Fix undefined names

bootstrap.py

@@ -169,7 +169,7 @@ def find_executable(target):
     # scripts from project configuration
     if "scripts" in config:
         for script_name in config["scripts"]:
-            if os.path.basename(script) == target:
+            if os.path.basename(script_name) == target:
                 return ("path", os.path.abspath(script_name))
     # entry-points from project configuration
     if "entry_points" in config:

src/PyMca5/PyMcaCore/LegacyStackROIBatch.py

@@ -317,6 +317,7 @@ def main(args):
     images = result["images"]
     nImages = images.shape[0]
 
+    fileRoot = args.fileRoot
     if not fileRoot:
         fileRoot = "images"
 

src/PyMca5/PyMcaCore/McaStackExport.py

@@ -45,10 +45,7 @@
     HAS_NEXUS_UTILS = False
     _logger.info("PyMca5.PyMcaIO.NexusUtils could not be imported")
 
-if sys.version_info < (3,):
-    strdtype = h5py.special_dtype(vlen=unicode)
-else:
-    strdtype = h5py.special_dtype(vlen=str)
+strdtype = h5py.special_dtype(vlen=str)
 
 def exportStackList(stackList, filename, channels=None, calibration=None):
     if hasattr(stackList, "data") and hasattr(stackList, "info"):

src/PyMca5/PyMcaCore/NexusTools.py

@@ -35,7 +35,7 @@
 import posixpath
 try:
     # try to import hdf5plugin
-    if hdf5plugin not in sys.modules:
+    if "hdf5plugin" not in sys.modules:
         import hdf5plugin
 except Exception:
     # but do not crash just because of it

src/PyMca5/PyMcaCore/StackBase.py

@@ -41,6 +41,7 @@
 import sys
 import glob
 import logging
+import copy
 
 logger = logging.getLogger(__name__)
 
@@ -167,11 +168,8 @@ def getPlugins(self):
                         del self.pluginInstanceDict[plugin]
                     if plugin in sys.modules:
                         if hasattr(sys.modules[plugin], targetMethod):
-                            if sys.version < '3.0':
-                                reload(sys.modules[plugin])
-                            else:
-                                import imp
-                                imp.reload(sys.modules[plugin])
+                            import importlib
+                            importlib.reload(sys.modules[plugin])
                     else:
                         try:
                             __import__(plugin)

src/PyMca5/PyMcaCore/XiaEdf.py

@@ -107,7 +107,7 @@ def reset(self):
         try:
             self.__readStat()
         except Exception:
-            raise XiaEdfError("Cannot parse header in <%s>"%filename)
+            raise XiaEdfError("Cannot parse header in <%s>" % self.filename)
 
     def __readStat(self):
         self.header= self.edf.GetHeader(0)

src/PyMca5/PyMcaGraph/PluginLoader.py

@@ -130,11 +130,8 @@ def getPlugins(self, method=None, directoryList=None, exceptions=False):
                         del self.pluginInstanceDict[plugin]
                     if plugin in sys.modules:
                         if hasattr(sys.modules[plugin], targetMethod):
-                            if sys.version.startswith('3'):
-                                import importlib
-                                importlib.reload(sys.modules[plugin])
-                            else:
-                                reload(sys.modules[plugin])
+                            import importlib
+                            importlib.reload(sys.modules[plugin])
                     else:
                         __import__(plugin)
                     if hasattr(sys.modules[plugin], targetMethod):

src/PyMca5/PyMcaGraph/backends/MatplotlibBackend.py

@@ -2496,6 +2496,11 @@ def addImage(self, data, legend=None, info=None,
         shape = data.shape
         if 0:
             # this supports non regularly spaced coordenates!!!!
+
+            if colormap is None:
+                colormap = self.getDefaultColormap()
+            cmap = self.__getColormap(colormap['name'])
+
             x = xmin + numpy.arange(w) * xScale[1]
             y = ymin + numpy.arange(h) * yScale[1]
             image = NonUniformImage(self.ax,
@@ -2505,8 +2510,6 @@ def addImage(self, data, legend=None, info=None,
                                     picker=picker,
                                     cmap=cmap)
 
