ngio 0.3.1__py3-none-any.whl → 0.3.3__py3-none-any.whl

ngio/common/_roi.py

@@ -57,6 +57,7 @@ class Roi(BaseModel):
             x_length=_to_raster(self.x_length, pixel_size.x, dim_x),
             y_length=_to_raster(self.y_length, pixel_size.y, dim_y),
             z_length=_to_raster(self.z_length, pixel_size.z, dim_z),
+            **self.model_extra,
         )
 
     def zoom(self, zoom_factor: float = 1) -> "Roi":
@@ -94,6 +95,7 @@ class RoiPixels(BaseModel):
             y_length=_to_world(self.y_length, pixel_size.y),
             z_length=_to_world(self.z_length, pixel_size.z),
             unit=pixel_size.space_unit,
+            **self.model_extra,
         )
 
     def to_slices(self) -> dict[str, slice]:

ngio/hcs/_plate.py

@@ -27,6 +27,7 @@ from ngio.ome_zarr_meta import (
 )
 from ngio.tables import (
     ConditionTable,
+    DefaultTableBackend,
     FeatureTable,
     GenericRoiTable,
     MaskingRoiTable,
@@ -199,7 +200,7 @@ class OmeZarrWell:
         )
 
 
-def _buil_extras(paths: Collection[str]) -> list[dict[str, str]]:
+def _build_extras(paths: Collection[str]) -> list[dict[str, str]]:
     """Build the extras for the images.
 
     Args:
@@ -944,7 +945,7 @@ class OmeZarrPlate:
         self,
         name: str,
         table: Table,
-        backend: TableBackend = "anndata",
+        backend: TableBackend = DefaultTableBackend,
         overwrite: bool = False,
     ) -> None:
         """Add a table to the image."""
@@ -1020,7 +1021,7 @@ class OmeZarrPlate:
                 if 'lazy', the table will be loaded as a lazy frame.
         """
         images = self.get_images(acquisition=acquisition)
-        extras = _buil_extras(images.keys())
+        extras = _build_extras(images.keys())
         return concatenate_image_tables(
             images=images.values(),
             extras=extras,
@@ -1054,7 +1055,7 @@ class OmeZarrPlate:
                 if 'lazy', the table will be loaded as a lazy frame.
         """
         images = self.get_images(acquisition=acquisition)
-        extras = _buil_extras(images.keys())
+        extras = _build_extras(images.keys())
         return concatenate_image_tables_as(
             images=images.values(),
             extras=extras,
@@ -1087,7 +1088,7 @@ class OmeZarrPlate:
                 if 'lazy', the table will be loaded as a lazy frame.
         """
         images = await self.get_images_async(acquisition=acquisition)
-        extras = _buil_extras(images.keys())
+        extras = _build_extras(images.keys())
         return await concatenate_image_tables_async(
             images=images.values(),
             extras=extras,
@@ -1121,7 +1122,7 @@ class OmeZarrPlate:
                 if 'lazy', the table will be loaded as a lazy frame.
         """
         images = await self.get_images_async(acquisition=acquisition)
-        extras = _buil_extras(images.keys())
+        extras = _build_extras(images.keys())
         return await concatenate_image_tables_as_async(
             images=images.values(),
             extras=extras,

ngio/images/_ome_zarr_container.py

@@ -23,6 +23,7 @@ from ngio.ome_zarr_meta.ngio_specs import (
 )
 from ngio.tables import (
     ConditionTable,
+    DefaultTableBackend,
     FeatureTable,
     GenericRoiTable,
     MaskingRoiTable,
@@ -501,7 +502,7 @@ class OmeZarrContainer:
         self,
         name: str,
         table: Table,
-        backend: TableBackend = "anndata",
+        backend: TableBackend = DefaultTableBackend,
         overwrite: bool = False,
     ) -> None:
         """Add a table to the image."""
@@ -831,7 +832,7 @@ def create_ome_zarr_from_array(
         axes_names=axes_names,
         name=name,
         chunks=chunks,
-        dtype=array.dtype,
+        dtype=str(array.dtype),
         overwrite=overwrite,
         version=version,
     )

ngio/tables/__init__.py

@@ -15,6 +15,7 @@ from ngio.tables._tables_container import (
     open_tables_container,
 )
 from ngio.tables.backends import (
+    DefaultTableBackend,
     ImplementedTableBackends,
     TableBackend,
     TableBackendProtocol,
@@ -23,6 +24,7 @@ from ngio.tables.v1._generic_table import GenericTable
 
