Merge branch 'py3k' into develop

        Comment a print statement in macroNode, which was put in after
2to3.

.gitignore

@@ -5,6 +5,7 @@
 *.so
 *.o
 *.DS_Store
+VERSION
 build/
 /node/
 /local/

bin/gpi_launch

@@ -1,4 +1,4 @@
-#!/usr/bin/env python # DEV
+#!/usr/bin/env python
 
 #    Copyright (C) 2014  Dignity Health
 #

bin/gpi_update

@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+#    Copyright (C) 2014  Dignity Health
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU Lesser General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU Lesser General Public License for more details.
+#
+#    You should have received a copy of the GNU Lesser General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+#    NO CLINICAL USE.  THE SOFTWARE IS NOT INTENDED FOR COMMERCIAL PURPOSES
+#    AND SHOULD BE USED ONLY FOR NON-COMMERCIAL RESEARCH PURPOSES.  THE
+#    SOFTWARE MAY NOT IN ANY EVENT BE USED FOR ANY CLINICAL OR DIAGNOSTIC
+#    PURPOSES.  YOU ACKNOWLEDGE AND AGREE THAT THE SOFTWARE IS NOT INTENDED FOR
+#    USE IN ANY HIGH RISK OR STRICT LIABILITY ACTIVITY, INCLUDING BUT NOT
+#    LIMITED TO LIFE SUPPORT OR EMERGENCY MEDICAL OPERATIONS OR USES.  LICENSOR
+#    MAKES NO WARRANTY AND HAS NOR LIABILITY ARISING FROM ANY USE OF THE
+#    SOFTWARE IN ANY HIGH RISK OR STRICT LIABILITY ACTIVITIES.
+
+import sys, os
+
+# Check for Anaconda PREFIX, or assume that THIS file location is the CWD.
+GPI_PREFIX = '/opt/anaconda1anaconda2anaconda3' # ANACONDA
+if GPI_PREFIX == '/opt/'+''.join(['anaconda'+str(i) for i in range(1,4)]):
+    GPI_PREFIX, _ = os.path.split(os.path.dirname(os.path.realpath(__file__)))
+
+GPI_LIB_DIR = os.path.join(GPI_PREFIX, 'lib')
+if GPI_LIB_DIR not in sys.path:
+    sys.path.insert(0, GPI_LIB_DIR)
+
+# gpi
+from gpi import update
+
+if __name__ == '__main__':
+    update.update()

gpi_py3k_env.yml

@@ -0,0 +1,35 @@
+name: py3k
+dependencies:
+- astyle=2.05.1=0
+- eigen=3.2.5=0
+- fftw=3.3.4=0
+- freetype=2.5.2=2
+- gpi=0.6.0=py3k
+- h5py=2.5.0=np19py35_3
+- hdf5=1.8.15.1=1
+- libpng=1.6.17=0
+- matplotlib=1.4.3=np19py35_3
+- numpy=1.9.2=py35_0
+- openssl=1.0.1k=1
+- pip=7.1.2=py35_0
+- psutil=3.2.0=py35_0
+- pyopengl=3.1.1a1=np19py35_0
+- pyparsing=2.0.3=py35_0
+- pyqt=4.11.3=py35_0
+- python=3.5.0=0
+- python-dateutil=2.4.2=py35_0
+- pytz=2015.4=py35_0
+- qt=4.8.6=3
+- readline=6.2=2
+- scipy=0.16.0=np19py35_1
+- setuptools=18.1=py35_0
+- sip=4.16.5=py35_0
+- six=1.9.0=py35_0
+- sqlite=3.8.4.1=1
+- tk=8.5.18=0
+- wheel=0.24.0=py35_0
+- xz=5.0.5=0
+- zlib=1.2.8=0
+- pip:
+  - qimage2ndarray==1.5
+

include/PyFI/PyFIArray_WrappedNUMPY.cpp

@@ -116,8 +116,8 @@ void printArray(Array<T> &in)
 {
     string code;
     code = "def func(in1):\n"
-           "    print type(in1), in1.dtype, in1.shape\n"
-           "    print in1\n";
+           "    print(type(in1), in1.dtype, in1.shape)\n"
+           "    print(in1)\n";
     PyCallable printer(code);
     printer.SetArg_Array(&in);
     printer.Run();

include/PyFI/PyFIMacros.h

@@ -110,26 +110,36 @@ inline T __PYFI_itself(T arg)
 #define PYFI_FUNCDESC_TEMPLATE(_nam, _tmpl, _desc) { #_nam "_" #_tmpl, (PyCFunction) __PYFI_itself(_nam <_tmpl>), METH_VARARGS|METH_KEYWORDS, _desc }
 #define PYFI_FUNCDESC_TERM() {NULL, NULL, 0, NULL}
 
