Merge pull request #66 from fractal-analytics-platform/update_ngio_version

adopt ngio 0.4

Author: lorenzocerrone

pixi.lock

@@ -2,7 +2,7 @@
 authors = [{ name = "lorenzo", email = "[email protected]" }]
 dependencies = [
     "streamlit>=1.50.0, <1.51.0",
-    "ngio>=0.3.2, <0.4.0",
+    "ngio==0.4.2",
     "plotly",
     "matplotlib",
     "orjson",
@@ -54,7 +54,7 @@ build-backend = "hatchling.build"
 source = "vcs"
 
 
-[tool.pixi.project]
+[tool.pixi.workspace]
 channels = ["conda-forge"]
 platforms = ["osx-arm64", "linux-64", "win-64"]
 

pyproject.toml

@@ -8,4 +8,3 @@
     __version__ = "uninstalled"
 __author__ = "Lorenzo Cerrone"
 __email__ = "[email protected]"
-

src/fractal_feature_explorer/__init__.py

@@ -9,6 +9,7 @@
 class FractalUserNonVerifiedException(ValueError):
     pass
 
+
 logger = get_logger(__name__)
 
 
@@ -60,7 +61,6 @@ def _verify_authentication(config: ProductionConfig):
             msg = f"Could not obtain Fractal user information from {current_user_url}."
             logger.info(msg)
             raise ValueError(msg)
-        
 
 
 def verify_authentication():

src/fractal_feature_explorer/authentication.py

@@ -54,7 +54,7 @@ def view_point(point: int, feature_df: pl.DataFrame) -> None:
         _show_point_info(point_dict)
         return
 
-    channels = container.image_meta.channel_labels
+    channels = container.channel_labels
     if len(channels) > 1:
         channel = st.selectbox(
             label="Select channel",

src/fractal_feature_explorer/pages/filters_page/_scatter_filter.py

@@ -2,9 +2,10 @@
 
 import polars as pl
 import streamlit as st
-from ngio.common import (
+from ngio.images._table_ops import (
     concatenate_image_tables_async,
     concatenate_image_tables_as_async,
+    list_image_tables_async,
 )
 from ngio.tables import FeatureTable
 from typing import Literal
@@ -16,7 +17,6 @@
     plate_name_from_url,
     extras_from_url,
 )
-from ngio.common import list_image_tables_async
 
 from streamlit.logger import get_logger
 
@@ -155,7 +155,7 @@ def _collect_condition_table_from_images_cached(
         concatenate_image_tables_async(
             images=images,
             extras=extras,
-            table_name=table_name,
+            name=table_name,
         )
     )
     condition_table = condition_table.lazy_frame.collect()
@@ -280,7 +280,7 @@ def _collect_feature_table_from_images_cached(
         concatenate_image_tables_as_async(
             images=images,
             extras=extras,
-            table_name=table_name,
+            name=table_name,
             table_cls=FeatureTable,
             mode="lazy",
         )

src/fractal_feature_explorer/pages/setup_page/_tables_io.py

@@ -11,7 +11,8 @@
     open_ome_zarr_container,
     open_ome_zarr_plate,
 )
-from ngio.common import Dimensions, Roi, list_image_tables_async
+from ngio.common import Dimensions, Roi
+from ngio.images._table_ops import list_image_tables_async
 from ngio.common._zoom import numpy_zoom
 from ngio.ome_zarr_meta.ngio_specs import PixelSize
 from ngio.tables import MaskingRoiTable
@@ -44,8 +45,8 @@ def _url_belongs_to_base(url: str, base_url: str) -> bool:
         logger.debug(f"Not including token for {url=}, case 1.")
         return False
     elif parsed_url.path is not None and (
-        parsed_base_url.path is not None and
-        not parsed_url.path.startswith(parsed_base_url.path)
+        parsed_base_url.path is not None
+        and not parsed_url.path.startswith(parsed_base_url.path)
     ):
         logger.debug(f"Not including token for {url=}, case 2.")
         return False
@@ -233,14 +234,12 @@ def roi_to_slice_kwargs(
     t_slice: int = 0,
 ) -> dict[str, slice | int | Iterable[int]]:
     """Convert a WorldCooROI to slice_kwargs."""
-    raster_roi = roi.to_pixel_roi(
-        pixel_size=pixel_size, dimensions=dimensions
-    ).to_slices()
+    raster_roi = roi.to_slicing_dict(pixel_size=pixel_size)
 
-    if dimensions.has_axis(axis_name="z"):
+    if dimensions.axes_handler.has_axis(axis_name="z"):
         raster_roi["z"] = z_slice  # type: ignore
 
-    if dimensions.has_axis(axis_name="t"):
+    if dimensions.axes_handler.has_axis(axis_name="t"):
         raster_roi["t"] = t_slice  # type: ignore
 
     return raster_roi  # type: ignore
@@ -292,7 +291,7 @@ def _get_image_array(
         ref_label=ref_label,
         fractal_token=fractal_token,
     )
-    roi = masking_roi.get(label=label)
+    roi = masking_roi.get_label(label=label)
     roi = roi.zoom(zoom_factor=zoom_factor)
     roi_slice = roi_to_slice_kwargs(
         roi=roi,
@@ -335,7 +334,7 @@ def _get_label_array(
         ref_label=ref_label,
         fractal_token=fractal_token,
     )
-    roi = masking_roi.get(label=label)
+    roi = masking_roi.get_label(label=label)
     roi = roi.zoom(zoom_factor=zoom_factor)
     roi_slice = roi_to_slice_kwargs(
         roi=roi,
@@ -408,7 +407,7 @@ def get_single_label_image(
     label_array = numpy_zoom(
         label_array,
         target_shape=image_rgba.shape[:2],
-        order=0,  # Always use nearest neighbor for labels
+        order="nearest",  # Always use nearest neighbor for labels
     )
 
     image_rgba[label_array > 0, 0] = 255