 __all__ = [
     "ConditionTable",
+    "DefaultTableBackend",
     "FeatureTable",
     "GenericRoiTable",
     "GenericTable",

ngio/tables/_abstract_table.py

@@ -10,6 +10,7 @@ from anndata import AnnData
 
 from ngio.tables.backends import (
     BackendMeta,
+    DefaultTableBackend,
     ImplementedTableBackends,
     TableBackend,
     TableBackendProtocol,
@@ -203,7 +204,7 @@ class AbstractBaseTable(ABC):
     def set_backend(
         self,
         handler: ZarrGroupHandler | None = None,
-        backend: TableBackend = "anndata",
+        backend: TableBackend = DefaultTableBackend,
     ) -> None:
         """Set the backend of the table."""
         if handler is None:

ngio/tables/_tables_container.py

@@ -8,6 +8,7 @@ import polars as pl
 
 from ngio.tables.backends import (
     BackendMeta,
+    DefaultTableBackend,
     TableBackend,
     TabularData,
 )
@@ -90,13 +91,13 @@ class Table(Protocol):
     def set_backend(
         self,
         handler: ZarrGroupHandler | None = None,
-        backend: TableBackend = "anndata",
+        backend: TableBackend = DefaultTableBackend,
     ) -> None:
         """Set the backend store and path for the table.
 
         Either a handler or a backend must be provided.
 
-        If the hanlder in none it will be inferred from the backend.
+        If the handler in none it will be inferred from the backend.
         If the backend is none, it will be inferred from the group attrs
         """
         ...
@@ -314,7 +315,7 @@ class TablesContainer:
         self,
         name: str,
         table: Table,
-        backend: TableBackend = "anndata",
+        backend: TableBackend = DefaultTableBackend,
         overwrite: bool = False,
     ) -> None:
         """Add a table to the group."""
@@ -406,7 +407,7 @@ def open_table_as(
 def write_table(
     store: StoreOrGroup,
     table: Table,
-    backend: TableBackend = "anndata",
+    backend: TableBackend = DefaultTableBackend,
     cache: bool = False,
     mode: AccessModeLiteral = "a",
     parallel_safe: bool = False,

ngio/tables/backends/__init__.py

@@ -6,6 +6,7 @@ from ngio.tables.backends._csv import CsvTableBackend
 from ngio.tables.backends._json import JsonTableBackend
 from ngio.tables.backends._parquet import ParquetTableBackend
 from ngio.tables.backends._table_backends import (
+    DefaultTableBackend,
     ImplementedTableBackends,
     TableBackend,
     TableBackendProtocol,
@@ -32,6 +33,7 @@ __all__ = [
     "AnnDataBackend",
     "BackendMeta",
     "CsvTableBackend",
+    "DefaultTableBackend",
     "ImplementedTableBackends",
     "JsonTableBackend",
     "ParquetTableBackend",

ngio/tables/backends/_abstract_backend.py

@@ -19,7 +19,7 @@ from ngio.utils import NgioValueError, ZarrGroupHandler
 class BackendMeta(BaseModel):
     """Metadata for the backend."""
 
-    backend: str = "anndata"
+    backend: str = "anndata_v1"
     index_key: str | None = None
     index_type: Literal["int", "str"] | None = None
 

ngio/tables/backends/_table_backends.py

@@ -223,3 +223,4 @@ ImplementedTableBackends().add_backend(
 )
 
 TableBackend = Literal["anndata", "json", "csv", "parquet"] | str | TableBackendProtocol
+DefaultTableBackend = "anndata_v1"

ngio/tables/v1/_condition_table.py

@@ -23,7 +23,7 @@ class ConditionTableV1(AbstractBaseTable):
     The condition table is a generic table that does not
     have a specific definition.
 
