minor cleanup with autopep8

.gitignore

@@ -83,3 +83,6 @@ tests/data
 .pytest_cache
 htmlcov
 docs/_build
+
+# pycharm
+.idea

pycorrfit/fit.py

@@ -492,9 +492,9 @@ def compute_weights(correlation, verbose=0, uselatex=False):
         ival = corr.fit_ival
         weight_data = corr.fit_weight_data
         weight_type = corr.fit_weight_type
-        #parameters = corr.fit_parameters
-        #parameters_range = corr.fit_parameters_range
-        #parameters_variable = corr.fit_parameters_variable
+        # parameters = corr.fit_parameters
+        # parameters_range = corr.fit_parameters_range
+        # parameters_variable = corr.fit_parameters_variable
 
         cdat = corr.correlation
         if cdat is None:
@@ -503,7 +503,7 @@ def compute_weights(correlation, verbose=0, uselatex=False):
         x_full = cdat[:, 0]
         y_full = cdat[:, 1]
         x_fit = cdatfit[:, 0]
-        #y_fit = cdatfit[:,1]
+        # y_fit = cdatfit[:,1]
 
         dataweights = np.ones_like(x_fit)
 
@@ -555,7 +555,7 @@ def compute_weights(correlation, verbose=0, uselatex=False):
                 return
             if verbose > 0:
                 # If plotting module is available:
-                #name = "spline fit: "+str(knotnumber)+" knots"
+                # name = "spline fit: "+str(knotnumber)+" knots"
                 # plotting.savePlotSingle(name, 1*x, 1*y, 1*ys,
                 #                         dirname=".",
                 #                         uselatex=uselatex)
@@ -641,8 +641,8 @@ def compute_weights(correlation, verbose=0, uselatex=False):
                 # start: counter on correlation array
                 start = i - weight_spread + offsetstart + ival[0] - offsetcrop
                 end = start + 2*weight_spread + 1 - offsetstart
-                #start = ival[0] - weight_spread + i
-                #end = ival[0] + weight_spread + i + 1
+                # start = ival[0] - weight_spread + i
+                # end = ival[0] + weight_spread + i + 1
                 diff = y - model(model_parms, x)
                 dataweights[i] = diff[start:end].std()
                 # The standard deviation at the end and the start of the
@@ -696,7 +696,7 @@ def fit_function(self, params, x, y, weights=1):
             tominimize = np.where(weights != 0,
                                   tominimize/weights, 0)
         # There might be NaN values because of zero weights:
-        #tominimize = tominimize[~np.isinf(tominimize)]
+        # tominimize = tominimize[~np.isinf(tominimize)]
         return tominimize
 
     def fit_function_scalar(self, parms, x, y, weights=1):

pycorrfit/gui/contribute.py

@@ -78,4 +78,4 @@ def on_button(self, event):
     "https://dx.doi.org/10.1093/bioinformatics/btu328",
     "https://github.com/sponsors/paulmueller",
     "https://liberapay.com/paulmueller",
-    ]
+]

pycorrfit/gui/edclasses.py

@@ -99,7 +99,7 @@ def save_figure(self, evt=None):
         if not filename.endswith(wildcard):
             filename += "."+wildcard
         dirname = dlg.GetDirectory()
-        #savename = os.path.join(dirname, filename)
+        # savename = os.path.join(dirname, filename)
         savename = filename
         try:
             self.canvas.figure.savefig(savename)
@@ -166,7 +166,7 @@ def __init__(self, parent, text, title):
         sizer = wx.BoxSizer(wx.VERTICAL)
         btnsizer = wx.BoxSizer()
         btn1 = wx.Button(self, wx.ID_YES)
-        #btn1.Bind(wx.EVT_BTN, self.YES)
+        # btn1.Bind(wx.EVT_BTN, self.YES)
         btnsizer.Add(btn1, 0, wx.ALL, 5)
         btnsizer.Add((1, -1), 0, wx.ALL, 5)
         btn2 = wx.Button(self, wx.ID_NO)

