Save a pandas dataframe as table in Image or pdf document with nice multi index display

Question

I'm trying to include a data frame with multi-index in a report in pdf. I would like to have a nice table output.

I have found these 2 solutions:

pandas.df -> HTML -> pdf

    import pandas as pd
    from IPython.display import HTML
    import pdfkit

    # df generation
    df = pd.read_csv(path_to_csv, sep =',')
    groupeddf = df.groupby('Cluster')
    res = groupeddf.describe([0.05, 0.5, 0.95])
    res.index.rename(['Cluster', 'stats'], inplace=True)

    res['Cluster'] = res.index.get_level_values('Cluster')
    res['stats'] = res.index.get_level_values('stats')
    populations = (res.iloc[(res.index.get_level_values('stats') == 'count'), \
                                                            0].values).tolist()
    res['population'] = [populations[i] for i in res.index.labels[0].values()]
    total_pop = sum(populations)
    res['frequency'] =(res['population']/total_pop).round(3)
    res.set_index(['Cluster', 'population','frequency', 'stats'], inplace=True)



    res1 = res.iloc[(res.index.get_level_values('stats') == '5%') |
    (res.index.get_level_values('stats') == 'mean') |
    (res.index.get_level_values('stats') == '50%') |
    (res.index.get_level_values('stats') == '95%')]
    res1 = res1.round(2)
    # saving the df     
    h = HTML(res1.to_html())
    my_file = open('test.html', 'w')
    my_file.write(h.data)
    my_file.close()


    options = {
        'orientation': 'Landscape'
        }
    with open('test.html') as f:
        pdfkit.from_file(f, 'out.pdf', options=options)

But this has a dependence on pdfkit which make it difficult to us. That's why I am trying to use pandas.df -> tex -> pdf (as mentioned in Export a Pandas dataframe as a table image )

    import pandas as pd
    import os
    # df generation              
    df = pd.read_csv(path_to_csv, sep =',')
    groupeddf = df.groupby('Cluster')
    res = groupeddf.describe([0.05, 0.5, 0.95])
    res.index.rename(['Cluster', 'stats'], inplace=True)

    res['Cluster'] = res.index.get_level_values('Cluster')
    res['stats'] = res.index.get_level_values('stats')
    populations = (res.iloc[(res.index.get_level_values('stats') == 'count'), \
                                                            0].values).tolist()
    res['population'] = [populations[i] for i in res.index.labels[0].values()]
    total_pop = sum(populations)
    res['frequency'] =(res['population']/total_pop).round(3)
    res.set_index(['Cluster', 'population','frequency', 'stats'], inplace=True)



    res1 = res.iloc[(res.index.get_level_values('stats') == '5%') |
    (res.index.get_level_values('stats') == 'mean') |
    (res.index.get_level_values('stats') == '50%') |
    (res.index.get_level_values('stats') == '95%')]
    res1 = res1.round(2)
    res1.rename(columns=lambda x: x.replace('_', ' '), inplace=True)    

    #latex
    template = r'''\documentclass[preview]{{standalone}}
    \usepackage{{booktabs}}
    \begin{{document}}
    {}
    \end{{document}}
    '''

    with open("outputfile.tex", "wb") as afile: 
        afile.write(template.format(res1.to_latex()))
    os.system("pdflatex outputfile.tex")

However, I am not familiar with latex, and I get this error :

  ! LaTeX Error: File `standalone.cls' not found.

 Type X to quit or <RETURN> to proceed,
 or enter a new name. (Default extension: cls)

Any idea about the error or the standard way to do pandas.df -> pdf ?

score 2 · Accepted Answer · answered Jul 04 '16 at 16:29

The solution that work for me: With pandas >= 0.17 I installed pdflatex. I copied latex package such as booktabs.sty, geography.sty and pdflscape.sty

import pandas as pd
import os
import math

def save_summary_table_as_pdf(path_to_csv, path_to_output_folder):
    pwd = os.getcwd()
    df = pd.read_csv(path_to_csv, sep =',')

