CHANGELOG

+0.3.2
+ - fix: refactor code for opening .dat files; moved from a Cython
+   module to a pure Python module due to errors on big-endian
+   systems (#17)
+0.3.1
+ - fix: console script entry point broken (#16)
+ - automate distribution to PyPI
+ - update documentation
 0.3.0
  - Move from Python 2 to Python 3 (#12)
  - Move to wxPython 4.0.1 (#12)

appveyor.yml

-clone_depth: 256
-build: off
-notifications:
-  - provider: Email
-    on_build_success: false
-    on_build_failure: false
-    on_build_status_changed: false
-environment:
-  matrix:
-    - PYTHON: "C:\\Miniconda36-x64"
-      PYTHON_VERSION: "3.6"
-      PYTHON_ARCH: "64"
-
-init:
-  - "ECHO %PYTHON% %PYTHON_VERSION% %PYTHON_ARCH%"
-
-install:
-  # Install InnoSetup and add to path
-  # Copied from
-  # https://github.com/Phonations/Joker/blob/master/appveyor.yml
-  - appveyor-retry choco install -y InnoSetup
-
-  # Prepend newly installed Python to the PATH of this build (this cannot be
-  # done from inside the powershell script as it would require to restart
-  # the parent CMD process).
-  - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
-
-  # CONDA installs
-  # Pinned versions are defined in .appveyor\pinned
-  - xcopy .appveyor\pinned %PYTHON%\conda-meta\ /Y
-  - "appveyor-retry conda install --yes --quiet matplotlib numpy pip scipy wxpython"
-  # Check that we have the expected version and architecture for Python
-  - "python --version"
-  - "pip install cython wheel"
-  - "pip install pyinstaller==3.3.1"
-  - "pip install -e ."
-  # Show the installed packages
-  - "pip freeze"
-
-test_script:
-  - "pip install coverage"
-  - "pip install codecov"
-  - "coverage run --source=pyscanfcs ./setup.py test"
-  - "coverage report -m"
-  - "codecov || exit 0"
-
-after_test:
-  # If tests are successful, create a whl package for the project.
-  - "python setup.py bdist_wheel"
-  - ps: "ls dist"
-  # Run pyinstaller
-  # This will create the "win7_innosetup.iss" file
-  - "pyinstaller -y --log-level=WARN .appveyor\\PyScanFCS_win7.spec"
-  # Create InnoSetup installers
-  # Set InnoSetup path here, because Cython complained about it.
-  - set PATH=%PATH%;"C:\\Program Files (x86)\\Inno Setup 5"
-  - iscc /Q win7_innosetup.iss
-
-artifacts:
-  # Archive the generated wheel package in the ci.appveyor.com build report.
-  - path: dist\*
-  # InnoSetup files
-  - path: Output\*
-
-deploy:
-  provider: GitHub
-  auth_token:
-    secure: TODO_not_set_yet
-  artifact: /.*\.exe/, /.*\.whl/
-  draft: true
-  prerelease: true
-  on:
-    branch: master                 # release from master branch only
-    appveyor_repo_tag: true        # deploy on tag push only

debian/changelog

+pyscanfcs (0.3.2+ds-1) unstable; urgency=medium
+
+  * New upstream version 0.3.2+ds <=> 0.3.1~gitd295b59+ds-1
+  * Upload to unstable
+  * Fix dversionmangle in d/watch
+
+ -- Alexandre Mestiashvili <mestia@debian.org>  Tue, 11 Dec 2018 09:33:28 +0000
+
+pyscanfcs (0.3.1~gitd295b59+ds-1) experimental; urgency=medium
+
+  * New upstream version 0.3.1~gitd295b59+ds
+  * Update Files-Excluded in d/copyright
+  * Drop patches which are parts of the release
+  * Update d/rules, remove not needed override_dh_fixperms
+  * Update d/watch, s/dfsg/ds/ for the suffix
+
+ -- Alexandre Mestiashvili <mestia@debian.org>  Thu, 29 Nov 2018 19:58:53 +0000
+
 pyscanfcs (0.3.0+dfsg-2) experimental; urgency=medium
 
