435 lines
21 KiB
Python
435 lines
21 KiB
Python
# -*- coding: UTF-8 -*-
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"""
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@Project ：MicroProduct
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@File ：LeafIndexMain.PY
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@Function ：主函数
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@Author ：SHJ
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@Date ：2022/11/07
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@Version ：2.0.0
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修改历史：
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[修改序列] [修改日期] [修改者] [修改内容]
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1 2022-6-27 李明明 1.增加配置文件config.ini; 2.修复快速图全黑的问题; 3.内部处理使用地理坐标系(4326)；
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"""
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from tool.algorithm.algtools.PreProcess import PreProcess as pp # 此行放在下面会报错，最好放在上面
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from tool.algorithm.xml.AlgXmlHandle import ManageAlgXML, CheckSource, InitPara # 导入xml文件读取与检查文件
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from tool.algorithm.algtools.logHandler import LogHandler
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from tool.algorithm.image.ImageHandle import ImageHandler
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from tool.algorithm.block.blockprocess import BlockProcess
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from tool.config.ConfigeHandle import Config as cf
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from tool.algorithm.xml.CreatMetafile import CreateMetafile
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from tool.algorithm.algtools.ROIAlg import ROIAlg as roi
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from tool.algorithm.algtools.filter.lee_Filter import Filter
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from LeafIndexXmlInfo import CreateDict, CreateStadardXmlFile
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from tool.csv.csvHandle import csvHandle
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import os
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import shutil
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import logging
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import datetime
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import glob
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import numpy as np
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import scipy.spatial.transform # 用于解决打包错误
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import scipy.spatial.transform._rotation_groups # 用于解决打包错误
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import scipy.special.cython_special # 用于解决打包错误
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from scipy.interpolate import griddata
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import sys
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import multiprocessing
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from tool.file.fileHandle import fileHandle
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cover_id_list = []
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threshold_of_ndvi_min = 0
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threshold_of_ndvi_max = 0
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multiprocessing_num = int(cf.get('multiprocessing_num'))
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leaf_index_value_min = float(cf.get('product_value_min'))
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leaf_index_value_max = float(cf.get('product_value_max'))
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FILTER_SISE = int(cf.get('filter_sise'))
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if cf.get('debug') == 'True':
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DEBUG = True
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else:
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DEBUG = False
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file = fileHandle(DEBUG)
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EXE_NAME = cf.get('exe_name')
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LogHandler.init_log_handler('run_log\\' + EXE_NAME)
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logger = logging.getLogger("mylog")
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csvh = csvHandle()
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env_str = os.path.split(os.path.realpath(__file__))[0]
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os.environ['PROJ_LIB'] = env_str
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class LeafIndexMain:
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"""
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叶面积指数主函数
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"""
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def __init__(self, alg_xml_path):
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self.alg_xml_path = alg_xml_path
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self.imageHandler = ImageHandler()
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self.BlockProcess = BlockProcess()
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self.__alg_xml_handler = ManageAlgXML(alg_xml_path)
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self.__check_handler = CheckSource(self.__alg_xml_handler)
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self.__workspace_path, self.__workspace_soimois_path,self.__workspace_soimois_path = None, None, None
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self.__input_paras, self.__processing_paras, self.__processing_paras = {}, {}, {}
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self.__out_para = None
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# 参考影像路径,坐标系
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self.__ref_img_path, self.__proj = '', ''
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# 宽/列数,高/行数
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self.__cols, self.__rows = 0, 0
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# 影像投影变换矩阵
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self.__geo = [0, 0, 0, 0, 0, 0]
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# 极化影像的名称
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self.__sar_tif_name = None
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def check_source(self):
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"""
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检查算法相关的配置文件，图像，辅助文件是否齐全
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"""
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env_str = os.getcwd()
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logger.info("sysdir: %s", env_str)
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if self.__check_handler.check_alg_xml() is False:
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return False
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if self.__check_handler.check_run_env() is False:
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return False
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self.__workspace_path = self.__alg_xml_handler.get_workspace_path()
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self.__create_work_space()
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self.__task_id = self.__alg_xml_handler.get_task_id()
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self.__input_paras = self.__alg_xml_handler.get_input_paras() # 获取输入文件夹中的数据名、类型、地址
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self.__out_para = os.path.join(self.__workspace_path,EXE_NAME, 'Output', r"LeafAreaIndexProduct.tar.gz")
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self.__alg_xml_handler.write_out_para("LeafAreaIndexProduct", self.__out_para) # 写入输出参数
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Polarization = self.__input_paras['Polarization']['ParaValue']
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if Polarization == "HV":
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self.__sar_tif_name = "HV"
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elif Polarization == "HH":
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self.__sar_tif_name = "HH"
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elif Polarization == "VV":
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self.__sar_tif_name = "VV"
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elif Polarization == 'empty' or Polarization == 'Empty' or Polarization == 'EMPTY':
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self.__sar_tif_name = 'empty'
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else:
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raise ValueError("input Para 'Polarization' is not 'HV'、'HH'、'VV'or 'empty'!")
