Merge pull request #123 from jpgill86/standalone-multi-windows

Allow standalone app to open multiple files, each in independent windows

ephyviewer/scripts.py

@@ -4,23 +4,39 @@
 import argparse
 from ephyviewer.datasource import HAVE_NEO
 from ephyviewer.standalone import all_neo_rawio_dict, rawio_gui_params
+from ephyviewer import __version__
 
 def launch_standalone_ephyviewer():
-    from ephyviewer.standalone import StandAloneViewer
+    from ephyviewer.standalone import WindowManager
     import pyqtgraph as pg
-    assert HAVE_NEO, 'Must have neo 0.6.0'
+    assert HAVE_NEO, 'Must have Neo >= 0.6.0'
     import neo
 
 
     argv = sys.argv[1:]
 
-    parser = argparse.ArgumentParser(description='tridesclous')
-    parser.add_argument('file_or_dir', help='', default=None, nargs='?')
-    parser.add_argument('-f', '--format', help='File format', default=None)
+    description = """
+    Visualize electrophysiological data stored in files readable with Neo's
+    RawIO classes
+    """
+    parser = argparse.ArgumentParser(description=description)
+    parser.add_argument('file_or_dir', default=None, nargs='?',
+                        help='an optional path to a data file or directory, '
+                             'which will be opened immediately (the file '
+                             'format will be inferred from the file '
+                             'extension, if possible; otherwise, --format is '
+                             'required)')
+    parser.add_argument('-V', '--version', action='version',
+                        version='ephyviewer {}'.format(__version__))
+    parser.add_argument('-f', '--format', default=None,
+                        help='specify one of the following formats to '
+                             'override the format detected automatically for '
+                             'file_or_dir: {}'.format(
+                             ', '.join(all_neo_rawio_dict.keys())))
 
     app = pg.mkQApp()
-    win = StandAloneViewer()
-    win.show()
+
+    manager = WindowManager()
 
     if len(argv)>=1:
         args = parser.parse_args(argv)
@@ -32,16 +48,19 @@ def launch_standalone_ephyviewer():
         else:
             neo_rawio_class = all_neo_rawio_dict.get(args.format, None)
 
-        assert neo_rawio_class is not None, 'Unknown format. Format list: ['+','.join(all_neo_rawio_dict.keys())+']'
+        assert neo_rawio_class is not None, 'Unknown format. Format list: {}'.format(', '.join(all_neo_rawio_dict.keys()))
 
         name = neo_rawio_class.__name__.replace('RawIO', '')
         if name in rawio_gui_params:
-            raise(Exception('This IO needs arguments. Do ephyviewer and use open menu'))
+            raise(Exception('This IO requires additional parameters. Run ephyviewer without arguments to input these via the GUI.'))
 
-        win.load_dataset(neo_rawio_class=neo_rawio_class, file_or_dir_names=[file_or_dir_name])
+        manager.load_dataset(neo_rawio_class=neo_rawio_class, file_or_dir_names=[file_or_dir_name])
 
+    else:
+        manager.open_dialog()
 
-    app.exec_()
+    if manager.windows:
+        app.exec_()
 
 if __name__=='__main__':
     launch_standalone_ephyviewer()

ephyviewer/standalone.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 #~ from __future__ import (unicode_literals, print_function, division, absolute_import)
 
+import gc
 from collections import OrderedDict
 
 from .myqt import QT, QT_MODE
@@ -39,23 +40,10 @@
 
 
 
-class StandAloneViewer(MainViewer):
+class WindowManager():
     def __init__(self):
 
