Replace numpy nan syntax since NaN was removed

as of numpy 2.0

src/VolumeRaytraceLFM/abstract_classes.py

@@ -471,8 +471,8 @@ def rays_through_vol(pixels_per_ml, naObj, nMedium, volume_ctr_um):
 
         # Angles that reach the pixels
         cam_pixels_azim = np.arctan2(jv - ml_ctr[1], iv - ml_ctr[0])
-        cam_pixels_azim[dist_from_ctr > ml_radius] = np.NaN
-        dist_from_ctr[dist_from_ctr > ml_radius] = np.NaN
+        cam_pixels_azim[dist_from_ctr > ml_radius] = np.nan
+        dist_from_ctr[dist_from_ctr > ml_radius] = np.nan
         cam_pixels_tilt = np.arcsin(dist_from_ctr / ml_radius * naObj / nMedium)
 
         # Plotting
@@ -490,7 +490,7 @@ def rays_through_vol(pixels_per_ml, naObj, nMedium, volume_ctr_um):
             volume_ctr_um[0] * np.tan(cam_pixels_tilt) * np.cos(cam_pixels_azim)
             + volume_ctr_um[2]
         )
-        ray_enter_x[np.isnan(ray_enter_y)] = np.NaN
+        ray_enter_x[np.isnan(ray_enter_y)] = np.nan
         ray_enter = np.array([ray_enter_x, ray_enter_y, ray_enter_z])
         vol_ctr_grid_tmp = np.array(
             [
@@ -1114,17 +1114,17 @@ def plot_rays(self, colormap="inferno", use_matplotlib=False):
                 all_x = np.empty((3 * len(x_entry)))
                 all_x[::3] = x_entry
                 all_x[1::3] = x_exit
-                all_x[2::3] = np.NaN
+                all_x[2::3] = np.nan
 
                 all_y = np.empty((3 * len(y_entry)))
                 all_y[::3] = y_entry
                 all_y[1::3] = y_exit
-                all_y[2::3] = np.NaN
+                all_y[2::3] = np.nan
 
                 all_z = np.empty((3 * len(z_entry)))
                 all_z[::3] = z_entry
                 all_z[1::3] = z_exit
-                all_z[2::3] = np.NaN
+                all_z[2::3] = np.nan
 
                 # prepare colors for each line
                 rgba = [ray_ix / len(all_x) for ray_ix in range(len(all_x))]

src/VolumeRaytraceLFM/birefringence_implementations.py

@@ -344,28 +344,28 @@ def plot_lines_plotly(
 
         # Don't plot zero values
         mask = delta_n == 0
-        x_base[mask] = np.NaN
-        y_base[mask] = np.NaN
-        z_base[mask] = np.NaN
-        x_tip[mask] = np.NaN
-        y_tip[mask] = np.NaN
-        z_tip[mask] = np.NaN
+        x_base[mask] = np.nan
+        y_base[mask] = np.nan
+        z_base[mask] = np.nan
+        x_tip[mask] = np.nan
+        y_tip[mask] = np.nan
+        z_tip[mask] = np.nan
 
         # Gather all rays in single arrays, to plot them all at once, placing NAN in between them
         array_size = 3 * len(x_base.flatten())
         # Prepare colormap
         all_x = np.empty((array_size))
         all_x[::3] = x_base.flatten()
         all_x[1::3] = x_tip.flatten()
-        all_x[2::3] = np.NaN
+        all_x[2::3] = np.nan
         all_y = np.empty((array_size))
         all_y[::3] = y_base.flatten()
         all_y[1::3] = y_tip.flatten()
-        all_y[2::3] = np.NaN
+        all_y[2::3] = np.nan
         all_z = np.empty((array_size))
         all_z[::3] = z_base.flatten()
         all_z[1::3] = z_tip.flatten()
-        all_z[2::3] = np.NaN
+        all_z[2::3] = np.nan
         # Compute colors
         all_color = np.empty((array_size))
         all_color[::3] = (

src/VolumeRaytraceLFM/visualization/plotting_rays.py

@@ -355,17 +355,17 @@ def plot_rays_at_sample(
             all_x = np.empty((3 * len(x_entry)))
             all_x[::3] = x_entry
             all_x[1::3] = x_exit
-            all_x[2::3] = np.NaN
+            all_x[2::3] = np.nan
 
             all_y = np.empty((3 * len(y_entry)))
             all_y[::3] = y_entry
             all_y[1::3] = y_exit
-            all_y[2::3] = np.NaN
+            all_y[2::3] = np.nan
 
             all_z = np.empty((3 * len(z_entry)))
             all_z[::3] = z_entry
             all_z[1::3] = z_exit
-            all_z[2::3] = np.NaN
+            all_z[2::3] = np.nan
 
             # prepare colors for each line
             rgba = [ray_ix / len(all_x) for ray_ix in range(len(all_x))]