Merge branch 'master' of https://git.lemmasoftware.org/akvo

akvo/gui/akvoGUI.py

@@ -35,14 +35,13 @@ version = pkg_resources.require("Akvo")[0].version
 import yaml
 # Writes out numpy arrays into Eigen vectors as serialized by Lemma
 class MatrixXr(yaml.YAMLObject):
-    yaml_tag = u'!MatrixXr'
-    def __init__(self, name, hp, ac, attacks):
-        self.name = name
-        self.hp = hp
-        self.ac = ac
-        self.attacks = attacks
-        def __repr__(self):
-            return "%s(name=%r, hp=%r, ac=%r, attacks=%r)" % (self.__class__.__name__, self.name, self.hp, self.ac, self.attacks)
+    yaml_tag = u'MatrixXr'
+    def __init__(self, rows, cols, data):
+        self.rows = rows
+        self.cols = cols
+        self.data = np.zeros((rows,cols))
+    def __repr__(self):
+        return "%s(rows=%r, cols=%r, data=%r)" % (self.__class__.__name__, self.rows, self.cols, self.data) 
 
 class VectorXr(yaml.YAMLObject):
     yaml_tag = r'VectorXr'
@@ -70,7 +69,7 @@ class AkvoYamlNode(yaml.YAMLObject):
         self.Import = {}
         self.Processing = OrderedDict() 
         #self.ProcessingFlow = []
-        #self.data = {}
+        #self.Data = {}
     # For going the other way, data import based on Yaml serialization, 
     def __repr__(self):
         return "%s(name=%r, Akvo_VESION=%r, Import=%r, Processing=%r)" % (
@@ -453,7 +452,6 @@ class ApplicationWindow(QtWidgets.QMainWindow):
         #INFO["samp"] = self.RAWDataProc.samp
         INFO["nPulseMoments"] = self.RAWDataProc.nPulseMoments
         #INFO["deadTime"] = self.RAWDataProc.deadTime
-        INFO["transFreq"] = self.RAWDataProc.transFreq.tolist()
         INFO["processed"] = "Akvo v. 1.0, on " + time.strftime("%d/%m/%Y")
         # Pulse current info
         ip = 0
@@ -503,10 +501,10 @@ class ApplicationWindow(QtWidgets.QMainWindow):
  
     def SavePreprocess(self):
      
-        if "Saved" not in self.YamlNode.Processing.keys():
-            self.YamlNode.Processing["Saved"] = []
-        self.YamlNode.Processing["Saved"].append(datetime.datetime.now().isoformat()) 
-        self.Log()
+        #if "Saved" not in self.YamlNode.Processing.keys():
+        #    self.YamlNode.Processing["Saved"] = []
+        #self.YamlNode.Processing["Saved"].append(datetime.datetime.now().isoformat()) 
+        #self.Log()
  
         import pickle, os 
         try:
@@ -608,10 +606,11 @@ class ApplicationWindow(QtWidgets.QMainWindow):
         #except KeyError:
         #    pass
        
-        if "Loaded" not in self.YamlNode.Processing.keys():
-            self.YamlNode.Processing["Loaded"] = []
-        self.YamlNode.Processing["Loaded"].append(datetime.datetime.now().isoformat()) 
-        self.Log()
+        # Remove "Saved" and "Loaded" from processing flow 
+        #if "Loaded" not in self.YamlNode.Processing.keys():
+        #    self.YamlNode.Processing["Loaded"] = []
+        #self.YamlNode.Processing["Loaded"].append(datetime.datetime.now().isoformat()) 
+        #self.Log()
  
         # If we got this far, enable all the widgets
         self.ui.lcdNumberTauPulse1.setEnabled(True)

akvo/tressel/filtfilt.py

@@ -35,11 +35,11 @@ def filtfilt(b,a,x):
     edge=ntaps*3
 
     if x.ndim != 1:
-        raise ValueError, "Filiflit is only accepting 1 dimension arrays."
+        raise ValueError("Filiflit is only accepting 1 dimension arrays.")
 
     #x must be bigger than edge
     if x.size < edge:
-        raise ValueError, "Input vector needs to be bigger than 3 * max(len(a),len(b)."
+        raise ValueError("Input vector needs to be bigger than 3 * max(len(a),len(b).")
 
     if len(a) < ntaps:
         a=r_[a,zeros(len(b)-len(a))]

setup.py

@@ -1,39 +1,21 @@
 #!/usr/bin/env python
-import sys
 
-# optionally use qt4
-# if sys.argv[1] == "build_ui":
-try:
-    from pyqt_distutils.build_ui import build_ui
-#         cmdclass = {'build_ui': build_ui}
-except ImportError:
-    build_ui = None  # user won't have pyqt_distutils when deploying
-#         cmdclass = {}
-# else:
-#     build_ui = None  # user won't have pyqt_distutils when deploying
-#     cmdclass = {}
-
-
-# Require PyQt5 and compiltion of GUI files via pyuic 
+# Requires PyQt5 and compiltion of GUI files via pyuic 
 from setuptools import setup, Extension
 from setuptools.command.build_py import build_py
-#from pyqt_distutils.build_ui import build_ui
+
+try:
+    from pyqt_distutils.build_ui import build_ui
+except:
+    print("Please install pyqt_distutils")
+    print( "(sudo) pip(3) install pyqt-distutils")
+    exit()
 
 class custom_build_py(build_py):
     def run(self):
         self.run_command('build_ui')
         build_py.run(self)
 
-try:
-    from Cython.Build import cythonize as cythonise
-except ImportError:
-    def cythonise(*args, **kwargs):
-        #from Cython.Build import cythonize
-        #return cythonize(*args, **kwargs)
-        return 
-
-#from distutils.core import setup
-
 setup(name='Akvo',
       version='1.0.5',
       description='Surface nuclear magnetic resonance workbench',
@@ -43,7 +25,10 @@ setup(name='Akvo',
       #setup_requires=['PyQt5'],
       setup_requires=[
         # Setuptools 18.0 properly handles Cython extensions.
-        'PyQt5', 'pyqt_distutils','setuptools>=18.0',
+        #'PyQt', 
+        'pyqt_distutils',
+        'PyQt5',
+        'setuptools>=18.0',
       ],
 #      ext_modules = cythonise("akvo/tressel/*.pyx"), 
 #      build_requires=['cython'],
@@ -65,12 +50,12 @@ setup(name='Akvo',
                   'akvo = akvo.gui.akvoGUI:main',                  
               ],              
           },
+      #cmdclass = cmdclass,
       # for forced build of pyuic
       cmdclass={
           'build_ui': build_ui,
           'build_py': custom_build_py,
       },
-      #cmdclass=cmdclass,
       # Mechanism to include auxiliary files
       include_package_data=True,
       package_data={