+#define PYFI_METHOD_TABLE(_nam_str) static struct PyModuleDef __pyfimstruct = { PyModuleDef_HEAD_INIT, _nam_str, NULL, -1, Methods };
+
+/* avoid this numpy macro return issue */
+void *numpy_import_array(void)
+{
+    import_array();
+    return NULL;
+}
+
 /* PyMODINIT_FUNC stringifications
  */
 #define STR_MOD_NAME1(_x) #_x
 #define STR_MOD_NAME(_x) STR_MOD_NAME1(_x)
-#define MAKE_FN_NAME(_x) PyMODINIT_FUNC init ## _x (void)
+#define MAKE_FN_NAME(_x) PyMODINIT_FUNC PyInit_ ## _x (void)
 #define FUNCTION_NAME(_x) MAKE_FN_NAME(_x)
 #define PYFI_MODINIT()      \
     FUNCTION_NAME(MOD_NAME) \
     {                       \
         PyObject *m;        \
-        m = Py_InitModule(STR_MOD_NAME(MOD_NAME), Methods); \
+        m = PyModule_Create(&__pyfimstruct); \
         if (m == NULL)      \
-            return;         \
-        import_array();     \
+            return NULL;         \
+        numpy_import_array();     \
+        return m; \
     }
 
 
 /* further simplify mod delcarations */
 #define PYFI_LIST_START_ PYFI_FUNCLIST = {
-#define PYFI_LIST_END_   PYFI_FUNCDESC_TERM() }; PYFI_MODINIT();
+#define PYFI_LIST_END_   PYFI_FUNCDESC_TERM() }; PYFI_METHOD_TABLE(STR_MOD_NAME(MOD_NAME)); PYFI_MODINIT();
 #define PYFI_DESC(_nam, _desc) PYFI_FUNCDESC(_nam, _desc),
 #define PYFI_T_DESC(_nam, _tmpl, _desc) PYFI_FUNCDESC_TEMPLATE(_nam, _tmpl, _desc),
 

include/PyFI/PyFunctionIF.cpp

@@ -381,15 +381,15 @@ void Parm_STRING::Convert_In(void)
     }
     else
     {
-        local_val = string(PyString_AsString(pyobj_ptr));
+        local_val = string(PyUnicode_AS_DATA(pyobj_ptr));
         val = (void *)&local_val;
     }
 }
 
 void Parm_STRING::Convert_Out(void)
 {
     /* new ref */
-    pyobj_ptr = PyString_FromString((*(string *)val).c_str());
+    pyobj_ptr = PyUnicode_FromString((*(string *)val).c_str());
 }
 
 /**** DOUBLE ****/
@@ -1403,6 +1403,12 @@ class PyCallable
                 delete *_arrays_itr;
         }
 
+        void *__import_array(void)
+        {
+            import_array(); /* required for using numpy arrays */
+            return NULL;
+        }
+
         /* 1) check if python has been initialized
         * 2) initialize numpy
         */
@@ -1412,7 +1418,7 @@ class PyCallable
             if (Py_IsInitialized() == 0)
             {
                 Py_Initialize();
-                import_array(); /* required for using numpy arrays */
+                __import_array(); /* required for using numpy arrays */
             }
             /*
             else
@@ -1681,7 +1687,7 @@ class PyCallable
             }
 
             /* convert to python string */
-            PyObject *pItem = PyString_FromString(in.c_str());
+            PyObject *pItem = PyUnicode_FromString(in.c_str());
 
             /* add to list */
             if (PyList_Append(_pArgList, pItem) != _PYCALLABLE_SUCCESS)
@@ -1845,7 +1851,7 @@ class PyCallable
                 * calling function, not sure what the behavior will
                 * be for this as it is. */
                 _PYFI_PYCALLABLE_ACQUIRE_GIL
-                string out = PyString_AsString(curVal);
+                string out = PyUnicode_AS_DATA(curVal);
                 _PYFI_PYCALLABLE_RELEASE_GIL
                 return(out);
             }

include/PyFI/embedded_script.py

@@ -26,10 +26,10 @@
 import numpy as np
 
 def script(in1, in2, in3):
-    print "start script"
-    print "in1:", in1, type(in1)
-    print "in2:", in2, type(in2)
-    print "in array: ", in3, type(in3)
-    print "end script"
+    print("start script")
+    print(("in1:", in1, type(in1)))
+    print(("in2:", in2, type(in2)))
+    print(("in array: ", in3, type(in3)))
+    print("end script")
     return (0, 1, np.array([1,2,3],dtype=np.float32))
 

include/PyFI/template_PyMOD.cpp

@@ -170,7 +170,9 @@ PYFI_FUNC(IFtest2)
 
