Use reshape/ravel to set numpy shape

src/PyMca5/PyMcaCore/PyMcaMatplotlibSave.py

@@ -658,7 +658,7 @@ def __postImage(self, ylim, filename):
     import sys
     if len(sys.argv) < 2:
         a=numpy.arange(1200.)
-        a.shape = 20, 60
+        a = a.reshape(20, 60)
         PyMcaMatplotlibSaveImage(a, "filename.png", colormap="rainbow")
         print("Image filename.png saved")
     else:

src/PyMca5/PyMcaCore/SpecFileDataSource.py

@@ -543,7 +543,7 @@ def getDataObject(self,key,selection=None):
                     output.data[i,:] = mcaData
                 #I have all the MCA data ready for image plot
                 if selectiontype == 'STACK':
-                    output.data.shape = 1, npoints, -1
+                    output.data = output.data.reshape(1, npoints, -1)
                     shape = output.data.shape
                     for i in range(len(shape)):
                         key = 'Dim_%d' % (i+1,)

src/PyMca5/PyMcaCore/StackBase.py

@@ -302,7 +302,7 @@ def stackUpdated(self, positioners=None):
                     numpy.add(self._stackImageData[i:i+step,:],
                               numpy.sum(tmpData, 2),
                               self._stackImageData[i:i+step,:])
-                    tmpData.shape = step*shape[1], shape[2]
+                    tmpData = tmpData.reshape(step*shape[1], shape[2])
                     tmpMax = numpy.nanmax(tmpData, axis=0)
                     numpy.add(mcaData0, numpy.sum(tmpData, 0), mcaData0)
                     mcaMax =numpy.max([mcaMax, tmpMax], axis=0)
@@ -317,7 +317,7 @@ def stackUpdated(self, positioners=None):
                 step = 1
                 for i in range(shape[0]):
                     tmpData = self._stack.data[i:i+step,:,:]
-                    tmpData.shape = tmpData.shape[1:]
+                    tmpData = tmpData.reshape(tmpData.shape[1:])
                     numpy.add(self._stackImageData,
                               tmpData,
                               self._stackImageData)
@@ -748,7 +748,7 @@ def calculateMcaDataObject(self, normalize=False, mask=None, mcamax=False):
                             row_dict[r].append(c)
                         for r in row_list:
                             tmpMcaData = self._stack.data[r:r + 1, row_dict[r], :]
-                            tmpMcaData.shape = -1, mcaData.shape[0]
+                            tmpMcaData = tmpMcaData.reshape(-1, mcaData.shape[0])
                             mcaData += numpy.sum(tmpMcaData, axis=0, dtype=numpy.float64)
                             if mcamax:
                                 mcaMax = numpy.max([mcaMax, numpy.max(tmpMcaData, axis=0)], axis=0)
@@ -793,7 +793,7 @@ def calculateMcaDataObject(self, normalize=False, mask=None, mcamax=False):
                             row_dict[r].append(c)
                         for r in row_list:
                             tmpMcaData = self._stack.data[r:r + 1, row_dict[r], :]
-                            tmpMcaData.shape = -1, mcaData.shape[0]
+                            tmpMcaData = tmpMcaData.reshape(-1, mcaData.shape[0])
                             mcaData += tmpMcaData.sum(axis=0, dtype=numpy.float64)
                             if mcamax:
                                 mcaMax = numpy.max([mcaMax, numpy.max(tmpMcaData, axis=0)], axis=0)
@@ -832,7 +832,7 @@ def calculateMcaDataObject(self, normalize=False, mask=None, mcamax=False):
         if "McaLiveTime" in self._stack.info:
             selectedPixels = actualSelectionMask > 0
             liveTime = self._stack.info["McaLiveTime"][:]
-            liveTime.shape = actualSelectionMask.shape
+            liveTime = liveTime.reshape(actualSelectionMask.shape)
             liveTime = liveTime[selectedPixels].sum()
             if normalize:
                 liveTime = liveTime / float(npixels)
@@ -940,7 +940,7 @@ def calculateROIImages(self, index1, index2, imiddle=None, energy=None):
                         minImage = numpy.zeros(leftImage.shape, numpy.int32)
                         for i in range(i1, i2):
                             tmpData = self._stack.data[i]
-                            tmpData.shape = leftImage.shape
+                            tmpData = tmpData.reshape(leftImage.shape)
                             if i == i1:
                                 minImageData = tmpData * 1.0
                                 maxImageData = tmpData * 1.0
@@ -974,7 +974,7 @@ def calculateROIImages(self, index1, index2, imiddle=None, energy=None):
                     istep = 1
                     for i in range(i1, i2):
                         tmpData = self._stack.data[i:i + istep]
-                        tmpData.shape = roiImage.shape
+                        tmpData = tmpData.reshape(roiImage.shape)
                         if i == i1:
                             minImageData = tmpData * 1.0
                             maxImageData = tmpData * 1.0