   * Add patch presumably fixing test failures on big-endian archs

debian/copyright

@@ -4,7 +4,7 @@ Source: https://github.com/FCS-analysis/PyScanFCS
 Files-Excluded:
  .appveyor
  .travis
- .appveyor.yml
+ appveyor.yml
  .travis.yml
  .readthedocs.yml
 

debian/patches/0001-force-little-endian-dtype-17.patch

-From 1950d60ab4824e18cd2964f8b4431881bec13116 Mon Sep 17 00:00:00 2001
-From: Paul Müller <dev@craban.de>
-Date: Sat, 24 Nov 2018 15:50:12 +0100
-Subject: [PATCH] force little-endian dtype (#17)
-
----
- pyscanfcs/sfcs_alg.pyx | 11 ++++-------
- 1 file changed, 4 insertions(+), 7 deletions(-)
-
-diff --git a/pyscanfcs/sfcs_alg.pyx b/pyscanfcs/sfcs_alg.pyx
-index 8cf5cbf..b7ee5d9 100755
---- a/pyscanfcs/sfcs_alg.pyx
-+++ b/pyscanfcs/sfcs_alg.pyx
-@@ -146,7 +146,6 @@ def bin_photon_events(np.ndarray[DTYPEuint32_t] data, double t_bin,
-     TempTrace.append(phot_c)
-     
-     NewFile.write(outdtype(TempTrace))
--    del TempTrace
-     NewFile.close()
-     return outfile
- 
-@@ -203,9 +202,9 @@ def open_dat(filename, callback=None, cb_kwargs={}):
-     File = open(filename, 'rb')
-     # 1st byte: get file format
-     # should be 16 - for 16 bit
--    fformat = int(np.fromfile(File, dtype="uint8", count=1))
-+    fformat = int(np.fromfile(File, dtype="<u1", count=1))
-     # 2nd byte: read system clock
--    system_clock = int(np.fromfile(File, dtype="uint8", count=1))
-+    system_clock = int(np.fromfile(File, dtype="<u1", count=1))
-     if fformat == 8:
-         # No 8 bit format supported
-         warnings.warn('8 bit format not supported.')
-@@ -213,7 +212,7 @@ def open_dat(filename, callback=None, cb_kwargs={}):
-         return system_clock, None
-     elif fformat == 32:
-         # (There is an utility to convert data to 32bit)
--        datData = np.fromfile(File, dtype="uint32", count=-1)
-+        datData = np.fromfile(File, dtype="<u4", count=-1)
-         File.close()
-         return system_clock, datData
-     elif fformat == 16:
-@@ -225,9 +224,8 @@ def open_dat(filename, callback=None, cb_kwargs={}):
-     # In case of 16 bit file format (assumed), read the rest of the file in
-     # 16 bit format.
-     # Load bunch of Data
--    Data = np.fromfile(File, dtype="uint16", count=-1)
-+    Data = np.fromfile(File, dtype="<u2", count=-1)
-     File.close()
--
-     # Now we need to check if there are any 0xFFFF values which would
-     # mean, that we do not yet have the true data in our array.
-     # There is 32 bit data after a 0xFFFF = 65535
-@@ -261,5 +259,4 @@ def open_dat(filename, callback=None, cb_kwargs={}):
- 
-     datData = np.delete(datData, zeroids)
- 
--    del Data
-     return system_clock, datData
--- 
-2.20.0.rc1
-

debian/patches/gui_scripts.patch

-Subject: Fix setup.py
-Forwarded: https://github.com/FCS-analysis/PyScanFCS/issues/16
-Author: Upstream
---- pyscanfcs.orig/setup.py
-+++ pyscanfcs/setup.py
-@@ -85,6 +85,6 @@
-                  ],
-     platforms=['ALL'],
-     entry_points={
--       "gui_scripts": ["{name:s}={name:s}:Main".format(**{"name":name})]
-+       "gui_scripts": ["pyscanfcs=pyscanfcs.gui_wx.main:Main"]
-        }
-     )

debian/patches/series

-0001-force-little-endian-dtype-17.patch
-gui_scripts.patch

debian/rules

@@ -47,10 +47,6 @@ override_dh_install:
 		debian/$(pkg)/usr/share/pixmaps
 	chmod -R 644 debian/$(pkg)/usr/share/doc/$(pkg)/examples/misc
 
-override_dh_fixperms:
-	dh_fixperms
-	chmod 644 debian/$(pkg)/usr/lib/$(pkg)/pyscanfcs/sfcs_alg.pyx
-
 override_dh_compress:
 	dh_compress -X$(PDF)
 

debian/watch

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

docs/conf.py

@@ -83,6 +83,7 @@ master_doc = 'index'
 
