From 69cf9c2bdb3a1d738630dcbc13d9d2ca8f1a2888 Mon Sep 17 00:00:00 2001
From: Johannes Hjorth <hjorth@kth.se>
Date: Thu, 5 Oct 2023 12:44:59 +0200
Subject: [PATCH] Updated remove_close_neurons

---
 snudda/place/place.py             |   2 +-
 snudda/place/region_mesh_redux.py | 129 ++++++++++++++++++++++++++++++
 2 files changed, 130 insertions(+), 1 deletion(-)
 create mode 100644 snudda/place/region_mesh_redux.py

diff --git a/snudda/place/place.py b/snudda/place/place.py
index 253c70283..a2567a47e 100644
--- a/snudda/place/place.py
+++ b/snudda/place/place.py
@@ -641,7 +641,7 @@ def get_projection_axon_location(self, source_position, proj_info, rng, patch_hu
         elif mapping == "source":
             xi = source_position
         else:
-            raise NotImplentedError(f"Unknown mapping '{mapping}'!")
+            raise NotImplementedError(f"Unknown mapping '{mapping}'!")
 
         if rotation is not None:
             target_rotation = griddata(points=rot_position,
diff --git a/snudda/place/region_mesh_redux.py b/snudda/place/region_mesh_redux.py
new file mode 100644
index 000000000..e84ba82aa
--- /dev/null
+++ b/snudda/place/region_mesh_redux.py
@@ -0,0 +1,129 @@
+
+import numpy as np
+from scipy.spatial import cKDTree
+
+
+class RegionMeshRedux:
+
+    def __init__(self):
+
+        pass
+
+    def load_mesh(self):
+
+        pass
+
+    def point_inside(self, point):
+
+        pass
+
+    def distance_to_border(self, point):
+
+        pass
+
+
+class NeuronPlacer:
+
+    # Improvement suggestion. Randomize only points within a mesh-voxel, then randomise
+    # within which of the mesh voxels the points should be placed.
+
+    def __init__(self, region_mesh: RegionMeshRedux, d_min: float, seed=None):
+
+        self.region_mesh = region_mesh
+        self.d_min = d_min
+
+        self.rng = np.random.default_rng(seed)
+
+        # Temp values, should be read from the 3d mesh + padding
+        self.cube_side = 1000e-6
+        self.cube_offset = np.array([1, 2, 5000])
+
+        # Use kdtree to avoid d_min overlaps
+
+        pass
+
+    def get_point_cloud(self, n):
+        points = self.rng.uniform(size=(n, 3), low=0, high=self.cube_side) + self.cube_offset
+
+        return points
+
+    def remove_close_neurons(self, points):
+
+        done = False
+
+        while not done:
+            points, done = self._remove_close_neurons_helper(points)
+
+        return points
+
+    def _remove_close_neurons_helper(self, points):
+
+        close_pairs = cKDTree(data=points).query_pairs(r=self.d_min)
+
+        if len(close_pairs) == 0:
+            return points, True
+
+        close_neurons = np.array(list(close_pairs), dtype=int)
+        unique, counts = np.unique(close_neurons, return_counts=True)
+
+        if max(counts) == 1:
+            # Only single pairs left, be smart about removing them, just pick one of each pair
+            remove_idx = close_neurons[np.arange(0, close_neurons.shape[0]),
+                                       self.rng.integers(low=0, high=2, size=close_neurons.shape[0])]
+
+        else:
+
+            # First remove worst offenders, with the most neighbours
+            # (but none with count 1, we do those separately
+            sort_idx = np.argsort(-counts)
+            sorted_offenders = unique[sort_idx]
+            sorted_counts = counts[sort_idx]
+
+            first_pair = np.argmax(sorted_counts == 1)
+            ten_percent = int(np.ceil(0.05*len(sorted_offenders)))
+
+            remove_idx = sorted_offenders[:min(first_pair, ten_percent)]
+
+        points = np.delete(points, remove_idx, axis=0)
+
+        print(f"n_points = {points.shape[0]}, prev_close_pairs = {len(close_pairs)}")
+
+        return points, False
+
+
+    def set_neuron_density(self, neuron_type, neuron_density):
+
+        pass
+
+    def place_neurons(self, neuron_type, number_of_neurons):
+
+        pass
+
+
+class NeuronBender:
+
+    def __init__(self):
+        pass
+
+# Goal for today:
+# - Function that returns N positions that are not within d_min of each other
+# - Within a given volume
+# - Also not colliding with already previously placed points.
+
+# Idea:
+# We want to have N positions.
+# Randomize M > N positions
+# Build a cKDTree
+# Find too close neighbours query_pairs(d_min)
+# Remove the worst offenders -- how?
+
+
+
+if __name__ == "__main__":
+
+    nep = NeuronPlacer(region_mesh=None, d_min=10e-6)
+    points = nep.get_point_cloud(n=1000000)
+    new_points = nep.remove_close_neurons(points)
+
+    import pdb
+    pdb.set_trace()
\ No newline at end of file