extract_PDF.qmd

---
title: "extract PDF file"
format: html
---

## extract PDF

从PDF里面提取出数据


```{r, include=FALSE}
library(tidyverse)
library(tabulizer) # 
# library(PDE)
library(pdftools)
```


### tabulizer 包 的测试

all_three = c(5,7,9,10,11,14:17,23,39,40),
all_two = c(6, 8, 12, 13, 18, 24, 25)

```{r}
f <- pdfs[1]

# 交互式提取不适合批量。
# extract_areas(f, pages = 1, output = "data.frame") -> df1

# out1 <- extract_tables(f, pages = 1, output = "data.frame")

out2 <- tabulizer::extract_text(f, page = 1)

out3 <- str_split(out2, '\n') |> unlist()

out3
```


```{r}
f <- pdfs[10]

out2 <- extract_text(f, page = 1)
out3 <- str_split(out2, '\n') |> unlist()

out3
```

```{r}
out3[[5]] |> str_split(' ')  |> unlist() -> a
b <- out3[[7]] |> str_split(' ') |> unlist()

bind_cols(as.data.frame(a), as.data.frame(b))


f1 <- function(i, l=out3){
  a <- l[[i]] |> str_split(' ') |> unlist()
}

```


```{r}
ll1 <- list()
all_three <- c(5,7,9,10,11,14:17,23,39,40)

for(i in seq_along(all_three)){
  print(all_three[[i]])
  x <- f1(all_three[[i]])
  ll1[[i]] <- x
}

df3 <- as.data.frame(ll1)
df3[1,2] <- '总体毛发密度'
names(df3) <- df3[1, ]
df3 <- df3[-1, ]
df3
```
```{r}
ll2 <- list()
all_two <- c(6,8,12,13,18,24,25)

for(i in seq_along(all_two)){
  x <- f1(all_two[[i]])
  ll2[[i]] <- x
}

df2 <- as.data.frame(ll2)
df2[1,2] <- '总体毛发数量'
names(df2) <- df2[1, ]
df2 <- df2[-1, ]
df2[2,] <- NA
df2
```

```{r}
ll3 <- list()
all_four <- c(19:22)

for(i in seq_along(all_four)){
  x <- f1(all_four[[i]])
  ll3[[i]] <- x
}

df4 <- as.data.frame(ll3)
names(df4) <- c('1根毛发', '1根毛发', '1根毛发', '4根毛发')
df4
```


### 批量脚本

start here!

```{r}
f1 <- function(i, l=out3){
  a <- l[[i]] |> str_split(' ') |> unlist()
}


extract_pdf2 <- function(f,
                         all_three = c(5,7,9,10,11,14:17,23,39,40),
                         all_two = c(6, 8, 12, 13, 18, 24, 25)
                         ) {
  f <- f
  out2 <- extract_text(f, page = 1)
  out3 <- str_split(out2, "\n") |> unlist()
  
  # 提取字符串长度为3的
  ll1 <- list()
  all_three <- all_three

  for (i in seq_along(all_three)) {
    x <- f1(all_three[[i]],out3)
    ll1[[i]] <- x
  }

  df3 <- as.data.frame(ll1)
  df3[1, 2] <- "总体毛发密度"
  names(df3) <- df3[1, ]
  df3 <- df3[-1, ]
  
  # 提取字符串长度为2的
  ll2 <- list()
  all_two <- all_two

  for (i in seq_along(all_two)) {
    x <- f1(all_two[[i]],out3)
    ll2[[i]] <- x
  }

  df2 <- as.data.frame(ll2)
  df2[1, 2] <- "总体毛发数量"
  names(df2) <- df2[1, ]
  df2 <- df2[-1, ]
  df2[2, ] <- NA
  
  final_df <- bind_cols(df3, df2) %>% as_tibble()
  
  final_df
}


extract_pdf <- function(f,
                        use_outlength = FALSE,
                        all_three = c(5,7,9,10,11,14:17,23,39,40),
                        all_two = c(6, 8, 12, 13, 18, 24, 25)
                        ) {
  f <- f
  out2 <- extract_text(f, page = 1)
  out3 <- str_split(out2, "\n") |> unlist()
  
  out3l <- length(out3)
  
  # 提取字符串长度为3的
  ll1 <- list()
  
  if(use_outlength){
    all_three <- c(5,7,9,10,11,14:17,23)
    all_three <- c(all_three, out3l-3, out3l-2)
  } else {
    all_three <- all_three
  }
  

  for (i in seq_along(all_three)) {
    x <- f1(all_three[[i]],out3)
    ll1[[i]] <- x
  }

  df3 <- as.data.frame(ll1)
  df3[1, 2] <- "总体毛发密度"
  names(df3) <- df3[1, ]
  df3 <- df3[-c(1,3), ]
  
  # 提取字符串长度为2的
  ll2 <- list()
  all_two <- all_two

  for (i in seq_along(all_two)) {
    x <- f1(all_two[[i]],out3)
    ll2[[i]] <- x
  }

  df2 <- as.data.frame(ll2)
  df2[1, 2] <- "总体毛发数量"
  names(df2) <- df2[1, ]
  df2 <- df2[-1, ]
  # df2[2, ] <- NA
  
  final_df <- bind_cols(df3, df2) %>% as_tibble()
  
  final_df
}
```