pycorrfit/gui/frontend.py

@@ -245,7 +245,7 @@ def add_fitting_tab(self, event=None, modelid=None, counter=None,
         # window is open.
         # Find Tool Statistics
         # Get open tools
-        #toolkeys = self.ToolsOpen.keys()
+        # toolkeys = self.ToolsOpen.keys()
         # for key in toolkeys:
         #    tool = self.ToolsOpen[key]
         #    try:
@@ -401,7 +401,7 @@ def MakeMenu(self):
         self.EnableToolCurrent(False)
         # Set events
         # File
-        #self.Bind(wx.EVT_MENU, self.OnLoadSingle, menuLoadSingle)
+        # self.Bind(wx.EVT_MENU, self.OnLoadSingle, menuLoadSingle)
         self.Bind(wx.EVT_MENU, self.OnLoadBatch, menuLoadBatch)
         self.Bind(wx.EVT_MENU, self.OnAddModel, menuAddModel)
         self.Bind(wx.EVT_MENU, self.OnCommSession, self.menuComm)
@@ -494,8 +494,8 @@ def OnAddModel(self, event=None, modfile=None):
             if dlg.ShowModal() == wx.ID_OK:
                 # Workaround since 0.7.5
                 (dirname, filename) = os.path.split(dlg.GetPath())
-                #filename = dlg.GetFilename()
-                #dirname = dlg.GetDirectory()
+                # filename = dlg.GetFilename()
+                # dirname = dlg.GetDirectory()
                 self.dirname = dirname
                 # Try to import a selected .txt file
             else:
@@ -764,8 +764,8 @@ def OnImportData(self, e=None):
             # The filename the page will get
             path = dlg.GetPath()            # Workaround since 0.7.5
             (self.dirname, self.filename) = os.path.split(path)
-            #self.filename = dlg.GetFilename()
-            #self.dirname = dlg.GetDirectory()
+            # self.filename = dlg.GetFilename()
+            # self.dirname = dlg.GetDirectory()
             try:
                 Stuff = readfiles.open_any(self.dirname, self.filename)
             except:
@@ -1076,7 +1076,7 @@ def OnLoadBatch(self, e=None, dataname=None):
             if dlgi.Update(j, "Loading data: "+afile)[0] == False:
                 dlgi.Destroy()
                 return
-            #Stuff = readfiles.openAny(self.dirname, afile)
+            # Stuff = readfiles.openAny(self.dirname, afile)
             try:
                 Stuff = readfiles.open_any(self.dirname, afile)
             except Exception as excpt:
@@ -1178,7 +1178,7 @@ def OnLoadBatch(self, e=None, dataname=None):
                         coords[k] = WorkType.index(keys[k])
                         WorkType[coords[k]] = None
                     Run[coords] = i + 1
-                #del WorkType
+                # del WorkType
         else:
             Run = [""] * len(Curveid)
         # Now we have a dictionary curvetypes with keys that name
@@ -1867,7 +1867,7 @@ def UnpackParameters(self, Parms, Page, init=False):
             Page.corr.fit_parameters_range = np.array(Parms[9])
         # If we want to add more stuff, we should do something like:
         # if len(Parms) >= 11:
-        ##       nextvalue = Parms[10]
+        # nextvalue = Parms[10]
         # Such that we are compatible to earlier versions of
         # PyCorrFit sessions.
 

pycorrfit/gui/page.py

@@ -78,7 +78,7 @@ def __init__(self, parent, counter, modelid, active_parms, tau=None):
         # This is necessary to prevent "Unsplit" of the SplitterWindow:
         self.sp.SetMinimumPaneSize(1)
         # Settings Section (left side)
-        #self.panelsettings = wx.Panel(self.sp, size=sizepanel)
+        # self.panelsettings = wx.Panel(self.sp, size=sizepanel)
         self.panelsettings = scrolled.ScrolledPanel(self.sp, size=sizepanel)
         self.panelsettings.SetupScrolling(scroll_x=False)
         # Setting up Plot (correlation + chi**2)
@@ -620,7 +620,7 @@ def PlotAll(self, event=None, trigger=None):
                     # if weights are from average or other, make sure that the
                     # dimensions are correct
                     if weights.shape[0] == self.corr.correlation.shape[0]:
-                        weights = weights[self.corr.fit_ival[0]                                          :self.corr.fit_ival[1]]
+                        weights = weights[self.corr.fit_ival[0]:self.corr.fit_ival[1]]
 
