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
@@ -343,4 +349,4 @@
  - Code cleanup: Opening data files is now handled internally differently.
 0.6.9
  - Initital GitHub commit
- 
\ No newline at end of file
+ 

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),
@@ -93,7 +94,7 @@ class Correlation(object):
         else:
             c = "CC"
         text = "{} correlation '{}' with {} traces".format(
-                c, self.title, len(self._traces))
+            c, self.title, len(self._traces))
         return text
 
     def background_replace(self, channel, background):
@@ -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
@@ -321,12 +323,13 @@ class Correlation(object):
         else:
             raise NotImplementedError("Unknown model identifier")
 
-        if newmodel != self._fit_model :
+        if newmodel != self._fit_model:
             self._fit_model = newmodel
             # 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
@@ -390,8 +393,8 @@ class Correlation(object):
         expect_shape = (self.fit_parameters.shape[0], 2)
         if value.shape != expect_shape:
             msg = "Expected shape of fit parameters: {} (vs {})".format(
-                                        expect_shape, value.shape
-                                        )
+                expect_shape, value.shape
+            )
             raise ValueError(msg)
         self._fit_parameters_range = value
 
@@ -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
@@ -408,7 +412,7 @@ class Correlation(object):
         expect_size = self.fit_parameters.shape[0]
         if value.shape[0] != expect_size:
             msg = "Fit parameter variables must have size {}!".format(
-                                                            expect_size)
+                expect_size)
             raise ValueError(msg)
         self._fit_parameters_variable = value
 
@@ -416,17 +420,18 @@ class Correlation(object):
     def lag_time(self):
         """logarithmic lag time axis"""
         if self.correlation is not None:
-            return self._correlation[:,0].copy()
+            return self._correlation[:, 0].copy()
         elif self._lag_time is not None:
             return self._lag_time
         else:
             # some default lag time
-            return 10**np.linspace(-6,8,1001)
+            return 10**np.linspace(-6, 8, 1001)
 
     @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
 
@@ -441,8 +446,8 @@ class Correlation(object):
         # perform parameter normalization
         lag = self.lag_time
         modeled = np.zeros((lag.shape[0], 2))
-        modeled[:,0] = lag
-        modeled[:,1] = self.fit_model(self.fit_parameters, lag)
+        modeled[:, 0] = lag
+        modeled[:, 1] = self.fit_model(self.fit_parameters, lag)
         return modeled.copy()
 
     @property
@@ -455,7 +460,7 @@ class Correlation(object):
     def modeled_plot(self):
         """fitted data values, same shape as self.correlation_fit"""
         toplot = self.modeled_fit
-        toplot[:,1] *= self.normalize_factor
+        toplot[:, 1] *= self.normalize_factor
         return toplot
 
     @property
@@ -479,14 +484,14 @@ class Correlation(object):
         if self.correlation is None:
             raise ValueError("Cannot compute residuals; No correlation given!")
         residuals = self.correlation.copy()
-        residuals[:,1] -= self.modeled[:,1]
+        residuals[:, 1] -= self.modeled[:, 1]
         return residuals
 
     @property
     def residuals_fit(self):
         """fit residuals, same shape as self.correlation_fit"""
         residuals_fit = self.correlation_fit.copy()
-        residuals_fit[:,1] -= self.modeled_fit[:,1]
+        residuals_fit[:, 1] -= self.modeled_fit[:, 1]
         return residuals_fit
 
     @property
@@ -495,7 +500,7 @@ class Correlation(object):
         cp = self.correlation_plot
         if cp is not None:
             residuals_plot = self.correlation_plot.copy()
-            residuals_plot[:,1] -= self.modeled_plot[:,1]
+            residuals_plot[:, 1] -= self.modeled_plot[:, 1]
             return residuals_plot
 
