ngio 0.3.4__py3-none-any.whl → 0.4.0__py3-none-any.whl

ngio/images/_create.py

@@ -1,8 +1,10 @@
 """Utility functions for working with OME-Zarr images."""
 
-from collections.abc import Collection
+from collections.abc import Sequence
 from typing import TypeVar
 
+from zarr.types import DIMENSION_SEPARATOR
+
 from ngio.common._pyramid import init_empty_pyramid
 from ngio.ome_zarr_meta import (
     NgioImageMeta,
@@ -29,7 +31,7 @@ _image_or_label_meta = TypeVar("_image_or_label_meta", NgioImageMeta, NgioLabelM
 def _init_generic_meta(
     meta_type: type[_image_or_label_meta],
     pixelsize: float,
-    axes_names: Collection[str],
+    axes_names: Sequence[str],
     z_spacing: float = 1.0,
     time_spacing: float = 1.0,
     levels: int | list[str] = 5,
@@ -80,7 +82,7 @@ def _init_generic_meta(
 
 def create_empty_label_container(
     store: StoreOrGroup,
-    shape: Collection[int],
+    shape: Sequence[int],
     pixelsize: float,
     z_spacing: float = 1.0,
     time_spacing: float = 1.0,
@@ -89,10 +91,12 @@ def create_empty_label_container(
     z_scaling_factor: float = 1.0,
     space_unit: SpaceUnits | str | None = DefaultSpaceUnit,
     time_unit: TimeUnits | str | None = DefaultTimeUnit,
-    axes_names: Collection[str] | None = None,
+    axes_names: Sequence[str] | None = None,
     name: str | None = None,
-    chunks: Collection[int] | None = None,
-    dtype: str = "uint16",
+    chunks: Sequence[int] | None = None,
+    dtype: str = "uint32",
+    dimension_separator: DIMENSION_SEPARATOR = "/",
+    compressor="default",
     overwrite: bool = False,
     version: NgffVersions = DefaultNgffVersion,
 ) -> ZarrGroupHandler:
@@ -100,7 +104,7 @@ def create_empty_label_container(
 
     Args:
         store (StoreOrGroup): The Zarr store or group to create the image in.
-        shape (Collection[int]): The shape of the image.
+        shape (Sequence[int]): The shape of the image.
         pixelsize (float): The pixel size in x and y dimensions.
         z_spacing (float, optional): The spacing between z slices. Defaults to 1.0.
         time_spacing (float, optional): The spacing between time points.
@@ -115,11 +119,14 @@ def create_empty_label_container(
             DefaultSpaceUnit.
         time_unit (TimeUnits, optional): The unit of time. Defaults to
             DefaultTimeUnit.
-        axes_names (Collection[str] | None, optional): The names of the axes.
+        axes_names (Sequence[str] | None, optional): The names of the axes.
             If None the canonical names are used. Defaults to None.
         name (str | None, optional): The name of the image. Defaults to None.
-        chunks (Collection[int] | None, optional): The chunk shape. If None the shape
+        chunks (Sequence[int] | None, optional): The chunk shape. If None the shape
             is used. Defaults to None.
+        dimension_separator (DIMENSION_SEPARATOR): The separator to use for
+            dimensions. Defaults to "/".
+        compressor: The compressor to use. Defaults to "default".
         dtype (str, optional): The data type of the image. Defaults to "uint16".
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
@@ -164,6 +171,8 @@ def create_empty_label_container(
         chunks=chunks,
         dtype=dtype,
         mode="a",
+        dimension_separator=dimension_separator,
+        compressor=compressor,
     )
     group_handler._mode = "r+"
     return group_handler
@@ -171,7 +180,7 @@ def create_empty_label_container(
 
