Fix bugs in code and clean up input parameters in growers

Change-Id: I6514a07a8d4a20f2a967d3e718b593aecf6cfa59

tns/generate/algorithms/abstractgrower.py

@@ -11,11 +11,12 @@ class AbstractAlgo(object):
     @abc.abstractmethod
     def __init__(self,
                  input_data,
-                 bif_method,
+                 params,
                  start_point):
         """Abstract TreeGrower Algorithm initialization.
         input_data: dictionary in which data used by the algorithm are stored
-        bif_method: bifurcation method, select from: bio_oriented, symmetric, directional
+        params: parameters needed for growth, it should include the bif_method
+        bifurcation method, select from: bio_oriented, symmetric, directional
         """
 
     @abc.abstractmethod

tns/generate/algorithms/basicgrower.py

@@ -9,13 +9,15 @@ class TrunkAlgo(AbstractAlgo):
 
     def __init__(self,
                  input_data,
-                 bif_method,
+                 params,
                  start_point):
         """
         input_data: saves all the data required for the growth
-        bif_method: selects the bifurcation method used for the growth
+        params: parameters needed for growth, it should include the bif_method
+        bifurcation method, select from: bio_oriented, symmetric, directional
         """
-        self.bif_method = bif_methods[bif_method]
+        self.bif_method = bif_methods[params["branching_method"]]
+        self.params = params
         self.input_data = input_data
         self.start_point = start_point
 

tns/generate/algorithms/common.py

@@ -5,7 +5,8 @@
 bif_methods = {'bio_oriented': rd.get_bif_bio_oriented,
                'symmetric': rd.get_bif_symmetric,
                'directional': rd.get_bif_directional, 
-               'random': rd.get_bif_random}
+               'random': rd.get_bif_random, 
+               'smooth': rd.get_bif_bio_smoothed}
 
 
 def init_ph_angles(ph_angles):
@@ -18,4 +19,3 @@ def init_ph_angles(ph_angles):
     bt_all = {round_num(p[1]): p[0] for p in ph_angles}
 
     return bif, term, angles, bt_all
-

tns/generate/algorithms/tmdgrower.py

@@ -13,15 +13,16 @@ class TMDAlgo(AbstractAlgo):
 
     def __init__(self,
                  input_data,
-                 bif_method,
+                 params,
                  start_point):
         """
         TMD basic grower
         input_data: saves all the data required for the growth
-        bif_method: selects the bifurcation method used for the growth
+        params: parameters needed for growth, it should include the bif_method
+        bifurcation method, select from: bio_oriented, symmetric, directional
         """
-
-        self.bif_method = bif_methods[bif_method]
+        self.bif_method = bif_methods[params["branching_method"]]
+        self.params = params
         self.ph_angles = sample.ph(input_data["persistence_diagram"])
         self.start_point = start_point
         self.bif = None

tns/generate/section.py

@@ -1,7 +1,7 @@
 import numpy as np
 from tns.morphmath import random_tree as rd
 from tns.morphmath.sample import ph_prob
-
+from scipy import stats
 
 class SectionGrower(object):
     '''Class for the section
@@ -76,6 +76,8 @@ def check_stop_ph(self, prob_function):
         scale = self.params["scale_prob"]
 
         currd = np.linalg.norm(np.subtract(self.points3D[-1], crit["ref"]))
+        # compute expected path length for a given target radial distance
+        # pathtarget = self.segs > 1.3 * np.abs(crit["bif"] - crit["term"])
 
         # Ensure that the section has at least two points
         if len(self.points3D) < 2:
@@ -87,6 +89,14 @@ def check_stop_ph(self, prob_function):
         elif ph_prob(prob_function, crit["term"] - currd):
             self.children = 0.
             return False
+        # Checks in too long path length is generated
+        # elif pathtarget:
+        #    # If target bif smaller
+        #    if crit["bif"] <= crit["term"]:
+        #        self.children = 2.
+        #    else:
+        #        self.children = 0.
+        #    return False
         else:
             return True
 
@@ -108,7 +118,6 @@ def generate(self):
         '''Creates a section with the selected parameters
            until at least one stop criterion is fulfilled.
         '''
-        from scipy import stats
         prob_function = stats.expon(loc=0, scale=self.params["scale_prob"])
 
         while self.check_stop_ph(prob_function):

tns/generate/tree.py

@@ -45,7 +45,7 @@ def __init__(self,
         grow_meth = growth_algorithms[self.params["growth_method"]]
 
         self.growth_algo = grow_meth(input_data=self.distr,
-                                     bif_method=self.params["branching_method"],
+                                     params=self.params,
                                      start_point=self.point)
 
         stop, num_sec = self.growth_algo.initialize()
@@ -54,6 +54,7 @@ def __init__(self,
                          direction=self.direction,
                          start_point=list(self.point),
                          stop=copy.deepcopy(stop),
+                         process='major',
                          children=2 if num_sec > 1 else 0)
 
     def add_section(self, parent, direction, start_point, stop, process=None, children=0):

tns/morphmath/random_tree.py

@@ -71,8 +71,8 @@ def get_bif_bio_smoothed(direction, angles):
     '''Input: init_phi, init_theta, dphi, dtheta.
     '''
     def smoothing(ang):
-        if np.abs(ang) > np.pi/2.:
-            return ang/2
+        if np.abs(ang) > np.pi:
+            return np.abs(ang)/2
         else:
             return ang
 
@@ -100,7 +100,7 @@ def get_bif_directional(direction, angles):
     dir1 = rt.vector_from_spherical(phi, theta)
     dir2 = rt.vector_from_spherical(phi - phi1, theta - theta1)
 
-    return (np.array(dir1), np.array(dir2))
+    return (np.array(direction), np.array(dir2))
 
 
 def get_bif_soma_repulsion(direction, angles, soma, curr_point):