New upstream version 0.9.0+dfsg

5 files changed, 214 insertions, 24 deletions

diff --git a/silx/app/view/About.py b/silx/app/view/About.py
index 07306ef..4b804f2 100644
--- a/silx/app/view/About.py
+++ b/silx/app/view/About.py
@@ -25,7 +25,7 @@
 
 __authors__ = ["V. Valls"]
 __license__ = "MIT"
-__date__ = "05/06/2018"
+__date__ = "05/07/2018"
 
 import sys
 
@@ -147,6 +147,15 @@ class About(qt.QDialog):
             template = '<b>%s</b> is <font color="red">not loaded</font>'
         return template % name
 
+    @staticmethod
+    def __formatOptionalFilters(name, isAvailable):
+        """Utils to format availability of features"""
+        if isAvailable:
+            template = '<b>%s</b> is <font color="green">available</font>'
+        else:
+            template = '<b>%s</b> is <font color="red">not available</font>'
+        return template % name
+
     def __updateText(self):
         """Update the content of the dialog according to the settings."""
         import silx._version
@@ -174,14 +183,29 @@ class About(qt.QDialog):
         </p>
         """
 
-        hdf5pluginLoaded = "hdf5plugin" in sys.modules
-        fabioLoaded = "fabio" in sys.modules
-        h5pyLoaded = "h5py" in sys.modules
-
-        optional_lib = []
-        optional_lib.append(self.__formatOptionalLibraries("FabIO", fabioLoaded))
-        optional_lib.append(self.__formatOptionalLibraries("H5py", h5pyLoaded))
-        optional_lib.append(self.__formatOptionalLibraries("hdf5plugin", hdf5pluginLoaded))
+        optionals = []
+        optionals.append(self.__formatOptionalLibraries("H5py", "h5py" in sys.modules))
+        optionals.append(self.__formatOptionalLibraries("FabIO", "fabio" in sys.modules))
+
+        try:
+            import h5py.version
+            if h5py.version.hdf5_version_tuple >= (1, 10, 2):
+                # Previous versions only return True if the filter was first used
+                # to decode a dataset
+                import h5py.h5z
+                FILTER_LZ4 = 32004
+                FILTER_BITSHUFFLE = 32008
+                filters = [
+                    ("HDF5 LZ4 filter", FILTER_LZ4),
+                    ("HDF5 Bitshuffle filter", FILTER_BITSHUFFLE),
+                ]
+                for name, filterId in filters:
+                    isAvailable = h5py.h5z.filter_avail(filterId)
+                    optionals.append(self.__formatOptionalFilters(name, isAvailable))
+            else:
+                optionals.append(self.__formatOptionalLibraries("hdf5plugin", "hdf5plugin" in sys.modules))
+        except ImportError:
+            pass
 
         # Access to the logo in SVG or PNG
         logo = icons.getQFile("../logo/silx")
@@ -194,7 +218,7 @@ class About(qt.QDialog):
             qt_binding=qt.BINDING,
             qt_version=qt.qVersion(),
             python_version=sys.version.replace("\n", "<br />"),
-            optional_lib="<br />".join(optional_lib),
+            optional_lib="<br />".join(optionals),
             silx_image_path=logo.fileName()
         )
 
diff --git a/silx/app/view/CustomNxdataWidget.py b/silx/app/view/CustomNxdataWidget.py
index 02ae6c0..72c9940 100644
--- a/silx/app/view/CustomNxdataWidget.py
+++ b/silx/app/view/CustomNxdataWidget.py
@@ -944,10 +944,10 @@ class CustomNxdataWidget(qt.QTreeView):
             if edited:
                 item.setAxesDatasets(datasets)
 
-        dataset = item.getSignalDataset()
-        newDataset = self.__replaceDatasetRoot(dataset, removedRoot, loadedRoot)
-        if dataset is not newDataset:
-            item.setSignalDataset(newDataset)
+            dataset = item.getSignalDataset()
+            newDataset = self.__replaceDatasetRoot(dataset, removedRoot, loadedRoot)
+            if dataset is not newDataset:
+                item.setSignalDataset(newDataset)
 
     def __replaceDatasetRoot(self, dataset, fromRoot, toRoot):
         """
diff --git a/silx/app/view/DataPanel.py b/silx/app/view/DataPanel.py
index 0653f74..5d87381 100644
--- a/silx/app/view/DataPanel.py
+++ b/silx/app/view/DataPanel.py
@@ -25,9 +25,10 @@
 
 __authors__ = ["V. Valls"]
 __license__ = "MIT"
-__date__ = "06/06/2018"
+__date__ = "12/10/2018"
 
 import logging
+import os.path
 
 from silx.gui import qt
 from silx.gui.data.DataViewerFrame import DataViewerFrame
@@ -45,6 +46,26 @@ class _HeaderLabel(qt.QLabel):
     def sizeHint(self):
         return qt.QSize(10, 30)
 