 def create_empty_image_container(
     store: StoreOrGroup,
-    shape: Collection[int],
+    shape: Sequence[int],
     pixelsize: float,
     z_spacing: float = 1.0,
     time_spacing: float = 1.0,
@@ -180,10 +189,12 @@ def create_empty_image_container(
     z_scaling_factor: float = 1.0,
     space_unit: SpaceUnits | str | None = DefaultSpaceUnit,
     time_unit: TimeUnits | str | None = DefaultTimeUnit,
-    axes_names: Collection[str] | None = None,
+    axes_names: Sequence[str] | None = None,
     name: str | None = None,
-    chunks: Collection[int] | None = None,
+    chunks: Sequence[int] | None = None,
     dtype: str = "uint16",
+    dimension_separator: DIMENSION_SEPARATOR = "/",
+    compressor="default",
     overwrite: bool = False,
     version: NgffVersions = DefaultNgffVersion,
 ) -> ZarrGroupHandler:
@@ -191,7 +202,7 @@ def create_empty_image_container(
 
     Args:
         store (StoreOrGroup): The Zarr store or group to create the image in.
-        shape (Collection[int]): The shape of the image.
+        shape (Sequence[int]): The shape of the image.
         pixelsize (float): The pixel size in x and y dimensions.
         z_spacing (float, optional): The spacing between z slices. Defaults to 1.0.
         time_spacing (float, optional): The spacing between time points.
@@ -206,12 +217,15 @@ def create_empty_image_container(
             DefaultSpaceUnit.
         time_unit (TimeUnits, optional): The unit of time. Defaults to
             DefaultTimeUnit.
-        axes_names (Collection[str] | None, optional): The names of the axes.
+        axes_names (Sequence[str] | None, optional): The names of the axes.
             If None the canonical names are used. Defaults to None.
         name (str | None, optional): The name of the image. Defaults to None.
-        chunks (Collection[int] | None, optional): The chunk shape. If None the shape
+        chunks (Sequence[int] | None, optional): The chunk shape. If None the shape
             is used. Defaults to None.
         dtype (str, optional): The data type of the image. Defaults to "uint16".
+        dimension_separator (DIMENSION_SEPARATOR): The separator to use for
+            dimensions. Defaults to "/".
+        compressor: The compressor to use. Defaults to "default".
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
         version (str, optional): The version of the OME-Zarr specification.
@@ -254,6 +268,8 @@ def create_empty_image_container(
         chunks=chunks,
         dtype=dtype,
         mode="a",
+        dimension_separator=dimension_separator,
+        compressor=compressor,
     )
 
     group_handler._mode = "r+"

