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blog:odborny:2025-05-07-command-line_tools_for_pdf_processing [2026/01/19 11:39] – Róbert Tothblog:odborny:2025-05-07-command-line_tools_for_pdf_processing [2026/05/15 13:10] (aktuálne) – Róbert Toth
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   * …   * …
  
-TODO+Due to the nature of the topic, this post is (and probably will remain) a work-in-progress. 
  
 ===== General: Overview of PDF-processing and manipulation tools ===== ===== General: Overview of PDF-processing and manipulation tools =====
  
 ==== Coherent PDF (cpdf) ==== ==== Coherent PDF (cpdf) ====
-  * **Download:**    https://www.coherentpdf.com/eval.html (fully functional demo)+  * **Download:**    https://www.coherentpdf.com/eval.html (fully functional demo) – the link at that page downloads all binaries, to select only needed binary, visit [[https://github.com/coherentgraphics/cpdf-binaries/|GitHub page]] and go to relevant folder.
   * **Changelog:**   https://www.coherentpdf.com/cpdfmanual/cpdfmanualap2.html#x26-177000B.1   * **Changelog:**   https://www.coherentpdf.com/cpdfmanual/cpdfmanualap2.html#x26-177000B.1
   * **Manual:**      https://www.coherentpdf.com/cpdfmanual/cpdfmanual.html   * **Manual:**      https://www.coherentpdf.com/cpdfmanual/cpdfmanual.html
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 ==== pdfcpu ==== ==== pdfcpu ====
   * **Download:**    https://github.com/pdfcpu/pdfcpu   * **Download:**    https://github.com/pdfcpu/pdfcpu
-  * **Changelog:**   https://pdfcpu.io/changelog.html+  * **Changelog:**   https://pdfcpu.io/changelog/
   * **Manual:**      https://pdfcpu.io/about/command_set   * **Manual:**      https://pdfcpu.io/about/command_set
  
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   * **Changelog:**   https://www.pdflabs.com/docs/pdftk-version-history/   * **Changelog:**   https://www.pdflabs.com/docs/pdftk-version-history/
   * **Manual:**      https://www.pdflabs.com/docs/pdftk-man-page/ ([[https://www.pdflabs.com/docs/pdftk-cli-examples/|examples here]])   * **Manual:**      https://www.pdflabs.com/docs/pdftk-man-page/ ([[https://www.pdflabs.com/docs/pdftk-cli-examples/|examples here]])
 +
 +==== QPDF ====
 +  * **Download:**    https://github.com/qpdf/qpdf/releases (for macOS using [[https://ports.macports.org/port/qpdf/details/|MacPorts QPDF port]])
 +  * **Changelog:**   https://qpdf.readthedocs.io/en/stable/release-notes.html
 +  * **Manual:**      https://qpdf.readthedocs.io/en/stable/cli.html
  
 <html> <html>
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 </html> </html>
  
-==== Other (non-tested) tools ==== +==== Other (non-/not-yet-tested) tools ==== 
-  * **QPDF:**        https://qpdf.sourceforge.io/ +TODO
-  * …+
 <html> <html>
 <!-- <!--
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 </html> </html>
  
-===== Minimize PDF size =====+ 
 +===== - Minimize PDF size =====
 **Example use-case:** Obvious. **Example use-case:** Obvious.
  
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 <code> <code>
 pdftk "in.pdf" output "out.pdf" compress pdftk "in.pdf" output "out.pdf" compress
 +</code>
 +
 +==== QPDF ====
 +[[https://qpdf.readthedocs.io/en/stable/cli.html#optimizing-file-size|Optimizing file size with qpdf]] suggests these flags to optimize file size:
 +  * **''[[https://qpdf.readthedocs.io/en/stable/cli.html#option-compress-streams|--compress-streams]]=y'':** This is the default, so it is not in fact needed.
 +  * **''[[https://qpdf.readthedocs.io/en/stable/cli.html#option-decode-level|--decode-level]]=generalized'':** Again, this is the default, so it is not in fact needed.
 +  * **''[[https://qpdf.readthedocs.io/en/stable/cli.html#option-recompress-flate|--recompress-flate]]'':** This forces recompression of already flate-compressed streams. This only make sense when combined with the ''--compression-level=9'' to achieve maximum compression.
 +  * **''[[https://qpdf.readthedocs.io/en/stable/cli.html#option-compression-level|--compression-level]]=9'':** Use maximum compression when flate-compressing PDF streams (the default is only ''6'').
 +  * **''[[https://qpdf.readthedocs.io/en/stable/cli.html#option-object-streams|--object-streams]]=generate'':** This will try to produce new object streams to lower file size as much as possible (the default is only ''preserve'').
 +So the resulting command is:
 +<code>
 +qpdf "in.pdf" --recompress-flate --compression-level=9 --object-streams=generate "out.pdf"
 </code> </code>
  
