schain-jc Commit - r1004:3c7daf19daec

0

schainpy/controller.py +22 -17

             import math
             import time
             from multiprocessing import Process, Queue, cpu_count
+            from profilehooks import profile, coverage
             import schainpy
             import schainpy.admin
             from schainpy.model import *
             from time import sleep
             def prettify(elem):
                 """Return a pretty-printed XML string for the Element.
                 """
                     print "Parameter[%s]: name = %s, value = %s, format = %s" %(self.id, self.name, self.value, self.format)
             class OperationConf():
                 id = None
                 name = None
                     parameterObj = self.getParameterObj(parameterName)
-            #         if not parameterObj:
+                #         if not parameterObj:
-            #             return None
+                    #             return None
                     value = parameterObj.getValue()
                     return procUnitObj
+                ## @profile
                 def run(self):
                     is_ok = False
                                                     opId = opConfObj.id,
                                                     )
-            #             total_time = time.time() - ini
+                    #             total_time = time.time() - ini
+                    #
-            #             if total_time > 0.002:
+                    #             if total_time > 0.002:
-            #                 print "%s::%s took %f seconds" %(self.name, opConfObj.name, total_time)
+                    #                 print "%s::%s took %f seconds" %(self.name, opConfObj.name, total_time)
                         is_ok = is_ok or sts
                     return opObj
-            #     def makeXml(self, projectElement):
+                    #     def makeXml(self, projectElement):
+                    #
-            #         procUnitElement = SubElement(projectElement, self.ELEMENTNAME)
+                    #         procUnitElement = SubElement(projectElement, self.ELEMENTNAME)
-            #         procUnitElement.set('id', str(self.id))
+                    #         procUnitElement.set('id', str(self.id))
-            #         procUnitElement.set('name', self.name)
+                    #         procUnitElement.set('name', self.name)
-            #         procUnitElement.set('datatype', self.datatype)
+                    #         procUnitElement.set('datatype', self.datatype)
-            #         procUnitElement.set('inputId', str(self.inputId))
+                    #         procUnitElement.set('inputId', str(self.inputId))
+                    #
-            #         for opConfObj in self.opConfObjList:
+                    #         for opConfObj in self.opConfObjList:
-            #             opConfObj.makeXml(procUnitElement)
+                    #             opConfObj.makeXml(procUnitElement)
                 def readXml(self, upElement):
                     raise NotImplementedError, "Use schainpy.controller_api.ControllerThread instead Project class"
                 def run(self):
                     print

0

schainpy/model/__init__.py +1 -1

             from data import *
             from io import *
             from proc import *
-            from graphics import *
+            #from graphics import *
             from utils import *

0

schainpy/model/graphics/jroplot_data.py +11 -3

             plt.ion()
             func = lambda x, pos: ('%s') %(datetime.datetime.fromtimestamp(x).strftime('%H:%M'))
+            fromtimestamp = lambda x, mintime : (datetime.datetime.utcfromtimestamp(mintime).replace(hour=(x + 5), minute=0) - d1970).total_seconds()
             d1970 = datetime.datetime(1970,1,1)
                     self.xrange = kwargs.get('xrange', 24)
                     self.ymin = kwargs.get('ymin', None)
                     self.ymax = kwargs.get('ymax', None)
-                    self.__MAXNUMY = kwargs.get('decimation', 80)
+                    self.__MAXNUMY = kwargs.get('decimation', 5000)
                     self.throttle_value = 5
                     self.times = []
                     #self.interactive = self.kwargs['parent']
                     self.z = np.array(self.z)
                     for n, ax in enumerate(self.axes):
                         x, y, z = self.fill_gaps(*self.decimate())
-                        xmin = self.min_time
+                        if self.xmin is None:
-                        xmax = xmin+self.xrange*60*60
+                            xmin = self.min_time
+                        else:
+                            xmin = fromtimestamp(int(self.xmin), self.min_time)
+                        if self.xmax is None:
+                            xmax = xmin + self.xrange*60*60
+                        else:
+                            xmax = xmin + (self.xmax - self.xmin) * 60 * 60
                         self.zmin = self.zmin if self.zmin else np.min(self.z)
                         self.zmax = self.zmax if self.zmax else np.max(self.z)
                         if ax.firsttime:

