From 144f93569879425d510192040b773e55b9122c63 Mon Sep 17 00:00:00 2001
From: Dan Howe <d.howe@wrl.unsw.edu.au>
Date: Mon, 9 Jul 2018 10:05:25 +1000
Subject: [PATCH] Fix repeated shp extension

---
 las_manipulation.py        |  2 +-
 outputs_2017088_Survey2.py | 24 ++++++++++++++++++++----
 2 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/las_manipulation.py b/las_manipulation.py
index a35caf5..2739730 100644
--- a/las_manipulation.py
+++ b/las_manipulation.py
@@ -326,7 +326,7 @@ def polygon_wave_runup(xyz_1m, direction, shp_name, set_check_value, distance_ch
     # Export polygon as shapefile
     df = gpd.GeoDataFrame(geometry=[Polygon(for_shape)])
     df.crs = {'init': 'epsg:283{}'.format(zone), 'no_defs': True}
-    df.to_file(shp_name + '.shp', driver='ESRI Shapefile')
+    df.to_file(shp_name, driver='ESRI Shapefile')
 
     return None
 
diff --git a/outputs_2017088_Survey2.py b/outputs_2017088_Survey2.py
index 661d0b3..9de895c 100644
--- a/outputs_2017088_Survey2.py
+++ b/outputs_2017088_Survey2.py
@@ -23,6 +23,8 @@ import xlsxwriter
 import math
 from cycler import cycler
 
+from survey_tools import call_lastools
+
 ###############################################################################
 ########################## FIXED INPUTS #######################################
 ######### UNCOMMENT THIS SECTION IF YOU WANT TO DEFINE EACH INPUT INDIVIDUALLY ######################
@@ -359,17 +361,19 @@ def remove_temp_files(directory):
 
 ###############################################################################
 ########################### RUN CODE ##########################################
+input_file = 'Parameter Files/las-manipulation-survey-2.xlsx'
 params_file=pd.read_excel(input_file, sheet_name="PARAMS")
 
 for i in range(0, len(params_file)): #0, len(params_file)
     print("Starting to process %s" % params_file['Beach'][i])
     beach=params_file['Beach'][i]
     survey_date=params_file['SURVEY DATE'][i]
-    input_las5=params_file['INPUT LAS4'][i]
-    crop_swash_poly=params_file['CROP SWASH POLY'][i]
+    original_las=params_file['INPUT LAS'][i]
+    classified_las_dir=params_file['LAS CLASSIFIED FOLDER'][i]
+    shp_swash_dir=params_file['SHP SWASH FOLDER'][i]
     heatmap_crop_poly=params_file['HEATMAP CROP POLY'][i]
-    final_las = params_file['FINAL LAS'][i]
-    heatmap_las = params_file['HEATMAP LAS'][i]
+    final_las = params_file['LAS FINAL FOLDER'][i]
+    # heatmap_las = params_file['HEATMAP LAS'][i]
     zone_MGA=params_file['ZONE MGA'][i]
     output_poly_name=params_file['OUTPUT POLY NAME'][i]
     path_2_output_poly=params_file['PATH TO OUTPUT'][i]
@@ -383,7 +387,19 @@ for i in range(0, len(params_file)): #0, len(params_file)
     tmp_dir=params_file['TEMP DIR'][i]
     int_dir=params_file['INTERIM DIR'][i]
 
+    # Get base name of input las
+    las_basename = os.path.splitext(os.path.basename(original_las))[0]
+
+    # Get name of input point cloud
+    input_las = os.path.join(classified_las_dir, las_basename + '.las')
+
+    # Get name of swash cropping polygon
+    crop_swash_poly = os.path.join(shp_swash_dir, las_basename + '.shp')
+
     # crop and get the output las
+    las_data = call_lastools('lasclip', input=input_las, output='-stdout',
+                             args=['-poly', crop_swash_poly], verbose=False)
+
     crop_las(input_las5, crop_swash_poly, final_las, path_2_lastools)
 
     #now crop out the heatmap las