 # General information about the project.
 project = 'PyScanFCS'
+github_project = 'FCS-analysis/' + project
 copyright = '2012, Paul Müller'
 author = 'Paul Müller'
 

docs/extensions/github_changelog.py

@@ -29,13 +29,13 @@ class IncludeDirective(Directive):
 
     def run(self):
         full_path = self.arguments[0]
-        project = self.state.document.settings.env.config.project
+        project = self.state.document.settings.env.config.github_project
 
         def insert_github_link(reobj):
             line = reobj.string
             instr = line[reobj.start():reobj.end()]
             issue = instr.strip("#()")
-            link = "https://github.com/RI-imaging/{}/issues/".format(project)
+            link = "https://github.com/{}/issues/".format(project)
             rstlink = "(`#{issue} <{link}{issue}>`_)".format(issue=issue,
                                                              link=link)
             return rstlink
@@ -70,5 +70,6 @@ class IncludeDirective(Directive):
 
 
 def setup(app):
+    app.add_config_value('github_project', "user/project", 'html')
     app.add_directive('include_changelog', IncludeDirective)
     return {'version': '0.1'}   # identifies the version of our extension

docs/sec_getting_started.rst

@@ -7,7 +7,7 @@ Installation
 - Windows installers for PyScanFCS are available at the `release page <https://github.com/FCS-analysis/PyScanFCS/releases>`_.
   Note: The installer is currently broken because astropy cannot be frozen, see https://github.com/astropy/astropy/issues/7052.
 - On Debian-based systems, install via ``apt-get install pyscanfcs``.
-- If you have Python 3.6 installed, you may install PyScanFCS via ``pip install pyscanfcs[GUI]``.
+- If you have Python 3.6 installed, you may install PyScanFCS via ``pip install pyscanfcs``.
   After the installation, type ``pyscanfcs`` in a command shell to start PyScanFCS.
 
 
@@ -15,7 +15,7 @@ Documentation
 -------------
 The documentation is in the process of being transferred entirely to
 readthedocs.org. Currently, the it is scattered across several
-places and it is most-likely outdated:
+places and it might be outdated:
 
-- Original LaTeX-based PDF file (outdated): https://github.com/FCS-analysis/PyScanFCS/wiki/PyScanFCS_doc.pdf
-- Wiki pages: https://github.com/FCS-analysis/PyScanFCS/wiki
+- Original LaTeX-based PDF file: https://github.com/FCS-analysis/PyScanFCS/wiki/PyScanFCS_doc.pdf
+- Book chapter in *Methods in Molecular Biology* (2013) on perpendicular line scanning FCS: https://arxiv.org/abs/1806.00070

pyscanfcs/__init__.py

 from . import fitting
 from . import openfile
-from . import sfcs_alg
 from . import util
 from ._version import version as __version__
 

pyscanfcs/_version.py

 #!/usr/bin/env python
-"""
-Determine package version for git repositories.
+"""Determine package version for git repositories from tags
 
 Each time this file is imported it checks if the ".git" folder is
 present and if so, obtains the version from the git history using
 `git describe`. This information is then stored in the file
 `_version_save.py` which is not versioned by git, but distributed
-along with e.g. pypi.
+along e.g. on PyPI.
 """
 from __future__ import print_function
 
@@ -15,7 +14,7 @@ from __future__ import print_function
 if True:  # pragma: no cover
     import imp
     import os
-    from os.path import join, abspath, dirname
+    from os.path import abspath, basename, dirname, join
     import subprocess
     import sys
     import time
@@ -24,12 +23,12 @@ if True:  # pragma: no cover
 
     def git_describe():
         """
-        Returns a string describing the version returned by the
+        Return a string describing the version returned by the
         command `git describe --tags HEAD`.
         If it is not possible to determine the correct version,
         then an empty string is returned.
         """
-        # make sure we are in a directory that belongs to the correct
+        # Make sure we are in a directory that belongs to the correct
         # repository.
         ourdir = dirname(abspath(__file__))
 