##### 对于01文件夹

```{r}
pdfs <- list.files(path = '/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/苏州开拓KX0826-CN-1004-女性雄秃项目-毛发镜报告1/KX-0826-CN-1004毛发镜分析', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )

s <- str_split(pdfs[[1]], '/')
patientID <- s[[1]][[10]]
visit <- s[[1]][[11]]
df1 <- extract_pdf(pdfs[[1]], use_outlength = FALSE)
df1[['patientID']] <- patientID
df1[['visit']] <- visit

for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- s[[1]][[10]]
  visit <- s[[1]][[11]]

  df <- extract_pdf(i, use_outlength = FALSE)
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('~/OneDrive/kintor/Daily_Work/extract_PDF/results_01.csv')
```

```{r}
s <- str_split(pdfs[[14]], '/')
patientID <- s[[1]][[10]]
visit <- s[[1]][[11]]
df1 <- extract_pdf(pdfs[[14]], use_outlength = FALSE, 
                   all_three = c(5,7,9,10,11,14:17,23,36)
                   )
df1[['patientID']] <- patientID
df1[['visit']] <- visit
```


##### 对于03文件夹

`all_three <- c(5, 7, 9, 10, 11, 14:17, 23, 35, 36)`

```{r}
pdfs <- list.files(path = '~/OneDrive/kintor/Daily_Work/extract_PDF/KX0826-CN-1002项目毛发评估报告/03中心毛发评估报告', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )
pdfs[1:3]
```
```{r}
all_three <- c(5, 7, 9, 10, 11, 14:17, 23, 35, 36)


s <- str_split(pdfs[[1]], '/')
patientID <- s[[1]][[10]]
visit <- s[[1]][[11]]
df1 <- extract_pdf(pdfs[[1]], all_three = all_three)
df1[['patientID']] <- patientID
df1[['visit']] <- visit
```

```{r}
for(i in pdfs[c(2,4,6,11,14,17)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- s[[1]][[10]]
  visit <- s[[1]][[11]]

  df <- extract_pdf(i, all_three = all_three)
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('~/OneDrive/kintor/Daily_Work/extract_PDF/results_03_1.csv')
```

```{r}
all_three <- c(5, 7, 9, 10, 11, 14:17, 23, 39, 40)


s <- str_split(pdfs[[3]], '/')
patientID <- s[[1]][[10]]
visit <- s[[1]][[11]]
df1 <- extract_pdf(pdfs[[3]], all_three = all_three)
df1[['patientID']] <- patientID
df1[['visit']] <- visit
```

```{r}
for(i in pdfs[c(5,7:10,12,13)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- s[[1]][[10]]
  visit <- s[[1]][[11]]

  df <- extract_pdf(i, all_three = all_three)
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('~/OneDrive/kintor/Daily_Work/extract_PDF/results_03_2.csv')
```


`all_three <- c(5, 7, 9, 10, 11, 14:17, 23, 31, 32)`

```{r}
s <- str_split(pdfs[[18]], '/')
patientID <- s[[1]][[10]]
visit <- s[[1]][[11]]
df1 <- extract_pdf(pdfs[[18]], use_outlength = TRUE)
df1[['patientID']] <- patientID
df1[['visit']] <- visit

for(i in pdfs[c(15, 16, 19:length(pdfs))]){
  print(i)
  s <- str_split(i, '/')
  patientID <- s[[1]][[10]]
  visit <- s[[1]][[11]]

  df <- extract_pdf(i, use_outlength = TRUE)
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('~/OneDrive/kintor/Daily_Work/extract_PDF/results_03_3.csv')

