Merge branch 'develop' of github.com:rproepp/spykeviewer into develop

CHANGELOG.rst

@@ -1,6 +1,14 @@
-Version 0.4.0
+* Data file path transform for starting plugins remotely.
+
+Version 0.4.1
 -------------
+* IPython 1.0 supported
+* IPython now supported as dock instead of external console
+* More explicit error messages on file loading failures.
+* Added "Start plugin remotely" to toolbar.
 
+Version 0.4.0
+-------------
 * Optional transparent lazy loading and lazy cascading for supported IOs.
 * Splash screen while loading the application.
 * Open files dialog as an alternative to the "Files" dock.
@@ -24,7 +32,6 @@ Version 0.4.0
 
 Version 0.3.0
 -------------
-
 * Added search and replace functionality to plugin editor (access with
   ``Ctrl`` + ``F`` and ``Ctrl`` + ``H``).
 * Added startup script. Can be modified using File->Edit startup script.

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2012, Robert Pröpper and conbtributors.
+Copyright (c) 2012-2014, Robert Pröpper and conbtributors.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
@@ -21,4 +21,4 @@ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

doc/source/api.rst

@@ -80,6 +80,16 @@ objects to access the main window and application and convenience functions.
         as for :class:`subprocess.Popen`, e.g.
         ``['--param1', 'first value', '-p2', '2']``. Default: ``[]``
 
+    remote_path_transform (function)
+        When the remote script is used to start plugins on a different
+        computer, the paths of data files can change. This function can be
+        used to change the path of all data files sent to a remote script.
+        For example, if the data files are in the same directory where the
+        plugin is started on the remote computer, you can strip the path and
+        just keep the filename:
+        ``spykeviewer.api.config.remote_path_transform = lambda x: os.path.split(x)[1]``
+        Default: The identity, paths are not changed.
+
 
 .. data:: spykeviewer.api.window
 
@@ -93,4 +103,4 @@ objects to access the main window and application and convenience functions.
 
 .. autofunction:: spykeviewer.api.start_plugin
 
-.. autofunction:: spykeviewer.api.get_plugin
+.. autofunction:: spykeviewer.api.get_plugin

spykeviewer/api.py

@@ -28,6 +28,8 @@ def __init__(self):
         self.autoselect_channels = True
         # Select all visible units in navigation by default
         self.autoselect_units = False
+        # Tranformation function for file paths when starting plugin remotely
+        self.remote_path_transform = lambda x: x
 
     def __setitem__(self, key, value):
         self.__dict__[key] = value
@@ -54,23 +56,26 @@ def start_plugin(name, current=None, selections=None):
         selections. If ``None``, the regular selections from the GUI
         are used.
     """
-    return window.start_plugin(name, current, selections)
+    return window.start_plugin(name, current, selections, False)
 
 
-def start_plugin_remote(name, current=None, selections=None):
+def start_plugin_remote(plugin, current=None, selections=None):
     """ Start first plugin with given name using the remote script.
     Raises a SpykeException if not exactly one plugins with
     this name exist.
 
-    :param str name: The name of the plugin. Should not include the
-        directory.
+    :param plugin: The name of the plugin or the plugin object. If this
+        is a string, it should not include the directory and the
+        plugin with this name will be started using the remote script.
+        If it is a plugin object, this plugin will be started using
+        the remote script.
     :param current: A DataProvider to use as current selection. If
         ``None``, the regular current selection from the GUI is used.
     :param list selections: A list of DataProvider objects to use as
         selections. If ``None``, the regular selections from the GUI
         are used.
     """
-    window.start_plugin_remote(name, current, selections)
+    window.start_plugin_remote(plugin, current, selections)
 
 
 def get_plugin(name):
@@ -98,4 +103,4 @@ def load_files(file_paths):
     :param list file_paths: The files to open as strings with the full
         file path.
     """
-    window.load_files(file_paths)
+    window.load_files(file_paths)

spykeviewer/ui/checkable_item_delegate.py

@@ -1,6 +1,7 @@
 from PyQt4.QtCore import Qt
 from PyQt4.QtGui import QStyledItemDelegate, QStyle, QApplication
 
+
 class CheckableItemDelegate(QStyledItemDelegate):
     """ A StyledItemDelegate for checkable items with support for both
     checkboxes and radio buttons.
@@ -21,8 +22,8 @@ def paint(self, painter, option, index):
 
         if index.data(CheckableItemDelegate.CheckTypeRole):
             # Size and spacing in current style
-            is_radio = index.data(CheckableItemDelegate.CheckTypeRole) ==\
-                       CheckableItemDelegate.RadioCheckType
+            is_radio = index.data(CheckableItemDelegate.CheckTypeRole) == \
+                CheckableItemDelegate.RadioCheckType
             if is_radio:
                 button_width = style.pixelMetric(
                     QStyle.PM_ExclusiveIndicatorWidth, option)
@@ -34,7 +35,6 @@ def paint(self, painter, option, index):
                 spacing = style.pixelMetric(
                     QStyle.PM_CheckBoxLabelSpacing, option)
 
