Merge pull request #129 from paulmueller/develop

Develop -> 0.8.9

ChangeLog.txt

@@ -1,14 +1,18 @@
-0.8.8-beta2
+0.8.9
 - Improved support for "ALV-7004" files (#104)
 - Increase resolution for image export
 - Load weights from PyCorrFit csv files 
 - Tool 'Overlay Curves': show cropped correlation curves
 - Tool 'Trace view': increase size of window (#93)
 - Tool 'Global fitting': remove forced, joint weights
+- Session comment dialog: more intuitive behavior (#116)
+- Improve plot export (#95)
 - Bugfixes:
-   - fitting algorithms did not work (#94)
-   - creating averages did not work (#123)
-   - ascii errors in statistics tool (#112)
+   - Weighted fits at borders of fit interval were
+     computed incorrectly due to integer division
+   - Fitting algorithms did not work (#94)
+   - Creating averages did not work (#123)
+   - ASCII errors in statistics tool (#112)
 - Under the hood:
    - Introduce new classes: Correlation, Fit, Trace
    - Code cleanup and rewrite to support planned features

pycorrfit/fcs_data_set.py

@@ -939,7 +939,7 @@ def compute_weights(correlation, verbose=0, uselatex=False):
 
             ## Calculation of variance
             # In some cases, the actual cropping interval from ival[0]
-            # ro ival[1] is chosen, such that the dataweights must be
+            # to ival[1] is chosen, such that the dataweights must be
             # calculated from unknown datapoints.
             # (e.g. points+endcrop > len(correlation)
             # We deal with this by multiplying dataweights with a factor
@@ -1045,7 +1045,6 @@ def compute_weights(correlation, verbose=0, uselatex=False):
             else:
                 raise ValueError, \
                   "`weights` must have length of full or cropped array."
-
 
         return dataweights
 

pycorrfit/plotting.py

@@ -141,20 +141,6 @@ def savePlotCorrelation(parent, dirname, Page, uselatex=False,
     labelweights = ur"Weights of fit"
     labels, parms = mdls.GetHumanReadableParms(Page.modelid,
                                                corr.fit_parameters)
-    ## According to issue #54, we remove fitting errors from plots
-    ## Error parameters with nice look
-    #errparmsblank = Page.parmoptim_error
-    #if errparmsblank is None:
-    #    errparms = None
-    #else:
-    #    errparms = dict()
-    #    for key in errparmsblank.keys():
-    #        newkey, newparm = mdls.GetHumanReadableParameterDict(Page.modelid,
-    #                                                    key, errparmsblank[key])
-    #        errparms[newkey] = newparm
-    #parmids = np.where(Page.active_parms[2])[0]
-    #labels = np.array(labels)[parmids]
-    #parms = np.array(parms)[parmids]
     if dataexp is None:
         if tabtitle.strip() == "":
             fitlabel = Page.corr.fit_model.name
@@ -199,18 +185,15 @@ def savePlotCorrelation(parent, dirname, Page, uselatex=False,
         ax = plt.subplot(111)
         #    ax = plt.axes()
     ax.semilogx()
+    # plot fit first
+    plt.plot(fit[:,0], fit[:,1], '-', label=fitlabel, lw=1.5,
+             color="blue")
     if dataexp is not None:
-        plt.plot(dataexp[:,0], dataexp[:,1], '-', color="darkgrey",
-                 label=tabtitle)
+        plt.plot(dataexp[:,0], dataexp[:,1], '-', color="black",
+                 alpha=.7, label=tabtitle, lw=1)
     else:
         plt.xlabel(ur'lag time $\tau$ [ms]')
-    # Plotting with error bars is very ugly if you have a lot of
-    # data points.
-    # We will use fill_between instead.
-    #plt.errorbar(fit[:,0], fit[:,1], yerr=weights, fmt='-',
-    #             label = fitlabel, lw=2.5, color="blue")
-    plt.plot(fit[:,0], fit[:,1], '-', label = fitlabel, lw=2.5,
-             color="blue")    
+
     if weights is not None and show_weights is True:
         plt.fill_between(weights[0][:,0],weights[0][:,1],weights[1][:,1],
                          color='cyan')
@@ -278,13 +261,16 @@ def savePlotCorrelation(parent, dirname, Page, uselatex=False,
             yLabelRes = "weighted "+ lb +"residuals"
         else:
             yLabelRes = "residuals"
-        plt.plot(resid[:,0], resid[:,1], '-', color="darkgrey", label=yLabelRes)
-        plt.xlabel(r'lag time $\tau$ [ms]')
-        plt.ylabel(yLabelRes, multialignment='center')
         minx = np.min(resid[:,0])
         maxx = np.max(resid[:,0])
         miny = np.min(resid[:,1])
         maxy = np.max(resid[:,1])
+        plt.hlines(0, minx, maxx, colors="orange")
+        plt.plot(resid[:,0], resid[:,1], '-', color="black",
+                 alpha=.85, label=yLabelRes, lw=1)
+        plt.xlabel(r'lag time $\tau$ [ms]')
+        plt.ylabel(yLabelRes, multialignment='center')
+
         ax2.set_xlim(minx, maxx)
         maxy = max(abs(maxy), abs(miny))
         ax2.set_ylim(-maxy, maxy)

