feat: check valid bbox

src/aind_exaspim_soma_detection/utils/img_util.py

@@ -58,8 +58,16 @@ def get_patch(img, voxel, shape, from_center=True):
         Patch extracted from the given image.
 
     """
+    # Get image patch coordiantes
     start, end = get_start_end(voxel, shape, from_center=from_center)
-    return img[0, 0, start[0]: end[0], start[1]: end[1], start[2]: end[2]]
+    valid_start = any([s < 0 for s in start])
+    valid_end = any([e > img.shape[i + 2] for i, e in enumerate(end)])
+
+    # Get image patch
+    if valid_start and valid_end: 
+        return img[0, 0, start[0]: end[0], start[1]: end[1], start[2]: end[2]]
+    else:
+        return np.zeros(shape)
 
 
 def sliding_window_coords_3d(img, window_shape, overlap):

src/aind_exaspim_soma_detection/utils/util.py

@@ -516,3 +516,33 @@ def sample_once(my_container):
 
     """
     return sample(my_container, 1)[0]
+
+
+def time_writer(t, unit="seconds"):
+    """
+    Converts a runtime "t" to a larger unit of time if applicable.
+
+    Parameters
+    ----------
+    t : float
+        Runtime.
+    unit : str, optional
+        Unit of time that "t" is expressed in.
+
+    Returns
+    -------
+    float
+        Runtime
+    str
+        Unit of time.
+
+    """
+    assert unit in ["seconds", "minutes", "hours"]
+    upd_unit = {"seconds": "minutes", "minutes": "hours"}
+    if t < 60 or unit == "hours":
+        return t, unit
+    else:
+        t /= 60
+        unit = upd_unit[unit]
+        t, unit = time_writer(t, unit=unit)
+    return t, unit