Merge pull request #134 from paulmueller/develop

Develop

Author: Paul Müller

ChangeLog.txt

@@ -1,3 +1,11 @@
+0.9.2
+- Bugfixes:
+  - "Slider Simulation"/"Parm Range" broken (#133)
+  - Computation of average intensity did not work
+    correctly for unequally spaced traces
+- Update .pt3 reader to version 8399ff7401
+- Import traces of .pt3 files (#118)
+  Warning: Absolute values for intensity might be wrong
 0.9.1
 - Tool 'Overlay curves': improve UI (#117)
 - Tool 'Statistics view': improve UI (#113)

appveyor.yml

@@ -10,6 +10,13 @@
 #  only:
 #  - master
 
+notifications:
+  - provider: Email
+    on_build_success: false
+    on_build_failure: false
+    on_build_status_changed: false
+
+
 environment:
 
   global:
@@ -51,18 +58,24 @@ install:
   # the parent CMD process).
   - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
 
-
   # Check that we have the expected version and architecture for Python
   - "python --version"
-  
+
+  # Install package-specific libraries
+  # CONDA installs
+  # Pinned versions are defined in freeze_appveyor\pinned
+  - xcopy freeze_appveyor\pinned %PYTHON%\conda-meta\ /Y
+  - "conda install --yes numpy"
+  - "conda install --yes pip"
+  - "conda install --yes scipy"
+  - "conda install --yes wxpython"
+  # PIP installs
   # Install the build dependencies of the project. 
   - "pip install cython"
   - "pip install wheel"
-  
   # Install package-specific libraries  
   - "pip install matplotlib"
   - "pip install sympy"
-  
   # Install pyinstaller
   - 'ECHO Downloading %PYWIN_DL%'
   - ps: (new-object net.webclient).DownloadFile("$env:PYWIN_DL", 'C:/pywin_inst.exe')

freeze_appveyor/Readme.md

@@ -0,0 +1,15 @@
+freeze_appveyor
+---------------
+
+files that are used by ../appveyor.yaml.
+
+- `install.ps1` : install Miniconda   
+  powershell script that donwloads and installs stuff
+
+- `pinned` : pin packages in Anaconda   
+  For example, NumPy is pinned to something <1.9.0, because
+  WxPython will not work with numpy>1.9.0 due to this bug:
+  http://trac.wxwidgets.org/ticket/16590
+
+- `run_with_compiler.cmd` : powershell tools   
+  Something required for running stuff on i386 and x64

freeze_appveyor/install.ps1

@@ -8,92 +8,12 @@ $GET_PIP_URL = "https://bootstrap.pypa.io/get-pip.py"
 $GET_PIP_PATH = "C:\get-pip.py"
 
 
-function DownloadPython ($python_version, $platform_suffix) {
-    $webclient = New-Object System.Net.WebClient
-    $filename = "python-" + $python_version + $platform_suffix + ".msi"
-    $url = $BASE_URL + $python_version + "/" + $filename
-
-    $basedir = $pwd.Path + "\"
-    $filepath = $basedir + $filename
-    if (Test-Path $filename) {
-        Write-Host "Reusing" $filepath
-        return $filepath
-    }
-
-    # Download and retry up to 3 times in case of network transient errors.
-    Write-Host "Downloading" $filename "from" $url
-    $retry_attempts = 2
-    for($i=0; $i -lt $retry_attempts; $i++){
-        try {
-            $webclient.DownloadFile($url, $filepath)
-            break
-        }
-        Catch [Exception]{
-            Start-Sleep 1
-        }
-   }
-   if (Test-Path $filepath) {
-       Write-Host "File saved at" $filepath
-   } else {
-       # Retry once to get the error message if any at the last try
-       $webclient.DownloadFile($url, $filepath)
-   }
-   return $filepath
-}
-
-
-function InstallPython ($python_version, $architecture, $python_home) {
-    Write-Host "Installing Python" $python_version "for" $architecture "bit architecture to" $python_home
-    if (Test-Path $python_home) {
-        Write-Host $python_home "already exists, skipping."
-        return $false
-    }
-    if ($architecture -eq "32") {
-        $platform_suffix = ""
-    } else {
-        $platform_suffix = ".amd64"
-    }
-    $msipath = DownloadPython $python_version $platform_suffix
-    Write-Host "Installing" $msipath "to" $python_home
-    $install_log = $python_home + ".log"
-    $install_args = "/qn /log $install_log /i $msipath TARGETDIR=$python_home"
-    $uninstall_args = "/qn /x $msipath"
-    RunCommand "msiexec.exe" $install_args
-    if (-not(Test-Path $python_home)) {
-        Write-Host "Python seems to be installed else-where, reinstalling."
-        RunCommand "msiexec.exe" $uninstall_args
-        RunCommand "msiexec.exe" $install_args
-    }
-    if (Test-Path $python_home) {
-        Write-Host "Python $python_version ($architecture) installation complete"
-    } else {
-        Write-Host "Failed to install Python in $python_home"
-        Get-Content -Path $install_log
-        Exit 1
-    }
-}
-
 function RunCommand ($command, $command_args) {
     Write-Host $command $command_args
     Start-Process -FilePath $command -ArgumentList $command_args -Wait -Passthru
 }
 
