CHANGELOG

+1.1.6
+ - fix: improve support for Confocor FCS file format
+   (see discussion in #37)
+ - ref: make pathlib.Path a standard in readfiles
+ - code cleanup
+ - drop support for Python<3.6
 1.1.5
  - docs: fix build with recent version of latex (#191)
 1.1.4

README.rst

@@ -17,7 +17,7 @@ at the `issues page <https://github.com/FCS-analysis/PyCorrFit/wiki/Creating-a-n
 
 
 .. |PyCorrFit| image:: https://raw.github.com/FCS-analysis/PyCorrFit/master/doc/Images/PyCorrFit_logo_dark.png
-.. |PyPI Version| image:: http://img.shields.io/pypi/v/PyCorrFit.svg
+.. |PyPI Version| image:: https://img.shields.io/pypi/v/PyCorrFit.svg
    :target: https://pypi.python.org/pypi/pycorrfit
 .. |Build Status Win| image:: https://img.shields.io/appveyor/ci/paulmueller/PyCorrFit/master.svg?label=win
    :target: https://ci.appveyor.com/project/paulmueller/pycorrfit

debian/changelog

+pycorrfit (1.1.6+dfsg-1) UNRELEASED; urgency=medium
+
+  * Update d/watch, normalize upstream version from d/changelog
+  * New upstream version 1.1.6+dfsg
+  * Bump Policy to 4.3.0
+  * Add X-Python3-Version: >= 3.6 to d/control
+  * Use debhelper-compat, drop d/compat
+
+ -- Alexandre Mestiashvili <mestia@debian.org>  Mon, 06 May 2019 10:44:58 +0200
+
 pycorrfit (1.1.5+dfsg-1) unstable; urgency=medium
 
   * New upstream version 1.1.5+dfsg

debian/compat

-11

debian/control

@@ -5,7 +5,7 @@ Uploaders: Alexandre Mestiashvili <mestia@debian.org>,
 Section: python
 Priority: optional
 Build-Depends: cython3,
-               debhelper (>= 11),
+               debhelper-compat (= 12),
                dh-python,
                faketime,
                imagemagick,
@@ -27,10 +27,11 @@ Build-Depends: cython3,
                texlive-latex-extra,
                texlive-latex-recommended,
                texlive-science
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/pycorrfit
 Vcs-Git: https://salsa.debian.org/med-team/pycorrfit.git
 Homepage: http://fcs-analysis.github.io/PyCorrFit/
+X-Python3-Version: >= 3.6
 
 Package: pycorrfit
 Architecture: any
@@ -44,7 +45,9 @@ Depends: python3-matplotlib,
          ${misc:Depends},
          ${python3:Depends},
          ${shlibs:Depends}
-Recommends: dvipng, texlive-latex-base, texlive-science
+Recommends: dvipng,
+            texlive-latex-base,
+            texlive-science
 Description: tool for fitting correlation curves on a logarithmic plot
  PyCorrFit is a general-purpose FCS evaluation software that,
  amongst other formats, supports the established Zeiss ConfoCor3 ~.fcs

debian/watch

 version=4
 opts=uversionmangle=s/(\d)[_\.\-\+]?((RC|rc|pre|dev|beta|alpha)\d*)$/$1~$2/,\
-filenamemangle=s/.+\/v?(\d\S*)\.tar\.gz/pycorrfit-$1\.tar\.gz/,dversionmangle=s/\+dfsg(\.\d+)?$//,repacksuffix=+dfsg,repack \
+filenamemangle=s/.+\/v?(\d\S*)\.tar\.gz/pycorrfit-$1\.tar\.gz/,dversionmangle=s/\+dfsg.*$//,repacksuffix=+dfsg,repack \
   https://github.com/paulmueller/PyCorrFit/tags .*/v?(\d\S*)\.tar\.gz

docs/index.rst

 .. _index:
 
-PyCorrFit documentation
-=======================
 
 .. image:: _static/PyCorrFit_logo_dark.png
 
+|
+
 Welcome to the documentation of PyCorrFit (version |release|), a data analysis software for
 fluorescence correlation spectroscopy (FCS).
 
+Documentation
+=============
 
 .. toctree::
-   :maxdepth: 1
-   :caption: Contents:
-
+   :maxdepth: 2
 
    sec_about
    sec_gallery
    sec_getting_started
    sec_contribute
+
+.. toctree::
+   :maxdepth: 1
+
    sec_changelog
 
 

pycorrfit/PyCorrFit.py

@@ -3,8 +3,7 @@ from os.path import dirname, abspath, split
 import sys
 
 sys.path = [split(abspath(dirname(__file__)))[0]] + sys.path
-
-from pycorrfit.gui import main
+from pycorrfit.gui import main  # noqa: E402
 
 
 if __name__ == "__main__":

pycorrfit/_version.py

@@ -138,4 +138,4 @@ if True:  # pragma: no cover
             save_version(longversion, versionfile)
 
     # PEP 440-conform development version:
-    version = ".dev".join(longversion.split("-")[:2])
+    version = ".post".join(longversion.split("-")[:2])

pycorrfit/correlation.py

@@ -12,6 +12,7 @@ from .trace import Trace
 class Correlation(object):
     """ unifies correlation curve handling
     """
+
     def __init__(self, backgrounds=[], correlation=None, corr_type="AC",
                  filename=None, fit_algorithm="Lev-Mar",
                  fit_model=6000, fit_ival=(0, 0),
@@ -144,7 +145,8 @@ class Correlation(object):
             elif isinstance(v, Trace):
                 backgrounds.append(v)
             else:
-                raise ValueError("Each background must be instance of Trace or ndarray")
+                raise ValueError(
+                    "Each background must be instance of Trace or ndarray")
         self._backgrounds = backgrounds
 