-    It is used to store informations about the particular conditions
+    It is used to store information about the particular conditions
     used to generate the data.
     - How much drug was used in the experiment
     - What treatment was used

ngio/tables/v1/_roi_table.py

@@ -47,11 +47,20 @@ REQUIRED_COLUMNS = [
 ORIGIN_COLUMNS = [
     "x_micrometer_original",
     "y_micrometer_original",
+    "z_micrometer_original",
 ]
 
 TRANSLATION_COLUMNS = ["translation_x", "translation_y", "translation_z"]
 
-PLATE_COLUMNS = ["plate_name", "row", "column", "path", "acquisition"]
+PLATE_COLUMNS = [
+    "plate_name",
+    "row",
+    "column",
+    "path_in_well",
+    "path_in_plate",
+    "acquisition_id",
+    "acquisition_name",
+]
 
 INDEX_COLUMNS = [
     "FieldIndex",
@@ -390,7 +399,8 @@ class MaskingRoiTableV1(GenericRoiTableV1):
             meta = MaskingRoiTableV1Meta()
 
         if reference_label is not None:
-            meta.region = RegionMeta(path=reference_label)
+            path = f"../labels/{reference_label}"
+            meta.region = RegionMeta(path=path)
 
         if meta.index_key is None:
             meta.index_key = "label"

ngio/utils/__init__.py

@@ -3,7 +3,11 @@
 import os
 
 from ngio.common._common_types import ArrayLike
-from ngio.utils._datasets import download_ome_zarr_dataset, list_ome_zarr_datasets
+from ngio.utils._datasets import (
+    download_ome_zarr_dataset,
+    list_ome_zarr_datasets,
+    print_datasets_infos,
+)
 from ngio.utils._errors import (
     NgioFileExistsError,
     NgioFileNotFoundError,
@@ -34,13 +38,13 @@ __all__ = [
     "NgioValueError",
     "StoreOrGroup",
     "ZarrGroupHandler",
-    # Datasets
+    # Other
     "download_ome_zarr_dataset",
-    # Fractal
     "fractal_fsspec_store",
     "list_ome_zarr_datasets",
     # Logger
     "ngio_logger",
     "open_group_wrapper",
+    "print_datasets_infos",
     "set_logger_level",
 ]

ngio/utils/_datasets.py

@@ -1,35 +1,124 @@
 """Download testing OME-Zarr datasets."""
 
