Improve coverage of core modules

examples/09_secondary_labeling/01_images_to_mip.py

@@ -1,43 +1,40 @@
 import json
+from typing import Any
 
 from devtools import debug
 
-from fractal_tasks_core.copy_ome_zarr import copy_ome_zarr
-from fractal_tasks_core.create_ome_zarr import create_ome_zarr
-from fractal_tasks_core.maximum_intensity_projection import (
+from fractal_tasks_core.tasks.copy_ome_zarr import copy_ome_zarr
+from fractal_tasks_core.tasks.create_ome_zarr import create_ome_zarr
+from fractal_tasks_core.tasks.maximum_intensity_projection import (
     maximum_intensity_projection,
 )
-from fractal_tasks_core.yokogawa_to_ome_zarr import yokogawa_to_ome_zarr
+from fractal_tasks_core.tasks.yokogawa_to_ome_zarr import yokogawa_to_ome_zarr
 
 
 allowed_channels = [
     {
         "wavelength_id": "A01_C01",
-        "colormap": "00FFFF",
-        "end": 2000,
+        "color": "00FFFF",
         "label": "Channel 1",
-        "start": 110,
+        "window": {"start": 110, "end": 2000},
     },
     {
         "wavelength_id": "A02_C02",
-        "colormap": "FF00FF",
-        "end": 500,
+        "color": "FF00FF",
         "label": "Channel 2",
-        "start": 110,
+        "window": {"start": 110, "end": 500},
     },
     {
         "wavelength_id": "A03_C03",
-        "colormap": "00FF00",
-        "end": 1600,
+        "color": "00FF00",
         "label": "Channel 3",
-        "start": 110,
+        "window": {"start": 110, "end": 1600},
     },
     {
         "wavelength_id": "A04_C04",
-        "colormap": "FFFF00",
-        "end": 1600,
+        "color": "FFFF00",
         "label": "Channel 4",
-        "start": 110,
+        "window": {"start": 110, "end": 1600},
     },
 ]
 
@@ -50,7 +47,7 @@
 img_path = "images/"
 zarr_path = "output/"
 zarr_path_mip = "output_mip/"
-metadata = {}
+metadata: dict[str, Any] = {}
 
 # Create zarr structure
 metadata_update = create_ome_zarr(
@@ -62,7 +59,6 @@
     allowed_channels=allowed_channels,
     num_levels=num_levels,
     coarsening_xy=coarsening_xy,
-    metadata_table="mrf_mlf",
 )
 metadata.update(metadata_update)
 debug(metadata)

examples/09_secondary_labeling/02_cellpose_two_steps_segmentation.py

@@ -4,7 +4,10 @@
 
 from devtools import debug
 
-from fractal_tasks_core.cellpose_segmentation import cellpose_segmentation
+from fractal_tasks_core.lib_input_models import Channel
+from fractal_tasks_core.tasks.cellpose_segmentation import (
+    cellpose_segmentation,
+)
 
 
 if os.path.exists("tmp"):
@@ -28,7 +31,7 @@
         output_path=zarr_path_mip,
         metadata=metadata,
         component=component,
-        wavelength_id="A01_C01",
+        channel=Channel(wavelength_id="A01_C01"),
         level=2,
         relabeling=True,
         diameter_level0=400.0,
@@ -50,7 +53,7 @@
         output_path=zarr_path_mip,
         metadata=metadata,
         component=component,
-        wavelength_id="A01_C01",
+        channel=Channel(wavelength_id="A01_C01"),
         level=2,
         relabeling=True,
         diameter_level0=20.0,