                     # perform some checks
                     if np.allclose(weights, np.ones_like(weights)):

pycorrfit/gui/plotting.py

@@ -27,7 +27,7 @@
 
 def greek2tex(char):
     """ Converts greek UTF-8 letters to latex """
-    #decchar = codecs.decode(char, "UTF-8")
+    # decchar = codecs.decode(char, "UTF-8")
     decchar = char
     repres = unicodedata.name(decchar).split(" ")
     # GREEK SMALL LETTER ALPHA
@@ -42,7 +42,7 @@ def greek2tex(char):
 
 def escapechars(string):
     """ For latex output, some characters have to be escaped with a "\\" """
-    #string = codecs.decode(string, "UTF-8")
+    # string = codecs.decode(string, "UTF-8")
     escapechars = ["#", "$", "%", "&", "~", "_", "\\", "{", "}"]
     retstr = r""
     for char in string:
@@ -64,20 +64,20 @@ def latexmath(string):
         return r"\mathrm{offset}"
     elif string == "SP":
         return r"\mathrm{SP}"
-    #string = codecs.decode(string, "UTF-8")
+    # string = codecs.decode(string, "UTF-8")
     unicodechars = dict()
-    #unicodechars["τ"] = r"\tau"
-    #unicodechars["µ"] = r"\mu"
+    # unicodechars["τ"] = r"\tau"
+    # unicodechars["µ"] = r"\mu"
     unicodechars["²"] = r"^2"
     unicodechars["³"] = r"^3"
     unicodechars["₁"] = r"_1"
     unicodechars["₂"] = r"_2"
     unicodechars["₃"] = r"_3"
     unicodechars["₀"] = r"_0"
-    #unicodechars["α"] = r"\alpha"
+    # unicodechars["α"] = r"\alpha"
     # We need lambda in here, because unicode names it lamda sometimes.
     unicodechars["λ"] = r"\lambda"
-    #unicodechars["η"] = r'\eta'
+    # unicodechars["η"] = r'\eta'
     unitchars = dict()
     unitchars["µ"] = r"\micro "
     items = string.split(" ", 1)
@@ -269,7 +269,7 @@ def savePlotCorrelation(parent, dirname, Page, uselatex=False,
     plt.text(xt, yt, text, size=12)
     if resid is not None:
         ax2 = plt.subplot(gs[1])
-        #ax2 = plt.axes()
+        # ax2 = plt.axes()
         ax2.semilogx()
         if Page.corr.is_weighted_fit:
             if uselatex == True:

pycorrfit/gui/tools/__init__.py

@@ -73,7 +73,7 @@
         ImpB[i][0], globals(), locals(), [ImpB[i][1]], 1))
     ToolsPassive.append(getattr(ModulePassive[i], ImpB[i][1]))
     # ModulePassive.append(importlib.import_module("tools."+ImpB[i][0]))
-    #ToolsPassive.append(getattr(ModulePassive[i], ImpB[i][1]))
+    # ToolsPassive.append(getattr(ModulePassive[i], ImpB[i][1]))
 
 ToolDict = dict()
 ToolDict["A"] = ToolsActive

pycorrfit/gui/tools/average.py

@@ -98,7 +98,7 @@ def OnPageChanged(self, page, trigger=None):
             self.panel.Disable()
             return
 
