ngio 0.2.0a3__tar.gz → 0.2.0b2__tar.gz

ngio-0.2.0b2/.github/scripts/download_data.sh

@@ -0,0 +1,97 @@
+#!/bin/bash
+# filepath: download_zarr_datasets.sh
+
+# Default download directory
+DOWNLOAD_DIR="data"
+
+# Create download directory if it doesn't exist
+mkdir -p "$DOWNLOAD_DIR"
+
+# Function to check MD5 hash
+check_md5() {
+    local file="$1"
+    local expected="$2"
+    
+    if [[ "$(uname)" == "Darwin" ]]; then
+        # macOS
+        actual=$(md5 -q "$file")
+    else
+        # Linux/Ubuntu
+        actual=$(md5sum "$file" | awk '{print $1}')
+    fi
+
+    echo "Expected: $expected"
+    echo "Actual: $actual"
+    
+    if [[ "$actual" == "$expected" ]]; then
+        return 0  # Success
+    else
+        return 1  # Failure
+    fi
+}
+
+# Function to download a file
+download_file() {
+    local url="$1"
+    local output="$2"
+    
+    echo "Downloading $url to $output..."
+    
+    if command -v curl &> /dev/null; then
+        curl -L -o "$output" "$url"
+    elif command -v wget &> /dev/null; then
+        wget -O "$output" "$url"
+    else
+        echo "Error: Neither curl nor wget is available. Please install one of them."
+        exit 1
+    fi
+}
+
+# Function to process a dataset
+process_dataset() {
+    local filename="$1"
+    local url="$2"
+    local expected_hash="$3"
+    
+    local file_path="$DOWNLOAD_DIR/$filename"
+    
+    echo "Processing $filename..."
+    
+    # Check if file exists and has the correct hash
+    if [[ -f "$file_path" ]] && check_md5 "$file_path" "$expected_hash"; then
+        echo "File exists and has the correct hash."
+    else
+        # File doesn't exist or has incorrect hash
+        if [[ -f "$file_path" ]]; then
+            echo "File exists but has incorrect hash. Redownloading..."
+        else
+            echo "File doesn't exist. Downloading..."
+        fi
+        
+        download_file "$url" "$file_path"
+        
+        # Verify the downloaded file
+        if check_md5 "$file_path" "$expected_hash"; then
+            echo "Download successful and hash verified."
+        else
+            echo "Error: Downloaded file has incorrect hash."
+            return 1
+        fi
+    fi
+    
+    echo "File is ready at $file_path"
+    return 0
+}
+
+# Process the CardioMyocyte dataset
+process_dataset "20200812-CardiomyocyteDifferentiation14-Cycle1.zarr.zip" \
+                "https://zenodo.org/records/13305156/files/20200812-CardiomyocyteDifferentiation14-Cycle1.zarr.zip" \
+                "efc21fe8d4ea3abab76226d8c166452c"
+
+process_dataset "20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr.zip" \
+                "https://zenodo.org/records/13305316/files/20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr.zip" \
+                "3ed3ea898e0ed42d397da2e1dbe40750"
+# To add more datasets, add more calls to process_dataset like this:
+# process_dataset "filename.zip" "download_url" "expected_md5_hash"
+
+echo "All datasets processed."

ngio-0.2.0b2/.github/workflows/build_docs.yml

@@ -0,0 +1,60 @@
+name: Build Docs
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+
+jobs:
+  download-test-ome-zarr:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Check and Download Artifacts
+        run: |
+          bash .github/scripts/download_data.sh
+
+  deploy:
+    name: Deploy Docs
+    needs: download-test-ome-zarr
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: 🐍 Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+          cache-dependency-path: "pyproject.toml"
+          cache: "pip"
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install -U pip
+          python -m pip install .[dev]
+          python -m pip install .[docs]
+
+      - name: Configure Git user
+        run: |
+          git config --local user.email "github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+        
+      - name: Deploy docs
+        run: |
+          VERSION=$(echo $GITHUB_REF | sed 's/refs\/tags\///' | sed 's/refs\/heads\///')
+          echo "Deploying version $VERSION"
+          # Check if the version is a stable release
+          # Meaning that starts with "v" and contains only numbers and dots
+          if [[ $GITHUB_REF == refs/tags/* ]] && [[ $VERSION =~ ^v[0-9.]+$ ]]; then
+            mike deploy --push --update-aliases $VERSION stable
+            mike set-default --push stable
+            echo "Deployed stable version"
+          else
+            mike deploy --push dev
+            echo "Deployed development version"
+          fi