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self.__processing_paras = InitPara.init_processing_paras(self.__input_paras)
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self.__processing_paras.update(self.get_tar_gz_inf(self.__processing_paras["sar_path0"]))
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logger.info('check_source success!')
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return True
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def get_tar_gz_inf(self, tar_gz_path):
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para_dic = {}
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name = os.path.split(tar_gz_path)[1].rstrip('.tar.gz')
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file_dir = os.path.join(self.__workspace_preprocessing_path, name + '\\')
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file.de_targz(tar_gz_path, file_dir)
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# 元文件字典
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para_dic.update(InitPara.get_meta_dic(InitPara.get_meta_paths(file_dir, name), name))
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# tif路径字典
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pol_dic = InitPara.get_polarization_mode(InitPara.get_tif_paths(file_dir, name))
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flag_list = [0, 0]
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if self.__sar_tif_name == 'empty':
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for key, in_tif_path in pol_dic.items():
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# 获取极化类型
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if 'HV' == key and flag_list[0] == 0:
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para_dic.update({'HV': in_tif_path})
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flag_list[0] = 1
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elif 'HH' == key and flag_list[0] == 0:
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para_dic.update({'HH': in_tif_path})
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flag_list[0] = 1
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elif 'VV' == key and flag_list[0] == 0:
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para_dic.update({'VV': in_tif_path})
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flag_list[0] = 1
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elif 'LocalIncidenceAngle' == key:
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para_dic.update({'LocalIncidenceAngle': in_tif_path})
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flag_list[1] = 1
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else:
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continue
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else:
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for key, in_tif_path in pol_dic.items():
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# 获取极化类型
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if self.__sar_tif_name == key and flag_list[0] == 0:
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para_dic.update({self.__sar_tif_name: in_tif_path})
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flag_list[0] = 1
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elif 'LocalIncidenceAngle' == key:
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para_dic.update({'LocalIncidenceAngle': in_tif_path})
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flag_list[1] = 1
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if flag_list != [1, 1]:
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raise Exception('There are not ' + self.__sar_tif_name + '、LocalIncidenceAngle or meta.xml in path:', tar_gz_path)
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return para_dic
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def __create_work_space(self):
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"""
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删除原有工作区文件夹,创建新工作区文件夹
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"""
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self.__workspace_preprocessing_path = self.__workspace_path + EXE_NAME + "\\Temporary\\preprocessing""\\"
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self.__workspace_preprocessed_path = self.__workspace_path + EXE_NAME + "\\Temporary\\preprocessed""\\"
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self.__workspace_processing_path = self.__workspace_path + EXE_NAME + "\\Temporary\\processing""\\"
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self.__workspace_maskcai_image_path = self.__workspace_path + EXE_NAME + "\\Temporary\\maskcai_image""\\"
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self.__workspace_maskcai_SoilMoi_path = self.__workspace_path + EXE_NAME + "\\Temporary\\maskcai_SoilMoi""\\"
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self.__workspace_maskcai_localang_path = self.__workspace_path + EXE_NAME + "\\Temporary\\maskcai_localang\\"
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self.__workspace_cai_sartif_path = self.__workspace_path + EXE_NAME + "\\Temporary\\cai_sartif""\\"
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self.__workspace_cai_SoilMoi_path = self.__workspace_path + EXE_NAME + "\\Temporary\\cai_SoilMoi""\\"
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self.__workspace_cai_localang_path = self.__workspace_path + EXE_NAME + "\\Temporary\\cai_localang""\\"
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self.__workspace_Leafindex_path = self.__workspace_path + EXE_NAME + "\\Temporary\\Leafindex""\\"
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self.__product_dic = self.__workspace_processing_path + "product\\"
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path_list = [self.__workspace_preprocessing_path, self.__workspace_preprocessed_path,
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self.__workspace_processing_path, self.__workspace_maskcai_image_path,
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self.__workspace_maskcai_SoilMoi_path, self.__workspace_maskcai_localang_path,
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self.__workspace_cai_sartif_path,
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self.__workspace_cai_SoilMoi_path, self.__workspace_cai_localang_path,
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self.__workspace_Leafindex_path]
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file.creat_dirs(path_list)
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logger.info('create new workspace success!')