-
-
             image.set_data(x, y, data)
             xmin, xmax = self.getGraphXLimits()
             ymin, ymax = self.getGraphYLimits()

src/PyMca5/PyMcaGui/io/QEdfFileWidget.py

@@ -1034,7 +1034,8 @@ def closeFile(self, filename=None):
         #print self.selection
         if (self.selection is not None) and filename in self.selection:
             nmca = 0
-            for key in self.selection[filename].keys():
+            mcakeys = list(self.selection[filename].keys())
+            for key in mcakeys:
                 nmca += len(self.selection[filename][key]['rows']) + len(self.selection[filename][key]['cols'])
             if nmca:
                 msg= "%d mca are linked to that EdfFile source.\n"% nmca

src/PyMca5/PyMcaGui/io/QSpsWidget.py

@@ -1048,7 +1048,7 @@ def getSelection(self):
     def __refreshSelection(self):
         return
         _logger.debug("__refreshSelection(self) called")
-        _logger.debug(selection)
+        _logger.debug(self.selection)
         if self.selection is not None:
             sel = self.selection.get(self.data.SourceName, {})
             selkeys = []

src/PyMca5/PyMcaGui/io/hdf5/DataViewerSelector.py

@@ -97,8 +97,8 @@ def _emitSignal(self, action="ADD"):
         ddict = {}
         ddict["action"] = action
         ddict["slice"] = self.getSelection()
-        shape = self.__data.shape
-        ddict["index"] = sel
+        # shape = self.__data.shape
+        # ddict["index"] = sel
         self.sigSliceSelectorSignal.emit(ddict)
 
     def setData(self, data, mode=None):

src/PyMca5/PyMcaGui/io/hdf5/HDF5McaTable.py

@@ -384,7 +384,7 @@ def setMcaSelection(self, ddict):
         if 0:
             if 'aliaslist' in keys:
                 aliaslist = ddict['aliaslist']
-            elif len(self.aliasList) == len(cntlist):
+            elif len(self.aliasList) == len(self.mcaList):
                 aliaslist = self.aliasList * 1
             else:
                 aliaslist = self.mcaList * 1
@@ -404,8 +404,7 @@ def setMcaSelection(self, ddict):
         self.mcaSelection = []
         self.mcaSelectionType = []
         for i in range(len(selection)):
-            idx = selection[idx]
-            if idx < len(mcalist):
+            if selection[i] < len(mcalist):
                 self.mcaSelection.append(selection[i])
                 self.mcaSelectionType.append(selectionType[i])
         self._update()

src/PyMca5/PyMcaGui/math/NNMAWindow.py

@@ -301,7 +301,7 @@ def setParameters(self, ddict):
         if "method" in ddict:
             self.buttonGroup.buttons()[ddict["method"]].setChecked(True)
         if "regions" in ddict:
-            self.regionsWidget.setRegions(regions)
+            self.regionsWidget.setRegions(ddict["regions"])
         return
 
     def getParameters(self):

src/PyMca5/PyMcaGui/math/PCAWindow.py

@@ -295,7 +295,7 @@ def setParameters(self, ddict):
             else:
                 self.binningCombo.setEnabled(False)
         if "regions" in ddict:
-            self.regionsWidget.setRegions(regions)
+            self.regionsWidget.setRegions(ddict["regions"])
         return
 
     def getParameters(self):

src/PyMca5/PyMcaGui/math/fitting/QScriptOption.py

@@ -301,7 +301,7 @@ def setdefaults(self, ddict):
         return
 
 def test():
-    a = qt.QApplication(sys.argv)
+    app = qt.QApplication(sys.argv)
     app.lastWindowClosed.connect(app.quit)
     #w = FieldSheet(fields=(["TextField",'Simple Entry'],
     #                       ["EntryField",'entry','MyLabel'],
@@ -317,7 +317,7 @@ def test():
     w=QScriptOption(name='QScriptOptions',sheets=(sheet1,sheet2),
                             default={'radio':1,'entry':'type here','label':1})
     w.show()
-    a.exec()
+    app.exec()
     print(w.output)
 