```


*新函数的测试*

```{r}
s <- str_split(pdfs[[1]], '/')
patientID <- s[[1]][[10]]
visit <- s[[1]][[11]]
df1 <- extract_pdf(pdfs[[1]], use_outlength = TRUE)
df1[['patientID']] <- patientID
df1[['visit']] <- visit

for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- s[[1]][[10]]
  visit <- s[[1]][[11]]

  df <- extract_pdf(i, use_outlength = TRUE)
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}


```

```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('~/OneDrive/kintor/Daily_Work/extract_PDF/results_03.csv')
```


##### 对于05文件夹

```{r}
all_three <- c(5, 7, 9, 10, 11, 14:17, 23, 36, 37)


pdfs <- list.files(path = '~/OneDrive/kintor/Daily_Work/extract_PDF/KX0826-CN-1002项目毛发评估报告/05中心毛发评估报告/05中心毛发评估报告', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )


```

```{r}
s <- str_split(pdfs[[1]], '/')
patientID <- s[[1]][[11]]
visit <- str_split(s[[1]][[12]], '-')[[1]][[5]]
df1 <- extract_pdf(pdfs[[1]])
df1[['patientID']] <- patientID
df1[['visit']] <- visit

for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- s[[1]][[11]]
  visit <- str_split(s[[1]][[12]], '-')[[1]][[5]]

  df <- extract_pdf(i)
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('~/OneDrive/kintor/Daily_Work/extract_PDF/results_05.csv')
```


##### 08文件夹

`all_three <- c(5, 7, 9, 10, 11, 14:17, 23, 39, 40)`

```{r}
pdfs <- list.files(path = '~/OneDrive/kintor/Daily_Work/extract_PDF/KX0826-CN-1002项目毛发评估报告/08毛发报告/毛发报告', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )

pdfs[1:5]
```
```{r}
s <- str_split(pdfs[[1]], '/')
patientID <- s[[1]][[11]]
visit <- str_split(s[[1]][[12]], '-')[[1]][[5]]
df1 <- extract_pdf(pdfs[[1]])
df1[['patientID']] <- patientID
df1[['visit']] <- visit
```

```{r}
for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- s[[1]][[11]]
  visit <- str_split(s[[1]][[12]], '-')[[1]][[5]]

  df <- extract_pdf(i)
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('~/OneDrive/kintor/Daily_Work/extract_PDF/results_08.csv')
```


##### 09文件夹

`all_three <- c(5, 7, 9, 10, 11, 14:17, 23, 36, 37)`

```{r}
pdfs <- list.files(path = '~/OneDrive/kintor/Daily_Work/extract_PDF/KX0826-CN-1002项目毛发评估报告/09中心毛发报告', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )

pdfs[1:5]
```
```{r}
s <- str_split(pdfs[[1]], '/')
patientID <- str_split(s[[1]][[11]], '_')[[1]][[2]]
# visit <- str_split(s[[1]][[12]], '-')[[1]][[5]]
df1 <- extract_pdf(pdfs[[1]])
df1[['patientID']] <- patientID
# df1[['visit']] <- visit
```

```{r}
for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- str_split(s[[1]][[11]], '_')[[1]][[2]]

  df <- extract_pdf(i)
  df[['patientID']] <- patientID
  # df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>%  
  mutate(visit = row_number()) %>% 
  select(patientID, visit, everything()) %>%
  write_excel_csv('~/OneDrive/kintor/Daily_Work/extract_PDF/results_09.csv')
```


##### 06文件夹

`all_three <- c(5, 7, 9, 10, 11, 14:17, 23, 33, 34)`

```{r}
pdfs <- list.files(path = '~/OneDrive/kintor/Daily_Work/extract_PDF/KX0826-CN-1002项目毛发评估报告/06中心微观照片及报告/06中心微观照片及报告', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )

pdfs[1:5]
```

```{r}
s <- str_split(pdfs[[1]], '/')
patientID <- s[[1]][[11]]
# visit <- str_split(s[[1]][[12]], '-')[[1]][[5]]
df1 <- extract_pdf(pdfs[[1]])
df1[['patientID']] <- patientID
# df1[['visit']] <- visit
```

```{r}
for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- s[[1]][[11]]

  df <- extract_pdf(i)
  df[['patientID']] <- patientID
  # df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>% 
  mutate(visit = row_number()) %>% 
  select(patientID, visit, everything()) %>%
  write_excel_csv('~/OneDrive/kintor/Daily_Work/extract_PDF/results_06.csv')
```