{ngio-0.2.0a3 → ngio-0.2.0b2}/.github/workflows/ci.yml

@@ -26,8 +26,24 @@ jobs:
       - uses: actions/checkout@v4
       - run: pipx run check-manifest
 
+  
+  download-test-ome-zarr:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Check and Download Artifacts
+        run: |
+          bash .github/scripts/download_data.sh
+      - name: Upload Artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: data
+          path: data
+
+
   test:
     name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    needs: download-test-ome-zarr
     runs-on: ${{ matrix.platform }}
     strategy:
       fail-fast: false
@@ -44,6 +60,15 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - uses: actions/download-artifact@v4
+        with:
+          name: data
+          path: data
+
+      - name: Check Artifacts
+        run: |
+          ls -l data
+
       - name: 🐍 Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:

{ngio-0.2.0a3 → ngio-0.2.0b2}/.gitignore

@@ -116,7 +116,10 @@ ENV/
 pixi.lock
 *.egg-info
 
+# Ignore all .zarr directories
 *.zarr
+# but allow .zarr in tests/data
+!tests/data/**/**/test_*.zarr
 
 # ignore data directory
 ./data/

{ngio-0.2.0a3 → ngio-0.2.0b2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.2.0a3
+Version: 0.2.0b2
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio
@@ -29,6 +29,7 @@ Requires-Dist: requests
 Requires-Dist: xarray
 Requires-Dist: zarr<3
 Provides-Extra: dev
+Requires-Dist: devtools; extra == 'dev'
 Requires-Dist: matplotlib; extra == 'dev'
 Requires-Dist: mypy; extra == 'dev'
 Requires-Dist: napari; extra == 'dev'
@@ -38,7 +39,9 @@ Requires-Dist: pre-commit; extra == 'dev'
 Requires-Dist: pyqt5; extra == 'dev'
 Requires-Dist: rich; extra == 'dev'
 Requires-Dist: ruff; extra == 'dev'
+Requires-Dist: scikit-image; extra == 'dev'
 Provides-Extra: docs
+Requires-Dist: mike; extra == 'docs'
 Requires-Dist: mkdocs; extra == 'docs'
 Requires-Dist: mkdocs-autorefs; extra == 'docs'
 Requires-Dist: mkdocs-git-committers-plugin-2; extra == 'docs'
@@ -50,6 +53,7 @@ Requires-Dist: scikit-image; extra == 'docs'
 Provides-Extra: test
 Requires-Dist: pytest; extra == 'test'
 Requires-Dist: pytest-cov; extra == 'test'
+Requires-Dist: scikit-image; extra == 'test'
 Description-Content-Type: text/markdown
 
 # NGIO - Next Generation file format IO
@@ -57,7 +61,7 @@ Description-Content-Type: text/markdown
 [![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/lorenzocerrone/ngio/raw/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/ngio.svg?color=green)](https://pypi.org/project/ngio)
 [![Python Version](https://img.shields.io/pypi/pyversions/ngio.svg?color=green)](https://python.org)
-[![CI](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml)
+[![CI](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml)
 [![codecov](https://codecov.io/gh/fractal-analytics-platform/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/fractal-analytics-platform/ngio)
 
 NGIO is a Python library to streamline OME-Zarr image analysis workflows.

{ngio-0.2.0a3 → ngio-0.2.0b2}/README.md

@@ -3,7 +3,7 @@
 [![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/lorenzocerrone/ngio/raw/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/ngio.svg?color=green)](https://pypi.org/project/ngio)
 [![Python Version](https://img.shields.io/pypi/pyversions/ngio.svg?color=green)](https://python.org)
-[![CI](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml)
+[![CI](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml)
 [![codecov](https://codecov.io/gh/fractal-analytics-platform/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/fractal-analytics-platform/ngio)
 
 NGIO is a Python library to streamline OME-Zarr image analysis workflows.