-
             # Draw default appearance shifted to right
             myOption = option
             left = myOption.rect.left()
@@ -51,26 +51,19 @@ def paint(self, painter, option, index):
                 myOption.state |= QStyle.State_Off
 
             if is_radio:
-                style.drawPrimitive(QStyle.PE_IndicatorRadioButton, myOption, painter)
+                style.drawPrimitive(
+                    QStyle.PE_IndicatorRadioButton, myOption, painter)
             else:
-                style.drawPrimitive(QStyle.PE_IndicatorCheckBox, myOption, painter)
+                style.drawPrimitive(
+                    QStyle.PE_IndicatorCheckBox, myOption, painter)
         else:
             QStyledItemDelegate.paint(self, painter, option, index)
 
     def sizeHint(self, option, index):
         s = QStyledItemDelegate.sizeHint(self, option, index)
-        # sizeHint is for some reason only called once, so set
-        # size globally
-        #if index.data(CheckableItemDelegate.CheckTypeRole):
-        #    # Determine size of check buttons in current style
-        #    #noinspection PyArgumentList
-        #    button_height = QApplication.style().pixelMetric(QStyle.PM_ExclusiveIndicatorHeight, option)
-        #    # Ensure that row is tall enough to draw check button
-        #    print button_height
-        #    s.setHeight(max(s.height(), button_height))
         radio_height = QApplication.style().pixelMetric(
             QStyle.PM_ExclusiveIndicatorHeight, option)
         check_height = QApplication.style().pixelMetric(
             QStyle.PM_IndicatorHeight, option)
         s.setHeight(max(s.height(), radio_height, check_height))
-        return s
+        return s

spykeviewer/ui/main_window.py

@@ -544,16 +544,21 @@ def run_command(self, cmd, history=True, new_prompt=True):
         # Duplicate stdout and stderr for console
         # Not using previous stdout, only stderr. Using StreamDuplicator
         # because spyder stream does not have flush() method...
-        ch = logging.StreamHandler()
-        ch.setLevel(logging.WARNING)
-        logger.addHandler(ch)
-
         sys.stdout = StreamDuplicator([sys.stdout])
         sys.stderr = StreamDuplicator([sys.stderr, sys.__stderr__])
 
+        # Set root logging handler to print all log warnings in console
+        ch = logging.StreamHandler()
+        ch.setLevel(logging.WARNING)
+        root_logger = logging.getLogger()
+        root_logger.addHandler(ch)
+
     def _append_python_history(self):
         self.browser.refresh_table()
-        self.history.append('\n' + self.console.history[-1])
+        try:
+            self.history.append('\n' + self.console.history[-1])
+        except IndexError:
+            pass  # Empty history, not a problem
         self.history.set_cursor_position('eof')
 
     def on_ipyDock_visibilityChanged(self, visible):
@@ -1118,7 +1123,8 @@ def _save_plugin_before_run(self):
                     return None
         return ana
 
-    def _run_plugin(self, plugin, current=None, selections=None):
+    def _run_plugin(self, plugin, current=None, selections=None,
+                    finish_progress=True):
         if current is None:
             current = self.provider
         if selections is None:
@@ -1141,7 +1147,8 @@ def _run_plugin(self, plugin, current=None, selections=None):
             traceback.print_exception(type(e), e, tb)
             return None
         finally:
-            self.progress.done()
+            if finish_progress:
+                self.progress.done()
 
     @pyqtSignature("")
     def on_actionEditPlugin_triggered(self):
@@ -1335,10 +1342,22 @@ def get_plugin(self, name):
 
         return plugins[0]
 
-    def start_plugin(self, name, current=None, selections=None):
+    def start_plugin(self, name, current=None, selections=None,
+                     finish_progress=True):
         """ Start first plugin with given name and return result of start()
         method. Raises a SpykeException if not exactly one plugins with
         this name exist.
+
+        :param str name: Name of the plugin (as specified by the get_name()
+            method in the plugin.
+        :param current: A DataProvider to use as current selection. If
+            ``None``, the regular current selection from the GUI is used.
+            Default: ``None``
+        :param list selections: A list of DataProvider objects to use as
+            selections. If ``None``, the regular selections from the GUI
+            are used. Default: ``None``
+        :param bool finish_progress: If ``True``, progress indicators are
+            closed automatically after the plugin finishes.
         """
         plugins = self.plugin_model.get_plugins_for_name(name)
         if not plugins:
@@ -1359,20 +1378,24 @@ def start_plugin(self, name, current=None, selections=None):
                     raise SpykeException(
                         'Multiple plugins named "%s" exist!' % name)
 
-        return self._run_plugin(plugins[0], current, selections)
+        return self._run_plugin(plugins[0], current, selections,
+                                finish_progress)
 