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   ; <color blue>Fonts</color> tab             : ✅ always on, with font subsetting turned on   ; <color blue>Fonts</color> tab             : ✅ always on, with font subsetting turned on
   ; <color blue>Transparency</color> tab      : 🚫 This causes optimisation to take extremely long time in some PDFs. My default is to have it turned off (and I cannot remember a situation when I actually needed to turn it on).   ; <color blue>Transparency</color> tab      : 🚫 This causes optimisation to take extremely long time in some PDFs. My default is to have it turned off (and I cannot remember a situation when I actually needed to turn it on).
-  ; <color blue>Discard Objects</color> tab   : ✅ Everything on, except **Discard bookmarks** (you never want that) and also **Convert smooth lines to curves** and **Detect and merge image fragments** (these are not needed in 99% of cases and they cause optimisation to take significantly longer, while they usually do not lower the PDF size at all). +  ; <color blue>Discard Objects</color> tab   : ✅ Everything on, except **Discard bookmarks** (you never want that) and also **Convert smooth lines to curves** and **Detect and merge image fragments** (these are not needed in 99% of cases and they cause optimisation to take significantly longer, while they usually do not lower the PDF size at all). You might also want to **Discard all Javascript actions**, but if there are any internal links (e.g. table of contents, references or index pointing to specific places in PDF), this causes them to disfunction. 
-  ; <color blue>Discard User Data</color> tab : ✅ Everything on.+  ; <color blue>Discard User Data</color> tab : ✅ Everything on. Note, however, that if you have any internal cross-references (e.g. clickable links from Contents page to specific parts of the document) in the PDF, you have to turn off **Discard all comments, forms and multimedia**, since this will also remove all these links.
   ; <color blue>Clean Up</color> tab          : ✅ Everything on.   ; <color blue>Clean Up</color> tab          : ✅ Everything on.
  
-===== Split each page of PDF into several pages (posterisation) =====+=== ❗️"Save as optimized PDF" in Acrobat breaks hyperlinks (internal cross-references)❗️ === 
 +This is just an addition to a note above under //<color blue>Discard User Data</color> tab//. I want to repeat it because it can seriously break your workflow and it is completely undocumented (and unexpected). 
 + 
 +Having **Discard all comments, forms and multimedia** (under **Discard User Data** tab) turned on while optimising PDF in Adobe Acrobat will also remove all internal cross-references (e.g. clickable links from Contents page to specific parts of the document). This was spotted [[https://graphicdesign.stackexchange.com/questions/68389/save-as-optimized-pdf-in-acrobat-breaks-hyperlinks-created-in-indesign|here on GraphicDesign stack exchange]]. 
 + 
 + 
 +===== - Split each page of PDF into several pages (posterisation) =====
 **Example use-case:** you have (scanned) pages where each PDF page contains two physical pages, and want to crop those into two. **Example use-case:** you have (scanned) pages where each PDF page contains two physical pages, and want to crop those into two.
  
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 The second step might also be done in Adobe Acrobat "Crop pages" function. The second step might also be done in Adobe Acrobat "Crop pages" function.
  
 +==== QPDF ====
 +N/A (not tested yet TODO)
  
-===== Crop pages of PDF =====+ 
 +===== - Crop pages of PDF =====
 See MuPDF documentation on [[https://mupdf.readthedocs.io/en/latest/mutool-trim.html#mutool-trim-defined-boxes|different PDF page boxes]] (media|crop|art|trim|bleed]box). See MuPDF documentation on [[https://mupdf.readthedocs.io/en/latest/mutool-trim.html#mutool-trim-defined-boxes|different PDF page boxes]] (media|crop|art|trim|bleed]box).
  
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 Note that Acrobat won't let you crop MediaBox, only other boxes (duh!). Note that Acrobat won't let you crop MediaBox, only other boxes (duh!).
   - Go to "Edit PDF" and then "Crop pages" function.   - Go to "Edit PDF" and then "Crop pages" function.
 +
 +==== QPDF ====
 +N/A (not tested yet TODO)
  
  
-===== Remove cropped content from PDF =====+===== - Remove cropped content from PDF =====
 **Example use-case:** You have cropped some pages but you want to actually remove the content, since otherwise it is only hidden but remains in PDF – this can be seen when you inspect the PDF in Adobe Acrobat via "Edit PDF" and zoom out the page – the cropped content will be selectable, although not visible, since it is out of the page margins. **Example use-case:** You have cropped some pages but you want to actually remove the content, since otherwise it is only hidden but remains in PDF – this can be seen when you inspect the PDF in Adobe Acrobat via "Edit PDF" and zoom out the page – the cropped content will be selectable, although not visible, since it is out of the page margins.
  