     def set_weights(self, type_name, data):
@@ -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/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():
@@ -90,19 +90,19 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 def SoftwareUsed():
     """Return some Information about the software used for this program"""
-    text = "Python "+sys.version+\
-           "\n\nModules:"+\
-           "\n - cython "+\
-           "\n - lmfit "+lmfit.__version__+\
-           "\n - matplotlib "+matplotlib.__version__+\
-           "\n - NumPy "+numpy.__version__+\
+    text = "Python "+sys.version +\
+           "\n\nModules:" +\
+           "\n - cython " +\
+           "\n - lmfit "+lmfit.__version__ +\
+           "\n - matplotlib "+matplotlib.__version__ +\
+           "\n - NumPy "+numpy.__version__ +\
            "\n - PyYAML "+yaml.__version__ +\
-           "\n - SciPy "+scipy.__version__+\
-           "\n - simplejson "+simplejson.__version__+\
+           "\n - SciPy "+scipy.__version__ +\
+           "\n - simplejson "+simplejson.__version__ +\
            "\n - sympy "+sympy.__version__ +\
            "\n - wxPython "+wx.__version__
     # Other software
-    text += "\n\nOther software:"+\
+    text += "\n\nOther software:" +\
             "\n - FCS_point_correlator ({})".format(read_pt3_scripts.version) +\
             "\n    PicoQuant file format for Python by Dominic Waithe"
     if hasattr(sys, 'frozen'):

pycorrfit/gui/edclasses.py

@@ -7,15 +7,16 @@ import traceback
 import warnings
 
 import matplotlib
-import wx 
+import wx
 
 
 # We do catch warnings about performing this before matplotlib.backends stuff
-#matplotlib.use('WXAgg') # Tells matplotlib to use WxWidgets
+# matplotlib.use('WXAgg') # Tells matplotlib to use WxWidgets
 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
 
@@ -24,10 +25,10 @@ class ChoicesDialog(wx.Dialog):
     def __init__(self, parent, dropdownlist, title, text):
         # parent is main frame
         self.parent = parent
-        #super(ChoicesDialog, self).__init__(parent=parent, 
+        # 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)
@@ -35,7 +36,7 @@ class ChoicesDialog(wx.Dialog):
         btnabort = wx.Button(panel, wx.ID_CANCEL)
         # Dropdown
         self.dropdown = wx.ComboBox(panel, -1, "", (15, 30),
-              wx.DefaultSize, dropdownlist, wx.CB_DROPDOWN|wx.CB_READONLY)
+                                    wx.DefaultSize, dropdownlist, wx.CB_DROPDOWN | wx.CB_READONLY)
         self.dropdown.SetSelection(0)
         # Bindings
         self.Bind(wx.EVT_BUTTON, self.OnOK, btnok)
@@ -50,19 +51,17 @@ class ChoicesDialog(wx.Dialog):
         topSizer.Add(btnSizer)
         panel.SetSizer(topSizer)
         topSizer.Fit(self)
-        #self.Show(True)
+        # self.Show(True)
         self.SetFocus()
 
