ngio 0.1.6__tar.gz → 0.2.0a1__tar.gz

{ngio-0.1.6 → ngio-0.2.0a1}/.github/workflows/build_docs.yml

@@ -21,22 +21,11 @@ jobs:
           python-version: "3.13"
           cache-dependency-path: "pyproject.toml"
           cache: "pip"
-      
-      - name: Download Dataset from Zenodo
-        run: |
-            mkdir -p data
-            wget -O data/dataset.zip https://zenodo.org/records/13305156/files/20200812-CardiomyocyteDifferentiation14-Cycle1.zarr.zip?download=1?
-            unzip -o data/dataset.zip -d data
-      - name: Download Dataset from Zenodo MIP
-        run: |
-            mkdir -p data
-            wget -O data/dataset.zip https://zenodo.org/records/13305316/files/20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr.zip?download=1?
-            unzip -o data/dataset.zip -d data      
 
       - name: Install Dependencies
         run: |
           python -m pip install -U pip
-          python -m pip install .[dev2]
+          python -m pip install .[dev]
           python -m pip install .[docs]
 
       - name: 📚 Build Docs

{ngio-0.1.6 → ngio-0.2.0a1}/.github/workflows/ci.yml

@@ -32,11 +32,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
-        # Skip Windows for now It's seems there are some issues with the
-        # ZarrV3 on Windows
+        python-version: ["3.11", "3.12", "3.13"]
         platform: [ubuntu-latest, macos-latest, windows-latest]
         # platform: [ubuntu-latest, macos-latest]
+        exclude:
+          - python-version: "3.11"
+            platform: windows-latest
+          - python-version: "3.12"
+            platform: windows-latest
 
     steps:
       - uses: actions/checkout@v4
@@ -78,30 +81,6 @@ jobs:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: /home/runner/work/ngio/ngio/coverage.xml
 
-  zarrv3:
-    name: Test zarr-python v3 compatibility
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: 🐍 Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
-          cache-dependency-path: "pyproject.toml"
-          cache: "pip"
-
-      - name: Install Dependencies
-        run: |
-          python -m pip install -U pip
-          # if running a cron job, we add the --pre flag to test against pre-releases
-          python -m pip install .[dev3] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
-
-      - name: 🧪 Run Tests
-        run: pytest
-        continue-on-error: true
-
   deploy:
     name: Deploy
     needs: test

{ngio-0.1.6 → ngio-0.2.0a1}/.gitignore

@@ -119,5 +119,13 @@ pixi.lock
 *.zarr
 
 # ignore data directory
-data/
-*.zip
+./data/
+*.zip
+
+src/ngio/_v01
+tests/_v01
+
+# Ignore locks
+*.lock
+
+benchmark/*

{ngio-0.1.6 → ngio-0.2.0a1}/.pre-commit-config.yaml

@@ -21,7 +21,7 @@ repos:
         args: [--force-exclude, --write-changes]
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.4.8
+    rev: v0.9.6
     hooks:
       - id: ruff
         args: [--fix]  # may also add '--unsafe-fixes'

