Update functions.html (IJ1 macro autocomplete in Fiji editor) #301
Conversation
The ImageJ website content moved from https://imagej.nih.gov/ij to https://imagej.net/ij.
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@bvandenbroek Thanks for the update. I compared this against https://imagej.net/ij/developer/macro/functions.html, which is where I would expect to find the latest macro functions documentation, and there are a lot of differences. It does not look clear-cut to me which one is "better" either: although the wsr.imagej.net copy has a much newer "last updated" date, it also introduces many HTML validity errors (e.g. removal of quotes), removes many "Requires 1.52o" type comments from various function docstrings, and even removes docstrings for some functions such as @rasband Could you please let us know which copy of functions.html is the canonical latest one? Then we can update the copy in this repository to reflect that, so that the Script Editor's autocompletion for ImageJ macros can function as smoothly as possible. |
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Hi @ctrueden , @bvandenbroek, @rasband, and also @haesleinhuepf Sorry for chiming in a little late to this PR, I just realized this was being discussed. First, some context for my intervention: I was already working on a branch to update several functions for the IJ macro autocompletion, as well as some of the code that deals with the parsing of the html to generate the suggestions. This started being discussed in this image.sc post. This update also incorporated some changes related to Fiji script editor update introduced by that time. The last update I pushed to this branch can be found here. At some point discussion in the forum pointed at some issues with the lexer, which made me postpone the PR to see if I could understand their inner workings (way over my skill level), and perhaps include a change in that same update. This was a clear error by my part. I ran out of time at the moment, put the project on hold, and here I am a little more than a year latter trying to catch up to finally release the original PR. Anyways, going back to this particular PR, I believe that the As a result of all this, I have the impression that it is not currently viable to just copy the latest version of the file that is being maintained by @rasband for the web. I think the function of both files is different enough to afford maintaining separate versions, although it is true that updating the one from the library implies some regex-replacing+diffing to track changes (this is what I have been doing). Other option would be to incorporate all these changes into the web version, and maybe writing a function to correctly translate internal anchors on the fly. What are your thoughts on this? Cheers, ** in my branch I proposed a slight change, using "name_2" instead of "name2" to avoid a problem with |
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The most up to date version of functions.html is at ` |
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@rasband Thanks for the quick reply I gathered a (rather lengthy) list of changes that could be made to bring this two versions closer together. You can check the details below. Click to expandA search of the disambiguated entries in my current branch gives this full list:
Additionally, an anchor should be included for this function
while these anchors should be added/updated using an underscore (instead of a space)
and the whole list of entries for Also, many references to the ImageJ version requirements are still missing:
There other minor issues that could be corrected/improved, but this is already a long list to start with. I feel like this is a lot of extra work that's unnecesarily falling upon you. That was the reason why I suggested keeping separate files, and offloading this burden to the ones contributing to/maintaining the autocompletion library. In this case, the html file in the library -for the lack of a better data format- could probably better be stripped of all the additional elements (headers, section links, letters, quote blocks, etc), so that it is clear that it's not just a copy of the web page. However, if you still prefer updating the web file (either for use as a template to copy, or just for the sake of uniformity), is there a way to help you in doing this? Also, if this is not the right place to discuss these issues, please let me know. Thanks again. |
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@ndefrancesco @rasband I am in favor of one single source of truth for this information. Maybe the |
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@ctrueden that'd be a really good solution! Then it'd be easy to modify the function parsing the entries to correctly redirect the embedded links to the right URL, so that the file maintains the right format to be served on the website(s). |
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I've worked on a proposal to merge the most important changes that I had identified into the current version of the functions.html file that @rasband is maintaining. You can check it in this repo: https://github.com/ndefrancesco/ImageJ-functions-doc-update. I started from the current version online at https://wsr.imagej.net/developer/macro/functions.html, and incrementally made the suggested modifications, plus some extra ones I had ready to incorporate. I tried to make the commits as specific as possible, so that it is easy to track what I've done. These changes are stucturally minimal, so that the way the page is rendered should not have mostly changed. If you consider these changes are acceptable, this could be a good starting point to work towards @ctrueden's idea. This should at least save @rasband some editing time. Please, let me know what you think. |
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Hi @ndefrancesco, @ctrueden, The merged functions.html file looks good so I added it to the ImageJ repository at https://github.com/imagej/ImageJ/blob/master/functions.html The commit does not appear on the list at https://github.com/imagej/ImageJ/commits/master/ij Is this because no files were changed? I did not modify build.xml to copy functions.html to ij.jar. I would prefer not to add this 190kb file to the ij.jar distributed with ImageJ. |
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Thanks, @rasband!
