)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/slimFunctionConfig.h.in ${CMAKE_CURRENT_BINARY_DIR}/slimFunctionConfig.h)
......
modules/slimFunction/slimFunction.i
View file @ abd3a5b6
......@@ -15,6 +15,7 @@
#include "unrefMesher.h"
#include "slimPreEvaluator.h"
#include "slimPreEvaluatorDistanceSHP.h"
#include "slimPreEvaluatorGeoTIFF.h"
%}
%import(module="dgpy.dgCommon") "dgCommon.i"
......@@ -36,3 +37,4 @@
%include "slimExportNetCDF.h"
%include "slimPreEvaluator.h"
%include "slimPreEvaluatorDistanceSHP.h"
%include "slimPreEvaluatorGeoTIFF.h"
modules/slimFunction/slimFunctionConfig.h.in
View file @ abd3a5b6
......@@ -7,4 +7,5 @@
#cmakedefine HAVE_PROJ
#cmakedefine HAVE_UNREF
#cmakedefine HAVE_FLANN
#cmakedefine HAVE_GEOTIFF
#endif
modules/slimFunction/slimPreEvaluatorGeoTIFF.cpp 0 → 100644
View file @ abd3a5b6
#include "slimFunctionConfig.h"
#ifdef HAVE_GEOTIFF
#include "slimPreEvaluatorGeoTIFF.h"
#include "xtiffio.h"
#include "geotiff.h"
#include "geovalues.h"
#include "geo_normalize.h" // projection and conversion to proj4
#include "tiffio.h"
#include "proj_api.h"
#include "dgMessage.h"
#include "dgConfig.h"
enum {SLIM_TIFF_UINT=1, SLIM_TIFF_INT=2, SLIM_TIFF_FLOAT=3};
enum {SLIM_TIFF_BYTE=1, SLIM_TIFF_INT16, SLIM_TIFF_INT32, SLIM_TIFF_INT64, SLIM_TIFF_UINT16, SLIM_TIFF_UINT32, SLIM_TIFF_UINT64, SLIM_TIFF_FLOAT32, SLIM_TIFF_FLOAT64};
static short buildType(short base, short size) {
if (size == 8) return SLIM_TIFF_BYTE;
if(base == SLIM_TIFF_INT && size == 16) return SLIM_TIFF_INT16;
if(base == SLIM_TIFF_INT && size == 32) return SLIM_TIFF_INT32;
if(base == SLIM_TIFF_INT && size == 64) return SLIM_TIFF_INT64;
if(base == SLIM_TIFF_UINT && size == 16) return SLIM_TIFF_UINT16;
if(base == SLIM_TIFF_UINT && size == 32) return SLIM_TIFF_UINT32;
if(base == SLIM_TIFF_UINT && size == 64) return SLIM_TIFF_UINT64;
if(base == SLIM_TIFF_FLOAT && size == 32) return SLIM_TIFF_FLOAT32;
if(base == SLIM_TIFF_FLOAT && size == 64) return SLIM_TIFF_FLOAT64;
Msg::Error("Unknown type in tiff file");
return 0;
}
static double _asDouble(char *data, short type, int i) {
switch (type) {
case SLIM_TIFF_BYTE: return ((uint8_t*)(data))[i];
case SLIM_TIFF_INT16: return ((int16_t*)(data))[i];
case SLIM_TIFF_INT32: return ((int32_t*)(data))[i];
case SLIM_TIFF_INT64: return ((int64_t*)(data))[i];
case SLIM_TIFF_UINT16: return ((uint16_t*)(data))[i];
case SLIM_TIFF_UINT32: return ((uint32_t*)(data))[i];
case SLIM_TIFF_UINT64: return ((uint64_t*)(data))[i];
case SLIM_TIFF_FLOAT32: return ((float*)(data))[i];
case SLIM_TIFF_FLOAT64: return ((double*)(data))[i];
}
return 0.;
}
slimPreEvaluatorGeoTIFF::slimPreEvaluatorGeoTIFF(const char *filename) {
_data = NULL;
_tiff = XTIFFOpen(filename, "r");
if(!_tiff)
Msg::Error("cannot open tiff file %s", filename);
_gtif = GTIFNew(_tiff);
if(!_gtif)
Msg::Error("cannot open tiff file %s", filename);
GTIFDefn defn;
if(GTIFGetDefn(_gtif, &defn))
_coordinateSystem = GTIFGetProj4Defn(&defn);
else
Msg::Error("cannot read coordinate system from tiff file");
