Merge pull request #1077 from vasole/np2toml

Adapt pyproject.toml

PyMca5/PyMcaCore/McaStackExport.py

@@ -2,7 +2,7 @@
 #
 # The PyMca X-Ray Fluorescence Toolkit
 #
-# Copyright (c) 2020-2023 European Synchrotron Radiation Facility
+# Copyright (c) 2020-2024 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF.
@@ -182,17 +182,17 @@ def exportStack(stack, h5object, path, channels=None, calibration=None):
     # get the calibration
     if calibration is None:
         calibration = info.get('McaCalib', [0.0, 1.0, 0.0])
-    h5g["calibration"] = numpy.array(calibration, copy=False)
+    h5g["calibration"] = numpy.asarray(calibration)
 
     # get the time
     for key in ["McaLiveTime", "live_time"]:
         if key in info and info[key] is not None:
             # TODO: live time can actually be elapsed time!!!
-            h5g["live_time"] =  numpy.array(info[key], copy=False)
+            h5g["live_time"] =  numpy.asarray(info[key])
 
     for key in ["preset_time", "elapsed_time"]:
         if key in info and info[key] is not None:
-            h5g[key] =  numpy.array(info[key], copy=False)
+            h5g[key] =  numpy.asarray(info[key])
 
     # get the channels
     if channels is None:
@@ -202,7 +202,7 @@ def exportStack(stack, h5object, path, channels=None, calibration=None):
                     channels = stack.x[0]
 
     if channels is not None:
-        h5g["channels"] = numpy.array(channels, copy=False)
+        h5g["channels"] = numpy.asarray(channels)
 
     # the positioners
     posKey = "positioners"
@@ -214,7 +214,7 @@ def exportStack(stack, h5object, path, channels=None, calibration=None):
             posGroup.attrs[att] = u"NXcollection"
         for key in info[posKey]:
             if key not in posGroup:
-                posGroup[key] = numpy.array(info[posKey][key], copy=False)
+                posGroup[key] = numpy.asarray(info[posKey][key])
 
     # the scales for the common rectangular map case
     if "xScale" in info and "yScale" in info:

PyMca5/PyMcaCore/StackBase.py

@@ -2,7 +2,7 @@
 #
 # The PyMca X-Ray Fluorescence Toolkit
 #
-# Copyright (c) 2004-2023 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2024 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF.
@@ -292,7 +292,10 @@ def stackUpdated(self, positioners=None):
                 self._stackImageData = numpy.zeros((shape[0], shape[1]),
                                                 dtype=numpy.float64)
                 mcaData0 = numpy.zeros((shape[2],), numpy.float64)
-                mcaMax = mcaData0 + numpy.NINF
+                if hasattr(numpy, "NINF"):
+                    mcaMax = mcaData0 + numpy.NINF
+                else:
+                    mcaMax = mcaData0 - numpy.inf
                 step = 1
                 for i in range(shape[0]):
                     tmpData = self._stack.data[i:i+step,:,:]
@@ -307,7 +310,10 @@ def stackUpdated(self, positioners=None):
                 self._stackImageData = numpy.zeros((shape[1], shape[2]),
                                                 dtype=numpy.float64)
                 mcaData0 = numpy.zeros((shape[0],), numpy.float64)
-                mcaMax = mcaData0 + numpy.NINF
+                if hasattr(numpy, "NINF"):
+                    mcaMax = mcaData0 + numpy.NINF
+                else:
+                    mcaMax = mcaData0 - numpy.inf
                 step = 1
                 for i in range(shape[0]):
                     tmpData = self._stack.data[i:i+step,:,:]

PyMca5/PyMcaCore/StackROIBatch.py

@@ -2,7 +2,7 @@
 #
 # The PyMca X-Ray Fluorescence Toolkit
 #
-# Copyright (c) 2004-2023 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2024 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF.
@@ -170,7 +170,7 @@ def idxmin(i): return i + 3 * nRois
                     rawSum = 0.0
                     netSum = 0.0
                 else:
-                    roichunk = numpy.array(chunk[:, idx[j]], copy=False, dtype=numpy.float64)
+                    roichunk = numpy.asarray(chunk[:, idx[j]], dtype=numpy.float64)
                     rawSum = roichunk.sum(axis=1, dtype=numpy.float64)
                     deltaX = xw[j][iXMaxList[j]] - xw[j][iXMinList[j]]
                     left = roichunk[:, iXMinList[j]]

PyMca5/PyMcaGraph/backends/GLSupport/GLPlotFrame.py

@@ -1031,7 +1031,7 @@ def _buildVerticesAndLabels(self):
         if not self.isY2Axis:
             extraVertices += self._y2Axis.displayCoords
 
-        extraVertices = np.array(extraVertices, copy=False, dtype=np.float32)
+        extraVertices = np.asarray(extraVertices, dtype=np.float32)
         vertices = np.append(vertices, extraVertices, axis=0)
 
         self._renderResources = (vertices, gridVertices, labels)