### pdftools

```{r}
pdf.text <- pdftools::pdf_text(f)
```


# 女性

## 对于01 site

all_three <- c(5, 7, 9, 10, 11, 14:17, 23, 39, 40)

```{r}
pdfs <- list.files(path = '/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/苏州开拓KX0826-CN-1004-女性雄秃项目-毛发镜报告1/KX-0826-CN-1004毛发镜分析', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )


```

```{r}
s <- str_split(pdfs[[1]], '/')
patientID <- s[[1]][[10]]
visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

df1 <- extract_pdf(pdfs[[1]])
df1[['patientID']] <- patientID
df1[['visit']] <- visit
```

```{r}
for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- s[[1]][[10]]
  visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

  df <- extract_pdf(i)
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/site_01.csv')
```

## 对于02site

all_three = c(5,7,9,10,11,14:17,23,40,41)

```{r}
pdfs <- list.files(path = '/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/苏州开拓KX0826-CN-1004-女性雄秃项目-毛发镜报告1/KX0826-02中心毛发报告', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )

head(pdfs)
```
```{r}
s <- str_split(pdfs[[1]], '/')
patientID <- s[[1]][[10]]
visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

df1 <- extract_pdf(pdfs[[1]],
                   all_three = c(5,7,9,10,11,14:17,23,40,41)
                   )
df1[['patientID']] <- patientID
df1[['visit']] <- visit
```

```{r}
for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- s[[1]][[10]]
  visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

  df <- extract_pdf(i,
                    all_three = c(5,7,9,10,11,14:17,23,40,41)
                    )
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```


```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/site_02.csv')
```


## 03 site

```{r}
pdfs <- list.files(path = '/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/苏州开拓KX0826-CN-1004-女性雄秃项目-毛发镜报告1/KX-0826-CN-1004 -03中心-北大一', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )
print(length(pdfs))

head(pdfs)
```

```{r}
s <- str_split(pdfs[[2]], '/')
patientID <- s[[1]][[10]]
visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

df1 <- extract_pdf(pdfs[[2]],
                   all_three = c(5,7,9,10,11,14:17,23,40,41)
                   )
df1[['patientID']] <- patientID
df1[['visit']] <- visit

View(df1)
```

```{r}
for(i in pdfs[3:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- s[[1]][[10]]
  visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

  df <- extract_pdf(i,
                    all_three = c(5,7,9,10,11,14:17,23,40,41)
                    )
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```


```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/site_03.csv')
```

## 04

```{r}
pdfs <- list.files(path = '/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/苏州开拓KX0826-CN-1004-女性雄秃项目-毛发镜报告1/KX0826-CN-1004-04中心-毛发评估报告', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )
print(length(pdfs))

head(pdfs)
```
```{r}
s <- str_split(pdfs[[1]], '/')
patientID <- str_split(s[[1]][[11]], '-')[[1]][[4]]
visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

df1 <- extract_pdf(pdfs[[1]],
                   all_three = c(5,7,9,10,11,14:17,23,39,40)
                   )
df1[['patientID']] <- patientID
df1[['visit']] <- visit

View(df1)
```


```{r}
for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- str_split(s[[1]][[11]], '-')[[1]][[4]]
  visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

  df <- extract_pdf(i,
                    all_three = c(5,7,9,10,11,14:17,23,39,40)
                    )
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```


```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/site_04.csv')
```

## 05

```{r}
pdfs <- list.files(path = '/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/苏州开拓KX0826-CN-1004-女性雄秃项目-毛发镜报告1/KX-0826-CN-1004 -05中心-重庆附一', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )
print(length(pdfs))

head(pdfs)
```
```{r}
s <- str_split(pdfs[[1]], '/')
patientID <- s[[1]][[10]]
visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

df1 <- extract_pdf(pdfs[[1]],
                   all_three = c(5,7,9,10,11,14:17,23,39,40)
                   )
df1[['patientID']] <- patientID
df1[['visit']] <- visit

