248 lines
8.7 KiB
C++
248 lines
8.7 KiB
C++
/*********************************************************************************************
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Description: 处理pubmed生成的txt文件，将处理结果放到mat文件中
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Copyright : All right reserved by ZheYuan.BJ
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Author : Zhang Zhonghai
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Date : 2023/09/18
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***********************************************************************************************/
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#include <iostream>
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#include <fstream>
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#include <vector>
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#include <string>
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#include <algorithm>
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#include <unordered_map>
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#include <mat.h>
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#include "common.h"
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#include "CommonLib/thread_pool.h"
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#include "CommonLib/matlab_io.h"
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#include "CommonLib/kthread.h"
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using namespace std;
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/* 将结果写入mat文件 */
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/* 将数据写入mat文件中，用给定的名称命名 */
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bool SavePubmed(const string& matPath,
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const vector<string>& vTgName,
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vector<unordered_map<string, string> >& vumPaperTagVal)
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{
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MATFile* pMatFile = matOpen(matPath.c_str(), "w"); //打开.mat文件
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if (pMatFile == nullptr) {
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cout << "filePath is error! " << matPath << endl;
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return false;
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}
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vector<const char*> vTgChars;
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for (auto& strTg : vTgName) {
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vTgChars.push_back(strTg.c_str());
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}
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// 创建结构体数据
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mxArray* mxStruct = mxCreateStructMatrix(1, 1, (int)vTgName.size(), vTgChars.data());
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// 创建cell matrix
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unordered_map<string, mxArray*> ummxCellMtx;
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for (auto & tgName : vTgName) {
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ummxCellMtx[tgName] = mxCreateCellMatrix(1, vumPaperTagVal.size());
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}
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// 遍历每一篇文章
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for (int i = 0; i < vumPaperTagVal.size(); ++i) {
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auto& umTagVal = vumPaperTagVal[i];
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// 遍历文章的每一个tag
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for (auto& tgName : vTgName) {
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mxArray* mxStr = mxCreateString(umTagVal[tgName].c_str());
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mxArray* pMxArr = ummxCellMtx[tgName];
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mxSetCell(pMxArr, i, mxStr);
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}
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}
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// 将cell matrix赋值给struct matrix
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for (auto& tgName : vTgName) {
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mxArray* pMxArr = ummxCellMtx[tgName];
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mxSetField(mxStruct, 0, tgName.c_str(), pMxArr);
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}
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// 将结构体写入mat，并命名为Tx
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matPutVariable(pMatFile, "Tx", mxStruct);
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// 将abstract信息写入mat，并命名为abs1
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matPutVariable(pMatFile, "abs1", ummxCellMtx["AB"]);
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matClose(pMatFile);
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return true;
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}
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/* 处理一篇文章 */
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struct ThreadParam { // 线程参数
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unordered_map<string, string> *pumTagContent;
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vector<string>* pvLineTag;
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vector<string>* pvTgName;
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int paperStartIdx;
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int paperEndIdx;
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unordered_map<string, string>* pumFullTagToTag;
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vector<string>* pvStrPubmedTxt;
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};
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//void ThreadProcessArticle(vector<ThreadParam>& vTP, long idx, int tid) {
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void ThreadProcessArticle(ThreadParam& param) {
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//ThreadParam& param = vTP[idx];
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unordered_map<string, string>& umTagContent = *param.pumTagContent;
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vector<string>& vLineTag = *param.pvLineTag;
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vector<string>& vTgName = *param.pvTgName;
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unordered_map<string, string>& umFullTagToTag = *param.pumFullTagToTag;
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vector<string>& vStrPubmedTxt = *param.pvStrPubmedTxt;
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int startIdx = param.paperStartIdx;
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int endIdx = param.paperEndIdx;
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for (int tgIdx = 0; tgIdx < vTgName.size(); ++tgIdx) {
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umTagContent[vTgName[tgIdx]] = ""; // 对每一个tag，设置一个新的string
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}
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for (int idx = startIdx; idx < endIdx; ++idx) { // 遍历当前文章的每一个tag内容
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string& fullTag = vLineTag[idx];
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auto tagItr = umFullTagToTag.find(fullTag);
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if (tagItr != umFullTagToTag.end()) { // 找到tag了
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const string& tag = tagItr->second;
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string& tagContent = umTagContent[tag];
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tagContent.append(vStrPubmedTxt[idx]);
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}
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}
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}
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// 命令行参数示例
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// ProcessPubmedTxt d:\Twirls\gat1\literatures\pubmed_tag.mat D:\Twirls\runtime\negatives\pubmed-multiplesc-set.txt d:\pubmed_txt.mat 12
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/*
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pubmed txt文件中包含多个文章的摘要信息，每个信息最前边有一个tag，每个tag对应的信息可能有一行，也可能多行，每个文章中间由一个空行隔开
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1. 读取预先提取的pubmed tags, 并将tags中的'-'和' '字符去掉，只留下纯字符串做tag
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2. 读取pubmed txt文件, 对所有文献根据tag进行拆分，同一个文献中，合并同一个tag的所有内容，空格隔开
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3. 去除一些冗余等内容， 将title和abstract合并，赋值给abstract
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4. 将结果写入mat文件
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*/
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void ProcessPubmedTxt(int argc, const char** argv) {
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// argv 1.pubmed tag.mat文件; 2.pubmed article.txt文件; 3.pubmed out.mat输出文件
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//
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if (argc < 4) {
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cout << "This program should take at least 3 arguments(1.pubmed tag.mat; 2. pubmed article.txt; 3. pubmed out.mat; [4. thread num])!" << endl;
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return;
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}
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clock_t begin, finish;
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int rowNum, colNum;