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def del_temp_workspace(self):
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"""
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临时工作区
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"""
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if DEBUG is True:
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return
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path = self.__workspace_path + EXE_NAME + r'\Temporary'
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if os.path.exists(path):
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file.del_folder(path)
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def preprocess_handle(self):
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"""
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预处理
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"""
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para_names = [self.__sar_tif_name, 'LocalIncidenceAngle', "NDVI", "surface_coverage"]
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ref_img_name = self.__sar_tif_name
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p = pp()
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self.__preprocessed_paras = p.preprocessing(para_names, ref_img_name,
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self.__processing_paras,
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self.__workspace_preprocessing_path,
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self.__workspace_preprocessed_path)
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self.__ref_img_path, self.__cols, self.__rows, self.__proj, self.__geo = p.get_ref_inf(
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self.__preprocessed_paras[ref_img_name])
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logger.info('preprocess_handle success!')
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logger.info('progress bar: 30%')
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def cal_roi(self):
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"""
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创建掩膜，并裁剪成统一范围
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"""
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# 1、利用叠掩区域生成局部入射角的Mask
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processing_path = self.__workspace_processing_path
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# 利用角度为nan生成Mask
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pp.check_LocalIncidenceAngle(self.__preprocessed_paras['LocalIncidenceAngle'], self.__preprocessed_paras['LocalIncidenceAngle'])
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angle_nan_mask_path = processing_path + 'angle_nan_mask.tif'
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roi.trans_tif2mask(angle_nan_mask_path, self.__preprocessed_paras['LocalIncidenceAngle'], np.nan)
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# 利用影像的有效范围生成MASK
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tif_nan_mask_path = processing_path + 'tif_mask_nan.tif'
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roi.trans_tif2mask(tif_nan_mask_path, self.__preprocessed_paras[self.__sar_tif_name], np.nan)
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# tif_zero_mask_path = processing_path + 'tif_mask_zero.tif'
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# roi.trans_tif2mask(tif_zero_mask_path, self.__preprocessed_paras[self.__sar_tif_name], 0,0)
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# 2、利用cover计算植被覆盖范围
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cover_mask_path = self.__workspace_processing_path + "SurfaceCover_mask.tif"
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cover_id_list = list(self.__processing_paras['CoveringIDs'].split(';'))
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cover_id_list = [int(num) for num in cover_id_list]
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roi.trans_cover2mask(cover_mask_path, self.__preprocessed_paras["surface_coverage"], cover_id_list)
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# 3、利用NDVI计算裸土范围该指数的输出值在 -1.0 和 1.0 之间，大部分表示植被量，
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# 负值主要根据云、水和雪而生成
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# 接近零的值则主要根据岩石和裸土而生成。
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# 较低的（小于等于 0.1）NDVI 值表示岩石、沙石或雪覆盖的贫瘠区域。
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# 中等值（0.2 至 0.3）表示灌木丛和草地
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# 较高的值（0.6 至 0.8）表示温带雨林和热带雨林。
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ndvi_mask_path = self.__workspace_processing_path + "Ndvi_mask.tif"
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ndvi_scope = list(self.__processing_paras['NDVIScope'].split(';'))
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threshold_of_ndvi_min = float(ndvi_scope[0])
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threshold_of_ndvi_max = float(ndvi_scope[1])
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roi.trans_tif2mask(ndvi_mask_path, self.__preprocessed_paras["NDVI"], threshold_of_ndvi_min, threshold_of_ndvi_max)
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logger.info('create masks success!')
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# 4、利用覆盖范围和裸土范围 生成总的MASK
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bare_land_mask_path = self.__workspace_processing_path + "bare_land_mask.tif"
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roi.combine_mask(bare_land_mask_path, ndvi_mask_path, cover_mask_path)
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roi.combine_mask(bare_land_mask_path, bare_land_mask_path, tif_nan_mask_path)
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# roi.combine_mask(bare_land_mask_path, bare_land_mask_path, tif_zero_mask_path)
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roi.combine_mask(bare_land_mask_path, bare_land_mask_path, angle_nan_mask_path)
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logger.info('combine_mask success!')
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# 5、使用ROI区域进行掩膜
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roi.cal_roi(self.__workspace_maskcai_localang_path + "LocalIncidenceAngle_preproed.tif",
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self.__preprocessed_paras["LocalIncidenceAngle"], bare_land_mask_path, background_value=1)
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logger.info('create ROI three image success!')
