Merge pull request #4100 from t20100/fix-deprecation

Dependencies: Fixed numpy v2 deprecation warnings

examples/plotStats.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # /*##########################################################################
 #
-# Copyright (c) 2016-2021 European Synchrotron Radiation Facility
+# Copyright (c) 2016-2024 European Synchrotron Radiation Facility
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -51,6 +51,11 @@
 import numpy
 import time
 
+try:
+    from numpy import trapezoid
+except ImportError:  # numpy v1 compatibility
+    from numpy import trapz as trapezoid
+
 
 class UpdateThread(threading.Thread):
     """Thread updating the curve of a :class:`~silx.gui.plot.Plot1D`
@@ -96,7 +101,7 @@ def __init__(self):
 
     def calculate(self, context):
         xData, yData = context.data
-        return numpy.trapz(x=xData, y=yData)
+        return trapezoid(x=xData, y=yData)
 
 
 class COM(StatBase):

src/silx/gui/plot/CurvesROIWidget.py

@@ -1,6 +1,6 @@
 # /*##########################################################################
 #
-# Copyright (c) 2004-2023 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2024 European Synchrotron Radiation Facility
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -37,6 +37,12 @@
 import sys
 import functools
 import numpy
+
+try:
+    from numpy import trapezoid
+except ImportError:  # numpy v1 compatibility
+    from numpy import trapz as trapezoid
+
 from silx.io import dictdump
 from silx.utils.weakref import WeakMethodProxy
 from silx.utils.proxy import docstring
@@ -1240,13 +1246,13 @@ def computeRawAndNetArea(self, curve):
         if x.size == 0:
             return 0.0, 0.0
 
-        rawArea = numpy.trapz(y, x=x)
+        rawArea = trapezoid(y, x=x)
         # to speed up and avoid an intersection calculation we are taking the
         # closest index to the ROI
         closestXLeftIndex = (numpy.abs(x - self.getFrom())).argmin()
         closestXRightIndex = (numpy.abs(x - self.getTo())).argmin()
         yBackground = y[closestXLeftIndex], y[closestXRightIndex]
-        background = numpy.trapz(yBackground, x=x)
+        background = trapezoid(yBackground, x=x)
         netArea = rawArea - background
         return rawArea, netArea
 

src/silx/gui/plot/items/_arc_roi.py

@@ -1,6 +1,6 @@
 # /*##########################################################################
 #
-# Copyright (c) 2018-2023 European Synchrotron Radiation Facility
+# Copyright (c) 2018-2024 European Synchrotron Radiation Facility
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -632,7 +632,12 @@ def _createGeometryFromControlPoints(self, start, mid, end, weight, closed=None)
                 center, start, end, radius, weight, startAngle, endAngle
             )
 
-        elif numpy.linalg.norm(numpy.cross(mid - start, end - start)) < 1e-5:
+        elif (
+            numpy.linalg.norm(
+                numpy.cross(numpy.append(mid - start, 0), numpy.append(end - start, 0))
+            )
+            < 1e-5
+        ):
             # Degenerated arc, it's a rectangle
             return _ArcGeometry.createRect(start, end, weight)
         else:

src/silx/gui/plot/items/scatter.py

@@ -1,6 +1,6 @@
 # /*##########################################################################
 #
-# Copyright (c) 2017-2023 European Synchrotron Radiation Facility
+# Copyright (c) 2017-2024 European Synchrotron Radiation Facility
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -713,7 +713,7 @@ def _addBackendRenderer(self, backend):
                         shape = shape[0], int(numpy.ceil(nbpoints / shape[0]))
 
                 if shape[0] < 2 or shape[1] < 2:  # Single line, at least 2 points
-                    points = numpy.ones((2, nbpoints, 2), dtype=numpy.float64)
+                    points = numpy.zeros((2, nbpoints, 3), dtype=numpy.float64)
                     # Use row/column major depending on shape, not on info value
                     gridOrder = "row" if shape[0] == 1 else "column"
 