{ngio-0.2.0a3 → ngio-0.2.0b2}/docs/notebooks/basic_usage.ipynb

@@ -22,11 +22,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from pathlib import Path\n",
+    "\n",
     "from ngio import open_omezarr_container\n",
     "from ngio.utils import download_ome_zarr_dataset\n",
     "\n",
-    "hcs_path = download_ome_zarr_dataset(\"CardiomyocyteSmallMip\")\n",
+    "# Download the dataset\n",
+    "download_dir = Path(\".\").absolute().parent.parent / \"data\"\n",
+    "hcs_path = download_ome_zarr_dataset(\"CardiomyocyteSmallMip\", download_dir=download_dir)\n",
     "image_path = hcs_path / \"B\" / \"03\" / \"0\"\n",
+    "\n",
+    "# Open the ome-zarr container\n",
     "omezarr_container = open_omezarr_container(image_path)"
    ]
   },
@@ -86,10 +92,10 @@
     "print(image)\n",
     "\n",
     "# 3. Get image from a specific pixel size using the pixel_size keyword\n",
-    "image = omezarr_container.get_image(\n",
-    "    pixel_size=PixelSize(x=0.65, y=0.65, z=1000), strict=True\n",
-    ")\n",
-    "print(image)"
+    "# image = omezarr_container.get_image(\n",
+    "#    pixel_size=PixelSize(x=0.65, y=0.65, z=1), strict=True\n",
+    "# )\n",
+    "print(image.pixel_size == PixelSize(x=0.325, y=0.325, z=1))"
    ]
   },
   {
@@ -287,6 +293,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import fsspec\n",
     "import fsspec.implementations.http\n",
     "\n",
     "url = (\n",
@@ -298,7 +305,6 @@
     "\n",
     "fs = fsspec.implementations.http.HTTPFileSystem(client_kwargs={})\n",
     "store = fs.get_mapper(url)\n",
-    "\n",
     "omezarr = open_omezarr_container(store)\n",
     "omezarr"
    ]
@@ -319,40 +325,6 @@
     "omezarr\n",
     "```"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from ngio import open_omezarr_container\n",
-    "from ngio.utils import fractal_fsspec_store\n",
-    "\n",
-    "store = fractal_fsspec_store(\n",
-    "    url=\"https://fractal.mls.uzh.ch/vizarr/data/data/active/lorcerr/fractal/104_altmeyer_10097/443_experiment3/AP411_U2OS.zarr/A/1/0\",\n",
-    "    fractal_token=\"eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJzdWIiOiI0MCIsImF1ZCI6WyJmYXN0YXBpLXVzZXJzOmF1dGgiXSwiZXhwIjoxNzQxMzY1NzY2fQ.wnpJSL6rtkKIoFeW7D31sVpEXeDcD0VrahwbF4CGbNI\",\n",
-    ")\n",
-    "omezarr = open_omezarr_container(store)\n",
-    "print(omezarr)\n",
-    "print(omezarr.get_image(path=\"3\").get_array())"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "omezarr.get_image(path=\"3\").get_array()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

{ngio-0.2.0a3 → ngio-0.2.0b2}/docs/notebooks/image.ipynb

@@ -15,13 +15,19 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from pathlib import Path\n",
+    "\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
     "from ngio import open_omezarr_container\n",
     "from ngio.utils import download_ome_zarr_dataset\n",
     "\n",
-    "hcs_path = download_ome_zarr_dataset(\"CardiomyocyteSmallMip\")\n",
+    "# Download the dataset\n",
+    "download_dir = Path(\".\").absolute().parent.parent / \"data\"\n",
+    "hcs_path = download_ome_zarr_dataset(\"CardiomyocyteSmallMip\", download_dir=download_dir)\n",
     "image_path = hcs_path / \"B\" / \"03\" / \"0\"\n",
+    "\n",
+    "# Open the ome-zarr container\n",
     "omezarr = open_omezarr_container(image_path)"
    ]
   },

{ngio-0.2.0a3 → ngio-0.2.0b2}/docs/notebooks/processing.ipynb

@@ -33,13 +33,19 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from pathlib import Path\n",
+    "\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
     "from ngio import open_omezarr_container\n",
     "from ngio.utils import download_ome_zarr_dataset\n",
     "\n",
-    "hcs_path = download_ome_zarr_dataset(\"CardiomyocyteTiny\")\n",
+    "# Download the dataset\n",
+    "download_dir = Path(\".\").absolute().parent.parent / \"data\"\n",
+    "hcs_path = download_ome_zarr_dataset(\"CardiomyocyteTiny\", download_dir=download_dir)\n",
     "image_path = hcs_path / \"B\" / \"03\" / \"0\"\n",
+    "\n",
+    "# Open the ome-zarr container\n",
     "omezarr = open_omezarr_container(image_path)"
    ]
   },

{ngio-0.2.0a3 → ngio-0.2.0b2}/mkdocs.yml

@@ -40,6 +40,8 @@ theme:
     - search.share
 
 extra:
+  version:
+    provider: mike
   social:
     - icon: fontawesome/brands/github
       link: "https://github.com/fractal-analytics-platform/ngio"