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return bare_land_mask_path
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def cal_leaf_index(self, vm_file, image_file, angle_file, v2_path, num):
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"""
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叶面积指数计算公式
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V1:植被层特征参数，V1设定为1
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v2：植被层特征参数，V2为叶面积指数
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A,B,C,D 经验系数
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vm 土壤体积含水量
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"""
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# 滤波
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# image_filter_path = v2_path.replace("LeafAreaIndexProduct","lee_filer_img")
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# f.lee_filter(image_file, image_filter_path, FILTER_SISE)
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a = self.__processing_paras["A"]
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b = self.__processing_paras["B"]
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c = self.__processing_paras["C"]
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d = self.__processing_paras["D"]
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k = self.__processing_paras["K"]
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m = self.__processing_paras["M"]
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v1 = 1
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vm_value = self.imageHandler.get_band_array(vm_file, 1)
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image_value = self.imageHandler.get_band_array(image_file, 1)
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# Filter.lee_filter_array(image_value, image_value, FILTER_SISE)
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angle = self.imageHandler.get_band_array(angle_file, 1)
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cos_angle_value = np.cos(angle)
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# 开始计算叶面积指数
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back_soil = c * vm_value - d
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t = (image_value - a * v1 * cos_angle_value) / (back_soil - a * v1 * cos_angle_value)
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where_0 = np.where(t <= 0)
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t[where_0] = 1
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array_v2 = -1 * (np.log(t)) * cos_angle_value / (2 * b)
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array_v2[where_0] = 0
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self.imageHandler.write_img(v2_path, self.__proj, self.__geo, array_v2)
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logger.info('block:%s cal LeafIndex success!', num)
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def create_soil_moisture_tif(self):
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"""
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创建土壤介电常数影像
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"""
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# 读取实测值，从经纬度坐标系转为图像坐标系
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measured_data_img = csvh.trans_measuredata(csvh.readcsv(self.__processing_paras['MeasuredData']), self.__ref_img_path)
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# 插值法生成土壤水分二维影像
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grid_x, grid_y = np.mgrid[0:self.__rows:1, 0:self.__cols:1]
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points = np.array(measured_data_img)[:, 0:2]
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values = np.array(measured_data_img)[:, 2].T
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grid_z0 = griddata(points, values, (grid_x, grid_y), method='nearest')
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self.__processing_paras['SoilMoisture'] = os.path.join(self.__workspace_maskcai_SoilMoi_path, 'soil_moisture.tif')
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self.imageHandler.write_img(self.__processing_paras['SoilMoisture'], self.__proj, self.__geo, grid_z0)
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logger.info('create soil_moisture image success!')
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logger.info('progress bar: 40%')
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def block_process(self,start):
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"""
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生成叶面积指数产品
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"""
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# 生成土壤水分影像
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self.create_soil_moisture_tif()
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shutil.copyfile(self.__preprocessed_paras[self.__sar_tif_name], self.__workspace_maskcai_image_path + self.__sar_tif_name+'.tif')
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logger.info('progress bar: 50%')
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block_size = self.BlockProcess.get_block_size(self.__rows, self.__cols)
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self.BlockProcess.cut(self.__workspace_maskcai_image_path, self.__workspace_cai_sartif_path, ['tif', 'tiff'], 'tif', block_size)
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self.BlockProcess.cut(self.__workspace_maskcai_localang_path, self.__workspace_cai_localang_path, ['tif', 'tiff'], 'tif', block_size)
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self.BlockProcess.cut(self.__workspace_maskcai_SoilMoi_path, self.__workspace_cai_SoilMoi_path, ['tif', 'tiff'], 'tif', block_size)
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logger.info('mask data image success!')
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# 计算每小块的叶面积指数
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in_tif_paths = list(glob.glob(os.path.join(self.__workspace_cai_sartif_path, '*.tif')))
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num = 0
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# 开启多进程处理
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processes_num = min([len(in_tif_paths), multiprocessing_num])
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Filter().lee_filter_multiprocess(in_tif_paths, in_tif_paths, FILTER_SISE, processes_num)
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pool = multiprocessing.Pool(processes=processes_num)
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pl = []
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for name in in_tif_paths:
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suffix = '_' + name.split('_')[-4] + "_" + name.split('_')[-3] + "_" + name.split('_')[-2] + "_" + \
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name.split('_')[-1]
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tif_path = name
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vm_path = self.__workspace_cai_SoilMoi_path + "soil_moisture" + suffix
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angle_path = self.__workspace_cai_localang_path + "LocalIncidenceAngle_preproed" + suffix
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v2_save_path = self.__workspace_Leafindex_path + "LeafAreaIndexProduct" + suffix
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pl.append(pool.apply_async(self.cal_leaf_index, (vm_path, tif_path, angle_path, v2_save_path, num)))
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logger.info('total:%s, block:%s calculating leaf_index!', len(in_tif_paths), num)
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num = num + 1
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pool.close()
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pool.join()
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logger.info('all img cal LeafIndex success!')