View(df1)
```

```{r}
for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- s[[1]][[10]]
  visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

  df <- extract_pdf(i,
                    all_three = c(5,7,9,10,11,14:17,23,39,40)
                    )
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/site_05.csv')
```

## 06 site


```{r}
pdfs <- list.files(path = '/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/苏州开拓KX0826-CN-1004-女性雄秃项目-毛发镜报告2/女秃报告南方皮肤病医院', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )
print(length(pdfs))

head(pdfs)
```
```{r}
s <- str_split(pdfs[[1]], '/')
patientID <- str_split(s[[1]][[10]], '-')[[1]][[4]]
visit <- str_split(s[[1]][[10]], '-')[[1]][[5]]

df1 <- extract_pdf(pdfs[[1]],
                   all_three = c(5,7,9,10,11,14:17,23,39,40)
                   )
df1[['patientID']] <- patientID
df1[['visit']] <- visit

View(df1)
```

```{r}
for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- str_split(s[[1]][[10]], '-')[[1]][[4]]
  visit <- str_split(s[[1]][[10]], '-')[[1]][[5]]

  df <- extract_pdf(i,
                    all_three = c(5,7,9,10,11,14:17,23,39,40)
                    )
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/site_06.csv')
```

## 07 site

```{r}
pdfs <- list.files(path = '/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/苏州开拓KX0826-CN-1004-女性雄秃项目-毛发镜报告2/KX-0826-CN-1004 -07中心-中日友好', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )
print(length(pdfs))

head(pdfs)
```
```{r}
s <- str_split(pdfs[[1]], '/')
patientID <- str_split(s[[1]][[10]], '-')[[1]][[2]]
visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

df1 <- extract_pdf(pdfs[[1]],
                   all_three = c(5,7,9,10,11,14:17,23,39,40)
                   )
df1[['patientID']] <- patientID
df1[['visit']] <- visit

View(df1)
```

```{r}
for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- str_split(s[[1]][[10]], '-')[[1]][[2]]
  visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

  df <- extract_pdf(i,
                    all_three = c(5,7,9,10,11,14:17,23,39,40)
                    )
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/site_07.csv')
```


## 08 site

```{r}
pdfs <- list.files(path = '/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/苏州开拓KX0826-CN-1004-女性雄秃项目-毛发镜报告2/KX0826-CN-1004-08中心毛发分析报告', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )
print(length(pdfs))

head(pdfs)
```
```{r}
s <- str_split(pdfs[[1]], '/')
patientID <- str_split(s[[1]][[10]], '-')[[1]][[5]]
visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

df1 <- extract_pdf(pdfs[[1]],
                   all_three = c(5,7,9,10,11,14:17,23,39,40)
                   )
df1[['patientID']] <- patientID
df1[['visit']] <- visit

View(df1)
```

```{r}
for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- str_split(s[[1]][[10]], '-')[[1]][[5]]
  visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

  df <- extract_pdf(i,
                    all_three = c(5,7,9,10,11,14:17,23,39,40)
                    )
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/site_08.csv')
```


## 09 site

```{r}
pdfs <- list.files(path = '/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/苏州开拓KX0826-CN-1004-女性雄秃项目-毛发镜报告2/KX-0826-CN-1004 -09中心-浙一', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )
print(length(pdfs))

head(pdfs)
```

## 10 site

```{r}
pdfs <- list.files(path = '/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/苏州开拓KX0826-CN-1004-女性雄秃项目-毛发镜报告2/KX-0826-CN-1004 -10中心-北京友谊', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )
print(length(pdfs))

head(pdfs)
```
```{r}
s <- str_split(pdfs[[1]], '/')
patientID <- s[[1]][[10]]
visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

df1 <- extract_pdf(pdfs[[1]],
                   all_three = c(5,7,9,10,11,14:17,23,39,40)
                   )
df1[['patientID']] <- patientID
df1[['visit']] <- visit

View(df1)
```

```{r}
for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- s[[1]][[10]]
  visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

  df <- extract_pdf(i,
                    all_three = c(5,7,9,10,11,14:17,23,39,40)
                    )
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/site_10.csv')
```


## 11 site

