Sc 50 disk backed operations (#94)

* SC_50 disk backed operations * SC_50 update comment * SC50 disk backed operations, reload * SC_50 disk backed, delete before load
saeyslab · Feb 14, 2025 · 5ff9d74 · 5ff9d74
1 parent 72c603a
commit 5ff9d74
Show file tree

Hide file tree

Showing 6 changed files with 7 additions and 7 deletions.
diff --git a/src/harpy/image/_manager.py b/src/harpy/image/_manager.py
@@ -154,8 +154,8 @@ def add_to_sdata(
             sdata[output_layer] = spatial_element
             if sdata.is_backed():
                 sdata.write_element(output_layer)
-                sdata_temp = read_zarr(sdata.path, selection=["images"])
                 del sdata[output_layer]
+                sdata_temp = read_zarr(sdata.path, selection=["images"])
                 sdata[output_layer] = sdata_temp[output_layer]
                 del sdata_temp
 
@@ -224,8 +224,8 @@ def add_to_sdata(
             sdata[output_layer] = spatial_element
             if sdata.is_backed():
                 sdata.write_element(output_layer)
-                sdata_temp = read_zarr(sdata.path, selection=["labels"])
                 del sdata[output_layer]
+                sdata_temp = read_zarr(sdata.path, selection=["labels"])
                 sdata[output_layer] = sdata_temp[output_layer]
                 del sdata_temp
 

diff --git a/src/harpy/image/pixel_clustering/_clustering.py b/src/harpy/image/pixel_clustering/_clustering.py
@@ -223,8 +223,8 @@ def _fix_name(layer: str | Iterable[str]):
             _labels_flowsom_name = f"labels_flowsom_{uuid.uuid4()}"
             sdata.images[_labels_flowsom_name] = se_intermediate
             sdata.write_element(_labels_flowsom_name)
-            sdata_temp = read_zarr(sdata.path, selection=["images"])
             del sdata[_labels_flowsom_name]
+            sdata_temp = read_zarr(sdata.path, selection=["images"])
             sdata[_labels_flowsom_name] = sdata_temp[_labels_flowsom_name]
             del sdata_temp
             _labels_flowsom = _get_spatial_element(sdata, layer=_labels_flowsom_name).data

diff --git a/src/harpy/points/_points.py b/src/harpy/points/_points.py
@@ -64,8 +64,8 @@ def add_points_layer(
         sdata[output_layer] = points
         if sdata.is_backed():
             sdata.write_element(output_layer)
-            sdata_temp = read_zarr(sdata.path, selection=["points"])
             del sdata[output_layer]
+            sdata_temp = read_zarr(sdata.path, selection=["points"])
             sdata[output_layer] = sdata_temp[output_layer]
             del sdata_temp
     return sdata
diff --git a/src/harpy/shape/_manager.py b/src/harpy/shape/_manager.py
@@ -207,8 +207,8 @@ def add_to_sdata(
             sdata[output_layer] = spatial_element
             if sdata.is_backed():
                 sdata.write_element(output_layer)
-                sdata_temp = read_zarr(sdata.path, selection=["shapes"])
                 del sdata[output_layer]
+                sdata_temp = read_zarr(sdata.path, selection=["shapes"])
                 sdata[output_layer] = sdata_temp[output_layer]
                 del sdata_temp
 

diff --git a/src/harpy/table/_manager.py b/src/harpy/table/_manager.py
@@ -61,8 +61,8 @@ def add_table(
             sdata[output_layer] = adata
             if sdata.is_backed():
                 sdata.write_element(output_layer)
-                sdata_temp = read_zarr(sdata.path, selection=["tables"])
                 del sdata[output_layer]
+                sdata_temp = read_zarr(sdata.path, selection=["tables"])
                 sdata[output_layer] = sdata_temp[output_layer]
                 del sdata_temp
 

diff --git a/src/harpy/utils/_io.py b/src/harpy/utils/_io.py
@@ -45,9 +45,9 @@ def _incremental_io_on_disk(
     sdata.write_element(output_layer)
     # b2. reload the new data into memory (because it has been written but in-memory it still points
     # from the backup location)
+    del sdata[output_layer]
     sdata_materialized = read_zarr(sdata.path, selection=[element_type])
     # to make sdata point to layer that is materialized, and keep object id.
-    del sdata[output_layer]
     sdata[output_layer] = sdata_materialized[output_layer]
     # c. remove the backup copy
     del sdata_materialized[new_output_layer]