     Array<float> arr_copy(*arr);
 
+    cout << "Printing using PyFI" << endl;
     coutv(arr_copy);
+    cout << "Printing using Numpy" << endl;
     Numpy::printArray(arr_copy);
 
     //arr_copy(1000);
@@ -222,7 +224,7 @@ PYFI_FUNC(IFtest2)
     coutv(*out);
 
     /* write your own function */
-    PyCallable mycode("def func(in1):\n  print \'in1\', in1\n  return 1\n");
+    PyCallable mycode("def func(in1):\n  print(\'in1\', in1)\n  return 1\n");
     mycode.SetArg_Long(777);
     coutv(mycode.GetReturn_Long());
 

include/PyFI/template_test.py

@@ -43,27 +43,27 @@
 
 
 # PYCALLABLE
-A = np.array(range(4), dtype=np.float32)
+A = np.array(list(range(4)), dtype=np.float32)
 A.shape = [2,2]
-print "A:", A
-print "Ainv:", npl.pinv(A)
+print("A:", A)
+print("Ainv:", npl.pinv(A))
 
-x = np.array(range(24), dtype=np.float32)
+x = np.array(list(range(24)), dtype=np.float32)
 x.shape = [4,3,2]
 
-print x
+print(x)
 
-print "matmult (PYTHON)"
-print "A: ", A
-print "AdotA: ", np.dot(A,A)
+print("matmult (PYTHON)")
+print("A: ", A)
+print("AdotA: ", np.dot(A,A))
 
 st = time.time()
 aarr, c = temp.IFtest2(x)
-print "IFtest time: ", time.time()-st
+print("IFtest time: ", time.time()-st)
 
-print c
+print(c)
 
-print "aarr:", aarr
+print("aarr:", aarr)
 
 
 temp.math_double()
@@ -76,16 +76,16 @@
 # testing the PyFI interface.
 def test(thetest, name):
     if thetest:
-        print '\t-'+name+' passed'
+        print('\t-'+name+' passed')
         return 1
     else:
-        print '\t-'+name+' failed'
+        print('\t-'+name+' failed')
         return 0
 
 
 
 
-print "\n\nInterface testing..."
+print("\n\nInterface testing...")
 mi = 111
 mf = 111.111
 ms = 'hello from python'
@@ -139,8 +139,8 @@ def test(thetest, name):
 cnt += test((kla == al).all(), 'mykwlarr') 
 tot += 1
 
-print '\nTest Summary:'
+print('\nTest Summary:')
 if cnt == tot:
-    print '\tSUCCESS: '+str(cnt)+'/'+str(tot)
+    print('\tSUCCESS: '+str(cnt)+'/'+str(tot))
 else:
-    print '\tFAILED: '+str(cnt)+'/'+str(tot)
+    print('\tFAILED: '+str(cnt)+'/'+str(tot))

include/PyFI/test.py

@@ -31,5 +31,5 @@
 x = np.array([1,2,3,4], dtype=np.float32)
 y = bm.add_one(x)
 
-print 'x: ', x
-print 'y: ', y
+print('x: ', x)
+print('y: ', y)

launch/GPI.app/Contents/Info.plist

@@ -7,7 +7,7 @@
 	<key>AMStayOpen</key>
 	<false/>
 	<key>BuildMachineOSBuild</key>
-	<string>12E39</string>
+	<string>11E53</string>
 	<key>CFBundleDevelopmentRegion</key>
 	<string>English</string>
 	<key>CFBundleDocumentTypes</key>
@@ -46,21 +46,21 @@
 	<key>CFBundleURLTypes</key>
 	<array/>
 	<key>CFBundleVersion</key>
-	<string>346</string>
+	<string>339.2</string>
 	<key>DTCompiler</key>
 	<string>com.apple.compilers.llvm.clang.1_0</string>
 	<key>DTPlatformBuild</key>
-	<string>4F250</string>
+	<string>11E53</string>
 	<key>DTPlatformVersion</key>
 	<string>GM</string>
 	<key>DTSDKBuild</key>
-	<string>12E39</string>
+	<string>11E53</string>
 	<key>DTSDKName</key>
 	<string></string>
 	<key>DTXcode</key>
-	<string>0440</string>
+	<string>0410</string>
 	<key>DTXcodeBuild</key>
-	<string>4F250</string>
+	<string>11E53</string>
 	<key>LSMinimumSystemVersion</key>
 	<string>10.5</string>
 	<key>LSMinimumSystemVersionByArchitecture</key>