     def OnOK(self, event=None):
         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:
@@ -70,8 +69,8 @@ def save_figure(self, evt=None):
         We want to be able to give parameters such as dirname and filename.
     """
     try:
-        parent=self.canvas.HACK_parent
-        fig=self.canvas.HACK_fig
+        parent = self.canvas.HACK_parent
+        fig = self.canvas.HACK_fig
         Page = self.canvas.HACK_Page
         add = self.canvas.HACK_append
         dirname = parent.dirname
@@ -89,8 +88,8 @@ def save_figure(self, evt=None):
         fieltypestring += formats[key]+"(*."+key+")|*."+key+"|"
     # remove last |
     fieltypestring = fieltypestring[:-1]
-    dlg = wx.FileDialog(parent, "Save figure", dirname, filename, 
-           fieltypestring, wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
+    dlg = wx.FileDialog(parent, "Save figure", dirname, filename,
+                        fieltypestring, wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT)
     # png is default
     dlg.SetFilterIndex(keys.index("png"))
     # user cannot do anything until he clicks "OK"
@@ -104,7 +103,7 @@ def save_figure(self, evt=None):
         savename = filename
         try:
             self.canvas.figure.savefig(savename)
-        except: # RuntimeError:
+        except:  # RuntimeError:
             # The file does not seem to be what it seems to be.
             info = sys.exc_info()
             errstr = "Could not latex output:\n"
@@ -113,8 +112,8 @@ def save_figure(self, evt=None):
             errstr += str(info[1])+"\n"
             for tb_item in traceback.format_tb(info[2]):
                 errstr += tb_item
-            wx.MessageDialog(parent, errstr, "Error", 
-                style=wx.ICON_ERROR|wx.OK|wx.STAY_ON_TOP)
+            wx.MessageDialog(parent, errstr, "Error",
+                             style=wx.ICON_ERROR | wx.OK | wx.STAY_ON_TOP)
     else:
         dirname = dlg.GetDirectory()
     try:
@@ -127,37 +126,39 @@ class MyScrolledDialog(wx.Dialog):
     def __init__(self, parent, overtext, readtext, title):
         wx.Dialog.__init__(self, parent, title=title)
         overtext = wx.StaticText(self, label=overtext)
-        text = wx.TextCtrl(self, -1, readtext, size=(500,400),
+        text = wx.TextCtrl(self, -1, readtext, size=(500, 400),
                            style=wx.TE_MULTILINE | wx.TE_READONLY)
-        sizer = wx.BoxSizer(wx.VERTICAL )
+        sizer = wx.BoxSizer(wx.VERTICAL)
         btnsizer = wx.BoxSizer()
-        btn = wx.Button(self, wx.ID_OK)#, "OK ")
+        btn = wx.Button(self, wx.ID_OK)  # , "OK ")
         btnsizer.Add(btn, 0, wx.ALL, 5)
-        btnsizer.Add((5,-1), 0, wx.ALL, 5)
-        btn = wx.Button(self, wx.ID_CANCEL)#, "Abort ")
+        btnsizer.Add((5, -1), 0, wx.ALL, 5)
+        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(text, 0, wx.EXPAND|wx.ALL, 5)   
-        sizer.Add(btnsizer, 0, wx.EXPAND|wx.ALIGN_CENTER_VERTICAL|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)
         self.SetSizerAndFit(sizer)
-        
-        
+
+
 class MyOKAbortDialog(wx.Dialog):
     def __init__(self, parent, text, title):
         wx.Dialog.__init__(self, parent, title=title)
         overtext = wx.StaticText(self, label=text)
-        sizer = wx.BoxSizer(wx.VERTICAL )
+        sizer = wx.BoxSizer(wx.VERTICAL)
         btnsizer = wx.BoxSizer()
-        btn = wx.Button(self, wx.ID_OK)#, "OK ")
+        btn = wx.Button(self, wx.ID_OK)  # , "OK ")
         btnsizer.Add(btn, 0, wx.ALL, 5)
-        btnsizer.Add((5,-1), 0, wx.ALL, 5)
-        btn = wx.Button(self, wx.ID_CANCEL)#, "Abort ")
+        btnsizer.Add((5, -1), 0, wx.ALL, 5)
+        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(overtext, 0, wx.EXPAND | wx.ALL, 5)
+        sizer.Add(btnsizer, 0, wx.EXPAND |
+                  wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
         self.SetSizerAndFit(sizer)
-        
-        
+
+
 class MyYesNoAbortDialog(wx.Dialog):
     def __init__(self, parent, text, title):
         wx.Dialog.__init__(self, parent, title=title)
@@ -167,18 +168,19 @@ class MyYesNoAbortDialog(wx.Dialog):
         btn1 = wx.Button(self, wx.ID_YES)
         #btn1.Bind(wx.EVT_BTN, self.YES)
         btnsizer.Add(btn1, 0, wx.ALL, 5)
-        btnsizer.Add((1,-1), 0, wx.ALL, 5)
+        btnsizer.Add((1, -1), 0, wx.ALL, 5)
         btn2 = wx.Button(self, wx.ID_NO)
         btnsizer.Add(btn2, 0, wx.ALL, 5)
-        btnsizer.Add((1,-1), 0, wx.ALL, 5)
+        btnsizer.Add((1, -1), 0, wx.ALL, 5)
         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(overtext, 0, wx.EXPAND | wx.ALL, 5)
+        sizer.Add(btnsizer, 0, wx.EXPAND |
+                  wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
         self.SetSizerAndFit(sizer)
         self.SetFocus()
         self.Show()
-        
+
     def YES(self, e):
         self.EndModal(wx.ID_YES)
 

pycorrfit/gui/icon.py

-#----------------------------------------------------------------------
+# ----------------------------------------------------------------------
 # This file was generated by /usr/bin/img2py
 #
 from wx.lib.embeddedimage import PyEmbeddedImage