@@ -67,8 +66,7 @@ if True:  # pragma: no cover
         return git_revision
 
     def load_version(versionfile):
-        """ load version from version_save.py
-        """
+        """load version from version_save.py"""
         longversion = ""
         try:
             _version_save = imp.load_source("_version_save", versionfile)
@@ -85,8 +83,7 @@ if True:  # pragma: no cover
         return longversion
 
     def save_version(version, versionfile):
-        """ save version to version_save.py
-        """
+        """save version to version_save.py"""
         data = "#!/usr/bin/env python\n" \
             + "# This file was created automatically\n" \
             + "longversion = '{VERSION}'\n"
@@ -97,7 +94,15 @@ if True:  # pragma: no cover
             msg = "Could not write package version to {}.".format(versionfile)
             warnings.warn(msg)
 
-    versionfile = join(dirname(abspath(__file__)), "_version_save.py")
+    hdir = dirname(abspath(__file__))
+    if basename(__file__) == "conf.py" and "name" in locals():
+        # This script is executed in conf.py from the docs directory
+        versionfile = join(join(join(hdir, ".."),
+                                name),  # noqa: F821
+                           "_version_save.py")
+    else:
+        # This script is imported as a module
+        versionfile = join(hdir, "_version_save.py")
 
     # Determine the accurate version
     longversion = ""

pyscanfcs/sfcs_alg.pyx → pyscanfcs/bin_pe.pyx

@@ -3,7 +3,6 @@ import warnings
 
 import numpy as np
 
-# See cython documentation for following stuff
 # "cimport" is used to import special compile-time information
 # about the numpy module (this is stored in a file numpy.pxd which is
 # currently part of the Cython distribution).
@@ -13,23 +12,18 @@ cimport numpy as np
 # type info object.
 DTYPEuint32 = np.uint32
 DTYPEuint16 = np.uint16
-DTYPEfloat32 = np.float32
 # "ctypedef" assigns a corresponding compile-time type to DTYPE_t. For
 # every type in the numpy module there's a corresponding compile-time
 # type with a _t-suffix.
 ctypedef np.uint32_t DTYPEuint32_t
 ctypedef np.uint16_t DTYPEuint16_t
-ctypedef np.float32_t DTYPEfloat32_t
+
+cimport cython
 
 # Negative indices are checked for and handled correctly. The code is
 # explicitly coded so that it doesn’t use negative indices, and it (hopefully)
 # always access within bounds. We can add a decorator to disable bounds
 # checking:
-cimport cython
-
-__all__ = ["bin_photon_events", "open_dat"]
-
-
 @cython.cdivision(True)
 @cython.boundscheck(False)  # turn of bounds-checking for entire function
 def bin_photon_events(np.ndarray[DTYPEuint32_t] data, double t_bin,
@@ -146,120 +140,5 @@ def bin_photon_events(np.ndarray[DTYPEuint32_t] data, double t_bin,
     TempTrace.append(phot_c)
     
