Recreated test dataset for Test_Landsat8_PreCollectionData. Replaced two...

Recreated test dataset for Test_Landsat8_PreCollectionData. Replaced two os.system calls with subcall_with_output.

Signed-off-by: Daniel Scheffler <danschef@gfz-potsdam.de>

HISTORY.rst

@@ -16,6 +16,8 @@ History
 * Fixed DeprecationsWarnings.
 * Replaced GMS_object._numba_array_merger() with GMS_object._merge_arrays which does not use numba (and is much faster).
 * Removed numba dependency.
+* Recreated test dataset for Test_Landsat8_PreCollectionData.
+* Replaced two os.system calls with subcall_with_out.
 
 
 0.18.3 (2020-04-06)

gms_preprocessing/algorithms/geoprocessing.py

@@ -672,6 +672,8 @@ class GEOPROCESSING(object):
             self.inDs = stack_in_mem
 
         else:  # CFG.inmem_serialization is False
+            from ..misc.helper_functions import subcall_with_output
+
             self.logger.info('Adding the following bands to Layerstack:')
             [self.logger.info(os.path.basename(i)) for i in layers_pathlist]
 
@@ -685,7 +687,12 @@ class GEOPROCESSING(object):
             str_layers_pathlist = ' '.join(layers_pathlist)
 
             if self.subset is None:
-                os.system("gdal_merge.py -q -o %s -of ENVI -seperate %s" % (path_output, str_layers_pathlist))
+                cmd = "gdal_merge.py -q -o %s -of ENVI -seperate %s" % (path_output, str_layers_pathlist)
+                output, exitcode, err = subcall_with_output(cmd)
+                if exitcode:
+                    raise RuntimeError(err)
+                if output:
+                    return output.decode('UTF-8')
                 # FIXME this changes the format of the projection (maybe a GDAL bug?)
                 # FIXME normalize by EPSG2WKT(WKT2EPSG(WKT))
             else:
@@ -698,8 +705,13 @@ class GEOPROCESSING(object):
                 LR_Ygeo = GT[3] + self.colEnd * GT[4] + self.rowEnd * GT[5]
                 ullr = '%s %s %s %s' % (UL_Xgeo, UL_Ygeo, LR_Xgeo, LR_Ygeo)
 
-                os.system(
-                    "gdal_merge.py -q -o %s -ul_lr %s -of ENVI -seperate %s" % (path_output, ullr, str_layers_pathlist))
+                cmd = "gdal_merge.py -q -o %s -ul_lr %s -of ENVI -seperate %s" \
+                      % (path_output, ullr, str_layers_pathlist)
+                output, exitcode, err = subcall_with_output(cmd)
+                if exitcode:
+                    raise RuntimeError(err)
+                if output:
+                    return output.decode('UTF-8')
 
                 if [GT, PR] == [(0.0, 1.0, 0.0, 0.0, 0.0, 1.0), '']:
                     # delete output map info in case of arbitrary coordinate system

gms_preprocessing/processing/pipeline.py

@@ -254,7 +254,7 @@ def L2B_map(L2A_obj):
 @EXC_H.log_uncaught_exceptions
 @update_proc_status
 def L2C_map(L2B_obj):
-    # type: (L2B_P.L2B_object) -> L2C_P.L2C_objec
+    # type: (L2B_P.L2B_object) -> L2C_P.L2C_object
     L2B_obj.block_at_system_overload(max_usage=CFG.critical_mem_usage)
     L2C_obj = L2C_P.L2C_object(L2B_obj)
     if CFG.exec_L2CP[1]: