Bash script edits to make stackSentinel.py faster in places (#225)

* plumb in num-process for time consuming steps

* refine num-process speed enhancements

* refine num-process speed enhancements

* dedicated function for writing batch processes

* refine num-process speed enhancements

* fix indents

Co-authored-by: Russell Grew <[email protected]>

Author: hardreddata

contrib/stack/topsStack/Stack.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+  #!/usr/bin/env python3
 ########################
 #Author: Heresh Fattahi
 
@@ -13,6 +13,7 @@
 maxNodes = 72
 
 
+
 class config(object):
     """
        A class representing the config file
@@ -242,6 +243,7 @@ def unwrapSnaphu(self, function):
         self.f.write('defomax : ' + self.defoMax + '\n')
         self.f.write('rlks : ' + self.rangeLooks + '\n')
         self.f.write('alks : ' + self.azimuthLooks + '\n')
+        self.f.write('numProcess : ' + self.numProcess + '\n')
 
     def denseOffset(self, function):
         self.f.write('###################################'+'\n')
@@ -258,6 +260,18 @@ def denseOffset(self, function):
         #self.f.write('ww : 256\n')
         #self.f.write('wh : 128\n')
 
+    def write_wrapper_config2run_file(self, configName, line_cnt, numProcess = 1):
+        # dispassionate list of commands for single process
+        if numProcess == 1:
+            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
+        # aggregate background commands between wait blocks for speed gains
+        elif numProcess > 1:
+            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + ' &\n')
+            if line_cnt == numProcess:
+                self.runf.write('wait\n\n')
+                line_cnt = 0
+        return line_cnt
+
     def finalize(self):
         self.f.close()
 
@@ -286,6 +300,7 @@ def unpackSLC(self, acquisitionDates, safe_dict):
         swath_path = self.work_dir
         os.makedirs(self.config_path, exist_ok=True)
 
+        line_cnt = 0
         for slcdate in acquisitionDates:
             configName = os.path.join(self.config_path,'config_unpack_'+slcdate)
             configObj = config(configName)
@@ -300,8 +315,10 @@ def unpackSLC(self, acquisitionDates, safe_dict):
             configObj.Sentinel1_TOPS('[Function-1]')
             configObj.topo('[Function-2]')
             configObj.finalize()
+            
+            line_cnt += 1
+            line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt)
             del configObj
-            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
 
     def unpackStackReferenceSLC(self, safe_dict):
         swath_path = self.work_dir
@@ -320,11 +337,14 @@ def unpackStackReferenceSLC(self, safe_dict):
         configObj.Sentinel1_TOPS('[Function-1]')
         configObj.topo('[Function-2]')
         configObj.finalize()
+
+        line_cnt = 1
+        line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt)
         del configObj
-        self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
 
     def unpackSecondarysSLC(self,  stackReferenceDate, secondaryList, safe_dict):
 
+        line_cnt = 0
         for secondary in secondaryList:
             configName = os.path.join(self.config_path,'config_secondary_'+secondary)
             outdir = os.path.join(self.work_dir,'secondarys/'+secondary)
@@ -337,11 +357,14 @@ def unpackSecondarysSLC(self,  stackReferenceDate, secondaryList, safe_dict):
             configObj.outDir = outdir
             configObj.Sentinel1_TOPS('[Function-1]')
             configObj.finalize()
+
+            line_cnt += 1
+            line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt, self.numProcess)
             del configObj
-            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName+'\n')
 
     def averageBaseline(self, stackReferenceDate, secondaryList):
 
+        line_cnt = 0
         for secondary in secondaryList:
             configName = os.path.join(self.config_path,'config_baseline_'+secondary)
             configObj = config(configName)
@@ -351,10 +374,14 @@ def averageBaseline(self, stackReferenceDate, secondaryList):
             configObj.baselineFile = os.path.join(self.work_dir,'baselines/' + stackReferenceDate +'_' + secondary + '/' + stackReferenceDate +'_'+ secondary  + '.txt')
             configObj.computeAverageBaseline('[Function-1]')
             configObj.finalize()
+
+            line_cnt += 1
+            line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt, self.numProcess)
             del configObj
-            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName+'\n')
 
     def gridBaseline(self, stackReferenceDate, secondaryList):
+
+        line_cnt = 0
         for secondary in secondaryList:
             configName = os.path.join(self.config_path,'config_baselinegrid_'+secondary)
             configObj = config(configName)
@@ -364,8 +391,10 @@ def gridBaseline(self, stackReferenceDate, secondaryList):
             configObj.baselineFile = os.path.join(self.work_dir, 'merged/baselines/' + secondary + '/' + secondary )
             configObj.computeGridBaseline('[Function-1]')
             configObj.finalize()
+
+            line_cnt += 1
+            line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt)
             del configObj
-            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName+'\n')
         # also add the reference in itself to be consistent with the SLC dir
         configName = os.path.join(self.config_path,'config_baselinegrid_reference')
         configObj = config(configName)
@@ -375,8 +404,10 @@ def gridBaseline(self, stackReferenceDate, secondaryList):
         configObj.baselineFile = os.path.join(self.work_dir, 'merged/baselines/' + stackReferenceDate + '/' + stackReferenceDate)
         configObj.computeGridBaseline('[Function-1]')
         configObj.finalize()
+
+        line_cnt = 1
+        line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt)
         del configObj
-        self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName+'\n')
 
 
     def extractOverlaps(self):
@@ -386,6 +417,7 @@ def extractOverlaps(self):
 
     def geo2rdr_offset(self, secondaryList, fullBurst='False'):
 
