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New Feature: internal links to tables and figures and headers #813

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GeraldLoeffler opened this issue Apr 4, 2013 · 138 comments
Open

New Feature: internal links to tables and figures and headers #813

GeraldLoeffler opened this issue Apr 4, 2013 · 138 comments

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@GeraldLoeffler
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@GeraldLoeffler GeraldLoeffler commented Apr 4, 2013

It's currently possible to include internal links to sections. I'd like to propose a similar feature for links to figures/images and tables.

It may make sense to provide this feature only if the figure/image or table that is being linked to has a caption. In that case Pandoc can today automatically generate a number for the figure or table and include it in the caption, e.g. "Figure 15".

At the most basic, the text of the link would be provided by the user, as is currently the case for links to sections.

Of course it would be very convenient if the automatically generated number for the figure or table would also be used for the text of the link, e.g. "as can be seen in Figure 15, blah", where "Figure 15" would be the internal link whose text is auto-generated from the figure it points to.

@kovla
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@kovla kovla commented May 3, 2013

That would be lovely indeed. In academic writing it is quite often necessary, and while automatic numbering of figures and tables is nice, it really should be linked to what is in the text.

@nichtich
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@nichtich nichtich commented May 21, 2013

One could use the figure caption as link target, similar to links to captions:

![la lune](lalune.jpg "Voyage to the moon")

...is shown in figure [la lune]...

And/or without automatic generation of link text:

...is shown in [the figure](#la-lune)...

See also issue #615 on automatic numbering of figures and tables in HTML output.

@liob
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@liob liob commented Jul 23, 2013

I concur. However, @nichtich suggestion breaks the current syntax. Maybe a less intrusive approach would be a syntax like:

![Voyage to the moon](lalune.jpg){la lune}

It would be great to be able to reference figures. As @nichtich said: it is nearly a requirement in academic writing.

@jgm
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@jgm jgm commented Jul 23, 2013

A more consistent format would be

![Voyage to the moon](lalune.jpg){#lalune}

See the current attribute format for headers.

@liob
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@liob liob commented Jul 27, 2013

indeed, that is a more consistent format.

About the implementation:
I see 2 major ways to implement this feature:

  1. Emulate something like the latex figure environment and output the figure as image with plain text underneath. Very much like figures are handled now in docx format, except that you put "Figure 1:" at the beginning. This would be the most portable way and should be fairly easy to implement in all format writers. However, than pandoc has to keep track of the references itself for cross referencing.
  2. Implement it the "proper" way in the corresponding format writer. Sticking with the docx example: Adding a caption to the image and then cross reference it in the text.

Can anybody (@jgm ?) make an educated guess on how much work either of the solutions will be?

@aaren
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@aaren aaren commented Sep 10, 2013

I agree - this is essential for academic writing. I wish I knew Haskell!

The current way around this, in the mailing list discussion, is functional but clumsy.

Would this mean using \autoref in the latex? Then from markdown input:

...is shown in [the figure](#la-lune)...

you would get the latex output:

...is shown in \autoref{la-lune}...
@AvverbioPronome
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@AvverbioPronome AvverbioPronome commented Sep 19, 2013

![Voyage to the moon](lalune.jpg){#lalune}

I just tried to write something like

Some text

![Bla blah](pic.png)   {#something}

Some other text

I was surprised that did not work. It showed the image without caption, and a raw "{#something}" afterwards.

I assumed curly braces were for assigning attributes to anything... :D

@CFCF
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@CFCF CFCF commented Nov 16, 2013

A workaround with numbered example lists is added to #904

For my purposes, this method works well with docx.

@Utsira
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@Utsira Utsira commented Mar 29, 2014

I agree that being able to reference figures is essential to academic writing. The workarounds linked to above aren't really satisfactory, in my opinion

![Voyage to the moon](lalune.jpg){#lalune} would be perfect

@jgm jgm added the enhancement label Mar 31, 2014
@srhb
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@srhb srhb commented Apr 24, 2014

Similar syntaxes would be very interesting for equations, too. In fact, why not adopt a completely general syntax? It would be especially nice if it could carry over to LaTeX bits, once you have to bail out and use say \begin{align} and friends.

@frederik-elwert
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@frederik-elwert frederik-elwert commented Apr 25, 2014

I have sympathy for the numbered example list approach, mainly for two reasons: Firstly, what we want are not really links but references, and secondly, the use case for numbered example lists is already close to, e.g., numbered equations. The example from the docs is close to a typical use case for figure references:

(@good)  This is a good example.

