Merge pull request #407 from vasole/warnings

Reduce the amount of warnings

PyMca5/PyMcaCore/NexusDataSource.py

@@ -2,7 +2,7 @@
 #
 # The PyMca X-Ray Fluorescence Toolkit
 #
-# Copyright (c) 2004-2018 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2019 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF by the Software group.
@@ -77,7 +77,7 @@ def h5py_sorting(object_list):
 
     try:
         if sorting_key != 'name':
-            sorting_list = [(o[sorting_key].value, o)
+            sorting_list = [(o[sorting_key][()], o)
                            for o in object_list]
             sorted_list = sorted(sorting_list, key=itemgetter(0))
             return [x[1] for x in sorted_list]
@@ -323,13 +323,13 @@ def getDataObject(self, key, selection=None):
                     mcaDatasetObjectPath = mcaObjectPaths[key]
                     dataset = None
                     if mcaDatasetObjectPath in h5File:
-                        dataset = h5File[mcaDatasetObjectPath].value
+                        dataset = h5File[mcaDatasetObjectPath][()]
                     elif "::" in mcaDatasetObjectPath:
                         fileName, path = mcaDatasetObjectPath.split()
                         if os.path.exists(fileName):
                             with h5py.File(fileName, "r") as h5:
                                 if path in h5:
-                                    dataset = h5[path].value
+                                    dataset = h5[path][()]
                     if dataset is None:
                         _logger.debug("Broken link? Ignoring key %s = %s",
                                       key, mcaDatasetObjectPath)
@@ -368,7 +368,7 @@ def getDataObject(self, key, selection=None):
                         if selection['mcaselectiontype'].lower() != "sum":
                             mcaData /= divider
                     else:
-                        mcaData = mcaData.value
+                        mcaData = mcaData[()]
                         divider = 1.0
                     if "McaLiveTime" in output.info:
                         if numpy.isscalar(output.info["McaLiveTime"]):
@@ -415,7 +415,7 @@ def getDataObject(self, key, selection=None):
                             _logger.info("Skipping object key %s" % key)
                             continue
                         output.info['MotorNames'].append(key)
-                        value = positioners[key].value
+                        value = positioners[key][()]
                         if hasattr(value, "size"):
                             if value.size > 1:
                                 if hasattr(value, "flat"):
@@ -436,7 +436,7 @@ def getDataObject(self, key, selection=None):
                 totalElements *= dim
             if totalElements < 2.0E7:
                 try:
-                    data = phynxFile[path].value
+                    data = phynxFile[path][()]
                 except MemoryError:
                     data = phynxFile[path]
                     pass
@@ -481,7 +481,7 @@ def getDataObject(self, key, selection=None):
                 if len(selection[cnt]) > 1:
                     for xidx in range(1, len(selection[cnt])):
                         path =  entry + selection['cntlist'][selection[cnt][xidx]]
-                        data = phynxFile[path].value
+                        data = phynxFile[path][()]
                         output.x.append(data)
             elif cnt == 'm':
                 #only one monitor

PyMca5/PyMcaCore/NexusTools.py

@@ -2,7 +2,7 @@
 #
 # The PyMca X-Ray Fluorescence Toolkit
 #
-# Copyright (c) 2018 European Synchrotron Radiation Facility
+# Copyright (c) 2018-2019 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF by the Software group.
@@ -78,7 +78,7 @@ def h5py_sorting(object_list):
 
     try:
         if sorting_key != 'name':
-            sorting_list = [(o[1][sorting_key].value, o)
+            sorting_list = [(o[1][sorting_key][()], o)
                            for o in object_list]
             sorted_list = sorted(sorting_list, key=itemgetter(0))
             return [x[1] for x in sorted_list]
@@ -500,7 +500,7 @@ def getScannedPositioners(h5file, path):
         if not len(scanned):
             entry = h5file[entry_name]
             if "title" in entry:
-                title = entry["title"].value
+                title = entry["title"][()]
                 if hasattr(title, "dtype"):
                     _logger.warning("entry title should be a string not an array")
                     if hasattr(title, "__len__"):
@@ -537,7 +537,7 @@ def getScannedPositioners(h5file, path):
     for entry in entries:
         print("Entry name = %s" % entry.name)
         if "title" in entry:
-            print("Entry title = %s" % entry["title"].value)
+            print("Entry title = %s" % entry["title"][()])
         measurement = getMeasurementGroup(h5, entry.name)
         if measurement is None:
             print("No measurement")