     @property
@@ -326,7 +328,8 @@ class Correlation(object):
             # overwrite fitting parameters
             self._fit_parameters = self._fit_model.default_values
             self._fit_parameters_variables = self._fit_model.default_variables
-            self._fit_parameters_range = np.zeros((len(self._fit_parameters), 2))
+            self._fit_parameters_range = np.zeros(
+                (len(self._fit_parameters), 2))
             self.normparm = None
 
     @property
@@ -399,7 +402,8 @@ class Correlation(object):
     def fit_parameters_variable(self):
         """which parameters are variable during fitting"""
         if self._fit_parameters_variable is None:
-            self._fit_parameters_variable = np.array(self.fit_model.default_variables, dtype=bool)
+            self._fit_parameters_variable = np.array(
+                self.fit_model.default_variables, dtype=bool)
         return self._fit_parameters_variable
 
     @fit_parameters_variable.setter
@@ -426,7 +430,8 @@ class Correlation(object):
     @lag_time.setter
     def lag_time(self, value):
         if self.correlation is not None:
-            warnings.warn("Setting lag time not possible, because of existing correlation")
+            warnings.warn(
+                "Setting lag time not possible, because of existing correlation")
         else:
             self._lag_time = value
 
@@ -532,7 +537,8 @@ class Correlation(object):
             elif isinstance(v, Trace):
                 traces.append(v)
             else:
-                raise ValueError("Each trace must be instance of Trace or ndarray")
+                raise ValueError(
+                    "Each trace must be instance of Trace or ndarray")
         self._traces = traces
 
         if len(self._traces) == 2:

pycorrfit/fit.py

@@ -7,9 +7,14 @@ import numpy as np
 import scipy.interpolate as spintp
 
 
+class StuckParameterWarning(UserWarning):
+    pass
+
+
 class Constraint(object):
     """ Class to translate fit constraints to lmfit syntax.
     """
+
     def __init__(self, constraint, fit_bool, fit_bounds, fit_values):
         """
         Parameters
@@ -160,7 +165,8 @@ class Constraint(object):
                 deltaname = "delta_{}_{}".format(p1["id"], p2["id"])
                 kwdelt = {}
                 kwdelt["name"] = deltaname
-                kwdelt["value"] = p2["bool"]*self.fit_values[p2["id"]] - self.fit_values[p1["id"]]
+                kwdelt["value"] = p2["bool"] * \
+                    self.fit_values[p2["id"]] - self.fit_values[p1["id"]]
                 kwdelt["vary"] = True
                 kwdelt["min"] = 0  # note: enforces "<=" (not "<")
                 kwdelt["max"] = np.inf
@@ -169,7 +175,8 @@ class Constraint(object):
                 kwp1["name"] = "parm{:04d}".format(p1["id"])
                 # this condition deals with negative numbers
                 kwp1["expr"] = "{MIN} if {COMP} < {MIN} else {MAX} if {COMP} > {MAX} else {COMP}".format(
-                                COMP="{}*parm{:04d}-{}+{:.14f}".format(p2["sign"], p2["id"], deltaname, ofs),
+                    COMP="{}*parm{:04d}-{}+{:.14f}".format(
+                        p2["sign"], p2["id"], deltaname, ofs),
                     MIN=self.fit_bounds[p1["id"]][0],
                     MAX=self.fit_bounds[p1["id"]][1])
                 kwargs = [kwdelt, kwp1]
@@ -181,16 +188,19 @@ class Constraint(object):
                 deltaname = "delta_{}_{}".format(p1["id"], p2["id"])
                 kwdelt = {}
                 kwdelt["name"] = deltaname
-                kwdelt["value"] = self.fit_values[p1["id"]] - p2["bool"]*self.fit_values[p2["id"]]
+                kwdelt["value"] = self.fit_values[p1["id"]] - \
+                    p2["bool"]*self.fit_values[p2["id"]]
                 kwdelt["vary"] = True
                 kwdelt["min"] = 0  # note: enforces ">=" (not ">")
-                kwdelt["max"] = np.inf #self.fit_bounds[p1["id"]][1] + max(-p2["sign"]*self.fit_bounds[p2["id"]]) - ofs
+                # self.fit_bounds[p1["id"]][1] + max(-p2["sign"]*self.fit_bounds[p2["id"]]) - ofs
+                kwdelt["max"] = np.inf
 
                 kwp1 = {}
                 kwp1["name"] = "parm{:04d}".format(p1["id"])
                 # this condition deals with negative numbers
                 kwp1["expr"] = "{MIN} if {COMP} < {MIN} else {MAX} if {COMP} > {MAX} else {COMP}".format(
-                                COMP="{}*parm{:04d}+{}+{:.14f}".format(p2["sign"], p2["id"], deltaname, ofs),
+                    COMP="{}*parm{:04d}+{}+{:.14f}".format(
+                        p2["sign"], p2["id"], deltaname, ofs),
                     MIN=self.fit_bounds[p1["id"]][0],
                     MAX=self.fit_bounds[p1["id"]][1])
 