As (@good) illustrates, ...

This mechanism can already be used for figure references, as CFCF pointed out:

![Figure (@primitive_hut): The primitive hut](Illustrations\primitive_hut.png)

As can be seen in Figure (@primitive_hut), huts may be primitive.

# Index of Figures

(@primitive_hut) *Primitive hut* from the frontispiece of Marc-Antoine Laugier’s 1755 second edition of *Esssay on Architecture*, illustration by Charles-Dominique-Joseph-Eisen.

However, there are a few drawbacks:

  • You currently need an index of figures, since example lists require the (@id) to be at the beginning of a line at least once.
  • You have to add the Figure (@id): bit to the caption manually.
  • This breaks LaTeX/PDF output, since LaTeX adds a “Figure” prefix itself.

Thus, a proper referencing scheme would need a bit additional thinking. Especially, PDF and HTML output should work alike, probably by pandoc adding the Figure: bit to HTML output, while leaving it to LaTeX in the PDF case. Additionally, this should also work for referencing numbered sections, like in see chapter (@mychapter).

@btel
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@btel btel commented Apr 25, 2014

Your workaround works as suggested, but I had to remove the parentheses when referencing the label, otherwise they were rendered in the output. After this modification my example looks like this:

Figure @figure is about being in time

![Figure @figure: Cubes](cubes.png)

(@figure) Figure 1

To remove the automatic numbering in LaTex (Figure 1:, etc.) you can add to the template:

\usepackage[labelformat=empty]{caption}

After rendering to pdf this produces the following output:

figure

@bitsgalore
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@bitsgalore bitsgalore commented May 8, 2014

Just came across this issue as well and ended up here. I'm also really in favor of support for the syntax suggested by @jgm above:

![Voyage to the moon](lalune.jpg){#lalune}

Especially since this is the standard way of dealing with this in PHP Markdown Extra:

http://michelf.ca/projects/php-markdown/extra/#spe-attr

@mangecoeur
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@mangecoeur mangecoeur commented Jul 10, 2014

Has there been any developments on this? It also seems to me that @jgm suggestiong

![Voyage to the moon](lalune.jpg){#lalune}

is the most consistent internally and with other tools. What would need to happen for this to be implemented?

@edwardabraham
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@edwardabraham edwardabraham commented Jul 23, 2014

I was wanting to add support for this addition to the syntax. When trying to replicate papers using markdown for the scholmd project, this is the feature that stands out as most needed by Pandoc . In short this can be addressed through the general use of {#lalune} for labelling elements, and of @lalune for referencing the number of the corresponding element. The syntax (@) may be used to number elements that are otherwise unnumbered.

A general syntax for labels {#lalune}, that are associated with the preceding element would allow for any element to be labelled (paragraphs, equations, tables, etc.). By associating the label with an element in the abstract syntax tree, the properties of the element would be available when the reference was made, and so they can be numbered appropriately. This syntax is already used in one context in Pandoc (section heading labels), and is used by PHP Markdown extra. For elements that don't have numbers, such as equations, the syntax (@) may be used (from the example_lists extension). So an equation would be numbered and labelled as $$ F = G{m_1 m_2 \over r^2$$ (@) {#gravity}. (An alternative could be to use the example_lists extension style and number and label it in one go as $$ F = G{m_1 m_2 \over r^2$$ (@gravity). There are clearly some details and edge cases to be thought through here.)

When the document is rendered, Pandoc would associate a number with each labelled element, based on its type, and its position in the document. This logic would need to be carried out in Pandoc, so that it was available to the range of back-end writers (including HTML). The philosophy would be similar to Pandoc-citeproc, which carries out its own formatting of citations, rather than delegating to writers that support this approach (such as bibtex for latex). An option would to have this behaviour depend on the backend (so that it in latex it inserts \label and \ref commands), but elsewhere it may insert calculated numbers, if referencing is not supported by the backend. This has the advantage that it will work easily in contexts where only a fragment of the document is rendered. If pandoc is calculating the numbering, a syntax would be needed for specifying the start numbers in a fragment that wasn't being compiled in stand alone mode.

Labelled elements may be linked to, with the @ symbol being used to indicate the reference. So
a trip to [the moon](@lalune) would be an anchor link to the element labelled {#lalune}. In this case the text is rendered as a trip to the moon.

The syntax The moon is illustrated in Figure @lalune may be used to insert the number of the referenced element, as well as a link to that element, with the text rendered as The moon is illustrated in Figure 1. This follows the syntax used for referencing numbered lists with the example_lists extension.

A further syntax could be to use square brackets [@lalune] to insert the type and number of the element that is referenced, similar to the behaviour of latex's \autoref command. So, the moon is illustrated in [@lalune] would be rendered as the moon is illustrated in Figure 1 (including a link to the anchor). To implement this feature would require some localisation or customisation capability, so that the word used to describe the element could be specified. In its simplest, this customisation could be put in the YAML header, with for example figure_label: Fig. if the style required a shortened label. The syntax for the reference, [@lalune], is the same as is used by the pandoc-citeproc library, so it would be overloading that usage to implement a self-citation. Pandoc would have the information on the context that is needed to either format it as a citation, or as a reference, assuming that there was no collision between the labels and the citation keys.

@kovla
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@kovla kovla commented Jul 23, 2014

@edwardabraham It must be pointed out that the syntax [@lalune] is already used in pandoc for bibliographical citations.

@timtylin
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@timtylin timtylin commented Jul 23, 2014

@kovla @edwardabraham I don't see why #lalune couldn't be used also as a reference to the defined symbol. With this scheme [the moon](#lalune) could be a normal text link to the figure, while [#lalune] could do the numbered reference thing as mentioned. In fact, I have a custom build of Pandoc that does exactly this.

@edwardabraham
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@edwardabraham edwardabraham commented Jul 24, 2014

@kovla The idea was to deliberately overload the [@lalune] syntax that is used for citations. The reason being that references to another part of the document are similar to citations (in essence they are self-citations). This has the benefit of avoiding introducing additional syntax. During processing the filter would identify which element the label was attached to, and use that information to appropriately format the text that is inserted into the document.

@evitaerc I prefer using the @ symbol, as it extends functionality that is already used by example_lists. Are you able to structure your pandoc build so that it may be implemented as a filter?

Note that this extension is [@lalune] a convenience and is not necessary, provided that the numbers are able to be accessed through the @lalune method.

@timtylin
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@timtylin timtylin commented Jul 24, 2014

@edwardabraham I tried the @ approach as well, but internal feedback in our lab showed that people get confused by what is a citation and what is an internal reference even when editing. The conclusion was that the mental model of keeping # for internal refs and using @ for external refs is the simplest to grok.

In fact, no one out of ten or so people have used example_lists (we are mostly writing extended abstracts and journal papers in the field of physics/engineering/applied math). When encountering a "list of scenarios" situation, the content was so static that people simply used literal numbers without issue.

Unfortunately the internal reference mechanism required heavy modification of the Markdown reader (additional state must be kept during the parsing process) and a custom AST, so I can't conceive of a filter implementation in the near future.

@elcritch
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@elcritch elcritch commented Jul 24, 2014

Personally, the # symbol and the {#label} syntax would be easier to understand and use. In my mind citations and internal references follow very distinct "mental models". Many academic papers use distinct numbering for figures, tables, and equations but the proposed syntaxes don't appear to have a way to support distinct numberings by type. It would be an important design criteria (I only got to skim the comments, hopefully its not a redundant suggestion).
@edwardabraham You mentioned the scholmd. Is it currently just a repository of ideas or have they implemented any of the academic markdown features?
@evitaerc Great work! Is it possible for you to propose submitting the changes to the pandoc project or alternately creating a github fork to allow others to experiment?

@mangecoeur
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@mangecoeur mangecoeur commented Jul 24, 2014

+1 for use of # symbol for internal references. But it's really important that the references can distinguish between equations, figures, and tables to have distinct numbering sequences.

There are two approaches to my mind

  1. make the "thing referenced" explicit in the tag, for instance using namespaces like #eqn.maxwells, #fig.hockeystick. Pandoc would have to track the objects in each namespace and format the references appropriately
  2. depend on pandoc's parser to know what type of thing is referenced and handle appropriately. So if you tag an image and then use a # reference pandoc automatically treats it as a "fig" reference, if you embed latex formula it because an equation reference etc. This would be cool but i suspect it would be a) complex and b) fragile - you get issues for instance if someone wants to embed an image for a formula.
@lierdakil
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@lierdakil lierdakil commented Mar 3, 2017

@ibutra, from https://github.com/lierdakil/pandoc-crossref#section-labels

You can also use autoSectionLabels variable to automatically prepend all section labels (automatically generated with pandoc included) with "sec:". Bear in mind that references can't contain periods, commas etc, so some auto-generated labels will still be unusable.