ngio/images/_create_synt_container.py

@@ -0,0 +1,138 @@
+"""Abstract class for handling OME-NGFF images."""
+
+from collections.abc import Sequence
+
+import numpy as np
+import PIL.Image
+from zarr.types import DIMENSION_SEPARATOR
+
+from ngio.common._synt_images_utils import fit_to_shape
+from ngio.images._ome_zarr_container import OmeZarrContainer, create_ome_zarr_from_array
+from ngio.ome_zarr_meta.ngio_specs import (
+    DefaultNgffVersion,
+    NgffVersions,
+)
+from ngio.resources import AVAILABLE_SAMPLES, SampleInfo, get_sample_info
+from ngio.tables import (
+    DefaultTableBackend,
+    TableBackend,
+)
+from ngio.utils import (
+    StoreOrGroup,
+)
+
+
+def create_synthetic_ome_zarr(
+    store: StoreOrGroup,
+    shape: Sequence[int],
+    reference_sample: AVAILABLE_SAMPLES | SampleInfo = "Cardiomyocyte",
+    levels: int | list[str] = 5,
+    xy_scaling_factor: float = 2,
+    z_scaling_factor: float = 1.0,
+    axes_names: Sequence[str] | None = None,
+    chunks: Sequence[int] | None = None,
+    channel_labels: list[str] | None = None,
+    channel_wavelengths: list[str] | None = None,
+    channel_colors: Sequence[str] | None = None,
+    channel_active: Sequence[bool] | None = None,
+    table_backend: TableBackend = DefaultTableBackend,
+    dimension_separator: DIMENSION_SEPARATOR = "/",
+    compressor="default",
+    overwrite: bool = False,
+    version: NgffVersions = DefaultNgffVersion,
+) -> OmeZarrContainer:
+    """Create an empty OME-Zarr image with the given shape and metadata.
+
+    Args:
+        store (StoreOrGroup): The Zarr store or group to create the image in.
+        shape (Sequence[int]): The shape of the image.
+        reference_sample (AVAILABLE_SAMPLES | SampleInfo): The reference sample to use.
+        levels (int | list[str], optional): The number of levels in the pyramid or a
+            list of level names. Defaults to 5.
+        xy_scaling_factor (float, optional): The down-scaling factor in x and y
+            dimensions. Defaults to 2.0.
+        z_scaling_factor (float, optional): The down-scaling factor in z dimension.
+            Defaults to 1.0.
+        axes_names (Sequence[str] | None, optional): The names of the axes.
+            If None the canonical names are used. Defaults to None.
+        chunks (Sequence[int] | None, optional): The chunk shape. If None the shape
+            is used. Defaults to None.
+        channel_labels (list[str] | None, optional): The labels of the channels.
+            Defaults to None.
+        channel_wavelengths (list[str] | None, optional): The wavelengths of the
+            channels. Defaults to None.
+        channel_colors (Sequence[str] | None, optional): The colors of the channels.
+            Defaults to None.
+        channel_active (Sequence[bool] | None, optional): Whether the channels are
+            active. Defaults to None.
+        table_backend (TableBackend): Table backend to be used to store tables
+        dimension_separator (DIMENSION_SEPARATOR): The separator to use for
+            dimensions. Defaults to "/".
+        compressor: The compressor to use. Defaults to "default".
+        overwrite (bool, optional): Whether to overwrite an existing image.
+            Defaults to True.
+        version (NgffVersion, optional): The version of the OME-Zarr specification.
+            Defaults to DefaultNgffVersion.
+    """
+    if isinstance(reference_sample, str):
+        sample_info = get_sample_info(reference_sample)
+    else:
+        sample_info = reference_sample
+
+    raw = np.asarray(PIL.Image.open(sample_info.img_path))
+    raw = fit_to_shape(arr=raw, out_shape=tuple(shape))
+    raw = raw / np.max(raw) * (2**16 - 1)
+    raw = raw.astype(np.uint16)
+    ome_zarr = create_ome_zarr_from_array(
+        store=store,
+        array=raw,
+        xy_pixelsize=sample_info.xy_pixelsize,
+        z_spacing=sample_info.z_spacing,
+        time_spacing=sample_info.time_spacing,
+        levels=levels,
+        xy_scaling_factor=xy_scaling_factor,
+        z_scaling_factor=z_scaling_factor,
+        space_unit=sample_info.space_unit,
+        time_unit=sample_info.time_unit,
+        axes_names=axes_names,
+        channel_labels=channel_labels,
+        channel_wavelengths=channel_wavelengths,
+        channel_colors=channel_colors,
+        channel_active=channel_active,
+        name=sample_info.name,
+        chunks=chunks,
+        overwrite=overwrite,
+        dimension_separator=dimension_separator,
+        compressor=compressor,
+        version=version,
+    )
+
+    image = ome_zarr.get_image()
+    well_table = image.build_image_roi_table()
+    ome_zarr.add_table("well_ROI_table", table=well_table, backend=table_backend)
+
+    for label_info in sample_info.labels:
+        ome_zarr.derive_label(name=label_info.name)
+        label = ome_zarr.get_label(name=label_info.name)
+
+        ref_label = np.asarray(PIL.Image.open(label_info.label_path))
+        ref_label = ref_label.astype(label_info.dtype)
+
+        ref_label = fit_to_shape(
+            arr=ref_label,
+            out_shape=label.shape,
+            ensure_unique_info=label_info.ensure_unique_labels,
+        )
+        ref_label = ref_label.astype(np.uint32)
+        label.set_array(ref_label)
+        label.consolidate()
+
+        if label_info.create_masking_table:
+            masking_table = label.build_masking_roi_table()
+            ome_zarr.add_table(
+                name=f"{label_info.name}_masking_table",
+                table=masking_table,
+                backend=table_backend,
+            )
+
+    return ome_zarr