@@ -202,10 +212,10 @@ class Constraint(object):
         return kwargs
 
 
-
 class Fit(object):
     """ Used for fitting FCS data to models.
     """
+
     def __init__(self, correlations=[], global_fit=False,
                  global_fit_variables=[],
                  uselatex=False, verbose=0):
@@ -320,8 +330,8 @@ class Fit(object):
             self.fit_parm_names = varin
             self.fit_bound = varbound
             self.constraints = []
-            warnings.warn("Constraints are not supported yet for global fitting.")
-
+            warnings.warn(
+                "Constraints are not supported yet for global fitting.")
 
             def parameters_global_to_local(parameters, iicorr, varin=varin,
                                            initpar=initpar,
@@ -337,7 +347,8 @@ class Fit(object):
                 for kk, pn in enumerate(mod.parameters[0]):
                     if pn in varin:
                         # edit that parameter
-                        fit_parm[kk] = parameters[np.where(np.array(varin)==pn)[0]]
+                        fit_parm[kk] = parameters[np.where(
+                            np.array(varin) == pn)[0]]
                 return fit_parm
 
             def parameters_local_to_global(parameters, iicorr, fit_parm,
@@ -351,7 +362,8 @@ class Fit(object):
                 for kk, pn in enumerate(mod.parameters[0]):
                     if pn in varin:
                         # edit that parameter
-                        parameters[np.where(np.array(varin)==pn)[0]] = fit_parm[kk]
+                        parameters[np.where(np.array(varin) == pn)[
+                            0]] = fit_parm[kk]
                 return parameters
 
             # Create function for fitting using ids
@@ -394,7 +406,6 @@ class Fit(object):
                 # save fit data in correlation class
                 corr.fit_results = self.get_fit_results(corr)
 
-
     def get_fit_results(self, correlation):
         """
         Return a dictionary with all information about the performed fit.
@@ -422,7 +433,6 @@ class Fit(object):
 
         return d
 
-
     @property
     def chi_squared(self):
         """ Calculate displayed Chi²
@@ -445,12 +455,11 @@ class Fit(object):
             variance = self.fit_weights**2
             chi2 = np.sum((self.y-fitted)**2/variance) / dof
         else:
-            chi2 = self.fit_function_scalar(self.fit_parm, self.x, self.y, self.fit_weights)
-
+            chi2 = self.fit_function_scalar(
+                self.fit_parm, self.x, self.y, self.fit_weights)
 
         return chi2
 
-
     @property
     def chi_squared_type(self):
         """ The type of Chi² that currently applies.
@@ -470,7 +479,6 @@ class Fit(object):
         else:
             raise ValueError("Unknown weight type!")
 
-
     @staticmethod
     def compute_weights(correlation, verbose=0, uselatex=False):
         """ computes and returns weights of the same length as
@@ -503,7 +511,8 @@ class Fit(object):
             weight_spread = int(weight_data)
         except:
             if verbose > 1:
-                warnings.warn("Could not get weight spread for spline. Setting it to 3.")
+                warnings.warn(
+                    "Could not get weight spread for spline. Setting it to 3.")
             weight_spread = 3
 
         if weight_type[:6] == "spline":
@@ -541,11 +550,11 @@ class Fit(object):
                 ys = spintp.splev(xs, tck, der=0)
             except:
                 if verbose > 0:
-                    raise ValueError("Could not find spline fit with "+\
+                    raise ValueError("Could not find spline fit with " +
                                      "{} knots.".format(knotnumber))
                 return
             if verbose > 0:
-                ## If plotting module is available:
+                # If plotting module is available:
                 #name = "spline fit: "+str(knotnumber)+" knots"
                 # plotting.savePlotSingle(name, 1*x, 1*y, 1*ys,
                 #                         dirname=".",
@@ -560,7 +569,7 @@ class Fit(object):
                     # Tell the user to install matplotlib
                     print("Couldn't import pylab! - not Plotting")
 
-            ## Calculation of variance
+            # Calculation of variance
             # In some cases, the actual cropping interval from ival[0]
             # to ival[1] is chosen, such that the dataweights must be
             # calculated from unknown datapoints.
@@ -646,7 +655,8 @@ class Fit(object):
                     dataweights[i] *= reference/dividor
                 # Do not substitute len(diff[start:end]) with end-start!
                 # It is not the same!
-                backset =  2*weight_spread + 1 - len(diff[start:end]) - offsetstart
+                backset = 2*weight_spread + 1 - \
+                    len(diff[start:end]) - offsetstart
                 if backset != 0:
                     reference = 2*weight_spread + 1
                     dividor = reference - backset
@@ -673,7 +683,6 @@ class Fit(object):
 
         return dataweights
 
-
     def fit_function(self, params, x, y, weights=1):
         """
         objective function that returns the residual (difference between
@@ -686,7 +695,7 @@ class Fit(object):
         with np.errstate(divide='ignore'):
             tominimize = np.where(weights != 0,
                                   tominimize/weights, 0)
-        ## There might be NaN values because of zero weights:
+        # There might be NaN values because of zero weights:
         #tominimize = tominimize[~np.isinf(tominimize)]
         return tominimize
 
