patchworks 0.3.0__tar.gz → 0.5.0__tar.gz

{patchworks-0.3.0 → patchworks-0.5.0}/.github/workflows/docs.yml

@@ -4,6 +4,10 @@ on:
   push:
     branches:
       - main
+  # Rebuild after each release so the version shown in the header refreshes.
+  release:
+    types: [published]
+  workflow_dispatch:
 
 permissions:
   contents: write

{patchworks-0.3.0 → patchworks-0.5.0}/.github/workflows/lint.yml

@@ -15,9 +15,11 @@ jobs:
       - name: ruff check
         uses: astral-sh/ruff-action@v3
         with:
+          version: "0.15.18"
           args: "check"
 
       - name: ruff format --check
         uses: astral-sh/ruff-action@v3
         with:
+          version: "0.15.18"
           args: "format --check"

{patchworks-0.3.0 → patchworks-0.5.0}/.github/workflows/release.yml

@@ -22,6 +22,9 @@ jobs:
         with:
           config: cliff.toml
           args: --latest --strip header
+        env:
+          # Lets git-cliff resolve commit authors to GitHub handles/avatars.
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Create GitHub release
         uses: softprops/action-gh-release@v2

{patchworks-0.3.0 → patchworks-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: patchworks
-Version: 0.3.0
+Version: 0.5.0
 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
@@ -24,6 +24,12 @@ Requires-Dist: zarr>=2.14
 Provides-Extra: all
 Requires-Dist: bioio; extra == 'all'
 Requires-Dist: bioio-bioformats; extra == 'all'
+Requires-Dist: bioio-czi; extra == 'all'
+Requires-Dist: bioio-lif; extra == 'all'
+Requires-Dist: bioio-nd2; extra == 'all'
+Requires-Dist: bioio-ome-tiff; extra == 'all'
+Requires-Dist: bioio-tifffile; extra == 'all'
+Requires-Dist: imaris-ims-file-reader; extra == 'all'
 Requires-Dist: nvidia-ml-py; extra == 'all'
 Requires-Dist: psutil; extra == 'all'
 Requires-Dist: scikit-image; extra == 'all'
@@ -31,6 +37,11 @@ Requires-Dist: tqdm; extra == 'all'
 Provides-Extra: bioio
 Requires-Dist: bioio; extra == 'bioio'
 Requires-Dist: bioio-bioformats; extra == 'bioio'
+Requires-Dist: bioio-czi; extra == 'bioio'
+Requires-Dist: bioio-lif; extra == 'bioio'
+Requires-Dist: bioio-nd2; extra == 'bioio'
+Requires-Dist: bioio-ome-tiff; extra == 'bioio'
+Requires-Dist: bioio-tifffile; extra == 'bioio'
 Provides-Extra: cellpose
 Requires-Dist: cellpose>=3.0; extra == 'cellpose'
 Provides-Extra: dev
@@ -44,6 +55,8 @@ Requires-Dist: mkdocs-material>=9.0; extra == 'docs'
 Requires-Dist: mkdocstrings[python]>=0.24; extra == 'docs'
 Provides-Extra: gpu
 Requires-Dist: nvidia-ml-py; extra == 'gpu'
+Provides-Extra: imaris
+Requires-Dist: imaris-ims-file-reader; extra == 'imaris'
 Provides-Extra: io
 Requires-Dist: psutil; extra == 'io'
 Requires-Dist: tqdm; extra == 'io'
@@ -61,7 +74,7 @@ Description-Content-Type: text/markdown
 > Tiled processing of arbitrarily large images — any image, any function.
 
 ```
-┌──────┬──────┬──────┐     fn(tile) → labels     ┌──────┬──────┬──────┐
+┌──────┬──────┬──────┐     fn(tile) → labels      ┌──────┬──────┬──────┐
 │ tile │ tile │ tile │  ─────────────────────►    │  1   │  2   │  3   │
 ├──────┼──────┼──────┤                            ├──────┼──────┼──────┤
 │ tile │ tile │ tile │                            │  4   │  5   │  6   │   globally
@@ -88,13 +101,16 @@ Optional extras:
 pip install "patchworks[gpu]"      # GPU VRAM querying (nvidia-ml-py)
 pip install "patchworks[cellpose]" # Cellpose plugin
 pip install "patchworks[bioio]"    # convert any image format to OME-ZARR
+pip install "patchworks[imaris]"   # convert Imaris .ims files to OME-ZARR
 pip install "patchworks[napari]"   # interactive napari viewer plugin
 pip install "patchworks[all]"      # Everything (except napari GUI)
 ```
 
-> `bioio` reads CZI/LIF/ND2/OME-TIFF/… — it ships with `bioio-bioformats`, the
-> Bio-Formats catch-all reader (needs a JVM). Add faster native readers where
-> you want them (e.g. `bioio-ome-tiff`, `bioio-czi`, `bioio-lif`, `bioio-nd2`).
+> `bioio` reads CZI/LIF/ND2/OME-TIFF/… The `[bioio]` extra bundles the common
+> native readers (`bioio-nd2`, `bioio-ome-tiff`, `bioio-czi`, `bioio-tifffile`,
+> `bioio-lif`) plus `bioio-bioformats`, the Bio-Formats catch-all reader (JVM).
+> `[imaris]` adds native `.ims` support (HDF5, no JVM). Physical pixel
+> calibration is read from the input and written into the OME-ZARR.
 