PyMca5/PyMcaGraph/backends/GLSupport/GLSupport.py

@@ -2,7 +2,7 @@
 #
 # The PyMca X-Ray Fluorescence Toolkit
 #
-# Copyright (c) 2004-2014 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2024 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF by the Software group.
@@ -117,7 +117,7 @@ class Shape2D(object):
     def __init__(self, points, fill='solid', stroke=True,
                  fillColor=(0., 0., 0., 1.), strokeColor=(0., 0., 0., 1.),
                  strokeClosed=True):
-        self.vertices = np.array(points, dtype=np.float32, copy=False)
+        self.vertices = np.asarray(points, dtype=np.float32)
         self.strokeClosed = strokeClosed
 
         self._indices = buildFillMaskIndices(len(self.vertices))

PyMca5/PyMcaGraph/backends/MatplotlibBackend.py

@@ -2,7 +2,7 @@
 #
 # The PyMca X-Ray Fluorescence Toolkit
 #
-# Copyright (c) 2004-2023 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2024 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF.
@@ -46,15 +46,15 @@
 # Problem on debian6 numpy version 1.4.1 unsigned longs give infinity
 #from numpy import nanmax, nanmin
 def nanmax(x):
-    x = numpy.array(x, copy=False)
+    x = numpy.asarray(x)
     x = x[numpy.isfinite(x)]
     if len(x):
         return x.max()
     else:
         return 0
 
 def nanmin(x):
-    x = numpy.array(x, copy=False)
+    x = numpy.asarray(x)
     x = x[numpy.isfinite(x)]
     if len(x):
         return x.min()
@@ -635,7 +635,7 @@ def _getDrawingColor(self):
         return color
 
     def onMouseMoved(self, event):
-        if DEBUG:
+        if 1 or DEBUG:
             print("onMouseMoved, event = ",event.xdata, event.ydata)
         if event.inaxes != self.ax:
             if DEBUG:
@@ -1700,8 +1700,8 @@ def addItem(self, x, y, legend, info=None, replace=False, replot=True, **kw):
         label = kw.get('label', legend)
         color = kw.get('color', 'black')
         fill = kw.get('fill', True)
-        xView = numpy.array(x, copy=False)
-        yView = numpy.array(y, copy=False)
+        xView = numpy.asarray(x)
+        yView = numpy.asarray(y)
         label = "__ITEM__" + label
         if shape in ["line", "hline", "vline"]:
             print("Not implemented")

PyMca5/PyMcaGraph/backends/_OpenGLPlotCanvas.py

@@ -2,7 +2,7 @@
 #
 # The PyMca X-Ray Fluorescence Toolkit
 #
-# Copyright (c) 2004-2015 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2024 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF by the Software group.
@@ -1323,7 +1323,7 @@ def addImage(self, data, legend=None, info=None,
                     RuntimeWarning)
                 data = np.array(data, dtype=np.float32, order='C')
             else:
-                data = np.array(data, copy=False, order='C')
+                data = np.asarray(data, order='C')
             assert data.dtype in (np.float32, np.uint8, np.uint16)
 
             if colormap is None:
@@ -1447,8 +1447,8 @@ def addItem(self, xList, yList, legend=None, info=None,
             yMin, yMax = yList
             yList = np.array((yMin, yMax, yMax, yMin))
         else:
-            xList = np.array(xList, copy=False)
-            yList = np.array(yList, copy=False)
+            xList = np.asarray(xList)
+            yList = np.asarray(yList)
 
         if self._plotFrame.xAxis.isLog and xList.min() <= 0.:
             raise RuntimeError(
@@ -1501,13 +1501,13 @@ def addCurve(self, x, y, legend=None, info=None,
         if legend is None:
             legend = self._UNNAMED_ITEM
 
-        x = np.array(x, dtype=np.float32, copy=False, order='C')
-        y = np.array(y, dtype=np.float32, copy=False, order='C')
+        x = np.asarray(x, dtype=np.float32, order='C')
+        y = np.asarray(y, dtype=np.float32, order='C')
         if xerror is not None:
-            xerror = np.array(xerror, dtype=np.float32, copy=False, order='C')
+            xerror = np.asarray(xerror, dtype=np.float32, order='C')
             assert np.all(xerror >= 0.)
         if yerror is not None:
-            yerror = np.array(yerror, dtype=np.float32, copy=False, order='C')
+            yerror = np.asarray(yerror, dtype=np.float32, order='C')
             assert np.all(yerror >= 0.)
 
         behaviors = set()

PyMca5/PyMcaGui/misc/NumpyArrayTableModel.py

@@ -1,5 +1,5 @@
 #/*##########################################################################
-# Copyright (C) 2004-2023 European Synchrotron Radiation Facility
+# Copyright (C) 2004-2024 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF.
@@ -230,13 +230,13 @@ def setArrayColors(self, bgcolors=None, fgcolors=None):
         errmsg = "Inconsistent shape for color array, should be %s or %s" % valid_shapes
 
         if bgcolors is not None:
-            bgcolors = numpy.array(bgcolors, copy=False)
+            bgcolors = numpy.asarray(bgcolors)
             assert bgcolors.shape in valid_shapes, errmsg
 