+        line_cnt = 0
         for secondary in secondaryList:
             reference = self.reference_date
             if fullBurst == 'True':
@@ -407,10 +439,14 @@ def geo2rdr_offset(self, secondaryList, fullBurst='False'):
                 configObj.overlapTrueOrFalse = 'True'
             configObj.geo2rdr('[Function-1]')
             configObj.finalize()
+
+            line_cnt += 1
+            line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt, self.numProcess)
             del configObj
-            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
 
     def resample_with_carrier(self, secondaryList, fullBurst='False'):
+
+        line_cnt = 0
         for secondary in secondaryList:
             reference = self.reference_date
             if fullBurst == 'True':
@@ -433,13 +469,17 @@ def resample_with_carrier(self, secondaryList, fullBurst='False'):
                 configObj.overlapTrueOrFalse = 'True'
             configObj.resamp_withCarrier('[Function-1]')
             configObj.finalize()
+
+            line_cnt += 1
+            line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt, self.numProcess)
             del configObj
-            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
+
 
     def pairs_misregistration(self, dateList, safe_dict):
         # generating overlap interferograms, estimate azimuth misregistration for each pair:
         pairs = []
         num_overlap_connections = int(self.num_overlap_connections) + 1
+
         for i in range(len(dateList)-1):
             for j in range(i+1,i+num_overlap_connections):
                 if j<len(dateList):
@@ -450,6 +490,8 @@ def pairs_misregistration(self, dateList, safe_dict):
             safe_dict[date].slc_overlap = os.path.join(self.work_dir , 'coreg_secondarys/'+date)
         safe_dict[self.reference_date].slc = os.path.join(self.work_dir , 'reference')
         safe_dict[self.reference_date].slc_overlap = os.path.join(self.work_dir , 'reference')
+
+        line_cnt = 0
         for pair in pairs:
             reference = pair[0]
             secondary = pair[1]
@@ -479,11 +521,12 @@ def pairs_misregistration(self, dateList, safe_dict):
             configObj.rangeMisreg('[Function-4]')
             configObj.finalize()
 
-            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
+            line_cnt += 1
+            line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt, self.numProcess)
+            del configObj
             ########################
 
 
-
     def timeseries_misregistration(self):
         #inverting the misregistration offsets of the overlap pairs to estimate the offsets of each date
         self.runf.write(self.text_cmd + 'invertMisreg.py -i ' + os.path.join(self.work_dir,'misreg/azimuth/pairs/') + ' -o ' + os.path.join(self.work_dir,'misreg/azimuth/dates/') + '\n')
@@ -499,6 +542,8 @@ def generate_burstIgram(self, dateList, safe_dict, pairs):
         for date in dateList:
             safe_dict[date].slc = os.path.join(self.work_dir, 'coreg_secondarys/'+date)
         safe_dict[self.reference_date].slc = os.path.join(self.work_dir , 'reference')
+
+        line_cnt = 0
         for pair in pairs:
             reference = pair[0]
             secondary = pair[1]
@@ -514,14 +559,19 @@ def generate_burstIgram(self, dateList, safe_dict, pairs):
             configObj.overlapTrueOrFalse = 'False'
             configObj.generateIgram('[Function-1]')
             configObj.finalize()
+
+            line_cnt += 1
+            line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt, self.numProcess)
             del configObj
 
-            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
+
 
     def igram_mergeBurst(self, dateList, safe_dict, pairs):
         for date in dateList:
             safe_dict[date].slc = os.path.join(self.work_dir, 'coreg_secondarys/'+date)
         safe_dict[self.reference_date].slc = os.path.join(self.work_dir , 'reference')
+
+        line_cnt = 0
         for pair in pairs:
             reference = pair[0]
             secondary = pair[1]
@@ -543,12 +593,14 @@ def igram_mergeBurst(self, dateList, safe_dict, pairs):
             configObj.stack = os.path.join(self.work_dir, 'stack')
             configObj.mergeBurst('[Function-1]')
             configObj.finalize()
-            del configObj
 
-            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
+            line_cnt += 1
+            line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt, self.numProcess)
+            del configObj
 
     def mergeSecondarySLC(self, secondaryList, virtual='True'):
 
+        line_cnt = 0
         for secondary in secondaryList:
             configName = os.path.join(self.config_path,'config_merge_' + secondary)
             configObj = config(configName)
@@ -566,7 +618,11 @@ def mergeSecondarySLC(self, secondaryList, virtual='True'):
             configObj.stack = os.path.join(self.work_dir, 'stack')
             configObj.mergeBurst('[Function-1]')
             configObj.finalize()
-            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
+
+            line_cnt += 1
+            line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt)
+            del configObj
+
 
     def mergeReference(self, stackReference, virtual='True'):
 