{ngio-0.2.0a3 → ngio-0.2.0b2}/pyproject.toml

@@ -51,18 +51,20 @@ dependencies = [
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies
 # "extras" (e.g. for `pip install .[test]`)
 [project.optional-dependencies]
-test = ["pytest", "pytest-cov"]
+test = ["pytest", "pytest-cov", "scikit-image"]
 
 dev = [
     "napari",
     "pyqt5",
     "matplotlib",
+    "devtools",
     "notebook",
     "mypy",
-    "pdbpp",      # https://github.com/pdbpp/pdbpp
+    "pdbpp",        # https://github.com/pdbpp/pdbpp
     "pre-commit",
-    "rich",       # https://github.com/Textualize/rich
+    "rich",         # https://github.com/Textualize/rich
     "ruff",
+    "scikit-image",
 ] # add anything else you like to have in your dev environment here
 
 docs = [
@@ -74,6 +76,7 @@ docs = [
     "mkdocs-git-revision-date-localized-plugin",
     "mkdocs-git-committers-plugin-2",
     "scikit-image",
+    "mike",
 ]
 
 
@@ -212,18 +215,12 @@ test13 = { features = ["py13", "test"], solve-group = "py13" }
 # dev env
 dev = { features = ["dev", "test"], solve-group = "py11" }
 
-
-[tool.pixi.feature.py11.tasks]
-pytest_test11 = "pytest"
+[tool.pixi.tasks]
+serve_docs = "mkdocs serve"
+run_tests = "pytest"
+clean_nb_data = "rm -rf ./docs/notebooks/**/*.zarr"
 test_nb = { cmd = "jupyter-execute ./docs/notebooks/*.ipynb" }
-
-[tool.pixi.feature.py12.tasks]
-pytest_test12 = "pytest"
-
-[tool.pixi.feature.py13.tasks]
-pytest_test13 = "pytest"
-
-[tool.pixi.feature.task-feat.tasks]
+test = { depends-on = ["run_tests", "clean_nb_data", "test_nb"] }
 pre_commit_install = "pre-commit install"
 
 ruff-fix-imports = "ruff check --select I --fix"
@@ -233,12 +230,3 @@ pre-commit = { cmd = "pre-commit run --all-files", depends-on = [
     "pre_commit_install",
     "ruff-format",
 ] }
-
-[tool.pixi.tasks]
-serve_docs = "mkdocs serve"
-test = { depends-on = [
-    "pytest_test11",
-    "pytest_test12",
-    "pytest_test13",
-    "test_nb",
-] }

{ngio-0.2.0a3 → ngio-0.2.0b2}/src/ngio/__init__.py

@@ -10,7 +10,7 @@ __author__ = "Lorenzo Cerrone"
 __email__ = "lorenzo.cerrone@uzh.ch"
 
 from ngio.common import ArrayLike, Dimensions
-from ngio.hcs import OmeZarrPlate, OmeZarrWell, open_omezarr_plate, open_omezarr_well
+from ngio.hcs import OmeZarrPlate, create_empty_plate, open_omezarr_plate
 from ngio.images import (
     Image,
     Label,
@@ -20,22 +20,22 @@ from ngio.images import (
     open_image,
     open_omezarr_container,
 )
-from ngio.ome_zarr_meta.ngio_specs import AxesSetup, PixelSize
+from ngio.ome_zarr_meta.ngio_specs import AxesSetup, ImageInWellPath, PixelSize
 
 __all__ = [
     "ArrayLike",
     "AxesSetup",
     "Dimensions",
     "Image",
+    "ImageInWellPath",
     "Label",
     "OmeZarrContainer",
     "OmeZarrPlate",
-    "OmeZarrWell",
     "PixelSize",
     "create_empty_omezarr",
+    "create_empty_plate",
     "create_omezarr_from_array",
     "open_image",
     "open_omezarr_container",
     "open_omezarr_plate",
-    "open_omezarr_well",
 ]

{ngio-0.2.0a3 → ngio-0.2.0b2}/src/ngio/common/__init__.py

@@ -1,6 +1,11 @@
 """Common classes and functions that are used across the package."""
 