-        #idsel = self.WXDropSelMod.GetSelection()
+        # idsel = self.WXDropSelMod.GetSelection()
         self.SetValues()
         # Set back user selection:
         # self.WXDropSelMod.SetSelection(idsel)
@@ -116,7 +116,7 @@ def OnAverage(self, evt=None):
         pages = list()
         UsedPagenumbers = list()
         # Reference page is the first page of the selection!
-        #referencePage = self.parent.notebook.GetCurrentPage()
+        # referencePage = self.parent.notebook.GetCurrentPage()
         referencePage = None
         for i in np.arange(self.parent.notebook.GetPageCount()):
             Page = self.parent.notebook.GetPage(i)

pycorrfit/gui/tools/background.py

@@ -248,8 +248,8 @@ def OnBrowse(self, event):
         if dlg.ShowModal() == wx.ID_OK:
             # Workaround since 0.7.5
             (dirname, filename) = os.path.split(dlg.GetPath())
-            #filename = dlg.GetFilename()
-            #dirname = dlg.GetDirectory()
+            # filename = dlg.GetFilename()
+            # dirname = dlg.GetDirectory()
             # Set parent dirname for user comfort
             self.parent.dirname = dirname
             try:
@@ -368,7 +368,7 @@ def OnImport(self, event):
         self.parent.Background.append(
             Trace(trace=self.trace, name=self.bgname.GetValue()))
         # Next two lines are taken care of by UpdateDropdown
-        #name = "{} ({:.2f} kHz)".format(self.bgname.GetValue(), self.average)
+        # name = "{} ({:.2f} kHz)".format(self.bgname.GetValue(), self.average)
         # self.BGlist.append(name)
         self.UpdateDropdown()
         self.btnremyall.Enable(True)
@@ -465,7 +465,7 @@ def OnRemove(self, event):
             # an error message.
             return
         # BG number
-        #item = self.dropdown.GetSelection()
+        # item = self.dropdown.GetSelection()
         # Apply to corresponding pages
         for i in np.arange(self.parent.notebook.GetPageCount()):
             Page = self.parent.notebook.GetPage(i)

pycorrfit/gui/tools/chooseimport.py

@@ -185,12 +185,12 @@ def OnSelected(self, keep, remove):
         # Set new button label
         for i in np.arange(len(keep)):
             keep[i] = int(keep[i])
-        #button = self.Buttons[self.buttonindex]
+        # button = self.Buttons[self.buttonindex]
         label = " ("+str(len(keep))+" curves)"
         # button.SetLabel(label)
         # Add new content to selected key
         SelectedKey = self.curvekeys[self.buttonindex]
-        #self.kept_curvedict[SelectedKey] = keep
+        # self.kept_curvedict[SelectedKey] = keep
         # If there are keys with the same amount of correlations,
         # these are assumed to be AC2, CC12, CC21 etc., so we will remove
         # items from them accordingly.

pycorrfit/gui/tools/overlaycurves.py

@@ -291,7 +291,7 @@ def __init__(self, parent, curvedict, wrapper=None, selkeys=None,
                    np.array((300, 30)))
         self.SetMinSize(minsize)
         # self.SetSize(minsize)
-        #self.SetMaxSize((9999, self.boxSizer.GetMinSize()[1]))
+        # self.SetMaxSize((9999, self.boxSizer.GetMinSize()[1]))
         # Canvas
         self.canvas = plot.PlotCanvas(self.bottom_sp)
         self.canvas.logScale = (True, False)

pycorrfit/gui/tools/simulation.py

@@ -386,7 +386,7 @@ def SetValues(self, event=None):
         self.valueB = ParmValues[idB]
         # Operator
         idop = self.dropop.GetSelection()
-        #keys = self.opdict.keys()
+        # keys = self.opdict.keys()
         opkey = self.oplist[idop]
         self.opfunc = self.opdict[opkey]
         # Parameter A