@@ -856,11 +865,12 @@ class Fit(object):
                 # write changes
                 self.fit_parm = parmsres
                 params = self.get_lmfitparm()
-                warnings.warn(u"PyCorrFit detected problems in fitting, "+\
-                              u"detected a stuck parameter, multiplied "+\
-                              u"it by {}, and fitted again. ".format(multby)+\
+                warnings.warn(u"PyCorrFit detected problems in fitting, " +
+                              u"detected a stuck parameter, multiplied " +
+                              u"it by {}, and fitted again. ".format(multby) +
                               u"The stuck parameters are: {}".format(
-                                np.array(self.fit_parm_names)[parmstuck]))
+                                  np.array(self.fit_parm_names)[parmstuck]),
+                              StuckParameterWarning)
             elif diff < 1e-8:
                 # Experience tells us this is good enough.
                 break
@@ -883,17 +893,16 @@ class Fit(object):
             try:
                 self.parmoptim_error = np.diag(covar)
             except:
-                warnings.warn("PyCorrFit Warning: Error estimate not "+\
-                              "possible, because we could not "+\
-                              "calculate covariance matrix. Please "+\
-                              "try reducing the number of fitting "+\
+                warnings.warn("PyCorrFit Warning: Error estimate not " +
+                              "possible, because we could not " +
+                              "calculate covariance matrix. Please " +
+                              "try reducing the number of fitting " +
                               "parameters.")
                 self.parmoptim_error = None
         else:
             self.parmoptim_error = None
 
 
-
 def GetAlgorithmStringList():
     """
         Get supported fitting algorithms as strings.

pycorrfit/gui/doc.py

@@ -61,10 +61,10 @@ def info(version):
         texta = textlin
     one = u"    PyCorrFit version "+version+"\n\n"
     two = u"\n\n    Supported file types:"
-    keys = readfiles.Filetypes.keys()
+    keys = readfiles.filetypes_dict.keys()
     keys = sorted(list(keys))
     for item in keys:
-        if item.split("|")[0] != readfiles.Allsupfilesstring:
+        if item.split("|")[0] != readfiles.ALL_SUP_STRING:
             two = two + "\n     - "+item.split("|")[0]
     lizenz = ""
     for line in licence().splitlines():

pycorrfit/gui/edclasses.py

@@ -15,7 +15,8 @@ import wx
 with warnings.catch_warnings():
     warnings.simplefilter("ignore")
     try:
-        matplotlib.use('WXAgg') # Tells matplotlib to use WxWidgets for dialogs
+        # Tells matplotlib to use WxWidgets for dialogs
+        matplotlib.use('WXAgg')
     except:
         pass
 
@@ -27,7 +28,7 @@ class ChoicesDialog(wx.Dialog):
         # super(ChoicesDialog, self).__init__(parent=parent,
         #    title=title)
         wx.Dialog.__init__(self, parent, -1, title)
-        ## Controls
+        # Controls
         panel = wx.Panel(self)
         # text1
         textopen = wx.StaticText(panel, label=text)
@@ -57,12 +58,10 @@ class ChoicesDialog(wx.Dialog):
         self.SelcetedID = self.dropdown.GetSelection()
         self.EndModal(wx.ID_OK)
 
-
     def OnAbort(self, event=None):
         self.EndModal(wx.ID_CANCEL)
 
 
-
 def save_figure(self, evt=None):
     """
         A substitude function for save in:
@@ -138,7 +137,8 @@ class MyScrolledDialog(wx.Dialog):
         btnsizer.Add(btn, 0, wx.ALL, 5)
         sizer.Add(overtext, 0, wx.EXPAND | wx.ALL, 5)
         sizer.Add(text, 0, wx.EXPAND | wx.ALL, 5)
-        sizer.Add(btnsizer, 0, wx.EXPAND|wx.ALIGN_CENTER_VERTICAL|wx.ALL, 5)   
+        sizer.Add(btnsizer, 0, wx.EXPAND |
+                  wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
         self.SetSizerAndFit(sizer)
 
 
@@ -154,7 +154,8 @@ class MyOKAbortDialog(wx.Dialog):
         btn = wx.Button(self, wx.ID_CANCEL)  # , "Abort ")
         btnsizer.Add(btn, 0, wx.ALL, 5)
         sizer.Add(overtext, 0, wx.EXPAND | wx.ALL, 5)
-        sizer.Add(btnsizer, 0, wx.EXPAND|wx.ALIGN_CENTER_VERTICAL|wx.ALL, 5)   
+        sizer.Add(btnsizer, 0, wx.EXPAND |
+                  wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
         self.SetSizerAndFit(sizer)
 
 
@@ -174,7 +175,8 @@ class MyYesNoAbortDialog(wx.Dialog):
         btn3 = wx.Button(self, wx.ID_CANCEL)
         btnsizer.Add(btn3, 0, wx.ALL, 5)
         sizer.Add(overtext, 0, wx.EXPAND | wx.ALL, 5)
-        sizer.Add(btnsizer, 0, wx.EXPAND|wx.ALIGN_CENTER_VERTICAL|wx.ALL, 5)   
+        sizer.Add(btnsizer, 0, wx.EXPAND |
+                  wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
         self.SetSizerAndFit(sizer)
         self.SetFocus()
         self.Show()

pycorrfit/gui/main.py

 """Main execution script"""
 from distutils.version import LooseVersion
-import os
 import sys
+import warnings
+
+import yaml
+import numpy as np
+import scipy
 
 
 class Fake(object):
     """ Fake module.
     """
+
     def __init__(self):
         self.__version__ = "0.0 unknown"
         self.version = "0.0 unknown"
@@ -21,12 +26,9 @@ except ImportError:
     matplotlib = Fake()
 # We do catch warnings about performing this before matplotlib.backends stuff
 # matplotlib.use('WXAgg') # Tells matplotlib to use WxWidgets
-import warnings
 with warnings.catch_warnings():
     warnings.simplefilter("ignore")
     matplotlib.use('WXAgg')  # Tells matplotlib to use WxWidgets for dialogs
-import numpy as np                  # NumPy
-import scipy
 
