ngio 0.2.6__tar.gz → 0.2.8__tar.gz

{ngio-0.2.6 → ngio-0.2.8}/PKG-INFO

@@ -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 → ngio-0.2.8}/src/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-0.2.6 → ngio-0.2.8}/src/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,