{ngio-0.1.6 → ngio-0.2.0a1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.1.6
+Version: 0.2.0a1
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio
@@ -10,54 +10,34 @@ License-File: LICENSE
 Classifier: Development Status :: 3 - Alpha
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Typing :: Typed
-Requires-Python: >=3.10
+Requires-Python: <3.14,>=3.11
 Requires-Dist: aiohttp
 Requires-Dist: anndata>=0.8.0
 Requires-Dist: dask[array]
+Requires-Dist: dask[distributed]
+Requires-Dist: filelock
 Requires-Dist: numpy
+Requires-Dist: ome-zarr-models
 Requires-Dist: pandas>=1.2.0
+Requires-Dist: pooch
 Requires-Dist: pydantic
 Requires-Dist: requests
-Provides-Extra: core
-Requires-Dist: dask-image; extra == 'core'
-Requires-Dist: dask[distributed]; extra == 'core'
-Requires-Dist: zarr<3; extra == 'core'
-Provides-Extra: dev2
-Requires-Dist: dask-image; extra == 'dev2'
-Requires-Dist: dask[distributed]; extra == 'dev2'
-Requires-Dist: ipython; extra == 'dev2'
-Requires-Dist: matplotlib; extra == 'dev2'
-Requires-Dist: mypy; extra == 'dev2'
-Requires-Dist: napari; extra == 'dev2'
-Requires-Dist: notebook; extra == 'dev2'
-Requires-Dist: pdbpp; extra == 'dev2'
-Requires-Dist: plotly; extra == 'dev2'
-Requires-Dist: pre-commit; extra == 'dev2'
-Requires-Dist: pyqt5; extra == 'dev2'
-Requires-Dist: pytest; extra == 'dev2'
-Requires-Dist: pytest-cov; extra == 'dev2'
-Requires-Dist: rich; extra == 'dev2'
-Requires-Dist: ruff; extra == 'dev2'
-Requires-Dist: scikit-image; extra == 'dev2'
-Requires-Dist: zarr<3; extra == 'dev2'
-Provides-Extra: dev3
-Requires-Dist: dask-image; extra == 'dev3'
-Requires-Dist: dask[distributed]; extra == 'dev3'
-Requires-Dist: ipython; extra == 'dev3'
-Requires-Dist: mypy; extra == 'dev3'
-Requires-Dist: notebook; extra == 'dev3'
-Requires-Dist: pdbpp; extra == 'dev3'
-Requires-Dist: pre-commit; extra == 'dev3'
-Requires-Dist: pytest; extra == 'dev3'
-Requires-Dist: pytest-cov; extra == 'dev3'
-Requires-Dist: rich; extra == 'dev3'
-Requires-Dist: ruff; extra == 'dev3'
-Requires-Dist: zarr==v3.0.0-alpha.4; extra == 'dev3'
+Requires-Dist: xarray
+Requires-Dist: zarr<3
+Provides-Extra: dev
+Requires-Dist: matplotlib; extra == 'dev'
+Requires-Dist: mypy; extra == 'dev'
+Requires-Dist: napari; extra == 'dev'
+Requires-Dist: notebook; extra == 'dev'
+Requires-Dist: pdbpp; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: pyqt5; extra == 'dev'
+Requires-Dist: rich; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
 Provides-Extra: docs
 Requires-Dist: mkdocs; extra == 'docs'
 Requires-Dist: mkdocs-autorefs; extra == 'docs'
@@ -70,7 +50,6 @@ Requires-Dist: scikit-image; extra == 'docs'
 Provides-Extra: test
 Requires-Dist: pytest; extra == 'test'
 Requires-Dist: pytest-cov; extra == 'test'
-Requires-Dist: zarr<3; extra == 'test'
 Description-Content-Type: text/markdown
 
