Я написал код python, который управляет большим количеством данных, и, следовательно, это занимает много времени. Итак, я узнал, что Китон и я начали менять свой код.

В основном, все, что я делал, - это изменить объявления функций (имя типа cdef (аргументы с типом переменной)), объявить переменные cdef с его типом и объявить классы cdef. Я пишу все .pyx с eclipse, и я компилирую команду python setup.py build_ext --inplace и запускаю ее с помощью eclipse.

Моя проблема в том, что сравнение python с скоростью cython, нет никакой разницы.

Я запускаю команду cython -a <file> чтобы сгенерировать html файл, и есть много желтых строк.

Я не знаю, что я делаю что-то неправильно, я должен включить что-то еще, и я не знаю, как удалить эти желтые строки.

Я просто вставляю несколько строк кода, что часть, которую я хотел бы ускорить, и потому, что код очень длинный.

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main.pyx

'''there are a lot of ndarray objects stored in a file and in this step I get each of them until there are no more items '''
cdef ReadWavePoints (WavePointManagement wavePointManagement, ColumnManagement columnManagement):
        cdef int runReadWavePoints

    wavePointManagement.OpenWavePointFileLoad(wavePointsFile)
    runReadWavePoints = 1

    while runReadWavePoints == 1:
        try:
            wavePointManagement.LoadWavePointFile()
            wavePointManagement.RoundCoordinates()
            wavePointManagement.SortWavePointList()
            GroupColumnsVoxels(wavePointManagement.GetWavePointList(), columnManagement)
        except:
            wavePointManagement.CloseWavePointFile()
            columnManagement.CloseWriteColumnFile()
            break

'''I check which points are in the same XYZ (voxel) and in the same XY (column)'''

cdef GroupColumnsVoxels (object wavePointList, ColumnManagement columnManagement):
    cdef int indexWavePointRef, indexWavePoint
    cdef int saved
    cdef double voxelValue
    cdef int sizeWavePointList

    sizeWavePointList = len(wavePointList)

    indexWavePointRef = 0

    while indexWavePointRef < sizeWavePointList - 1:
        saved = 0
        voxelValue = (wavePointList[indexWavePointRef]).GetValue()
        for indexWavePoint in xrange(indexWavePointRef + 1, len(wavePointList)):
            if (wavePointList[indexWavePointRef]).GetX() == (wavePointList[indexWavePoint]).GetX() and (wavePointList[indexWavePointRef]).GetY() == (wavePointList[indexWavePoint]).GetY():
                if (wavePointList[indexWavePointRef]).GetZ() == (wavePointList[indexWavePoint]).GetZ():
                    if voxelValue < (wavePointList[indexWavePoint]).GetValue():
                        voxelValue = (wavePointList[indexWavePoint]).GetValue()
                else:
                    saved = 1
                    CheckVoxel((wavePointList[indexWavePointRef]).GetX(), (wavePointList[indexWavePointRef]).GetY(), (wavePointList[indexWavePointRef]).GetZ(), voxelValue)
                    indexWavePointRef = indexWavePoint
                    if indexWavePointRef == sizeWavePointList - 1:
                        CheckVoxel((wavePointList[indexWavePointRef]).GetX(), (wavePointList[indexWavePointRef]).GetY(), (wavePointList[indexWavePointRef]).GetZ(), (wavePointList[indexWavePointRef]).GetValue())
                    break
            else:
                saved = 1
                CheckVoxel((wavePointList[indexWavePointRef]).GetX(), (wavePointList[indexWavePointRef]).GetY(), (wavePointList[indexWavePointRef]).GetZ(), voxelValue)
                columnObject = columnInstance.Column((wavePointList[indexWavePointRef]).GetX(), (wavePointList[indexWavePointRef]).GetY())
                columnManagement.AddColumn(columnObject)
                MaximumHeightColumn((wavePointList[indexWavePointRef]).GetX(), (wavePointList[indexWavePointRef]).GetY(), (wavePointList[indexWavePointRef]).GetZ()) 
                indexWavePointRef = indexWavePoint
                break
        if saved == 0:
            CheckVoxel((wavePointList[indexWavePointRef]).GetX(), (wavePointList[indexWavePointRef]).GetY(), (wavePointList[indexWavePointRef]).GetZ(), voxelValue)
            indexWavePointRef = indexWavePoint
    columnObject = columnInstance.Column((wavePointList[indexWavePointRef]).GetX(), (wavePointList[indexWavePointRef]).GetY())
    columnManagement.AddColumn(columnObject)
    MaximumHeightColumn((wavePointList[indexWavePointRef]).GetX(), (wavePointList[indexWavePointRef]).GetY(), (wavePointList[indexWavePointRef]).GetZ())



