Fix some pylint warnings

Author: PierreRaybaut

sigima_/algorithms/image.py

@@ -710,6 +710,7 @@ def remove_overlapping_disks(coords: np.ndarray) -> np.ndarray:
     return coords
 
 
+# pylint: disable=too-many-positional-arguments
 def find_blobs_opencv(
     data: np.ndarray,
     min_threshold: float | None = None,

sigima_/computation/base.py

@@ -265,6 +265,8 @@ def dst_n_to_1(
     return dst
 
 
+# TODO: `src2` is not used for now, but it may be used in the future, should we keep it?
+# pylint: disable=unused-argument
 def dst_2_to_1(
     src1: SignalObj | ImageObj,
     src2: SignalObj | ImageObj,

sigima_/computation/image/extraction.py

@@ -236,7 +236,7 @@ def update_from_obj(self, obj: ImageObj) -> None:
         self.x0 = obj.xc
         self.y0 = obj.yc
 
-    def choice_callback(self, item, value):
+    def choice_callback(self, item, value):  # pylint: disable=unused-argument
         """Callback for choice item"""
         if value == "centroid":
             self.y0, self.x0 = alg.get_centroid_fourier(self.__obj.get_masked_view())

sigima_/computation/image/fourier.py

@@ -50,7 +50,7 @@ def update_from_obj(self, obj: ImageObj) -> None:
         self.__obj = obj
         self.choice_callback(None, self.strategy)
 
-    def choice_callback(self, item, value):
+    def choice_callback(self, item, value):  # pylint: disable=unused-argument
         """Callback to update padding values"""
         if self.__obj is None:
             return

sigima_/computation/image/geometry.py

@@ -178,6 +178,7 @@ def rotate270(src: ImageObj) -> ImageObj:
     return dst
 
 
+# pylint: disable=unused-argument
 def hflip_coords(dst: ImageObj, src: ImageObj, coords: np.ndarray) -> None:
     """Apply HFlip to coords"""
     coords[:, ::2] = dst.x0 + dst.width - coords[:, ::2]
@@ -199,6 +200,7 @@ def fliph(src: ImageObj) -> ImageObj:
     return dst
 
 
+# pylint: disable=unused-argument
 def vflip_coords(dst: ImageObj, src: ImageObj, coords: np.ndarray) -> None:
     """Apply VFlip to coords"""
     coords[:, 1::2] = dst.y0 + dst.height - coords[:, 1::2]

sigima_/obj/base.py

@@ -15,13 +15,6 @@
 from copy import deepcopy
 from typing import Any, Generic, Iterator, Literal, Type, TypeVar
 
-if sys.version_info >= (3, 11):
-    # Use Self from typing module in Python 3.11+
-    from typing import Self
-else:
-    # Use Self from typing_extensions module in Python < 3.11
-    from typing_extensions import Self
-
 import guidata.dataset as gds
 import numpy as np
 import pandas as pd
@@ -31,6 +24,13 @@
 from sigima_.algorithms import coordinates
 from sigima_.algorithms.datatypes import is_integer_dtype
 
+if sys.version_info >= (3, 11):
+    # Use Self from typing module in Python 3.11+
+    from typing import Self
+else:
+    # Use Self from typing_extensions module in Python < 3.11
+    from typing_extensions import Self
+
 ROI_KEY = "_roi_"
 
 
@@ -624,8 +624,6 @@ class BaseObjMeta(abc.ABCMeta, gds.DataSetMeta):
 class NoDefaultOption:
     """Marker class for metadata option without default value"""
 
-    pass
-
 
 class BaseObj(Generic[TypeROI], metaclass=BaseObjMeta):
     """Object (signal/image) interface"""
@@ -876,7 +874,8 @@ def transform_coords(
         self,
         coords: np.ndarray,
         orig: BaseObj[TypeROI],
-        func: Callable,
+        func: Callable[[BaseObj[TypeROI], BaseObj[TypeROI], np.ndarray], None]
+        | Callable[[BaseObj[TypeROI], BaseObj[TypeROI], np.ndarray, gds.DataSet], None],
         param: gds.DataSet | None,
     ) -> None:
         """Transform coordinates
@@ -893,7 +892,11 @@ def transform_coords(
             func(self, orig, coords, param)
 
     def transform_shapes(
-        self, orig: BaseObj[TypeROI], func: Callable, param: gds.DataSet | None = None
+        self,
+        orig: BaseObj[TypeROI],
+        func: Callable[[BaseObj[TypeROI], BaseObj[TypeROI], np.ndarray], None]
+        | Callable[[BaseObj[TypeROI], BaseObj[TypeROI], np.ndarray, gds.DataSet], None],
+        param: gds.DataSet | None = None,
     ) -> None:
         """Apply transform function to result shape / annotations coordinates.
 

sigima_/obj/image.py

@@ -881,6 +881,7 @@ def get_data(self, roi_index: int | None = None) -> np.ndarray:
             view.mask = np.isnan(self.data)
             return view
         single_roi = self.roi.get_single_roi(roi_index)
+        # pylint: disable=unbalanced-tuple-unpacking
         x0, y0, x1, y1 = self.physical_to_indices(single_roi.get_bounding_box(self))
         return self.get_masked_view()[y0:y1, x0:x1]