-        navigation_params = {}
-        MainViewer.__init__(self, debug=False, settings_name=None, **navigation_params)
-
-        self.navigation_dock.hide()
-
-        self.create_actions_and_menu()
-
-
-    def create_actions_and_menu(self):
-        self.file_menu = self.menuBar().addMenu(self.tr("File"))
-
-        do_open = QT.QAction('&Open', self, shortcut = "Ctrl+O")
-        do_open.triggered.connect(self.open_dialog)
-        self.file_menu.addAction(do_open)
+        self.windows = []
 
     def open_dialog(self):
         dia = RawNeoOpenDialog()
@@ -74,17 +62,32 @@ def load_dataset(self, neo_rawio_class=None, file_or_dir_names=[], io_params={})
             kargs['dirname'] = file_or_dir_names[0]
         kargs.update(io_params)
 
-        self.neorawio = neo_rawio_class(**kargs)
-        self.neorawio.parse_header()
-        print(self.neorawio)
+        neorawio = neo_rawio_class(**kargs)
+        neorawio.parse_header()
+        print(neorawio)
 
-        self.navigation_dock.show()
+        # initialize a new main window and populate viewers
+        navigation_params = {}
+        win = MainViewer(debug=False, settings_name=None, **navigation_params)
+        sources = get_sources_from_neo_rawio(neorawio)
+        compose_mainviewer_from_sources(sources, mainviewer=win)
 
-        #TODO clear all
-        sources = get_sources_from_neo_rawio(self.neorawio)
+        # add menus
+        file_menu = win.menuBar().addMenu(win.tr("File"))
+        do_open = QT.QAction('&Open', win, shortcut = "Ctrl+O")
+        do_open.triggered.connect(self.open_dialog)
+        file_menu.addAction(do_open)
 
+        # store a reference to the window to prevent it from going out of scope
+        # immediately and being destroyed
+        self.windows.append(win)
 
-        compose_mainviewer_from_sources(sources, mainviewer=self)
+        # delete window on close so that memory and file resources are released
+        win.setAttribute(QT.WA_DeleteOnClose, True)
+        win.destroyed.connect(
+            lambda qobject, i=len(self.windows)-1: self.free_resources(i))
+
+        win.show()
 
         #~ for i, sig_source in enumerate(sources['signal']):
             #~ view = TraceViewer(source=sig_source, name='signal {}'.format(i))
@@ -108,6 +111,27 @@ def load_dataset(self, neo_rawio_class=None, file_or_dir_names=[], io_params={})
             #~ view = EventList(source=ep_source, name='Event list')
             #~ self.add_view(view, location='bottom',  orientation='horizontal')
 
+    def free_resources(self, i):
+        """
+        Run garbage collection to unlock files and free memory for the closed
+        window with index ``i``.
+        Data files opened by Neo in lazy mode remain locked for as long as the
+        RawIO objects pointing to them exist in memory. Normally such objects
+        would be automatically garbage collected when they go out of scope,
+        i.e., when the window that created them is closed. However, due to an
+        issue in Neo, circular references to these objects are always created,
+        so they persist even after the window is closed. This function performs
+        a manual garbage collection after a window has been closed to clean up
+        any lingering Neo objects that keep files locked. For more info about
+        the issue, see https://github.com/NeuralEnsemble/python-neo/issues/684.
+        """
+
+        # first remove the last remaining reference to the closed window
+        self.windows[i] = None
+
+        # run garbage collection
+        gc.collect()
+
 
 
 

ephyviewer/tests/test_standalone.py

@@ -1,16 +1,17 @@
 
 
 
-from ephyviewer.standalone import StandAloneViewer, RawNeoOpenDialog
+from ephyviewer.standalone import WindowManager, RawNeoOpenDialog
 import pyqtgraph as pg
 
 
 
-def test_StandAloneViewer():
+def test_WindowManager():
     app = pg.mkQApp()
-    win = StandAloneViewer()
-    win.show()
-    app.exec_()
+    manager = WindowManager()
+    manager.open_dialog()
+    if manager.windows:
+        app.exec_()
 
 
 def test_RawNeoOpenDialog():
@@ -24,5 +25,5 @@ def test_RawNeoOpenDialog():
 
 
 if __name__=='__main__':
-    test_StandAloneViewer()
+    test_WindowManager()
     #~ test_RawNeoOpenDialog()