     NewFile.write(outdtype(TempTrace))
-    del TempTrace
     NewFile.close()
     return outfile
-
-
-@cython.cdivision(True)
-@cython.boundscheck(False)  # turn of bounds-checking for entire function
-def open_dat(filename, callback=None, cb_kwargs={}):
-    """Load "Flex02-12D" correlator.com files
-
-    We open a .dat file as produced by the "Flex02-12D" correlator in photon
-    history recorder mode.
-    The file contains the time differences between single photon events.
-
-    Parameters
-    ----------
-    filename : str
-        Path to file
-    callback : callable or None
-        Callback function to be called throughout the algorithm. If the
-        return value of `callback` is not None, the function will abort.
-        Number of function calls: 3
-    cb_kwargs : dict, optional
-        Keyword arguments for `callback` (e.g. "pid" of process).
-
-    Returns
-    -------
-    system_clock, datData
-        The system clock in MHz and the photon time event stream.
-        Returns (None, None) if the progress was aborted through the
-        callback function.
-
-
-    Notes
-    -----
-    Raw data file format (taken from manual):
-     1. The file records the difference in system clock ticks (1/60 us)
-        between photon event.
-     2. The first byte identifies the format of the file 8 : 8 bit, 16: 16 bit
-     3. The second byte identifies the system clock. 60MHz.
-     4. The time unit is 1/system clock.
-     5. 16 bit format. Each WORD (2 bytes) represents a photon event,
-        time = WORD/system clock, unless the value is 0xFFFF, in which case,
-        the following four bytes represent a photon event.
-     6. 8 bit format: Each BYTE represents a photon event unless the value is
-        0xFF, in which case, the BYTE means 255 clock ticks passed without a
-        photon event. For example 0A 0B FF 08 means there are three
-        photon events. The time series are 0x0A+1, 0x0B+1, 0xFF+8+1.
-
-    """
-    cdef np.ndarray[DTYPEuint16_t] Data
-    cdef np.ndarray[DTYPEuint32_t] datData
-    cdef int i, N
-    # open file
-    File = open(filename, 'rb')
-    # 1st byte: get file format
-    # should be 16 - for 16 bit
-    fformat = int(np.fromfile(File, dtype="uint8", count=1))
-    # 2nd byte: read system clock
-    system_clock = int(np.fromfile(File, dtype="uint8", count=1))
-    if fformat == 8:
-        # No 8 bit format supported
-        warnings.warn('8 bit format not supported.')
-        File.close()
-        return system_clock, None
-    elif fformat == 32:
-        # (There is an utility to convert data to 32bit)
-        datData = np.fromfile(File, dtype="uint32", count=-1)
-        File.close()
-        return system_clock, datData
-    elif fformat == 16:
-        pass
-    else:
-        warnings.warn("Unknown format: {} bit".format(fformat))
-        File.close()
-        return system_clock, None
-    # In case of 16 bit file format (assumed), read the rest of the file in
-    # 16 bit format.
-    # Load bunch of Data
-    Data = np.fromfile(File, dtype="uint16", count=-1)
-    File.close()
-
-    # Now we need to check if there are any 0xFFFF values which would
-    # mean, that we do not yet have the true data in our array.
-    # There is 32 bit data after a 0xFFFF = 65535
-    if callback is not None:
-        ret = callback(**cb_kwargs)
-        if ret is not None:
-            return None, None
-
-    occurrences = np.where(Data == 65535)[0]
-    N = len(occurrences)
-
-    if callback is not None:
-        ret = callback(**cb_kwargs)
-        if ret is not None:
-            return None, None
-
-    # Make a 32 bit array
-    datData = np.uint32(Data)
-    datData[occurrences] = np.uint32(
-        Data[occurrences + 1]) + np.uint32(Data[occurrences + 2]) * 65536
-
-    if callback is not None:
-        ret = callback(**cb_kwargs)
-        if ret is not None:
-            return None, None
-
-    # Now delete the zeros
-    zeroids = np.zeros(N * 2)
-    zeroids[::2] = occurrences + 1
-    zeroids[1::2] = occurrences + 2
-
-    datData = np.delete(datData, zeroids)
-
-    del Data
-    return system_clock, datData

pyscanfcs/gui_wx/doc.py

@@ -139,7 +139,8 @@ PyScanFCS) in numerous ways:
    \tfamiliar with reStrucuredText or LaTeX, you might be able to help
    \tout with the online documentation.
 
-5. \tPlease cite: Müller et al. Bioinformatics 30(17): 2532–2533, 2014
+5. \tPlease cite: Müller et al. Methods in Molecular Biology, 1076,
+   \t(635–51), 2014.
 
 If you are planning to contribute to PyScanFCS, please contact me via
 the PyScanFCS issue page on GitHub such that we may coordinate a pull

pyscanfcs/gui_wx/main.py

@@ -28,7 +28,7 @@ from wx.lib.scrolledpanel import ScrolledPanel
 
 from .. import fitting
 from .. import openfile
-from .. import sfcs_alg
+from .. import bin_pe
 from .. import util
 
 from . import doc
@@ -230,22 +230,6 @@ maximum. \n The data achieved will automatically be updated within the main prog
                 self.redline = self.axes.vlines(
                     ltime, self.ymin, self.ymax, color='red')
 
-                # Tried with gaussian fit
-                #amplitudes = self.ampl[start:stop]
-                #frequencies = self.freq[start:stop]
-                #argmax = np.argmax(amplitudes)
-                # Get gaussian function and optimal parameters
-                ## popt = [freq, ampl, sigma]
-                ## gauss(popt, frequencies)
-                #popt, gauss = sfcs_alg.FitGaussian(amplitudes, frequencies, argmax)
-                #self.pnt.t_linescan = 1./popt[0]
-                #lenplot = 1000
-                #ids_plot = np.linspace(start,stop,lenplot, endpoint=False)
-                #freq_plot = np.linspace(frequencies[0],frequencies[-1],lenplot, endpoint=False)
-                #a = np.argmax(gauss(popt, freq_plot))
-                #self.pnt.t_linescan = 1./freq_plot[a]
-                #self.redline =  self.axes.plot(ids_plot, gauss(popt, freq_plot), '-', color='red')
-
                 self.canvas.draw()
                 # Plot the results
                 # Set check box to True: "use cycle time"
@@ -383,7 +367,7 @@ class MyFrame(wx.Frame):
 
         print("Creating file {} ({})".format(outfile, outdtype.__name__))
 