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"
@@ -20,13 +25,10 @@ try:
 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
+# matplotlib.use('WXAgg') # Tells matplotlib to use WxWidgets
 with warnings.catch_warnings():
     warnings.simplefilter("ignore")
-    matplotlib.use('WXAgg') # Tells matplotlib to use WxWidgets for dialogs
-import numpy as np                  # NumPy
-import scipy
+    matplotlib.use('WXAgg')  # Tells matplotlib to use WxWidgets for dialogs
 
 
 # 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+\
-              " | Required: "+name+" "+ required)
+        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

@@ -31,12 +31,12 @@ def parseString2Pagenum(parent, string, nodialog=False):
         return PageNumbers
     except:
         if nodialog is False:
-            errstring = "Invalid syntax in page selection: "+string+\
-                        ". Please use a comma separated list with"+\
+            errstring = "Invalid syntax in page selection: "+string +\
+                        ". Please use a comma separated list with" +\
                         " optional dashes, e.g. '1-3,6,8'."
             try:
                 wx.MessageDialog(parent, errstring, "Error",
-                                  style=wx.ICON_ERROR|wx.OK|wx.STAY_ON_TOP)
+                                 style=wx.ICON_ERROR | wx.OK | wx.STAY_ON_TOP)
             except:
                 raise ValueError(errstring)
         else:
@@ -110,4 +110,3 @@ def getMainIcon(pxlength=32):
     iconBMP = wx.Bitmap(image)
     iconICO = wx.Icon(iconBMP)
     return iconICO
-

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):
@@ -103,7 +104,7 @@ def latexmath(string):
         else:
             anew += char
     # lower case
-    lcitems = anew.split("_",1)
+    lcitems = anew.split("_", 1)
     if len(lcitems) > 1:
         anew = lcitems[0]+"_{\\text{"+lcitems[1]+"}}"
     return anew + r" \hspace{0.3em} \mathrm{"+b+r"}"
@@ -154,7 +155,7 @@ def savePlotCorrelation(parent, dirname, Page, uselatex=False,
 
     weights = Page.weights_plot_fill_area
     tabtitle = Page.tabtitle.GetValue()
-    #fitlabel = ur"Fit model: "+str(mdls.modeldict[Page.modelid][0])
+    # fitlabel = ur"Fit model: "+str(mdls.modeldict[Page.modelid][0])
     fitlabel = Page.corr.fit_model.name
     labelweights = r"Weights of fit"
     labels, parms = mdls.GetHumanReadableParms(Page.modelid,
@@ -168,22 +169,23 @@ 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
     r31 = find_program("gs")[0]
-    r32 = find_program("mgs")[0] # from miktex
-    r3 = max(r31,r32)
+    r32 = find_program("mgs")[0]  # from miktex
+    r3 = max(r31, r32)
     if r1+r2+r3 < 3:
         uselatex = False
     if uselatex == True:
         rcParams['text.usetex'] = True
         rcParams['text.latex.unicode'] = True
         rcParams['font.family'] = 'serif'
-        rcParams['text.latex.preamble']=[r"""\usepackage{amsmath}
+        rcParams['text.latex.preamble'] = [r"""\usepackage{amsmath}
                                             \usepackage[utf8x]{inputenc}
                                             \usepackage{amssymb}
                                             \usepackage{siunitx}"""]
@@ -191,31 +193,31 @@ def savePlotCorrelation(parent, dirname, Page, uselatex=False,
         tabtitle = r"{\normalsize "+escapechars(tabtitle)+r"}"
         labelweights = r"{\normalsize "+escapechars(labelweights)+r"}"
     else:
-        rcParams['text.usetex']=False
+        rcParams['text.usetex'] = False
     # create plot
     # plt.plot(x, y, '.', label = 'original data', markersize=5)
-    fig=plt.figure()
+    fig = plt.figure()
     wtit = "Correlation #{:04d}_{}".format(int(Page.counter.strip(":# ")),
-                                     Page.title.strip())
+                                           Page.title.strip())
     fig.canvas.set_window_title(wtit)
     if resid is not None:
-        gs = gridspec.GridSpec(2, 1, height_ratios=[5,1])
+        gs = gridspec.GridSpec(2, 1, height_ratios=[5, 1])
         ax = plt.subplot(gs[0])
     else:
         ax = plt.subplot(111)
         #    ax = plt.axes()
     ax.semilogx()
     # plot fit first
-    plt.plot(fit[:,0], fit[:,1], '-', label=fitlabel, lw=1.5,
+    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="black",
+        plt.plot(dataexp[:, 0], dataexp[:, 1], '-', color="black",
                  alpha=.7, label=tabtitle, lw=1)
     else:
         plt.xlabel(r'lag time $\tau$ [ms]')
 
