Simplified patch export method

model_server/extensions/chaeo/products.py

@@ -92,11 +92,6 @@ def get_patches_from_zmask_meta(
         focus_metric: str = None,
         **kwargs
 ) -> pd.DataFrame:
-    # patches = []
-
-    # for mi in zmask_meta:
-    # dfe = roiset.get_df().assign(patch=object())
-    # for i, roi in enumerate(dfe.itertuples()):
 
     def _make_patch(roi):
         patch3d = roiset.acc_raw.data[roi.slice]
@@ -161,41 +156,21 @@ def get_patches_from_zmask_meta(
 
         if pad_to:
             patch = pad(patch, pad_to)
-
-        # patches.append(patch)
         return patch
-        # dfe.loc[i, 'patch'] = patch
+
     dfe = roiset.get_df()
     dfe['patch'] = roiset.get_df().apply(lambda r: _make_patch(r), axis=1)
     return dfe
 
-    # if not make_3d and pc == 1:
-    #     return MonoPatchStack(patches)
-    # else:
-    #     return Multichannel3dPatchStack(patches)
 
 def export_patches_from_zstack(
         where: Path,
-        # stack: GenericImageDataAccessor,
-        # zmask_meta: list,
         roiset,
-        rescale_clip: float = 0.0,
-        pad_to: int = 256,
-        make_3d: bool = False,
         prefix='patch',
-        focus_metric: str = None,
         **kwargs
 ):
-    patches_df = get_patches_from_zmask_meta(
-        roiset,
-        # stack,
-        # zmask_meta,
-        # rescale_clip=rescale_clip,
-        pad_to=pad_to,
-        make_3d=make_3d,
-        focus_metric=focus_metric,
-        **kwargs
-    )
+    make_3d = kwargs.get('make_3d', False)
+    patches_df = get_patches_from_zmask_meta(roiset, **kwargs)
 
     pc = roiset.acc_raw.chroma
     patches = list(patches_df['patch'])
@@ -204,13 +179,8 @@ def export_patches_from_zstack(
     else:
         patches_acc = Multichannel3dPatchStack(patches)
 
-    exported = []
-    for i, roi in enumerate(roiset.get_df().itertuples()):  # just used for label info
-    # for i in range(0, len(zmask_meta)):
-    #     mi = zmask_meta[i]
+    def _export_patch(roi):
         patch = patches_acc.iat_yxcz(i)
-        # obj = mi['info']
-        # idx = mi['df_index']
         ext = 'tif' if make_3d else 'png'
         fname = f'{prefix}-la{roi.label:04d}-zi{roi.zi:04d}.{ext}'
 
@@ -223,6 +193,11 @@ def export_patches_from_zstack(
             'df_index': roi.Index,
             'patch_filename': fname,
         })
+
+    exported = []
+    for i, roi in enumerate(patches_df.itertuples()):  # just used for label info
+        _export_patch(roi)
+
     return exported