+import shutil
 from pathlib import Path
+from typing import Literal
 
 import pooch
 
 from ngio.utils._errors import NgioValueError
 
+
+class UnzipAndRename(pooch.Unzip):
+    """Unzip and rename the extracted directory."""
+
+    def __init__(
+        self,
+        extract_dir: str = "",
+        out_name: str = "ome-zarr.zarr",
+        re_unzip: bool = True,
+        **kwargs,
+    ):
+        super().__init__(extract_dir=extract_dir, **kwargs)
+        self.out_name = out_name
+        self.re_unzip = re_unzip
+
+    def output_file(self) -> Path:
+        """Return the output file path."""
+        if self.extract_dir is None:
+            raise NgioValueError("extract_dir must be set for UnzipAndRename.")
+
+        return Path(self.extract_dir) / self.out_name
+
+    def _extract_file(self, fname, extract_dir):
+        """Extract the file and rename it."""
+        output_path = self.output_file()
+        if output_path.exists() and not self.re_unzip:
+            # Nothing to do, the file already exists and we are not re-unzipping
+            return None
+
+        tmp_dir = Path(extract_dir) / "tmp"
+        super()._extract_file(fname, tmp_dir)
+
+        list_extracted_dirs = tmp_dir.iterdir()
+        # Keep only if ends with .zarr
+        list_extracted_dirs = filter(
+            lambda x: x.name.endswith(".zarr"),
+            list_extracted_dirs,
+        )
+        list_extracted_dirs = list(list_extracted_dirs)
+        if len(list_extracted_dirs) != 1:
+            raise NgioValueError(
+                "Expected one directory to be extracted, "
+                f"got {len(list_extracted_dirs)}."
+            )
+
+        extracted_dir = list_extracted_dirs[0]
+        if output_path.exists():
+            shutil.rmtree(output_path, ignore_errors=True)
+
+        extracted_dir.rename(output_path)
+        # Clean up the temporary directory
+        shutil.rmtree(tmp_dir, ignore_errors=True)
+
+
 _ome_zarr_zoo = {
     "CardiomyocyteTiny": {
         "url": "https://zenodo.org/records/13305156/files/20200812-CardiomyocyteDifferentiation14-Cycle1.zarr.zip",
         "known_hash": "md5:efc21fe8d4ea3abab76226d8c166452c",
-        "fname": "20200812-CardiomyocyteDifferentiation14-Cycle1.zarr.zip",
-        "processor": pooch.Unzip(extract_dir=""),
+        "fname": "20200812-CardiomyocyteDifferentiation14-Cycle1-tiny.zarr.zip",
+        "description": "Tiny cardiomyocyte dataset 3D (32MB).",
+    },
+    "CardiomyocyteTinyMip": {
+        "url": "https://zenodo.org/records/13305156/files/20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr.zip",
+        "known_hash": "md5:51809479777cafbe9ac0f9fa5636aa95",
+        "fname": "20200812-CardiomyocyteDifferentiation14-Cycle1-tiny-mip.zarr.zip",
+        "description": "Tiny cardiomyocyte dataset 2D MIP (16.4MB).",
+    },
+    "CardiomyocyteSmall": {
+        "url": "https://zenodo.org/records/13305316/files/20200812-CardiomyocyteDifferentiation14-Cycle1.zarr.zip",
+        "known_hash": "md5:d5752ed4b72a9092a0290b3c04c0b9c2",
+        "fname": "20200812-CardiomyocyteDifferentiation14-Cycle1-small.zarr.zip",
+        "description": "Small cardiomyocyte dataset 3D (750MB).",
     },
     "CardiomyocyteSmallMip": {
         "url": "https://zenodo.org/records/13305316/files/20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr.zip",
         "known_hash": "md5:3ed3ea898e0ed42d397da2e1dbe40750",
+        "fname": "20200812-CardiomyocyteDifferentiation14-Cycle1-small-mip.zarr.zip",
+        "description": "Small cardiomyocyte dataset 2D MIP (106MB).",
+    },
+    "CardiomyocyteMediumMip": {
+        "url": "https://zenodo.org/records/14826000/files/20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr.zip",
+        "known_hash": "md5:3f932bbf7fc0577f58b97471707816a1",
         "fname": "20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr.zip",
-        "processor": pooch.Unzip(extract_dir=""),
+        "description": "Medium cardiomyocyte dataset 2D MIP (30GB).",
     },
 }
 
+AVAILABLE_DATASETS = Literal[
+    "CardiomyocyteTiny",
+    "CardiomyocyteTinyMip",
+    "CardiomyocyteSmall",
+    "CardiomyocyteSmallMip",
+    "CardiomyocyteMediumMip",
+]
+
 
 def list_ome_zarr_datasets() -> list[str]:
     """List available OME-Zarr datasets."""
     return list(_ome_zarr_zoo.keys())
 
 
+def print_datasets_infos() -> None:
+    for dataset_name, dataset_info in _ome_zarr_zoo.items():
+        print(f"{dataset_name} - Description: {dataset_info['description']}")
+
+
 def download_ome_zarr_dataset(
-    dataset_name: str,
+    dataset_name: AVAILABLE_DATASETS | str,
     download_dir: str | Path = "data",
+    re_unzip: bool = True,
+    progressbar: bool = False,
 ) -> Path:
     """Download an OME-Zarr dataset.
 