 # NGIO - Next Generation file format IO

{ngio-0.1.6 → ngio-0.2.0a1}/docs/notebooks/basic_usage.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# OME-Zarr Image Exploration\n",
     "\n",
-    "In this notebook we will show how to use the 'NgffImage' class to explore and manage an OME-NGFF image.\n",
+    "In this notebook we will show how to use the 'OmeZarr Container' class to explore and manage an OME-NGFF image.\n",
     "\n",
     "For this example we will use a small example image that can be downloaded from the following link: [example ome-zarr](https://zenodo.org/records/13305156)\n",
     "\n",
@@ -19,10 +19,10 @@
     "```\n",
     "from the root of the repository.\n",
     "\n",
-    "## NgffImage\n",
+    "## OmeZarr Container\n",
     "\n",
-    "The `NgffImage` provides a high-level interface to read, write and manipulate NGFF images.\n",
-    "A `NgffImage` can be created from a storelike object (e.g. a path to a directory, or a url) or from a `zarr.Group` object. "
+    "The `OmeZarr Container` provides a high-level interface to read, write and manipulate NGFF images.\n",
+    "A `OmeZarr Container` can be created from a storelike object (e.g. a path to a directory, or a url) or from a `zarr.Group` object. "
    ]
   },
   {
@@ -31,11 +31,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ngio.core import NgffImage\n",
+    "from ngio import open_omezarr_container\n",
+    "from ngio.utils import download_ome_zarr_dataset\n",
     "\n",
-    "# Ngio can stream data from any fsspec-compatible store\n",
-    "path = \"../../data/20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr/B/03/0\"\n",
-    "ngff_image = NgffImage(path, \"r\")"
+    "hcs_path = download_ome_zarr_dataset(\"CardiomyocyteSmallMip\")\n",
+    "image_path = hcs_path / \"B\" / \"03\" / \"0\"\n",
+    "omezarr_container = open_omezarr_container(image_path)"
    ]
   },
   {
@@ -43,7 +44,7 @@
    "metadata": {},
    "source": [
     "\n",
-    "The `ngff_image` object provides a high-level interface to read, write and manipulate OME-Zarr images.\n",
+    "The `omezarr_container` object provides a high-level interface to read, write and manipulate OME-Zarr images.\n",
     "\n",
     "Print the image will show some overview information like:\n",
     "* The path to the image\n",
@@ -58,14 +59,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(ngff_image)"
+    "print(omezarr_container)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "From the `NgffImage` object we can easily access access the image data (at any resolution level), the labels and the tables."
+    "From the `OmeZarr Container` object we can easily access access the image data (at any resolution level), the labels and the tables."
    ]
   },
   {
@@ -83,18 +84,18 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ngio.ngff_meta import PixelSize\n",
+    "from ngio import PixelSize\n",
     "\n",
     "# 1. Get image from highest resolution (default)\n",
-    "image = ngff_image.get_image()\n",
+    "image = omezarr_container.get_image()\n",
     "print(image)\n",
     "\n",
     "# 2. Get image from a specific level using the path keyword\n",
-    "image = ngff_image.get_image(path=\"1\")\n",
+    "image = omezarr_container.get_image(path=\"1\")\n",
     "print(image)\n",
     "\n",
     "# 3. Get image from a specific pixel size using the pixel_size keyword\n",
-    "image = ngff_image.get_image(pixel_size=PixelSize(x=0.65, y=0.65, z=1))\n",
+    "image = omezarr_container.get_image(pixel_size=PixelSize(x=0.65, y=0.65, z=1))\n",
     "print(image)"
    ]
   },
@@ -112,7 +113,6 @@
    "outputs": [],
    "source": [
     "print(\"Shape\", image.shape)\n",
-    "print(\"Axes\", image.axes_names)\n",
     "print(\"PixelSize\", image.pixel_size)\n",
     "print(\"Dimensions\", image.dimensions)\n",
     "print(\"Channel Names\", image.channel_labels)"
@@ -137,19 +137,7 @@
    "metadata": {},
    "source": [
     "`ngio` design is to always provide the data in a canonical axis order (`t`, `c`, `z`, `y`, `x`) no matter what is the order on disk.  \n",
-    "The `Image` object provides methods to access the data in this order.  \n",
-    "If you want to access data or metadata in the on-disk order, you can by using `on_disk_{method_name}` methods.\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print(\"On-disk shape\", image.on_disk_shape)\n",
-    "print(\"On-disk array\", image.on_disk_array)\n",
-    "print(\"On-disk dask array\", image.on_disk_dask_array)"
+    "The `Image` object provides methods to access the data in this order.  \n"
    ]
   },
   {