src/PyMca5/PyMcaGraph/Colormap.py

@@ -130,7 +130,7 @@ def applyColormap(data, colormap='gray', norm='linear', bounds=None):
 
 if __name__ == "__main__":
     data = np.arange(1024 * 1024.)
-    data.shape = 1024, -1
+    data = data.reshape(1024, -1)
 
     for colormap in COLORMAPS:
         pixmap, _ = applyColormap(data, colormap)

src/PyMca5/PyMcaGraph/backends/GLSupport/GLPlotCurve.py

@@ -1163,7 +1163,7 @@ def prepare(self, isXLog, isYLog):
 
             if self.fill is not None:
                 xData = self.xData[:]
-                xData.shape = xData.size, 1
+                xData = xData.reshape(xData.size, 1)
                 zero = np.array((1e-32,), dtype=self.yData.dtype)
 
                 # Add one point before data: (x0, 0.)

src/PyMca5/PyMcaGraph/backends/GLSupport/PlotEvents.py

@@ -50,7 +50,7 @@ def prepareDrawingSignal(event, type_, points, parameters=None):
     eventDict['event'] = event
     eventDict['type'] = type_
     points = np.array(points, dtype=np.float32)
-    points.shape = -1, 2
+    points = points.reshape(-1, 2)
     eventDict['points'] = points
     eventDict['xdata'] = points[:, 0]
     eventDict['ydata'] = points[:, 1]

src/PyMca5/PyMcaGraph/backends/GLUTOpenGLBackend.py

@@ -113,7 +113,7 @@ def glutMouseMoved(self, xPixel, yPixel):
     w = Plot(None, backend=GLUTOpenGLBackend)
     size = 4096
     data = np.arange(float(size)*size, dtype=np.dtype(np.float32))
-    data.shape = size, size
+    data = data.reshape(size, size)
 
     colormap = {'name': 'gray', 'normalization': 'linear',
                 'autoscale': True, 'vmin': 0.0, 'vmax': 1.0,

src/PyMca5/PyMcaGraph/backends/MatplotlibBackend.py

@@ -1217,7 +1217,7 @@ def _emitDrawingSignal(self, event="drawingFinished"):
         #print(dir(self._drawingPatch))
         a = self._drawingPatch.get_xy()
         ddict['points'] = numpy.array(a)
-        ddict['points'].shape = -1, 2
+        ddict['points'] = ddict['points'].reshape(-1, 2)
         ddict['xdata'] = ddict['points'][:, 0]
         ddict['ydata'] = ddict['points'][:, 1]
         #print(numpyvstack(a))
@@ -1751,8 +1751,8 @@ def addItem(self, x, y, legend, info=None, replace=False, replot=True, **kw):
             if fill:
                 item.set_hatch('.')
         elif shape in ['polygon']:
-            xView.shape = 1, -1
-            yView.shape = 1, -1
+            xView = xView.reshape(1, -1)
+            yView = yView.reshape(1, -1)
             item = Polygon(numpyvstack((xView, yView)).T,
                             closed=True,
                             fill=False,
@@ -2858,7 +2858,7 @@ def main(parent=None):
     w.replot()
     #w.invertYAxis(True)
     data = numpy.arange(1000.*1000)
-    data.shape = 10000,100
+    data = data.reshape(10000, 100)
     #plot.replot()
     #w.invertYAxis(True)
     #w.replot()

src/PyMca5/PyMcaGraph/backends/OSMesaGLBackend.py

@@ -251,7 +251,7 @@ def getWidgetHandle(self):
 
     size = 1024
     data = np.arange(float(size)*size, dtype=np.uint16)
-    data.shape = size, size
+    data = data.reshape(size, size)
 
     colormap = {'name': 'gray', 'normalization': 'linear',
                 'autoscale': True, 'vmin': 0.0, 'vmax': 1.0,

src/PyMca5/PyMcaGraph/backends/OpenGLBackend.py

@@ -152,7 +152,7 @@ def resizeGL(self, width, height):
 
     size = 4096
     data = np.arange(float(size)*size, dtype=np.dtype(np.float32))
-    data.shape = size, size
+    data = data.reshape(size, size)
 
     colormap = {'name': 'gray', 'normalization': 'linear',
                 'autoscale': True, 'vmin': 0.0, 'vmax': 1.0,

src/PyMca5/PyMcaGraph/ctools/_ctools/cython/Colormap.pyx

@@ -135,7 +135,7 @@ def dataToRGBAColormap(data,
                            c_nanColorPtr,
                            &c_pixmap[0, 0])
 