0

schainpy/model/io/jroIO_base.py +4 -7

                         return 0
             #         if self.online:
             #             self.__jumpToLastBlock()
-                    print 'xxxx'
                     if self.flagIsNewFile:
                         self.lastUTTime = self.basicHeaderObj.utc
                         if not(self.setNextFile()):
                             return 0
                         else:
                             return 1
-                    print 'xxxx'
                     #if self.server is None:
                     currentSize = self.fileSize - self.fp.tell()
                     neededSize = self.processingHeaderObj.blockSize + self.basicHeaderSize
                 def readNextBlock(self):
                     #Skip block out of startTime and endTime
                     while True:
-                        print 'cxxxx'
                         if not(self.__setNewBlock()):
                             print 'returning'
                             return 0
-                        print 'dxxx'
                         if not(self.readBlock()):
                             return 0

0

schainpy/model/io/jroIO_voltage.py 0 -2

                         Si un bloque leido no es un bloque valido
                     """
-                    print 'READ BLOCK'
                     # if self.server is not None:
                     #     self.zBlock = self.receiver.recv()
                     #     self.zHeader = self.zBlock[:24]
                     try:
                         junk = junk.reshape( (self.processingHeaderObj.profilesPerBlock, self.processingHeaderObj.nHeights, self.systemHeaderObj.nChannels) )
-                        print'junked'
                     except:
                         #print "The read block (%3d) has not enough data" %self.nReadBlocks

