Merge pull request #101 from ZELLMECHANIK-DRESDEN/develop

Version 0.6.5

CHANGELOG

@@ -1,9 +1,17 @@
+0.6.5
+- Sessions are now autosaved every 60s (#97)
+- Bugfixes:
+  - Loading of sessions with hierarchy children failed (#99)
+  - Reduced a memory leak for new analyses that resulted in frequent
+    memory errors (should be less frequent now)
 0.6.4
 - Bugfixes:
   - Batch analysis: Individual measurement parameters not preserved (#96)
   - Legend plot: >9 measurements cannot be displayed in legend at
     the same time. Introduced new config key "Legend Autoscaled" (#91) 
 - New filter hierarchy allows to investigate subpopulations (#87, #63)
+- dclab
+  - Add InertiaRatio and InertiaRatioRaw to tdms files (typo)
 0.6.3
 - Bugfixes:
   - Regression: Excluded events plotted on top of filtered events (#86)

appveyor.yml

@@ -6,7 +6,8 @@
 
 # Do not use shallow_clone, because coveralls needs a git repository
 #shallow_clone: true
-clone_depth: 10
+# Use large clone depth so that a tag is included for versioning
+clone_depth: 256
 
 
 # Only build master branch
@@ -86,6 +87,7 @@ install:
   # https://ci.appveyor.com/project/paulmueller/shapeout/build/1.0.152#L504
   - "pip freeze"
   # PIP installs
+  - "pip install appdirs"
   - "pip install nptdms"
   # install pyper (R)
   - "pip install pyper"

requirements.txt

@@ -1,3 +1,4 @@
+appdirs
 chaco>=4.1.0
 cffi>=0.8.2
 dclab>=0.1.0

setup.py

@@ -43,7 +43,7 @@
             'GUI':  ["wxPython", "chaco", "opencv"],
             # kiwisolver?
         },
-        install_requires=["dclab", "NumPy>=1.7.0", "SciPy>=0.10.0",
+        install_requires=["appdirs", "dclab", "NumPy>=1.7.0", "SciPy>=0.10.0",
                           "pyper"],
         setup_requires=['pytest-runner'],
         tests_require=["pytest", "urllib3"],

shapeout/ShapeOut.py

@@ -32,6 +32,7 @@ def main():
     # close the splash screen
     splash.terminate()
     # launch application
+    app.frame.InitRun()
     app.MainLoop()
 
 

shapeout/__main__.py

@@ -58,19 +58,20 @@ def prepare_app():
         warnings.warn(_("Could not determine ShapeOut version."))
         version = None
 
+    app.frame = frontend.Frame(version)
+
+    return app
+
+if __name__ == "__main__":
     # get session file
     session_file = None
     for arg in sys.argv:
         if arg.endswith(".zmso"):
-            print("\nLoading Session "+arg)
+            print("\nUsing Session "+arg)
             session_file=arg
         else:
             print("Ignoring command line parameter: "+arg)
 
-    app.frame = frontend.Frame(version, session_file=session_file)
-
-    return app
-
-if __name__ == "__main__":
     app = prepare_app()
+    app.frame.InitRun(session_file=session_file)
     app.MainLoop()

shapeout/analysis.py

@@ -11,6 +11,7 @@
 import copy
 import numpy as np
 import os
+import sys
 import warnings
 
 # dclab imports
@@ -53,6 +54,41 @@ def __init__(self, data, search_path="./"):
                              " .tdms files: {}".format(data))
 