It's because no files in the https://github.com/imagej/ImageJ/commits/master i.e. drop the
That is unfortunate, but I understand the reluctance. I will figure out how to bundle it into imagej-legacy.jar at the linked version of Another option might be to download it on demand from https://imagej.net/ij/developer/macro/functions.html, although IIRC there was some performance reason that @haesleinhuepf did not originally want to do that... I guess because the network requests are too slow for autocomplete, and if we cache it then it can get out of sync as ij.jar evolves, so we would need to check at least once per JVM startup or daily or some such, whether the locally cached Regardless, I will need to create some server-side infrastructure to make this committed @rasband What if I change https://imagej.net/ij/source/ not to be manually maintained, but rather just pulled from GitHub once an hour? Then I can symlink |
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I decided to include functions.html with ij.jar. It makes things simpler and the file is not that large after compression. I updated Jerome's FunctionFinder tool (cmd-shift-f in ImageJ's macro editor) to use this file. I also removed all the 'Requires 1.52x' strings. "Requires" is only intended to be used with recently added functions. |
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@ctrueden: “What if I change https://imagej.net/ij/source/ not to be manually maintained, but rather just pulled from GitHub once an hour? Then I can symlink functions.html from there to the other locations.” Sounds like a good plan. The files in that directory have not been updated in 7 months. |
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I have reconfigured https://imagej.net/ij/source/ to automatically pull from GitHub once an hour. There was another copy of the sources at https://imagej.net/ij/download/tools/source/, which I have now symlinked to I also reconfigured all existing copies of All previous copies of the source code, and previous copies of
These last two |
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@ctrueden I'm currently working on a new version of the IJ macro autocompletion to incorporate these changes. I've already managed to load |
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@ndefrancesco Oops, I was working on it also! I'll push the branch that I have. |
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@ndefrancesco OK, take a look at this: I got it far enough along to compile, but have not tested it whatsoever yet. But hopefully it illustrates what I'm thinking? It avoids shipping If you have time to test it, I would appreciate it! |
This new version of the file is now also included in the ImageJ repo and served in the imagej.net web. Functions up to 1.54f are included. The logic that parses new functions families (`Color.`, `Image.`, `Property.` and `RoiManager.`) as well as the one that resolves relative links to full URLs was updated to match the web version. See this discussion: imagej#301 (comment)
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@ctrueden Thanks for the update! I had some time to test that branch. It seems to work fine using the web version of the html file if the ij.jar version is missing, but it's not picking it up when it's present. I guess it should be easy to solve (it works ok in the previous implementation) but I'm not entirely sure what's going on with this new one. There is, anyway, an aspect of that approach that I would prefer avoiding. It is true that if ImageJ is up to date (in this moment, beyond the latest stable release), there will be no need to fetch any file from an external resource. But in the case that imagej-legacy is updated without updating ImageJ (which can certainly happen during the transition, and will happen due to other circumstances), there will be an absolute need for a live internet connection for it to work, and as there's no caching of the file, that would happen every time it's launched. I personally dislike that option, as it's quite limiting. On the other hand, the cost of having a (probably redundant) copy of the file [~48k compressed] will ensure that any version of ImageJ prior to 1.54g will have an up to date (and beyond) autocompletion, and any new version will be as updated as possible, with no need for connectivity in any case. I have prepared a new branch where I gathered a bunch of commits from my previous attempt (with changes that have been already tested) and some new ones regarding this new file, including some logic needed to correctly parse this version (relative links, new function families). You can check it out here: https://github.com/ndefrancesco/imagej-legacy/tree/autocompletion_2023 In this case, I took the route of keeping a static copy of the file as fallback. Anyway, I think that the rest of the changes are fitting irrespective of what's the final decision regarding the way to handle a possibly missing Let me know what you think and how you suggest we move forward. Thanks! |
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This pull request has been mentioned on Image.sc Forum. There might be relevant details there: https://forum.image.sc/t/how-to-type-non-smart-quotation-marks-in-the-fiji-macro-editor/84909/3 |
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Hi @ctrueden @ndefrancesco @rasband, |
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This pull request has been mentioned on Image.sc Forum. There might be relevant details there: https://forum.image.sc/t/remove-plots-or-fits-from-a-plot-profile-chart/54740/8 |
Update for the IJ1 macro autocomplete functions in the Fiji editor.
The page is copied from the new location: https://wsr.imagej.net/developer/macro/functions.html