pycorrfit/gui/tools/statistics.py

@@ -132,10 +132,10 @@ def __init__(self, parent):
         GridAll.Add(self.WXavg)
         GridAll.Add(textsd)
         GridAll.Add(self.WXsd)
-        #Psizer = wx.BoxSizer(wx.HORIZONTAL)
+        # Psizer = wx.BoxSizer(wx.HORIZONTAL)
         # Psizer.Add(Pagetext)
         # Psizer.Add(self.WXTextPages)
-        #DDsizer = wx.BoxSizer(wx.HORIZONTAL)
+        # DDsizer = wx.BoxSizer(wx.HORIZONTAL)
         # DDsizer.Add(DDtext)
         # DDsizer.Add(self.WXDropdown)
         # self.topSizer.Add(Psizer)
@@ -344,8 +344,8 @@ def OnChooseValues(self, event=None):
         """
         Info, checked = self.GetListOfAllParameters(
             return_std_checked=True)
-        #headcounter = 0
-        #headlen = len(head)
+        # headcounter = 0
+        # headlen = len(head)
         # We will sort the checkboxes in more than one column if there
         # are more than *maxitemsincolumn*
         maxitemsincolumn = np.float64(19)
@@ -354,10 +354,10 @@ def OnChooseValues(self, event=None):
         for i in np.arange(Sizernumber):
             self.boxsizerlist.append(wx.BoxSizer(wx.VERTICAL))
         # Start at -1 so the indexes will start at 0 (see below).
-        #itemcount = -1
+        # itemcount = -1
         for i in range(len(Info)):
-            #itemcount += 1
-            #headcounter += 1
+            # itemcount += 1
+            # headcounter += 1
             checkbox = wx.CheckBox(self.panel, label=Info[i][0])
             # if headcounter <= headlen:
             #    checkbox.SetValue(True)
@@ -405,7 +405,7 @@ def OnDropDown(self, e=None):
 
         # Get plot parameters
         DDselid = self.WXDropdown.GetSelection()
-        #[label, key] = self.PlotParms[DDselid]
+        # [label, key] = self.PlotParms[DDselid]
         label = self.PlotParms[DDselid]
         # Get potential pages
         pages = list()
@@ -450,7 +450,7 @@ def OnDropDown(self, e=None):
         else:
             # Plot data
             plotavg = [[0.5, avg], [maxpage+.5, avg]]
-            #lineclear = plot.PolyLine(plotavg, colour="black")
+            # lineclear = plot.PolyLine(plotavg, colour="black")
             lineclear = plot.PolyMarker(plotavg, colour="black")
             plotlist.append(lineclear)
             # Update Text control

pycorrfit/gui/wxutils.py

@@ -133,11 +133,11 @@ def GetValue(self):
         string = wx.TextCtrl.GetValue(self)
         if string == PCFFloatTextCtrl.float2string(self._PCFvalue):
             # use internal value: more accurate
-            #print("internal", self._PCFvalue)
+            # print("internal", self._PCFvalue)
             return self._PCFvalue
         else:
             # new value
-            #print("external", string)
+            # print("external", string)
             return PCFFloatTextCtrl.string2float(string)
 
     @staticmethod

pycorrfit/models/MODEL_TIRF_1C.py

@@ -117,8 +117,8 @@ def MoreInfo_6000(parms, countrate=None):
         Effective particle number in detection area:
         [6] N_eff = A_eff * C_2D
     """
-    #D = parms[0]
-    #sigma = parms[1]
+    # D = parms[0]
+    # sigma = parms[1]
     a = parms[2]
     Conc = parms[3]
     Info = list()
@@ -158,7 +158,7 @@ def MoreInfo_6010(parms, countrate):
     # 3D Model TIR square
     # 3D TIR (□xσ/exp),Simple 3D diffusion w/ TIR, fct.CF_Gxyz_square_tir
     # D [10 µm²/s],σ [100 nm],a [100 nm],d_eva [100 nm],[conc.] [1000 /µm³]
-    #sigma = parms[1]
+    # sigma = parms[1]
     a = parms[2]
     d_eva = parms[3]
     conc = parms[4]