How to include a figure in PDF format?

[roaldarbol]

Description

When including a PDF as an image, which is quite common for academic papers, it renders as a scroll box with little height. The basic example could look like this (I have also attempted to add e.g. {height=100%} to no avail):

:::{#fig-myfigure}

![](figure-1.pdf)

My caption
:::

...which renders like this:

I guess the underlying issue is that it is inserted as in a PDF reader; I would expect it to render as a normal figure when it is inside a #fig div. Is there anyway to make it so?
Thanks in advance!

[mcanouil]

Please provide a fully reproducible example not a snippet out of context.

I will guess, the format is HTML.
I'm afraid a PDF is not an image, it's a binary format, thus it requires third party to be read which leads Pandoc to use iframe in HTML.
That's beyond Quarto or Pandoc control, that's how HTML works.

[roaldarbol]

It is indeed HTML. MyST converts PDFs to images with imagemagick before rendering, so I imagined a similar functionality to be present in Quarto, since many journals recommend submitting figures in PDF (e.g. nature, science, journal of experimental biology) hence the question. Thanks for the answer. :-)

[mcanouil]

Quarto does not depend on imagemagick and will very unlikely do so.
You can make a Lua filter to do that if you want.

PS: I am perfectly aware of journals guidelines (I spent more than 10 years in academia).

[roaldarbol]

Oh, that wasn't meant to sound like I questioned you - apologies of it sounded that way; it was just to ensure context, just as you explained PDF format although I've also spent 10 years in academia and know what it is - doesn't mean I didn't think it was relevant information. :-)

Fair game regarding the imagemagick dependency, I may have a look at how to make a Lua filter then.

[mcanouil]

Oh, that wasn't meant to sound like I questioned you - apologies of it sounded that way; it was just to ensure context, just as you explained PDF format although I've also spent 10 years in academia and know what it is - doesn't mean I didn't think it was relevant information. :-)

All is fine, I was only giving context on my background ;)

Fair game regarding the imagemagick dependency, I may have a look at how to make a Lua filter then.

See https://github.com/search?q=lua%20imagemagick&type=repositories to get you started.

https://quarto.org/docs/extensions/filters.html

[roaldarbol]

Thanks for the links! I'll report back if I get around to making one. ;)

[roaldarbol]

Ended up creating a Lua filter which converts PDF files to .webp format with some help from ChatGPT, which does this quite nicely. You can tweak the imagemagick settings a to your liking.

pdf-to-webp.lua, which I've for now just placed in the base of my workspace:

1. Converts .pdf to .webp in the source folder.
2. Except if a webp file is already generated
3. Checks whether the source .pdf file has changed, in which case it re-converts

---

EDIT: I've made the filter into an extension which can be found here: https://github.com/roaldarbol/pdf-to-image

---

-- Lua filter for Quarto to convert PDF images to WebP only in HTML output

-- Check if the current output format is HTML
local is_html = (quarto and quarto.doc.is_format("html"))

-- Function to check if a file exists
local function file_exists(name)
  local f = io.open(name, "r")
  if f then f:close() end
  return f ~= nil
end

-- Function to get the modification time of a file using a shell command
local function file_mod_time(name)
  local handle = io.popen('stat -f "%m" "' .. name .. '"') -- macOS or BSD
  local result = handle:read("*a")
  handle:close()
  
  return tonumber(result)
end

function Image(elem)
  -- Only proceed if output format is HTML and the image is a PDF
  if is_html and elem.src:match("%.pdf$") then
    -- Define new filename for the WebP version
    local webp_src = elem.src:gsub("%.pdf$", ".webp")

    -- Check if WebP file exists and compare modification times
    local pdf_time = file_mod_time(elem.src)
    local webp_time = file_exists(webp_src) and file_mod_time(webp_src)

    -- If WebP doesn't exist or the PDF is newer, convert PDF to WebP
    if not webp_time or (pdf_time and pdf_time > webp_time) then
      -- Run the ImageMagick command to convert PDF to WebP
      os.execute(string.format('magick -density 600 -colorspace RGB "%s" "%s"', elem.src, webp_src))
    end

    -- Update image source to the new or existing WebP file
    elem.src = webp_src
  end

  return elem
end

And added it in _quarto.yml:

format:
  html:
    filters:
      - pdf-to-webp.lua

[mcanouil]

Thanks for sharing your filter.

[roaldarbol]

Thanks for the pointers! Fun trying something new! 😄