Enable Python 3.5 for zorro only (No PySide==No Automator)

CHANGELOG.txt

@@ -12,6 +12,8 @@ ZORRO 0.7.3
   initial classes.
 * ReliablePy was moved to the mrcz package, as it is not really dependant on 
   Zorro.
+* Installing on Python 3.5 is now possible, but it will not install Automator, 
+  only Zorro and Numexprz.
 
 
 ZORRO 0.7.2

LICENSE.txt

@@ -25,7 +25,7 @@ OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISE
 OF THE POSSIBILITY OF SUCH DAMAGE.
 
 
-=====Numexprz is released under the MIT License=====
+=====Numexprz is released under the BSD 2-clause License=====
 
 Copyright (c) 2007,2008  David M. Cooke <david.m.cooke@gmail.com>
 Copyright (c) 2009,2010  Francesc Alted <faltet@pytables.org>

README.rst

@@ -29,7 +29,7 @@ Zorro is MIT license.
 
 
 Automator 
---------
+---------
 
 The Automator for Zorro and 2dx is a GUI interface to Zorro.
 

automator/__version__.py

@@ -1 +1 @@
-__version__ = '0.7.2b0'
+__version__ = '0.7.3b0'

automator/setup.py

@@ -29,6 +29,7 @@ def configuration( parent_package='', top_path=None ):
     config.add_data_files( ('', 'automator/*.ini') )
     config.add_data_files( ("", "automator/*.ui" ) )
     config.add_data_files( ("", "automator/*.txt" ) )    
+
     config.make_config_py()
     return config
 

requirements.txt

@@ -1,6 +1,5 @@
 numpy>=1.8
 scipy>=0.12.0
 pyfftw >= 0.10.4
-pyside >= 1.2
 matplotlib >= 1.4
 mrcz >= 0.0.1

setup.py

@@ -2,7 +2,7 @@
 ###################################################################
 #  Zorro Dose-fractionated Image Registration Software
 #
-#      License: Limited GNU Public License
+#      License: BSD
 #      Author:  Robert A. McLeod
 #
 #  See LICENSE.txt for details about copyright and
@@ -80,7 +80,7 @@
 major_ver = 0
 minor_ver = 7
 nano_ver = 3
-branch = 'b0'
+branch = 'b1'
 
 version = "%d.%d.%d%s" % (major_ver, minor_ver, nano_ver, branch)
 
@@ -91,9 +91,13 @@
     fh.write( "__version__ = '" + version + "'\n" )
 
 
+INSTALL_AUTOMATOR = True
 if sys.version_info < (2, 7):
     raise RuntimeError( "ZorroAutomator requires python 2.7 or greater" )
-
+if sys.version_info > (3, 4):
+    print( "WARNING: PySide is not compatible with Python > 3.5, Automator will not be installed" )
+    INSTALL_AUTOMATOR = False
+
 # Always prefer setuptools over distutils
 try:
     import setuptools
@@ -126,8 +130,9 @@ def configuration(parent_package=None,top_path=None):
     os.chdir( here )
     config.add_subpackage('numexprz')
     os.chdir( here )
-    config.add_subpackage('automator')
-    os.chdir( here )
+    if INSTALL_AUTOMATOR:
+        config.add_subpackage('automator')
+        os.chdir( here )
 
     config.add_data_files( (".", 'README.rst') )
     config.add_data_files( (".", "LICENSE.txt") )
@@ -153,7 +158,7 @@ def setup_zorro():
                       author='Robert A. McLeod',
                       author_email='robert.mcleod@unibas.ch',
                       url='https://github.com/C-CINA/Zorro',
-                      license='MIT',
+                      license='BSD',
                       packages=[], # DON'T INLCUDE subpackages here in setuptools...
                       install_requires=requirements,
                       setup_requires=requirements,
@@ -164,6 +169,11 @@ def setup_zorro():
                                             "ims = zorro.zorro_plotting:main" ],
                           },
                       # See https://pypi.python.org/pypi?%3Aaction=list_classifiers
+                      extras_require={
+                            ':python_version <= "3.4"': [
+                                'pyside',
+                            ],
+                        },
                       classifiers=[
                             # How mature is this project? Common values are
                             #   3 - Alpha
@@ -184,6 +194,7 @@ def setup_zorro():
                             'Programming Language :: Python :: 2.7',
                             'Programming Language :: Python :: 3',
                             'Programming Language :: Python :: 3.4',
+                            'Programming Language :: Python :: 3.5',
 
                             # OS
                             'Operating System :: POSIX',

zorro/__version__.py

@@ -1 +1 @@
-__version__ = '0.7.2b0'
+__version__ = '0.7.3b0'

zorro/extract.py

@@ -9,13 +9,14 @@
 from __future__ import division, print_function, absolute_import
 
 import numpy as np
-from . import  (ReliablePy, zorro_util, zorro)
+from . import  (zorro_util, zorro)
 import time
 import os, os.path, glob
 import scipy.ndimage
 import re
 import collections
 import mrcz
+from mrcz import ReliablePy
 
 # For a multiprocessing, maybe I should use subprocess pool and a master process?  That would avoid having to 
 # any of the Python MPI libraries.  Then again maybe I should just learn mpi4py, likely it would be a 

zorro/zorro.py

@@ -138,7 +138,7 @@ def __init__( self ):
         # for 'hot' in filterMode
         self.hotpixInfo = { u"logisticK":6.0, u"relax":0.925, u"maxSigma":8.0, u"psf": u"K2",
                            u"guessHotpix":0, u"guessDeadpix":0, u"decorrOutliers":False,
-                           u"cutoffLower":-4.0, u"cutoffUpper":3.25 }
+                           u"cutoffLower":-4.0, u"cutoffUpper":3.25, u"neighborPix":0 }
 
 
         self.FFTSum = None
@@ -2633,7 +2633,8 @@ def errorNormCDF( params ):
         neighbourlyOutlierMask = nz.evaluate( "neighbourlyOutlierMask > neighbourThres" )
         neighbourlyIndices = np.where( nz.evaluate( "neighbourlyOutlierMask > neighbourThres" ) )
         bestMean = bestNorm.x[0] / m
-        print( "Number of neighbourly outlier pixels: %d" % len(neighbourlyIndices[0]) )
+        print( "Number of neighborly outlier pixels: %d" % len(neighbourlyIndices[0]) )
+        self.hotpixInfo[u'neighborPix'] = len(neighbourlyIndices[0])
         neighbourFilt = np.zeros_like( psfFiltMean )
         for (nY, nX) in zip( neighbourlyIndices[0], neighbourlyIndices[1] ):
             # We'll use 5x5 here, substituting the bestMean if it's all garbage