short int nsample, sampleformat, bitspersample;
if(TIFFGetField(_tiff, TIFFTAG_IMAGEWIDTH, &_sizex) != 1 ||
TIFFGetField(_tiff, TIFFTAG_IMAGELENGTH, &_sizey) != 1 ||
TIFFGetField(_tiff, TIFFTAG_SAMPLESPERPIXEL, &nsample) != 1 ||
TIFFGetField(_tiff, TIFFTAG_BITSPERSAMPLE, &bitspersample) != 1) {
Msg::Error("invalid tiff file");
}
if(TIFFGetField( _tiff, TIFFTAG_SAMPLEFORMAT, &sampleformat) != 1){
sampleformat = 1;
}
_dataType = buildType(sampleformat, bitspersample);
short int rasterType;
if(GTIFKeyGet( _gtif, GTRasterTypeGeoKey, &rasterType, 0, 1) != 1)
rasterType = 1;
if(GTIFKeyGet( _gtif, GTModelTypeGeoKey, &_modelType, 0, 1) != 1)
Msg::Error("no model type defined in geotiff file");
if(_modelType == ModelGeographic && GTIFKeyGet( _gtif, GeogAngularUnitsGeoKey, &_angularUnit, 0, 1) == 1)
if(_angularUnit != Angular_Degree)
Msg::Error("geotiff unit is not decimal degrees (Angular_Degree)");
printf("model type : %i\n", _modelType);
/*
double *tiepoint;
int count;
TIFFGetField(_tiff, TIFFTAG_GEOTIEPOINTS, &count, &tiepoint);
TIFFGetField(_tiff, TIFFTAG_GEOPIXELSCALE, &count, &tiepoint);
*/
_data = new char[bitspersample/8*_sizex*_sizey];
for (int i = 0; i < _sizey; ++i) {
if(TIFFReadScanline(_tiff, _data+i*_sizex*bitspersample/8, i, 0) !=1)
Msg::Error("error reading tiff file %s", filename);
}
}
std::string slimPreEvaluatorGeoTIFF::coordinateSystem() {
return _coordinateSystem;
}
double slimPreEvaluatorGeoTIFF::evaluate(double x, double y, double z) {
if(_modelType==2){
x*=180/M_PI;
y*=180/M_PI;
}
if(!GTIFPCSToImage(_gtif, &x, &y))
return 0;
int x0 = std::min(_sizex-1,std::max(0, (int)floor(x)));
int x1 = std::min(_sizex-1,std::max(0, (int)ceil(x)));
int y0 = std::min(_sizey-1,std::max(0, (int)floor(y)));
int y1 = std::min(_sizey-1,std::max(0, (int)ceil(y)));
double a = x-x0;
double b = y-y0;
return
(1-b)*(1-a)*(_asDouble(_data, _dataType, y0*_sizex+x0))
+(1-b)*( a)*(_asDouble(_data, _dataType, y0*_sizex+x1))
+( b)*(1-a)*(_asDouble(_data, _dataType, y1*_sizex+x0))
+( b)*( a)*(_asDouble(_data, _dataType, y1*_sizex+x1));
}
slimPreEvaluatorGeoTIFF::~slimPreEvaluatorGeoTIFF() {
if(_gtif)
GTIFFree(_gtif);
if (_tiff)
XTIFFClose(_tiff);
if (_data)
delete []_data;
}
#endif
modules/slimFunction/slimPreEvaluatorGeoTIFF.h 0 → 100644
View file @ abd3a5b6
#ifndef SLIM_PRE_GEOTIFF_H_
#define SLIM_PRE_GEOTIFF_H_
#include "slimFunctionConfig.h"
#ifdef HAVE_GEOTIFF
#include "slimPreEvaluator.h"
#include "unrefMesher.h"
#undef HAVE_STRINGS_H
#undef HAVE_STRING_H
#undef HAVE_STDLIB_H
typedef struct tiff TIFF;
typedef struct gtiff GTIF;
class slimPreEvaluatorGeoTIFF : public slimPreEvaluator{
TIFF *_tiff;
GTIF *_gtif;
std::string _coordinateSystem;
short _modelType;
short _angularUnit;
short _dataType;
int _sizex, _sizey;
char *_data;
public:
slimPreEvaluatorGeoTIFF(const char *filename);
double evaluate(double x, double y, double z);
std::string coordinateSystem();
~slimPreEvaluatorGeoTIFF();
};
#endif
#endif
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