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   - Run preflight and the script   - Run preflight and the script
  
 +==== QPDF ====
 +N/A (not tested yet TODO)
  
-===== Text in Calibri-created PDF files cannot be copied/searched in Preview =====+ 
 +===== - Text in Calibri-created PDF files cannot be copied/searched in Preview =====
 Preview app (or any PDFkit-based PDF viewer, such as Skim) cannot search/copy text from PDFs generated by Calibri. This is because the PDF created in such way uses CID Fonts, something which Preview app based on Apple's PDFKit does not support. Preview app (or any PDFkit-based PDF viewer, such as Skim) cannot search/copy text from PDFs generated by Calibri. This is because the PDF created in such way uses CID Fonts, something which Preview app based on Apple's PDFKit does not support.
  
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-===== Decompress the whole PDF for editing in text editor =====+===== - Decompress the whole PDF for editing in text editor =====
 **Example use-case:** There are some cases when you need to see or edit the actual text contents of the PDF. For example, there are some metadata at the level of individual pages (like ) which no existing program will actually clean (Acrobat "Find hidden information" lists them, but keeps them there when you select to remove them). **Example use-case:** There are some cases when you need to see or edit the actual text contents of the PDF. For example, there are some metadata at the level of individual pages (like ) which no existing program will actually clean (Acrobat "Find hidden information" lists them, but keeps them there when you select to remove them).
  
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 </code> </code>
 As mentioned by manual, ''[[https://www.coherentpdf.com/cpdfmanual/cpdfmanualch1.html#x5-360001.12|-no-preserve-objstm]]'' will remove data from separate object streams and put them back into normal flow of PDF, which should make the PDF easier for direct editing. As mentioned by manual, ''[[https://www.coherentpdf.com/cpdfmanual/cpdfmanualch1.html#x5-360001.12|-no-preserve-objstm]]'' will remove data from separate object streams and put them back into normal flow of PDF, which should make the PDF easier for direct editing.
 +
 +<color red>**Warning:**</color> After processing a PDF using this command (with or without the ''-no-preserve-objstm'' switch), I have not been able to use Adobe Acrobat's "Optimize" or "Compare documents" function on it ever again – no matter how much tinkering, document-processing, transforming and cleaning I did on the PDF. So I consider this method to be unreliable if you want to maintain Adobe Acrobat compatibility (which I always do).
  
 ==== MuPDF (mutool) ==== ==== MuPDF (mutool) ====
 [[https://mupdf.readthedocs.io/en/1.24.0/mutool-clean.html|mutool clean]]: [[https://mupdf.readthedocs.io/en/1.24.0/mutool-clean.html|mutool clean]]:
 <code> <code>
-mutool clean -d [-a] "in.pdf" "out.pdf"+mutool clean -d "in.pdf" "out.pdf"
 </code> </code>
-''mutool clean'' is specifically stated by developer as designated to "make a PDF file human editable" and to "expand compressed streams", so this is the command to go. There are two switches which deal with PDF decompression: +''mutool clean'' is specifically stated by developer as designated to "make a PDF file human editable" and to "expand compressed streams", so this is the command to go. 
-  * **''-d'' (Decompress streams):** the basic switch for decompressing the whole file, + 
-  * **''-a'' (ASCII hex encode binary streams):** this safely encodes binary streams so that there should be no problems when editing the PDF in text editor.+There is one additional switch which deals with PDF decompression: **''-a''**, which ASCII-hex-encodes binary streams. This safely encodes binary streams so that there should be no problems when editing the PDF in text editor. However, this forces almost //**all**// streams in PDF to be encoded, which makes the whole PDF human-unreadable, so it is not really helpful. 
 + 
 +Of all tested tools, ''mutool clean'' is the only one which maintains original object reference numbers (e.g. ''/Metadata 22 0 R'' referencing object #22). 
 + 
 +<color red>**Warning:**</color> After processing a PDF using this command (with or without the ''-a'' switch), I have not been able to use Adobe Acrobat's "Optimize" or "Compare documents" function on it ever again – no matter how much tinkering, document-processing, transforming and cleaning I did on the PDF. So I consider this method to be unreliable if you want to maintain Adobe Acrobat compatibility (which I always do).
  