PyMca5/PyMcaGui/io/hdf5/HDF5Info.py

@@ -1,5 +1,5 @@
 #/*##########################################################################
-# Copyright (C) 2004-2017 V.A. Sole, European Synchrotron Radiation Facility
+# Copyright (C) 2004-2019 V.A. Sole, European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF by the Software group.
@@ -390,19 +390,19 @@ def getInfo(hdf5File, node):
             if hasattr(data, 'shape'):
                 shape = data.shape
                 if not len(shape):
-                    ddict['general']['Value'] = "%s" % data.value
+                    ddict['general']['Value'] = "%s" % data[()]
                 elif shape[0] == 1:
-                    ddict['general']['Value'] = "%s" % data.value[0]
+                    ddict['general']['Value'] = "%s" % data[0]
                 else:
                     print("Warning: Node %s not fully understood" % node)
-                    ddict['general']['Value'] = "%s" % data.value
+                    ddict['general']['Value'] = "%s" % data[()]
         elif hasattr(data, 'shape'):
             shape = data.shape
             if len(shape) == 1:
                 if shape[0] == 1:
-                    ddict['general']['Value'] = "%s" % data.value[0]
+                    ddict['general']['Value'] = "%s" % data[0]
             elif len(shape) == 0:
-                ddict['general']['Value'] = "%s" % data.value
+                ddict['general']['Value'] = "%s" % data[()]
     if hasattr(data, "keys"):
         ddict['general']['members'] = list(data.keys())
     elif hasattr(data, "listnames"):
@@ -425,27 +425,28 @@ def getInfo(hdf5File, node):
                    ("%s" % dtype).startswith("|O"):
                     if not len(shape):
                         ddict['general'][member]['Shape'] = ""
-                        ddict['general'][member]['Value'] = "%s" % memberObject.value
+                        ddict['general'][member]['Value'] = "%s" % memberObject[()]
                     else:
                         ddict['general'][member]['Shape'] = shape[0]
-                        ddict['general'][member]['Value'] = "%s" % memberObject.value[0]
+                        if shape[0] > 0:
+                            ddict['general'][member]['Value'] = "%s" % memberObject[0]
                     continue
                 if not len(shape):
                     ddict['general'][member]['Shape'] = ""
-                    ddict['general'][member]['Value'] = "%s" % memberObject.value
+                    ddict['general'][member]['Value'] = "%s" % memberObject[()]
                     continue
                 ddict['general'][member]['Shape'] = "%d" % shape[0]
                 for i in range(1, len(shape)):
                     ddict['general'][member]['Shape'] += " x %d" % shape[i]
                 if len(shape) == 1:
                     if shape[0] == 1:
-                        ddict['general'][member]['Value'] = "%s" % memberObject.value[0]
-                    else:
-                        ddict['general'][member]['Value'] = "%s, ..., %s" % (memberObject.value[0],
-                                                                             memberObject.value[-1])
+                        ddict['general'][member]['Value'] = "%s" % memberObject[0]
+                    elif shape[0] > 1:
+                        ddict['general'][member]['Value'] = "%s, ..., %s" % (memberObject[0],
+                                                                             memberObject[-1])
                 elif len(shape) == 2:
-                    ddict['general'][member]['Value'] = "%s, ..., %s" % (memberObject.value[0],
-                                                                         memberObject.value[-1])
+                    ddict['general'][member]['Value'] = "%s, ..., %s" % (memberObject[0],
+                                                                         memberObject[-1])
                 else:
                     pass
         else:

PyMca5/PyMcaGui/io/hdf5/HDF5Widget.py

@@ -1,5 +1,5 @@
 #/*##########################################################################
-# Copyright (C) 2004-2018 V.A. Sole, ESRF - D. Dale CHESS
+# Copyright (C) 2004-2019 V.A. Sole, ESRF - D. Dale CHESS
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF by the Software group.
@@ -105,7 +105,7 @@ def h5py_sorting(object_list):
 
     try:
         if sorting_key != 'name':
-            sorting_list = [(o[1][sorting_key].value, o)
+            sorting_list = [(o[1][sorting_key][()], o)
                            for o in object_list]
             sorted_list = sorted(sorting_list, key=itemgetter(0))
             return [x[1] for x in sorted_list]
@@ -429,10 +429,10 @@ def data(self, index, role):
                                 if len(children[idx].getNode().shape):
                                     #stored as an array of strings!!!
                                     #return just the first item
-                                    return MyQVariant("%s" % children[idx].getNode().value[0])
+                                    return MyQVariant("%s" % children[idx].getNode()[()][0])
                                 else:
                                     #stored as a string
-                                    return MyQVariant("%s" % children[idx].getNode().value)
+                                    return MyQVariant("%s" % children[idx].getNode()[()])
                 return MyQVariant(item.type)
             if column == 2:
                 return MyQVariant(item.shape)

PyMca5/PyMcaGui/pymca/PyMcaMain.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 #/*##########################################################################
-# Copyright (C) 2004-2018 V.A. Sole, European Synchrotron Radiation Facility
+# Copyright (C) 2004-2019 V.A. Sole, European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF by the Software group.
@@ -135,7 +135,13 @@
             if hasattr(qt, 'QOpenGLWidget'):
                 print("Warning: OpenGL backend not fully supported")
 try:
-    # try to import silx prior to import matplotlib
+    if (sys.version_info < (3,)) and ("PyQt4.QtCore" in sys.modules):
+        # PyQt4 is the most reliable binding at the ESRF for python 2
+        import silx
+        silxLogger = logging.getLogger("silx.DEPRECATION")
+        silxLogger.setLevel(logging.CRITICAL)
+    # try to import silx prior to importing matplotlib to prevent
+    # unnecessary warning
     import silx.gui.plot
 except:
     pass

PyMca5/PyMcaGui/pymca/QStackWidget.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 #/*##########################################################################
-# Copyright (C) 2004-2018 V.A. Sole, European Synchrotron Radiation Facility
+# Copyright (C) 2004-2019 V.A. Sole, European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
 # the ESRF by the Software group.
@@ -88,8 +88,13 @@
 else:
     QString = qt.safe_str
 try:
-    # try to import silx prior to importing matplotlib
-    # to prevent unnecessary warning
+    if (sys.version_info < (3,)) and ("PyQt4.QtCore" in sys.modules):
+        # PyQt4 is the most reliable binding at the ESRF for python 2
+        import silx
+        silxLogger = logging.getLogger("silx.DEPRECATION")
+        silxLogger.setLevel(logging.CRITICAL)
+    # try to import silx prior to importing matplotlib to prevent
+    # unnecessary warning
     import silx.gui.plot
 except:
     pass