ENH: improve ROI based filtering

TimeSeries/s2theia.py

@@ -161,7 +161,12 @@ class S2TheiaTilePipeline:
             er.SetParameterString('in', bnd)
             er.SetParameterString('mode', 'fit')
             er.SetParameterString('mode.fit.vect', roi)
-            er.Execute()
+            try:
+                er.Execute()
+            except Exception as e:
+                if not 'Extraction Region not consistent with output image' in str(e):
+                    print(e)
+                return False
             arr = er.GetImageAsNumpyArray('out')
             if (np.sum(arr != cls.NDT) / (arr.shape[0]*arr.shape[1])) <= min_surf:
                 return False
@@ -219,25 +224,31 @@ class S2TheiaTilePipeline:
                     self.input_dates = [self.input_dates[i] for i in idx]
                     self.tile_cloud_percentage = [self.tile_cloud_percentage[i] for i in idx]
 
-                self.set_input_epsg()
-                self.output_epsg = self.input_epsg
-                self.output_dates = self.input_dates
-
-                for img in self.image_list:
-                    for p in self.PTRN_ful:
-                        ifn, ofn = self.get_file(img, p)
-                        self.append(to_otb_pipeline(ifn), ofn, self.REF_TYPE, 'out', is_output=True)
-                    for p in self.PTRN_msk:
-                        ifn, ofn = self.get_file(img, p)
-                        self.append(to_otb_pipeline(ifn), ofn, self.MSK_TYPE, 'out', is_output=True)
+                if len(self.image_list) > 0:
+                    self.set_input_epsg()
+                    self.output_epsg = self.input_epsg
+                    self.output_dates = self.input_dates
+
+                    for img in self.image_list:
+                        for p in self.PTRN_ful:
+                            ifn, ofn = self.get_file(img, p)
+                            self.append(to_otb_pipeline(ifn), ofn, self.REF_TYPE, 'out', is_output=True)
+                        for p in self.PTRN_msk:
+                            ifn, ofn = self.get_file(img, p)
+                            self.append(to_otb_pipeline(ifn), ofn, self.MSK_TYPE, 'out', is_output=True)
+                else:
+                    warnings.warn('Empty pipeline after filtering for tile {}.'.format(self.tile_id))
 
         else:
-            warnings.warn('Empty pipeline. Need to set preprocessed inputs?')
+            warnings.warn('Empty pipeline at init. Need to set preprocessed inputs?')
 
     def __del__(self):
         if os.path.exists(self.temp_fld):
             shutil.rmtree(self.temp_fld)
 
+    def is_empty(self):
+        return len(self.image_list) == 0
+
     def reset(self):
         self.pipe = []
         self.files = []
@@ -775,20 +786,25 @@ class S2TheiaPipeline:
     _tile_id = S2TilePipeline._tile_id
     tiles = []
 
-    def __init__(self, fld, temp_fld='/tmp', input_date_interval=None, max_clouds_percentage=None):
+    def __init__(self, fld, temp_fld='/tmp', input_date_interval=None, max_clouds_percentage=None, roi=None):
         self.folder = fld
         self.temp_fld = temp_fld
         self.input_date_interval = input_date_interval
         self.max_clouds_percentage = max_clouds_percentage
+        self.roi = roi
         self.tile_list = set()
         img_list = [os.path.abspath(x) for x in glob.glob(os.path.join(self.folder, self.S2TilePipeline.PTRN_dir))
                     if os.path.isdir(x) or os.path.splitext(x)[-1] == '.zip']
         [self.tile_list.add(self._tile_id(x)) for x in img_list if self._check(x)]
         assert all([self.S2TilePipeline(fld, t, dummy_read=True) for t in self.tile_list])
-        self.tiles = [self.S2TilePipeline(fld, t, self.temp_fld, self.input_date_interval, self.max_clouds_percentage) for t in self.tile_list]
+        self.tiles = [self.S2TilePipeline(fld, t, self.temp_fld, self.input_date_interval, self.max_clouds_percentage, filter_by_roi=self.roi) for t in self.tile_list]
+        self.tiles = [x for x in self.tiles if not x.is_empty()]
         self.output_dates = None
-        self.roi = None
-        self.output_epsg = self.tiles[0].input_epsg
+
+        if len(self.tiles) > 0:
+            self.output_epsg = self.tiles[0].input_epsg
+        else:
+            warnings.warn('Empty pipeline for the given image path.')
 
     def __del__(self):
         for x in self.tiles:
@@ -824,6 +840,7 @@ class S2TheiaPipeline:
             for t in self.tiles:
                 t.preprocess()
                 if self.roi is not None:
+                    print('Clipping')
                     t.clip(self.roi)
                 if align:
                     if type(align_to) == str and os.path.exists(align_to):

Workflows/operations.py

@@ -40,9 +40,9 @@ def preprocess_s2(in_fld, out_fld, output_dates_file=None, roi=None,
     else:
         raise ValueError("Unsupported/non-valid provider")
 
-    s2 = S2Processor(in_fld, temp_fld=out_fld)
-    if roi is not None:
-        s2.set_roi(roi)
+    s2 = S2Processor(in_fld, temp_fld=out_fld, roi=roi)
+    #if roi is not None:
+    #    s2.set_roi(roi)
     if output_dates_file is not None:
         s2.set_output_dates_by_file(output_dates_file)
     else: