Merge pull request #141 from FCS-analysis/develop

version 0.9.4

Author: Paul Müller

.travis.yml

@@ -104,4 +104,4 @@ deploy:
     - "${RELEASE_PKG_FILEA}"
   on:
     tags: true
-    repo: paulmueller/PyCorrFit
+    repo: FCS-analysis/PyCorrFit

ChangeLog.txt

@@ -1,3 +1,11 @@
+0.9.4
+- Batch control allows to select individual parameters (#108)
+- Allow to exclude pages from batch fitting (#107)
+- Bugfixes:
+  - Fix `ValueError` in parameter display
+  - Possibly fixed error with `yaml.safe_dump`
+    on Mac OSx 10.8.5
+  - Make sure background is lower than signal (#137)
 0.9.3
 - Fitting: migrate to lmfit
   - This introduces a new dependency for building PyCorrFit.

PKG-INFO

@@ -2,11 +2,11 @@ Metadata-Version: 1.0
 Name: pycorrfit
 Version: 0.8.0
 Summary: UNKNOWN
-Home-page: https://github.com/paulmueller/PyCorrFit
+Home-page: https://github.com/FCS-analysis/PyCorrFit
 Author: Paul Mueller
 Author-email: paul.mueller@biotec.tu-dresden.de
 License: GPL v2
-Description: ![PyCorrFit](https://raw.github.com/paulmueller/PyCorrFit/master/doc-src/Images/PyCorrFit_logo_dark.png)
+Description: ![PyCorrFit](https://raw.github.com/FCS-analysis/PyCorrFit/master/doc-src/Images/PyCorrFit_logo_dark.png)
         =========
 
         This repository contains the source code of PyCorrFit - a scientific tool for fitting
@@ -24,10 +24,10 @@ Description: ![PyCorrFit](https://raw.github.com/paulmueller/PyCorrFit/master/do
         information, visit the official homepage at http://pycorrfit.craban.de.
 
 
-        - [Download the latest version](https://github.com/paulmueller/PyCorrFit/releases)  
-        - [Documentation](https://github.com/paulmueller/PyCorrFit/raw/master/PyCorrFit_doc.pdf)
-        - [Run PyCorrFit from source](https://github.com/paulmueller/PyCorrFit/wiki/Running-PyCorrFit-from-source)
-        - [Write model functions](https://github.com/paulmueller/PyCorrFit/wiki/Writing-model-functions)
-        - [Need help?](https://github.com/paulmueller/PyCorrFit/wiki/Creating-a-new-issue)
+        - [Download the latest version](https://github.com/FCS-analysis/PyCorrFit/releases)  
+        - [Documentation](https://github.com/FCS-analysis/PyCorrFit/raw/master/PyCorrFit_doc.pdf)
+        - [Run PyCorrFit from source](https://github.com/FCS-analysis/PyCorrFit/wiki/Running-PyCorrFit-from-source)
+        - [Write model functions](https://github.com/FCS-analysis/PyCorrFit/wiki/Writing-model-functions)
+        - [Need help?](https://github.com/FCS-analysis/PyCorrFit/wiki/Creating-a-new-issue)
 
 Platform: UNKNOWN

README.md

@@ -1,8 +1,8 @@
-![PyCorrFit](https://raw.github.com/paulmueller/PyCorrFit/master/doc/Images/PyCorrFit_logo_dark.png)
+![PyCorrFit](https://raw.github.com/FCS-analysis/PyCorrFit/master/doc/Images/PyCorrFit_logo_dark.png)
 =========
 [![PyPI](http://img.shields.io/pypi/v/PyCorrFit.svg)](https://pypi.python.org/pypi/pycorrfit)
 [![Build Win](https://img.shields.io/appveyor/ci/paulmueller/PyCorrFit/master.svg?label=build_win)](https://ci.appveyor.com/project/paulmueller/pycorrfit)
-[![Build Mac](https://img.shields.io/travis/paulmueller/PyCorrFit/master.svg?label=build_mac)](https://travis-ci.org/paulmueller/PyCorrFit)
+[![Build Mac](https://img.shields.io/travis/FCS-analysis/PyCorrFit/master.svg?label=build_mac)](https://travis-ci.org/FCS-analysis/PyCorrFit)
 
 
 
@@ -21,8 +21,8 @@ with different excitation geometries like total internal reflection (TIR). For m
 information, visit the official homepage at http://pycorrfit.craban.de.
 
 
-- [Download the latest version](https://github.com/paulmueller/PyCorrFit/releases)  
-- [Documentation](https://github.com/paulmueller/PyCorrFit/wiki/PyCorrFit_doc.pdf)
-- [Run PyCorrFit from source](https://github.com/paulmueller/PyCorrFit/wiki/Running-from-source)
-- [Write your own model functions](https://github.com/paulmueller/PyCorrFit/wiki/Writing-model-functions)
-- [Need help?](https://github.com/paulmueller/PyCorrFit/wiki/Creating-a-new-issue)
+- [Download the latest version](https://github.com/FCS-analysis/PyCorrFit/releases)  
+- [Documentation](https://github.com/FCS-analysis/PyCorrFit/wiki/PyCorrFit_doc.pdf)
+- [Run PyCorrFit from source](https://github.com/FCS-analysis/PyCorrFit/wiki/Running-from-source)
+- [Write your own model functions](https://github.com/FCS-analysis/PyCorrFit/wiki/Writing-model-functions)
+- [Need help?](https://github.com/FCS-analysis/PyCorrFit/wiki/Creating-a-new-issue)

Readme.txt

@@ -18,11 +18,11 @@ This package provides the Python module `pycorrfit` and its graphical user inter
 graphical user interface is written with wxPython. A HowTo for the installation of the 
 latest version of PyCorrFit using pip can be found there:
 
-https://github.com/paulmueller/PyCorrFit/wiki/Installation_pip
+https://github.com/FCS-analysis/PyCorrFit/wiki/Installation_pip
 
 Further reading:
 
-- Latest downloads: https://github.com/paulmueller/PyCorrFit/releases   
-- Documentation: https://github.com/paulmueller/PyCorrFit/wiki/PyCorrFit_doc.pdf  
-- Write model functions: https://github.com/paulmueller/PyCorrFit/wiki/Writing-model-functions   
-- Need help? https://github.com/paulmueller/PyCorrFit/wiki/Creating-a-new-issue   
+- Latest downloads: https://github.com/FCS-analysis/PyCorrFit/releases   
+- Documentation: https://github.com/FCS-analysis/PyCorrFit/wiki/PyCorrFit_doc.pdf  
+- Write model functions: https://github.com/FCS-analysis/PyCorrFit/wiki/Writing-model-functions   
+- Need help? https://github.com/FCS-analysis/PyCorrFit/wiki/Creating-a-new-issue   

doc/PyCorrFit_doc_content.tex

@@ -2,7 +2,7 @@ \section{Introduction}
 \label{sec:intro}
 \subsection{Preface}
 \label{sec:intro.prefa}
-\textit{PyCorrFit} emerged from my work in the Schwille Lab\footnote{\url{http://www.biochem.mpg.de/en/rd/schwille/}} at the Biotechnology Center of the TU Dresden in 2011/2012. Since then, the program has been further developed based on numerous input from FCS users, in particular Franziska Thomas, Grzesiek Chwastek, Janine Tittel, and Thomas Weidemann. The program source code is available at GitHub\footnote{\url{https://github.com/paulmueller/PyCorrFit}}. Please do not hesitate to sign up and add a feature request. If you you find a bug, please let us know via GitHub.\\
+\textit{PyCorrFit} emerged from my work in the Schwille Lab\footnote{\url{http://www.biochem.mpg.de/en/rd/schwille/}} at the Biotechnology Center of the TU Dresden in 2011/2012. Since then, the program has been further developed based on numerous input from FCS users, in particular Franziska Thomas, Grzesiek Chwastek, Janine Tittel, and Thomas Weidemann. The program source code is available at GitHub\footnote{\url{https://github.com/FCS-analysis/PyCorrFit}}. Please do not hesitate to sign up and add a feature request. If you you find a bug, please let us know via GitHub.\\
 
 \noindent \textit{PyCorrFit} was written to simplify the work with experimentally obtained correlation curves. These can be processed independently (operating system, location, time). PyCorrFit supports commonly used file formats and enables users to allocate and organize their data in a simple way.\\
 