examples/tools/lib_inspect_ROI_table.py

@@ -0,0 +1,49 @@
+from typing import Sequence
+
+import anndata as ad
+
+from fractal_tasks_core.lib_regions_of_interest import (
+    convert_ROI_table_to_indices,
+)
+
+
+def _inspect_ROI_table(
+    path: str,
+    full_res_pxl_sizes_zyx: Sequence[float],
+    level: int = 0,
+    coarsening_xy: int = 2,
+) -> None:
+    """
+    Description
+
+    :param dummy: this is just a placeholder
+    :type dummy: int
+    """
+
+    print(f"{full_res_pxl_sizes_zyx=}")
+
+    adata = ad.read_zarr(path)
+    df = adata.to_df()
+    print("table")
+    print(df)
+    print()
+
+    try:
+        list_indices = convert_ROI_table_to_indices(
+            adata,
+            level=level,
+            coarsening_xy=coarsening_xy,
+            full_res_pxl_sizes_zyx=full_res_pxl_sizes_zyx,
+            # verbose=True,
+        )
+        print()
+        print(f"level:         {level}")
+        print(f"coarsening_xy: {coarsening_xy}")
+        print("list_indices:")
+        for indices in list_indices:
+            print(indices)
+        print()
+    except KeyError as e:
+        print("Something went wrong in convert_ROI_table_to_indices\n", str(e))
+
+    return df

fractal_tasks_core/lib_masked_loading.py

@@ -32,7 +32,7 @@
 def _preprocess_input(
     image_array: np.ndarray,
     *,
-    region: tuple[slice],
+    region: tuple[slice, ...],
     current_label_path: str,
     ROI_table_path: str,
     ROI_positional_index: int,
@@ -90,7 +90,7 @@
 
     # Check that image data are 4D (CZYX) - FIXME issue 340
     if not image_array.ndim == 4:
         raise ValueError(
             "_preprocess_input requires a 4D "
             f"image_array argument, but {image_array.shape=}"
         )
@@ -101,13 +101,13 @@
     logger.info(f"[_preprocess_input] {ROI_table_path=}")
     logger.info(f"[_preprocess_input] {attrs.asdict()=}")
     if not attrs["type"] == "ngff:region_table":
         raise ValueError("Wrong attributes for {ROI_table_path}:\n{attrs}")
     label_relative_path = attrs["region"]["path"]
     column_name = attrs["instance_key"]
 
     # Check that ROI_table.obs has the right column and extract label_value
     if column_name not in ROI_table.obs.columns:
         raise ValueError(
             'In _preprocess_input, "{column_name}" '
             f" missing in {ROI_table.obs.columns=}"
         )

fractal_tasks_core/lib_pyramid_creation.py

@@ -16,6 +16,7 @@
 """
 import pathlib
 from typing import Callable
+from typing import Optional
 from typing import Sequence
 from typing import Union
 
@@ -29,9 +30,9 @@ def build_pyramid(
     overwrite: bool = False,
     num_levels: int = 2,
     coarsening_xy: int = 2,
-    chunksize: Sequence[int] = None,
-    aggregation_function: Callable = None,
-):
+    chunksize: Optional[Sequence[int]] = None,
+    aggregation_function: Optional[Callable] = None,
+) -> None:
 
     """
     Starting from on-disk highest-resolution data, build and write to disk a
@@ -59,7 +60,7 @@ def build_pyramid(
     # Check the number of axes and identify YX dimensions
     ndims = len(data_highres.shape)
     if ndims not in [2, 3, 4]:
-        raise Exception("{data_highres.shape=}, ndims not in [2,3,4]")
+        raise ValueError(f"{data_highres.shape=}, ndims not in [2,3,4]")
     y_axis = ndims - 2
     x_axis = ndims - 1
 
