minor bug fix

fractal-analytics-platform · Nov 14, 2024 · 97e7682 · 97e7682
1 parent e4c2bf0
commit 97e7682
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diff --git a/docs/notebooks/basic_usage.ipynb b/docs/notebooks/basic_usage.ipynb
@@ -55,7 +55,7 @@
     "print(ngff_image)\n",
     "image = ngff_image.get_image()\n",
     "print(image)\n",
-    "nuclei = ngff_image.label.get_label(\"nuclei\")\n",
+    "nuclei = ngff_image.labels.get_label(\"nuclei\")\n",
     "print(nuclei)\n"
    ]
   },
@@ -106,9 +106,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(\"List of Labels: \", ngff_image.label.list())\n",
+    "print(\"List of Labels: \", ngff_image.labels.list())\n",
     "\n",
-    "label_nuclei = ngff_image.label.get_label(\"nuclei\", path=\"0\")\n",
+    "label_nuclei = ngff_image.labels.get_label(\"nuclei\", path=\"0\")\n",
     "print(f\"{label_nuclei.shape=}\")\n",
     "print(f\"{label_nuclei.pixel_size=}\")"
    ]
@@ -133,10 +133,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(\"List of Tables: \", ngff_image.table.list())\n",
-    "print(\" - Feature tables: \", ngff_image.table.list(table_type='feature_table'))\n",
-    "print(\" - Roi tables: \", ngff_image.table.list(table_type='roi_table'))\n",
-    "print(\" - Masking Roi tables: \", ngff_image.table.list(table_type='masking_roi_table'))"
+    "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'))"
    ]
   },
   {
@@ -146,7 +146,7 @@
    "outputs": [],
    "source": [
     "# Loading a table\n",
-    "feature_table = ngff_image.table.get_table(\"regionprops_DAPI\")\n",
+    "feature_table = ngff_image.tables.get_table(\"regionprops_DAPI\")\n",
     "feature_table.table"
    ]
   },
@@ -157,7 +157,7 @@
    "outputs": [],
    "source": [
     "# Loading a roi table\n",
-    "roi_table = ngff_image.table.get_table(\"FOV_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",

diff --git a/docs/notebooks/image.ipynb b/docs/notebooks/image.ipynb
@@ -294,17 +294,24 @@
     "feat_df = pd.DataFrame.from_records(list_of_records)\n",
     "\n",
     "# Create a new feature table\n",
-    "feat_table = ngff_image.table.new(name='new_feature_table',\n",
+    "feat_table = ngff_image.tables.new(name='new_feature_table',\n",
     "                     label_image='../nuclei',\n",
     "                     table_type='feature_table',\n",
     "                     overwrite=True)\n",
     "\n",
-    "print(f\"New list of feature table: {ngff_image.table.list(table_type='feature_table')}\")\n",
+    "print(f\"New list of feature table: {ngff_image.tables.list(table_type='feature_table')}\")\n",
     "feat_table.set_table(feat_df)\n",
     "feat_table.consolidate()\n",
     "\n",
     "feat_table.table"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

diff --git a/docs/notebooks/processing.ipynb b/docs/notebooks/processing.ipynb
@@ -81,7 +81,7 @@
     "print(\"MIP image loaded with shape:\", mip_image.shape)\n",
     "\n",
     "# Get a ROI table\n",
-    "roi_table = ngff_image.table.get_table(\"FOV_ROI_table\")\n",
+    "roi_table = ngff_image.tables.get_table(\"FOV_ROI_table\")\n",
     "print(\"ROI table loaded with\", len(roi_table.rois), \"ROIs\")\n",
     "\n",
     "# For each ROI in the table\n",
@@ -157,7 +157,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mip_roi_table = mip_ngff.table.new(\"FOV_ROI_table\", overwrite=True)\n",
+    "mip_roi_table = mip_ngff.tables.new(\"FOV_ROI_table\", overwrite=True)\n",
     "\n",
     "roi_list = []\n",
     "for roi in roi_table.rois:\n",
@@ -221,7 +221,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "nuclei_image = mip_ngff.label.derive(name=\"nuclei\", overwrite=True)"
+    "nuclei_image = mip_ngff.labels.derive(name=\"nuclei\", overwrite=True)"
    ]
   },
   {
@@ -242,7 +242,7 @@
     "print(\"Source image loaded with shape:\", source_image.shape)\n",
     "\n",
     "# Get a ROI table\n",
-    "roi_table = mip_ngff.table.get_table(\"FOV_ROI_table\")\n",
+    "roi_table = mip_ngff.tables.get_table(\"FOV_ROI_table\")\n",
     "print(\"ROI table loaded with\", len(roi_table.rois), \"ROIs\")\n",
     "\n",
     "# Find the DAPI channel\n",

diff --git a/pyproject.toml b/pyproject.toml
@@ -149,16 +149,12 @@ skip-magic-trailing-comma = false # default is false
 [tool.mypy]
 files = "src/**/"
 strict = true
+ignore_missing_imports = true
 disallow_any_generics = false
 disallow_subclassing_any = false
 show_error_codes = true
 pretty = true
 
-# # module specific overrides
-[[tool.mypy.overrides]]
-module = ["numpy.*", "dask.*", "zarr.*"]
-ignore_errors = true
-
 # https://docs.pytest.org/
 [tool.pytest.ini_options]
 minversion = "7.0"

diff --git a/src/ngio/core/image_like_handler.py b/src/ngio/core/image_like_handler.py
@@ -10,7 +10,6 @@
 
 from ngio.core.dimensions import Dimensions
 from ngio.core.roi import WorldCooROI
-from ngio.core.utils import Lock
 from ngio.io import AccessModeLiteral, StoreOrGroup, open_group_wrapper
 from ngio.ngff_meta import (
     Dataset,
@@ -23,6 +22,11 @@
 from ngio.utils import ngio_logger
 from ngio.utils._common_types import ArrayLike
 
+try:
+    from dask.distributed import Lock
+except ImportError:
+    Lock = None  # type: ignore
+
 
 class ImageLike:
     """A class to handle OME-NGFF images stored in Zarr format.