@@ -727,19 +727,14 @@ def _addBackendRenderer(self, backend):
                     # Add a second line that will be clipped in the end
                     points[1, :-1] = (
                         points[0, :-1]
-                        + numpy.cross(points[0, 1:] - points[0, :-1], (0.0, 0.0, 1.0))[
-                            :, :2
-                        ]
+                        + numpy.cross(points[0, 1:] - points[0, :-1], (0.0, 0.0, 1.0))
                     )
                     points[1, -1] = (
                         points[0, -1]
-                        + numpy.cross(points[0, -1] - points[0, -2], (0.0, 0.0, 1.0))[
-                            :2
-                        ]
+                        + numpy.cross(points[0, -1] - points[0, -2], (0.0, 0.0, 1.0))
                     )
 
-                    points.shape = 2, nbpoints, 2  # Use same shape for both orders
-                    coords, indices = _quadrilateral_grid_as_triangles(points)
+                    points = points[:, :, :2]
 
                 elif gridOrder == "row":  # row-major order
                     if nbpoints != numpy.prod(shape):

src/silx/gui/plot/test/testCurvesROIWidget.py

@@ -1,6 +1,6 @@
 # /*##########################################################################
 #
-# Copyright (c) 2016-2023 European Synchrotron Radiation Facility
+# Copyright (c) 2016-2024 European Synchrotron Radiation Facility
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -32,6 +32,11 @@
 import os.path
 import numpy
 
+try:
+    from numpy import trapezoid
+except ImportError:  # numpy v1 compatibility
+    from numpy import trapz as trapezoid
+
 from silx.gui import qt
 from silx.gui.plot import items
 from silx.gui.plot import Plot1D
@@ -171,7 +176,7 @@ def testAreaCalculation(self):
 
         self.assertEqual(
             roi_pos.computeRawAndNetArea(posCurve),
-            (numpy.trapz(y=[10, 20], x=[10, 20]), 0.0),
+            (trapezoid(y=[10, 20], x=[10, 20]), 0.0),
         )
         self.assertEqual(roi_pos.computeRawAndNetArea(negCurve), (0.0, 0.0))
         self.assertEqual(roi_neg.computeRawAndNetArea(posCurve), ((0.0), 0.0))

src/silx/opencl/sift/alignment.py

@@ -3,7 +3,7 @@
 #    Project: Sift implementation in Python + OpenCL
 #             https://github.com/silx-kit/silx
 #
-#    Copyright (C) 2013-2018  European Synchrotron Radiation Facility, Grenoble, France
+#    Copyright (C) 2013-2024  European Synchrotron Radiation Facility, Grenoble, France
 #
 # Permission is hereby granted, free of charge, to any person
 # obtaining a copy of this software and associated documentation
@@ -324,8 +324,8 @@ def align(
                     [transform_matrix[5], transform_matrix[2]], dtype=numpy.float32
                 )
                 matrix = numpy.empty((2, 2), dtype=numpy.float32)
-                matrix[0, 0], matrix[0, 1] = transform_matrix[4], transform_matrix[3]
-                matrix[1, 0], matrix[1, 1] = transform_matrix[1], transform_matrix[0]
+                matrix[0, 0], matrix[0, 1] = transform_matrix[4, 0], transform_matrix[3, 0]
+                matrix[1, 0], matrix[1, 1] = transform_matrix[1, 0], transform_matrix[0, 0]
             if double_check and (
                 len_match >= 3 * 6
             ):  # and abs(matrix - numpy.identity(2)).max() > 0.1:
@@ -348,12 +348,12 @@ def align(
                     )
                     matrix = numpy.empty((2, 2), dtype=numpy.float32)
                     matrix[0, 0], matrix[0, 1] = (
-                        transform_matrix[4],
-                        transform_matrix[3],
+                        transform_matrix[4, 0],
+                        transform_matrix[3, 0],
                     )
                     matrix[1, 0], matrix[1, 1] = (
-                        transform_matrix[1],
-                        transform_matrix[0],
+                        transform_matrix[1, 0],
+                        transform_matrix[0, 0],
                     )
             if relative:  # update stable part to perform a relative alignment
                 self.ref_kp = kp