From 0ef791f9f681450aaaadf544921b927c41d77dd7 2017-04-17 22:28:52
From: Juan C. Valdez <juan.espinoza@jro.igp.gob.pe>
Date: 2017-04-17 22:28:52
Subject: [PATCH] Add C extension for hildebrand_sekhon noise estimation and update requirements versions in setup

---

diff --git a/schainpy/model/data/jrodata.py b/schainpy/model/data/jrodata.py
index bc94ee7..6cd9c1d 100644
--- a/schainpy/model/data/jrodata.py
+++ b/schainpy/model/data/jrodata.py
@@ -9,6 +9,8 @@ import numpy
 import datetime
 
 from jroheaderIO import SystemHeader, RadarControllerHeader
+from schainpy import cSchain
+
 
 def getNumpyDtype(dataTypeCode):
     
@@ -64,41 +66,45 @@ def hildebrand_sekhon(data, navg):
     """
     
     sortdata = numpy.sort(data,axis=None)
-    lenOfData = len(sortdata)
-    nums_min = lenOfData*0.2
-    
-    if nums_min <= 5:
-        nums_min = 5
+#     lenOfData = len(sortdata)
+#     nums_min = lenOfData*0.2
+#     
+#     if nums_min <= 5:
+#         nums_min = 5
+# 
+#     sump = 0.
+#     
+#     sumq = 0.
+#     
+#     j = 0
+#     
+#     cont = 1
+#     
+#     while((cont==1)and(j<lenOfData)):
+#         
+#         sump += sortdata[j]
+#         
+#         sumq += sortdata[j]**2
+#         
+#         if j > nums_min:
+#             rtest = float(j)/(j-1) + 1.0/navg
+#             if ((sumq*j) > (rtest*sump**2)):
+#                 j = j - 1
+#                 sump  = sump - sortdata[j]
+#                 sumq =  sumq - sortdata[j]**2
+#                 cont = 0
+#         
+#         j += 1
+#         
+#     lnoise = sump /j
+# 
+#     return lnoise
+
+    return cSchain.hildebrand_sekhon(sortdata, navg)
 
-    sump = 0.
-    
-    sumq = 0.
-    
-    j = 0
-    
-    cont = 1
-    
-    while((cont==1)and(j<lenOfData)):
-        
-        sump += sortdata[j]
-        
-        sumq += sortdata[j]**2
-        
-        if j > nums_min:
-            rtest = float(j)/(j-1) + 1.0/navg
-            if ((sumq*j) > (rtest*sump**2)):
-                j = j - 1
-                sump  = sump - sortdata[j]
-                sumq =  sumq - sortdata[j]**2
-                cont = 0
-        
-        j += 1
-        
-    lnoise = sump /j
-#     stdv = numpy.sqrt((sumq - lnoise**2)/(j - 1))
-    return lnoise   
 
 class Beam:
+    
     def __init__(self):
         self.codeList = []
         self.azimuthList = []
diff --git a/schainpy/model/proc/extensions.c b/schainpy/model/proc/extensions.c
new file mode 100644
index 0000000..8117e99
--- /dev/null
+++ b/schainpy/model/proc/extensions.c
@@ -0,0 +1,55 @@
+#include <Python.h>
+#include <numpy/arrayobject.h>
+#include <math.h>
+
+static PyObject *hildebrand_sekhon(PyObject *self, PyObject *args);
+
+static PyMethodDef extensionsMethods[] = {
+   { "hildebrand_sekhon", (PyCFunction)hildebrand_sekhon, METH_VARARGS, "get noise with" },
+   { NULL, NULL, 0, NULL }
+};
+
+PyMODINIT_FUNC initcSchain() {
+  Py_InitModule("cSchain", extensionsMethods);
+  import_array();
+}
+
+static PyObject *hildebrand_sekhon(PyObject *self, PyObject *args) {
+   /* Do your stuff here. */
+  double navg;
+  PyObject *data_obj, *data_array;
+
+  if (!PyArg_ParseTuple(args, "Od", &data_obj, &navg)) return NULL;
+  data_array = PyArray_FROM_OTF(data_obj, NPY_FLOAT64, NPY_IN_ARRAY);
+  if (data_array == NULL) {
+      Py_XDECREF(data_array);
+      Py_XDECREF(data_obj);
+      return NULL;
+  }
+  double *sortdata = (double*)PyArray_DATA(data_array);
+  int lenOfData = (int)PyArray_SIZE(data_array) ;
+  double nums_min = lenOfData*0.2;
+  if (nums_min <= 5) nums_min = 5;
+  double sump = 0;
+  double sumq = 0;
+  int j = 0;
+  int cont = 1;
+  double rtest = 0;
+  while ((cont == 1) && (j < lenOfData)) {
+    sump = sump + sortdata[j];
+    sumq = sumq + pow(sortdata[j], 2);
+    if (j > nums_min) {
+      rtest = (double)j/(j-1) + 1/navg;
+      if ((sumq*j) > (rtest*pow(sump, 2))) {
+        j = j - 1;
+        sump = sump - sortdata[j];
+        sumq = sumq - pow(sortdata[j],2);
+        cont = 0;
+      }
+    }
+    j = j + 1;
+  }
+
+  double lnoise = sump / j;
+  return Py_BuildValue("d", lnoise);
+}
diff --git a/setup.py b/setup.py
index a2e379b..a0f14e8 100644
--- a/setup.py
+++ b/setup.py
@@ -1,7 +1,7 @@
 '''
 Created on Jul 16, 2014
 
-@author: @author: Miguel Urco
+@author: Miguel Urco
 '''
 
 from schainpy import __version__
@@ -26,6 +26,7 @@ setup(name="schainpy",
                     'schainpy.gui.viewcontroller',
                     'schainpy.gui.viewer',
                     'schainpy.gui.viewer.windows'},
+        ext_package='schainpy',
         py_modules=[''],
         package_data={'': ['schain.conf.template'],
                       'schainpy.gui.figures': ['*.png','*.jpg'],
@@ -33,13 +34,15 @@ setup(name="schainpy",
         include_package_data=False,
         scripts =['schainpy/gui/schainGUI',
                   'schainpy/scripts/schain'],
+        ext_modules=[Extension("cSchain", ["schainpy/model/proc/extensions.c"])],
         install_requires=[
-                          "scipy >= 0.9.0",
-                          "h5py >= 2.0.1",
-                          "matplotlib >= 1.0.0",
-                          "pyfits >= 2.0.0",
-                          "numpy >= 1.6.0",
-                          "paramiko",
-                          "paho-mqtt"                       
+                          "scipy >= 0.14.0",
+                          "h5py >= 2.2.1",
+                          "matplotlib >= 1.4.2",
+                          "pyfits >= 3.4",
+                          "numpy >= 1.11.2",
+                          "paramiko >= 2.1.2",
+                          "paho-mqtt >= 1.2",
+                          "zmq",
                           ],
       )
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