0

schainpy/model/proc/extensions.c +85 -4

@@ -1,12 +1,22
		1	#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
		2	#define NUM_CPY_THREADS 8
1	#include <Python.h>	3	#include <Python.h>
2	#include <numpy/arrayobject.h>	4	#include <numpy/arrayobject.h>
3	#include <math.h>	5	#include <math.h>
		6	#include <complex.h>
		7	#include <time.h>
4		8
		9	// void printArr(int *array);
5	static PyObject hildebrand_sekhon(PyObject self, PyObject *args);	10	static PyObject hildebrand_sekhon(PyObject self, PyObject *args);
		11	static PyObject correlateByBlock(PyObject self, PyObject *args);
		12	#ifndef PyMODINIT_FUNC /* declarations for DLL import/export */
		13	#define PyMODINIT_FUNC void
		14	#endif
6		15
7	static PyMethodDef extensionsMethods[] = {	16	static PyMethodDef extensionsMethods[] = {
8	{ "hildebrand_sekhon", (PyCFunction)hildebrand_sekhon, METH_VARARGS, "get noise with" },	17	{ "correlateByBlock", (PyCFunction)correlateByBlock, METH_VARARGS, "get correlation by block" },
9	{ NULL, NULL, 0, NULL }	18	{ "hildebrand_sekhon", (PyCFunction)hildebrand_sekhon, METH_VARARGS, "get noise with hildebrand_sekhon" },
		19	{ NULL, NULL, 0, NULL }
10	};	20	};
11		21
12	PyMODINIT_FUNC initcSchain() {	22	PyMODINIT_FUNC initcSchain() {
@@ -14,13 +24,83 PyMODINIT_FUNC initcSchain() {
14	import_array();	24	import_array();
15	}	25	}
16		26
		27	static PyObject correlateByBlock(PyObject self, PyObject *args) {
		28
		29	// int x = (int) malloc(4000000 * 216 * sizeof(int));;
		30	// int a = 5;
		31	// x = &a;
		32	// int b = 6;
		33	// x = &b;
		34	// printf("Antes de imprimir x \n");
		35	// printf("%d \n", x[0]);
		36
		37	PyObject data_obj1, data_obj2;
		38	PyArrayObject data_array1, data_array2, correlateRow, out, dataRow, codeRow; //, ,
		39	int mode;
		40
		41	if (!PyArg_ParseTuple(args, "OOi", &data_obj1, &data_obj2, &mode)) return NULL;
		42
		43	data_array1 = (PyArrayObject *) PyArray_FROM_OTF(data_obj1, NPY_COMPLEX128, NPY_ARRAY_DEFAULT);
		44	data_array2 = (PyArrayObject *) PyArray_FROM_OTF(data_obj2, NPY_FLOAT64, NPY_ARRAY_DEFAULT);
		45
		46	npy_intp dims[1];
		47	dims[0] = 200;
		48	npy_intp dims_code[1];
		49	dims_code[0] = 16;
		50
		51	double complex * dataRaw;
		52	double * codeRaw;
		53	dataRaw = (double complex*) PyArray_DATA(data_array1);
		54	codeRaw = (double *) PyArray_DATA(data_array2);
		55	double complex ** outC = malloc(40000200sizeof(double complex));
		56	int i;
		57
		58	clock_t start = clock();
		59	for(i=0; i<40000; i++){
		60	// codeRow = PyArray_SimpleNewFromData(1, dims_code, NPY_FLOAT64, codeRaw + 16 * i);
		61	// dataRow = PyArray_SimpleNewFromData(1, dims, NPY_COMPLEX128, dataRaw + 200 * i);
		62	// Py_INCREF(codeRow);
		63	// Py_INCREF(dataRow);
		64	// PyArray_ENABLEFLAGS(codeRow, NPY_ARRAY_OWNDATA);
		65	// PyArray_ENABLEFLAGS(dataRow, NPY_ARRAY_OWNDATA);
		66	correlateRow = (PyArrayObject ) PyArray_Correlate2(PyArray_SimpleNewFromData(1, dims_code, NPY_FLOAT64, codeRaw + 16 i), PyArray_SimpleNewFromData(1, dims, NPY_COMPLEX128, dataRaw + 200 * i), (npy_intp) 2);
		67	//Py_INCREF(correlateRow);
		68	// PyArray_ENABLEFLAGS(correlateRow, NPY_ARRAY_OWNDATA);
		69	memcpy(outC + 200i, (double complex) PyArray_DATA(correlateRow), 200 * sizeof(double complex));
		70
		71	Py_DECREF(correlateRow);
		72	// Py_DECREF(codeRow);
		73	// Py_DECREF(dataRow);
		74	}
		75	clock_t end = clock();
		76	float seconds = (float)(end - start) / CLOCKS_PER_SEC;
		77	printf("%f", seconds);
		78	//
		79	npy_intp dimsret[2];
		80	dimsret[0] = 40000;
		81	dimsret[1] = 200;
		82	out = PyArray_SimpleNewFromData(2, dimsret, NPY_COMPLEX128, outC);
		83	PyArray_ENABLEFLAGS(out, NPY_ARRAY_OWNDATA);
		84	//Py_INCREF(out);
		85	Py_DECREF(data_array1);
		86	Py_DECREF(data_array2);
		87	// PyArray_DebugPrint(out);
		88	// Py_DECREF(data_obj2);
		89	// Py_DECREF(data_obj1);
		90	// Py_DECREF(codeRow);
		91	// Py_DECREF(dataRow);
		92	// free(dataRaw);
		93	// free(codeRaw);
		94
		95	return PyArray_Return(out);
		96	}
		97
17	static PyObject hildebrand_sekhon(PyObject self, PyObject *args) {	98	static PyObject hildebrand_sekhon(PyObject self, PyObject *args) {
18	/* Do your stuff here. */
19	double navg;	99	double navg;
20	PyObject data_obj, data_array;	100	PyObject data_obj, data_array;
21		101
22	if (!PyArg_ParseTuple(args, "Od", &data_obj, &navg)) return NULL;	102	if (!PyArg_ParseTuple(args, "Od", &data_obj, &navg)) return NULL;
23	data_array = PyArray_FROM_OTF(data_obj, NPY_FLOAT64, NPY_~~IN_~~ARRAY);	103	data_array = PyArray_FROM_OTF(data_obj, NPY_FLOAT64, NPY_ARRAY_DEFAULT);
24	if (data_array == NULL) {	104	if (data_array == NULL) {
25	Py_XDECREF(data_array);	105	Py_XDECREF(data_array);
26	Py_XDECREF(data_obj);	106	Py_XDECREF(data_obj);
@@ -56,3 +136,4 static PyObject hildebrand_sekhon(PyObject self, PyObject *args) {
56		136
57	return Py_BuildValue("d", lnoise);	137	return Py_BuildValue("d", lnoise);
58	}	138	}
		139