 
 # Sympy is optional:
@@ -38,16 +40,14 @@ except ImportError:
     # We create a fake module sympy with a __version__ property.
     # This way users can run PyCorrFit without having installed sympy.
     sympy = Fake()
+
 # We must not import wx here. frontend/gui does that. If we do import wx here,
 # somehow unicode characters will not be displayed correctly on windows.
 # import wx
-import yaml
-
-## Continue with the import:
-sys.path.append(os.path.abspath(os.path.dirname(__file__)))
 
-from . import doc
-from . import frontend as gui              # The actual program
+# Continue with the import:
+from . import frontend as gui  # noqa: E402
+from . import doc  # noqa: E402
 
 
 def CheckVersion(given, required, name):
@@ -62,22 +62,22 @@ def CheckVersion(given, required, name):
         print(" WARNING: Could not verify version of "+name+".")
         return
     if req > giv:
-        print(" WARNING: You are using "+name+" v. "+given+\
+        print(" WARNING: You are using "+name+" v. "+given +
               " | Required: "+name+" " + required)
     else:
         print(" OK: "+name+" v. "+given+" | "+required+" required")
 
 
-## Start gui
+# Start gui
 def Main():
 
-    ## VERSION
+    # VERSION
     version = doc.__version__
     __version__ = version
 
     print(gui.doc.info(version))
 
-    ## Check important module versions
+    # Check important module versions
     print("\n\nChecking module versions...")
     CheckVersion(matplotlib.__version__, "2.2.2", "matplotlib")
     CheckVersion(np.__version__, "1.14.2", "NumPy")
@@ -86,7 +86,7 @@ def Main():
     CheckVersion(sympy.__version__, "1.1.1", "sympy")
     CheckVersion(gui.wx.__version__, "4.0.1", "wxPython")
 
-    ## Start gui
+    # Start gui
     app = gui.MyApp(False)
 
     frame = gui.MyFrame(None, -1, version)

pycorrfit/gui/misc.py

@@ -110,4 +110,3 @@ def getMainIcon(pxlength=32):
     iconBMP = wx.Bitmap(image)
     iconICO = wx.Icon(iconBMP)
     return iconICO
-

pycorrfit/gui/page.py

@@ -19,11 +19,11 @@ from . import tools
 from . import wxutils
 
 
-
 class FittingPanel(wx.Panel):
     """
     Those are the Panels that show the fitting dialogs with the Plots.
     """
+
     def __init__(self, parent, counter, modelid, active_parms, tau=None):
         """ Initialize with given parameters. """
         wx.Panel.__init__(self, parent=parent, id=wx.ID_ANY)
@@ -47,7 +47,6 @@ class FittingPanel(wx.Panel):
         self.weighted_fittype_id = 0  # integer (drop down item)
         self.weighted_nuvar = 3  # bins for std-dev. (left and rigth)
 
-
         # The weights that are plotted in the page
         # This is set by the PlotAll function
         self.weights_plot_fill_area = None
@@ -66,7 +65,7 @@ class FittingPanel(wx.Panel):
 
         # Tool statistics uses this list:
         self.StatisticsCheckboxes = None
-        ### Splitter window
+        # Splitter window
         # Sizes
         size = parent.notebook.GetSize()
         tabsize = 33
@@ -78,11 +77,11 @@ class FittingPanel(wx.Panel):
         self.sp = wx.SplitterWindow(self, size=size, style=wx.SP_3DSASH)
         # This is necessary to prevent "Unsplit" of the SplitterWindow:
         self.sp.SetMinimumPaneSize(1)
-        ## Settings Section (left side)
+        # Settings Section (left side)
         #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)
+        # Setting up Plot (correlation + chi**2)
         self.spcanvas = wx.SplitterWindow(self.sp, size=sizecanvas,
                                           style=wx.SP_3DSASH)
         # This is necessary to prevent "Unsplit" of the SplitterWindow:
@@ -256,7 +255,6 @@ class FittingPanel(wx.Panel):
         # function, write them back.
         self.apply_parameters_reverse()
 
-
     def apply_parameters_reverse(self, event=None):
         """ Read the values from the pages parameters and write
             it to the GUI form.
@@ -295,14 +293,12 @@ class FittingPanel(wx.Panel):
         self.AlgorithmDropdown.SetSelection(idalg)
         self.updateChi2()
 
-
     def calculate_corr(self):
         """
         Calculate model correlation function
         """
         return self.corr.modeled
 
-
     def Fit_enable_fitting(self):
         """ Enable the fitting button and the weighted fit control"""
         # self.Fitbox = [ fitbox, weightedfitdrop, fittext, fittext2,
@@ -314,7 +310,6 @@ class FittingPanel(wx.Panel):
         self.Fitbox[7].Enable()
         self.Fitbox[8].Enable()
 
-
     def Fit_function(self, event=None, noplots=False, trigger=None):
         """ Calls the fit function.
 
