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_modules/forestatrisk/data/country_compute.html

@@ -112,7 +112,7 @@ <h1>Source code for forestatrisk.data.country_compute</h1><div class="highlight"
 <span class="kn">from</span> <span class="nn">.compute</span> <span class="kn">import</span> <span class="n">compute_biomass_avitabile</span><span class="p">,</span> <span class="n">compute_osm</span>
 <span class="kn">from</span> <span class="nn">.compute</span> <span class="kn">import</span> <span class="n">compute_srtm</span><span class="p">,</span> <span class="n">compute_wdpa</span>
 <span class="kn">from</span> <span class="nn">.compute</span> <span class="kn">import</span> <span class="n">compute_forest</span>
-<span class="kn">from</span> <span class="nn">.extent_shp</span> <span class="kn">import</span> <span class="n">extent_shp</span>
+<span class="kn">from</span> <span class="nn">.get_vector_extent</span> <span class="kn">import</span> <span class="n">get_vector_extent</span>
 
 
 <div class="viewcode-block" id="country_compute">
@@ -156,21 +156,21 @@ <h1>Source code for forestatrisk.data.country_compute</h1><div class="highlight"
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="c1"># Reproject GADM</span>
-    <span class="n">ofile</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">temp_dir</span><span class="p">,</span> <span class="s2">&quot;ctry_PROJ.shp&quot;</span><span class="p">)</span>
-    <span class="n">ifile</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">temp_dir</span><span class="p">,</span> <span class="s2">&quot;gadm36_&quot;</span> <span class="o">+</span> <span class="n">iso3</span> <span class="o">+</span> <span class="s2">&quot;_0.shp&quot;</span><span class="p">)</span>
+    <span class="n">ofile</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">temp_dir</span><span class="p">,</span> <span class="s2">&quot;ctry_PROJ.gpkg&quot;</span><span class="p">)</span>
+    <span class="n">ifile</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">temp_dir</span><span class="p">,</span> <span class="s2">&quot;gadm41_&quot;</span> <span class="o">+</span> <span class="n">iso3</span> <span class="o">+</span> <span class="s2">&quot;_0.gpkg&quot;</span><span class="p">)</span>
     <span class="n">param</span> <span class="o">=</span> <span class="n">gdal</span><span class="o">.</span><span class="n">VectorTranslateOptions</span><span class="p">(</span>
         <span class="n">accessMode</span><span class="o">=</span><span class="s2">&quot;overwrite&quot;</span><span class="p">,</span>
         <span class="n">srcSRS</span><span class="o">=</span><span class="s2">&quot;EPSG:4326&quot;</span><span class="p">,</span>
         <span class="n">dstSRS</span><span class="o">=</span><span class="n">proj</span><span class="p">,</span>
         <span class="n">reproject</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
-        <span class="nb">format</span><span class="o">=</span><span class="s2">&quot;ESRI Shapefile&quot;</span><span class="p">,</span>
+        <span class="nb">format</span><span class="o">=</span><span class="s2">&quot;GPKG&quot;</span><span class="p">,</span>
         <span class="n">layerCreationOptions</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;ENCODING=UTF-8&quot;</span><span class="p">],</span>
     <span class="p">)</span>
     <span class="n">gdal</span><span class="o">.</span><span class="n">VectorTranslate</span><span class="p">(</span><span class="n">ofile</span><span class="p">,</span> <span class="n">ifile</span><span class="p">,</span> <span class="n">options</span><span class="o">=</span><span class="n">param</span><span class="p">)</span>
 
     <span class="c1"># Compute extent</span>
-    <span class="n">ifile</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">temp_dir</span><span class="p">,</span> <span class="s2">&quot;ctry_PROJ.shp&quot;</span><span class="p">)</span>
-    <span class="n">extent_proj</span> <span class="o">=</span> <span class="n">extent_shp</span><span class="p">(</span><span class="n">ifile</span><span class="p">)</span>
+    <span class="n">ifile</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">temp_dir</span><span class="p">,</span> <span class="s2">&quot;ctry_PROJ.gpkg&quot;</span><span class="p">)</span>
+    <span class="n">extent_proj</span> <span class="o">=</span> <span class="n">get_vector_extent</span><span class="p">(</span><span class="n">ifile</span><span class="p">)</span>
 
     <span class="c1"># Region with buffer of 5km</span>
     <span class="n">xmin_reg</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">floor</span><span class="p">(</span><span class="n">extent_proj</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="mi">5000</span><span class="p">)</span>