-        sfcs_alg.bin_photon_events(Data, t_bin, binshift=eb,
+        bin_pe.bin_photon_events(Data, t_bin, binshift=eb,
                                  outfile=outfile,
                                  outdtype=outdtype,
                                  callback=wxdlg.Iterate)
@@ -418,7 +402,7 @@ class MyFrame(wx.Frame):
 
         print("Creating file {} ({})".format(outfile, outdtype.__name__))
 
-        sfcs_alg.bin_photon_events(Data, t_bin, binshift=eb,
+        bin_pe.bin_photon_events(Data, t_bin, binshift=eb,
                                    outfile=outfile,
                                    outdtype=outdtype,
                                    callback=wxdlg.Iterate)
@@ -1287,8 +1271,8 @@ class MyFrame(wx.Frame):
 
                     wxdlg = uilayer.wxdlg(parent=self, steps=3,
                                           title="Importing dat file...")
-                    datData2 = sfcs_alg.open_dat(
-                        path, callback=wxdlg.Iterate)[1]
+                    datData2 = openfile.openDAT(
+                        path, callback=wxdlg.Iterate)["data_stream"]
                     wxdlg.Finalize()
 
                     # Bin to obtain intData2
@@ -1719,8 +1703,9 @@ class MyFrame(wx.Frame):
 
         wxdlg = uilayer.wxdlg(parent=self, steps=3,
                               title="Importing dat file...")
-        self.system_clock, self.datData = sfcs_alg.open_dat(
-            filename, callback=wxdlg.Iterate)
+        info = openfile.openDAT(filename, callback=wxdlg.Iterate)
+        self.system_clock = info["system_clock"]
+        self.datData = info["data_stream"]
         wxdlg.Finalize()
 
         self.GetTotalTime()

pyscanfcs/openfile.py

 """filetype definitions"""
 import astropy.io.fits
+import numpy as np
 from skimage.external import tifffile
 
-from . import sfcs_alg
 
-
-def openAny(fname, callback=None):
+def openAny(path, callback=None):
     """load any supported file type"""
     methods = methods_binned.copy()
     methods.update(methods_stream)
 
