Optimize aligning

pygmtsar/pygmtsar/PRM_gmtsar.py

@@ -238,6 +238,8 @@ def resamp(self, repeatPRM, repeatSLC_tofile, interp, debug=False):
         if not isinstance(repeatPRM, PRM):
             raise Exception('Argument should be PRM class instance')
 
+        SLC_tmpname = os.path.split(repeatSLC_tofile)[-1] + '.tmp'
+
         pipe1 = os.pipe()
         os.write(pipe1[1], bytearray(repeatPRM.to_str(), 'utf8'))
         os.close(pipe1[1])
@@ -254,23 +256,24 @@ def resamp(self, repeatPRM, repeatSLC_tofile, interp, debug=False):
         #                     stderr=subprocess.PIPE, pass_fds=[pipe1[0], pipe2[1]],
         #                     cwd=cwd, encoding='utf8', shell=True)
         argv = ['resamp', f'/dev/stdin', f'/dev/fd/{pipe1[0]}',
-                f'/dev/fd/{pipe2[1]}', '/dev/stdout', str(interp)]
+                f'/dev/fd/{pipe2[1]}', SLC_tmpname, str(interp)]
         if debug:
             print ('DEBUG: argv', argv)
         cwd = os.path.dirname(self.filename) if self.filename is not None else '.'
+        if debug:
+            print ('DEBUG: cwd', cwd)
         p = subprocess.Popen(argv, stdin=subprocess.PIPE, stdout=subprocess.PIPE,
                              stderr=subprocess.PIPE, pass_fds=[pipe1[0], pipe2[1]],
                              cwd=cwd)
         stdout_data, stderr_data = p.communicate(input=bytearray(self.to_str(), 'utf8'))
 
-        # print errors and notifications
         if len(stderr_data) > 0 and debug:
             print ('DEBUG: resamp', stderr_data.decode('utf8'))
 
-        # save big SLC binary file
-        with open(repeatSLC_tofile, 'wb') as f:
-            f.write(stdout_data)
-
+        # rename the file to the persistent name
+        if os.path.exists(repeatSLC_tofile + '.tmp'):
+            os.rename(repeatSLC_tofile + '.tmp', repeatSLC_tofile)
+        
         # PRM file should be small text
         data = os.read(pipe2[0],int(10e6))
         return PRM.from_str(data.decode('utf8'))

pygmtsar/pygmtsar/Stack_align.py

@@ -827,7 +827,6 @@ def compute_align(self, geometry='auto', dates=None, n_jobs=-1, degrees=12.0/360
             List of dates to process. If None, process all scenes. Default is None.
         n_jobs : int, optional
             Number of parallel processing jobs. n_jobs=-1 means all processor cores are used. Default is -1.
-        joblib_aligning_backend: str or None, optional
 
         Returns
         -------
@@ -845,6 +844,9 @@ def compute_align(self, geometry='auto', dates=None, n_jobs=-1, degrees=12.0/360
         # supress warnings about unary_union future behaviour to replace None by empty collection 
         warnings.filterwarnings('ignore')
 
+        if joblib_aligning_backend is not None:
+            print('Note: the joblib_aligning_backend argument has been removed from the compute_align() function.')
+
         if dates is None:
             dates = self.df.index.unique()
         dates_rep = [date for date in dates if date != self.reference]
@@ -854,7 +856,6 @@ def compute_align(self, geometry='auto', dates=None, n_jobs=-1, degrees=12.0/360
         if n_jobs is None or debug == True:
             print ('Note: sequential joblib processing is applied when "n_jobs" is None or "debug" is True.')
             joblib_backend = 'sequential'
-            joblib_aligning_backend = 'sequential'
         else:
             joblib_backend = None
 
@@ -866,7 +867,7 @@ def compute_align(self, geometry='auto', dates=None, n_jobs=-1, degrees=12.0/360
         # prepare secondary images
         with self.tqdm_joblib(tqdm(desc='Aligning Repeat', total=len(dates_rep)*len(subswaths))) as progress_bar:
             # threading backend is the only one working inside Docker container to run multiple binaries in parallel
-            joblib.Parallel(n_jobs=n_jobs, backend=joblib_aligning_backend)(joblib.delayed(self._align_rep_subswath)(subswath, date, degrees=degrees, debug=debug) \
+            joblib.Parallel(n_jobs=n_jobs, backend=joblib_backend)(joblib.delayed(self._align_rep_subswath)(subswath, date, degrees=degrees, debug=debug) \
                                            for date in dates_rep for subswath in subswaths)
 
         if len(subswaths) > 1: