ENH: started coding new interface.

VHR/segmentation.py

 import sys
-sys.path.append("../Common")
+sys.path.append('../Common')
 
 from Common.otb_numpy_proc import to_otb_pipeline
 import os.path
@@ -47,11 +47,20 @@ def lsgrm_process_tile(input_image, params : LSGRMParams, tile_width, tile_heigh
 
 
 def lsgrm(input_image, params : LSGRMParams, out_seg, n_proc=None, memory=None, roi=None, remove_graph=True, force_parallel=False):
-    # Define default number of threads and memory amount
+    # Check output file type
+    ext = os.path.splitext(out_seg)[-1]
+    if ext in ['.tif']:
+        vectorize = False
+    elif ext in ['.shp', '.gpkg', 'gml']:
+        vectorize = True
+    else:
+        raise ValueError('Output type {} not recognized/supported.'.format(ext))
+
+    # Define default number of threads (half) and memory amount (3/4 of available)
     if n_proc is None:
-        n_proc = mp.cpu_count()
+        n_proc = round(mp.cpu_count() / 2)
     if memory is None:
-        memory = psutil.virtual_memory().available
+        memory = round(psutil.virtual_memory().available * 0.75)
     else:
         memory *= 1e6
 
@@ -92,17 +101,72 @@ def lsgrm(input_image, params : LSGRMParams, out_seg, n_proc=None, memory=None,
         agg_app = otb.Registry.CreateApplication('AssembleGRMGraphs')
         agg_app.SetParameterInputImage('in', in_img.GetParameterOutputImage('out'))
         agg_app.SetParameterString('graph', graph)
-        agg_app.SetParameterString('out', out_seg)
         agg_app.SetParameterFloat('threshold', params.threshold)
         agg_app.SetParameterFloat('criterion.bs.cw', params.color_weight)
         agg_app.SetParameterFloat('criterion.bs.sw', params.spatial_weight)
         agg_app.SetParameterString('tiling', 'user')
         agg_app.SetParameterInt('tiling.user.sizex', nominal_tw)
         agg_app.SetParameterInt('tiling.user.sizey', nominal_th)
-        agg_app.ExecuteAndWriteOutput()
+        #agg_app.ExecuteAndWriteOutput()
+
+        if vectorize:
+            agg_app.Execute()
+            vec_app = otb.Registry.CreateApplication('SimpleVectorization')
+            vec_app.SetParameterInputImage('in', agg_app.GetParameterOutputImage('out'))
+            vec_app.SetParameterString('out', out_seg)
+            vec_app.ExecuteAndWriteOutput()
+        else:
+            agg_app.SetParameterString('out', out_seg)
+            agg_app.ExecuteAndWriteOutput()
+            write_qgis_seg_style(out_seg.replace(ext, '.qml'))
 
         if remove_graph:
             for f in chain(*graph_files):
                 os.remove(f)
 
