clean-up (#13)

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="griml",
-    version="0.1.0",
+    version="0.1.1",
     author="Penelope How",
     author_email="pho@geus.dk",
     description="A workflow for classifying lakes from satellite imagery and compiling lake inventories",
@@ -34,4 +34,9 @@
     package_data={"griml.test": ["*"]},
     python_requires=">=3.8",
     install_requires=['geopandas', 'pandas', 'scipy', 'Shapely', 'rasterio'],
+    entry_points={
+    'console_scripts': [
+        'griml = griml.test.process_cli:griml'
+    ],
+},
 )

src/griml/convert/convert.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 from griml.convert import raster_to_vector
-import glob
+import glob, os
 from pathlib import Path
 
 def convert(indir, proj, band_info, startdate, enddate, outdir=None):
@@ -41,15 +41,12 @@ def convert(indir, proj, band_info, startdate, enddate, outdir=None):
 
 if __name__ == "__main__": 
 
-    # Define file attributes
-    indir = list(glob.glob('/home/pho/Desktop/python_workspace/GrIML/other/iml_2017/binary_images/*.tif'))
-    outdir = '/home/pho/Desktop/python_workspace/GrIML/other/iml_2017/vectors/'
+    infile = os.path.join(os.path.dirname(griml.__file__),'test/test_north_greenland.tif')
     proj = 'EPSG:3413'
     band_info = [{'b_number':1, 'method':'VIS', 'source':'S2'},
                  {'b_number':2, 'method':'SAR', 'source':'S1'},
                  {'b_number':3, 'method':'DEM', 'source':'ARCTICDEM'}]
     start='20170701'
     end='20170831'
 
-    # Perform conversion
-    convert(indir, outdir, proj, band_info, start, end)    
+    convert([infile], proj, band_info, start, end)          

src/griml/filter/filter_vectors.py

@@ -5,6 +5,7 @@
 from griml.load import load
 import geopandas as gpd
 from pathlib import Path
+import os
 
 def filter_vectors(inlist, margin_file, outdir=None, min_area=0.05):
     '''Filter vectors by area and margin proximity
@@ -66,8 +67,6 @@ def filter_vectors(inlist, margin_file, outdir=None, min_area=0.05):
 
 
 if __name__ == "__main__": 
-    infile1 = '../test/test_icemask.shp'
-    margin_buff = gpd.read_file(infile1)
-
-    infile2 = ['../test/test_filter.shp']       
-    filter_vectors(infile2, margin_buff)
+    infile1 = os.path.join(os.path.dirname(griml.__file__),'test/test_filter.shp')
+    infile2 = os.path.join(os.path.dirname(griml.__file__),'test/test_icemask.shp')       
+    filter_vectors([infile1], infile2)

src/griml/load/load.py

@@ -69,12 +69,10 @@ def is_geo_object(typ):
     else:
         return False
 
-if __name__ == "__main__": 
-    infile1 = '../test/test_icemask.shp'
+if __name__ == "__main__":
+
+    infile1 = os.path.join(os.path.dirname(griml.__file__),'test/test_icemask.shp') 
     test1 = load(infile1)
 
     g = gpd.read_file(infile1)
     test2 = load(g)
-
-    infile2 = '../test/test_icemsak.shp'
-    test2 = load(infile2)

src/griml/merge/merge_vectors.py

@@ -108,6 +108,6 @@ def _dissolve_vectors(gdf):
     return gdf2
 
 if __name__ == "__main__": 
-        infile1 = '../test/test_merge_1.shp'
-        infile2 = '../test/test_merge_2.shp'               
-        vectors = merge_vectors([infile1,infile2]) 
+    infile1 = os.path.join(os.path.dirname(griml.__file__),'test/test_merge_1.shp') 
+    infile2 = os.path.join(os.path.dirname(griml.__file__),'test/test_merge_2.shp')                  
+    merge_vectors([infile1,infile2])

src/griml/metadata/add_metadata.py

@@ -36,13 +36,7 @@ def add_metadata(iml, names, regions, outfile=None):
 