Generating labels for figures/tables/other has another drawback. Right now, the default behavior in pandoc-crossref is to ignore unlabelled elements (since this is least intrusive), so

![Caption](image) 

will be an unnumbered (or rather, unprocessed) figure.

This kind of behavior is useful for informal writing, when you don't need to number the figures you're not referencing. Also for running pandoc-crossref on documents that don't need cross-referencing at all, f.ex. from an automated script.

@jgm, for figures, a better (more concise) source of auto identifiers is probably not a title, but a filename (or rather, basename). Tables and listings are another matter, and I don't think it's feasible for math.

@gappleto97
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@gappleto97 gappleto97 commented Apr 19, 2017

For RST the syntax should be much easier. Just use the already-available name field:

.. figure:: image.png
    :name: example
    :alt: an image

    This is the caption
@DaveJarvis
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@DaveJarvis DaveJarvis commented Apr 28, 2017

see Example (14)
...
see Figure 5

FWIW, the Markdown should not include the caption type text (e.g., "Equation", "Table", "Figure") as that is presentation logic. That is, without changing the source, it should be possible to replace "Figure" with "Illustration" throughout the output document.

Here are a few others, which suggests that the solution should be caption type agnostic. The complete set of possible captions is fairly long and we probably shouldn't try to restrain the syntax to a particular subset as some could get missed, such as:

see Listing (14)
see Algorithm 5

Thus with the text, As seen in Figure @fig:force, the word "Figure" is redundant (the @fig already signifies the caption is a figure). With that particular syntax, As seen in @fig:force allows the rendering component (e.g., LaTeX, ConTeXt, etc.) to determine what caption type text to inject, if any.

@sjackman
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@sjackman sjackman commented Apr 28, 2017

The above is also helpful when referencing multiple items, for example
As shown in @fig:a;@fig:b => As shown in Figures 1 and 2
and ranges
As shown in @fig:a;@fig:b;@fig:c => As shown in Figures 1–3

@mangecoeur
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@mangecoeur mangecoeur commented May 30, 2017

Hopefully, if this is built into core pandoc the docx could gain the ability to output 'real' reference fields (using the office xml reference tags). This would allow you to post-process fields in Word, for example to generate tables of figures and tables of tables (Word can generate these when caption fields are used).

@Hipomenes
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@Hipomenes Hipomenes commented Jun 22, 2017

Here it goes again... How does one cross-reference figures in Pandoc?

Thanks!

@iandol
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@iandol iandol commented Jun 22, 2017

For the moment you should use filters, either pandoc-crossref (installs via homebrew if you use a Mac: brew install pandoc-crossref) or pandoc-fignos (you need a working python install). Personally I do all my writing in Scrivener, which has its own crossref system that outputs to Pandoc so don't use these myself.

@jgm jgm changed the title New Feature: internal links to tables and figures New Feature: internal links to tables and figures and headers Aug 13, 2017
@jgm jgm removed this from the pandoc 2.0 milestone Aug 20, 2017
@petterreinholdtsen
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@petterreinholdtsen petterreinholdtsen commented Feb 25, 2018

It would be great if pandoc by default would support adding image/figure IDs and cross references when converting markdown to docbook. This would ensure the software needed is available in Debian.

I am currently typesetting a set of books using a Markdown->Docbook pipeline, and need a way to reference figures in the text.

@ikcalB
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@ikcalB ikcalB commented Jul 27, 2018

@jgm is there any progress an this inside the main tree, or would you suggest using the filter pandoc-crossref?

@mb21
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@mb21 mb21 commented Jul 27, 2018

for now, use pandoc-crossref

@esnahn
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@esnahn esnahn commented Dec 15, 2018

I hope there was an option to interpret links as numberings instead of hyperlinks, for but not limited to non-electronic media. Something like ![Figure fig#. Caption](/path/file.png) and [fig.](Figure fig#. Caption), stripping all automated stuff except the numbering.

@tomduck
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@tomduck tomduck commented Sep 18, 2019

I am pleased to announce the 2.0.0 release of the pandoc-xnos filter suite:

  • pandoc-fignos, for numbering figures and figure references;
  • pandoc-eqnos, for numbering equations and equation references;
  • pandoc-tablenos, for numbering tables and table references; and
  • pandoc-secnos, for numbering section references (pandoc does the section numbering).

The filters emerged from recommendations made by the community in this thread, and in particular this post by @scaramouche1.

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