Merge branch 'develop' of https://gitlab.irstea.fr/raffaele.gaetano/moringav2 into develop

OK

OBIA/segmentation.py

 import sys
+
+import rasterio
+from osgeo import gdal
 from Common.otb_numpy_proc import to_otb_pipeline
 import os.path
 import otbApplication as otb
 import multiprocessing as mp
-from math import sqrt, floor
+from math import sqrt, floor, ceil
 from itertools import product, chain
 from dataclasses import dataclass
 import psutil
-from skimage.measure import regionprops
+from skimage.measure import regionprops, label
 from tqdm import tqdm
 import numpy as np
 
@@ -22,6 +25,77 @@ class LSGRMParams:
     n_first_iter: int = 8
     margin: int = 100
 
+def grm_process_tile(input_image, params : LSGRMParams, tile_width, tile_height, tile_idx, out_img, roi):
+
+    if roi is None:
+        in_img = to_otb_pipeline(input_image)
+    elif os.path.exists(roi):
+        in_img = otb.Registry.CreateApplication('ExtractROI')
+        in_img.SetParameterString('in', input_image)
+        in_img.SetParameterString('mode', 'fit')
+        in_img.SetParameterString('mode.fit.vect', roi)
+        in_img.Execute()
+    else:
+        print('ROI provided but cannot find file.')
+        sys.exit(-1)
+
+    W, H = in_img.GetImageSize('out')
+
+    startx = 0 if tile_idx[0] == 0 else tile_idx[0] * tile_width - params.margin
+    starty = 0 if tile_idx[1] == 0 else tile_idx[1] * tile_height - params.margin
+    endx = W if tile_width * (tile_idx[0] + 1) >= W else tile_width * (tile_idx[0] + 1) + params.margin
+    endy = H if tile_height * (tile_idx[1] + 1) >= H else tile_height * (tile_idx[1] + 1) + params.margin
+
+    tile = otb.Registry.CreateApplication('ExtractROI')
+    tile.SetParameterInputImage('in', in_img.GetParameterOutputImage('out'))
+    tile.SetParameterInt('startx', startx)
+    tile.SetParameterInt('starty', starty)
+    tile.SetParameterInt('sizex', endx - startx)
+    tile.SetParameterInt('sizey', endy - starty)
+    tile.Execute()
+
+    out_fn = '{}_{}_{}.tif'.format(os.path.splitext(out_img)[0], tile_idx[1], tile_idx[0])
+
+    seg_app = otb.Registry.CreateApplication('GenericRegionMerging')
+    seg_app.SetParameterInputImage('in', tile.GetParameterOutputImage('out'))
+    seg_app.SetParameterFloat('threshold', params.threshold)
+    seg_app.SetParameterFloat('cw', params.color_weight)
+    seg_app.SetParameterFloat('sw', params.spatial_weight)
+    seg_app.SetParameterInt('niter', params.n_first_iter)
+    seg_app.Execute()
+
+    tie_lines = (0 if starty == 0 else params.margin,
+                 0 if startx == 0 else params.margin,
+                 0, 0)
+
+    tie_lines = (tie_lines[0], tie_lines[1],
+                 H if endy == H else tile_height + tie_lines[0],
+                 W if endx == W else tile_width + tie_lines[1])
+
+    seg = seg_app.ExportImage('out')
+    op = regionprops(seg['array'][:,:,0].astype(np.int32))
+    to_del = []
+    for o in op:
+        if not (tie_lines[0] <= o.bbox[0] < tie_lines[2]
+                and tie_lines[1] <= o.bbox[1] < tie_lines[3]):
+            # This one to check if a potentially deleted object trespass the overlap area,
+            # in which case it is kept.
+            if not (2*params.margin <= o.bbox[2] < tile_height and
+                    2*params.margin <= o.bbox[3] < tile_width):
+                to_del.append(o.label)
+    seg['array'][np.isin(seg['array'], to_del)] = 0
+    seg['array'], nlab = label(seg['array'], background=0, connectivity=1, return_num=True)
+    seg['array'] = np.ascontiguousarray(seg['array']).astype(float)
+
+    out_img = otb.Registry.CreateApplication('ExtractROI')
+    out_img.ImportImage('in', seg)
+    out_img.SetParameterString('out', out_fn)
+    out_img.SetParameterOutputImagePixelType('out', otb.ImagePixelType_uint32)
+    out_img.ExecuteAndWriteOutput()
+
+    return out_fn, nlab
+
+
 def lsgrm_process_tile(input_image, params : LSGRMParams, tile_width, tile_height, tile_idx, out_graph, roi=None):
     if roi is None:
         in_img = to_otb_pipeline(input_image)
@@ -52,6 +126,113 @@ def lsgrm_process_tile(input_image, params : LSGRMParams, tile_width, tile_heigh
             out_graph + '_edge_{}_{}.bin'.format(tile_idx[1], tile_idx[0]),
             out_graph + '_edgeMargin_{}_{}.bin'.format(tile_idx[1], tile_idx[0])]
 
