Current fixes

aydin/features/groups/correlation.py

@@ -151,9 +151,7 @@ def _correlate(
             for axis in range(image.ndim):
 
                 # prepare shape:
-                shape = [
-                    1,
-                ] * image.ndim
+                shape = [1] * image.ndim
                 shape[axis] = kernel.shape[0]
 
                 # reshape kernel:

aydin/gui/_qt/custom_widgets/program_flow_diagram.py

@@ -47,6 +47,7 @@ def __init__(self, parent):
             "HCR (Royer)": examples_single.royerlab_hcr,
             "Blastocyst Fracking (Maitre)": examples_single.maitre_mouse,
             "OpenCell ARHGAP21 (Leonetti)": examples_single.leonetti_arhgap21,
+            "OpenCell ANKRD11  (Leonetti)": examples_single.leonetti_ankrd11,
         }
         for item in menu_items.keys():
             action = menu.addAction(item)

aydin/io/datasets.py

@@ -185,6 +185,10 @@ def get_array(self):
         '1arq6nj4oiJaxG7dPHjhYVTSYXM2Czpgx',
         'Leonetti_OC-FOV_ARHGAP21_ENSG00000107863_CID000556_FID00030711_stack.tif',
     )
+    leonetti_ankrd11 = (
+        '1Bl0WlEPeDe8MmlWy8_KaZS9QKthvSDHM',
+        'Leonetti_OC-FOV_ANKRD11_ENSG00000167522_CID001385_FID00033338_stack.tif',
+    )
 
     # XYZ
     huang_fixed_pattern_noise = (

aydin/util/crop/demo/demo_sf_rep_crop.py

@@ -54,8 +54,7 @@ def _crop_fun():
 if __name__ == "__main__":
 
     demo_super_fast_representative_crop(
-        examples_single.royerlab_hcr.get_array().squeeze(),
-        crop_size=1_000_000,
+        examples_single.royerlab_hcr.get_array().squeeze(), crop_size=1_000_000
     )
 
     demo_super_fast_representative_crop(

aydin/util/crop/super_fast_rep_crop.py

@@ -46,7 +46,7 @@ def _downscale(length):
 
         # Compute zoom factor
         zoom_per_axis = tuple(
-            1.0 / d if s > 1 else 1 for d, s in zip(downscale_factor, image.shape)
+            1.0 / d if s > d else 1 for d, s in zip(downscale_factor, image.shape)
         )
         lprint(f"zoom_per_axis: {zoom_per_axis}")
 

aydin/util/edge_filter/fast_edge_filter.py

@@ -9,13 +9,9 @@ def fast_edge_filter(array: ArrayLike, axis: int = 0, gpu: bool = True):
     # Cast to float:
     array = array.astype(dtype=numpy.float32, copy=False)
 
-    negative = [
-        '0',
-    ] * array.ndim
+    negative = ['0'] * array.ndim
     negative[axis] = '-1'
-    positive = [
-        '0',
-    ] * array.ndim
+    positive = ['0'] * array.ndim
     positive[axis] = '+1'
 
     kernel_str = f"""