Does not crop the classified las file

README.md

@@ -63,7 +63,7 @@ python las_outputs.py param-files/survey-1*.yaml param-files/survey-2*.yaml
 Example usage:
 
 ```
-C:\Python27\ArcGIS10.5\python generate_heatmaps.py param-files\survey-2*.yaml
+C:/Python27/ArcGIS10.4/python generate_heatmaps.py param-files/survey-2*.yaml
 
 ```
 
@@ -76,29 +76,5 @@ C:\Python27\ArcGIS10.5\python generate_heatmaps.py param-files\survey-2*.yaml
 Example usage:
 
 ```
-C:\Python27\ArcGIS10.5\python plot_heatmaps.py param-files\survey-2-avoca.yaml
+C:/Python27/ArcGIS10.4/python plot_heatmaps.py param-files/survey-2-avoca.yaml
-```
-
-### 7. Export 0.7 m contour for DSAS trend analysis
-`extract_contours.py` extracts a predefined contour (say 0.7 m AHD) and outputs it in a format suitable for DSAS shoreline trend analysis.
-
-Example usage:
-```
-python extract_contours.py
-```
-
-## polyline_to_points.py
-This script interpolates points along transects in a shapefile.
-
-Example usage:
-
-```
-# Extract points at default spacing (1m)
-$ python polyline_to_points.py path/to/shp
-
-# Extract points at 5m increments
-$ python polyline_to_points.py -s 5 path/to/shp
-
-# Use profile names from field "ProfileID" in the attribute table at 1 m spacing
-$ python polyline_to_points.py -f ProfileID -s 1 path/to/shp
 ```

generate_heatmaps.py

@@ -72,10 +72,10 @@ def process(yaml_name):
         raise ValueError('No previous survey date provided')
 
     # Set paths for raster files
-    current_raster = os.path.join(input_tif_dir, base_name + '_DEM.tif')
+    current_raster = os.path.join(input_tif_dir, base_name + '.tif')
     previous_base_name = re.sub('\d+', previous_date, base_name)
-    previous_raster = os.path.join(input_tif_dir, previous_base_name + '_DEM.tif')
+    previous_raster = os.path.join(input_tif_dir, previous_base_name + '.tif')
-    heatmap_raster = os.path.join(output_tif_dir, base_name + '_heatmap.tif')
+    heatmap_raster = os.path.join(output_tif_dir, base_name + '.tif')
 
     print('processing {}'.format(beach))
 

las_manipulation.py

@@ -407,7 +407,7 @@ def process(yaml_file):
     print('Interpolating to grid...')
     xyz_name = os.path.join(tmp_dir, las_basename + '.xyz')
     call_lastools('blast2dem', input=las_classified_name, output=xyz_name,
-                  args=['-step', 1], verbose=False)
+                  args=['-step', 0.1], verbose=False)
 
     # Make runup clipping mask from gridded point cloud
     print('Calculating runup clipping mask...')

las_outputs.py

@@ -129,7 +129,7 @@ def plot_profiles(profile_name, csv_output_dir, graph_loc, ch_limits, delta_vol,
                     backgroundcolor='#ffffff', linespacing=1.5)
 
     ax.legend(edgecolor='none', facecolor='#ffffff', fontsize=9, labelspacing=1)
-              loc='lower left', bbox_to_anchor=(1.02,0))
+
     ax.xaxis.set_minor_locator(MultipleLocator(5))
     ax.yaxis.set_minor_locator(MultipleLocator(0.5))
     ax.xaxis.grid(True, which='minor', color='k', linewidth=0.5, alpha=0.3)
@@ -190,14 +190,15 @@ def calculate_volumes(profile_name, current_survey_date, previous_survey_date,
     volumes = volumes.sort_index()
     volumes.to_csv(csv_vol)
 
-    # Get most recent volume difference for current profile
-    current_date_idx = volumes.columns.get_loc('Volume_' + current_survey_date)
-    previous_date_idx = volumes.columns.get_loc('Volume_' + previous_survey_date)
 
-    if previous_date_idx < 0:
+
+    if previous_survey_date=="nan":
         # Return None if there is only one survey
         delta_vol = None
     else:
+        # Get most recent volume difference for current profile
+        current_date_idx = volumes.columns.get_loc('Volume_' + current_survey_date)
+        previous_date_idx = volumes.columns.get_loc('Volume_' + previous_survey_date)
         previous_vol = volumes.loc[profile_name][previous_date_idx]
         current_vol = volumes.loc[profile_name][current_date_idx]
         delta_vol = current_vol - previous_vol
@@ -239,32 +240,11 @@ def process(yaml_file):
     # Get name of swash cropping polygon
     crop_swash_poly = os.path.join(shp_swash_dir, las_basename + '.shp')
 