```{r}
pdfs <- list.files(path = '/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/苏州开拓KX0826-CN-1004-女性雄秃项目-毛发镜报告2/11中心毛发镜照片', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )
print(length(pdfs))

head(pdfs)
```

```{r}
s <- str_split(pdfs[[1]], '/')
patientID <- str_split(s[[1]][[10]], '-')[[1]][[4]]
visit <- str_split(s[[1]][[10]], '-')[[1]][[5]]

df1 <- extract_pdf(pdfs[[1]],
                   all_three = c(5,7,9,10,11,14:17,23,39,40)
                   )
df1[['patientID']] <- patientID
df1[['visit']] <- visit

View(df1)
```

```{r}
for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- str_split(s[[1]][[10]], '-')[[1]][[4]]
  visit <- str_split(s[[1]][[10]], '-')[[1]][[5]]

  df <- extract_pdf(i,
                    all_three = c(5,7,9,10,11,14:17,23,39,40)
                    )
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/site_11.csv')
```

## 13 site

```{r}
pdfs <- list.files(path = '/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/苏州开拓KX0826-CN-1004-女性雄秃项目-毛发镜报告2/KX-0826-CN-1004 -13中心-河北一', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )
print(length(pdfs))

head(pdfs)
```

```{r}
s <- str_split(pdfs[[1]], '/')
patientID <- s[[1]][[10]]
visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

df1 <- extract_pdf(pdfs[[1]],
                   all_three = c(5,7,9,10,11,14:17,23,39,40)
                   )
df1[['patientID']] <- patientID
df1[['visit']] <- visit

View(df1)
```

```{r}
for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- s[[1]][[10]]
  visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

  df <- extract_pdf(i,
                    all_three = c(5,7,9,10,11,14:17,23,39,40)
                    )
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/site_13.csv')
```

## 14 site

```{r}
pdfs <- list.files(path = '/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/苏州开拓KX0826-CN-1004-女性雄秃项目-毛发镜报告2/KX-0826-CN-1004 -14中心-深圳人民', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )
print(length(pdfs))

head(pdfs)
```
```{r}
s <- str_split(pdfs[[1]], '/')
patientID <- str_split(s[[1]][[11]], '-')[[1]][[4]]
visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

df1 <- extract_pdf(pdfs[[1]],
                   all_three = c(5,7,9,10,11,14:17,23,39,40)
                   )
df1[['patientID']] <- patientID
df1[['visit']] <- visit

View(df1)
```

```{r}
for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- str_split(s[[1]][[11]], '-')[[1]][[4]]
  visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

  df <- extract_pdf(i,
                    all_three = c(5,7,9,10,11,14:17,23,39,40)
                    )
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/site_14.csv')
```

## 15 site

```{r}
pdfs <- list.files(path = '/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/苏州开拓KX0826-CN-1004-女性雄秃项目-毛发镜报告2/KX-0826-CN-1004 -15中心-西安交大二', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )
print(length(pdfs))

head(pdfs)
```
```{r}
s <- str_split(pdfs[[1]], '/')
patientID <- s[[1]][[10]]
visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

df1 <- extract_pdf(pdfs[[1]],
                   all_three = c(5,7,9,10,11,14:17,23,39,40)
                   )
df1[['patientID']] <- patientID
df1[['visit']] <- visit

View(df1)
```

```{r}
for(i in pdfs[2:length(pdfs)]){
  print(i)
  s <- str_split(i, '/')
  patientID <- s[[1]][[10]]
  visit <- str_split(s[[1]][[11]], '-')[[1]][[5]]

  df <- extract_pdf(i,
                    all_three = c(5,7,9,10,11,14:17,23,39,40)
                    )
  df[['patientID']] <- patientID
  df[['visit']] <- visit
  # print(df)
  
  df1 <- bind_rows(df1, df)
}
```

```{r}
df1 %>% select(patientID, visit, everything()) %>% 
  write_excel_csv('/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/site_15.csv')
```

## 16 site

```{r}
pdfs <- list.files(path = '/Users/congliu/OneDrive/kintor/Daily_Work/KX826_CN1004/苏州开拓KX0826-CN-1004-女性雄秃项目-毛发镜报告2/KX0826-CN-1004毛发评估表', recursive = TRUE, 
           pattern = '.pdf',
           full.names = TRUE
           )
print(length(pdfs))

head(pdfs)
```
```{r}

```