+    def minimumSizeHint(self):
+        return qt.QSize(10, 30)
+
+    def setData(self, filename, path):
+        if filename == "" and path == "":
+            text = ""
+        elif filename == "":
+            text = path
+        else:
+            text = "%s::%s" % (filename, path)
+        self.setText(text)
+        tooltip = ""
+        template = "<li><b>%s</b>: %s</li>"
+        tooltip += template % ("Directory", os.path.dirname(filename))
+        tooltip += template % ("File name", os.path.basename(filename))
+        tooltip += template % ("Data path", path)
+        tooltip = "<ul>%s</ul>" % tooltip
+        tooltip = "<html>%s</html>" % tooltip
+        self.setToolTip(tooltip)
+
     def paintEvent(self, event):
         painter = qt.QPainter(self)
 
@@ -101,14 +122,14 @@ class DataPanel(qt.QWidget):
             self.__dataTitle.setVisible(True)
             if hasattr(data, "name"):
                 if hasattr(data, "file"):
-                    label = str(data.file.filename)
-                    label += "::"
+                    filename = str(data.file.filename)
                 else:
-                    label = ""
-                label += data.name
+                    filename = ""
+                path = data.name
             else:
-                label = ""
-            self.__dataTitle.setText(label)
+                filename = ""
+                path = ""
+            self.__dataTitle.setData(filename, path)
 
     def setCustomDataItem(self, item):
         self.__customNxdataItem = item
diff --git a/silx/app/view/Viewer.py b/silx/app/view/Viewer.py
index 8f5db60..88ff989 100644
--- a/silx/app/view/Viewer.py
+++ b/silx/app/view/Viewer.py
@@ -25,7 +25,7 @@
 
 __authors__ = ["V. Valls"]
 __license__ = "MIT"
-__date__ = "25/06/2018"
+__date__ = "08/10/2018"
 
 
 import os
@@ -146,6 +146,18 @@ class Viewer(qt.QMainWindow):
         toolbar.setStyleSheet("QToolBar { border: 0px }")
 
         action = qt.QAction(toolbar)
+        action.setIcon(icons.getQIcon("view-refresh"))
+        action.setText("Refresh")
+        action.setToolTip("Refresh all selected items")
+        action.triggered.connect(self.__refreshSelected)
+        action.setShortcut(qt.QKeySequence(qt.Qt.ControlModifier + qt.Qt.Key_Plus))
+        toolbar.addAction(action)
+        treeView.addAction(action)
+        self.__refreshAction = action
+
+        toolbar.addSeparator()
+
+        action = qt.QAction(toolbar)
         action.setIcon(icons.getQIcon("tree-expand-all"))
         action.setText("Expand all")
         action.setToolTip("Expand all selected items")
@@ -173,6 +185,135 @@ class Viewer(qt.QMainWindow):
         layout.addWidget(treeView)
         return widget
 