@@ -54,10 +54,10 @@ \subsubsection{Software}
 For Windows XP and later, stand-alone binary executables are available from the download page. 
 \item \textbf{Ubuntu/Debian.}
 PyCorrFit is available from the Debian repositories and can be installed via the operating systems packaging tool (e.g. \texttt{apt-get install pycorrfit}).
-\item\textbf{PyPI.} To run \textit{PyCorrFit} on any other operating system, the installation of Python v.2.7 is required. \textit{PyCorrFit} is included in the Python package index (PyPI, \url{http://pypi.python.org/pypi/pip}) and can be installed via\footnote{See also the wiki article at \url{https://github.com/paulmueller/PyCorrFit/wiki/Installation_pip}}
+\item\textbf{PyPI.} To run \textit{PyCorrFit} on any other operating system, the installation of Python v.2.7 is required. \textit{PyCorrFit} is included in the Python package index (PyPI, \url{http://pypi.python.org/pypi/pip}) and can be installed via\footnote{See also the wiki article at \url{https://github.com/FCS-analysis/PyCorrFit/wiki/Installation_pip}}
 \texttt{pip~install~pycorrfit$\!$[GUI]}.
 \item \textbf{Sources.}
-You can also directly download the source code at any developmental stage\footnote{See also the wiki article at \url{https://github.com/paulmueller/PyCorrFit/wiki/Running-from-source}}.
+You can also directly download the source code at any developmental stage\footnote{See also the wiki article at \url{https://github.com/FCS-analysis/PyCorrFit/wiki/Running-from-source}}.
 \end{itemize}
 
 
@@ -203,10 +203,14 @@ \subsubsection{Tools / Batch control}
 \label{sec:menub.tools.batch}
 By default, the current page is taken as a reference to perform automated fitting. A batch is defined as the ensemble of correlation data sets (pages) assigned to the same model function within a session. A session can therefore have several batches, even for the same data. 
 
-For fitting, it is crucial to carefully define the starting parameters, whether parameters should be fixed or varied, the range of values which make physically sense, and other options offered within the \textit{Main window}. By executing \textit{Apply to applicable pages}, these settings are transferred to all other pages assigned to the same fit model. Note that this includes the range of lag times (lag time channels) which may have been changed with the \textit{Data range }tool for individual pages.
+For fitting, it is crucial to carefully define the starting parameters, whether parameters should be fixed or varied, the range of values which make physically sense, and other options offered within the \textit{Main window}. By executing \textit{Apply to applicable pages}, these settings are transferred to all other pages assigned to the same fit model. Note that this includes the range of lag times (lag time channels) which may have been changed with the \textit{Data range} tool for individual pages.
+
+It is possible to prevent the application of fitting parameters to individual pages by checking the \textit{prevent batch modification} checkbox in the \textit{Model parameters} box of a page.
 
 The button \textit{Fit applicable pages} then performs fitting on all pages of the same batch. Alternatively, the user can define an external source of parameters as a reference, i.e. the first page of some \textit{Other session} (*.pcfs). However, this assumes a consistent assignment of model functions.
 
+
+
 \subsubsection{Tools / Global fitting}
 \label{sec:menub.tools.globa}
 Global fitting is useful when experimental curves share the same values for certain physical parameters. For example, due to physical constraints in two-focus FCS both autocorrelation curves and  cross-correlation curves should adopt the same values for the diffusion time $\tau_\mathrm{diff}$ and the number of particles $n$. A global fit can be applied such that $n$ and $\tau_\mathrm{diff}$ are identical for all data sets. All curves are added to a single array. In contrast to fixing the shared parameters across a batch, in \textit{Global fitting} $\chi^2$  is minimized for all data sets simultaneously (see \hyref{Section}{sec:theor.nonle}). To perform \textit{Global fitting}, a subset of curves has to be selected by typing the numbers into the input field or by highlighting the pages via the \textit{Overlay curves} tool. 
@@ -731,6 +735,6 @@ \subsubsection{Algorithms}
 \input{PyCorrFit_doc_models}
 