@@ -327,7 +322,6 @@ class FittingPanel(wx.Panel):
         """
         tools.batchcontrol.FitProgressDlg(self, self)
 
-
     def Fit_finalize(self, trigger):
         """ Things that need be done after fitting
         """
@@ -350,7 +344,6 @@ class FittingPanel(wx.Panel):
         # update displayed chi2
         self.updateChi2()
 
-
     def Fit_WeightedFitCheck(self, event=None):
         """ Enable Or disable variance calculation, dependent on
             "Weighted Fit" checkbox
@@ -371,7 +364,6 @@ class FittingPanel(wx.Panel):
             self.Fitbox[4].Disable()
             self.Fitbox[5].Disable()
 
-
     def MakeStaticBoxSizer(self, boxlabel):
         """ Create a Box with check boxes (fit yes/no) and possibilities to
             change initial values for fitting.
@@ -410,26 +402,25 @@ class FittingPanel(wx.Panel):
         sizer.Add(sizerh)
         return sizer, check, spin
 
-
     def OnAmplitudeCheck(self, event=None):
         """ Enable/Disable BG rate text line.
             New feature introduced in 0.7.8
         """
         modelid = self.corr.fit_model.id
-        ## Normalization to a certain parameter in plots
+        # Normalization to a certain parameter in plots
         # Find all parameters that start with an "N"
         # ? and "C" ?
         # Create List
         normlist = list()
         normlist.append("None")
-        ## Add parameters
+        # Add parameters
         parameterlist = list()
         for i in np.arange(len(self.active_parms[0])):
             label = self.active_parms[0][i]
             if label[0].lower() == "n":
                 normlist.append("*"+label)
                 parameterlist.append(i)
-        ## Add supplementary parameters
+        # Add supplementary parameters
         # Get them from models
         supplement = mdls.GetMoreInfo(modelid, self)
         if supplement is not None:
@@ -457,7 +448,7 @@ class FittingPanel(wx.Panel):
         # Set dropdown values
         self.AmplitudeInfo[2].SetItems(normlist)
         self.AmplitudeInfo[2].SetSelection(normsel)
-        ## Plot intensities
+        # Plot intensities
         # Quick reminder:
         # self.AmplitudeInfo = [ [intlabel1, intlabel2],
         #                       [bgspin1, bgspin2],
@@ -473,10 +464,10 @@ class FittingPanel(wx.Panel):
         else:
             self.AmplitudeInfo[0][1].Disable()
         # Background
-        ## self.parent.Background[self.bgselected][i]
-        ## [0] average signal [kHz]
-        ## [1] signal name (edited by user)
-        ## [2] signal trace (tuple) ([ms], [kHz])
+        # self.parent.Background[self.bgselected][i]
+        # [0] average signal [kHz]
+        # [1] signal name (edited by user)
+        # [2] signal trace (tuple) ([ms], [kHz])
         if len(self.corr.backgrounds) >= 1:
             self.AmplitudeInfo[1][0].SetValue(
                 self.corr.backgrounds[0].countrate)
@@ -495,7 +486,6 @@ class FittingPanel(wx.Panel):
         for item in self.WXAmplitudeCCOnlyStuff:
             item.Enable(boolval)
 
-
     def OnBGSpinChanged(self, e):
         """ Calls tools.background.ApplyAutomaticBackground
             to update background information
@@ -529,7 +519,6 @@ class FittingPanel(wx.Panel):
                                                   self.parent)
         e.Skip()
 
-
     def OnTitleChanged(self, e):
         modelid = self.corr.fit_model.id
         pid = self.parent.notebook.GetPageIndex(self)
@@ -563,7 +552,6 @@ class FittingPanel(wx.Panel):
                 pass
             self.parent.RangeSelector = None
 
-
     def OnSize(self, event):
         """ Resize the fitting Panel, when Window is resized. """
         size = self.parent.notebook.GetSize()
@@ -571,7 +559,6 @@ class FittingPanel(wx.Panel):
         size[1] = size[1] - tabsize
         self.sp.SetSize(size)
 
-
     def PlotAll(self, event=None, trigger=None):
         """
         This function plots the whole correlation and residuals canvas.
@@ -598,12 +585,12 @@ class FittingPanel(wx.Panel):
                 return
             else:
                 self.InitialPlot = True
-        ## Enable/Disable, set values frontend normalization
+        # Enable/Disable, set values frontend normalization
         self.OnAmplitudeCheck()
-        ## Apply parameters
+        # Apply parameters
         self.apply_parameters()
         # Calculate correlation function from parameters
-        ## Drawing of correlation plot
+        # Drawing of correlation plot
         # Plots corr.correlation_fit and the calcualted correlation function
         # self.datacorr into the upper canvas.
         # Create a line @ y=zero:
@@ -640,7 +627,8 @@ class FittingPanel(wx.Panel):
                         weights = 0
                     elif weights.shape[0] != self.corr.modeled_fit.shape[0]:
                         # non-matching weigths
-                        warnings.warn("Unmatching weights found. Probably from previous data set.")
+                        warnings.warn(
+                            "Unmatching weights found. Probably from previous data set.")
                         weights = 0
 
                     # Add the weights to the graph.
@@ -656,8 +644,9 @@ class FittingPanel(wx.Panel):
                     if np.all(w[:, 0] == self.corr.correlation_fit[:, 0]):
                         pass
                     else:
-                        raise ValueError("This should not have happened: size of weights is wrong.")
-                    ## Normalization with self.normfactor
+                        raise ValueError(
+                            "This should not have happened: size of weights is wrong.")
+                    # Normalization with self.normfactor
                     w1[:, 1] *= self.corr.normalize_factor
                     w2[:, 1] *= self.corr.normalize_factor
                     self.weights_plot_fill_area = [w1, w2]
@@ -670,7 +659,7 @@ class FittingPanel(wx.Panel):
             else:
                 self.weights_plot_fill_area = None
 