+def get_ls_seg_parameter(input_image, roi=None, margin=0, n_proc=None, memory=None, force_parallel=False):
+    # Define default number of threads (half) and memory amount (3/4 of available)
+    if n_proc is None:
+        n_proc = round(mp.cpu_count() / 2)
+    if memory is None:
+        memory = round(psutil.virtual_memory().available * 0.75)
+    else:
+        memory *= 1e6
+
+    if roi is None:
+        in_img = to_otb_pipeline(input_image)
+    elif os.path.exists(roi):
+        in_img = otb.Registry.CreateApplication('ExtractROI')
+        in_img.SetParameterString('in', input_image)
+        in_img.SetParameterString('mode', 'fit')
+        in_img.SetParameterString('mode.fit.vect', roi)
+        in_img.Execute()
+    else:
+        print('ROI provided but cannot find file.')
+        sys.exit(-1)
+
+    # Get image size
+    W, H = in_img.GetImageSize('out')
+
+    # adapt memory amount to force fitting the number of cores
+    if force_parallel and memory > (W * H * node_size) and W > margin and H > margin:
+        memory = W * H * node_size
+
+    # Compute optimal tile size
+    T = (memory / n_proc) / node_size  # approx. pixels per tile with margins
+    tile_width_wmarg, tile_height_wmarg = floor(sqrt(T * W / H)), floor(sqrt(T * H / W))
+    nominal_tw, nominal_th = tile_width_wmarg - 2 * margin, tile_height_wmarg - 2 * margin
+    n_tiles_x, n_tiles_y = max(1, ceil(W / nominal_tw)), max(1, ceil(H / nominal_th))
+
+    return in_img, n_tiles_x, n_tiles_y, nominal_tw, nominal_th
+
+def lsgrm_light(input_image, params : LSGRMParams, out_seg, n_proc=None, memory=None,
+                roi=None, force_parallel=False, remove_tiles_if_useless=True):
+    # Check output file type
+    ext = os.path.splitext(out_seg)[-1]
+    if ext == '.vrt':
+        mode = 'vrt'
+    elif ext in ['.tif']:
+        mode = 'raster'
+    elif ext in ['.shp', '.gml', '.gpkg']:
+        mode = 'vector'
+    else:
+        raise ValueError('Output type {} not supported.'.format(ext))
+
+    in_img, n_tiles_x, n_tiles_y, nominal_tw, nominal_th = get_ls_seg_parameter(input_image, roi, params.margin, n_proc,
+                                                                        memory, force_parallel)
+
+    print('[INFO] Using a layout of {} x {} tiles.'.format(n_tiles_x,n_tiles_y))
+    print('[INFO] Nominal tile size w/margin: {} x {} pixels'.format(nominal_tw+2*params.margin,
+                                                                     nominal_th+2*params.margin))
+
+    if (n_tiles_x == 1 and n_tiles_y == 1):
+        # Fallback to classical GRM
+        print('[INFO] Fallback to one-tile GRM.')
+        grm = otb.Registry.CreateApplication('GenericRegionMerging')
+        grm.SetParameterInputImage('in', in_img.GetParameterOutputImage('out'))
+        grm.SetParameterFloat('threshold', params.threshold)
+        grm.SetParameterFloat('cw', params.color_weight)
+        grm.SetParameterFloat('sw', params.spatial_weight)
+        grm.SetParameterString('out', out_seg)
+        grm.SetParameterOutputImagePixelType('out', otb.ImagePixelType_uint32)
+        grm.ExecuteAndWriteOutput()
+    else:
+        tile_index_list = product(range(n_tiles_x), range(n_tiles_y))
+        arg_list = [(input_image, params, nominal_tw, nominal_th, x, out_seg, roi) for x in tile_index_list]
+        with mp.Pool(n_proc) as p:
+            out_tiles = p.starmap(grm_process_tile, arg_list)
+        cumul_label = 0
+        for f,l in out_tiles:
+            if cumul_label > 0:
+                with rasterio.open(f, 'r+') as tile:
+                    arr = tile.read(1)
+                    arr[arr>0] += cumul_label
+                    tile.write(arr, indexes=1)
+                    tile.nodata = 0
+            cumul_label += l
+
+        print('[INFO] Output mode {}.'.format(mode))
+        if mode == 'vrt':
+            vrtopt = gdal.BuildVRTOptions(separate=False, srcNodata=0, VRTNodata=0)
+            gdal.BuildVRT(out_seg, [x[0] for x in out_tiles], options=vrtopt)
+        elif mode in ['raster', 'vector']:
+            mos = otb.Registry.CreateApplication('Mosaic')
+            mos.SetParameterStringList('il', [x[0] for x in out_tiles])
+            mos.SetParameterInt('nodata', 0)
+            if mode == 'raster':
+                mos.SetParameterOutputImagePixelType('out', otb.ImagePixelType_uint32)
+                mos.SetParameterString('out', out_seg)
+                mos.ExecuteAndWriteOutput()
+            elif mode == 'vector':
+                mos.Execute()
+                vec = otb.Registry.CreateApplication('SimpleVectorization')
+                vec.SetParameterInputImage('in', mos.GetParameterOutputImage('out'))
+                vec.SetParameterString('out', out_seg)
+                vec.ExecuteAndWriteOutput()
+            if remove_tiles_if_useless:
+                [os.remove(x[0]) for x in out_tiles]
+
+    return out_seg
+
+
+
 
 def lsgrm(input_image, params : LSGRMParams, out_seg, n_proc=None, memory=None, roi=None, remove_graph=True, force_parallel=False):
     # Check output file type

docker/dockerfile

@@ -100,6 +100,7 @@ ENV LD_LIBRARY_PATH="/opt/otb/lib:$LD_LIBRARY_PATH"
 ENV OTB_APPLICATION_PATH="/opt/otb/lib/otb/applications"
 ENV PROJ_LIB="$DEPS_INSTALL_PREFIX/share/proj"
 ENV GDAL_DATA="$DEPS_INSTALL_PREFIX/share/gdal"
+ENV OTB_LOGGER_LEVEL="CRITICAL"
 
 RUN useradd -s /bin/bash -m ubuntu
 USER ubuntu