Focus 3d patches now brought into workflow parameters

extensions/chaeo/products.py

@@ -13,6 +13,16 @@ from extensions.chaeo.annotators import draw_box_on_patch
 from model_server.accessors import GenericImageDataAccessor
 from model_server.process import pad, rescale, resample_to_8bit
 
+def _focus_metrics():
+    return {
+        'max_intensity': lambda x: np.max(x),
+        'stdev': lambda x: np.std(x),
+        'max_sobel': lambda x: np.max(sobel(x)),
+        'rms_sobel': lambda x: sqrt(np.mean(sobel(x) ** 2)),
+        'entropy': lambda x: shannon_entropy(x),
+        'moment': lambda x: moment(x.flatten(), moment=2),
+    }
+
 def _write_patch_to_file(where, fname, data):
     ext = fname.split('.')[-1].upper()
     where.mkdir(parents=True, exist_ok=True)
@@ -41,6 +51,7 @@ def export_patches_from_zstack(
         pad_to: int = 256,
         make_3d: bool = False,
         prefix='patch',
+        focus_metric: str = None,
         **kwargs
 ):
     assert stack.chroma == 1, 'Expecting monochromatic image data'
@@ -65,7 +76,9 @@ def export_patches_from_zstack(
             patch = patch3d
 
         # make a 2d patch, find optimal z-position determined by focus_metric function
-        elif foc := kwargs.get('focus_metric'):
+        elif focus_metric is not None:
+            foc = _focus_metrics()[focus_metric]
+
             sp_sl = np.s_[y0: y1, x0: x1, :, :]
             subpatch = patch3d[sp_sl]
 
@@ -125,14 +138,7 @@ def export_3d_patches_with_focus_metrics(
 
     def get_zstack_focus_metrics(zs):
         nz = zs.shape[3]
-        me = {
-            'max_intensity': lambda x: np.max(x),
-            'stdev': lambda x: np.std(x),
-            'max_sobel': lambda x: np.max(sobel(x)),
-            'rms_sobel': lambda x: sqrt(np.mean(sobel(x) ** 2)),
-            'entropy': lambda x: shannon_entropy(x),
-            'moment': lambda x: moment(x.flatten(), moment=2),
-        }
+        me = _focus_metrics()
         dd = {}
         for zi in range(0, nz):
             spf = zs[:, :, :, zi]

extensions/chaeo/workflows.py

@@ -60,33 +60,29 @@ def export_patches_from_multichannel_zstack(
     zmask_acc = InMemoryDataAccessor(zmask)
     ti.click('generate_zmasks')
 
-    # export patches
-    import numpy as np
-    from skimage.filters import gaussian, sobel
-
-    # def zs_projector(zs):
-    #     sigma = 1.5
-    #     blur = gaussian(sobel(zs), sigma)
-    #     argmax = np.argmax(blur, axis=3, keepdims=True)
-    #     return np.take_along_axis(zs, argmax, axis=3)
-    #
-    # def zs_annotate_best_focus(zs):
-    #     pass
-
     files = export_patches_from_zstack(
-        # Path(where_output) / '2d_patches',
         Path(where_output) / '3d_patches',
         stack.get_one_channel_data(patches_channel),
         zmask_meta,
         prefix=fstem,
-        # draw_bounding_box=True,
         draw_bounding_box=False,
         rescale_clip=0.0,
-        # projector=zs_projector,
         make_3d=True,
     )
     ti.click('export_patches')
 
+    files = export_patches_from_zstack(
+        Path(where_output) / '2d_patches',
+        stack.get_one_channel_data(patches_channel),
+        zmask_meta,
+        prefix=fstem,
+        draw_bounding_box=False,
+        rescale_clip=0.0,
+        make_3d=False,
+        focus_metric='max_sobel',
+    )
+    ti.click('export_patches')
+
     # export annotated zstack
     annotated = InMemoryDataAccessor(
         draw_boxes_on_3d_image(