_modules/forestatrisk/data/download/download_gadm.html

@@ -102,45 +102,30 @@ <h1>Source code for forestatrisk.data.download.download_gadm</h1><div class="hig
 <span></span><span class="sd">&quot;&quot;&quot;Download GADM data.&quot;&quot;&quot;</span>
 
 <span class="kn">import</span> <span class="nn">os</span>
-<span class="kn">from</span> <span class="nn">zipfile</span> <span class="kn">import</span> <span class="n">ZipFile</span>
 <span class="kn">from</span> <span class="nn">urllib.request</span> <span class="kn">import</span> <span class="n">urlretrieve</span>
 
-<span class="kn">from</span> <span class="nn">...misc</span> <span class="kn">import</span> <span class="n">make_dir</span>
-
 
 <div class="viewcode-block" id="download_gadm">
 <a class="viewcode-back" href="../../../../python_api/forestatrisk.data.html#forestatrisk.data.download.download_gadm">[docs]</a>
-<span class="k">def</span> <span class="nf">download_gadm</span><span class="p">(</span><span class="n">iso3</span><span class="p">,</span> <span class="n">output_dir</span><span class="o">=</span><span class="s2">&quot;.&quot;</span><span class="p">):</span>
+<span class="k">def</span> <span class="nf">download_gadm</span><span class="p">(</span><span class="n">iso3</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Download GADM data for a country.</span>
 
 <span class="sd">    Download GADM (Global Administrative Areas) for a specific</span>
 <span class="sd">    country. See `&lt;https://gadm.org&gt;`_\\ .</span>
 
 <span class="sd">    :param iso3: Country ISO 3166-1 alpha-3 code.</span>
 
-<span class="sd">    :param output_dir: Directory where data is downloaded. Default to</span>
-<span class="sd">        current working directory.</span>
+<span class="sd">    :param output_file: Path to output GPKG file.</span>
 
 <span class="sd">    &quot;&quot;&quot;</span>
 
-    <span class="c1"># Create directory</span>
-    <span class="n">make_dir</span><span class="p">(</span><span class="n">output_dir</span><span class="p">)</span>
-
-    <span class="c1"># Check for existing data</span>
-    <span class="n">shp_name</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">output_dir</span><span class="p">,</span> <span class="s2">&quot;gadm41_&quot;</span> <span class="o">+</span> <span class="n">iso3</span> <span class="o">+</span> <span class="s2">&quot;_0.shp&quot;</span><span class="p">)</span>
-    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">shp_name</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">True</span><span class="p">:</span>
-
-        <span class="c1"># Download the zipfile from gadm.org</span>
-        <span class="n">fname</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">output_dir</span><span class="p">,</span> <span class="n">iso3</span> <span class="o">+</span> <span class="s2">&quot;_shp.zip&quot;</span><span class="p">)</span>
-        <span class="n">url</span> <span class="o">=</span> <span class="p">(</span>
-            <span class="s2">&quot;https://geodata.ucdavis.edu/gadm/gadm4.1/&quot;</span>
-            <span class="s2">&quot;shp/gadm41_&quot;</span> <span class="o">+</span> <span class="n">iso3</span> <span class="o">+</span> <span class="s2">&quot;_shp.zip&quot;</span>
-        <span class="p">)</span>
-        <span class="n">urlretrieve</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">fname</span><span class="p">)</span>
+    <span class="c1"># Check for existing file</span>
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
 
-        <span class="c1"># Extract files from zip</span>
-        <span class="k">with</span> <span class="n">ZipFile</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
-            <span class="n">file</span><span class="o">.</span><span class="n">extractall</span><span class="p">(</span><span class="n">output_dir</span><span class="p">)</span></div>
+        <span class="c1"># Download the file from gadm.org</span>
+        <span class="n">url</span> <span class="o">=</span> <span class="p">(</span><span class="s2">&quot;https://geodata.ucdavis.edu/gadm/gadm4.1/&quot;</span>
+               <span class="sa">f</span><span class="s2">&quot;gpkg/gadm41_</span><span class="si">{</span><span class="n">iso3</span><span class="si">}</span><span class="s2">.gpkg&quot;</span><span class="p">)</span>
+        <span class="n">urlretrieve</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">output_file</span><span class="p">)</span></div>
 
 
 