@@ -38,16 +127,28 @@ def download_ome_zarr_dataset(
     Args:
         dataset_name (str): The dataset name.
         download_dir (str): The download directory. Defaults to "data".
+        re_unzip (bool): If True, it will unzip the dataset even if it already exists.
+        progressbar (bool): If True, show a progress bar during download.
     """
     if dataset_name not in _ome_zarr_zoo:
         raise NgioValueError(f"Dataset {dataset_name} not found in the OME-Zarr zoo.")
-    ome_zarr_url = _ome_zarr_zoo[dataset_name]
+    zenodo_infos = _ome_zarr_zoo[dataset_name]
+
+    fname = zenodo_infos["fname"]
+    zarrname = fname.replace(".zip", "")
+
+    processor = UnzipAndRename(
+        extract_dir="",
+        out_name=zarrname,
+        re_unzip=re_unzip,
+    )
+
     pooch.retrieve(
+        url=zenodo_infos["url"],
+        known_hash=zenodo_infos["known_hash"],
+        fname=fname,
         path=download_dir,
-        **ome_zarr_url,
+        processor=processor,
+        progressbar=progressbar,
     )
-    path = Path(download_dir) / ome_zarr_url["fname"]
-
-    if isinstance(ome_zarr_url["processor"], pooch.Unzip):
-        path = path.with_suffix("")
-    return path
+    return processor.output_file()

{ngio-0.3.1.dist-info → ngio-0.3.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.3.1
+Version: 0.3.3
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/fractal-analytics-platform/ngio
 Project-URL: repository, https://github.com/fractal-analytics-platform/ngio