pycorrfit/readfiles/read_ASC_ALV.py

@@ -366,10 +366,10 @@ def openASC_ALV_7004_USB(path):
            0.35156         129.67148          74.58858         129.67148          74.58858
            0.46875         134.57133          79.53957         134.57133          79.53957
     [...]
-      29.29688         143.78307          79.06236         143.78307          79.06236
-      29.41406         154.80135          82.87147         154.80135          82.87147
-      29.53125         187.43013          89.61197         187.43013          89.61197
-      29.64844         137.82655          77.71597         137.82655          77.71597
+          29.29688         143.78307          79.06236         143.78307          79.06236
+          29.41406         154.80135          82.87147         154.80135          82.87147
+          29.53125         187.43013          89.61197         187.43013          89.61197
+          29.64844         137.82655          77.71597         137.82655          77.71597
     [...]
 
 

pycorrfit/tools/comment.py

@@ -5,8 +5,7 @@
 Module tools - comment
 Edit the sessions' comment.
 """
-
-
+from __future__ import print_function
 import wx
 
 
@@ -29,28 +28,25 @@ def __init__(self, parent):
         self.panel = wx.Panel(self)
         self.control = wx.TextCtrl(self.panel, style=wx.TE_MULTILINE, 
                         size=initial_sizec, value=self.parent.SessionComment)
+        self.Bind(wx.EVT_TEXT, self.OnTextChanged, self.control)
         text = wx.StaticText(self.panel, 
                    label="Session comments will be saved in the  session file.")
         # buttons
-        btnclose = wx.Button(self.panel, wx.ID_ANY, 'Close')
-        btnokay = wx.Button(self.panel, wx.ID_ANY, 'OK')
-        self.Bind(wx.EVT_BUTTON, self.OnClose, btnclose)
-        self.Bind(wx.EVT_BUTTON, self.OnOkay, btnokay)
+        btnsave = wx.Button(self.panel, wx.ID_SAVE, 'Save Comment')
+        self.Bind(wx.EVT_BUTTON, self.OnSave, btnsave)
         #sizers
         self.topSizer = wx.BoxSizer(wx.VERTICAL)
-        buttonsizer = wx.BoxSizer(wx.HORIZONTAL)
-        buttonsizer.Add(btnclose, 1)
-        buttonsizer.Add(btnokay, 1)
         self.topSizer.Add(text)
-        self.topSizer.Add(buttonsizer)
         self.topSizer.Add(self.control)
+        self.topSizer.Add(btnsave, 1, wx.RIGHT | wx.EXPAND)
         self.panel.SetSizer(self.topSizer)
         self.topSizer.Fit(self)
         #Icon
         if parent.MainIcon is not None:
             wx.Frame.SetIcon(self, parent.MainIcon)
         self.Show(True)
         wx.EVT_SIZE(self, self.OnSize)
+        self.text_changed = False
 
 
     def OnSize(self, event):
@@ -60,12 +56,24 @@ def OnSize(self, event):
         self.control.SetSize(sizec)
 
