added some verbose option

copro/scripts/postprocessing/avg_over_time.py

@@ -13,11 +13,12 @@
 @click.option('-c', '--column', help='column name', default='chance_of_conflict', type=str)
 @click.option('--geojson/--no-geojson', help='save output to geojson or not', default=False)
 @click.option('--png/--no-png', help='save output to png or not', default=True)
+@click.option('--verbose/--no-verbose', help='verbose on/off', default=False)
 @click.argument('input_dir', type=click.Path())
 @click.argument('output_dir',type=click.Path())
 @click.argument('selected_polygons', type=click.Path())
 
-def main(input_dir=None, output_dir=None, selected_polygons=None, start_year=None, end_year=None, geojson=None, png=None, column=None):
+def main(input_dir=None, output_dir=None, selected_polygons=None, start_year=None, end_year=None, geojson=None, png=None, column=None, verbose=None):
     """Post-processing script to calculate average model output over a user-specifeid period or all output geojson-files.
     """    
 
@@ -50,7 +51,7 @@ def main(input_dir=None, output_dir=None, selected_polygons=None, start_year=Non
             # if the year-suffix of geojson-file matches year in period, add to list
             year = int(str(str(os.path.basename(fo)).rsplit('.')[0]).rsplit('_')[-1])
             if year in period:
-                print('adding to selection')
+                if verbose: print('adding to selection')
                 selected_files.append(fo)
     # if not end/start time is specified, use all geojson-files in input-dir
     else:
@@ -65,7 +66,7 @@ def main(input_dir=None, output_dir=None, selected_polygons=None, start_year=Non
     # go through all geojson-files left over after selection step
     for geojson in selected_files:
         # read files and convert to datatrame
-        click.echo('reading file {}'.format(geojson))
+        if verbose: click.echo('reading file {}'.format(geojson))
         gdf = gpd.read_file(geojson, driver='GeoJSON')
         df = pd.DataFrame(gdf)
         # append to dataframe 
@@ -76,7 +77,8 @@ def main(input_dir=None, output_dir=None, selected_polygons=None, start_year=Non
     y_out = pd.DataFrame()
     # get all unique IDs of polygons
     y_out['ID'] = y_df.ID.unique()
-    if column = 'chance_of_conflict'
+    click.echo('reading from column {}'.format(column))
+    if column == 'chance_of_conflict':
         # add number of predictiosn made over all selected years
         y_out = pd.merge(y_out, y_df.nr_predictions.groupby(y_df.ID).sum().to_frame(), on='ID')
         # add number of predicted conflicts over all selected years
@@ -99,8 +101,8 @@ def main(input_dir=None, output_dir=None, selected_polygons=None, start_year=Non
 
     # if specified, save as geojson-file to output-dir
     if geojson:
-        click.echo('saving to {}'.format(os.path.abspath(os.path.join(output_dir, 'merged_output_{}.geojson'.format(suffix)))))
-        gdf_out.to_file(os.path.abspath(os.path.join(output_dir, 'merged_output_{}.geojson'.format(suffix))), driver='GeoJSON')
+        click.echo('saving to {}'.format(os.path.abspath(os.path.join(output_dir, '{}_merged_{}.geojson'.format(column, suffix)))))
+        gdf_out.to_file(os.path.abspath(os.path.join(output_dir, '{}_merged_{}.geojson'.format(column, suffix))), driver='GeoJSON')
 
     # if specified, save as png-file to output-dir
     if png:
@@ -111,8 +113,8 @@ def main(input_dir=None, output_dir=None, selected_polygons=None, start_year=Non
                         legend=True,
                         legend_kwds={'label': column, 'orientation': "vertical"})
 