@@ -585,7 +641,10 @@ def mergeReference(self, stackReference, virtual='True'):
         configObj.multiLook = 'False'
         configObj.mergeBurst('[Function-1]')
         configObj.finalize()
-        self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
+
+        line_cnt = 1
+        line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt)
+        del configObj
 
         geometryList = ['lat*rdr', 'lon*rdr', 'los*rdr', 'hgt*rdr', 'shadowMask*rdr','incLocal*rdr']
         multiookToolDict = {'lat*rdr': 'gdal', 'lon*rdr': 'gdal', 'los*rdr': 'gdal' , 'hgt*rdr':"gdal", 'shadowMask*rdr':"isce",'incLocal*rdr':"gdal"}
@@ -610,10 +669,14 @@ def mergeReference(self, stackReference, virtual='True'):
             configObj.stack = os.path.join(self.work_dir, 'stack')
             configObj.mergeBurst('[Function-1]')
             configObj.finalize()
-            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
+
+            line_cnt += 1
+            line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt)
+            del configObj
 
     def mergeSLC(self, aquisitionDates, virtual='True'):
 
+        line_cnt  = 0
         for slcdate in aquisitionDates:
             configName = os.path.join(self.config_path,'config_merge_' + slcdate)
             configObj = config(configName)
@@ -630,9 +693,14 @@ def mergeSLC(self, aquisitionDates, virtual='True'):
             configObj.stack = os.path.join(self.work_dir, 'stack')
             configObj.mergeBurst('[Function-1]')
             configObj.finalize()
-            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
+
+            line_cnt += 1
+            line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt)
+
 
             geometryList = ['lat*rdr', 'lon*rdr', 'los*rdr', 'hgt*rdr', 'shadowMask*rdr','incLocal*rdr']
+            
+            g_line_cnt = 0
             for i in range(len(geometryList)):
                 pattern = geometryList[i]
                 configName = os.path.join(self.config_path,'config_merge_' + slcdate + '_' +pattern.split('*')[0])
@@ -650,10 +718,14 @@ def mergeSLC(self, aquisitionDates, virtual='True'):
                 configObj.stack = os.path.join(self.work_dir, 'stack')
                 configObj.mergeBurst('[Function-1]')
                 configObj.finalize()
-                self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
+                
+                g_line_cnt += 1
+                g_line_cnt = configObj.write_wrapper_config2run_file(configName, g_line_cnt)
+                del configObj
 
     def filter_coherence(self, pairs):
 
+        line_cnt = 0
         for pair in pairs:
             reference = pair[0]
             secondary = pair[1]
@@ -673,9 +745,15 @@ def filter_coherence(self, pairs):
             #configObj.filtStrength = str(self.filtStrength)
             configObj.FilterAndCoherence('[Function-1]')
             configObj.finalize()
-            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
+
+            line_cnt += 1
+            line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt, self.numProcess)
+            del configObj
+
 
     def unwrap(self, pairs):
+
+        line_cnt = 0
         for pair in pairs:
             reference = pair[0]
             secondary = pair[1]
@@ -693,10 +771,14 @@ def unwrap(self, pairs):
             configObj.unwMethod = self.unwMethod
             configObj.unwrap('[Function-1]')
             configObj.finalize()
-            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
+
+            line_cnt += 1
+            line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt, self.numProcess)
+            del configObj
 
     def denseOffsets(self, pairs):
 
+        line_cnt = 0
         for pair in pairs:
             reference = pair[0]
             secondary = pair[1]
@@ -709,9 +791,10 @@ def denseOffsets(self, pairs):
             configObj.output = os.path.join(self.work_dir , 'merged/dense_offsets/'+reference+'_'+secondary + '/'  + reference+'_'+secondary)
             configObj.denseOffset('[Function-1]')
             configObj.finalize()
-            del configObj
-            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
 
+            line_cnt += 1
+            line_cnt = configObj.write_wrapper_config2run_file(configName, line_cnt)
+            del configObj
 
     def finalize(self):
         self.runf.close()
@@ -966,8 +1049,6 @@ def get_orbit(self, orbitDir, workDir, margin=60.0):
               self.orbit =  orbitFile[0]
               self.orbitType = 'restituted'
 
-
-
 # an example for writing job files when using clusters
 
 """

contrib/stack/topsStack/stackSentinel.py

@@ -167,7 +167,7 @@ def createParser():
                         help='Allow App to use GPU when available')
 
     parser.add_argument('--num-proc', '--num-process', dest='numProcess', type=int, default=1,
-                        help='number of parallel processes (for topo only) (default: %(default)s).')
+                        help='number of parallel processes (where applicable) (default: %(default)s).')
 
     parser.add_argument('-u', '--unw_method', dest='unwMethod', type=str, default='snaphu', choices=['icu', 'snaphu'],
                         help='Unwrapping method (default: %(default)s).')