@@ -72,7 +73,7 @@ def build_pyramid(
     for ind_level in range(1, num_levels):
         # Verify that coarsening is doable
         if min(previous_level.shape[-2:]) < coarsening_xy:
-            raise Exception(
+            raise ValueError(
                 f"ERROR: at {ind_level}-th level, "
                 f"coarsening_xy={coarsening_xy} "
                 f"but previous level has shape {previous_level.shape}"

fractal_tasks_core/lib_regions_of_interest.py

@@ -272,48 +272,6 @@ def convert_ROI_table_to_indices(
     return list_indices
 
 
-def _inspect_ROI_table(
-    path: str,
-    full_res_pxl_sizes_zyx: Sequence[float],
-    level: int = 0,
-    coarsening_xy: int = 2,
-) -> None:
-    """
-    Description
-
-    :param dummy: this is just a placeholder
-    :type dummy: int
-    """
-
-    print(f"{full_res_pxl_sizes_zyx=}")
-
-    adata = ad.read_zarr(path)
-    df = adata.to_df()
-    print("table")
-    print(df)
-    print()
-
-    try:
-        list_indices = convert_ROI_table_to_indices(
-            adata,
-            level=level,
-            coarsening_xy=coarsening_xy,
-            full_res_pxl_sizes_zyx=full_res_pxl_sizes_zyx,
-            # verbose=True,
-        )
-        print()
-        print(f"level:         {level}")
-        print(f"coarsening_xy: {coarsening_xy}")
-        print("list_indices:")
-        for indices in list_indices:
-            print(indices)
-        print()
-    except KeyError as e:
-        print("Something went wrong in convert_ROI_table_to_indices\n", str(e))
-
-    return df
-
-
 def array_to_bounding_box_table(
     mask_array: np.ndarray, pxl_sizes_zyx: list[float]
 ) -> pd.DataFrame:

fractal_tasks_core/lib_upscale_array.py

@@ -15,17 +15,17 @@
 """
 import logging
 import warnings
+from typing import Optional
 from typing import Sequence
-from typing import Tuple
 
 import numpy as np
 
 
 def upscale_array(
     *,
     array: np.ndarray,
-    target_shape: Tuple[int],
-    axis: Sequence[int] = None,
+    target_shape: tuple[int, ...],
+    axis: Optional[Sequence[int]] = None,
     pad_with_zeros: bool = False,
     warn_if_inhomogeneous: bool = False,
 ) -> np.ndarray:
@@ -57,6 +57,8 @@ def upscale_array(
 
     if len(array_shape) != len(target_shape):
         raise ValueError(f"{info} Dimensions-number mismatch.")
+    if axis == []:
+        raise ValueError(f"{info} Empty axis list")
     if min(axis) < 0:
         raise ValueError(f"{info} Negative axis specification not allowed.")
 
@@ -92,7 +94,7 @@ def upscale_array(
     # Raise a warning if upscaling is non-homogeneous across all axis
     if warn_if_inhomogeneous:
         if len(set(upscale_factors.values())) > 1:
-            warnings.warn(info)
+            warnings.warn(f"{info} (inhomogeneous)")
 
     # Upscale array, via np.repeat
     upscaled_array = array
@@ -130,10 +132,10 @@ def upscale_array(
 
 def convert_region_to_low_res(
     *,
-    highres_region: Tuple[slice],
-    lowres_shape: Tuple[int],
-    highres_shape: Tuple[int],
-) -> Tuple[slice]:
+    highres_region: tuple[slice, ...],
+    lowres_shape: tuple[int, ...],
+    highres_shape: tuple[int, ...],
+) -> tuple[slice, ...]:
     """
     Convert a region defined for a high-resolution array to the corresponding
     region for a low-resolution array

tests/.gitignore

@@ -1,3 +1,4 @@
 *_zenodo_*
 data/*_zenodo_*
 data/fake_multiplex
+activate_venv.sh

tests/data/omero/channels_list.json

@@ -8,5 +8,15 @@
         "label": "label_2",
         "wavelength_id": "wavelength_id_2",
         "window": {"start":0, "end": 180}
+    },
+    {
+        "label": "label_3",
+        "wavelength_id": "wavelength_id_3",
+        "window": {"start":0, "end": 180}
+    },
+    {
+        "label": "label_4",
+        "wavelength_id": "wavelength_id_4",
+        "window": {"start":0, "end": 180}
     }
 ]