Numpy 内存错误

如何解决Numpy 内存错误

我正在堆叠大量栅格来计算 2 个月卫星数据的中位数，当数据具有 10m 分辨率时，这很有效。

因为我在 20m 分辨率数据上运行相同的函数（-> 光栅应该是列和行的 1/2），所以我得到了内存错误。

除了初始卫星数据的波段之外，我没有更改任何内容。

我知道数据量很大，因为时间长，空间范围也很大，但它仍然适用于较小的分辨率。

我正在 Anaconda 中使用 python3.6 开发虚拟机，该机器有 128 GB RAM 和 16 个 VCPus。

错误信息：

<class 'numpy.core._exceptions._ArrayMemoryError'>,((563,256,55296),dtype('int64')) -> always
<class 'MemoryError'>,((506,54528),dtype('bool')) -> sometimes

以下是合并代码，其中 file_list 是链接：

import os

from typing import List
from osgeo import gdal
import numpy as np
import glob


def build_vrt(vrt: str,files: List[str],resample_name: str) -> None:
    """builds .vrt file which will hold information needed for overlay
    Args:
        vrt (:obj:`string`): name of vrt file,which will be created
        files (:obj:`list`): list of file names for merging
        resample_name (:obj:`string`): name of resampling method
    """

    options = gdal.BuildVRTOptions(srcNodata=-9999)
    gdal.BuildVRT(destName=vrt,srcDSOrSrcDSTab=files,options=options)
    add_pixel_fn(vrt,resample_name)


def add_pixel_fn(filename: str,resample_name: str) -> None:
    """inserts pixel-function into vrt file named 'filename'
    Args:
        filename (:obj:`string`): name of file,into which the function will be inserted
        resample_name (:obj:`string`): name of resampling method
    """

    header = """  <VRTRasterBand dataType="uInt16" band="1" subClass="VRTDerivedRasterBand">"""
    contents = """
    <PixelFunctionType>{0}</PixelFunctionType>
    <PixelFunctionLanguage>Python</PixelFunctionLanguage>
    <PixelFunctionCode><![CDATA[{1}]]>
    </PixelFunctionCode>"""

    lines = open(filename,'r').readlines()
    lines[3] = header  # FIX ME: 3 is a hand constant
    lines.insert(4,contents.format(resample_name,get_resample(resample_name)))
    open(filename,'w').write("".join(lines))


def get_resample(name: str) -> str:
    """retrieves code for resampling method
    Args:
        name (:obj:`string`): name of resampling method
    Returns:
        method :obj:`string`: code of resample method
    """

    methods = {
        "median":
        """
import numpy as np
    def median(in_ar,out_ar,xoff,yoff,xsize,ysize,raster_xsize,raster_ysize,buf_radius,gt,**kwargs):
        div = np.zeros((len(in_ar),in_ar[0].shape[0],in_ar[0].shape[1]),dtype=np.float16)
        for i in range(len(in_ar)):
            div[i,:,:] = np.where(in_ar[i] != 0,in_ar[i],np.nan)

        y = np.nanmedian(div,axis=0)

        np.clip(y,y.min(),y.max(),out = out_ar)
"""}

if name not in methods:
    raise ValueError(
        "ERROR: Unrecognized resampling method (see documentation): '{}'.".
        format(name))

return methods[name]


def merge(files: List[str],output_file: str,resample: str = "average") -> None:
    """merges list of files using specific resample method for overlapping parts
    Args:
        files (:obj:`list[string]`): list of files to merge
        output_file (:obj:`string`): name of output file
        resample (:obj:`string`): name of resampling method
    """
    #des=r"E:\naser\code_de\output\test\_vrt.vrt"
    des=os.getcwd() + "/_vrt.vrt"
    print("1")
    build_vrt(des,files,resample)
    print("2")
    gdal.SetConfigOption('GDAL_VRT_ENABLE_PYTHON','YES')
    print("3")
    translateoptions = gdal.TranslateOptions(gdal.ParseCommandLine("-of Gtiff -ot UINT16 -co TILED=YES -co COMPRESS=LZW BIGTIFF=YES NUM_THREADS=ALL_CPUS -a_nodata 0"))
    gdal.SetConfigOption("GDAL_CACHEMAX","512")
    gdal.Translate(destName=output_file,srcDS=des,options=translateoptions)
    print("4")
    gdal.SetConfigOption('GDAL_VRT_ENABLE_PYTHON',None)
    print("5")
    if os.path.isfile(des):
        os.remove(des)



def mergeAll(file_list,Outname,resample):
    merge(file_list,resample)

是否有合理的解释来解释为什么会发生这种情况？或者我能做什么？

解决方法

您的虚拟机内存似乎已超出可用容量。

解决方法可能是尝试to increase it。或者重新设计您的程序以分块工作（批处理），这样您就可以批量访问您的数据，而不是将所有文件加载到内存中。