 ---
 

{patchworks-0.3.0 → patchworks-0.5.0}/README.md

@@ -8,7 +8,7 @@
 > Tiled processing of arbitrarily large images — any image, any function.
 
 ```
-┌──────┬──────┬──────┐     fn(tile) → labels     ┌──────┬──────┬──────┐
+┌──────┬──────┬──────┐     fn(tile) → labels      ┌──────┬──────┬──────┐
 │ tile │ tile │ tile │  ─────────────────────►    │  1   │  2   │  3   │
 ├──────┼──────┼──────┤                            ├──────┼──────┼──────┤
 │ tile │ tile │ tile │                            │  4   │  5   │  6   │   globally
@@ -35,13 +35,16 @@ Optional extras:
 pip install "patchworks[gpu]"      # GPU VRAM querying (nvidia-ml-py)
 pip install "patchworks[cellpose]" # Cellpose plugin
 pip install "patchworks[bioio]"    # convert any image format to OME-ZARR
+pip install "patchworks[imaris]"   # convert Imaris .ims files to OME-ZARR
 pip install "patchworks[napari]"   # interactive napari viewer plugin
 pip install "patchworks[all]"      # Everything (except napari GUI)
 ```
 
-> `bioio` reads CZI/LIF/ND2/OME-TIFF/… — it ships with `bioio-bioformats`, the
-> Bio-Formats catch-all reader (needs a JVM). Add faster native readers where
-> you want them (e.g. `bioio-ome-tiff`, `bioio-czi`, `bioio-lif`, `bioio-nd2`).
+> `bioio` reads CZI/LIF/ND2/OME-TIFF/… The `[bioio]` extra bundles the common
+> native readers (`bioio-nd2`, `bioio-ome-tiff`, `bioio-czi`, `bioio-tifffile`,
+> `bioio-lif`) plus `bioio-bioformats`, the Bio-Formats catch-all reader (JVM).
+> `[imaris]` adds native `.ims` support (HDF5, no JVM). Physical pixel
+> calibration is read from the input and written into the OME-ZARR.
 
 ---
 

{patchworks-0.3.0 → patchworks-0.5.0}/cliff.toml

@@ -8,12 +8,11 @@ body = """
 - {% if commit.scope %}**{{ commit.scope }}**: {% endif %}{{ commit.message | split(pat="\n") | first }}
 {% endfor %}
 {% endfor %}\
-{% set contributors = commits | map(attribute="author.name") | unique | sort -%}
-{% if contributors | length > 0 %}
+{% if github.contributors | length > 0 %}
 ### 👥 Contributors
 
-{% for name in contributors %}\
-- {{ name }}
+{% for contributor in github.contributors | sort(attribute="username") %}\
+* @{{ contributor.username }}
 {% endfor %}
 {% endif %}\
 """
@@ -47,3 +46,7 @@ commit_parsers = [
 filter_commits = true
 tag_pattern = "v[0-9].*"
 sort_commits = "oldest"
+
+[remote.github]
+owner = "imcf"
+repo = "patchworks"

{patchworks-0.3.0 → patchworks-0.5.0}/docs/guide/ome_zarr_napari.md

@@ -38,19 +38,33 @@ existed.
 
 ## Convert any image to OME-ZARR
 
-`to_ome_zarr` accepts a dask/NumPy array, an existing `.zarr` store, or **any
-file format** readable by [bioio](https://github.com/bioio-devs/bioio) (CZI,
-LIF, ND2, OME-TIFF, …). File inputs are read **lazily** — pixels stream from
-disk and are written level by level through dask, so terabyte images convert in
-bounded RAM.
+`to_ome_zarr` accepts a dask/NumPy array, an existing `.zarr` store, an
+**Imaris `.ims`** file, or **any format** readable by
+[bioio](https://github.com/bioio-devs/bioio) (CZI, LIF, ND2, OME-TIFF, …). File
+inputs are read **lazily**.
 
 ```python
 from patchworks.plugins.ome_zarr import to_ome_zarr
 
-# From a proprietary microscope file (lazy, via bioio):
-to_ome_zarr("scan.czi", "scan.zarr", n_levels=5)
+to_ome_zarr("scan.czi", "scan.zarr", n_levels=5)   # via bioio
+to_ome_zarr("scan.ims", "scan.zarr")               # Imaris, native HDF5
 ```
 
