patchworks 1.3.0__tar.gz → 1.3.1__tar.gz

{patchworks-1.3.0 → patchworks-1.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: patchworks
-Version: 1.3.0
+Version: 1.3.1
 Summary: Tiled processing of arbitrarily large images with globally consistent labels
 Project-URL: Homepage, https://github.com/imcf/patchworks
 Project-URL: Issues, https://github.com/imcf/patchworks/issues

{patchworks-1.3.0 → patchworks-1.3.1}/docs/guide/ome_zarr_napari.md

@@ -152,6 +152,16 @@ just one channel instead: `view_in_napari("scan.zarr", channel=0)`.
     napari ships in `patchworks[all]`, or install just it with
     `pip install "patchworks[napari]"`.
 
+!!! tip "Measuring all the objects"
+    Once labels are loaded, use
+    [napari-chunked-regionprops](https://github.com/imcf/napari-chunked-regionprops)'s
+    "Measure" dock widget for area/centroid/intensity stats — it works
+    out-of-core straight off the Labels layer's backing dask/zarr array, so
+    it scales to the same huge label images `tile_process` writes, unlike
+    plain `skimage.measure.regionprops`. Bundled in `patchworks[napari]`. See
+    [Measurements](snakemake.md#measurements-fast-whole-volume-regionprops)
+    for the non-interactive/headless equivalent.
+
 ## End-to-end
 
 ```python

{patchworks-1.3.0 → patchworks-1.3.1}/docs/guide/snakemake.md

@@ -361,10 +361,20 @@ needs `pip install "patchworks[dog]"` in the segment jobs' environment.
 ## Measurements (fast, whole-volume regionprops)
 
 `skimage.measure.regionprops` needs the full labelled + intensity array in
-RAM — fine for one tile, not for a hundred-thousand-object OME-ZARR. Use
-[`dask-image`](https://image.dask.org)'s `ndmeasure`, which computes directly
-on the dask/zarr-backed arrays, chunk-parallel, without materializing the
-volume:
+RAM — fine for one tile, not for a hundred-thousand-object OME-ZARR.
+
+**Interactively, in napari**, this is what
+[napari-chunked-regionprops](https://github.com/imcf/napari-chunked-regionprops)
+is for — its "Measure" dock widget computes area/centroid/intensity stats
+directly off a Labels layer's dask/zarr-backed array, out-of-core, and scales
+with chunk count rather than object count. It's the best fit for measuring
+*every* object in a store this size, not just a cropped region — see
+[View image + labels in napari](ome_zarr_napari.md#view-image--labels-in-napari).
+Bundled in `patchworks[napari]`.
+
+**Headless/scripted**, use [`dask-image`](https://image.dask.org)'s
+`ndmeasure`, which computes directly on the dask/zarr-backed arrays,
+chunk-parallel, without materializing the volume:
 
 ```bash
 pip install dask-image
@@ -392,7 +402,10 @@ For interactively inspecting individual cells by clicking in the viewer
 (not all objects at once), the
 [napari-skimage-regionprops](https://github.com/haesleinhuepf/napari-skimage-regionprops)
 plugin's table widget works well — point it at a cropped region rather than
-the full volume, since it loads its input fully into memory.
+the full volume, since it loads its input fully into memory. For measuring
+*all* objects at once, use
+[napari-chunked-regionprops](https://github.com/imcf/napari-chunked-regionprops)
+instead (see above) — it doesn't have this in-memory limitation.
 
 ## Custom segmentation function
 

{patchworks-1.3.0 → patchworks-1.3.1}/pyproject.toml

@@ -72,11 +72,12 @@ imaris = ["imaris-ims-file-reader"]
 # - lxml-html-clean: napari's notebook_display imports lxml.html.clean, split
 #   into a separate package in lxml >= 5.2 (else ImportError on Viewer()).
 # - glasbey: distinct high-contrast label LUTs for view_in_napari.
-# - napari-chunked-regionprops: out-of-core regionprops-style measurements
-#   (area/centroid/intensity stats) for huge Labels layers, straight off
-#   their backing dask/zarr arrays — the "Measure" dock widget. Formerly
-#   napari-dask-ndmeasure; renamed when its engine dropped dask_image.ndmeasure
-#   for a chunk-local map/merge that scales with chunk count, not object count.
+# - napari-chunked-regionprops (https://github.com/imcf/napari-chunked-regionprops):
+#   out-of-core regionprops-style measurements (area/centroid/intensity
+#   stats) for huge Labels layers, straight off their backing dask/zarr
+#   arrays — the "Measure" dock widget. Formerly napari-dask-ndmeasure;
+#   renamed when its engine dropped dask_image.ndmeasure for a chunk-local
+#   map/merge that scales with chunk count, not object count.
 # - pyqt6 < 6.10: PyQt6-Qt6 6.10.2's Windows wheel fails to import (`DLL load
 #   failed while importing QtWidgets: The specified procedure could not be
 #   found`) — confirmed unrelated to napari/qtpy, reproduces on a bare

{patchworks-1.3.0 → patchworks-1.3.1}/src/patchworks/plugins/napari.py

@@ -187,8 +187,8 @@ def _label_hint(path: Union[str, Path]) -> dict[str, Any]:
     during the merge) — the exact id set is then ``range(1, n_objects +
     1)`` by construction, with no scan needed. Passed through as a Labels
     layer's ``metadata`` so a downstream consumer (e.g.
-    napari-chunked-regionprops) can use it instead of re-deriving the id
-    set from the array itself.
+    napari-chunked-regionprops, https://github.com/imcf/napari-chunked-regionprops)
+    can use it instead of re-deriving the id set from the array itself.
 
     Parameters
     ----------

{patchworks-1.3.0 → patchworks-1.3.1}/src/patchworks/plugins/ome_zarr.py

@@ -1083,8 +1083,10 @@ def register_labels(
         ``sequential_labels=True``, which means ``ids == range(1, n_objects
         + 1)`` by construction). When given, written into the label group's
         attrs as ``n_objects``/``sequential_labels`` so a downstream reader
-        (e.g. napari-chunked-regionprops) can use the known id set instead
-        of re-deriving it with a full-volume scan of its own.
+        (e.g. napari-chunked-regionprops,
+        https://github.com/imcf/napari-chunked-regionprops) can use the
+        known id set instead of re-deriving it with a full-volume scan of
+        its own.
 
     Returns
     -------