Added script to generate a list of valid tiles

2.combine_mask_and_fragmentation_tiles.py

+# -*- coding: utf-8 -*-
+"""
+Created on Thu Oct 19 16:25:58 2023
+
+@author: no67wuwu
+
+
+work: combine the rasters to get the final fragmentation with land
+
+"""
+#%%
+import sys
+sys.path.insert(0,r"I:\biocon\Emmanuel_Oceguera\projects\2023_03_NaturaConnect\tools")
+import MacPyver as mp
+#%%
+import os
+from glob import glob
+import numpy as np
+
+frag_path = r"S:\Emmanuel_OcegueraConchas\fragmentation_estonia_test\frag_raster"
+land_path = r"S:\Emmanuel_OcegueraConchas\fragmentation_estonia_test\land_raster"
+out_path = r"S:\Emmanuel_OcegueraConchas\fragmentation_estonia_test\frag_and_land"
+
+# Get a list of tile filenames
+tiles = [x[-15:] for x in glob(frag_path + os.sep + '*.tif')]
+
+for t in tiles:
+    frag_p = frag_path + os.sep + 'frag_tile_' + t
+    land_p = land_path + os.sep + 'mask_tile_' + t
+    
+    frag = mp.raster.tiff.read_tif(frag_p)
+    land = mp.raster.tiff.read_tif(land_p)
+    
+    out = np.where((frag==9) & (land==1), 9, land)
+    
+    mp.raster.tiff.write_tif(frag_p, out_path + os.sep + 'lf_comb_' + t, out, 6, nodata=0, option="COMPRESS=DEFLATE")
+
+#%%
+# # Import necessary libraries
+# import os
+# from glob import glob
+# import numpy as np
+
+# # Define the paths for input rasters and output directory
+# frag_path = r"S:\Emmanuel_OcegueraConchas\Fragmentation\frag_raster"
+# land_path = r"S:\Emmanuel_OcegueraConchas\Fragmentation\land_raster"
+# out_path = r"S:\Emmanuel_OcegueraConchas\Fragmentation\frag_land"
+
+# # Get a list of tile filenames
+# tiles_2 = [os.path.basename(x) for x in glob(os.path.join(frag_path, '*.tif'))]
+
+# # Loop through the tiles and combine the rasters
+# for t in tiles:
+#     frag_p = os.path.join(frag_path, 'frag_tile_' + t)
+#     land_p = os.path.join(land_path, 'mask_tile_' + t)
+#     out_p = os.path.join(out_path, 'lf_comb_' + t)
+
+#     # Read the frag and land rasters
+#     frag = mp.raster.tiff.read_tif(frag_p)
+#     land = mp.raster.tiff.read_tif(land_p)
+
+#     # Combine the rasters
+#     out = np.where((frag == 9) & (land == 1), 9, land)
+
+#     # Write the combined raster to the output directory
+#     mp.raster.tiff.write_tif(frag_p, out_p, out, 6, nodata=0, option="COMPRESS=DEFLATE")

3.generate_list_valid_tiles.py

+# -*- coding: utf-8 -*-
+"""
+Created on Mon Oct 23 16:05:56 2023
+
+@author: no67wuwu
+"""
+
+import os
+
+import subprocess
+
+from glob import glob
+
+
+# Define the function
+def get_stdout(cmd, verbose=False):
+    """
+    send command to the commandline and fetch the return
+    
+    oprion verbose: will also print the return
+    
+    from http://blog.kagesenshi.org/2008/02/teeing-python-subprocesspopen-output.html
+    """
+    p = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+    stdout = []
+    while True:
+        line = p.stdout.readline()
+        line = line.decode('utf-8') # Decode the bytes into a string
+        line = line.replace('\n','').replace('\r','')
+        if line != '':
+            stdout.append(line)
+        if verbose:
+            print(line),
+        if line == '' and p.poll() != None: #p.poll is checking if the process is still running 
+                                            #is it is running it returns None
+            break
+    return stdout
+
+# Define the pathe where all the combined files are
+# path = r'S:\Emmanuel_OcegueraConchas\Fragmentation\frag_and_land\*.tif'
+path = r"S:\Emmanuel_OcegueraConchas\fragmentation_estonia_test\frag_and_land\*.tif"
+
+# get the list of all the files
+files = glob(path)
+
+# Define the gdal command 
+cmd = 'gdalinfo -stats %s'
+
+# Open a text file in writing modus. This file will be used to store the paths of the tif files that meet cetain criteria
+vrt_imgs = open(r'S:\Emmanuel_OcegueraConchas\fragmentation_estonia_test\valid_tiles.txt', 'w')
+
+for f in files:
+    stats = get_stdout(cmd %f)
+    if not stats[0].startswith('ERROR'):
+        vrt_imgs.write(f+'\n')
+    else:
+        print ('not considered: %s' %f.split(os.sep)[-1])
+        
+vrt_imgs.close()