+### Pixel calibration
+
+The physical voxel size is read from the input — bioio's `physical_pixel_sizes`,
+the Imaris resolution metadata, or an existing OME-ZARR's scale — and written
+into the NGFF `coordinateTransformations` (in micrometers), so calibration is
+preserved regardless of input. Override or supply it for bare arrays with
+`pixel_size={"z": 2.0, "y": 0.32, "x": 0.32}`.
+
+### Won't OOM
+
+Each pyramid level is built by reading the **previous level back from disk**
+and streaming the downsampled result out through dask with bounded chunks. The
+graph never chains level-on-level and no whole plane/volume is held in RAM, so
+terabyte images convert in bounded memory.
+
 !!! note "Install the readers you need"
     `pip install "patchworks[bioio]"` pulls `bioio` plus the `bioio-bioformats`
     catch-all reader (needs a JVM). For speed, add native readers for your

{patchworks-0.3.0 → patchworks-0.5.0}/mkdocs.yml

@@ -22,9 +22,11 @@ theme:
   - content.code.annotate
   - content.code.copy
   - content.tabs.link
-  - navigation.tabs
+  - navigation.expand
+  - navigation.sections
   - navigation.top
   - navigation.footer
+  - toc.integrate
   - search.highlight
   - search.share
 

{patchworks-0.3.0 → patchworks-0.5.0}/pyproject.toml

@@ -43,15 +43,24 @@ io = ["psutil", "tqdm"]
 cellpose = ["cellpose>=3.0"]
 gpu = ["nvidia-ml-py"]
 # bioio enables converting any image format (CZI, LIF, ND2, OME-TIFF, …) to
-# OME-ZARR. bioio-bioformats is the Bio-Formats catch-all reader (needs a JVM);
-# add narrower native readers too where you want them (bioio-ome-tiff,
-# bioio-czi, bioio-lif, bioio-nd2) as they are faster than going through Java.
-bioio = ["bioio", "bioio-bioformats"]
+# OME-ZARR. Ships the common native readers (faster than going through Java)
+# plus bioio-bioformats, the Bio-Formats catch-all reader (needs a JVM).
+bioio = [
+    "bioio",
+    "bioio-bioformats",
+    "bioio-nd2",
+    "bioio-ome-tiff",
+    "bioio-czi",
+    "bioio-tifffile",
+    "bioio-lif",
+]
+# imaris reads .ims files natively (HDF5, no JVM) for OME-ZARR conversion.
+imaris = ["imaris-ims-file-reader"]
 # napari enables the interactive viewer plugin (GUI-heavy, kept out of [all]).
 napari = ["napari[all]"]
 dev = ["pytest", "pytest-cov", "scikit-image", "psutil", "tqdm"]
 docs = ["mkdocs-material>=9.0", "mkdocstrings[python]>=0.24"]
-all = ["patchworks[io,gpu,bioio]", "psutil", "tqdm", "scikit-image"]
+all = ["patchworks[io,gpu,bioio,imaris]", "psutil", "tqdm", "scikit-image"]
 
 [project.urls]
 Homepage = "https://github.com/imcf/patchworks"

{patchworks-0.3.0 → patchworks-0.5.0}/src/patchworks/_io.py

@@ -47,8 +47,11 @@ def load_ome_zarr(
     (128, 2048, 2048)
     """
     root = zarr.open_group(str(store_path), mode="r")
+    # OME-ZARR 0.5 nests under "ome" key; older stores use "multiscales" directly
+    _attrs = dict(root.attrs)
+    _ms = _attrs.get("multiscales") or _attrs.get("ome", {}).get("multiscales")
     try:
-        path = root.attrs["multiscales"][0]["datasets"][level]["path"]
+        path = _ms[0]["datasets"][level]["path"]
     except (KeyError, IndexError, TypeError) as exc:
         raise ValueError(
             f"Cannot read OME-ZARR multiscales metadata at level {level} "
@@ -157,8 +160,12 @@ def estimate_empty_tiles(
     z_src: Any = None
     if isinstance(image, (str, Path)):
         _root = zarr.open_group(str(image), mode="r")
+        _rattr = dict(_root.attrs)
+        _rms = _rattr.get("multiscales") or _rattr.get("ome", {}).get(
+            "multiscales"
+        )
         try:
-            _zpath = _root.attrs["multiscales"][0]["datasets"][level]["path"]
+            _zpath = _rms[0]["datasets"][level]["path"]
         except (KeyError, IndexError, TypeError) as exc:
             raise ValueError(
                 f"Cannot read OME-ZARR multiscales metadata at level {level} "