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As any Common Lisp coder knows, a REPL is an incredibly useful tool. It can be used not just for development, but for running all sorts of tasks. Personally, I don't bother making my Lisp tools into executable scripts and just run them directly from SLIME. As such, any operation that requires leaving the REPL is quite inconvenient. For me, one such operation was viewing image files, for example in conjunction with my match-client:match tool. So lately I've been researching various methods to incorporate this functionality into the normal REPL workflow. Below, I present 3 methods that can be used to achieve this.

Open in external program

This one's easy. When you want to view a file, launch an external process with your favorite image viewer. On Windows a shell command consisting of the image filename would launch the associated application, on Linux it's necessary to provide the name of the image viewer.

(defvar *image-app* nil) ;; set it to '("eog") or something

(defun view-file-native (file)
  (let ((ns (uiop:native-namestring file)))
    (uiop:launch-program (if *image-app*
                             (append *image-app* (list ns))
                             (uiop:escape-shell-token ns)))))

Note that uiop:launch-program is used instead of uiop:run-program. The difference is that launch- is non-blocking - you can continue to work in your REPL while the image is displayed, whereas run- will not return until you close the image viewer.

Also note that when the first argument to run/launch-program is a string, it is not escaped, so I have to do it manually. And if the first argument is a list, it must be a program and a list of its arguments, so merely using (list ns) wouldn’t work on Windows.

Inline image in REPL

The disadvantage of the previous method is that the external program might steal focus, appear on top of your REPL and disrupt your workflow. And it's well known that Emacs can do everything, including viewing images, so why not use that?

In fact, SLIME has a plugin specifically for displaying images in REPL, slime-media. However it’s difficult to find any information on how to use it. Eventually I figured out that SWANK (SLIME’s CL backend) needs to send an event :write-image with appropriate arguments and slime-media's handler will display it right in the REPL. The easiest way is to just send the file path. The second argument is the resulting image's string value. If you copy-paste (sorry, "kill-yank") it in the repl, it would act just like if you typed this string.

(swank::send-to-emacs '(:write-image "/path/to/test.png" "test"))

You can even send raw image data using this method. I don't have anything on hand to generate raw image data so here's some code that reads from a file, converts it to a base64 string and sends it over SWANK.

(with-open-file (in "/path/to/test.png" :direction :input  :element-type '(unsigned-byte 8))
                (let* ((arr (make-array (file-length in) :element-type '(unsigned-byte 8)))
                       (b64 (progn (read-sequence arr in) (cl-base64:usb8-array-to-base64-string arr))))
                  (swank::send-to-emacs `(:write-image ((:data ,b64 :type swank-io-package::png)) "12345"))))

Note that the first argument to :write-image must be a list with a single element, which is itself a plist containing :data and :type keys. :data must be a base64-encoded raw image data. :type must be a symbol in swank-io-package. It’s not exactly convenient, so if you’re going to use this functionality a helper function/macro might be necessary.

Image in a SLIME popup buffer

Inline images are not always convenient. They can’t be resized, and will take up as much space as is necessary to display them. Meanwhile EMACS itself has a built-in image viewer (image-mode) which can fit images to width or height of a buffer. And SLIME has a concept of a “popup buffer” which is for example used by macroexpander (C-c C-m) to display the result of a macro expansion in a separate window.

Interestingly, slime-media.el defines an event :popup-buffer but it seems impossible to trigger it from SWANK. It is however a useful code reference for how to create the popup buffer in ELisp. This time we won’t bother with “events” and just straight up execute some ELisp code using swank::eval-in-emacs. However by default, this feature is disabled on Emacs-side, so you’ll have to set Emacs variable slime-enable-evaluate-in-emacs to t in order for this method to work.

Also Emacs must be compiled with ImageMagick for the resizing functionality to work.