_modules/forestatrisk/data/download/download_srtm.html

@@ -114,8 +114,9 @@ <h1>Source code for forestatrisk.data.download.download_srtm</h1><div class="hig
     <span class="kn">from</span> <span class="nn">urllib2</span> <span class="kn">import</span> <span class="n">HTTPError</span>  <span class="c1"># HTTPError with Python 2</span>
 
 <span class="kn">from</span> <span class="nn">...misc</span> <span class="kn">import</span> <span class="n">make_dir</span>
-<span class="kn">from</span> <span class="nn">..extent_shp</span> <span class="kn">import</span> <span class="n">extent_shp</span>
+<span class="kn">from</span> <span class="nn">..get_vector_extent</span> <span class="kn">import</span> <span class="n">get_vector_extent</span>
 <span class="kn">from</span> <span class="nn">.tiles_srtm</span> <span class="kn">import</span> <span class="n">tiles_srtm</span>
+<span class="kn">from</span> <span class="nn">.download_gadm</span> <span class="kn">import</span> <span class="n">download_gadm</span>
 
 
 <div class="viewcode-block" id="download_srtm">
@@ -141,23 +142,12 @@ <h1>Source code for forestatrisk.data.download.download_srtm</h1><div class="hig
     <span class="n">make_dir</span><span class="p">(</span><span class="n">output_dir</span><span class="p">)</span>
 
     <span class="c1"># Check for existing data</span>
-    <span class="n">shp_name</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">output_dir</span><span class="p">,</span> <span class="s2">&quot;gadm36_&quot;</span> <span class="o">+</span> <span class="n">iso3</span> <span class="o">+</span> <span class="s2">&quot;_0.shp&quot;</span><span class="p">)</span>
-    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">shp_name</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">True</span><span class="p">:</span>
-
-        <span class="c1"># Download the zipfile from gadm.org</span>
-        <span class="n">fname</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">output_dir</span><span class="p">,</span> <span class="n">iso3</span> <span class="o">+</span> <span class="s2">&quot;_shp.zip&quot;</span><span class="p">)</span>
-        <span class="n">url</span> <span class="o">=</span> <span class="p">(</span>
-            <span class="s2">&quot;https://biogeo.ucdavis.edu/data/gadm3.6/&quot;</span>
-            <span class="s2">&quot;shp/gadm36_&quot;</span> <span class="o">+</span> <span class="n">iso3</span> <span class="o">+</span> <span class="s2">&quot;_shp.zip&quot;</span>
-        <span class="p">)</span>
-        <span class="n">urlretrieve</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">fname</span><span class="p">)</span>
-
-        <span class="c1"># Extract files from zip</span>
-        <span class="k">with</span> <span class="n">ZipFile</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
-            <span class="n">file</span><span class="o">.</span><span class="n">extractall</span><span class="p">(</span><span class="n">output_dir</span><span class="p">)</span>
+    <span class="n">gpkg_name</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">output_dir</span><span class="p">,</span> <span class="s2">&quot;gadm41_&quot;</span> <span class="o">+</span> <span class="n">iso3</span> <span class="o">+</span> <span class="s2">&quot;_0.gpkg&quot;</span><span class="p">)</span>
+    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">gpkg_name</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">True</span><span class="p">:</span>
+        <span class="n">download_gadm</span><span class="p">(</span><span class="n">iso3</span><span class="p">,</span> <span class="n">gpkg_name</span><span class="p">)</span>
 
     <span class="c1"># Compute extent and SRTM tiles</span>
-    <span class="n">extent_latlong</span> <span class="o">=</span> <span class="n">extent_shp</span><span class="p">(</span><span class="n">shp_name</span><span class="p">)</span>
+    <span class="n">extent_latlong</span> <span class="o">=</span> <span class="n">get_vector_extent</span><span class="p">(</span><span class="n">gpkg_name</span><span class="p">)</span>
     <span class="n">tiles_long</span><span class="p">,</span> <span class="n">tiles_lat</span> <span class="o">=</span> <span class="n">tiles_srtm</span><span class="p">(</span><span class="n">extent_latlong</span><span class="p">)</span>
     <span class="n">tiles_long</span> <span class="o">=</span> <span class="n">tiles_long</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;-&quot;</span><span class="p">)</span>
     <span class="n">tiles_lat</span> <span class="o">=</span> <span class="n">tiles_lat</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;-&quot;</span><span class="p">)</span>