if output folder doesnt exist, create it

.vscode/settings.json

+{
+    "python.formatting.provider": "black"
+}
\ No newline at end of file

PyNutil/generate_target_slice.py

+import numpy as np
+
+
+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))))
+    print(X_size, Z_size)
+    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_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

PyNutil/main.py

@@ -5,6 +5,7 @@ from .counting_and_load import label_points, pixel_count_per_region
 import json
 import pandas as pd
 from datetime import datetime
+import os
 
 
 class PyNutil:
@@ -218,6 +219,9 @@ class PyNutil:
             If the pixel coordinates have not been extracted.
 
         """
+        if not os.path.exists(output_folder):
+            os.makedirs(output_folder)
+
         if not hasattr(self, "pixel_points"):
             raise ValueError("Please run get_coordinates before running save_analysis")
 

workflows/calculate_objects_per_region.py

+import cv2
+from skimage import measure
+
+
+# read the segmentation image
+segmentation_path = ""
+segmentation = cv2.imread(segmentation_path)
+# apply get centroids and area function
+
+# try to label the coordinates
+
+# try to save the coordinates to a csv file