-            ## Plot Correlation curves
+            # Plot Correlation curves
             # Plot both, experimental and calculated data
             # Normalization with self.normfactor, new feature in 0.7.8
             datacorr_norm = self.corr.modeled_plot
@@ -686,7 +675,7 @@ class FittingPanel(wx.Panel):
                                          xLabel=u'lag time τ [ms]', yLabel=u'G(τ)')
 
             self.canvascorr.Draw(PlotCorr)
-            ## Calculate residuals
+            # Calculate residuals
             resid_norm = self.corr.residuals_plot
             lineres = plot.PolyLine(resid_norm, legend='', colour=colfit,
                                     width=width)
@@ -711,7 +700,6 @@ class FittingPanel(wx.Panel):
         self.Refresh()
         self.parent.OnFNBPageChanged(trigger=trigger)
 
-
     def settings(self):
         """ Here we define, what should be displayed at the left side
             of the fitting page/tab.
@@ -769,8 +757,9 @@ class FittingPanel(wx.Panel):
         box1.Add(horzs)
         # Set horizontal size
         box1.SetMinSize((horizontalsize, -1))
-        ## More info
-        normbox = wx.StaticBox(self.panelsettings, label="Amplitude corrections")
+        # More info
+        normbox = wx.StaticBox(
+            self.panelsettings, label="Amplitude corrections")
         miscsizer = wx.StaticBoxSizer(normbox, wx.VERTICAL)
         miscsizer.SetMinSize((horizontalsize, -1))
         # Intensities and Background
@@ -797,7 +786,7 @@ class FittingPanel(wx.Panel):
         sizeint.Add(intlabel2)
         sizeint.Add(bgspin2)
         miscsizer.Add(sizeint)
-        ## Normalize to n?
+        # Normalize to n?
         textnor = wx.StaticText(self.panelsettings, label="Plot normalization")
         miscsizer.Add(textnor)
         normtoNDropdown = wx.ComboBox(self.panelsettings)
@@ -808,7 +797,7 @@ class FittingPanel(wx.Panel):
                               normtoNDropdown, textnor]
         self.WXAmplitudeCCOnlyStuff = [chtext2, intlabel2, bgspin2]
         self.panelsettings.sizer.Add(miscsizer, 0, wx.EXPAND, 0)
-        ## Add fitting Box
+        # Add fitting Box
         fitbox = wx.StaticBox(self.panelsettings, label="Fitting options")
         fitsizer = wx.StaticBoxSizer(fitbox, wx.VERTICAL)
         fitsizer.SetMinSize((horizontalsize, -1))
@@ -834,7 +823,8 @@ class FittingPanel(wx.Panel):
         fitsizer.Add(fittext2)
         fitsizerspin = wx.BoxSizer(wx.HORIZONTAL)
         fittextvar = wx.StaticText(self.panelsettings, label="j = ")
-        fitspin = wx.SpinCtrl(self.panelsettings, -1, initial=3, min=1, max=100)
+        fitspin = wx.SpinCtrl(self.panelsettings, -1,
+                              initial=3, min=1, max=100)
         fitsizerspin.Add(fittextvar)
         fitsizerspin.Add(fitspin)
         fitsizer.Add(fitsizerspin)
@@ -854,8 +844,9 @@ class FittingPanel(wx.Panel):
         self.Bind(wx.EVT_BUTTON, self.Fit_function, buttonfit)
         fitbuttonsizer.Add(buttonfit)
 
-        ## add shortcut
-        acctbl = wx.AcceleratorTable([(wx.ACCEL_CTRL, ord('F'), buttonfit.GetId())])
+        # add shortcut
+        acctbl = wx.AcceleratorTable(
+            [(wx.ACCEL_CTRL, ord('F'), buttonfit.GetId())])
         self.SetAcceleratorTable(acctbl)
         ##
 
@@ -879,7 +870,6 @@ class FittingPanel(wx.Panel):
         self.panelsettings.sizer.Fit(self.panelsettings)
         self.parent.Layout()
 
-
     def updateChi2(self):
         """
         updates the self.WXTextChi2 text control

pycorrfit/gui/plotting.py

@@ -13,15 +13,16 @@ import re
 with warnings.catch_warnings():
     warnings.simplefilter("ignore")
     matplotlib.use('WXAgg')  # Tells matplotlib to use WxWidgets for dialogs
-import matplotlib.gridspec as gridspec
-import matplotlib.pyplot as plt
 # Text rendering with matplotlib
 from matplotlib import rcParams
-import unicodedata
+import matplotlib.pyplot as plt
+import matplotlib.gridspec as gridspec
 
 # For finding latex tools
-from pycorrfit.meta import find_program
-from pycorrfit import models as mdls
+import unicodedata
+
+from .. import models as mdls
+from ..meta import find_program
 
 
 def greek2tex(char):
@@ -168,9 +169,10 @@ def savePlotCorrelation(parent, dirname, Page, uselatex=False,
         if tabtitle.strip() == "":
             tabtitle = "page"+str(Page.counter).strip().strip(":")
     if Page.corr.normparm is not None:
-        fitlabel += r", normalized to "+Page.corr.fit_model.parameters[0][Page.corr.normparm]
+        fitlabel += r", normalized to " + \
+            Page.corr.fit_model.parameters[0][Page.corr.normparm]
 
