Working With PDF Files

The Portable Document Format, or PDF, is a standard fixed-layout file type that is a good file type to use when publishing data that will not need to be edited. For example, it is a good file type to use when publishing the final version of a figure or submitting the final draft of a paper or grant application. In general, PDF files will preserve formatting and appear identical on different systems that can view them. PDF files are also able to include both vector and bitmap image data, which also allows them to preserve the full quality of figures that contain both bitmap image data and text and other vector graphics data.

The Figure Editing and Image Preparation Workshop, which is available here, has information on how to prepare high-quality figures and explains lots of important concepts that are relevant when generating PDF files.

Creating PDFs

There are many ways to create PDF files. Current versions of Microsoft Office, such as Office 2013 for Windows or Office 2011 for OS X can save directly to PDF format. To generate a PDF from a Word, Excel, and/or PowerPoint file, simply open the file in the corresponding Office application, then go to File, select Save As, then select PDF as the format/file type.

OpenOffice Draw, which is useful for creating figures, can be used to save directly to PDF by navigating to the File menu and selecting Export As PDF. When generating a PDF file in this way, unless there is a requirement to do otherwise, make sure that Lossless compression is selected in the Images section of the General tab in the PDF Options window that appears when saving. Many of the advanced options for generating PDFs in this way with OpenOffice are discussed in the Figure Editing and Image Preparation Workshop.

When using programs, such as a web browser, that do not have the option to save directly to PDF, there are various ways to generate PDF files.

On an OS X computer, PDFs can be generated from most applications by preparing to print a document (for example, by going to the File menu and selecting Print in most applications) and then clicking the PDF button in the lower-left corner of the print window and selecting Save As PDF. The system will then prompt for a file name and location and will generate a PDF file.

On a Windows computer, it may not be possible to save directly to PDF from some programs. However, it is possible to generate an Open XML Paper Specification, or XPS, file from most programs by preparing to print a document (for example, by going to the File menu and selecting Print in most applications) and then selecting the Microsoft XPS Document Writer as the printer, adjusting the print formatting options as necessary, and clicking Print. The system will then display the Save Print Output As window. Be sure to select XPS Document (*.xps) from the Save as type pulldown menu; do not use the OpenXPS Document (*.oxps) type as this type is not as well supported at the moment. Select a location to save the file, enter a file name, and click Save.

It is possible to convert an XPS file to a PDF file in several ways. If the XPS file does not contain any confidential information, one way to generate a PDF file from an XPS is to upload an XPS file to Google Drive, then view the file in Google Drive and print the file using Google Drive's print tool, which will generate a PDF version that can be downloaded and saved. Again, it is critical to ensure that no confidential data are in the XPS file when using this conversion service as this process discloses data to third parties (i.e., Google).

Another method to convert an XPS file to a PDF is to go to a Windows computer with Adobe Acrobat Professional installed, such as the PedOnc Core imaging workstations, and open Adobe Acrobat Professional. From the File menu in Adobe Acrobat Pro, select Open. In the lower-right corner of the Open window that appears, select All Files from the pull-down menu, then open the XPS file that will be converted. Once the file is open, go to the File menu and select Save As, then save the file as a PDF.

Editing PDFs

To edit existing PDF files, you will need Adobe Acrobat Professional. On a system with Acrobat Pro installed, for example, one of the PedOnc Core imaging workstations, open Acrobat Pro then go to the File menu, select Open, and open the PDF file you want to edit.

To extract or add pages, click Tools, then Pages and use the options listed to delete, extract, replace, or insert pages.

To reduce a PDF file's size, open the PDF in Acrobat Pro, then go to the File menu and select Save As. Select Adobe PDF Files, Optimized and click the Settings button to select options to change the formatting of the PDF file. It is important to note that modifying the way that data is stored in a PDF file can reduce the PDF's quality, so be sure to use appropriate settings to preserve quality.