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logger.info('progress bar: 80%')
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ref_tif_path = self.__ref_img_path
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date_type = 'float32'
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self.BlockProcess.combine(self.__workspace_Leafindex_path, self.__cols, self.__rows, self.__workspace_processing_path + "combine", 'tif', ['tif'], date_type)
|
||
# 添加地理信息
|
||
out_path = self.__workspace_processing_path + "combine\\LeafAreaIndexProduct.tif"
|
||
self.BlockProcess.assign_spatial_reference_byfile(ref_tif_path, out_path)
|
||
|
||
# 截取roi区域
|
||
bare_land_mask_path = self.cal_roi()
|
||
product_path = self.__product_dic + "LeafAreaIndexProduct.tif"
|
||
roi.cal_roi(product_path, out_path, bare_land_mask_path, background_value=np.nan)
|
||
|
||
logger.info('block_process finished!')
|
||
|
||
proj, geos, data = self.imageHandler.read_img(product_path)
|
||
data[data < leaf_index_value_min] = leaf_index_value_min
|
||
data[data > leaf_index_value_max] = leaf_index_value_max
|
||
self.imageHandler.write_img(product_path, proj, geos, data)
|
||
# 生成快视图
|
||
self.imageHandler.write_quick_view(product_path)
|
||
|
||
|
||
xml_path = "./model_meta.xml"
|
||
tem_folder = self.__workspace_path + EXE_NAME + r"\Temporary""\\"
|
||
image_path = product_path
|
||
out_path1 = os.path.join(tem_folder, "trans_geo_projcs.tif")
|
||
out_path2 = os.path.join(tem_folder, "trans_projcs_geo.tif")
|
||
par_dict = CreateDict(image_path, out_path1, out_path2).calu_nature(start)
|
||
model_xml_path = os.path.join(tem_folder, "creat_standard.meta.xml") # 输出xml路径
|
||
|
||
id_min = 0
|
||
id_max = 0
|
||
for id in cover_id_list:
|
||
if id < id_min:
|
||
id_min = id
|
||
if id > id_max:
|
||
id_max = id
|
||
set_threshold = [id_max, id_min, threshold_of_ndvi_min, threshold_of_ndvi_max]
|
||
|
||
CreateStadardXmlFile(xml_path, self.alg_xml_path, par_dict, set_threshold, model_xml_path).create_standard_xml()
|
||
|
||
SrcImagePath = self.__input_paras["SAR"]['ParaValue']
|
||
paths = SrcImagePath.split(';')
|
||
SrcImageName=os.path.split(paths[0])[1].split('.tar.gz')[0]
|
||
if len(paths) >= 2:
|
||
for i in range(1, len(paths)):
|
||
SrcImageName = SrcImageName+";"+os.path.split(paths[i])[1].split('.tar.gz')[0]
|
||
meta_xml_path = self.__product_dic+EXE_NAME+"Product.meta.xml"
|
||
CreateMetafile(self.__processing_paras['META'], self.alg_xml_path, model_xml_path, meta_xml_path).process(SrcImageName)
|
||
|
||
# 文件夹打包
|
||
file.make_targz(self.__out_para, self.__product_dic)
|
||
logger.info('process_handle success!')
|
||
logger.info('progress bar: 100%')
|
||
|
||
def process_handle(self,start):
|
||
self.cal_roi()
|
||
self.block_process(start)
|
||
return True
|
||
|
||
|
||
if __name__ == '__main__':
|
||
multiprocessing.freeze_support() # 解决多进程打包错误
|
||
start = datetime.datetime.now()
|
||
try:
|
||
if len(sys.argv) < 2:
|
||
xml_path = 'LeafAreaIndex.xml'
|
||
else:
|
||
xml_path = sys.argv[1]
|
||
main_handler = LeafIndexMain(xml_path)
|
||
if main_handler.check_source() is False:
|
||
raise Exception('check_source() failed!')
|
||
if main_handler.preprocess_handle() is False:
|
||
raise Exception('preprocess_handle() failed!')
|
||
if main_handler.process_handle(start) is False:
|
||
raise Exception('process_handle() failed!')
|
||
logger.info('successful production of ' + EXE_NAME + ' products!')
|
||
except Exception:
|
||
logger.exception('run-time error!')
|
||
finally:
|
||
main_handler.del_temp_workspace()
|
||
|
||
end = datetime.datetime.now()
|
||
msg = 'running use time: %s ' % (end - start)
|
||
logger.info(msg)
|