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I have a lot of pdf files and E-books , which do not have bookmarks for different chapters. Is there any software(preferably in gnu/linux) that could help me generate those automatically?windows software would also help.

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Maybe http://www.florian-diesch.de/software/pdfrecycle/ can help you, together with some shell scripts to create bookmark commands from a table of contents (using pdftotext or similar).

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My first suggestion would be to look at jPDFbookmarks.

You can also insert bookmarks using pdflatex with the hyperref package, even into a pre-existing PDF through the pdfpages package.

But I worry about the requirement that this ought to be done "automatically" -- that's going to be tricky. What exactly should a script or program "look for" in order to know where to insert a bookmark? The semantic notion of "Chapter" is not known to the PDF; PDFs just record what character or image or vector element goes where and what size, font, etc. Without the bookmarks, it doesn't contain information about chapter beginnings. Still, with some clever scripting it might be possible to whip up some artificial intelligence, especially if your PDFs are very consistent in how they're made, or have tables of contents in predictable formts. (Though of course if you have the source documents, you may want to go back to them.)

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