Add plotting script for correction files

utils/plot_correction_files.py

@@ -0,0 +1,140 @@
+import numpy as np
+from matplotlib import pyplot as plt
+import glob
+import re
+import math
+import rasterio as rio
+import argparse
+import os
+
+"""
+This script plots the original interferogram, the corresponding correction file, 
+and the resulting corrected interferogram from a PyRate directory with already,
+processed data. directories are given as user arguments to the script, and the
+number of plots is determined by a number range given by user. 
+
+Usage: python3 plot_correction_files.py <IFG_DIR> <CORRECTION_DIR> <CORRECTED_DIR> <SAVE_DIR> <FIRST_IFG> <LAST_IFG>
+
+Command-line arguments:
+           IFG_DIR       - full path to uncorrected interferograms in PyRate.
+    CORRECTION_DIR       - full path to correction files in PyRate.
+     CORRECTED_DIR       - full path to corrected interferograms in PyRate.
+          SAVE_DIR       - full path to directory where images will be saved (needs to exist).
+         FIRST_IFG       - first IFG in range of IFGs to plot (e.g. 1 to start plotting at 1st IFG in directory).
+          LAST_IFG       - last IFG in range of IFGs to plot (e.g. 37 will plot up until the 37th IFG in directory).
+"""
+
+# Arguments
+parser = argparse.ArgumentParser(description="Script to plot correction files with uncorrected and corrected interferogram")
+parser.add_argument("IFG_DIR", type=str, help="full path to uncorrected interferograms in PyRate")
+parser.add_argument("CORRECTION_FILE_DIR", type=str, help="full path to correction files in PyRate")
+parser.add_argument("CORRECTED_IFG_DIR", type=str, help="full path to corrected interferograms in PyRate")
+parser.add_argument("SAVE_DIR", type=str, help="full path to directory where images will be saved")
+parser.add_argument("FIRST_IFG", type=int, help="first IFG in range of IFGs to plot (e.g. 1 to start plotting at first IFG in directory)")
+parser.add_argument("LAST_IFG", type=int, help="last IFG in range of IFGs to plot (e.g. 37 will plot up until the 37th IFG in directory)")
+args = parser.parse_args()
+
+
+
+# Directories and variable from user agruments
+ifg_dir = os.path.abspath(args.IFG_DIR)
+corr_dir = os.path.abspath(args.CORRECTION_FILE_DIR)
+tempml_dir = os.path.abspath(args.CORRECTED_IFG_DIR)
+save_dir = os.path.abspath(args.SAVE_DIR)
+
+first_ifg_num = args.FIRST_IFG - 1
+last_ifg_num = args.LAST_IFG - 1
+
+
+# Create Lists
+ifg_list = []
+for file in glob.glob(f'{ifg_dir}/*ifg.tif'):
+    ifg_list.append(file)
+
+corr_list = []
+for file in glob.glob(f'{corr_dir}/*.npy'):
+    corr_list.append(file)
+
+tempml_list = []
+for file in glob.glob(f'{tempml_dir}/*ifg.tif'):
+    tempml_list.append(file)
+
+# Sort
+ifg_list.sort()
+corr_list.sort()
+tempml_list.sort()
+
+for i in range(first_ifg_num, last_ifg_num + 1):    
+
+    # Read data
+    with rio.open(ifg_list[i]) as src:
+        ifg = src.read(1)
+        ifg[ifg==0.0] = np.nan
+        mask = np.isnan(ifg)
+
+        # convert to mm 
+        ifg = ifg * 1000 * (0.0562356424 / (4 * math.pi))
+
+    corr =  np.load(corr_list[i])
+    corr[mask] = np.nan
+
+
+    with rio.open(tempml_list[i]) as src:
+        ifg_corr = src.read(1)
+
+    # Identify Date Pair
+    date_pair_list_ifg = re.findall(r'\d{8}-\d{8}', ifg_list[i])
+    date_pair_string_ifg = date_pair_list_ifg[0]
+
+    date_pair_list_corr = re.findall(r'\d{8}-\d{8}', corr_list[i])
+    date_pair_string_corr = date_pair_list_corr[0]
+
+    date_pair_list_ifgcorr = re.findall(r'\d{8}-\d{8}', tempml_list[i])
+    date_pair_string_ifgcorr = date_pair_list_ifgcorr[0]
+
+    # Check the Date-pairs are the same in case of mismatched files saved into the directories
+    if date_pair_string_ifg == date_pair_string_corr and date_pair_string_ifg == date_pair_string_ifgcorr:
+
+         print(f'\nPlotting for {date_pair_string_ifg}...\n')
+        pass
+
+    else:
+
+        print(f'\nERROR: Interferogram datepair mismatch at {date_pair_string_ifg}, check that directories have the same interferograms.\n')
+        break
+
+
+    # Plot
+    climit = 100
+    fig, ax = plt.subplots(1,3, figsize=(6, 3))
+
+    # IFG
+    s0 = ax[0].imshow(ifg-np.nanmedian(ifg), cmap='bwr', clim=(-1*climit, climit))
+    ax[0].set_axis_off()
+
+    # CORRECTION FILE
+    s1 =ax[1].imshow(corr-np.nanmedian(corr), cmap='bwr', clim=(-1*climit, climit))
+    ax[1].set_axis_off()
+
+    # IFG CORRECTED
+    s2 = ax[2].imshow(ifg_corr-np.nanmedian(ifg_corr), cmap='bwr', clim=(-1*climit,climit))
+    ax[2].set_axis_off()
+
+    # Extra
+    fig.colorbar(s0, ax=ax[0], location='bottom', label='mm')
+    fig.colorbar(s1, ax=ax[1], location='bottom', label='mm')
+    fig.colorbar(s2, ax=ax[2], location='bottom', label='mm')
+
+    fig.set_facecolor('grey')
+
+    fig.tight_layout()
+
+    # Title
+    ax[1].set_title(f'{date_pair_string_ifg}', fontsize=10, fontweight='bold')
+
+    plt.savefig(f'{save_dir}/{date_pair_string_ifg}.png', dpi=300)
+
+    plt.close()
+
+    i = i + 1
+