File size: 4,746 Bytes
9f29b8f | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 | #!pip install PyMuPDF
import pandas as pd
import numpy as np
import fitz
import os
from datetime import datetime
def collate_pdfs(pdf_dir,project=None,samples=None,save_dir=None,addlabel=True):
'''
cobbles together a proper order to merge all the generated pdfs after the fact
#example combining outputs from batch run (keeps samples separate)
for proj in projects:
for sample in samples[proj]:
pdf_dir = os.path.join(batch_dir[proj],sample+'_run')
#print(pdf_dir)
collate_pdfs(pdf_dir,project='HSPB5_'+sample+'_'+proj,save_dir=batch_dir[proj])
'''
now = datetime.now()
date = now.strftime("%d%b%Y")
def categorize(df,types,search_col,new_col):
for i,type in enumerate(types):
df[type] = np.where(df[search_col].str.contains(type),str(i)+type,'')
df[new_col]=''
# for type in types:
# df[new_col] += pdf_info[type]
df[new_col] = df.apply(lambda x: max(x[types],key=len),axis=1)
df = df.drop(types,axis=1)
return df
def add_header(mfile,header_text):
for page in mfile:
prect = page.rect
header_rect = fitz.Rect(0, 10, prect.width-10,30) # height 20 points
page.insert_textbox(header_rect, header_text,
fontname="hebo", color= fitz.pdfcolor["blue"],
align=fitz.TEXT_ALIGN_RIGHT)
return mfile
output_types = ['IndFits','BootFits','ndeut']
pdfs = [ f for f in os.listdir(pdf_dir) if f[-4:]=='.pdf' ]
pdfs = [ p for p in pdfs if p[0:5]=='hxex_']
pdf_info = pd.DataFrame({'file':pdfs})
pdf_info = categorize(pdf_info,output_types,'file','type')
if samples is not None:
samples = samples if isinstance(samples,list) else [samples]
pdf_info = categorize(pdf_info,samples,'file','sample')
else: pdf_info['sample'] = ''
if project is not None: proj_str = project+'_'
else: proj_str = ''
if save_dir is None: save_dir = pdf_dir
pdf_info[['start_res','end_res']] = ''
pdf_info['start_res'] = pdf_info['file'].str[:-4].str.split('-',n=1,).str[0].str[-4:].astype('Int64')
pdf_info['end_res'] = pdf_info['file'].str[:-4].str.split('-',n=1,).str[1].str[0:4].astype('Int64')
pdf_info['charge'] = pdf_info['file'].str[:-4].str.split('_').str[-3].str[1:].astype('Int64')
#pdf_info['data_id'].str[:-4].str.split('_').str[1].astype('Int64')
pdf_info = pdf_info.sort_values(['start_res','end_res','sample','charge','type']).reset_index(drop=True)
pdf_info['type'] = pdf_info['type'].str[1:]
pdf_info['sample'] = pdf_info['sample'].str[1:]
#display(pdf_info)
sorted_pdfs = pdf_info['file'].values
sorted_pdfs = [s for s in sorted_pdfs if '_all_' not in s]
sorted_pdfs_Ind = [s for s in sorted_pdfs if 'Ind' in s]
sorted_pdfs_BootFits = [s for s in sorted_pdfs if 'BootFits' in s]
sorted_pdfs_ndeut = [s for s in sorted_pdfs if 'ndeut' in s]
#sorted_pdfs
result = fitz.open()
for pdf in sorted_pdfs:
with fitz.open(os.path.join(pdf_dir,pdf)) as mfile:
if addlabel:
data_id = pdf.split('_')[1]
header_text = "data_id: "+data_id
mfile = add_header(mfile,header_text)
result.insert_pdf(mfile)
result.save(os.path.join(save_dir,'hxex_all_plots_'+proj_str+date+'.pdf'))
result = fitz.open()
for pdf in sorted_pdfs_Ind:
with fitz.open(os.path.join(pdf_dir,pdf)) as mfile:
if addlabel:
data_id = pdf.split('_')[1]
header_text = "data_id: "+data_id
mfile = add_header(mfile,header_text)
result.insert_pdf(mfile)
result.save(os.path.join(save_dir,'hxex_all_IndFits_'+proj_str+date+'.pdf'))
result = fitz.open()
for pdf in sorted_pdfs_BootFits:
with fitz.open(os.path.join(pdf_dir,pdf)) as mfile:
if addlabel:
data_id = pdf.split('_')[1]
header_text = "data_id: "+data_id
mfile = add_header(mfile,header_text)
result.insert_pdf(mfile)
result.save(os.path.join(save_dir,'hxex_all_BootFits_'+proj_str+date+'.pdf'))
result = fitz.open()
for pdf in sorted_pdfs_ndeut:
with fitz.open(os.path.join(pdf_dir,pdf)) as mfile:
if addlabel:
data_id = pdf.split('_')[1]
header_text = "data_id: "+data_id
mfile = add_header(mfile,header_text)
result.insert_pdf(mfile)
result.save(os.path.join(save_dir,'hxex_all_ndeutBoot_'+proj_str+date+'.pdf'))
return
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