     for key in list(methods.keys()):
-        if fname.endswith(key):
-            return methods[key](fname, callback)
-
-
-def openDAT(fname, callback=None):
-    system_clock, intensity_data = sfcs_alg.open_dat(fname, callback)
-    info = dict()
-    info["data_stream"] = intensity_data
-    info["system_clock"] = system_clock
+        if path.endswith(key):
+            return methods[key](path, callback)
+
+
+def openDAT(path, callback=None, cb_kwargs={}):
+    """Load "Flex02-12D" correlator.com files
+
+    We open a .dat file as produced by the "Flex02-12D" correlator in photon
+    history recorder mode.
+    The file contains the time differences between single photon events.
+
+    Parameters
+    ----------
+    path : str
+        Path to file
+    callback : callable or None
+        Callback function to be called throughout the algorithm. If the
+        return value of `callback` is not None, the function will abort.
+        Number of function calls: 3
+    cb_kwargs : dict, optional
+        Keyword arguments for `callback` (e.g. "pid" of process).
+
+    Returns
+    -------
+    info: dict
+        Dictionary containing the "system_clock" in MHz and the
+        "data_stream" (photon arrival time event stream).
+        Returns `None` if the progress was aborted through the
+        callback function.
+
+
+    Notes
+    -----
+    Raw data file format (taken from manual):
+     1. The file records the difference in system clock ticks (1/60 us)
+        between photon event.
+     2. The first byte identifies the format of the file 8 : 8 bit, 16: 16 bit
+     3. The second byte identifies the system clock. 60MHz.
+     4. The time unit is 1/system clock.
+     5. 16 bit format. Each WORD (2 bytes) represents a photon event,
+        time = WORD/system clock, unless the value is 0xFFFF, in which case,
+        the following four bytes represent a photon event.
+     6. 8 bit format: Each BYTE represents a photon event unless the value is
+        0xFF, in which case, the BYTE means 255 clock ticks passed without a
+        photon event. For example 0A 0B FF 08 means there are three
+        photon events. The time series are 0x0A+1, 0x0B+1, 0xFF+8+1.
+
+    """
+    # open file
+    filed = open(path, 'rb')
+    # 1st byte: get file format
+    # should be 16 - for 16 bit
+    fformat = int(np.fromfile(filed, dtype="<u1", count=1))
+    # 2nd byte: read system clock
+    system_clock = int(np.fromfile(filed, dtype="<u1", count=1))
+    if fformat == 8:
+        # No 8 bit format supported
+        raise ValueError("8 bit format not supported!")
+    elif fformat == 32:
+        # (There is an utility to convert data to 32bit)
+        data = np.fromfile(filed, dtype="<u4", count=-1)
+    elif fformat == 16:
+        # convert 16bit to 32bit
+        # Read the rest of the file in 16 bit format.
+        # Load bunch of Data
+        data16 = np.fromfile(filed, dtype="<u2", count=-1)
+        # Now we need to check if there are any 0xFFFF values which would
+        # mean, that we do not yet have the true data in our array.
+        # There is 32 bit data after a 0xFFFF = 65535
+        if callback is not None:
+            ret = callback(**cb_kwargs)
+            if ret is not None:
+                return
+
+        # occurences of large values
+        occ = np.where(data16 == 65535)[0]
+        N = len(occ)
+
+        if callback is not None:
+            ret = callback(**cb_kwargs)
+            if ret is not None:
+                return
+
+        # Make a 32 bit array
+        data = np.uint32(data16)
+        data[occ] = data16[occ + 1] + data16[occ + 2] * 65536
+
+        if callback is not None:
+            ret = callback(**cb_kwargs)
+            if ret is not None:
+                return None
+
+        # Now delete the zeros
+        zeroids = np.zeros(N * 2, dtype=int)
+        zeroids[::2] = occ + 1
+        zeroids[1::2] = occ + 2
+        data = np.delete(data, zeroids)
+    else:
+        raise ValueError("Unknown format: {} bit".format(fformat))
+    filed.close()
+
+    info = {"data_stream": data,
+            "system_clock": system_clock
+            }
 
     return info
 

setup.py

@@ -18,8 +18,8 @@ except ImportError:
           "with this setup script will not work:", sys.exc_info())
     extensions = []
 else:
-    extensions = [Extension("pyscanfcs.sfcs_alg",
-                            sources=["pyscanfcs/sfcs_alg.pyx"],
+    extensions = [Extension("pyscanfcs.bin_pe",
+                            sources=["pyscanfcs/bin_pe.pyx"],
                             include_dirs=[np.get_include()]
                             )
                  ]
@@ -85,6 +85,6 @@ setup(
                  ],
     platforms=['ALL'],
     entry_points={
-       "gui_scripts": ["{name:s}={name:s}:Main".format(**{"name":name})]
+       "gui_scripts": ["pyscanfcs=pyscanfcs.gui_wx.main:Main"]
        }
     )

tests/test_sfcs_alg.py → tests/test_bin_pe.py

-import pathlib
-
 import numpy as np
 
-from pyscanfcs import sfcs_alg
-
-
-def test_open_dat():
-    here = pathlib.Path(__file__).parent
-    f16 = here / "data/n2000_7.0ms_16bit.dat"
-    f32 = here / "data/n2000_7.0ms_32bit.dat"
-    r16, d16 = sfcs_alg.open_dat(str(f16))
-    r32, d32 = sfcs_alg.open_dat(str(f32))
-    assert r16 == 60
-    assert r32 == 60
-    assert np.all(d16==d32)
-    assert np.all(d16[-5:] == np.array([1, 1, 21420, 21418, 21420]))
+from pyscanfcs import bin_pe
 
 
 def test_bin_photon_events():
@@ -25,7 +11,7 @@ def test_bin_photon_events():
                      # blank
                      8, 1, 1,  # 28
                      ], dtype=np.uint32)
-    binf = sfcs_alg.bin_photon_events(data=data, t_bin=5.0001)
+    binf = bin_pe.bin_photon_events(data=data, t_bin=5.0001)
     binned = np.fromfile(binf, dtype="uint16", count=-1)
     assert np.all(binned == np.array([1, 3, 4, 3, 0, 3]))