         self._bgcolors = bgcolors
 
         if fgcolors is not None:
-            fgcolors = numpy.array(fgcolors, copy=False)
+            fgcolors = numpy.asarray(fgcolors)
             assert fgcolors.shape in valid_shapes, errmsg
 
         self._fgcolors = fgcolors

PyMca5/PyMcaGui/physics/xas/XASNormalizationWindow.py

@@ -2,7 +2,7 @@
 #
 # The PyMca X-Ray Fluorescence Toolkit
 #
-# Copyright (c) 2004-2023 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2024 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF.
@@ -280,7 +280,7 @@ def __init__(self, parent, spectrum, energy=None):
             self.energy = numpy.arange(len(spectrum)).astype(numpy.float64)
         else:
             self.energy = energy
-        self.spectrum = numpy.array(spectrum, dtype=numpy.float64, copy=False) 
+        self.spectrum = numpy.asarray(spectrum, dtype=numpy.float64) 
         self.parametersWidget = XASNormalizationParametersWidget(self)
         self.graph = PlotWindow.PlotWindow(self, backend=backend,
                                            plugins=False, newplot=False)

PyMca5/PyMcaGui/plotting/ImageView.py

@@ -2,10 +2,10 @@
 #
 # The PyMca X-Ray Fluorescence Toolkit
 #
-# Copyright (c) 2004-2016 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2024 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
-# the ESRF by the Software group.
+# the ESRF.
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -26,7 +26,7 @@
 # THE SOFTWARE.
 #
 # ###########################################################################*/
-__author__ = "T. Vincent - ESRF Data Analysis"
+__author__ = "T. Vincent - ESRF"
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
@@ -754,7 +754,11 @@ def setImage(self, image, origin=(0, 0), scale=(1., 1.),
             self._imagePlot.removeImage(self._imageLegend, replot=False)
             return
 
-        data = np.array(image, order='C', copy=copy)
+        if copy:
+            data = np.array(image, order='C', copy=True)
+        else:
+            data = np.asarray(image, order='C')
+
         assert data.size != 0
         assert len(data.shape) == 2
         height, width = data.shape

PyMca5/PyMcaGui/plotting/MaskScatterWidget.py

@@ -1,5 +1,5 @@
 #/*##########################################################################
-# Copyright (C) 2004-2023 European Synchrotron Radiation Facility
+# Copyright (C) 2004-2024 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF.
@@ -383,7 +383,7 @@ def setSelectionMask(self, mask=None, plot=True):
             self._selectionMask = mask
         else:
             x, y = selectionCurve[0:2]
-            x = numpy.array(x, copy=False)
+            x = numpy.asarray(x)
             if hasattr(mask, "size"):
                 if mask.size == x.size:
                     if self._selectionMask is None:

PyMca5/PyMcaGui/plotting/ScatterPlotCorrelatorWidget.py

@@ -1,8 +1,8 @@
 #/*##########################################################################
-# Copyright (C) 2004-2015 V.A. Sole, European Synchrotron Radiation Facility
+# Copyright (C) 2004-2024 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
-# the ESRF by the Software group.
+# the ESRF.
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -23,7 +23,7 @@
 # THE SOFTWARE.
 #
 #############################################################################*/
-__author__ = "V.A. Sole - ESRF Data Analysis"
+__author__ = "V.A. Sole - ESRF"
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
@@ -87,7 +87,10 @@ def setSelectableItemList(self, items, labels=None, copy=True):
 
     def addSelectableItem(self, item, label=None, copy=True):
         # we always keep a copy by default
-        item = numpy.array(item, dtype=numpy.float32, copy=copy)
+        if copy:
+            item = numpy.array(item, dtype=numpy.float32, copy=True)
+        else:
+            item = numpy.asarray(item, dtype=numpy.float32)
         if label is None:
             label = "Unnamed 00"
             i = 0

PyMca5/PyMcaGui/plotting/SilxMaskImageWidget.py

@@ -1,5 +1,5 @@
 # /*#########################################################################
-# Copyright (C) 2004-2023 European Synchrotron Radiation Facility
+# Copyright (C) 2004-2024 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF.
@@ -142,7 +142,7 @@ def setSelectionMask(self, mask, copy=True):
                  The mask can be cropped or padded to fit active image,
                  the returned shape is that of the active image.
         """
-        mask = numpy.array(mask, copy=False, dtype=numpy.uint8)
+        mask = numpy.asarray(mask, dtype=numpy.uint8)
         if len(mask.shape) != 2:
             # _logger.error('Not an image, shape: %d', len(mask.shape))
             return None

PyMca5/PyMcaGui/pymca/QPyMcaMatplotlibSave1D.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 #/*##########################################################################
-# Copyright (C) 2004-2023 European Synchrotron Radiation Facility
+# Copyright (C) 2004-2024 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF.
@@ -482,8 +482,8 @@ def addDataToPlot(self, x, y, legend = None,
                       linestyle = None,
                       marker=None,
                       alias = None,**kw):
-        x = numpy.array(x, copy=False)
-        y = numpy.array(y, copy=False)
+        x = numpy.asarray(x)
+        y = numpy.asarray(y)
         if self.limitsSet is not None:
             n = self._filterData(x, y)
             if not len(n):