 if __name__ == "__main__":

src/PyMca5/PyMcaGui/physics/xrf/QPeriodicTable.py

@@ -430,7 +430,7 @@ def __init__(self, master=None, name=None, fl=0, detailed=1, single=0):
         self.detailed= (detailed==1)
 
         try:
-            strlist= QStringList()
+            strlist= qt.QStringList()
         except Exception:
             strlist= []
         strlist.append("Z")

src/PyMca5/PyMcaGui/plotting/PlotWidget.py

@@ -80,8 +80,10 @@ def __init__(self, parent=None, backend=None,
         self.setGraphYLabel("Y")
         self.setCallback(callback)
 
+        self._legends = legends
+
     def showLegends(self, flag=True):
-        if legends:
+        if self._legends:
             _logger.warning("Legends widget to be implemented")
 
     def graphCallback(self, ddict=None):

src/PyMca5/PyMcaGui/pymca/ImageListStatsWidget.py

@@ -81,7 +81,7 @@ def setImageList(self, images, image_names=None):
             self.imageList = images
             if image_names is None:
                 self.imageNames = []
-                for i in range(nimages):
+                for i in range(len(images)):
                     self.imageNames.append("Image %02d" % i)
             else:
                 self.imageNames = image_names

src/PyMca5/PyMcaGui/pymca/LegacyPyMcaBatch.py

@@ -585,7 +585,7 @@ def __getFileType(self,inputfile):
         except Exception:
             qt.QMessageBox.critical(self,
                                     sys.exc_info()[0],
-                                    'I do not know what to do with file\n %s' % ffile)
+                                    'I do not know what to do with file\n %s' % inputfile)
             self.raise_()
             return None
 

src/PyMca5/PyMcaGui/pymca/McaWindow.py

@@ -175,7 +175,7 @@ def mcaSimpleFitSignal(self):
             self.__simplefitcalibration = calib
             calibrationOrder = curveinfo.get('McaCalibOrder', 2)
             if calibrationOrder == 'TOF':
-                x = calib[2] + calib[0] / pow(x - alib[1],2)
+                x = calib[2] + calib[0] / pow(x - calib[1],2)
             else:
                 x = calib[0] + calib[1] * x + calib[2] * x * x
             self.simplefit.setdata(x=x,y=y,

src/PyMca5/PyMcaGui/pymca/PyMcaBatch.py

@@ -1102,7 +1102,7 @@ def __getFileType(self,inputfile):
         except Exception:
             qt.QMessageBox.critical(self,
                                     sys.exc_info()[0],
-                                    'I do not know what to do with file\n %s' % ffile)
+                                    'I do not know what to do with file\n %s' % inputfile)
             self.raise_()
             return None
 

src/PyMca5/PyMcaGui/pymca/PyMcaMain.py

@@ -51,6 +51,14 @@
 from PyMca5.PyMcaGui.io import PyMcaFileDialogs
 QTVERSION = qt.qVersion()
 
+try:
+    import silx
+    # try to import silx prior to importing matplotlib to prevent
+    # unnecessary warning
+    import silx.gui.plot
+except Exception:
+    pass
+
 from PyMca5.PyMcaGui.pymca import PyMcaMdi
 IconDict = PyMcaMdi.IconDict
 IconDict0 = PyMcaMdi.IconDict0
@@ -167,12 +175,11 @@
 from PyMca5.PyMcaIO import ConfigDict
 from PyMca5 import PyMcaDirs
 
-XIA_CORRECT = False
 try:
     from PyMca5.PyMcaCore import XiaCorrect
     XIA_CORRECT = True
 except Exception:
-    pass
+    XIA_CORRECT = False
 
 SOURCESLIST = QDispatcher.QDataSource.source_types.keys()
 

src/PyMca5/PyMcaGui/pymca/PyMcaMdi.py

@@ -196,7 +196,7 @@ def onWinToolMenu(self, idx):
         self.onWinToolAction()
 
     def onWinToolAction(self):
-            apply(self.winToolMenuAction, ())
+        apply(self.winToolMenuAction, ())
 
