Add grower for axon trunks

Only trivial axon trunks are synthesized to allow axon grafing in
another process.

Change-Id: Iec4d2998c769834d82bfae33951a4b649198e3c6

tests/data/axon_trunk_distribution.json

@@ -0,0 +1,90 @@
+{
+    "apical": {},
+    "basal": {
+        "filtration_metric": "trunk_length",
+        "num_trees": {
+            "data": {
+                "bins": [
+                    4
+                ],
+                "weights": [
+                    1
+                ]
+            }
+        },
+        "trunk": {
+            "azimuth": {
+                "uniform": {
+                    "max": 0.0,
+                    "min": 3.141592653589793
+                }
+            },
+            "orientation_deviation": {
+                "data": {
+                    "bins": [
+                        0.09586683335089932,
+                        0.39001954178950027,
+                        1.174426764292436,
+                        1.566630375543904,
+                        2.9393430149240416
+                    ],
+                    "weights": [
+                        4,
+                        3,
+                        1,
+                        1,
+                        2
+                    ]
+                }
+            }
+        }
+    },
+    "axon": {
+        "filtration_metric": "trunk_length",
+        "num_trees": {
+            "data": {
+                "bins": [
+                    1
+                ],
+                "weights": [
+                    1
+                ]
+            }
+        },
+        "trunk": {
+            "azimuth": {
+                "uniform": {
+                    "max": 0.0,
+                    "min": 3.141592653589793
+                }
+            },
+            "orientation_deviation": {
+                "data": {
+                    "bins": [
+                        0.09586683335089932,
+                        0.39001954178950027,
+                        1.174426764292436,
+                        1.566630375543904,
+                        2.9393430149240416
+                    ],
+                    "weights": [
+                        4,
+                        3,
+                        1,
+                        1,
+                        2
+                    ]
+                }
+            }
+        }
+    },
+    "soma": {
+        "size": {
+            "norm": {
+                "mean": 9.024144162609812,
+                "std": 3.5462697985669935
+            }
+        }
+    },
+"diameter": {"method": "default"}
+}

tests/data/axon_trunk_parameters.json

@@ -0,0 +1,16 @@
+{"axon": {"randomness": 0.0,
+           "metric": "trunk_length",
+           "targeting": 0.2,
+           "radius": 0.3,
+           "num_seg": 999,
+           "orientation": null,
+           "growth_method": "axon_trunk",
+           "branching_method": "bio_oriented",
+           "modify": null,
+           "tree_type": 2,
+           "step_size": {"norm":{"mean":1.0, "std":0.2}}},
+"origin": [0.0,
+           0.0,
+           0.0],
+"grow_types": ["axon"],
+"diameter_params": {"method": "default"}}

tests/test_neuron_functional.py

@@ -6,7 +6,6 @@
 Finally, we need to check the TMD of the produced cells.
 '''
 
-
 from tempfile import TemporaryDirectory
 import json
 import os
@@ -178,6 +177,19 @@ def test_breaker_of_tmd_algo():
     assert_array_almost_equal(n.sections[169].points[-1], np.array([117.20551, -41.12157, 189.57013]), decimal=5)
     assert_array_almost_equal(n.sections[122].points[-1], np.array([ 77.08879, 115.79825,  -0.99393]), decimal=5)
 
+
+def test_axon_grower():
+    '''Test axon grower, which should only grow trunks with 1 section to allow later axon grafting.
+
+    The num_seg value in the parameters is set to 999 but only 1 segment should be synthesized.
+    '''
+    _test_full('radial_distances',
+               'axon_trunk_distribution.json',
+               'axon_trunk_parameters.json',
+               'test_axon_grower.h5',
+               None)
+
+
 def test_basic_grower():
     _test_full('radial_distances',
                'bio_trunk_distribution.json',

tns/generate/algorithms/basicgrower.py

@@ -58,3 +58,18 @@ def extend(self, current_section):
            until at least one stop criterion is fulfilled.
         '''
         return current_section.next()
+
+
+class AxonAlgo(TrunkAlgo):
+    """TreeGrower of axon growth.
+
+    Only a trunk with one segment is synthesized and another process is supposed to gaft an actual
+    axon on this trunk.
+    """
+
+    def __init__(self, *args, **kwargs):
+        # Force num_seg in params to 1
+        params = kwargs.get("params", None) or args[1]
+        params["num_seg"] = 1
+
+        super().__init__(*args, **kwargs)

tns/generate/tree.py

@@ -23,6 +23,7 @@
 growth_algorithms = {'tmd': tmdgrower.TMDAlgo,
                      'tmd_apical': tmdgrower.TMDApicalAlgo,
                      'tmd_gradient': tmdgrower.TMDGradientAlgo,
+                     'axon_trunk': basicgrower.AxonAlgo,
                      'trunk': basicgrower.TrunkAlgo}
 
 section_growers = {'radial_distances': SectionGrowerTMD,

tns/schemas/parameters.json

@@ -16,7 +16,7 @@
                 "bias_length": {"type": "number"},
                 "branching_method": {"type": "string"},
                 "growth_method": {"type": "string",
-                                  "enum": ["tmd", "tmd_gradient", "tmd_apical", "trunk"]},
+                                  "enum": ["tmd", "tmd_gradient", "tmd_apical", "axon_trunk", "trunk"]},
                 "has_apical_tuft": {"type": "boolean"},
                 "metric": {"type": "string"},
                 "modify": {"oneOf": [{"type": "object"}, {"type": "null"}]},
@@ -64,7 +64,7 @@
                            {"$ref": "#/definitions/neurite"}]},
         "basal": {"$ref": "#/definitions/neurite"},
         "grow_types": {"type": "array",
-                       "items": {"type": "string", "enum": ["basal", "apical"]}
+                       "items": {"type": "string", "enum": ["basal", "apical", "axon"]}
                        },
         "origin": {"$ref": "#/definitions/point"},
         "diameter_params": {

tns/version.py

@@ -1,2 +1,2 @@
 """ tns version """
-VERSION = "2.3.0"
+VERSION = "2.3.1.dev0"