@@ -167,9 +155,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(\"List of Labels: \", ngff_image.labels.list())\n",
+    "print(\"List of Labels: \", omezarr_container.list_labels())\n",
     "\n",
-    "label_nuclei = ngff_image.labels.get_label(\"nuclei\", path=\"0\")\n",
+    "label_nuclei = omezarr_container.get_label(\"nuclei\", path=\"0\")\n",
     "print(label_nuclei)"
    ]
   },
@@ -193,10 +181,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(\"List of Tables: \", ngff_image.tables.list())\n",
-    "print(\" - Feature tables: \", ngff_image.tables.list(table_type=\"feature_table\"))\n",
-    "print(\" - Roi tables: \", ngff_image.tables.list(table_type=\"roi_table\"))\n",
-    "print(\" - Masking Roi tables: \", ngff_image.tables.list(table_type=\"masking_roi_table\"))"
+    "print(\"List of Tables: \", omezarr_container.list_tables())"
    ]
   },
   {
@@ -206,8 +191,8 @@
    "outputs": [],
    "source": [
     "# Loading a table\n",
-    "feature_table = ngff_image.tables.get_table(\"regionprops_DAPI\")\n",
-    "feature_table.table"
+    "feature_table = omezarr_container.get_table(\"regionprops_DAPI\")\n",
+    "feature_table.dataframe"
    ]
   },
   {
@@ -217,12 +202,9 @@
    "outputs": [],
    "source": [
     "# Loading a roi table\n",
-    "roi_table = ngff_image.tables.get_table(\"FOV_ROI_table\")\n",
-    "\n",
-    "print(f\"{roi_table.field_indexes=}\")\n",
-    "print(f\"{roi_table.get_roi('FOV_1')=}\")\n",
+    "roi_table = omezarr_container.get_table(\"FOV_ROI_table\")\n",
     "\n",
-    "roi_table.table"
+    "print(f\"{roi_table.get('FOV_1')=}\")"
    ]
   },
   {
@@ -241,10 +223,10 @@
     "import matplotlib.pyplot as plt\n",
     "\n",
     "# Plotting a single ROI\n",
-    "roi = roi_table.get_roi(\"FOV_1\")\n",
-    "roi_data = image.get_array_from_roi(roi, c=0, mode=\"numpy\")\n",
+    "roi = roi_table.get(\"FOV_1\")\n",
+    "roi_data = image.get_roi(roi, c=0, mode=\"numpy\")\n",
     "plt.title(\"ROI: FOV_1\")\n",
-    "plt.imshow(roi_data[0], cmap=\"gray\")\n",
+    "plt.imshow(roi_data[0, 0], cmap=\"gray\")\n",
     "plt.axis(\"off\")\n",
     "plt.show()"
    ]
@@ -267,19 +249,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "new_ngff_image = ngff_image.derive_new_image(\n",
-    "    \"../../data/new_ome.zarr\", name=\"new_image\"\n",
-    ")\n",
-    "print(new_ngff_image)"
+    "new_omezarr_image = omezarr_container.derive_image(\"data/new_ome.zarr\", overwrite=True)\n",
+    "print(new_omezarr_image)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Steam an NgffImage over HTTP\n",
+    "## Steam an OmeZarr over HTTP\n",
     "\n",
-    "The `NgffImage` class can also be used to stream an image over HTTP. This is useful when the image is stored on a remote server and you want to access it without downloading the entire image. All features of the `NgffImage` class are available when streaming an image over HTTP (besides anything that requires writing to the image)."
+    "The `OmeZarr` class can also be used to stream an image over HTTP. This is useful when the image is stored on a remote server and you want to access it without downloading the entire image. All features of the `OmeZarr` class are available when streaming an image over HTTP (besides anything that requires writing to the image)."
    ]
   },
   {
@@ -288,20 +268,33 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ngio.core.utils import get_fsspec_http_store\n",
+    "import fsspec.implementations.http\n",
+    "\n",
+    "url = (\n",
+    "    \"https://raw.githubusercontent.com/\"\n",
+    "    \"fractal-analytics-platform/fractal-ome-zarr-examples/\"\n",
+    "    \"refs/heads/main/v04/\"\n",
+    "    \"20200812-CardiomyocyteDifferentiation14-Cycle1_B_03_mip.zarr/\"\n",
+    ")\n",
     "\n",
-    "# Ngio can stream data from any fsspec-compatible store\n",
-    "url = \"https://raw.githubusercontent.com/fractal-analytics-platform/fractal-ome-zarr-examples/refs/heads/main/v04/20200812-CardiomyocyteDifferentiation14-Cycle1_B_03_mip.zarr/\"\n",
-    "store = get_fsspec_http_store(url)\n",
-    "ngff_image = NgffImage(store, \"r\")\n",
+    "fs = fsspec.implementations.http.HTTPFileSystem(client_kwargs={})\n",
+    "store = fs.get_mapper(url)\n",
     "\n",
-    "print(ngff_image)"
+    "omezarr = open_omezarr_container(store)\n",
+    "omezarr"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "ngio",
+   "display_name": "dev",
    "language": "python",
    "name": "python3"
   },
@@ -315,7 +308,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.7"
+   "version": "3.11.11"
   }
  },
  "nbformat": 4,