     #
     # Mdi windows geometry

src/PyMca5/PyMcaGui/pymca/QDispatcher.py

@@ -199,6 +199,7 @@ def _addSelectionSlot(self, sel_list, event=None):
                             #the clients will be able to retrieve the data
                             #the problem is that 10 clients will requiere
                             #10 read outs
+                            import weakref
                             ddict["sourcereference"] = weakref.ref(source)
                             selectionList.append(ddict)
                         if lastEvent != event:

src/PyMca5/PyMcaGui/pymca/QStackWidget.py

@@ -708,9 +708,9 @@ def loadSecondaryStack(self):
             for i in range(len(stack)):
                 if stack[i] is not None:
                     secondary = QStackWidget(primary=False,
-                                         rgbwidget=widget.rgbWidget)
+                                         rgbwidget=self.rgbWidget)
                     secondary.setStack(stack[i])
-                    widget.addSecondary(secondary)
+                    self.addSecondary(secondary)
                     stack[i] = None
         else:
             secondary = QStackWidget(rgbwidget=self.rgbWidget,

src/PyMca5/PyMcaGui/pymca/SilxScanWindow.py

@@ -784,7 +784,7 @@ def getPrintPreviewTitle(self):
                 # no need to add a second one
                 return title
         except Exception:
-            logger.warning('Problem accessing ScanWindow plot title')
+            _logger.warning('Problem accessing ScanWindow plot title')
         if self.scanWindowInfoWidget is not None:
             if not self.infoDockWidget.isHidden():
                 info = self.scanWindowInfoWidget.getInfo()

src/PyMca5/PyMcaGui/pymca/SilxScatterWindow.py

@@ -151,7 +151,7 @@ def _addSelection(self, selectionlist):
                         break
                 if not gotIt:
                     raise ValueError("Unmatched dimensions following C order")
-                data = data.reshape(xsize, *oldDataShape[i+1:])
+                data = data.reshape(x.size, *oldDataShape[i+1:])
                 nscatter = data.shape[0]
             else:
                 raise ValueError("Unmatched dimensions among axes and signals")

src/PyMca5/PyMcaGui/pymca/StackPluginResultsWindow.py

@@ -180,7 +180,7 @@ def setStackPluginResults(
             self.imageList = images
             if image_names is None:
                 self.imageNames = []
-                for i in range(nimages):
+                for i in range(len(images)):
                     self.imageNames.append("Image %02d" % i)
             else:
                 self.imageNames = image_names

src/PyMca5/PyMcaIO/ArraySave.py

@@ -48,10 +48,7 @@
 HDF5 = True
 try:
     import h5py
-    if sys.version_info < (3, ):
-        text_dtype = h5py.special_dtype(vlen=unicode)
-    else:
-        text_dtype = h5py.special_dtype(vlen=str)
+    text_dtype = h5py.special_dtype(vlen=str)
 except ImportError:
     HDF5 = False
 

src/PyMca5/PyMcaIO/BAXSCSVFileParser.py

@@ -135,7 +135,7 @@ def scanno(self):
         """
         Gives back the number of scans in the file
         """
-        return len(self_scan)
+        return len(self._scan)
 
     def list(self):
         return "1:1"

src/PyMca5/PyMcaIO/MarCCD.py

@@ -36,11 +36,12 @@
 
 class MarCCD(object):
     def __init__(self, filename):
-        if isinstance(filename, file):
-            fd = filename
-        else:
+        if isinstance(filename, str):
             # make sure we work with bytes
             fd = open(filename, 'rb')
+        else:
+            fd = filename
+
         order = fd.read(2)
         if order == "II":
             #intel, little endian
@@ -74,7 +75,7 @@ def __init__(self, filename):
         data = data.reshape(info["nfast"], info["nslow"])
         self.__data = data
         self.__info = info
-        if not isinstance(filename, file):
+        if isinstance(filename, str):
             fd.close()
 
     def getData(self, *var, **kw):