 
-function InstallPip ($python_home) {
-    $pip_path = $python_home + "\Scripts\pip.exe"
-    $python_path = $python_home + "\python.exe"
-    if (-not(Test-Path $pip_path)) {
-        Write-Host "Installing pip..."
-        $webclient = New-Object System.Net.WebClient
-        $webclient.DownloadFile($GET_PIP_URL, $GET_PIP_PATH)
-        Write-Host "Executing:" $python_path $GET_PIP_PATH
-        Start-Process -FilePath "$python_path" -ArgumentList "$GET_PIP_PATH" -Wait -Passthru
-    } else {
-        Write-Host "pip already installed."
-    }
-}
-
-
 function DownloadMiniconda ($python_version, $platform_suffix) {
     $webclient = New-Object System.Net.WebClient
     if ($python_version -eq "3.4") {
@@ -159,60 +79,8 @@ function InstallMiniconda ($python_version, $architecture, $python_home) {
 }
 
 
-function InstallMinicondaPip ($python_home) {
-    $pip_path = $python_home + "\Scripts\pip.exe"
-    $conda_path = $python_home + "\Scripts\conda.exe"
-    if (-not(Test-Path $pip_path)) {
-        Write-Host "Installing pip..."
-        $args = "install --yes pip"
-        Write-Host $conda_path $args
-        Start-Process -FilePath "$conda_path" -ArgumentList $args -Wait -Passthru
-    } else {
-        Write-Host "pip already installed."
-    }
-}
-
-
-function InstallMinicondaNumpy ($python_home) {
-    $conda_path = $python_home + "\Scripts\conda.exe"
-    Write-Host "Installing numpy..."
-    # Current WxPython will not work with numpy>1.9.0 due to this bug:
-    # http://trac.wxwidgets.org/ticket/16590
-    #$args = "install --yes numpy"
-    $args = "install --yes 'numpy<1.9.0'"
-    Write-Host $conda_path $args
-    Start-Process -FilePath "$conda_path" -ArgumentList $args -Wait -Passthru
-}
-
-function InstallMinicondaScipy ($python_home) {
-    $conda_path = $python_home + "\Scripts\conda.exe"
-    Write-Host "Installing scipy..."
-    # Current WxPython will not work with numpy>1.9.0 due to this bug:
-    # http://trac.wxwidgets.org/ticket/16590
-    #$args = "install --yes scipy"
-    $args = "install --yes scipy numpy=1.8"
-    Write-Host $conda_path $args
-    Start-Process -FilePath "$conda_path" -ArgumentList $args -Wait -Passthru
-}
-
-
-function InstallMinicondaWxpython ($python_home) {
-    $conda_path = $python_home + "\Scripts\conda.exe"
-    Write-Host "Installing wxpython..."
-    $args = "install --yes wxpython"
-    Write-Host $conda_path $args
-    Start-Process -FilePath "$conda_path" -ArgumentList $args -Wait -Passthru
-}
-
-
 function main () {
-    #InstallPython $env:PYTHON_VERSION $env:PYTHON_ARCH $env:PYTHON
-    #InstallPip $env:PYTHON
     InstallMiniconda $env:PYTHON_VERSION $env:PYTHON_ARCH $env:PYTHON
-    InstallMinicondaPip $env:PYTHON
-    InstallMinicondaNumpy $env:PYTHON
-    InstallMinicondaScipy $env:PYTHON
-    InstallMinicondaWxpython $env:PYTHON
 }
 
 main

freeze_appveyor/pinned

@@ -0,0 +1 @@
+numpy 1.8.*

pycorrfit/doc.py

@@ -41,6 +41,7 @@ def __init__(self):
 import yaml
 
 import readfiles
+from readfiles import read_pt3_scripts
 
 
 def GetLocationOfFile(filename):
@@ -155,7 +156,7 @@ def SoftwareUsed():
            "\n - wxPython "+wx.__version__
     # Other software
     text += "\n\nOther software:"+\
-            "\n - FCS_point_correlator (9311a5c15e)" +\
+            "\n - FCS_point_correlator ({})".format(read_pt3_scripts.version) +\
             "\n    PicoQuant file format for Python by Dominic Waithe"
     if hasattr(sys, 'frozen'):
         pyinst = "\n\nThis executable has been created using PyInstaller."

