Merge 90a0d07 into 9810954

AxonDeepSeg/visualization/simulate_axons.py

@@ -0,0 +1,52 @@
+import numpy as np
+from scipy.misc import imrotate
+import imageio
+import AxonDeepSeg.ads_utils
+
+class SimulateAxons:
+
+    def __init__(self, image_dims=[1000,1000]):
+        self.width = image_dims[0]
+        self.height = image_dims[1]
+        self.origin = [self.width/2, self.height/2]
+
+        # Initialize image
+        self.image = np.zeros([self.width, self.height], dtype=np.uint8)
+
+    def generate_axon(self, axon_radius, center=None, gratio = 0.7, axon_angle = 0, plane_angle = 0, eccentricity = 0):
+        if center is None:
+            center=self.origin
+
+        axon_major_axis_radius = axon_radius/np.cos(np.deg2rad(plane_angle))
+
+        if eccentricity != 0:
+            axon_minor_axis_radius = np.sqrt(axon_radius**2-(eccentricity*axon_radius)**2)
+        else:
+            axon_minor_axis_radius = axon_radius
+
+        x = np.arange(0, self.width)
+        y = np.arange(0, self.height)
+        axon = (x[np.newaxis,:]-center[0])**2/(axon_major_axis_radius**2) + (y[:,np.newaxis]-center[1])**2/(axon_minor_axis_radius**2) < 1
+
+        myelin_outer = (x[np.newaxis,:]-center[0])**2/(axon_major_axis_radius/gratio)**2 + (y[:,np.newaxis]-center[1])**2/(axon_minor_axis_radius/gratio)**2 < 1
+        myelin = (myelin_outer ^ axon)
+
+        # Convert to int befor rotate
+        axon = np.ndarray.astype(axon, int)
+        myelin = np.ndarray.astype(myelin, int)
+
+        axon = imrotate(axon, axon_angle, 'nearest')
+        myelin = imrotate(myelin, axon_angle, 'nearest')
+
+        # Convert back to bool
+        axon = np.ndarray.astype(axon, bool)
+        myelin = np.ndarray.astype(myelin, bool)
+
+        self.image[axon & (self.image==0)]=255
+        self.image[myelin & (self.image==0)]=127
+
+    def save(self, filename="SimulatedAxons.png"):
+        imageio.imwrite(filename, self.image)
+
+    def reset(self):
+        self.image = np.zeros([self.width, self.height], dtype=np.uint8)