ngio 0.2.6__py3-none-any.whl → 0.2.8__py3-none-any.whl

ngio/hcs/plate.py

@@ -399,7 +399,7 @@ class OmeZarrPlate:
         acquisition_id: int | None = None,
         acquisition_name: str | None = None,
         atomic: bool = False,
-    ) -> StoreOrGroup | None:
+    ) -> str:
         """Add an image to an ome-zarr plate."""
         if image_path is not None:
             image_path = path_in_well_validation(path=image_path)
@@ -450,8 +450,8 @@ class OmeZarrPlate:
             meta_handler._group_handler.clean_cache()
 
         if image_path is not None:
-            return group_handler.get_group(image_path, create_mode=True)
-        return None
+            return f"{well_path}/{image_path}"
+        return well_path
 
     def atomic_add_image(
         self,
@@ -460,14 +460,14 @@ class OmeZarrPlate:
         image_path: str,
         acquisition_id: int | None = None,
         acquisition_name: str | None = None,
-    ) -> StoreOrGroup:
+    ) -> str:
         """Parallel safe version of add_image."""
         if image_path is None:
             raise ValueError(
                 "Image path cannot be None for atomic add_image. "
                 "If your intent is to add a well, use add_well instead."
             )
-        group = self._add_image(
+        path = self._add_image(
             row=row,
             column=column,
             image_path=image_path,
@@ -475,12 +475,7 @@ class OmeZarrPlate:
             acquisition_name=acquisition_name,
             atomic=True,
         )
-        if group is None:
-            raise ValueError(
-                f"Some error occurred while adding image {image_path} "
-                f"to well {row}{column}."
-            )
-        return group
+        return path
 
     def add_image(
         self,
@@ -489,14 +484,14 @@ class OmeZarrPlate:
         image_path: str,
         acquisition_id: int | None = None,
         acquisition_name: str | None = None,
-    ) -> StoreOrGroup:
+    ) -> str:
         """Add an image to an ome-zarr plate."""
         if image_path is None:
             raise ValueError(
                 "Image path cannot be None for atomic add_image. "
                 "If your intent is to add a well, use add_well instead."
             )
-        group = self._add_image(
+        path = self._add_image(
             row=row,
             column=column,
             image_path=image_path,
@@ -504,12 +499,7 @@ class OmeZarrPlate:
             acquisition_name=acquisition_name,
             atomic=False,
         )
-        if group is None:
-            raise ValueError(
-                f"Some error occurred while adding image {image_path} "
-                f"to well {row}{column}."
-            )
-        return group
+        return path
 
     def add_well(
         self,

ngio/ome_zarr_meta/ngio_specs/_channels.py

@@ -9,7 +9,7 @@ from enum import Enum
 from typing import Any, TypeVar
 
 import numpy as np
-from pydantic import BaseModel, ConfigDict, Field, field_validator
+from pydantic import BaseModel, ConfigDict, Field, field_validator, model_validator
 
 from ngio.utils import NgioValidationError, NgioValueError
 
@@ -124,7 +124,6 @@ class ChannelVisualisation(BaseModel):
     model_config = ConfigDict(extra="allow", frozen=True)
 
     @field_validator("color", mode="after")
-    @classmethod
     def validate_color(cls, value: str | NgioColors) -> str:
         """Color validator.
 
@@ -145,6 +144,33 @@ class ChannelVisualisation(BaseModel):
         else:
             raise NgioValueError(f"Invalid color {value}.")
 
+    @model_validator(mode="before")
+    def check_start_end(cls, data):
+        """Check that the start and end values are valid.
+
+        If the start and end values are equal, set the end value to start + 1
+        """
+        start = data.get("start", None)
+        end = data.get("end", None)
+        if start is None or end is None:
+            return data
+        if abs(end - start) < 1e-6:
+            data["end"] = start + 1
+        return data
+
+    @model_validator(mode="after")
+    def check_model(self) -> "ChannelVisualisation":
+        """Check that the start and end values are within the min and max values."""
+        if self.start < self.min or self.start > self.max:
+            raise NgioValidationError(
+                f"Start value {self.start} is out of range [{self.min}, {self.max}]"
+            )
+        if self.end < self.min or self.end > self.max:
+            raise NgioValidationError(
+                f"End value {self.end} is out of range [{self.min}, {self.max}]"
+            )
+        return self
+
     @classmethod
     def default_init(
         cls,

{ngio-0.2.6.dist-info → ngio-0.2.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.2.6
+Version: 0.2.8
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio

{ngio-0.2.6.dist-info → ngio-0.2.8.dist-info}/RECORD

@@ -10,7 +10,7 @@ ngio/common/_roi.py,sha256=dq1iVT8-G_zWuxcYWJeHfviBSbPgsyKUcDL3Vg6jx6I,5122
 ngio/common/_slicer.py,sha256=AKpwXRncOmF9nhjKYma0C_41WqAgSv860beKGx-aw-0,3075
 ngio/common/_zoom.py,sha256=KsURa5VuixmpbAAY5-6obmuQV8vfiHKZqBxZDXvchpM,5473
 ngio/hcs/__init__.py,sha256=5oAYT_454WGhms97kxo8gS4_rKHtFf_x-9uu8M_VeVM,356
-ngio/hcs/plate.py,sha256=zmhHXRsoc4s_-bPccYCH9rqoYg419j-T-NF-OojXRZM,30509
+ngio/hcs/plate.py,sha256=WmUw8qZgWUPBBTqtV8lh_7T0vtRzMkAmduM8b969Ni4,30082
 ngio/images/__init__.py,sha256=DYbXAdBgPxyjBRdJrWvU0UnBRI0gUMmx9KaJ-Bucvz4,533
 ngio/images/abstract_image.py,sha256=8PNQPZjiDz-pcTFXSJAVw7nUr4yL_iRwqDEUTKkAnp0,10266
 ngio/images/create.py,sha256=XYn30m_2OSZeHHASYHc3eK9u_gZIYy9wo6mGdRGaq5c,9473
@@ -22,7 +22,7 @@ ngio/ome_zarr_meta/__init__.py,sha256=oZ8PEsWM7U0KwzpsnvVfX9k4UfuTz5sZ8B6B9eY5hy
 ngio/ome_zarr_meta/_meta_handlers.py,sha256=BLvYt5PONYrWkEb2XgEiAXR_OX9rfeX_C0eEqen0jQA,25549
 ngio/ome_zarr_meta/ngio_specs/__init__.py,sha256=05NQukZG0nNvjzf8AKWGu7PhjhQcImGSAOK3D3Bg-Js,1786
 ngio/ome_zarr_meta/ngio_specs/_axes.py,sha256=Kqe9T7LWa_9o3UWS5uzALyyNluIhXxWhDGxWY4-GIo8,16707
-ngio/ome_zarr_meta/ngio_specs/_channels.py,sha256=piK_SZ1Oay2_f2Sq4BFMOadMYc2yI1itfH075qxFznc,14085
+ngio/ome_zarr_meta/ngio_specs/_channels.py,sha256=2L-HM9K1Xu4qRI2MiXPqgCuHdCBRydEW1StThcqEuvY,15120
 ngio/ome_zarr_meta/ngio_specs/_dataset.py,sha256=hY8ogPPxvCgVg6k02t3zUr24lasYrvnxBd1iPEigdG4,5892
 ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py,sha256=uh345KQmEQtslIyMmLK9sB-NbjPYxi0Y9FuYIFhd3Rc,17465
 ngio/ome_zarr_meta/ngio_specs/_ngio_image.py,sha256=8E38Mgw-l0Ff1nkmCJIzo64G_paAVhM8xktUS_V5egY,17960
@@ -51,7 +51,7 @@ ngio/utils/_errors.py,sha256=pKQ12LUjQLYE1nUawemA5h7HsgznjaSvV1n2PQU33N0,759
 ngio/utils/_fractal_fsspec_store.py,sha256=7qoGLiLi8JQFh9Ej_z5WNwQQuWrujb0f6p9nj8ocsS8,548
 ngio/utils/_logger.py,sha256=HIuqD_2ShfFGDswBddcouStbKfL0Vz_ah8cAIFGhbS8,888
 ngio/utils/_zarr_utils.py,sha256=qOI-HL2HsfFLCj_yxsTR-aq4oHpSqS9KR13aEIvhGDY,13593
-ngio-0.2.6.dist-info/METADATA,sha256=jlhKK6wPZ-us8oK16tnxrItPYQwYFcHO7HPraMjMbyI,5215
-ngio-0.2.6.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ngio-0.2.6.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.2.6.dist-info/RECORD,,
+ngio-0.2.8.dist-info/METADATA,sha256=Rf7imDRysf67wo02l22A8DX2TjeWQLndDdzPp48YncY,5215
+ngio-0.2.8.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ngio-0.2.8.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.2.8.dist-info/RECORD,,