{ngio-0.3.1.dist-info → ngio-0.3.3.dist-info}/RECORD

@@ -6,19 +6,19 @@ ngio/common/_common_types.py,sha256=OkAYNSNjZkixL1MI-HPBVuXamheFBr862uJ4PvTxmhk,
 ngio/common/_dimensions.py,sha256=UV2XulWaROb3Y2f4fv27ZkTIu-MoS53U26aDkrv-_lk,3900
 ngio/common/_masking_roi.py,sha256=-o6meGP17iTXEbkO9aGh1VX2drkc2laIcRJvCy_pRRM,4919
 ngio/common/_pyramid.py,sha256=SJzPauuduuqcm9B7nFCJhMTzIg6Knjsnp4CY4lN61Is,7411
-ngio/common/_roi.py,sha256=dq1iVT8-G_zWuxcYWJeHfviBSbPgsyKUcDL3Vg6jx6I,5122
+ngio/common/_roi.py,sha256=xJZ3vSusxhM1wXOizyjPbgzYhneva4IlhaWQc13Kuk4,5186
 ngio/common/_slicer.py,sha256=AKpwXRncOmF9nhjKYma0C_41WqAgSv860beKGx-aw-0,3075
 ngio/common/_table_ops.py,sha256=ToNR7F053l1dubVv-gvBD-523T10HnE2UzqeU2BuNy8,15494
 ngio/common/_zoom.py,sha256=KsURa5VuixmpbAAY5-6obmuQV8vfiHKZqBxZDXvchpM,5473
 ngio/hcs/__init__.py,sha256=G8j9vD-liLeB_UeGtKYIgshWvJnUA6ks9GwjvWBLdHs,357
-ngio/hcs/_plate.py,sha256=Z8M3slG5t16MYvPwvAzj-e9O4yAswWZp7_EDBlAxiHc,44225
+ngio/hcs/_plate.py,sha256=o-Myg1sPUT9mCfYjHOuUTIpm2Nl0siacmuztGoPcYc0,44265
 ngio/images/__init__.py,sha256=PlYvbHOMvZLDgn_PeGrytOEU3e_-AO8GWpRjEqoX_Gw,536
 ngio/images/_abstract_image.py,sha256=8PNQPZjiDz-pcTFXSJAVw7nUr4yL_iRwqDEUTKkAnp0,10266
 ngio/images/_create.py,sha256=XYn30m_2OSZeHHASYHc3eK9u_gZIYy9wo6mGdRGaq5c,9473
 ngio/images/_image.py,sha256=B9MTk3Cei-FBR4jbhSujTSNcKM_ySape28yXR_JlY0A,17980
 ngio/images/_label.py,sha256=Q1vPrXDcjJ7Gdd0wDz6NCVYQLNe1Ae6YDI4iK0oq31s,10557
 ngio/images/_masked_image.py,sha256=sd6aQetNVwtDkwUvKX-lssQyHzt5m-CYZL8ZFkwDSn8,8533
-ngio/images/_ome_zarr_container.py,sha256=hRx_8CPtFpxQUcprTT4_k5L5pjMUJ6t4wJaYr1tyljw,31181
+ngio/images/_ome_zarr_container.py,sha256=CygzzFMYFT35ztLSPKe6iKLzCtgCnVWk8M9xOj6Tc5U,31221
 ngio/ome_zarr_meta/__init__.py,sha256=oZ8PEsWM7U0KwzpsnvVfX9k4UfuTz5sZ8B6B9eY5hyY,1193
 ngio/ome_zarr_meta/_meta_handlers.py,sha256=ctknNDT8jxwyvxQf9on5gW31H1tRRsnneO38GT2UXoE,25880
 ngio/ome_zarr_meta/ngio_specs/__init__.py,sha256=05NQukZG0nNvjzf8AKWGu7PhjhQcImGSAOK3D3Bg-Js,1786
@@ -31,31 +31,31 @@ ngio/ome_zarr_meta/ngio_specs/_pixel_size.py,sha256=5TT8250XdCKUnk3OwZeyXIMNFKOg
 ngio/ome_zarr_meta/v04/__init__.py,sha256=dJRzzxyYc81kf-0Hip_bqvbdManaM8XTdQX2meWyCSs,583
 ngio/ome_zarr_meta/v04/_custom_models.py,sha256=5GxiDERvLuvq4QvApcA6EiKLS6hLFX1R0R_9rSaa85A,530
 ngio/ome_zarr_meta/v04/_v04_spec_utils.py,sha256=05tEr2eEP_XVIfBMOAWLT7lzJV4KS5eYrpK8l94tn3w,15876
-ngio/tables/__init__.py,sha256=rJGcyQUlHQb_ZbeMM9ICD8_mhTE2X9H5nKp0J-z9tMM,825
-ngio/tables/_abstract_table.py,sha256=naAeDsPTVjDUOnAxj_57UWXApg_nyWCsWdZ0f7bm740,8169
-ngio/tables/_tables_container.py,sha256=a2NNExiP1HqFVJ6HPLn0nEkYHLdf2LONVz5OxoH7OkY,12118
-ngio/tables/backends/__init__.py,sha256=tx97ZkK5kF_sAGU2kf_ZI9JxbOXn8GVjE0rUUq9h-QM,1525
-ngio/tables/backends/_abstract_backend.py,sha256=jtai3AqcLNZyxYyK0rernbMtcwxWhWAahCS0fPlMNls,7454
+ngio/tables/__init__.py,sha256=_BV3sclNMLITu_J8_3DkkUrCB6Kro0HzeWLDCD1ivKM,877
+ngio/tables/_abstract_table.py,sha256=rwGa47TzbFmosucBWVfFq6JEXtgGvOdUVtU9DIelV88,8204
+ngio/tables/_tables_container.py,sha256=3xmpREaN671l40MPprnl1BD-VoOb6xfjECb5mNoMW0w,12173
+ngio/tables/backends/__init__.py,sha256=nQZVazwTL1IHU08gL-BZcFZd7Cehhbc_AsJ3t3XSps0,1577
+ngio/tables/backends/_abstract_backend.py,sha256=tsbHzSPTX88fiCbVc8khXv5aN68ck6HKG8r5OHkY3S8,7457
 ngio/tables/backends/_anndata.py,sha256=8RX2NO15CLxys3p6gw54Nd-_0WATU4WBlNndX06wvzI,2587
 ngio/tables/backends/_anndata_utils.py,sha256=DBWIcR0btnH-DIvDvzlcnMXoYhhtXc9DstryiOP0Qsg,3122
 ngio/tables/backends/_csv.py,sha256=Ev61D-AUKo4LIhXRmWPJgYbHI7eQdxiajQR574DevEM,932
 ngio/tables/backends/_json.py,sha256=1ZsEuXDJm1rOZV_KjFm8CB0qhv7L1W7L2EGWPf4q_p0,3137
 ngio/tables/backends/_non_zarr_backends.py,sha256=SvPPhT6n5TrKUOyV1mNcdHQK49huZ5lwR8EVe9MdydM,7254
 ngio/tables/backends/_parquet.py,sha256=ic-p86h8lce8q9luBJGRzy6vxlWyJvA0-2l5cUD6OqY,1398
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