 ==== pdfcpu ==== ==== pdfcpu ====
-[[https://pdfcpu.io/core/TODO|pdfcpu TODO]]: +pdfcpu does not seem to support decompressing PDFs.
-<code> +
-pdfcpu TODO "in.pdf" "out.pdf" +
-</code>+
  
 ==== PDFtk server (pdftk) ==== ==== PDFtk server (pdftk) ====
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 pdftk "in.pdf" output "out.pdf" uncompress pdftk "in.pdf" output "out.pdf" uncompress
 </code> </code>
 +PDFtk separates individual PDF dictionary elements by newlines (''0A''). E.g. a page definition looks like this:
 +<code>
 +<<
 +/pdftk_PageNum 7
 +/Metadata 23 0 R
 +/Rotate 0
 +/Resources 24 0 R
 +/Type /Page
 +/Parent 25 0 R
 +/Contents 26 0 R
 +/MediaBox [0 0 370.158 591.26]
 +/CropBox [0 0 370.158 591.26]
 +>>
 +</code>
 +It also adds its own elements (e.g. ''/pdftk_PageNum'').
 +
 +
 +==== QPDF ====
 +[[https://qpdf.readthedocs.io/en/stable/cli.html#option-stream-data|qpdf --stream-data=uncompress]]:
 +<code>
 +qpdf "in.pdf" --stream-data=uncompress "out_qpdf.pdf"
 +</code>
 +This will effectively equivalent to using both [[https://qpdf.readthedocs.io/en/stable/cli.html#option-compress-streams|--compress-streams=n]] and [[https://qpdf.readthedocs.io/en/stable/cli.html#option-decode-level|--decode-level=generalized]].
 +
 +There is also another switch, ''[[https://qpdf.readthedocs.io/en/stable/cli.html#option-qdf|--qdf]]'', which TODO
 +
 +QPDF currently [[https://github.com/qpdf/qpdf/issues/339|does not support]] maintaining the original object ID.
 +
 +
 +===== - Resetting PDF page coordinates (remove CropBox/MediaBox shift) =====
 +**Example use-case:** you have a PDF with pages consisting of scanned images, which are cropped accordingly so that each page is the same size and the real scanned page is situated properly inside the PDF page. You want to OCR these pages (using Adobe Acrobat's OCR to "Editable text & images"). However, while doing OCR, Acrobat also resets all the page coordinates to (0,0), which causes some other page elements (e.g. annotations, internal hyperlinks etc.) to become improperly shifted away. So the solution in this case is to manually reset these coordinates in the original PDF before trying to OCR it.
 +
 +==== TL;DR: Summary first ====
 +<color blue/lightgrey>**Conclusion:** Use Coherent PDF's ''-upright'' method below. No other tool is capable of doing this.</color>
 +
 +==== Coherent PDF (cpdf) ====
 +Although listed under "Rotating Pages" section, the [[https://www.coherentpdf.com/cpdfmanual/cpdfmanualch3.html#x6-560003.4|cpdf -upright]] method also "makes sure the media box has its origin at (0,0), changing other boxes to compensate" – which is exactly what we wanted! And it is //this// easy:
 +<code>
 +cpdf -upright "in.pdf" -o "out.pdf"
 +</code>
 +
 +
 +===== - Make Adobe Acrobat appear in "Open with" menu for images =====
 +  * **Example use-case #1:** You want to create PDF from image //quickly//. When you open an image in Adobe Acrobat, it automatically converts it to PDF file. This //would be// perfect, if Acrobat actually allowed you to open image files directly.
 +  * **Example use-case #2:** You have a series of scanned pages which you want to combine into a PDF. When you open several images with Acrobat, it will automatically ask you whether you want to combine them into single PDF file. Again, this would be perfect, if you were allowed to open those images in Acrobat…
 +
 +Adobe Acrobat is perfectly capable of opening common image types (e.g. ''*.jpg'', ''*.png'' or ''*.tiff'' files) and in this case, it automatically converts them to PDF file. Yet, it does not register itself as an app for opening those files. This means that you must:
 +  * either manually locate the ''Adobe Acrobat.app'' through ''Open with → Other…'' command each time you want to open an image in Acrobat,
 +  * //or// you can open the image from Acrobat, but in this case you must click the ''Options'' button in Open menu and select ''All files'' under ''Show:'' menu – otherwise you won't be able to select image files in the Open menu (they will be greyed-out). Again, you have to do this every single time you want to open an image in Acrobat.