 
-    def OnClose(self, event=None):
+    def OnClose(self, e=None):
         self.parent.filemenu.Check(self.parent.menuComm.GetId(), False)
+        if self.text_changed:
+            # ask the user to save or discard.
+            dlg = wx.MessageDialog(self, "Save comment?",
+                                   "Do you want to save the current changes?",
+                                   style=wx.YES_NO)
+            if dlg.ShowModal() == wx.ID_YES:
+                self.OnSave()
         self.Destroy()
 
+    def OnTextChanged(self, e=None):
+        """ When the user changes the text
+        """
+        self.text_changed = True
 
-    def OnOkay(self, event):
+    def OnSave(self, e=None):
         self.parent.SessionComment = self.control.GetValue()
+        self.text_changed = False
         self.OnClose()
 

pycorrfit/tools/info.py

@@ -107,7 +107,7 @@ def GetPageInfo(self, Page):
         corr = Page.corr
 
         # Get model information
-        model = [corr.fit_model.description_short, Page.tabtitle.GetValue(), corr.fit_model.id]
+        model = corr.fit_model
         parms = corr.fit_parameters
         fct = corr.fit_model.function.__name__
         InfoDict["version"] = [Page.parent.version]
@@ -117,29 +117,30 @@ def GetPageInfo(self, Page):
         if len(model[1]) == 0:
             # Prevent saving no title
             model[1] = "NoName"
-        Title.append(["filename/title", model[1] ]) 
-        Title.append(["Model ID", str(model[2]) ]) 
-        Title.append(["Model name", model[0] ]) 
-        Title.append(["Model function", fct ]) 
-        Title.append(["Page number", Page.counter[1:-2] ]) 
+        Title.append(["filename/title", Page.title])
+        Title.append(["Model species", model.components])
+        Title.append(["Model name", model.name])
+        Title.append(["Model ID", str(model.id)]) 
+        Title.append(["Model function", fct]) 
+        Title.append(["Page number", Page.counter[1:-2]]) 
         ## Parameters
         Parameters = list()
         # Use this function to determine human readable parameters, if possible
-        Units, Newparameters = mdls.GetHumanReadableParms(model[2], parms)
+        Units, Newparameters = mdls.GetHumanReadableParms(model.id, parms)
         # Add Parameters
         for i in np.arange(len(parms)):
             Parameters.append([ Units[i], Newparameters[i] ])
         InfoDict["parameters"] = Parameters
         # Add some more information if available
         # Info is a dictionary or None
-        MoreInfo = mdls.GetMoreInfo(model[2], Page)
+        MoreInfo = mdls.GetMoreInfo(model.id, Page)
         if MoreInfo is not None:
             InfoDict["supplement"] = MoreInfo
             # Try to get the dictionary entry of a model
             try:
                 # This function should return all important information
                 # that can be calculated from the given parameters.
-                func_info = mdls.supplement[model[2]]
+                func_info = mdls.supplement[model.id]
             except KeyError:
                 # No information available
                 pass
@@ -198,7 +199,7 @@ def GetPageInfo(self, Page):
                     errors = corr.fit_results["fit error estimation"]
                     for err, par in zip(errors, fitparms):
                         nam, val = mdls.GetHumanReadableParameterDict( 
-                                                model[2], [par], [err])
+                                                model.id, [par], [err])
                         Fitting.append(["Err "+nam[0], val[0]])
 
                 InfoDict["fitting"] = Fitting