diff --git a/algorithm_config.yaml b/algorithm_config.yaml
index 2c2924ed90bb465ae47ed2e27ae6f379b83385ab..2527eb1add4c955393c859058b9f7599223747c6 100644
--- a/algorithm_config.yaml
+++ b/algorithm_config.yaml
@@ -1,6 +1,6 @@
description: Estimates canopy height from InSAR coherence and LiDAR data
algo_name: ich
-version: 0.5.2
+version: 0.5.3
environment: ubuntu
repository_url: https://repo.maap-project.org/bnarayanarao/insar_forest_height.git
docker_url: mas.maap-project.org/root/maap-workspaces/base_images/python:v4.1.0
@@ -27,3 +27,5 @@ inputs:
download: False
- name: filter
download: False
+ - name: minshots
+ download: False
diff --git a/ich.sh b/ich.sh
index 2a7c5a6c90140697488f0ee5240e1df58cefd4a5..256caedd4e86bf325dcdaa2999b2c07f3dfb864b 100644
--- a/ich.sh
+++ b/ich.sh
@@ -23,6 +23,7 @@ options=()
[[ "${5:-}" != "-" ]] && options+=("--algorithm" "${5}")
[[ "${6:-}" != "-" ]] && options+=("--overlap" "${6}")
[[ "${7:-}" != "-" ]] && options+=("--filter" "${7}")
+[[ "${7:-}" != "-" ]] && options+=("--minshots" "${8}")
# Run the Python script with the determined options
${ich_py} --correlationFile "${correlationFile}" --cal_ht "${cal_ht}" "${options[@]}"
\ No newline at end of file
diff --git a/src/ich/InSAR_canopy_height.py b/src/ich/InSAR_canopy_height.py
index aff3a140fb42b0abb676662b129ee8ec96f4aff8..92ea0bfcb88f2da19f31ebc5ba9787351206d143 100644
--- a/src/ich/InSAR_canopy_height.py
+++ b/src/ich/InSAR_canopy_height.py
@@ -5,22 +5,11 @@ Created on Thu Dec 27 14:40:29 2023
@author: Narayanarao
"""
+__version__ = "0.5.3"
-import argparse,os,sys,warnings,time
-
-import numpy as np, pandas as pd
+import argparse,warnings
+import numpy as np
from osgeo import gdal
-from scipy import interpolate
-import matplotlib.pyplot as plt
-from matplotlib import cm
-from matplotlib.colors import Normalize
-
-from scipy.stats import linregress
-from skimage.util.shape import view_as_blocks
-from mpl_toolkits.axes_grid1 import make_axes_locatable
-from scipy.interpolate import griddata
-from tqdm import tqdm
-from scipy.interpolate import interpn
gdal.UseExceptions()
warnings.filterwarnings('ignore')
warnings.filterwarnings('error')
@@ -35,6 +24,13 @@ from args_in import rvog_inverse
##########################################################################
parser = argparse.ArgumentParser()
+parser.add_argument(
+ "--version",
+ action="version",
+ version=f"%(prog)s {__version__}",
+ help="Show version information"
+)
+
parser.add_argument("-c", "--correlationFile", dest = "corFile", help="correlation file [0,1]")
parser.add_argument("-l", "--cal_ht", dest = "lidarFile", help="Calibration height file e.g. LiDAR heights in (m)")
parser.add_argument("-ll", "--lower_limit",dest ="htl", default = None ,help="lower limit of canopy height (m)", type=int)
@@ -43,7 +39,8 @@ parser.add_argument("-w", "--window",dest = "window_size", default = 10, help="c
parser.add_argument("-val", "--validation",dest = "validation", default = 0, help="fraction to split cross validation", type=float)
parser.add_argument("-al", "--algorithm",dest = "algo", default = 1, help="Algorithm Type", type=int)