 +
 +==== Solution: Manually adding images as Acrobat-recognized file types ====
 +  - Locate ''info.plist'' file under ''Adobe Acrobat.app → Contents''
 +  - Make a backup copy of the file (this will ask for a password, since Acrobat installs itself with extra permissions).
 +  - Open ''info.plist'' file with editor and locate a ''<nowiki><key>CFBundleDocumentTypes</key></nowiki>'' line.
 +  - Add the following lines to the beginning of the ''<array>'' section – like this:<WRAP prewrap><code xml>
 +<key>CFBundleDocumentTypes</key>
 +<array>
 + <!-- FurloSK BEGIN: added jpg, tiff, png extensions -->
 + <!-- after changing, run this command to refresh system associations:
 + /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -f "/Applications/Adobe Acrobat DC/Adobe Acrobat.app/"
 + -->
 + <dict>
 + <key>CFBundleTypeName</key>
 + <string>JPEG Image</string>
 + <key>CFBundleTypeRole</key>
 + <string>Viewer</string>
 + <key>LSHandlerRank</key>
 + <string>Alternate</string>
 + <key>LSItemContentTypes</key>
 + <array>
 + <string>public.jpeg</string>
 + </array>
 + </dict>
 + <dict>
 + <key>CFBundleTypeName</key>
 + <string>Portable Network Graphics Image</string>
 + <key>CFBundleTypeRole</key>
 + <string>Viewer</string>
 + <key>LSHandlerRank</key>
 + <string>Alternate</string>
 + <key>LSItemContentTypes</key>
 + <array>
 + <string>public.png</string>
 + </array>
 + </dict>
 + <dict>
 + <key>CFBundleTypeName</key>
 + <string>TIFF Image</string>
 + <key>CFBundleTypeRole</key>
 + <string>Viewer</string>
 + <key>LSHandlerRank</key>
 + <string>Alternate</string>
 + <key>LSItemContentTypes</key>
 + <array>
 + <string>public.tiff</string>
 + </array>
 + </dict>
 + <!-- FurloSK END: added jpg, tiff, png extensions -->
 + <!-- … continuing with the default Document Types -->
 + <dict>
 + <key>CFBundleTypeExtensions</key>
 + <array>
 + <string>acrobatsecuritysettings</string>
 + </array>
 + …
 +</code></WRAP>
 +  - After this, force macOS to refresh file types associations from Acrobat by running:<WRAP prewrap><code>
 +/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -f "/Applications/Adobe Acrobat DC/Adobe Acrobat.app/"
 +</code></WRAP>
 +  - Done! ''Open with'' menu should now list Adobe Acrobat for ''*.jpg'', ''*.png'' or ''*.tiff'' file types.
 +
 +=== Possible code-signing issue ("Signature not valid" warning) ===
 +This is not happening specifically with Acrobat, but generally speaking, when you change an app's ''Info.plist'' file (or, for that matter, any other resource inside the App bundle) and that app is signed, its _CodeSignature will no longer be valid and you might be unable to re-run the app. In that case, you need to force app re-signing with this command: <code>codesign --force --deep --sign - /Applications/Adobe Acrobat DC/Adobe Acrobat.app</code>
 +
 +Original source: [[https://www.reddit.com/r/MacOS/comments/1ddq9lf/comment/l8841yp/|Reddit]]
 +
  
  
 +===== New cases to come… =====
 <html> <html>
 +<!-- ———————————————————————————————————————————————————————————————————————————————————————————————
 +———————————————————————————————————————————————————————————————————————————————————————————————  -->
 <!-- New Case Template BEGIN <!-- New Case Template BEGIN
-===== New Case TODO =====+===== - New Case TODO =====
 **Example use-case:** TODO. **Example use-case:** TODO.
  
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 <code> <code>
 pdftk "in.pdf" output "out.pdf" TODO pdftk "in.pdf" output "out.pdf" TODO
 +</code>
 +
 +==== QPDF ====
 +[[https://qpdf.readthedocs.io/en/stable/cli.html#TODO|qpdf --TODO]]:
 +<code>
 +qpdf "in.pdf" --TODO "out.pdf"
 </code> </code>
 --><!-- New Case Template END --> --><!-- New Case Template END -->
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 ===== Comments ===== ===== Comments =====
blog/odborny/2025-05-07-command-line_tools_for_pdf_processing.1768819146.txt.gz · Posledná úprava: 2026/01/19 11:39 od Róbert Toth