-    def start_plugin_remote(self, name, current=None, selections=None):
-        """ Start first plugin with given name remotely. Does not return
-        any value. Raises a SpykeException if not exactly one plugins with
-        this name exist.
+    def start_plugin_remote(self, plugin, current=None, selections=None):
+        """ Start given plugin (or plugin with given name) remotely.
+        Does not return any value. Raises a SpykeException if not
+        exactly one plugins with this name exist.
         """
-        plugins = self.plugin_model.get_plugins_for_name(name)
-        if not plugins:
-            raise SpykeException('No plugin named "%s" exists!' % name)
-        if len(plugins) > 1:
-            raise SpykeException('Multiple plugins named "%s" exist!' % name)
+        if not isinstance(plugin, AnalysisPlugin):
+            plugins = self.plugin_model.get_plugins_for_name(plugin)
+            if not plugins:
+                raise SpykeException('No plugin named "%s" exists!' % plugin)
+            if len(plugins) > 1:
+                raise SpykeException(
+                    'Multiple plugins named "%s" exist!' % plugin)
+            plugin = plugins[0]
 
-        self._execute_remote_plugin(plugins[0], current, selections)
+        self._execute_remote_plugin(plugin, current, selections)
 
     def on_file_available(self, available):
         """ Callback when availability of a file for a plugin changes.
@@ -1395,6 +1418,7 @@ def on_actionSettings_triggered(self):
             self.selection_path = settings.selection_path()
             self.filter_path = settings.filter_path()
             self.remote_script = settings.remote_script()
+            AnalysisPlugin.data_dir = settings.data_path()
             self.plugin_paths = settings.plugin_paths()
             if self.plugin_paths:
                 self.pluginEditorDock.set_default_path(self.plugin_paths[-1])
@@ -1503,6 +1527,7 @@ def closeEvent(self, event):
         settings.setValue('selectionPath', self.selection_path)
         settings.setValue('filterPath', self.filter_path)
         settings.setValue('remoteScript', self.remote_script)
+        settings.setValue('dataPath', AnalysisPlugin.data_dir)
 
         # Save plugin configurations
         configs = self.get_plugin_configs()

spykeviewer/ui/main_window_neo.py

@@ -18,11 +18,12 @@
 from spykeutils.plugin.data_provider_stored import NeoStoredProvider
 from spykeutils.plugin import io_plugin
 
-from main_window import MainWindow
+from .main_window import MainWindow
 from ..plugin_framework.data_provider_viewer import NeoViewerProvider
-from neo_navigation import NeoNavigationDock
-from dir_files_dialog import DirFilesDialog
-import io_settings
+from .neo_navigation import NeoNavigationDock
+from .dir_files_dialog import DirFilesDialog
+from . import io_settings
+from .. import api
 
 logger = logging.getLogger('spykeviewer')
 
@@ -172,9 +173,14 @@ def __init__(self, paths):
             QThread.__init__(self)
             self.paths = paths
             self.blocks = []
+            self.error = None
 
         def run(self):
-            self.blocks = NeoDataProvider.get_blocks(self.paths[0])
+            try:
+                self.blocks = NeoDataProvider.get_blocks(self.paths[0])
+            except Exception as e:
+                self.error = e
+                raise
 
     def load_files(self, file_paths):
         self.progress.begin('Loading data files...')
@@ -217,13 +223,30 @@ def load_file_callback(self):
         # Load worker thread finished
         blocks = self.load_worker.blocks
         if blocks is None:
-            logger.error('Could not read "%s"' %
+            QMessageBox.critical(
+                self, 'File could not be loaded',
+                'Could not read "%s": No suitable IO found.' %
+                self.load_worker.paths[0])
+            logger.error('Could not read "%s": No suitable IO found.' %
                          self.load_worker.paths[0])
             self.progress.done()
             self.load_progress.reset()
             self.raise_()
             return
 
+        if self.load_worker.error:
+            QMessageBox.critical(
+                self, 'File could not be loaded',
+                'While loading "%s", the following error occured:'
+                '\n\n%s\n%s\n\nSee the console for more details.' % (
+                    self.load_worker.paths[0],
+                    type(self.load_worker.error).__name__,
+                    str(self.load_worker.error)))
+            self.progress.done()
+            self.load_progress.reset()
+            self.raise_()
+            return
+
         for block in blocks:
             name = block.name
             if not name or name == 'One segment only':
@@ -539,6 +562,8 @@ def _execute_remote_plugin(self, plugin, current=None, selections=None):
             sl.append(s.data_dict())
 
         io_plugin_files = []
+        transform_path = getattr(api.config, 'remote_path_transform',
+                                 lambda x: x)
         for s in sl:
             if s['type'] != 'Neo':
                 continue
@@ -550,6 +575,7 @@ def _execute_remote_plugin(self, plugin, current=None, selections=None):
                                         '%s is not a known IO class!' % b[2])
                     if getattr(io, '_is_spyke_plugin', False):
                         io_plugin_files.append(io._python_file)
+                b[1] = transform_path(b[1])
 
         selections = json.dumps(sl, sort_keys=True, indent=2)
         config = pickle.dumps(plugin.get_parameters())
@@ -560,4 +586,4 @@ def _execute_remote_plugin(self, plugin, current=None, selections=None):
     def closeEvent(self, event):
         super(MainWindowNeo, self).closeEvent(event)
 
-        NeoDataProvider.clear()
+        NeoDataProvider.clear()