'''I check if the data stored in a voxel is lower than the new one; if its the case, I store it'''  

cdef CheckVoxel (double X, double Y, double Z, double newValue):
    cdef object bandVoxel, structvalCheckVoxel, out_str
    cdef tuple valueCheckVoxel

    bandVoxel = datasetVoxels.GetRasterBand(int(math.floor(Z/0.3))+1)
    structvalCheckVoxel = bandVoxel.ReadRaster(int(math.floor((X-Xmin)/0.25)), int(math.floor((Ymax-Y)/0.25)), 1, 1, buf_type=gdal.GDT_Float32)
    valueCheckVoxel = struct.unpack('f', structvalCheckVoxel)

    if newValue > valueCheckVoxel[0]:
        out_str = struct.pack('f', newValue)
        bandVoxel.WriteRaster(int(math.floor((X-Xmin)/0.25)), int(math.floor((Ymax-Y)/0.25)), 1, 1, out_str)

'''I check if this point has the highest Z and I store this information'''    
cdef MaximumHeightColumn(double X, double Y, double newZ):
        cdef object bandMetricMaximumHeightColumn, structvalMaximumHeightColumn, out_strMaximumHeightColumn
    cdef tuple valueMaximumHeightColumn

    bandMetricMaximumHeightColumn = datasetMetrics.GetRasterBand(10)
    structvalMaximumHeightColumn = bandMetricMaximumHeightColumn.ReadRaster(int(math.floor((X-Xmin)/0.25)), int(math.floor((Ymax-Y)/0.25)), 1, 1, buf_type=gdal.GDT_Float32)
    valueMaximumHeightColumn = struct.unpack('f', structvalMaximumHeightColumn)

    if newZ > round(valueMaximumHeightColumn[0], 1):
        out_strMaximumHeightColumn = struct.pack('f', newZ)
        bandMetricMaximumHeightColumn.WriteRaster(int(math.floor((X-Xmin)/0.25)), int(math.floor((Ymax-Y)/0.25)), 1, 1, out_strMaximumHeightColumn)

---

WavePointManagement.pyx

'''this class serializes, rounds and sorts the points of each ndarray'''
import cPickle as pickle
import numpy as np
cimport numpy as np
import math

cdef class WavePointManagement(object):
    '''
    This class manages all the points extracted from the waveform
    '''
    cdef object fileObject, wavePointList
    __slots__ = ('wavePointList', 'fileObject')

    def __cinit__(self):
        '''
        Constructor
        '''

        self.fileObject = None
        self.wavePointList = np.array([])

    cdef object GetWavePointList(self):
        return self.wavePointList

    cdef void OpenWavePointFileLoad (self, object fileName):
        self.fileObject = file(fileName, 'rb')

    cdef void LoadWavePointFile (self):
        self.wavePointList = None
        self.wavePointList = pickle.load(self.fileObject)

    cdef void SortWavePointList (self):
        self.wavePointList = sorted(self.wavePointList, key=lambda k: (k.x, k.y, k.z))

    cdef void RoundCoordinates (self):
        cdef int indexPointObject, sizeWavePointList

        for pointObject in self.GetWavePointList():
            pointObject.SetX(round(math.floor(pointObject.GetX()/0.25)*0.25, 2))
            pointObject.SetY(round(math.ceil(pointObject.GetY()/0.25)*0.25, 2))
            pointObject.SetZ(round(math.floor(pointObject.GetZ()/0.3)*0.3, 1))

    cdef void CloseWavePointFile(self):
        self.fileObject.close()

---

setup.py

from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext

import numpy

ext = Extension("main", ["main.pyx"], include_dirs = [numpy.get_include()])

setup (ext_modules=[ext], 
       cmdclass = {'build_ext' : build_ext}
       )

---

test_cython.py

'''this is the file I run with eclipse after compiling'''
from main import main

main()

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Как я могу ускорить этот код?