pycorrfit/fcs_data_set.py

@@ -7,6 +7,7 @@
 
 import hashlib
 import numpy as np
+import scipy.integrate as spintg
 import scipy.interpolate as spintp
 import scipy.optimize as spopt
 import warnings
@@ -61,7 +62,9 @@ def __repr__(self):
     @property
     def countrate(self):
         if self._countrate is None:
-            self._countrate = np.average(self._trace[:,1])
+            #self._countrate = np.average(self._trace[:,1])
+            # Take into account traces that have arbitrary sampling
+            self._countrate = spintg.simps(self._trace[:,1], self._trace[:,0]) / self.duration
         return self._countrate
 
     @countrate.setter

pycorrfit/readfiles/read_FCS_Confocor3.py

@@ -7,6 +7,7 @@
 import numpy as np
 import warnings
 
+from . import util
 
 def openFCS(dirname, filename):
     """ 
@@ -128,37 +129,8 @@ def openFCS_Multiple(dirname, filename):
                         trace.append( (np.float(row[3])*1000,
                                        np.float(row[4])/1000) )
                     trace = np.array(trace)
-                    # The trace is too big. Wee need to bin it.
-                    if len(trace) >= 500:
-                        # We want about 500 bins
-                        # We need to sum over intervals of length *teiler*
-                        teiler = int(len(trace)/500)
-                        newlength = len(trace)/teiler
-                        newsignal = np.zeros(newlength)
-                        # Simultaneously sum over all intervals
-                        for j in np.arange(teiler):
-                            newsignal = \
-                                 newsignal+trace[j:newlength*teiler:teiler][:,1]
-                        newsignal = 1.* newsignal / teiler
-                        newtimes = trace[teiler-1:newlength*teiler:teiler][:,0]
-                        if len(trace)%teiler != 0:
-                            # We have a rest signal
-                            # We average it and add it to the trace
-                            rest = trace[newlength*teiler:][:,1]
-                            lrest = len(rest)
-                            rest = np.array([sum(rest)/lrest])
-                            newsignal = np.concatenate((newsignal, rest),
-                                                       axis=0)
-                            timerest = np.array([trace[-1][0]])
-                            newtimes = np.concatenate((newtimes, timerest),
-                                                      axis=0)
-                        newtrace=np.zeros((len(newtimes),2))
-                        newtrace[:,0] = newtimes
-                        newtrace[:,1] = newsignal
-                    else:
-                        # Declare newtrace -
-                        # otherwise we have a problem down three lines ;)
-                        newtrace = trace
+                    # If the trace is too big. Wee need to bin it.
+                    newtrace = util.downsample_trace(trace)
                     # Finally add the trace to the list
                     traces.append(newtrace)
                     if FoundType[:2] != "AC":
@@ -370,37 +342,8 @@ def openFCS_Single(dirname, filename):
                         # So we need to put some factors here
                         trace.append( (np.float(row[0])*1000, np.float(row[1])) )
                     trace = np.array(trace)
-                    # The trace is too big. Wee need to bin it.
-                    if len(trace) >= 500:
-                        # We want about 500 bins
-                        # We need to sum over intervals of length *teiler*
-                        teiler = int(len(trace)/500)
-                        newlength = len(trace)/teiler
-                        newsignal = np.zeros(newlength)
-                        # Simultaneously sum over all intervals
-                        for j in np.arange(teiler):
-                            newsignal = \
-                                 newsignal+trace[j:newlength*teiler:teiler][:,1]
-                        newsignal = 1.* newsignal / teiler
-                        newtimes = trace[teiler-1:newlength*teiler:teiler][:,0]
-                        if len(trace)%teiler != 0:
-                            # We have a rest signal
-                            # We average it and add it to the trace
-                            rest = trace[newlength*teiler:][:,1]
-                            lrest = len(rest)
-                            rest = np.array([sum(rest)/lrest])
-                            newsignal = np.concatenate((newsignal, rest),
-                                                       axis=0)
-                            timerest = np.array([trace[-1][0]])
-                            newtimes = np.concatenate((newtimes, timerest),
-                                                      axis=0)
-                        newtrace=np.zeros((len(newtimes),2))
-                        newtrace[:,0] = newtimes
-                        newtrace[:,1] = newsignal
-                    else:
-                        # Declare newtrace -
-                        # otherwise we have a problem down three lines ;)
-                        newtrace = trace
+                    # If the trace is too big. Wee need to bin it.
+                    newtrace = util.downsample_trace(trace)
                 tracecurve = False
         if fcscurve == True:
             if Alldata[i].partition("=")[0].strip() == "##NPOINTS":