ngio 0.2.7__py3-none-any.whl → 0.2.9__py3-none-any.whl

ngio/ome_zarr_meta/ngio_specs/_axes.py

@@ -2,15 +2,12 @@
 
 from collections.abc import Collection
 from enum import Enum
-from logging import Logger
 from typing import Literal, TypeVar
 
 import numpy as np
 from pydantic import BaseModel, ConfigDict, Field
 
-from ngio.utils import NgioValidationError, NgioValueError
-
-logger = Logger(__name__)
+from ngio.utils import NgioValidationError, NgioValueError, ngio_logger
 
 T = TypeVar("T")
 
@@ -102,20 +99,20 @@ class Axis(BaseModel):
     def implicit_type_cast(self, cast_type: AxisType) -> "Axis":
         unit = self.unit
         if self.axis_type != cast_type:
-            logger.warning(
+            ngio_logger.warning(
                 f"Axis {self.on_disk_name} has type {self.axis_type}. "
                 f"Casting to {cast_type}."
             )
 
         if cast_type == AxisType.time and unit is None:
-            logger.warning(
+            ngio_logger.warning(
                 f"Time axis {self.on_disk_name} has unit {self.unit}. "
                 f"Casting to {DefaultSpaceUnit}."
             )
             unit = DefaultTimeUnit
 
         if cast_type == AxisType.space and unit is None:
-            logger.warning(
+            ngio_logger.warning(
                 f"Space axis {self.on_disk_name} has unit {unit}. "
                 f"Casting to {DefaultSpaceUnit}."
             )

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-0.2.7.dist-info → ngio-0.2.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.2.7
+Version: 0.2.9
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio

{ngio-0.2.7.dist-info → ngio-0.2.9.dist-info}/RECORD

@@ -21,8 +21,8 @@ ngio/images/ome_zarr_container.py,sha256=-9bbzNtsVAjU1X_h78Lr5LOV0JXtOiWVWqmt3DF
 ngio/ome_zarr_meta/__init__.py,sha256=oZ8PEsWM7U0KwzpsnvVfX9k4UfuTz5sZ8B6B9eY5hyY,1193
 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/_axes.py,sha256=tHtx6NfBgDcCgDk9CosjIjw1KZJ2qi0i_eoLgrdiEWw,16681
+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-0.2.7.dist-info/METADATA,sha256=DI47tFwc8OP-d0nuqNHv4pSUhg15pJiU2uUDmiq9Q-U,5215
-ngio-0.2.7.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ngio-0.2.7.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.2.7.dist-info/RECORD,,
+ngio-0.2.9.dist-info/METADATA,sha256=3hSjDhHlP2G3U8g1HcTNO5bQWGBEB0S1FLSMwDh4RlQ,5215
+ngio-0.2.9.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ngio-0.2.9.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.2.9.dist-info/RECORD,,