Changed MIP fct (not using SimpleITK anymore)

brick/processing/plot.py

@@ -41,18 +41,12 @@ import mpl_toolkits.mplot3d as p3_
 import numpy as np_
 import skimage.measure as ms_
 
-import SimpleITK as sitk
 
-
-def MaximumIntensityProjectionZ(img: array_t, cmap: str ='tab20', output_image_file_name: str = None) -> None:
+def MaximumIntensityProjectionZ(img: array_t, cmap: str ='tab20', axis: int = 0, output_image_file_name: str = None) -> None:
     """ Maximum Image Projection on the Z axis. """
     #
-    image = sitk.GetImageFromArray(img)
-    # image_size = image.GetSize()
-    # print('Image Size = ', image_size)
-    projection = sitk.MaximumProjection(image, 2)
-    np_img = sitk.GetArrayFromImage(projection)
-    pl_.imshow(np_img[0, :, :], cmap=cmap)
+    xy = np_.amax(img, axis=axis)
+    pl_.imshow(xy, cmap=cmap)
     pl_.show(block=True)
     if output_image_file_name is not None:
         pl_.imsave(output_image_file_name, np_img[0, :, :], cmap=cmap)

nutrimorph.py

@@ -342,7 +342,7 @@ po_.MaximumIntensityProjectionZ(ext_nfo['lmp_ext'])
 
 # Extract the graph of each extension of a soma
 print('\n--- Graph extraction\n')
-ext_map = skl_map_t.FromShapeMap(ext_nfo['lmp_ext'], store_widths=True, skeletonize=False, do_post_thinning=False)
+ext_map = skl_map_t.FromShapeMap(ext_nfo['lmp_ext'], store_widths=True, skeletonize=False)  # , do_post_thinning=True
 ext_skl_graph = skl_graph_t.FromSkeleton(ext_map)
 
 # --- Some info about the skeleton graphs
@@ -381,3 +381,23 @@ ext_skl_graph = ge_.FindGraphsRoot(somas, ext_skl_graph)
 elapsed_time = tm_.gmtime(tm_.time() - start_time)
 print(f"\nElapsed Time={tm_.strftime('%Hh %Mm %Ss', elapsed_time)}")
 print(f"DONE: {tm_.strftime('%a, %b %d %Y @ %H:%M:%S')}")
+
+
+# for node_id,node_id2, edge_nfo in ext_skl_graph.edges.data('as_edge_t'):
+# ...     if (ext_skl_graph.degree[node_id] == 1) or (ext_skl_graph.degree[node_id2] == 1):
+# ...         print(edge_nfo.sites)
+
+# # Pour un soma donne
+# # primary_extension_sites = tuple(set(zip(*extension.sites) for extension in soma.extensions)
+# primary_extension_uids = tuple(extension.uid for extension in soma.extensions)
+# for node_id,node_id2, edge_nfo in ext_skl_graph.edges.data('as_edge_t'):
+#     if (ext_skl_graph.degree[node_id] == 1) or (ext_skl_graph.degree[node_id2] == 1):
+#         ext_uid = np_.unique(ext_nfo['lmp'][edge_nfo.sites])[1]
+#         if ext_uid in primary_extension_uids:
+#             if ext_skl_graph.degree[node_id] == 1:
+#                 root_node = node_id
+#             else:
+#                 root_node = node_id2
+#         # print(edge_nfo.sites)
+#         # edge_sites = set(zip(*edge_nfo.sites))
+#         # intersections = map(in)
\ No newline at end of file