 
+    def _clear(self):
+        """Remove all attributes from this instance, making it unusable
+        
+        It is difficult to control how the chaco plots refer to a measurement
+        object.
+        
+        """
+        import gc
+        for _i in range(len(self.measurements)):
+            mm = self.measurements.pop(0)
+            # Deleting all the data in measurements!
+            attrs = dclab.definitions.rdv
+            attrs += ["_filter_"+a for a in attrs]
+            attrs += ["_filter", "_plot_filter", "_Downsampled_Scatter"]
+            for a in attrs:
+                if hasattr(mm, a):
+                    b = getattr(mm, a)
+                    del b
+            # Also delete fluorescence curves
+            for tr in list(mm.traces.keys()):
+                t = mm.traces.pop(tr)
+                del t
+            del mm.traces
+            refs = gc.get_referrers(mm)
+            for r in refs:
+                if hasattr(r, "delplot"):
+                    r.delplot()
+                    import IPython
+                    IPython.embed()
+                del r
+            del mm
+        dclab.cached.Cache.clear_cache()
+        gc.collect()
+
+
     def _ImportDumped(self, indexname, search_path="./"):
         """ Loads data from index file as saved using `self.DumpData`.
         
@@ -96,8 +132,12 @@ def _ImportDumped(self, indexname, search_path="./"):
                     ids = [mm.identifier for mm in measmts if mm is not None]
                     mms = [mm for mm in measmts if mm is not None]
                     if idhp in ids:
+                        # parent exists
                         hparent = mms[ids.index(idhp)]  
                         mm = RTDC_DataSet(hparent=hparent)
+                    else:
+                        # parent doesn't exist - try again in next loop
+                        continue
                 else:
                     tloc = session_get_tdms_file(data, search_path)
                     mm = RTDC_DataSet(tloc)
@@ -195,9 +235,8 @@ def DumpData(self, directory, fullout=False, rel_path="./"):
         for i in range(len(out)):
             out[i] += "\r\n"
 
-        index = codecs.open(indexname, "w", "utf-8")
-        index.writelines(out)
-        index.close()
+        with codecs.open(indexname, "w", "utf-8") as index:
+            index.writelines(out)
 
         # Dump polygons
         if len(PolygonFilter.instances) > 0:

shapeout/gui/autosave.py

@@ -0,0 +1,77 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+""" ShapeOut - autosaving of sessions
+"""
+from __future__ import division, print_function
+
+import appdirs
+import os
+import time
+import wx
+import wx.lib.delayedresult as delayedresult
+
+from . import session
+
+cache_dir = appdirs.user_cache_dir(appname="ShapeOut")
+autosave_file = os.path.join(cache_dir, "autosave.zmso")
+
+
+def mkdir_p(adir):
+    """Recursively create a directory"""
+    adir = os.path.abspath(adir)
+    while not os.path.exists(adir):
+        try:
+            os.mkdir(adir)
+        except:
+            mkdir_p(os.path.dirname(adir))
+
+
+def _autosave_consumer(delayedresult, parent):
+    parent.StatusBar.SetStatusText("Autosaving...")
+    tempname = autosave_file+".tmp"
+    mkdir_p(cache_dir)
+    try:
+        session.save_session(tempname, parent.analysis)
+    except:
+        parent.StatusBar.SetStatusText("Autosaving failed!")
+        if os.path.exists(tempname):
+            os.remove(tempname)
+    else:
+        if os.path.exists(autosave_file):
+            os.remove(autosave_file)
+        os.rename(tempname, autosave_file)
+        parent.StatusBar.SetStatusText("")
+    autosave_run(parent)
+
+
+def _autosave_worker(parent, interval):
+    """Runs in the background and performs autosaving"""
+    time.sleep(interval)
+
+
+def autosave_run(parent, interval=60):
+    """Runs in the background and performs autosaving"""
+    delayedresult.startWorker(_autosave_consumer,
+                              _autosave_worker,
+                              wargs=(parent, interval,),
+                              cargs=(parent,))
+
+
+def check_recover(parent):
+    """Check for a recovery file and ask if user wants to restore
+    
+    Returns True if a session was restored. False otherwise.
+    """
+    if os.path.exists(autosave_file):
+        message="Autosaved session found. Restore?"
+        dlg = wx.MessageDialog(parent,
+                               caption=_("Missing tdms files for session"),
+                               message=message,
+                               style=wx.YES|wx.NO,
+                               )
+        mod = dlg.ShowModal()
+        dlg.Destroy()
+        if mod == wx.ID_YES:
+            session.open_session(autosave_file, parent)
+            return True
+    return False