-        click.echo('saving to {}'.format(os.path.abspath(os.path.join(output_dir, 'merged_output_{}.png'.format(suffix)))))
-        plt.savefig(os.path.abspath(os.path.join(output_dir, 'merged_output_{}.png'.format(suffix))), dpi=300, bbox_inches='tight')
+        click.echo('saving to {}'.format(os.path.abspath(os.path.join(output_dir, '{}_merged_{}.png'.format(column, suffix)))))
+        plt.savefig(os.path.abspath(os.path.join(output_dir, '{}_merged_{}.png'.format(column, suffix))), dpi=300, bbox_inches='tight')
         plt.close()
 
 if __name__ == '__main__':

copro/scripts/postprocessing/geojson2gif.py

@@ -47,12 +47,12 @@ def main(input_dir=None, column=None, color_map=None, minimum_value=None, maximu
 
         ax.set_title(str(year))
         click.echo('saving plot to png-folder')
-        plt.savefig(os.path.join(png_dir, 'plt{}.png'.format(year)), dpi=300, bbox_inches='tight')
+        plt.savefig(os.path.join(png_dir, 'plt_{}_{}.png'.format(column, year)), dpi=300, bbox_inches='tight')
 
     click.echo('creating GIF from saved plots')
     # based on: https://pillow.readthedocs.io/en/stable/handbook/image-file-formats.html#gif
-    fp_in = os.path.join(png_dir, '*.png')
-    fp_out = os.path.join(output_dir, 'conflict_over_time.gif')
+    fp_in = os.path.join(png_dir, '*_{}_{}.png'.format(column, year))
+    fp_out = os.path.join(output_dir, '{}_over_time.gif'.format(column))
     img, *imgs = [Image.open(f) for f in sorted(glob.glob(fp_in))]
     img.save(fp=fp_out, format='GIF', append_images=imgs, save_all=True, duration=500, loop=0)
 

copro/scripts/postprocessing/plot_prediction_dev.py

@@ -10,10 +10,11 @@
 @click.option('-id', '--polygon-id', multiple=True, type=int)
 @click.option('-c', '--column', help='column name', default='chance_of_conflict', type=str)
 @click.option('-t', '--title', help='title for plot and file_object name', type=str)
+@click.option('--verbose/--no-verbose', help='verbose on/off', default=False)
 @click.argument('input-dir', type=click.Path())
 @click.argument('output-dir', type=click.Path())
 
-def main(input_dir=None, polygon_id=None, column=None, title=None, output_dir=None):
+def main(input_dir=None, polygon_id=None, column=None, title=None, output_dir=None, verbose=None):
     """Quick and dirty function to plot the develoment of a column in the outputted geojson-files over time.
     """
 
@@ -32,15 +33,15 @@ def main(input_dir=None, polygon_id=None, column=None, title=None, output_dir=No
 
     print('retrieving values from column {}'.format(column))
     for geojson in all_files:
-        print('reading file {}'.format(geojson))
+        if verbose: print('reading file {}'.format(geojson))
         gdf = gpd.read_file(geojson, driver='GeoJSON')
         df = pd.DataFrame(gdf.drop(columns='geometry'))
 
         year = int(str(str(os.path.basename(geojson)).rsplit('.')[0]).rsplit('_')[-1])
         years.append(year)
 
         for idx in polygon_id:
-            print('sampling ID {}'.format(idx))
+            if verbose: print('sampling ID {}'.format(idx))
 
             if idx not in df.ID.values: 
                 print('WARNING: ID {} is not in {} - NaN set'.format(idx, geojson))
@@ -59,7 +60,7 @@ def main(input_dir=None, polygon_id=None, column=None, title=None, output_dir=No
         click.echo('creating output folder {}'.format(os.path.abspath(output_dir)))
         os.makedirs(os.path.abspath(output_dir))
 
-    df.to_csv(os.path.abspath(os.path.join(output_dir, 'prediction_dev.csv')))
+    df.to_csv(os.path.abspath(os.path.join(output_dir, '{}_dev.csv'.format(column))))
 
     fig, axes = plt.subplots(nrows=len(polygon_id), ncols=1, sharex=True)
     df.plot(subplots=True, ax=axes)
@@ -68,7 +69,7 @@ def main(input_dir=None, polygon_id=None, column=None, title=None, output_dir=No
         ax.set_yticks(np.arange(0, 1.1, 1))
     if title != None:
         ax.set_title(str(title))
-    plt.savefig(os.path.abspath(os.path.join(output_dir, 'prediction_dev.png')), dpi=300, bbox_inches='tight')
+    plt.savefig(os.path.abspath(os.path.join(output_dir, '{}_dev.png'.format(column))), dpi=300, bbox_inches='tight')
 
 if __name__ == '__main__':