         return out_seg
+
+def write_qgis_seg_style(out_file, line_color='255,255,0,255', line_width=0.46):
+    with open(out_file, 'wb') as f:
+        f.writelines(
+            ["<!DOCTYPE qgis PUBLIC 'http://mrcc.com/qgis.dtd' 'SYSTEM'>",
+             "<qgis styleCategories=\"Symbology\" version=\"3.14.1-Pi\">",
+             "  <renderer-v2 forceraster=\"0\" type=\"singleSymbol\" symbollevels=\"0\" enableorderby=\"0\">",
+             "    <symbols>",
+             "      <symbol alpha=\"1\" clip_to_extent=\"1\" name=\"0\" type=\"fill\" force_rhr=\"0\">",
+             "        <layer class=\"SimpleLine\" locked=\"0\" enabled=\"1\" pass=\"0\">",
+             "          <prop k=\"capstyle\" v=\"square\"/>",
+             "          <prop k=\"customdash\" v=\"5;2\"/>",
+             "          <prop k=\"customdash_map_unit_scale\" v=\"3x:0,0,0,0,0,0\"/>",
+             "          <prop k=\"customdash_unit\" v=\"MM\"/>",
+             "          <prop k=\"draw_inside_polygon\" v=\"0\"/>",
+             "          <prop k=\"joinstyle\" v=\"bevel\"/>",
+             "          <prop k=\"line_color\" v=\"{}\"/>".format(line_color),
+             "          <prop k=\"line_style\" v=\"solid\"/>",
+             "          <prop k=\"line_width\" v=\"{}\"/>".format(line_width),
+             "          <prop k=\"line_width_unit\" v=\"MM\"/>",
+             "          <prop k=\"offset\" v=\"0\"/>",
+             "          <prop k=\"offset_map_unit_scale\" v=\"3x:0,0,0,0,0,0\"/>",
+             "          <prop k=\"offset_unit\" v=\"MM\"/>",
+             "          <prop k=\"ring_filter\" v=\"0\"/>",
+             "          <prop k=\"use_custom_dash\" v=\"0\"/>",
+             "          <prop k=\"width_map_unit_scale\" v=\"3x:0,0,0,0,0,0\"/>",
+             "          <data_defined_properties>",
+             "            <Option type=\"Map\">",
+             "              <Option name=\"name\" value=\"\" type=\"QString\"/>",
+             "              <Option name=\"properties\"/>",
+             "              <Option name=\"type\" value=\"collection\" type=\"QString\"/>",
+             "            </Option>",
+             "          </data_defined_properties>",
+             "        </layer>",
+             "      </symbol>",
+             "    </symbols>",
+             "    <rotation/>",
+             "    <sizescale/>",
+             "  </renderer-v2>",
+             "  <blendMode>0</blendMode>",
+             "  <featureBlendMode>0</featureBlendMode>",
+             "  <layerGeometryType>2</layerGeometryType>",
+             "</qgis>"]
+        )
+        return out_file
\ No newline at end of file

moringa.py

+import sys
+import argparse
+import VHR.segmentation
+
+def run_segmentation(img, threshold, cw, sw , out_seg,
+                     n_first_iter, margin, n_proc, memory,
+                     remove_graph, force_parallel):
+    params = VHR.segmentation.LSGRMParams(threshold, cw, sw, n_first_iter, margin)
+    VHR.segmentation.lsgrm(img,params,out_seg,n_proc,memory,None,remove_graph,force_parallel)
+    return
+
+def main(args):
+    parser = argparse.ArgumentParser(prog="moringa", add_help=False)
+    subpar = parser.add_subparsers(dest="cmd")
+
+    prepr = subpar.add_parser("preprocess", help="Performs basic time series preprocessing (unimplemented).",
+                              formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    # Put arguments and options here
+
+    segmt = subpar.add_parser("segment", help="Performs (large scale Baatz-Shape) segmentation of an input image.",
+                              formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    segmt.add_argument("img", type=str, help="Path to the image to segment.")
+    segmt.add_argument("threshold", type=float, help="Threshold for the heterogeneity criterion in Baatz-Shape.")
+    segmt.add_argument("--cw", type=float, nargs="?", default=0.5, help="Color weight in Baatz-Shape criterion.")
+    segmt.add_argument("--sw", type=float, nargs="?", default=0.5, help="Spatial weight in Baatz-Shape criterion.")
+    segmt.add_argument("--n_first_iter", type=int, nargs="?", default=12, help="Number of iterations for parallel tile processing.")
+    segmt.add_argument("--tile_margin", type=int, nargs="?", default=100, help="Margin for tile overlap.")
+    segmt.add_argument("--n_proc", type=int, help="Number of cores to use.")
+    segmt.add_argument("--mem_limit", type=int, help="Memory limit in MB.")
+    segmt.add_argument("--keep_graph", help="Keep the graph files (.bin) after segmentation.", action='store_true')
+    segmt.add_argument("--force_parallel", help="Force the parallelization of the process even if the full graph fits in memory.", action='store_true')
+
+
+
+
+    if len(args) == 1:
+        parser.print_help()
+        sys.exit(0)
+
+    arg = parser.parse_args()
+
+    if arg.cmd == "preprocess":
+        print('Not yet implemented.')
+
+    if arg.cmd == "segment":
+        print(arg.force_parallel)
+        print('Here.')
+
+    return 0
+
+if __name__ == "__main__":
+    main(sys.argv)