Several minor improvements / WIP

src/geomtree/affine_transform.py

@@ -94,6 +94,7 @@ class AffineTransform(object):
         from visu_core.matplotlib.colormap import plain_colormap
         from visu_core.vtk.actor import vtk_actor
         from visu_core.vtk.polydata import face_scalar_property_polydata
+
         #TODO : doc + correct scale (in visu_core)
         qr = np.sqrt(chi2.ppf(alpha, 3))
         T = self.linear

src/geomtree/geomdag.py

-def assign_ids_to_dag(dag, t, tree_type):
-    # a deplacer dans treex ?
-    node = t.get_attribute(tree_type + '_equivalence_class')
-    attr = dag.get_attribute(node)
-    if "tree_ids" in attr.keys():
-        tree_id = attr['tree_ids']
-    else:
-        tree_id = []
-    tree_id.append(t.my_id)
-    dag.add_attribute_to_node("tree_ids", tree_id, node)
-    for child in t.my_children:
-        assign_ids_to_dag(dag, child, tree_type)
+

src/geomtree/geomtree.py

@@ -39,14 +39,13 @@ class GeomTree(Tree):
     #         child.update_relative_geometry()
 
     def get_actor(self,axis=False,alpha=0.95,opacity=0.2,relative=False, show_ellipsoid=True):
-        from visu_core.vtk.primitive_actors import segment_primitive, point_cloud_primitive
         actors = []
         i=1
         self.__get_recursive_actor(actors,i,axis,alpha,opacity,relative,show_ellipsoid)
         return actors
 
     def __get_recursive_actor(self,actors,i,axis,alpha,opacity,relative,show_ellipsoid):
-
+        from visu_core.vtk.primitive_actors import segment_primitive, point_cloud_primitive
         if show_ellipsoid:
             if relative:
                 actors += self.my_relative_geometry.get_actor(color='glasbey_' + str(i), axis=axis, alpha=alpha,
@@ -68,7 +67,7 @@ class GeomTree(Tree):
                 d = child.my_relative_geometry.translation
             else:
                 d = child.my_absolute_geometry.translation
-            actors+=[segment_primitive(c,d,color='#808080')]
+            actors+=[segment_primitive(c,d,color='#808080',lw=1)] ### epaisseur du segment ! #TODO: gerer par un argument l'epaisseur
             child.__get_recursive_actor(actors,i,axis,alpha,opacity,relative,show_ellipsoid)
 
     def apply_tf(self,tf,relative=False):
@@ -92,15 +91,15 @@ def align_centers(t1,t2,tree_type="unordered", rmsd=True):
     """
     If the two trees are isomorphic, find the best alignment of centers of the two trees via Kabsch algorithm
     """
-    assert t1.is_isomorphic_to(t2, tree_type), "Trees are not isomorphic"
+    bool, mapp = t1.is_isomorphic_to(t2, tree_type,mapping=True)
+
+    assert bool, "Trees are not isomorphic"
 
     geom1 = t1.get_geometry()
     geom2 = t2.get_geometry()
 
-    # TODO: s'occuper mieux des isomorphismes, la ça marche par la grace divine et la chance
-
-    p = np.array([geom1[k].translation for k in geom1.keys()])
-    q = np.array([geom2[k].translation for k in geom2.keys()])
+    p=np.array([geom1[k].translation for k in mapp.keys()])
+    q=np.array([geom2[mapp[k]].translation for k in mapp.keys()])
 
     if rmsd:
         print("RMSD before processing : ", np.linalg.norm(p - q)/np.sqrt(len(p)))
@@ -123,21 +122,24 @@ def align_centers(t1,t2,tree_type="unordered", rmsd=True):
     tf = AffineTransform()
     tf.set_parameters(linear=R, translation=cp - R @ cq)
 
+    #return tf.inverse(), np.linalg.norm(p - q)/np.sqrt(len(p))
     return tf, np.linalg.norm(p - q)/np.sqrt(len(p))
 
 def tree_hellinger_distance(t1,t2,tree_type="unordered",relative=[False,False]):
 
-    assert t1.is_isomorphic_to(t2, tree_type), "Trees are not isomorphic"
+    bool, mapp = t1.is_isomorphic_to(t2, tree_type,mapping=True)
+
+    assert bool, "Trees are not isomorphic"
 
     geomu = t1.get_geometry(relative=relative[0])
     geomv = t2.get_geometry(relative=relative[1])
 
-    p = [geomu[k] for k in geomu.keys()]
-    q = [geomv[k] for k in geomv.keys()]
+    p=np.array([geomu[k] for k in mapp.keys()])
+    q=np.array([geomv[mapp[k]] for k in mapp.keys()])
     f = 0
     for i in range(len(p)):
         f += hellinger_distance(p[i], q[i])
-    return f
+    return f/t1.get_property('size') #pour rester dans [0,1]
 
 def tree_to_geomtree(t):
     gt = GeomTree(random_transform())
@@ -151,4 +153,13 @@ def tree_to_geomtree(t):
 # vtk_display_actors(actors,background=(0.9,0.9,0.9))
 
 
-
+# from geomtree import *
+# from visu_core.vtk.actor import vtk_display_actors as display
+#
+# tf=random_transform()
+#
+# pc1 = tf.sample_points(n=1000,method='uniform')
+# pc2 = tf.sample_points(n=1000)
+#
+# display(tf.get_actor(opacity=0.1)+pc2.get_actor(glyph='sphere',scale=0.1))
+# display(tf.get_actor(opacity=0.1,alpha=chi2.cdf(1,3))+pc1.get_actor(glyph='sphere',scale=0.1))

src/geomtree/point_cloud.py

@@ -224,7 +224,7 @@ class PointCloud(object):
         return abs(np.log10(l1/l2)) < np.log10(evidence)
 
     def intersection_filter_bis(self,tf1,tf2,evidence=10):
-        K = 2 * np.log(evidence)
+        K = 2 * np.log(evidence) #TODO: vérifier que 2 est correct
         filter=[]
         for vec in self.cloud:
             m1 = mahalanobis(vec, tf1.translation, inv(tf1.get_covariance_matrix()))**2