initial commit for a bunch of files I didnt commit properly

src/resource_use/preparing_grid_resource_use.py

+# -*- coding: utf-8 -*-
+"""
+Spyder Editor
+
+# script to prepare the grid with the resource use information
+"""
+
+
+import numpy as np
+import MacPyver as mp
+import os
+ 
+ 
+"""
+# absence 
+os.system("gdal_rasterize \
+-l absence_shape_rep \
+-burn 1 \
+-ot Float32 \
+-te -1751798.359 1267454.241  -629798.359 2560454.241 -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_rep.shp \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_rep.tif")
+
+os.system("gdal_rasterize \
+-l absence_shape_rep \
+-burn 1 \
+-ot Float32 \
+ -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_rep.shp \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_rep.tif")
+
+os.system("gdalwarp \
+-t_srs '+proj=aea +lat_1=7 +lat_2=-32 +lat_0=-15 +lon_0=125 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs' \
+-ot Float64 -r bilinear \
+-te -1751798.359 1267454.241 -629798.359 2560454.241 \
+-ts 1122 1293 \
+-overwrite  \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_rep.tif \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_repro_res.tif"
+)
+
+os.system("gdalwarp \
+-t_srs '+proj=aea +lat_1=7 +lat_2=-32 +lat_0=-15 +lon_0=125 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs' \
+-ot Float64 -r near \
+-te -1751798.359 1267454.241 -629798.359 2560454.241 \
+-ts 1122 1293 \
+-overwrite  \
+/homes/mv39zilo/work/Borneo/data/future/grid.tif \
+/homes/mv39zilo/work/Borneo/data/future/grid_repro_res.tif"
+)
+
+
+
+"""
+
+
+
+
+
+absence_path = "/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_repro_res.tif"
+absence = mp.tiff.read_tif(absence_path, 1)
+
+grid_layer_path = "/homes/mv39zilo/work/Borneo/data/future/grid_repro_res.tif"
+grid = mp.tiff.read_tif(grid_layer_path, 1)
+
+
+grid = np.where(absence == 0, grid, 0)    
+np.unique(grid)
+
+
+# now assigning number for each resource use
+# 0 - absence       
+# 1 - plantation
+# 2 - deforestation
+# 3 - landcover change
+# 4 - logging
+# 5 - other 
+
+
+gaveau_defor_path = "/homes/mv39zilo/work/Borneo/data/predictors/raw_data/Remaining_forest_in_2015_and_deforestation_1973-2015/REGIONBorneo_FCDefDeg_1973to2015_CIFOR_repro_res.tif"
+gaveau_defor_raw = mp.tiff.read_tif(gaveau_defor_path, 1)
+gaveau_deforested = np.where((gaveau_defor_raw > 6 ) & 
+                              (gaveau_defor_raw < 10), 1, 0)
+gaveau_logged = np.where(gaveau_defor_raw == 2, 1, 0)
+
+#plantation                       
+plantation_path = "/homes/mv39zilo/work/Borneo/data/predictors/raw_data/Land_cover_trajectory_before_oil-palm_and_pulpwood_establishment/raster_plantation.tif"
+plantations = mp.tiff.read_tif(plantation_path, 1)                              
+
+#non habitat
+crisp_2000_path = "/homes/mv39zilo/work/Borneo/analysis/model_prep_and_running/results/resource_use//crisp_2000_repro_res.tif"
+crisp_2000 = mp.tiff.read_tif(crisp_2000_path, 1)
+crisp_2010_path = "/homes/mv39zilo/work/Borneo/analysis/model_prep_and_running/results/resource_use/crisp_2010_repro_res.tif"
+crisp_2010 = mp.tiff.read_tif(crisp_2010_path, 1)
+crisp_2015_path = "/homes/mv39zilo/work/Borneo/analysis/model_prep_and_running/results/resource_use/crisp_2015_repro_res.tif"
+crisp_2015 = mp.tiff.read_tif(crisp_2015_path, 1)
+
+cover_change = np.where(((crisp_2000 > 2 ) & (crisp_2000 < 7)) & ((crisp_2010 > 6 ) |(crisp_2010 == 1 ) | (crisp_2015 > 6) | (crisp_2015 == 1 ) ), 1, 0)
+
+# we can save some computing time by only considering
+# the grid and not everything, because abundance will only be
+# in rid
+grid = np.where((plantations == 1) & 
+                 (grid == 1), 1 , grid)
+grid = np.where((gaveau_deforested  == 1)& 
+                 (grid == 1), 2 , grid)
+grid = np.where((cover_change == 1)& 
+                 (grid == 1), 3 , grid)
+grid = np.where((gaveau_logged == 1) & 
+                 (grid == 1), 4 , grid)
+grid = np.where((grid == 1) &
+                (plantations == 0) &
+                (gaveau_deforested  == 0) & 
+                (cover_change == 0) &
+                (gaveau_logged == 0), 5 , grid)
+                
+np.unique(grid)
+
+mp.tiff.write_tif(file_with_srid = grid_layer_path, 
+                   full_output_name = "/homes/mv39zilo/work/Borneo/data/resource_use/resource_use_grid.tif",
+                   data =  grid, 
+                   dtype = 0)  
+                   
+
+"""
+# test
+indir = "/homes/mv39zilo/work/Borneo/analysis/model_prep_and_running/results/resource_use"
+abundance_layer_path = indir + "/abundance_pred_2015_no_absence.tif"
+# read the data
+abundance_data = mp.tiff.read_tif(abundance_layer_path, 1)
+
+test = np.where((grid == 0) &
+                (abundance_data > 0), abundance_data, 0)
+np.sum(test)
+mp.tiff.write_tif(file_with_srid = grid_layer_path, 
+                   full_output_name = "/homes/mv39zilo/work/Borneo/data/bootstrap/test.tif",
+                   data =  test, 
+                   dtype = 4)  
+"""                
+# rasterize borneo with info on country or province
+                   
+"""
+os.system("gdal_rasterize \
+-a ID_1 \
+-l Borneo \
+-ot Float32 \
+-te -1751798.359 1267454.241  -629798.359 2560454.241 -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo.shp \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_province.tif")
+
+os.system("gdal_rasterize \
+-a ID_1 \
+-l Borneo \
+-ot Float32 \
+ -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo.shp \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_province.tif")
+
+os.system("gdalwarp \
+-r near -t_srs '+proj=aea +lat_1=7 +lat_2=-32 +lat_0=-15 +lon_0=125 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs' \
+-te -1751798.359 1267454.241  -629798.359 2560454.241 -ts 1122 1293 \
+-overwrite \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_province.tif \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo__province_repro_res.tif")
+
+os.system("gdal_rasterize \
+-a ID_0 \
+-l Borneo \
+-ot Float32 \
+-te -1751798.359 1267454.241  -629798.359 2560454.241 -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo.shp \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_country.tif")
+
+os.system("gdal_rasterize \
+-a ID_0 \
+-l Borneo \
+-ot Float32 \
+ -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo.shp \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_country.tif")
+
+os.system("gdalwarp \
+-r near -t_srs '+proj=aea +lat_1=7 +lat_2=-32 +lat_0=-15 +lon_0=125 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs' \
+-te -1751798.359 1267454.241  -629798.359 2560454.241 -ts 1122 1293 \
+-overwrite \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_country.tif \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_country_repro_res.tif")
+
+"""