0

schainpy/model/proc/jroproc_voltage.py +36 -9

             import sys
             import numpy
+            from profilehooks import profile
             from scipy import interpolate
+            from schainpy import cSchain
             from jroproc_base import ProcessingUnit, Operation
             from schainpy.model.data.jrodata import Voltage
+            from time import time
             class VoltageProc(ProcessingUnit):
                     self.times = None
                     self.osamp = None
-            #         self.__setValues = False
+                #         self.__setValues = False
                     self.isConfig = False
                 def setup(self, code, osamp, dataOut):
                     return self.datadecTime
+                #@profile
+                def oldCorrelate(self, i, data, code_block):
+                    profilesList = xrange(self.__nProfiles)
+                    for j in profilesList:
+                            self.datadecTime[i,j,:] = numpy.correlate(data[i,j,:], code_block[j,:], mode='full')[self.nBaud-1:]
+                @profile
                 def __convolutionByBlockInTime(self, data):
                     repetitions = self.__nProfiles / self.nCode
                     junk = numpy.lib.stride_tricks.as_strided(self.code, (repetitions, self.code.size), (0, self.code.itemsize))
                     junk = junk.flatten()
                     code_block = numpy.reshape(junk, (self.nCode*repetitions, self.nBaud))
-                    for i in range(self.__nChannels):
-                        for j in range(self.__nProfiles):
+                    # def toVectorize(a,b):
-                            print self.datadecTime[i,j,:].shape
+                    #     return numpy.correlate(a,b, mode='full')
-                            print numpy.correlate(data[i,j,:], code_block[j,:], mode='full')[self.nBaud-1:].shape
+                    # vectorized = numpy.vectorize(toVectorize, signature='(n),(m)->(k)')
-                            self.datadecTime[i,j,:] = numpy.correlate(data[i,j,:], code_block[j,:], mode='full')[self.nBaud-1:]
+                    a = time()
+                    for i in range(self.__nChannels):
+                    #     self.datadecTime[i,:,:] = numpy.array([numpy.correlate(data[i,j,:], code_block[j,:], mode='full')[self.nBaud-1:] for j in profilesList ])
+                        # def func(i, j):
+                        #     self.datadecTime[i,j,:] = numpy.correlate(data[i,j,:], code_block[j,:], mode='full')[self.nBaud-1:]
+                        # map(lambda j: func(i, j), range(self.__nProfiles))
+                        #print data[i,:,:].shape
+                        # self.datadecTime[i,:,:] = vectorized(data[i,:,:], code_block[:,:])[:,self.nBaud-1:]
+                        self.oldCorrelate(i, data, code_block)
+                        print self.datadecTime[i,:,:]
+                        # print data[i,:,:]
+                        # print cSchain.correlateByBlock(data[i,:,:], code_block, 2)
+                        self.datadecTime[i,:,:] = cSchain.correlateByBlock(data[i,:,:], code_block, 2)
+                        print self.datadecTime[i,:,:]
+                        #print self.datadecTime[i,:,:].shape
+                    print time() - a
                     return self.datadecTime
                 def __convolutionByBlockInFreq(self, data):
                     return data
                 def run(self, dataOut, code=None, nCode=None, nBaud=None, mode = 0, osamp=None, times=None):
                     if dataOut.flagDecodeData:
                         print "Fail decoding: Code is not defined."
                         return
+                    self.__nProfiles = dataOut.nProfiles
                     datadec = None
                     if mode == 3:
                         mode = 0

