new implementation of target slice that exactly matches QuickNII

PyNutil/generate_target_slice.py

 import numpy as np
+import math
 
+def generate_target_slize(ouv, atlas):
+    width = None
+    height = None
+    ox, oy, oz, ux, uy, uz, vx, vy, vz = ouv
+    width = np.floor(math.hypot(ux,uy,uz)).astype(int) + 1
+    height = np.floor(math.hypot(vx,vy,vz)).astype(int) + 1
+    data = np.zeros((width, height), dtype=np.uint32).flatten()
+    xdim, ydim, zdim = atlas.shape
+    y_values = np.arange(height)
+    x_values = np.arange(width)
+    hx = ox + vx * (y_values / height)
+    hy = oy + vy * (y_values / height)
+    hz = oz + vz * (y_values / height)
+    wx = ux * (x_values / width)
+    wy = uy * (x_values / width)
+    wz = uz * (x_values / width)
+    lx = np.floor(hx[:, None] + wx).astype(int) 
+    ly = np.floor(hy[:, None] + wy).astype(int) 
+    lz = np.floor(hz[:, None] + wz).astype(int) 
+    valid_indices = (0 <= lx) & (lx < xdim) & (0 <= ly) & (ly < ydim) & (0 <= lz) & (lz < zdim)
+    valid_indices = valid_indices.flatten()
+    lxf = lx.flatten()
+    lyf = ly.flatten()
+    lzf = lz.flatten()
+    valid_lx = lxf[valid_indices]
+    valid_ly = lyf[valid_indices]
+    valid_lz = lzf[valid_indices]
+    atlas_slice = atlas[valid_lx,valid_ly,valid_lz]
+    data[valid_indices] = atlas_slice
+    data_im = data.reshape((height, width))
+    return data_im
 
-def generate_target_slice(alignment, volume):
-    Ox, Oy, Oz, Ux, Uy, Uz, Vx, Vy, Vz = alignment
-    ##just for mouse for now
-    bounds = [455, 527, 319]
-    X_size = np.sqrt(np.sum(np.square((Ux, Uy, Uz))))
-    Z_size = np.sqrt(np.sum(np.square((Vx, Vy, Vz))))
-    X_size = np.round(X_size).astype(int)
-    Z_size = np.round(Z_size).astype(int)
-    # make this into a grid (0,0) to (320,456)
-    Uarange = np.arange(0, 1, 1 / X_size)
-    Varange = np.arange(0, 1, 1 / Z_size)
-    Ugrid, Vgrid = np.meshgrid(Uarange, Varange)
-    Ugrid_x = Ugrid * Ux
-    Ugrid_y = Ugrid * Uy
-    Ugrid_z = Ugrid * Uz
-    Vgrid_x = Vgrid * Vx
-    Vgrid_y = Vgrid * Vy
-    Vgrid_z = Vgrid * Vz
-
-    X_Coords = (Ugrid_x + Vgrid_x).flatten() + Ox
-    Y_Coords = (Ugrid_y + Vgrid_y).flatten() + Oy
-    Z_Coords = (Ugrid_z + Vgrid_z).flatten() + Oz
-
-    X_Coords = np.round(X_Coords).astype(int)
-    Y_Coords = np.round(Y_Coords).astype(int)
-    Z_Coords = np.round(Z_Coords).astype(int)
-
-    out_bounds_Coords = (
-        (X_Coords > bounds[0])
-        | (Y_Coords > bounds[1])
-        | (Z_Coords > bounds[2])
-        | (X_Coords < 0)
-        | (Y_Coords < 0)
-        | (Z_Coords < 0)
-    )
-    X_pad = X_Coords.copy()
-    Y_pad = Y_Coords.copy()
-    Z_pad = Z_Coords.copy()
-
-    X_pad[out_bounds_Coords] = 0
-    Y_pad[out_bounds_Coords] = 0
-    Z_pad[out_bounds_Coords] = 0
-
-    regions = volume[X_pad, Y_pad, Z_pad]
-    ##this is a quick hack to solve rounding errors
-    C = len(regions)
-    compare = C - X_size * Z_size
-    if abs(compare) == X_size:
-        if compare > 0:
-            Z_size += 1
-        if compare < 0:
-            Z_size -= 1
-    elif abs(C - X_size * Z_size) == Z_size:
-        if compare > 0:
-            X_size += 1
-        if compare < 0:
-            X_size -= 1
-    elif abs(C - X_size * Z_size) == Z_size + X_size:
-        if compare > 0:
-            X_size += 1
-            Z_size += 1
-        if compare < 0:
-            X_size -= 1
-            Z_size -= 1
-    elif abs(C - X_size * Z_size) == Z_size - X_size:
-        if compare > 0:
-            X_size += 1
-            Z_size -= 1
-        if compare < 0:
-            X_size -= 1
-            Z_size += 1
-    elif abs(C - X_size * Z_size) == X_size - Z_size:
-        if compare > 0:
-            X_size -= 1
-            Z_size += 1
-        if compare < 0:
-            X_size += 1
-            Z_size -= 1
-    regions = regions.reshape((abs(Z_size), abs(X_size)))
-    return regions