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vector<string> vTg;
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vector<string> vTgName;
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vector<unordered_map<string, string> > vumPaperTagVal;
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unordered_map<string, string> umFullTagToTag; // 完整tag与tag的映射，如“PMID- ”：“PMID”
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/* 读取pubmed tags */
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ReadMtxString(argv[1], "tg", vTg, &rowNum, &colNum);
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/* 1. 去掉tags里的'-'和' '字符，得到纯净的tag */
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begin = clock();
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vTgName = vTg;
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for (int i = 0; i < vTg.size(); ++i) {
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int pos = 0;
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for (int j = 0; j < vTg[i].size(); ++j) {
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if (vTg[i][j] != ' ' && vTg[i][j] != '-') { // 去掉tag中的空格和'-'字符，生成tag name
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vTgName[i][pos++] = vTg[i][j];
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}
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}
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vTgName[i].resize(pos);
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umFullTagToTag[vTg[i]] = vTgName[i];
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}
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finish = clock();
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cout << "process tag Total time: " << (double)(finish - begin) / CLOCKS_PER_SEC << " s" << endl;
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/* 2. 读取pubmed txt文件，先读入后处理 */
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ifstream ifsPubmedTxt(argv[2]);
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vector<string> vStrPubmedTxt;
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vector<string> vLineTag;
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vector<int> vPaperStartIdx;
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string blankTag = " "; // 5个空格
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string strLine;
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string fullTag;
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int curPos = 0;
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vPaperStartIdx.push_back(curPos); // 添加初始索引
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const int FULL_TAG_LEN = 5;
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begin = clock();
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while (getline(ifsPubmedTxt, strLine)) { // 读取内容时候去掉了行尾的换行符
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while (strLine.back() == ' ') strLine.pop_back(); // 去掉行尾的空格
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if (strLine.size() == 0) { // 新的paper
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vPaperStartIdx.push_back(curPos);
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continue;
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}
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fullTag = strLine.substr(0, 5);
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if (fullTag == blankTag) { // 这一行的内容还是属于上一个tag的
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string& lastTagConteng = vStrPubmedTxt.back();
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lastTagConteng.append(strLine.substr(FULL_TAG_LEN)); // 最前边包含了一个空格
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}
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else {
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vStrPubmedTxt.push_back(strLine.substr(FULL_TAG_LEN));
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vLineTag.push_back(fullTag);
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curPos++;
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}
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}
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vPaperStartIdx.push_back(curPos); // 比文章多1，最后一个记录结束位置
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finish = clock();
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cout << "read txt Total time: " << (double)(finish - begin) / CLOCKS_PER_SEC << " s" << endl;
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/* 处理每一篇文章 */
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int numThread = 1;
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if (argc >= 5) numThread = atoi(argv[4]);
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if (numThread < 1) numThread = 1;
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ThreadPool thPool(numThread);
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vumPaperTagVal.resize(vPaperStartIdx.size()-1);
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vector<thread> vT;
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vector<ThreadParam> vTP(vPaperStartIdx.size() - 1);
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begin = clock();
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for (int i = 0; i < vTP.size(); ++i) {
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vTP[i] = { &vumPaperTagVal[i], &vLineTag, &vTgName, vPaperStartIdx[i], vPaperStartIdx[i + 1], &umFullTagToTag, &vStrPubmedTxt };
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}
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kt_for(numThread, ThreadProcessArticle, vTP);
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finish = clock();
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cout << "kt for Total time: " << (double)(finish - begin) / CLOCKS_PER_SEC << " s" << endl;
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/* 去除没有摘要的文章 */
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begin = clock();
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const string abstractTag = "AB";
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for (auto itr = vumPaperTagVal.begin(); itr != vumPaperTagVal.end(); ) {
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if ((*itr)[abstractTag].size() == 0) {
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itr = vumPaperTagVal.erase(itr);
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}
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else {
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itr++;
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}
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}
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finish = clock();
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cout << "remove no AB Total time: " << (double)(finish - begin) / CLOCKS_PER_SEC << " s" << endl;
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/* 根据PMID，去除冗余 */
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begin = clock();
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unordered_map<string, int> umPMID;
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const string pmidTag = "PMID";
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for (auto itr = vumPaperTagVal.begin(); itr != vumPaperTagVal.end(); ) {
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if (umPMID.find((*itr)[pmidTag]) != umPMID.end()) {
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// out << "duplicate " << (*itr)[pmidTag] << endl;
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itr = vumPaperTagVal.erase(itr);
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}
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else {
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umPMID[(*itr)[pmidTag]] = 1;
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itr++;
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}
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}
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finish = clock();
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cout << "remove duplication Total time : " << (double)(finish - begin) / CLOCKS_PER_SEC << " s" << endl;
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/* 将title和abstract合并，赋值给abstract */
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begin = clock();
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const string titleTag = "TI";
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for (auto itr = vumPaperTagVal.begin(); itr != vumPaperTagVal.end(); itr++) {
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string& abstractStr = (*itr)[abstractTag];
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abstractStr = (*itr)[titleTag] + " " + abstractStr; // 可能会有性能损失，不过影响不大
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}
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finish = clock();
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cout << "merge abs and title Total time : " << (double)(finish - begin) / CLOCKS_PER_SEC << " s" << endl;
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// 关闭txt文件
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ifsPubmedTxt.close();
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/* 将处理后的数据写入mat文件，mat中的变量名称分别为Tx和abs1 */
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begin = clock();
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SavePubmed(argv[3], vTgName, vumPaperTagVal);
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finish = clock();
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cout << "write to MAT Total time: " << (double)(finish - begin) / CLOCKS_PER_SEC << " s" << endl;
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} |