0

schainpy/scripts/JASMET30_MetDet.py +3 -3

             # path = '/mnt/jars/2016_08/NOCHE'
             # path = '/media/joscanoa/DATA_JASMET/JASMET/2016_08/DIA'
             # path = '/media/joscanoa/DATA_JASMET/JASMET/2016_08/NOCHE'
-            path = '/media/nanosat/NewVolumen/JASMET/2016_08/DIA'
+            path = '/home/nanosat/data/jasmet'
             #Path para los graficos
             pathfig = os.path.join(os.environ['HOME'],'Pictures/JASMET30/201608/graphics')
             pathfile = os.path.join(os.environ['HOME'],'Pictures/JASMET30/201608/meteor')
             #Fechas para busqueda de archivos
-            startDate = '2016/08/29'
+            startDate = '2010/08/29'
-            endDate = '2016/09/11'
+            endDate = '2017/09/11'
             #Horas para busqueda de archivos
             startTime = '00:00:00'
             endTime = '23:59:59'

0

schainpy/scripts/schain.xml +1 -1

	@@ -1,1 +1,1
	1	<Project description="JASMET Wind Estimation" id="005" name="script05"><ReadUnit datatype="ParamReader" id="51" inputId="0" name="ParamReader"><Operation id="511" name="run" priority="1" type="self"><Parameter format="str" id="5111" name="datatype" value="ParamReader" /><Parameter format="str" id="5112" name="path" value="/home/nanosat/Pictures/JASMET30_mp/201608/meteor" /><Parameter format="date" id="5113" name="startDate" value="2016/08/29" /><Parameter format="date" id="5114" name="endDate" value="2016/09/11" /><Parameter format="time" id="5115" name="startTime" value="00:00:00" /><Parameter format="time" id="5116" name="endTime" value="23:59:59" /><Parameter format="int" id="5118" name="walk" value="1" /></Operation></ReadUnit><ProcUnit datatype="ParametersProc" id="52" inputId="51" name="ParametersProc"><Operation id="521" name="run" priority="1" type="self" /><Operation id="522" name="CorrectSMPhases" priority="2" type="other"><Parameter format="floatlist" id="5221" name="phaseOffsets" value="-5.86, -0.93, -7.29, 23.35" /></Operation><Operation id="523" name="SkyMapPlot" priority="3" type="other"><Parameter format="int" id="5231" name="id" value="1" /><Parameter format="str" id="5232" name="wintitle" value="Sky Map" /><Parameter format="bool" id="5233" name="save" value="1" /><Parameter format="str" id="5234" name="figpath" value="/home/nanosat/Pictures/JASMET30_mp/201608/graphics" /><Parameter format="int" id="5235" name="ftp" value="1" /><Parameter format="int" id="5236" name="exp_code" value="15" /><Parameter format="int" id="5237" name="sub_exp_code" value="1" /><Parameter format="int" id="5238" name="tmin" value="0" /><Parameter format="int" id="5239" name="tmax" value="24" /></Operation><Operation id="524" name="WindProfiler" priority="4" type="other"><Parameter format="str" id="5241" name="technique" value="Meteors" /><Parameter format="float" id="5242" name="nHours" value="1" /><Parameter format="float" id="5243" name="hmin" value="70" /><Parameter format="float" id="5244" name="hmax" value="120" /></Operation><Operation id="525" name="WindProfilerPlot" priority="5" type="other"><Parameter format="int" id="5251" name="id" value="2" /><Parameter format="str" id="5252" name="wintitle" value="Wind Profiler" /><Parameter format="bool" id="5253" name="save" value="1" /><Parameter format="str" id="5254" name="figpath" value="/home/nanosat/Pictures/JASMET30_mp/201608/graphics" /><Parameter format="int" id="5255" name="zmin" value="-140" /><Parameter format="int" id="5256" name="zmax" value="140" /><Parameter format="float" id="5257" name="xmin" value="0" /><Parameter format="float" id="5258" name="xmax" value="24" /><Parameter format="float" id="5259" name="ymin" value="70" /><Parameter format="float" id="5260" name="ymax" value="110" /></Operation><Operation id="526" name="ParamWriter" priority="6" type="other"><Parameter format="str" id="5261" name="path" value="/home/nanosat/Pictures/JASMET30_mp/201608/phase" /><Parameter format="int" id="5262" name="blocksPerFile" value="1000" /><Parameter format="list" id="5263" name="metadataList" value="type,outputInterval,timeZone" /><Parameter format="list" id="5264" name="dataList" value="data_output,utctime" /></Operation></ProcUnit></Project> No