-    # Crop point cloud to swash boundary
-    print('Cropping swash...')
-    las_data = call_lastools('lasclip', input=input_las, output='-stdout',
-                             args=['-poly', crop_swash_poly], verbose=False)
-
-    # Export classified, clipped las for delivery to client
-    las_name = os.path.join(output_las_dir, las_basename + '.las')
-    with open (las_name, 'wb') as f:
-        f.write(las_data)
-
-    # Apply sea-side clipping polygon
-    print('Cropping back of beach...')
-    las_data = call_lastools('lasclip', input=las_data, output='-stdout',
-                             args=['-poly', crop_heatmap_poly], verbose=False)
-
-
-    # Create clipping polygon for heatmap raster
-    print('Creating heat map cropping polygon...')
-    shp_name = os.path.join(output_poly_dir, las_basename + '.shp')
-    call_lastools('lasboundary', input=las_data, output=shp_name, verbose=False)
-
     # Make a raster from point cloud
     print('Creating heat map raster...')
-    tif_name = os.path.join(output_tif_dir, las_basename + '_DEM.tif')
+    tif_name = os.path.join(output_tif_dir, las_basename + '.tif')
-    call_lastools('las2dem', input=las_data, output=tif_name,
+    call_lastools('blast2dem', input=input_las, output=tif_name,
-                  args=['-step', 1, '-keep_class', 2], verbose=False)
+                  args=['-step', 0.1, '-keep_class', 2], verbose=True)
     # IF THIS STEP ISN'T WORKING:
         # might mean there are no data lines
         # trying running with args=['-step', 1, '-keep_class', 2, '-rescale', 0.001,0.001,0.001]
@@ -274,7 +254,7 @@ def process(yaml_file):
     # Extract elevations along profiles from triangulated surface
     print('Extracting profile elevations...')
     df = extract_pts(
-        las_data,
+        input_las,
         cp_csv,
         survey_date,
         beach,

plot_heatmaps.py

@@ -70,7 +70,7 @@ def process(yaml_name):
         raise ValueError('No previous survey date provided')
 
     # Set paths for raster files
-    heatmap_raster = os.path.join(input_tif_dir, base_name + '_heatmap.tif')
+    heatmap_raster = os.path.join(input_tif_dir, base_name + '.tif')
 
     print('processing {}'.format(beach))
     mxd = arcpy.mapping.MapDocument(mxd_name)

polyline_to_points.py

@@ -1,92 +0,0 @@
-"""polyline_to_points.py
-Extract interpolated points along transects in a shapefile.
-
-D. Howe
-d.howe@wrl.unsw.edu.au
-2020-02-19
-"""
-import sys
-import argparse
-import numpy as np
-import pandas as pd
-import geopandas as gpd
-from shapely.geometry import LineString
-
-
-def extract(shp_path, spacing=1, field=None):
-
-    rows = []
-    shp = gpd.read_file(shp_path)
-
-    if field is None:
-        # Assume profile name is second field in shapefile
-        field = shp.columns[1]
-
-    for i, line in shp.iterrows():
-        g = line.geometry
-        chainages = np.arange(0, g.length, step=spacing)
-        for chainage in chainages:
-            easting, northing = g.interpolate(chainage).xy
-
-            row = {
-                'ProfileNum': line[field],
-                'Easting': easting[0],
-                'Northing': northing[0],
-                'Chainage': chainage,
-            }
-            rows.append(row)
-
-    # Create output dataframe
-    df = pd.DataFrame(rows)
-
-    # Re-order columns
-    df = df[['ProfileNum', 'Easting', 'Northing', 'Chainage']]
-
-    # Export to csv
-    csv_path = shp_path.replace('.shp', '.csv')
-    df.to_csv(csv_path, index=False)
-
-
-def main():
-    example_text = """examples:
-    # Extract points at default spacing (1m)
-    $ python polyline_to_points.py path/to/shp
-
-    # Extract points at 5m increments
-    $ python polyline_to_points.py -s 5 path/to/shp
-
-    # Use profile names from field "ProfileID" in the attribute table
-    $ python polyline_to_points.py -f ProfileID path/to/shp
-    """
-    # Set up command line arguments
-    parser = argparse.ArgumentParser(
-        epilog=example_text,
-        formatter_class=argparse.RawDescriptionHelpFormatter)
-    parser.add_argument('shp_path',
-                        metavar='SHAPEFILE',
-                        help='path to input shapefile')
-    parser.add_argument('-s',
-                        '--spacing',
-                        metavar='SPACING',
-                        default=1,
-                        type=int,
-                        help='space between points (default=1)')
-    parser.add_argument('-f',
-                        '--field',
-                        metavar='FIELDNAME',
-                        help='profile field name in attribute table')
-
-    # Print usage if no arguments are provided
-    if len(sys.argv) == 1:
-        parser.print_help(sys.stderr)
-        sys.exit(1)
-
-    # Parse arguments
-    args = parser.parse_args()
-
-    # Combine images
-    extract(**vars(args))
-
-
-if __name__ == '__main__':
-    main()