-    ## Check if we can use latex for plotting:
+    # Check if we can use latex for plotting:
     r1 = find_program("latex")[0]
     r2 = find_program("dvipng")[0]
     # Ghostscript
@@ -240,7 +242,7 @@ def savePlotCorrelation(parent, dirname, Page, uselatex=False,
         text += r'\['
         text += r'\begin{split}'
         text += genLatexText(parms, labels)
-        ## According to issue #54, we remove fitting errors from plots
+        # According to issue #54, we remove fitting errors from plots
         # if errparms is not None:
         #    keys = errparms.keys()
         #    keys.sort()
@@ -252,15 +254,13 @@ def savePlotCorrelation(parent, dirname, Page, uselatex=False,
         text = r""
         for i in np.arange(len(parms)):
             text += u"{} = {:.3g}\n".format(labels[i], parms[i])
-        ## According to issue #54, we remove fitting errors from plots
+        # According to issue #54, we remove fitting errors from plots
         # if errparms is not None:
         #    keys = errparms.keys()
         #    keys.sort()
         #    for key in keys:
         #        text += "Err "+key+" = " + str(errparms[key]) +"\n"
 
-
-
     logmax = np.log10(xmax)
     logmin = np.log10(xmin)
     logtext = 0.6*(logmax-logmin)+logmin
@@ -294,14 +294,13 @@ def savePlotCorrelation(parent, dirname, Page, uselatex=False,
         ax2.set_ylim(-maxy, maxy)
         ticks = ax2.get_yticks()
         ax2.set_yticks([ticks[0], ticks[-1], 0])
-    ## Hack
+    # Hack
     # We need this for hacking. See edclasses.
     fig.canvas.HACK_parent = parent
     fig.canvas.HACK_fig = fig
     fig.canvas.HACK_Page = Page
     fig.canvas.HACK_append = ".png"
 
-
     # Legend outside of plot
     # Decrease size of plot to fit legend
     box = ax.get_position()
@@ -317,7 +316,6 @@ def savePlotCorrelation(parent, dirname, Page, uselatex=False,
     ax.legend(loc='upper center', bbox_to_anchor=(0.5, -0.55),
               prop={'size': 9})
 
-
     if verbose == True:
         plt.show()
     else:
@@ -364,7 +362,7 @@ def savePlotTrace(parent, dirname, Page, uselatex=False, verbose=False):
     for ii, tr in enumerate(traces):
         labels.append("Channel {}: {}".format(ii+1, tr.name))
 
-    ## Check if we can use latex for plotting:
+    # Check if we can use latex for plotting:
     r1 = find_program("latex")[0]
     r2 = find_program("dvipng")[0]
     # Ghostscript
@@ -417,7 +415,7 @@ def savePlotTrace(parent, dirname, Page, uselatex=False, verbose=False):
                prop={'size': 9},
                )
 
-    ## Hack
+    # Hack
     # We need this for hacking. See edclasses.
     fig.canvas.HACK_parent = parent
     fig.canvas.HACK_fig = fig
@@ -441,5 +439,6 @@ def savePlotTrace(parent, dirname, Page, uselatex=False, verbose=False):
         except:
             pass
 
+
 # set dpi to 300
 matplotlib.rcParams['savefig.dpi'] = 300

pycorrfit/gui/threaded_progress.py

@@ -20,6 +20,7 @@ class KThread(threading.Thread):
     thread will not actually be killed until the next Python statement is
     executed.
     """
+
     def __init__(self, *args, **keywords):
         threading.Thread.__init__(self, *args, **keywords)
         self.killed = False
@@ -53,9 +54,9 @@ class KThread(threading.Thread):
         self.killed = True
 
 
-
 class WorkerThread(KThread):
     """Worker Thread Class."""
+
     def __init__(self, target, args, kwargs):
         """Init Worker Thread Class."""
         KThread.__init__(self)
@@ -142,7 +143,6 @@ class ThreadedProgressDlg(object):
         if not messages:
             messages = ["item {} of {}".format(a+1, nums) for a in range(nums)]
 
-
         time1 = time.time()
         sty = wx.PD_SMOOTH | wx.PD_AUTO_HIDE | wx.PD_CAN_ABORT
         if len(targets) > 1:
@@ -207,11 +207,11 @@ class ThreadedProgressDlg(object):
         pass
 
 
-
 if __name__ == "__main__":
     # GUI Frame class that spins off the worker thread
     class MainFrame(wx.Frame):
         """Class MainFrame."""
+
         def __init__(self, parent, aid):
             """Create the MainFrame."""
             wx.Frame.__init__(self, parent, aid, 'Thread Test')
@@ -219,13 +219,13 @@ if __name__ == "__main__":
             # Dumb sample frame with two buttons
             but = wx.Button(self, wx.ID_ANY, 'Start Progress', pos=(0, 0))
 
-
             self.Bind(wx.EVT_BUTTON, self.OnStart, but)
 
         def OnStart(self, event):
             """Start Computation."""
             # Trigger the worker thread unless it's already busy
             arguments = [test_class(a) for a in range(10)]
+
             def method(x):
                 x.arg *= 1.1
                 time.sleep(1)
@@ -233,9 +233,9 @@ if __name__ == "__main__":
             print(tp.index_aborted)
             print([a.arg for a in arguments])
 
-
     class MainApp(wx.App):
         """Class Main App."""
+
         def OnInit(self):
             """Init Main App."""
             self.frame = MainFrame(None, -1)
@@ -247,6 +247,5 @@ if __name__ == "__main__":
         def __init__(self, arg):
             self.arg = arg
 
-
     app = MainApp(0)
     app.MainLoop()