-from ngio.common._array_pipe import get_pipe, set_pipe
+from ngio.common._array_pipe import (
+    get_masked_pipe,
+    get_pipe,
+    set_masked_pipe,
+    set_pipe,
+)
 from ngio.common._axes_transforms import (
     transform_dask_array,
     transform_list,
@@ -8,8 +13,9 @@ from ngio.common._axes_transforms import (
 )
 from ngio.common._common_types import ArrayLike
 from ngio.common._dimensions import Dimensions
+from ngio.common._masking_roi import compute_masking_roi
 from ngio.common._pyramid import consolidate_pyramid, init_empty_pyramid, on_disk_zoom
-from ngio.common._roi import RasterCooROI, WorldCooROI
+from ngio.common._roi import RasterCooROI, WorldCooROI, roi_to_slice_kwargs
 from ngio.common._slicer import (
     SliceTransform,
     compute_and_slices,
@@ -27,16 +33,20 @@ __all__ = [
     "SliceTransform",
     "WorldCooROI",
     "compute_and_slices",
+    "compute_masking_roi",
     "consolidate_pyramid",
     "dask_get_slice",
     "dask_set_slice",
     "dask_zoom",
+    "get_masked_pipe",
     "get_pipe",
     "init_empty_pyramid",
     "numpy_get_slice",
     "numpy_set_slice",
     "numpy_zoom",
     "on_disk_zoom",
+    "roi_to_slice_kwargs",
+    "set_masked_pipe",
     "set_pipe",
     "transform_dask_array",
     "transform_list",

{ngio-0.2.0a3 → ngio-0.2.0b2}/src/ngio/common/_array_pipe.py

@@ -158,3 +158,109 @@ def set_pipe(
         )
     else:
         raise NgioValueError("Unknown patch type, expected numpy, dask or delayed.")
+
+
+def _mask_pipe_common(
+    array: zarr.Array,
+    label_array: zarr.Array,
+    label: int,
+    *,
+    dimensions_array: Dimensions,
+    dimensions_label: Dimensions,
+    axes_order: Collection[str] | None = None,
+    mode: Literal["numpy", "dask", "delayed"] = "numpy",
+    **slice_kwargs: slice | int | Iterable[int],
+):
+    array_patch = get_pipe(
+        array,
+        dimensions=dimensions_array,
+        axes_order=axes_order,
+        mode=mode,
+        **slice_kwargs,
+    )
+
+    if "c" in slice_kwargs.keys():
+        # This makes the strong assumption that the
+        # user is passing the channel axis as "c"
+        # This will fail if the channel axis is queried
+        # with a different on-disk name
+        slice_kwargs.pop("c")
+
+    label_patch = get_pipe(
+        label_array,
+        dimensions=dimensions_label,
+        axes_order=axes_order,
+        mode=mode,
+        **slice_kwargs,
+    )
+
+    if isinstance(array_patch, np.ndarray):
+        label_patch = np.broadcast_to(label_patch, array_patch.shape)
+    elif isinstance(array_patch, dask.array.Array):
+        label_patch = dask.array.broadcast_to(label_patch, array_patch.shape)
+    else:
+        raise NgioValueError(f"Mode {mode} not yet supported for masked array.")
+
+    mask = label_patch == label
+    return array_patch, mask
+
+
+def get_masked_pipe(
+    array: zarr.Array,
+    label_array: zarr.Array,
+    label: int,
+    *,
+    dimensions_array: Dimensions,
+    dimensions_label: Dimensions,
+    axes_order: Collection[str] | None = None,
+    mode: Literal["numpy", "dask", "delayed"] = "numpy",
+    **slice_kwargs: slice | int | Iterable[int],
+):
+    array_patch, mask = _mask_pipe_common(
+        array=array,
+        label_array=label_array,
+        label=label,
+        dimensions_array=dimensions_array,
+        dimensions_label=dimensions_label,
+        axes_order=axes_order,
+        mode=mode,
+        **slice_kwargs,
+    )
+    array_patch[~mask] = 0
+    return array_patch
+
+
+def set_masked_pipe(
+    array: zarr.Array,
+    label_array: zarr.Array,
+    label: int,
+    patch: ArrayLike,
+    *,
+    dimensions_array: Dimensions,
+    dimensions_label: Dimensions,
+    axes_order: Collection[str] | None = None,
+    **slice_kwargs: slice | int | Iterable[int],
+):
+    if isinstance(patch, dask.array.Array):
+        mode = "dask"
+    elif isinstance(patch, np.ndarray):
+        mode = "numpy"
+    else:
+        raise NgioValueError(
+            "Mode not yet supported for masked array. Expected a numpy or dask array."
+        )
+
+    array_patch, mask = _mask_pipe_common(
+        array=array,
+        label_array=label_array,
+        label=label,
+        dimensions_array=dimensions_array,
+        dimensions_label=dimensions_label,
+        axes_order=axes_order,
+        mode=mode,
+        **slice_kwargs,
+    )
+    patch = np.where(mask, patch, array_patch)
+    set_pipe(
+        array, patch, dimensions=dimensions_array, axes_order=axes_order, **slice_kwargs
+    )