     if weights is not None and show_weights is True:
-        plt.fill_between(weights[0][:,0],weights[0][:,1],weights[1][:,1],
+        plt.fill_between(weights[0][:, 0], weights[0][:, 1], weights[1][:, 1],
                          color='cyan')
         # fake legend:
         p = plt.Rectangle((0, 0), 0, 0, color='cyan',
@@ -223,16 +225,16 @@ def savePlotCorrelation(parent, dirname, Page, uselatex=False,
         ax.add_patch(p)
     plt.ylabel('correlation')
     if dataexp is not None:
-        mind = np.min([ dataexp[:,1], fit[:,1]])
-        maxd = np.max([ dataexp[:,1], fit[:,1]])
+        mind = np.min([dataexp[:, 1], fit[:, 1]])
+        maxd = np.max([dataexp[:, 1], fit[:, 1]])
     else:
-        mind = np.min(fit[:,1])
-        maxd = np.max(fit[:,1])
+        mind = np.min(fit[:, 1])
+        maxd = np.max(fit[:, 1])
     ymin = mind - (maxd - mind)/20.
     ymax = maxd + (maxd - mind)/20.
     ax.set_ylim(bottom=ymin, top=ymax)
-    xmin = np.min(fit[:,0])
-    xmax = np.max(fit[:,0])
+    xmin = np.min(fit[:, 0])
+    xmax = np.max(fit[:, 0])
     ax.set_xlim(xmin, xmax)
     # Add some nice text:
     if uselatex == True and len(parms) != 0:
@@ -240,8 +242,8 @@ 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
-        #if errparms is not None:
+        # According to issue #54, we remove fitting errors from plots
+        # if errparms is not None:
         #    keys = errparms.keys()
         #    keys.sort()
         #    for key in keys:
@@ -252,21 +254,19 @@ 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
-        #if errparms is not None:
+        # 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
     xt = 10**(logtext)
     yt = 0.3*ymax
-    plt.text(xt,yt,text, size=12)
+    plt.text(xt, yt, text, size=12)
     if resid is not None:
         ax2 = plt.subplot(gs[1])
         #ax2 = plt.axes()
@@ -276,15 +276,15 @@ def savePlotCorrelation(parent, dirname, Page, uselatex=False,
                 lb = r"\newline \indent "
             else:
                 lb = "\n"
-            yLabelRes = "weighted "+ lb +"residuals"
+            yLabelRes = "weighted " + lb + "residuals"
         else:
             yLabelRes = "residuals"
-        minx = np.min(resid[:,0])
-        maxx = np.max(resid[:,0])
-        miny = np.min(resid[:,1])
-        maxy = np.max(resid[:,1])
+        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",
+        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')
@@ -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()
@@ -312,11 +311,10 @@ def savePlotCorrelation(parent, dirname, Page, uselatex=False,
     if resid is not None:
         box2 = ax2.get_position()
         ax2.set_position([box2.x0, box2.y0 + box.height * 0.2,
-                     box2.width, box2.height])
+                          box2.width, box2.height])
 
     ax.legend(loc='upper center', bbox_to_anchor=(0.5, -0.55),
-              prop={'size':9})
-
+              prop={'size': 9})
 