parser.add_argument("-ol", "--overlap",dest = "window_overlap", default = 0, help="window overlap fraction", type=float)
-parser.add_argument("-f", "--filter",dest = "filt_parm", default = 0, help="filter/smoothen the calibation parameters", type=int)
+parser.add_argument("-f", "--filter",dest = "filt_parm", default = 0, help="filter/smoothen the calibration parameters", type=int)
+parser.add_argument("-ms", "--minshots",dest = "minshots", default = 3, help="Minimum number of GEDI shots per window", type=int)
args = parser.parse_args()
diff --git a/src/ich/algo.py b/src/ich/algo.py
index 8497b4c6b244dacc1997c14e8f0cf65310ac9f9a..c406e13439a725b7b77729992b944b2db08aaf53 100644
--- a/src/ich/algo.py
+++ b/src/ich/algo.py
@@ -65,7 +65,7 @@ def arc_sinc_fast(x, c_param):
#################################################
def process_st_window(win, temp_cor, temp_lidar, args):
- parm = cal_(temp_cor, temp_lidar, args.htl, args.htg)
+ parm = cal_(temp_cor, temp_lidar, args.htl, args.htg, args.minshots)
mask = temp_lidar.copy()
mask[~np.isnan(mask)] = 1
@@ -169,7 +169,7 @@ def arc_sinc(x, c_param):
# return y
return y
-def cal_(temp_cor, temp_gedi, htl, htg):
+def cal_(temp_cor, temp_gedi, htl, htg,minshots=3):
try:
# temp_cor = cor.copy()
# temp_gedi = gedi.copy()
@@ -214,9 +214,12 @@ def cal_(temp_cor, temp_gedi, htl, htg):
if tempdf.empty:
return [0, 0, 0, 0, 0, 0]
elif nn>6:
- tempdf_coarse = tempdf[tempdf['N'] > 3].sort_values(by=['rmse'], ascending=True)
- tempdf_coarse = tempdf_coarse[tempdf_coarse['inv'] > 0.5]
-
+ if minshots>1:
+ tempdf_coarse = tempdf[tempdf['N'] >= minshots].sort_values(by=['rmse'], ascending=True)
+ tempdf_coarse = tempdf_coarse[tempdf_coarse['inv'] > 0.5]
+ else:
+ tempdf_coarse = tempdf.sort_values(by=['rmse'], ascending=True)
+
sCoarse = np.round(tempdf_coarse.iloc[0]['S'], 2)
cCoarse = np.round(tempdf_coarse.iloc[0]['C'], 2)
@@ -249,7 +252,10 @@ def cal_(temp_cor, temp_gedi, htl, htg):
del result
tempdf.dropna(subset=['rmse'], inplace=True)
# if nn>6:
- tempdf = tempdf[tempdf['N'] > 3].sort_values(by=['rmse'], ascending=True)
+ if minshots>1:
+ tempdf = tempdf[tempdf['N'] >= minshots].sort_values(by=['rmse'], ascending=True)
+ else:
+ tempdf = tempdf.sort_values(by=['rmse'], ascending=True)
if tempdf.empty and sCoarse==0:
return [0, 0, 0, 0, 0,0]
diff --git a/src/ich/args_in.py b/src/ich/args_in.py
index 549d4a6f0fd578b010980ae5e114b250134f2147..db7c82659d387b02f64ca8466c18dc82619ceaa5 100644
--- a/src/ich/args_in.py
+++ b/src/ich/args_in.py
@@ -49,7 +49,7 @@ def rvog_inverse(args):
try:
t0 = time.time()
- print( "-corFile {} -lidarFile {} -htl {} -htg {} -window_size {} -validation {} -algo {} -window_overlap {} -filt_parm {}".format(
+ print( "-corFile {} -lidarFile {} -htl {} -htg {} -window_size {} -validation {} -algo {} -window_overlap {} -filt_parm {} -minshots {}".format(
args.corFile,
args.lidarFile,
args.htl,
@@ -58,7 +58,8 @@ def rvog_inverse(args):
args.validation,
args.algo,
args.window_overlap,
- args.filt_parm
+ args.filt_parm,
+ args.minshots
))
lidar_ht = read_bin(args.lidarFile)