Add locks to fix racing conditions

opendm/dem/commands.py

@@ -6,6 +6,7 @@ import math
 import time
 import shutil
 import functools
+import threading
 from joblib import delayed, Parallel
 from opendm.system import run
 from opendm import point_cloud
@@ -314,7 +315,7 @@ def median_smoothing(geotiff_path, output_path, smoothing_iterations=1, window_s
     log.ODM_INFO('Starting smoothing...')
 
     # imgout needs to be 'w+' (write/read) to work in place for all the iterations but the first
-    with rasterio.open(geotiff_path) as img, rasterio.open(output_path, 'w+', BIGTIFF="IF_SAFER", **img.profile) as imgout:
+    with rasterio.open(geotiff_path, num_threads=num_workers,) as img, rasterio.open(output_path, "w+", BIGTIFF="IF_SAFER", num_threds=num_workers, **img.profile) as imgout:
         nodata = img.nodatavals[0]
         dtype = img.dtypes[0]
         shape = img.shape
@@ -329,19 +330,26 @@ def median_smoothing(geotiff_path, output_path, smoothing_iterations=1, window_s
 
             filter = functools.partial(ndimage.median_filter, size=9, output=dtype, mode='nearest')
 
+            # We cannot read/write to the same file from multiple threads without causing race conditions. 
+            # To safely read/write from multiple threads, we use a lock to protect the DatasetReader/Writer.
+            read_lock = threading.Lock()
+            write_lock = threading.Lock()
+
             # threading backend and GIL released filter are important for memory efficiency and multi-core performance
-            Parallel(n_jobs=num_workers, backend='threading')(delayed(window_filter_2d)(img, imgout, nodata , window, 9, filter) for window in windows)
+            Parallel(n_jobs=num_workers, backend='threading')(delayed(window_filter_2d)(img, imgout, nodata , window, 9, filter, read_lock, write_lock) for window in windows)
 
             # After the first iteration, modifications are done in place
             if i == 0:
                 img = imgout
+                # We now read and write to the same file
+                read_lock = write_lock
 
 
     log.ODM_INFO('Completed smoothing to create %s in %s' % (output_path, datetime.now() - start))
     return output_path
 
 
-def window_filter_2d(img, imgout, nodata, window, kernel_size, filter):
+def window_filter_2d(img, imgout, nodata, window, kernel_size, filter, read_lock, write_lock):
     """
     Apply a filter to dem within a window, expects to work with kernal based filters
 
@@ -350,6 +358,8 @@ def window_filter_2d(img, imgout, nodata, window, kernel_size, filter):
     :param window: the window to apply the filter, should be a list contains row start, col_start, row_end, col_end
     :param kernel_size: the size of the kernel for the filter, works with odd numbers, need to test if it works with even numbers
     :param filter: the filter function which takes a 2d array as input and filter results as output.
+    :param read_lock: threading lock for the read operation
+    :param write_lock: threading lock for the write operation
     """
     shape = img.shape[:2]
     if window[0] < 0 or window[1] < 0 or window[2] > shape[0] or window[3] > shape[1]:
@@ -360,7 +370,8 @@ def window_filter_2d(img, imgout, nodata, window, kernel_size, filter):
     width = expanded_window[3] - expanded_window[1]
     height = expanded_window[2] - expanded_window[0]
     rasterio_window = rasterio.windows.Window(col_off=expanded_window[1], row_off=expanded_window[0], width=width, height=height)
-    win_arr = img.read(indexes=1, window=rasterio_window)
+    with read_lock:
+        win_arr = img.read(indexes=1, window=rasterio_window)
 
     # Should have a better way to handle nodata, similar to the way the filter algorithms handle the border (reflection, nearest, interpolation, etc).
     # For now will follow the old approach to guarantee identical outputs
@@ -373,7 +384,8 @@ def window_filter_2d(img, imgout, nodata, window, kernel_size, filter):
     width = window[3] - window[1]
     height = window[2] - window[0]
     rasterio_window = rasterio.windows.Window(col_off=window[1], row_off=window[0], width=width, height=height)
-    imgout.write(win_arr, indexes=1, window=rasterio_window)
+    with write_lock:
+        imgout.write(win_arr, indexes=1, window=rasterio_window)
 
 
 def get_dem_radius_steps(stats_file, steps, resolution, multiplier = 1.0):