    #data preparation
    groupeddf = df.groupby('Cluster')
    res = groupeddf.describe([0.05, 0.5, 0.95])
    res.index.rename(['Cluster', 'Stats'], inplace=True)

    res['cluster'] = res.index.get_level_values('Cluster')
    res['stats'] = res.index.get_level_values('Stats')
    populations = (res.iloc[(res.index.get_level_values('Stats') == 'count'), \
                                                            0].values).tolist()
    res['population'] = [populations[i] for i in res.index.labels[0].values()]
    total_pop = sum(populations)
    res['frequency'] =(res['population']/total_pop).round(3)
    res.set_index(['cluster', 'population','frequency', 'stats'], inplace=True)
    res1 = res.iloc[(res.index.get_level_values('stats') == '5%') |
    (res.index.get_level_values('stats') == 'mean') |
    (res.index.get_level_values('stats') == '50%') |
    (res.index.get_level_values('stats') == '95%')]
    res1 = res1.round(2)
    res1.rename(columns=lambda x: x.replace('_', ' '), inplace=True)  

    #latex
    nbpages = int(math.ceil(res1.shape[0]*1.0/40))

    templatetop = r'''\documentclass[a3paper, 5pt]{article}
    \usepackage{booktabs}
    \usepackage{pdflscape}
    \usepackage[a4paper,bindingoffset=0.2in,%
            left=0.25in,right=0.25in,top=1in,bottom=1in,%
            footskip=.25in]{geometry}
    \begin{document}
    \begin{landscape}
    \pagenumbering{gobble}
    \oddsidemargin = 0pt
    \hoffset = -0.25in
    \topmargin = 1pt
    \headheight = 0pt
    \headsep = 0pt
    '''
    templatebottom = '''
    \end{landscape}
    \end{document}
    '''
    output_folder_path_abs = path_to_output_folder
    output_tex = os.path.join(output_folder_path_abs, 
    "clustering_summary_table.tex")

    with open(output_tex, "wb") as afile: 
        afile.write(templatetop +'\n')
        for i in range(0, nbpages):
            afile.write(res1.iloc[(i*40):((i+1)*40), :].to_latex() +'\n' + 
                                                """\pagenumbering{gobble}""")
        afile.write(templatebottom +'\n')
    os.chdir(output_folder_path_abs)
    os.system('pdflatex clustering_summary_table.tex')
    os.chdir(pwd)
    os.remove(output_tex)
    os.remove(os.path.join(path_to_output_folder, 
                                           'clustering_summary_table.aux'))
    os.remove(os.path.join(path_to_output_folder, 
                                           'clustering_summary_table.log'))

if __name__ == "__main__":
    print 'begin generate pdf table about clustering'
    import argparse
    parser = argparse.ArgumentParser()
    parser.add_argument("path_to_csv")
    parser.add_argument("outputfolder")
    args = vars(parser.parse_args())
    filedir = os.path.abspath(os.path.dirname(__file__))
    output_folder_path_abs = os.path.abspath(args['outputfolder'])
    input_folder_path_abs = os.path.abspath(args['path_to_csv'])
    # copy the user package latex to the folder
    os.system('scp '
    +os.path.abspath(os.path.join(filedir, 'userpackagelatex/booktabs.sty'))+
    ' ' +output_folder_path_abs)
    os.system('scp '
    +os.path.abspath(os.path.join(filedir, 'userpackagelatex/geography.sty'))+
    ' ' +output_folder_path_abs)
    os.system('scp '
    +os.path.abspath(os.path.join(filedir, 'userpackagelatex/pdflscape.sty'))+
    ' ' +output_folder_path_abs)
    save_summary_table_as_pdf(input_folder_path_abs, output_folder_path_abs)
    os.remove(os.path.join(output_folder_path_abs, 'booktabs.sty'))
    os.remove(os.path.join(output_folder_path_abs, 'geography.sty'))
    os.remove(os.path.join(output_folder_path_abs, 'pdflscape.sty'))

score 0 · Answer 2 · answered Jun 29 '16 at 10:43

0

Well one way is to use markdown. You can use df.to_html(). This converts the dataframe into a html table. From there you can put the generated html into a markdown file (.md) and use a package to convert markdown to pdf. https://www.npmjs.com/package/markdown-pdf

Would this be a good alternative?

answered Jun 29 '16 at 10:43

SerialDev

2,777
20
34

The first solution I have written (df -> HTML -> pdf) is working on my machine, however, the code can not run a a distant machine where I do not have the rights to install PDFkit. I guess I would be the same for makedown-pdf. That is why I need to limit dependencies as much as I can. – Luce Philibert Jun 29 '16 at 11:23
markdown-pdf isn't able to resize the pdf so it only contains the table – Chaoste Jul 29 '17 at 14:38

Save a pandas dataframe as table in Image or pdf document with nice multi index display

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