{ngio-0.1.6 → ngio-0.2.0a1}/docs/notebooks/image.ipynb

@@ -18,10 +18,11 @@
     "import matplotlib.pyplot as plt\n",
     "\n",
     "from ngio.core.ngff_image import NgffImage\n",
+    "from ngio.utils import download_ome_zarr_dataset\n",
     "\n",
-    "ngff_image = NgffImage(\n",
-    "    \"../../data/20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr/B/03/0\"\n",
-    ")"
+    "hcs_path = download_ome_zarr_dataset(\"CardiomyocyteSmallMip\")\n",
+    "image_path = hcs_path / \"B\" / \"03\" / \"0\"\n",
+    "ngff_image = NgffImage(image_path)"
    ]
   },
   {
@@ -317,11 +318,18 @@
     "\n",
     "feat_table.table"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "ngio",
+   "display_name": "dev",
    "language": "python",
    "name": "python3"
   },
@@ -335,7 +343,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.7"
+   "version": "3.11.11"
   }
  },
  "nbformat": 4,

{ngio-0.1.6 → ngio-0.2.0a1}/docs/notebooks/processing.ipynb

@@ -36,10 +36,11 @@
     "import matplotlib.pyplot as plt\n",
     "\n",
     "from ngio.core import NgffImage\n",
+    "from ngio.utils import download_ome_zarr_dataset\n",
     "\n",
-    "ngff_image = NgffImage(\n",
-    "    \"../../data/20200812-CardiomyocyteDifferentiation14-Cycle1.zarr/B/03/0\"\n",
-    ")"
+    "hcs_path = download_ome_zarr_dataset(\"CardiomyocyteTiny\")\n",
+    "image_path = hcs_path / \"B\" / \"03\" / \"0\"\n",
+    "ngff_image = NgffImage(image_path)"
    ]
   },
   {
@@ -56,7 +57,7 @@
    "outputs": [],
    "source": [
     "mip_ngff = ngff_image.derive_new_image(\n",
-    "    \"../../data/20200812-CardiomyocyteDifferentiation14-Cycle1.zarr/B/03/0_mip\",\n",
+    "    \"data/20200812-CardiomyocyteDifferentiation14-Cycle1.zarr/B/03/0_mip\",\n",
     "    name=\"MIP\",\n",
     "    on_disk_shape=(1, 1, 2160, 5120),\n",
     ")"
@@ -292,7 +293,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "dev2",
+   "display_name": "dev",
    "language": "python",
    "name": "python3"
   },
@@ -306,7 +307,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.15"
+   "version": "3.11.11"
   }
  },
  "nbformat": 4,