 
 if __name__ == "__main__": 
-    # indir = "/home/pho/python_workspace/GrIML/other/iml_2017/merged_vectors/griml_2017_inventory.shp"
-    indir = "/home/pho/python_workspace/GrIML/other/iml_2017/inspected_vectors/lakes_all-0000000000-0000037888_filtered.shp"
-
-
-    infile_names = '/home/pho/python_workspace/GrIML/other/datasets/placenames/oqaasileriffik_placenames.shp'
-    infile_regions = '/home/pho/python_workspace/GrIML/other/datasets/drainage_basins/greenland_basins_polarstereo.shp'
-
-
-    outfile = "/home/pho/python_workspace/GrIML/other/iml_2017/metadata_vectors/griml_2017_inventory_final.shp"
-    add_metadata(indir, infile_names, infile_regions, outfile)
+    infile1 = os.path.join(os.path.dirname(griml.__file__),'test/test_merge_2.shp')
+    infile2 = os.path.join(os.path.dirname(griml.__file__),'test/test_placenames.shp')
+    infile3 = os.path.join(os.path.dirname(griml.__file__),'test/greenland_basins_polarstereo.shp')
+    add_metadata(infile1, infile2, infile3)

src/griml/metadata/assign_names.py

@@ -84,15 +84,4 @@ def _compile_names(gdf):
                     placenames.append(v['Alternativ'])
                 else:
                     placenames.append(None)
-    return placenames 
-
-
-if __name__ == "__main__": 
-
-    # Define file attributes
-    infile = '/home/pho/Desktop/python_workspace/GrIML/src/griml/test/test_merge_1.shp'
-    names = '/home/pho/Desktop/python_workspace/GrIML/other/datasets/placenames/oqaasileriffik_placenames_polarstereo.shp'
-
-
-    # Perform conversion
-    a = assign_names(infile, names)
+    return placenames

src/griml/metadata/assign_regions.py

@@ -68,19 +68,4 @@ def _get_nearest_polygon(gdfA, gdfB, gdfB_cols=['subregion'], distance=100000.0)
     gdf.loc[gdf['dist']>=distance, 'subregion'] = 'Unknown'
 
     gdf = gdf.drop(columns=['dist'])   
-    return gdf
-
-
-if __name__ == "__main__": 
-
-    # Define file attributes
-    infile = '/home/pho/Desktop/python_workspace/GrIML/src/griml/test/test_merge_1.shp'
-    regions = '/home/pho/python_workspace/GrIML/other/datasets/drainage_basins/greenland_basins_polarstereo.shp'
-    regions=gpd.read_file(regions)
-
-    regions_dissolve = regions.dissolve(by='subregion')
-
-
-    # Perform conversion
-    a = assign_regions(infile, regions)
-
+    return gdf    

src/griml/test/process_cli.py

@@ -24,6 +24,8 @@ def parse_griml_arguments():
                         help='File path to ice margin for spatial filtering')
     parser.add_argument('-n', '--names_file', type=str, required=True, 
                         help='File path to placenames file for metadata population')
+    parser.add_argument('-r', '--regions_file', type=str, required=True, 
+                        help='File path to regions/drainage basin file for metadata population')                       
     parser.add_argument('-p', '--proj', type=str, default='EPSG:3413', 
                         required=False, help='Projection (of input and output)')
     parser.add_argument('-s', '--steps', type=str, default='1111', 
@@ -46,7 +48,7 @@ def check_dir(d):
         os.mkdir(d)
 
 
-def griml_process():
+def griml():
     '''Perform processing workflow'''
     args = parse_griml_arguments()
 
@@ -127,6 +129,6 @@ def griml_process():
         print('Reading from ' + src)
         print('Writing to ' + str(dest))
 
-        add_metadata(src, args.names_file, str(dest))
+        add_metadata(src, args.names_file, args.regions_file, str(dest))
 
     print('Finished')

src/griml/test/process_example.py

@@ -79,7 +79,8 @@
 print('Writing to ' + dest)
 
 infile_names = str(root_dir.joinpath('datasets/placenames/oqaasileriffik_placenames.shp'))
+infile_basins = str(root_dir.joinpath('datasets/drainage_basins/greenland_basins_polarstereo.shp'))
 
-add_metadata(src, infile_names, dest)
+add_metadata(src, infile_names, infile_basins, dest)
 
 print('Finished')