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I am writing my thesis, which is currently approx 30 pages long. When I convert it to a PDF-file, the file size is 52.3 MB, which is unbelievably big. I have used 14 images, in which I have rescaled to a smaller size. Furthermore, I have used 5 tables in which 2 have overfull/underfull boxes.

These are the packages I am using:

\documentclass[11pt, a4paper]{report}
\usepackage[utf8]{inputenc}
\usepackage{graphicx}
\usepackage{amsmath} 
\usepackage[hidelinks]{hyperref}
\usepackage{nomencl}
\usepackage{float}
\usepackage{textcomp}
\usepackage[version=3]{mhchem}
\usepackage{booktabs}
\usepackage[margin=0.9in]{geometry}
\parskip=0.05in

The code I use for images (here is one of the images on my thesis):

\begin{figure}[H]
\caption{Cross section of fresh concrete subject to different types of separation \cite{Bur}.}
\centering
\label{sep}
\includegraphics[width=100mm,scale=0.5]{../Figurer/sep}
\end{figure}

and the code Im using for most of my tables (code from one of the tables):

\begin{table}[H]
\centering
\footnotesize
\caption{Concrete mix proportions \cite{Cengiz}}
\resizebox{\textwidth}{!}{%
\begin{tabular}{p{1cm} p{1cm} p{1.4cm} p{1cm} p{1.5cm} p{1.5cm} p{1.5cm} p{1.5cm} p{1cm}} \toprule
{Mixture no} & {Cement [kg/$m^3$]} & {Fly Ash [kg/$m^3$]} & {Sand [kg/$m^3$]} & {Gravel [kg/$m^3$]} & {Water [kg/$m^3$]} & {Optimum W/C} & {Actual W/(FA+C)} & {SP [l/$m^3$]}\\ \midrule
    M0  & 400 & - & 600 & 1200 & 220 & - & 0.55 & -\\
    M1  & 120 & 280 & 600 & 1200 & 112 & 0.29 & 0.28 & 5.6\\
    M2  & 120 & 280 & 600 & 1200 & 116 & 0.29 & 0.29 & -\\
    M3 & 200 & 200 & 600 & 1200 & 132 & 0.30 & 0.33 & 5.6\\
    M4 & 200 & 200 & 600 & 1200 & 120 & 0.30 & 0.30 & - \\
   \bottomrule
   \label{mix}
\end{tabular}%
}
\end{table}

Why is my PDF file so large?

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Turns out that there is nothing wrong with the OPs files or LaTeX setup. By mistake, the OP had not realised that running pdflatex, actually generates a PDF file on disk and that the PDF viewer in the editor is just showing that PDF from disk.

Instead the OP chose to print the PDF to disk as a PDF (this might be normal in for example older versions of Word, nowadays even Word has a Save as PDF feature). Printing a file often means decompressing it and its contents, aka all images in the file. So saving the printed file as a PDF, most likely saves the PDF with all of its contents uncompressed, thus resulting in a very large file on disk.

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