-    pixmap.shape = data.shape + (4,)
+    pixmap = pixmap.reshape(data.shape + (4,))
     return pixmap, (c_start, c_end)
 
 def fastLog10(double value):

src/PyMca5/PyMcaGraph/ctools/_ctools/test/testColormap.py

@@ -128,7 +128,7 @@ def buildControlPixmap(data, colormap, start=None, end=None,
                                  dtype=np.uint32)
 
         pixmap = np.take(colormap, indices, axis=0)
-        pixmap.shape = data.shape + (4,)
+        pixmap = pixmap.reshape(data.shape + (4,))
         return np.ascontiguousarray(pixmap)
 
     @staticmethod
@@ -158,7 +158,7 @@ def buildSPSLUTRedPixmap(data, start=None, end=None, isLog10=False):
                                                 (start, end),
                                                 (0, 255),
                                                 1)
-        pixmap.shape = data.shape[0], data.shape[1], 4
+        pixmap = pixmap.reshape(data.shape[0], data.shape[1], 4)
 
         return pixmap
 
@@ -188,8 +188,8 @@ def _testColormap(self, data, colormap, start, end, control=None,
                 # Only works with red colormap and even size
                 # as it needs 2D data
                 if len(data.shape) == 1:
-                    data.shape = data.size // 2, -1
-                    pixmap.shape = data.shape + (4,)
+                    data = data.reshape(data.size // 2, -1)
+                    pixmap = pixmap.reshape(data.shape + (4,))
                 control = self.buildSPSLUTRedPixmap(data, start, end, isLog10)
                 controlType = 'SPS LUT'
 
@@ -243,7 +243,7 @@ def testNoData(self):
             for isLog10 in (False, True):
                 data = np.array((), dtype=dtype)
                 result = np.array((), dtype=np.uint8)
-                result.shape = 0, 4
+                result = result.reshape(0, 4)
                 duration = self._testColormap(data, self.COLORMAPS['red 256'],
                                               None, None, result, isLog10)
                 self._log('No data', 'red 256', dtype, len(data), (None, None),
@@ -359,7 +359,7 @@ def test2DData(self):
                         # Increasing values
                         data = np.arange(size * size, dtype=dtype)
                         data = np.nan_to_num(data)
-                        data.shape = size, size
+                        data = data.reshape(size, size)
                         duration = self._testColormap(data, colormap,
                                                       start, end)
 
@@ -493,7 +493,7 @@ def test2DDataAllPositive(self):
                         # Increasing values
                         data = np.arange(size * size, dtype=dtype) + 1
                         data = np.nan_to_num(data)
-                        data.shape = size, size
+                        data = data.reshape(size, size)
                         duration = self._testColormap(data, colormap,
                                                       start, end,
                                                       isLog10=True)

src/PyMca5/PyMcaGui/io/QEdfFileWidget.py

@@ -987,7 +987,7 @@ def getPixmapFromData(self, data, colormap):
                                 (colormap[2],colormap[3]),
                                 (0,255), 1)
 
-        pixmap.shape = [data.shape[0], data.shape[1], 4]
+        pixmap = pixmap.reshape(data.shape[0], data.shape[1], 4)
         if not goodData:
             pixmap[finiteData < 1] = 255
         return pixmap

src/PyMca5/PyMcaGui/math/FFTAlignmentWindow.py

@@ -295,7 +295,7 @@ def __init__(self, parent=None):
 
     def setDummyStack(self):
         dummyStack = numpy.arange(2 * 128 *256)
-        dummyStack.shape = 2, 128, 256
+        dummyStack = dummyStack.reshape(2, 128, 256)
         self.setStack(dummyStack, index=0)
 
     def getParameters(self):