 \section{Troubleshooting}
-If you are having problems with PyCorrFit, you might find the solution in the frequently asked questions\footnote{\url{https://github.com/paulmueller/PyCorrFit/wiki/Frequently-Asked-Questions-\%28FAQ\%29}} or on other pages in the \textit{PyCorrFit} 
-wiki\footnote{\url{https://github.com/paulmueller/PyCorrFit/wiki}}.
+If you are having problems with PyCorrFit, you might find the solution in the frequently asked questions\footnote{\url{https://github.com/FCS-analysis/PyCorrFit/wiki/Frequently-Asked-Questions-\%28FAQ\%29}} or on other pages in the \textit{PyCorrFit} 
+wiki\footnote{\url{https://github.com/FCS-analysis/PyCorrFit/wiki}}.
 There you will also find instructions on how to contact us to file a bug or to request a feature.

doc/README.md

@@ -1,5 +1,5 @@
 This folder contains the TeX-source of the 
-[PyCorrFit documentation](https://github.com/paulmueller/PyCorrFit/wiki/PyCorrFit_doc.pdf).
+[PyCorrFit documentation](https://github.com/FCS-analysis/PyCorrFit/wiki/PyCorrFit_doc.pdf).
 
 If, for some reason, you wish to compile it yourself, you will need a 
 working LaTeX distribution.

pycorrfit/doc.py

@@ -185,6 +185,6 @@ def SoftwareUsed():
 
 
 # Github homepage
-GitChLog = "https://raw.github.com/paulmueller/PyCorrFit/master/ChangeLog.txt"
-GitHome = "https://github.com/paulmueller/PyCorrFit"
-GitWiki = "https://github.com/paulmueller/PyCorrFit/wiki"
+GitChLog = "https://raw.github.com/FCS-analysis/PyCorrFit/master/ChangeLog.txt"
+GitHome = "https://github.com/FCS-analysis/PyCorrFit"
+GitWiki = "https://github.com/FCS-analysis/PyCorrFit/wiki"

pycorrfit/fcs_data_set.py

@@ -188,8 +188,6 @@ def __init__(self, backgrounds=[], correlation=None, corr_type="AC",
         self.fit_weight_type = fit_weight_type
         self.fit_weight_parameters = fit_weight_data
 
-        # lock prevents any changes to the parameters
-        self.lock_parameters = False
         self.normparm = normparm
         self.title = title
         self.traces = traces
@@ -452,17 +450,16 @@ def fit_weight_data(self, value):
     @property
     def fit_parameters(self):
         """parameters that were fitted/will be used for fitting"""
+        # Do not return `self._fit_parameters.copy()`, because
+        # some methods of PyCorrFit depende on the array being
+        # accessible and changeable with indices.
         return self._fit_parameters
 
     @fit_parameters.setter
     def fit_parameters(self, value):
         # must unlock parameters, if change is required
         value = np.array(value)
-        if self.lock_parameters == False:
-            self._fit_parameters = self.check_parms(value)
-        else:
-            warnings.warn("Correlation {}: fixed parameters unchanged.".
-                          format(self.uid))
+        self._fit_parameters = self.check_parms(value)
 
     @property
     def fit_parameters_range(self):

pycorrfit/frontend.py

@@ -1429,9 +1429,17 @@ def OnOpenSession(self, e=None, sessionfile=None):
         except:
             pass
         try:
-            Infodict["Preferences"] # not used yet
+            prefdict = Infodict["Preferences"]
         except:
             pass
+        else:
+            for key in prefdict:
+                if key == "Pages prevent batch modification":
+                    for pid in prefdict[key]:
+                        for i in np.arange(N):
+                            page = self.notebook.GetPage(i)
+                            if page.counter.strip("#: ") == pid:
+                                page.prevent_batch_modification = True
         if self.notebook.GetPageCount() > 0:
             # Enable the "Current" Menu
             self.EnableToolCurrent(True)
@@ -1591,6 +1599,14 @@ def OnSaveSession(self,e=None):
             Infodict["External Weights"][counter] = external_weights
         # Append Session Comment:
         Infodict["Comments"]["Session"] = self.SessionComment
+        # Protected pages:
+        protpage = []
+        for i in np.arange(N):
+            # Set Page 
+            Page = self.notebook.GetPage(i)
+            if Page.prevent_batch_modification:
+                protpage.append(Page.counter.strip("#: "))
+        Infodict["Preferences"]["Pages prevent batch modification"] = protpage
         # File dialog
         dlg = wx.FileDialog(self, "Save session file", self.dirname, "",
                             "PyCorrFit session (*.pcfs)|*.pcfs|All files (*.*)|*.*",