     if verbose == True:
         plt.show()
@@ -364,44 +362,44 @@ 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
     r31 = find_program("gs")[0]
     r32 = find_program("mgs")[0]
-    r3 = max(r31,r32)
+    r3 = max(r31, r32)
     if r1+r2+r3 < 3:
         uselatex = False
     if uselatex == True:
-        rcParams['text.usetex']=True
-        rcParams['text.latex.unicode']=True
-        rcParams['font.family']='serif'
-        rcParams['text.latex.preamble']=[r"\usepackage{amsmath}"]
+        rcParams['text.usetex'] = True
+        rcParams['text.latex.unicode'] = True
+        rcParams['font.family'] = 'serif'
+        rcParams['text.latex.preamble'] = [r"\usepackage{amsmath}"]
         for i in np.arange(len(labels)):
             labels[i] = r"{\normalsize "+escapechars(labels[i])+r"}"
     else:
-        rcParams['text.usetex']=False
+        rcParams['text.usetex'] = False
     # create plot
     # plt.plot(x, y, '.', label = 'original data', markersize=5)
-    fig=plt.figure(figsize=(10,3))
+    fig = plt.figure(figsize=(10, 3))
     wtit = "Trace #{:04d}_{}".format(int(Page.counter.strip(":# ")),
                                      Page.title.strip())
     fig.canvas.set_window_title(wtit)
     ax = plt.subplot(111)
     for i in np.arange(len(traces)):
         # Columns
-        time = traces[i][:,0]*timefactor
-        intensity = traces[i][:,1]
+        time = traces[i][:, 0]*timefactor
+        intensity = traces[i][:, 1]
         plt.plot(time, intensity, '-',
-                 label = labels[i],
+                 label=labels[i],
                  lw=1)
     # set plot boundaries
     maxy = -np.infty
     miny = np.infty
     for tr in traces:
-        maxy = max(np.max(tr[:,1]), maxy)
-        miny = min(np.min(tr[:,1]), miny)
+        maxy = max(np.max(tr[:, 1]), maxy)
+        miny = min(np.min(tr[:, 1]), miny)
     ax.set_ylim(miny, maxy)
 
     plt.ylabel('count rate [kHz]')
@@ -414,17 +412,17 @@ def savePlotTrace(parent, dirname, Page, uselatex=False, verbose=False):
                      box.width, box.height * 0.9])
     plt.legend(loc='upper center',
                bbox_to_anchor=(0.5, -0.35),
-               prop={'size':9},
+               prop={'size': 9},
                )
 
-    ## 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 = "_trace.png"
 
-    plt.tight_layout(rect=(.001,.34,.999,1.0))
+    plt.tight_layout(rect=(.001, .34, .999, 1.0))
 
     if verbose == True:
         plt.show()
@@ -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)
@@ -134,21 +135,20 @@ class ThreadedProgressDlg(object):
         elif isinstance(args, list):
             # convenience-convert args to tuples
             if not isinstance(args[0], tuple):
-                args = [ (t,) for t in args ]
+                args = [(t,) for t in args]
 
         if isinstance(kwargs, dict):
             kwargs = [kwargs]*nums
 
         if not messages:
-            messages = [ "item {} of {}".format(a+1, nums) for a in range(nums) ]
-
+            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
+        sty = wx.PD_SMOOTH | wx.PD_AUTO_HIDE | wx.PD_CAN_ABORT
         if len(targets) > 1:
-            sty = sty|wx.PD_REMAINING_TIME
+            sty = sty | wx.PD_REMAINING_TIME
         dlgargs = [title, "initializing..."]
-        dlgkwargs = {"maximum":nums, "parent":parent, "style":sty }
+        dlgkwargs = {"maximum": nums, "parent": parent, "style": sty}
         dlg = None
 
         self.aborted = False
@@ -166,7 +166,7 @@ class ThreadedProgressDlg(object):
                     dlg = wx.ProgressDialog(*dlgargs, **dlgkwargs)
                     wx.EndBusyCursor()
 
-                init=False
+                init = False
                 time.sleep(.01)
                 if dlg:
                     if len(targets) == 1:
@@ -207,25 +207,25 @@ 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')
 
             # Dumb sample frame with two buttons
-            but = wx.Button(self, wx.ID_ANY, 'Start Progress', pos=(0,0))
-
+            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) ]
+            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()
\ No newline at end of file
+    app.MainLoop()