+    def __refreshSelected(self):
+        """Refresh all selected items
+        """
+        qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
+
+        selection = self.__treeview.selectionModel()
+        indexes = selection.selectedIndexes()
+        selectedItems = []
+        model = self.__treeview.model()
+        h5files = set([])
+        while len(indexes) > 0:
+            index = indexes.pop(0)
+            if index.column() != 0:
+                continue
+            h5 = model.data(index, role=silx.gui.hdf5.Hdf5TreeModel.H5PY_OBJECT_ROLE)
+            rootIndex = index
+            # Reach the root of the tree
+            while rootIndex.parent().isValid():
+                rootIndex = rootIndex.parent()
+            rootRow = rootIndex.row()
+            relativePath = self.__getRelativePath(model, rootIndex, index)
+            selectedItems.append((rootRow, relativePath))
+            h5files.add(h5.file)
+
+        if len(h5files) == 0:
+            qt.QApplication.restoreOverrideCursor()
+            return
+
+        model = self.__treeview.findHdf5TreeModel()
+        for h5 in h5files:
+            self.__synchronizeH5pyObject(h5)
+
+        model = self.__treeview.model()
+        itemSelection = qt.QItemSelection()
+        for rootRow, relativePath in selectedItems:
+            rootIndex = model.index(rootRow, 0, qt.QModelIndex())
+            index = self.__indexFromPath(model, rootIndex, relativePath)
+            if index is None:
+                continue
+            indexEnd = model.index(index.row(), model.columnCount() - 1, index.parent())
+            itemSelection.select(index, indexEnd)
+        selection.select(itemSelection, qt.QItemSelectionModel.ClearAndSelect)
+
+        qt.QApplication.restoreOverrideCursor()
+
+    def __synchronizeH5pyObject(self, h5):
+        model = self.__treeview.findHdf5TreeModel()
+        # This is buggy right now while h5py do not allow to close a file
+        # while references are still used.
+        # FIXME: The architecture have to be reworked to support this feature.
+        # model.synchronizeH5pyObject(h5)
+
+        filename = h5.filename
+        row = model.h5pyObjectRow(h5)
+        index = self.__treeview.model().index(row, 0, qt.QModelIndex())
+        paths = self.__getPathFromExpandedNodes(self.__treeview, index)
+        model.removeH5pyObject(h5)
+        model.insertFile(filename, row)
+        index = self.__treeview.model().index(row, 0, qt.QModelIndex())
+        self.__expandNodesFromPaths(self.__treeview, index, paths)
+
+    def __getRelativePath(self, model, rootIndex, index):
+        """Returns a relative path from an index to his rootIndex.
+
+        If the path is empty the index is also the rootIndex.
+        """
+        path = ""
+        while index.isValid():
+            if index == rootIndex:
+                return path
+            name = model.data(index)
+            if path == "":
+                path = name
+            else:
+                path = name + "/" + path
+            index = index.parent()
+
+        # index is not a children of rootIndex
+        raise ValueError("index is not a children of the rootIndex")
+
+    def __getPathFromExpandedNodes(self, view, rootIndex):
+        """Return relative path from the root index of the extended nodes"""
+        model = view.model()
+        rootPath = None
+        paths = []
+        indexes = [rootIndex]
+        while len(indexes):
+            index = indexes.pop(0)
+            if not view.isExpanded(index):
+                continue
+
+            node = model.data(index, role=silx.gui.hdf5.Hdf5TreeModel.H5PY_ITEM_ROLE)
+            path = node._getCanonicalName()
+            if rootPath is None:
+                rootPath = path
+            path = path[len(rootPath):]
+            paths.append(path)
+
+            for child in range(model.rowCount(index)):
+                childIndex = model.index(child, 0, index)
+                indexes.append(childIndex)
+        return paths
+
+    def __indexFromPath(self, model, rootIndex, path):
+        elements = path.split("/")
+        if elements[0] == "":
+            elements.pop(0)
+        index = rootIndex
+        while len(elements) != 0:
+            element = elements.pop(0)
+            found = False
+            for child in range(model.rowCount(index)):
+                childIndex = model.index(child, 0, index)
+                name = model.data(childIndex)
+                if element == name:
+                    index = childIndex
+                    found = True
+                    break
+            if not found:
+                return None
+        return index
+
+    def __expandNodesFromPaths(self, view, rootIndex, paths):
+        model = view.model()
+        for path in paths:
+            index = self.__indexFromPath(model, rootIndex, path)
+            if index is not None:
+                view.setExpanded(index, True)
+
     def __expandAllSelected(self):
         """Expand all selected items of the tree.
 
@@ -185,6 +326,8 @@ class Viewer(qt.QMainWindow):
         model = self.__treeview.model()
         while len(indexes) > 0:
             index = indexes.pop(0)
+            if index.column() != 0:
+                continue
             if isinstance(index, tuple):
                 index, depth = index
             else:
@@ -211,6 +354,8 @@ class Viewer(qt.QMainWindow):
         model = self.__treeview.model()
         while len(indexes) > 0:
             index = indexes.pop(0)
+            if index.column() != 0:
+                continue
             if isinstance(index, tuple):
                 index, depth = index
             else:
@@ -682,5 +827,5 @@ class Viewer(qt.QMainWindow):
                 action.triggered.connect(lambda: self.__treeview.findHdf5TreeModel().removeH5pyObject(h5))
                 menu.addAction(action)
                 action = qt.QAction("Synchronize %s" % obj.local_filename, event.source())
-                action.triggered.connect(lambda: self.__treeview.findHdf5TreeModel().synchronizeH5pyObject(h5))
+                action.triggered.connect(lambda: self.__synchronizeH5pyObject(h5))
                 menu.addAction(action)
diff --git a/silx/app/view/test/test_view.py b/silx/app/view/test/test_view.py
index 010cda5..ebcd405 100644
--- a/silx/app/view/test/test_view.py
+++ b/silx/app/view/test/test_view.py
@@ -46,7 +46,7 @@ from silx.app.view.About import About
 from silx.app.view.DataPanel import DataPanel
 from silx.app.view.CustomNxdataWidget import CustomNxdataWidget
 from silx.gui.hdf5._utils import Hdf5DatasetMimeData
-from silx.gui.test.utils import TestCaseQt
+from silx.gui.utils.testutils import TestCaseQt
 from silx.io import commonh5
 
 _tmpDirectory = None