src/PyMca5/PyMcaGui/math/NNMADialog.py

@@ -123,14 +123,14 @@ def _calculateSlot(self):
                     images, eigenvalues, eigenvectors = threadResult
                 except Exception:
                     if isinstance(data, numpy.ndarray):
-                        self._data.shape = old_shape
+                        self._data = self._data.reshape(*old_shape)
                     msg = qt.QMessageBox(self)
                     msg.setIcon(qt.QMessageBox.Critical)
                     msg.setText("%s" % sys.exc_info()[1])
                     msg.exec()
                     return
             if isinstance(self._data, numpy.ndarray):
-                self._data.shape = old_shape
+                self._data = self._data.reshape(*old_shape)
             _logger.debug("NNMA Elapsed = %s", time.time() - t0)
             self.nnmaWindow.setPCAData(images,
                                        eigenvalues,

src/PyMca5/PyMcaGui/math/NNMAWindow.py

@@ -272,15 +272,15 @@ def updatePlot(self):
         binning = int(self.binningCombo.currentText())
         x = self._x * 1.0
         y = self._y * 1.0
-        x.shape = 1, -1
-        y.shape = 1, -1
+        x = x.reshape(1, -1)
+        y = y.reshape(1, -1)
         r, c = x.shape
-        x.shape = r, int(c / binning), binning
-        y.shape = r, int(c / binning), binning
+        x = x.reshape(r, int(c / binning), binning)
+        y = y.reshape(r, int(c / binning), binning)
         x = x.sum(axis=-1, dtype=numpy.float32) / binning
         y = y.sum(axis=-1, dtype=numpy.float32)
-        x.shape = -1
-        y.shape = -1
+        x = numpy.ravel(x)
+        y = numpy.ravel(y)
         self._binnedX = x
         self._binnedY = y
         if self.graph:
@@ -411,7 +411,7 @@ def test():
     app.lastWindowClosed.connect(app.quit)
     container = NNMAWindow()
     data = numpy.arange(20000)
-    data.shape = 2, 100, 100
+    data = data.reshape(2, 100, 100)
     data[1, 0:100, 0:50] = 100
     container.setPCAData(
         data,

src/PyMca5/PyMcaGui/math/PCADialog.py

@@ -145,14 +145,14 @@ def _calculateSlot(self):
                     images, eigenvalues, eigenvectors = threadResult
                 except Exception:
                     if isinstance(data, numpy.ndarray):
-                        self._data.shape = old_shape
+                        self._data = self._data.reshape(*old_shape)
                     msg = qt.QMessageBox(self)
                     msg.setIcon(qt.QMessageBox.Critical)
                     msg.setText("%s" % sys.exc_info()[1])
                     msg.exec()
                     return
             if isinstance(self._data, numpy.ndarray):
-                self._data.shape = old_shape
+                self._data = self._data.reshape(old_shape)
             _logger.debug("PCA Elapsed = %s", time.time() - t0)
             methodlabel = pcaParameters.get('methodlabel', "")
             imagenames = None

src/PyMca5/PyMcaGui/math/PCAWindow.py

@@ -263,15 +263,15 @@ def updatePlot(self):
         binning = int(self.binningCombo.currentText())
         x = self._x * 1.0
         y = self._y * 1.0
-        x.shape = 1, -1
-        y.shape = 1, -1
+        x = x.reshape(1, -1)
+        y = y.reshape(1, -1)
         r, c = x.shape
-        x.shape = r, int(c / binning), binning
-        y.shape = r, int(c / binning), binning
+        x = x.reshape(r, int(c / binning), binning)
+        y = y.reshape(r, int(c / binning), binning)
         x = x.sum(axis=-1, dtype=numpy.float32) / binning
         y = y.sum(axis=-1, dtype=numpy.float32)
-        x.shape = -1
-        y.shape = -1
+        x = numpy.ravel(x)
+        y = numpy.ravel(y)
         self._binnedX = x
         self._binnedY = y
         self.graph.addCurve(x, y, legend=self._legend, replace=True)
@@ -712,7 +712,7 @@ def test():
     app.lastWindowClosed.connect(app.quit)
     container = PCAWindow()
     data = numpy.arange(20000)
-    data.shape = 2, 100, 100
+    data = data.reshape(2, 100, 100)
     data[1, 0:100, 0:50] = 100
     container.setPCAData(
         data,

src/PyMca5/PyMcaGui/math/SIFTAlignmentWindow.py

@@ -291,7 +291,7 @@ def __init__(self, parent=None):
 
     def setDummyStack(self):
         dummyStack = numpy.arange(2 * 128 *256)
-        dummyStack.shape = 2, 128, 256
+        dummyStack = dummyStack.reshape(2, 128, 256)
         self.setStack(dummyStack, index=0)
 
     def getParameters(self):