This project was inspired by and built upon org-pdfview from @markus1189.

You can now install org-pdftools and org-noter-pdftools from MELPA!

Run M-x pdf-tools-install after installation of pdftools if you haven’t done before.

(use-package org-noter
  :config
  ;; Your org-noter config ........
  (require 'org-noter-pdftools))

(use-package org-pdftools
  :hook (org-mode . org-pdftools-setup-link))

(use-package org-noter-pdftools
  :after org-noter
  :config
  ;; Add a function to ensure precise note is inserted
  (defun org-noter-pdftools-insert-precise-note (&optional toggle-no-questions)
    (interactive "P")
    (org-noter--with-valid-session
     (let ((org-noter-insert-note-no-questions (if toggle-no-questions
                                                   (not org-noter-insert-note-no-questions)
                                                 org-noter-insert-note-no-questions))
           (org-pdftools-use-isearch-link t)
           (org-pdftools-use-freepointer-annot t))
       (org-noter-insert-note (org-noter--get-precise-info)))))

  ;; fix https://github.com/weirdNox/org-noter/pull/93/commits/f8349ae7575e599f375de1be6be2d0d5de4e6cbf
  (defun org-noter-set-start-location (&optional arg)
    "When opening a session with this document, go to the current location.
With a prefix ARG, remove start location."
    (interactive "P")
    (org-noter--with-valid-session
     (let ((inhibit-read-only t)
           (ast (org-noter--parse-root))
           (location (org-noter--doc-approx-location (when (called-interactively-p 'any) 'interactive))))
       (with-current-buffer (org-noter--session-notes-buffer session)
         (org-with-wide-buffer
          (goto-char (org-element-property :begin ast))
          (if arg
              (org-entry-delete nil org-noter-property-note-location)
            (org-entry-put nil org-noter-property-note-location
                           (org-noter--pretty-print-location location))))))))
  (with-eval-after-load 'pdf-annot
    (add-hook 'pdf-annot-activate-handler-functions #'org-noter-pdftools-jump-to-note)))

• Incorporated https://github.com/weirdNox/org-noter/pull/93/commits/f8349ae7575e599f375de1be6be2d0d5de4e6cbf in Usage README
• Added customizable variable org-pdftools-use-isearch-link and org-pdftools-use-freepointer-annot to control whether you will get prompt to create isearch/freepointer link if no existing annotations are found

In order to link a specific page of a .pdf-file in an org-file, use the following syntax:

[[pdf:~/file.pdf::3][Link to page 3]]

When browsing a pdftools-buffer you can use org-store-link (by default C-c l) to get a link to this location withing the pdf – even while marking some content in the .pdf. Then use org-insert-link (by default C-c C-l) to create a link to this page and this place on the page:

[[pdf:~/file.pdf::5++0.00;;annot-5-0][file.pdf: Page 5; Quoting: some text]]

The provided function includes:

• [X] (Sort-of) backward compatibility with org-pdfview: simply change the link prefix from pdfview: to pdf:.
• [X] The reason this URL prefix change was proposed is that pdftools: links can also point to pdf-occur searchs. Multi-file search is also supported.
• [X] There is also support for pdf-isearch.
• [X] Beyond the original link implementation that stores only file path and page number, now you can store the precise location of annotations.
• [X] If there are selected texts on the current PDF page, it will be marked-up using pdf-tools markup functions (by default, underline) automatically and the corresponding annotation id is stored in the link.
• HTML exported link now have a “#page=n” postfix, which should make browsers like Chrome open the corresponding page.
• You can now customize the link description format using org-pdftools-get-desc-function
• Added org-noter-pdftools-embed-org-note-to-pdf, org-noter-pdftools-embed-all-org-note-to-pdf to copy one or all org-noter annotation headings (the ones with a annot-id and org-pdftools link) to the corresponding PDF file.
• Added org-noter-pdftools-embed-org-buffer-to-pdf to copy the whole org-noter buffer to a annotation in the left upper corner of the first page in the PDF.
• Added org-noter-pdftools-jump-to-note config in the README.
• The prefix of pdftools link can now be customized using org-pdftools-link-prefix, and the default is now set to “pdf”
• The org-pdftools-search-string-separator is now set to ?? to avoid org fontification problem
• You can now specify how the path of pdf is stored using two function:
• org-pdftools-path-generator takes buffer-file-name as an argument, and output a translated path. Default to abbreviate-file-name
• org-pdftools-path-resolver takes a translated path as an argument and translate it back to absolute path. Default to expand-file-name

You can use the vanilla org-noter now.

• [X] Integrate with org-noter, such that org-noter can remember the precise location (in the resolution of the exact annotation).
• [X] Jump from a PDF annotation to a associated org-heading org-noter-sync-* and org-noter-jump-to-heading.
• [X] Transform old org-noter notes to newer ones and sync with the corresponding PDF. org-noter-convert-old-notes
• [-] PDF annotation will have full and synced information with the associated org-note. (Besides the note content, each annotate will record the IDs of the corresponding org heading and potentially even it’s parent org heading, such that tree-rebuild is possible.)

This is the first step of a set of overhauls of Emacs PDF notetaking experience. The features below are planned (either in this package or as PR to other packages):

• [-] Optionally grab image/text excerpt from the PDF and insert below the corresponding org-heading. Please refer to pdf-view-extract-region-image, not sure what’s the best way to integrate it.
• [ ] Link export with image/text-based excerpt from the PDF.
• [ ] (Long-term) Org <-> PDF Annotation converter.