newline at end of file		1	<Project description="JASMET Meteor Detection" id="002" name="script02"><ReadUnit datatype="VoltageReader" id="21" inputId="0" name="VoltageReader"><Operation id="211" name="run" priority="1" type="self"><Parameter format="str" id="2111" name="datatype" value="VoltageReader" /><Parameter format="str" id="2112" name="path" value="/home/nanosat/data/jasmet" /><Parameter format="date" id="2113" name="startDate" value="2010/08/29" /><Parameter format="date" id="2114" name="endDate" value="2017/09/11" /><Parameter format="time" id="2115" name="startTime" value="00:00:00" /><Parameter format="time" id="2116" name="endTime" value="23:59:59" /><Parameter format="int" id="2118" name="delay" value="30" /><Parameter format="int" id="2119" name="blocktime" value="100" /><Parameter format="int" id="2120" name="getblock" value="1" /><Parameter format="int" id="2121" name="walk" value="1" /><Parameter format="int" id="2122" name="online" value="0" /></Operation><Operation id="212" name="printNumberOfBlock" priority="2" type="self" /></ReadUnit><ProcUnit datatype="VoltageProc" id="22" inputId="21" name="VoltageProc"><Operation id="221" name="run" priority="1" type="self" /><Operation id="222" name="selectChannels" priority="2" type="self"><Parameter format="intlist" id="2221" name="channelList" value="0,1,2,3,4" /></Operation><Operation id="223" name="setRadarFrequency" priority="3" type="self"><Parameter format="float" id="2231" name="frequency" value="30.e6" /></Operation><Operation id="224" name="interpolateHeights" priority="4" type="self"><Parameter format="int" id="2241" name="topLim" value="73" /><Parameter format="int" id="2242" name="botLim" value="71" /></Operation><Operation id="225" name="Decoder" priority="5" type="other" /><Operation id="226" name="CohInt" priority="6" type="other"><Parameter format="int" id="2261" name="n" value="2" /></Operation></ProcUnit><ProcUnit datatype="ParametersProc" id="23" inputId="22" name="ParametersProc"><Operation id="231" name="run" priority="1" type="self" /><Operation id="232" name="SMDetection" priority="2" type="other"><Parameter format="float" id="2321" name="azimuth" value="45" /><Parameter format="float" id="2322" name="hmin" value="60" /><Parameter format="float" id="2323" name="hmax" value="120" /></Operation><Operation id="233" name="ParamWriter" priority="3" type="other"><Parameter format="str" id="2331" name="path" value="/home/nanosat/Pictures/JASMET30/201608/meteor" /><Parameter format="int" id="2332" name="blocksPerFile" value="1000" /><Parameter format="list" id="2333" name="metadataList" value="type,heightList,paramInterval,timeZone" /><Parameter format="list" id="2334" name="dataList" value="data_param,utctime" /><Parameter format="int" id="2335" name="mode" value="2" /></Operation></ProcUnit></Project> No newline at end of file

0

setup.py +8 -1

             from schainpy import __version__
             from setuptools import setup, Extension
+            import numpy
             setup(name="schainpy",
                   version=__version__,
                     ],
                   },
                   scripts=['schainpy/gui/schainGUI'],
-                  ext_modules=[Extension("cSchain", ["schainpy/model/proc/extensions.c"], include_dirs=[numpy.get_include()])],
+                  ext_modules=[
+                      Extension("cSchain",
+                        ["schainpy/model/proc/extensions.c"],
+                        include_dirs=[numpy.get_include()],
+                        #extra_compile_args=['-Werror'],
+                      )
+                    ],
                   install_requires=[
                                   "scipy >= 0.14.0",
                                   "h5py >= 2.2.1",

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schainpy/scripts/150km_January_longPulse.py removed 0 -185

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schainpy/scripts/150km_jicamarca.xml removed 0 -61

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schainpy/scripts/JASMET30_Online_spc.py removed 0 -118

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