Anyway, the code to view file in the popup buffer looks like this:

(defun view-file-slime (file &key (bufname "*image-viewer*"))
  (let ((ns (namestring file)))
    (swank::eval-in-emacs
     `(progn
        (slime-with-popup-buffer (,bufname :connection t :package t)
          (insert-image (create-image ,ns))
          (image-mode)
          (setf buffer-file-name ,ns)
          (not-modified)
          (image-toggle-display-image))
        ;; try to resize the image after the buffer is displayed
        (with-current-buffer ,bufname (image-toggle-display-image))))))
    ))

Arriving to this solution has required reading image-mode’s source code to understand what exactly makes image-mode behave just like if the image file was opened in Emacs via C-x C-f. First off, image-mode can be a major and a minor mode - and the minor mode is not nearly as useful. slime-with-popup-buffer has a :mode keyword argument but it would cause image-mode to be set before the image is inserted, and it will be a minor mode in this case! Therefore (image-mode) must be called after insert-image.

Next, the buffer must satisfy several conditions in order to get image data from the filename and not from the buffer itself. Technically it shouldn’t be necessary, but I couldn’t get auto resizing to work when data-p is true. So I set buffer-file-name to image’s filename and set not-modified flag on.

Next, image-toggle-display-image is called to possibly resize the image according to image-mode settings. It's called outside of slime-with-popup-buffer for the following reason: the buffer might not yet be visible and have any specific dimensions assigned to it, and therefore resizing will do nothing.

Here’s an example of how calling this function looks in Emacs.

The position of the popup buffer depends on whether the original Emacs window is wide enough or not. I think it looks better when it’s divided vertically. Use M-x image-transform-fit-to-height or M-x image-transform-fit-to-width to set up the auto-resizing method (it gets remembered for future images). Unfortunately there’s no way to fit both height and width, at least with vanilla Emacs. I prefer fit-to-width because in case the image is too tall, it is possible to scroll the image vertically with M-PgDn and M-PgUp from the other buffer. Unlike other image-mode buffers, this buffer supports a shortcut q to close itself, as well as various SLIME shortcuts, for example C-c C-z to return to the REPL.

That's it for now, hope you enjoyed this overview and if you happen to know a better way to display images in Emacs, I would be interested to hear about it.

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Basecamp’s newest product HEY has lived on Kubernetes since development first began. While our applications are majestic monoliths, a product like HEY has numerous supporting services that run along-side the main app like our mail pipeline (Postfix and friends), Resque (and Resque Scheduler), and nginx, making Kubernetes a great orchestration option for us. As you… keep reading

In our computational study, we use molecular simulations to substantiate a hypothetical mechanism for glycosidic bond cleavage in the presence of a single catalytic acid at the active site of the mutant D10N HiCel45A. In addition to discussing this plausible mechanism from the context of structurally related MltA lytic transglycosylase and subfamily C GH45s, we also suggest the implications of the plausible mechanism for our current understanding of the action of expansins and lytic transglycosylases. As correctly pointed out by Professor Cosgrove (1), there is large body of evidence, a significant portion of which was regrettably not discussed in our paper, that suggests that expansins are incapable of lytic action on polysaccharide substrates. Whereas these insights do not change the results or the conclusions of our article, we would like to thank Professor Cosgrove for these additional insights. In particular, our main point with respect to expansins is that our results suggest the possibility that expansins are capable of nonhydrolytic lytic activity. Our intention was not to suggest this was the mechanism of expansins, but that it should be considered based on our results and the similarity of the active sites.The molecular mechanisms of how expansins enable cell wall expansion remains to be fully understood. Whereas our proposed mechanism resulting in the formation of the 1,6-anhdro product might be found in expansins and might contribute to the mode of action of expansins, we would like to emphasize that the intent of this study was only to suggest this as a...

In bacteria, the restart of stalled DNA replication forks requires the DNA helicase PriA. PriA can recognize and remodel abandoned DNA replication forks, unwind DNA in the 3'-to-5' direction, and facilitate the loading of the helicase DnaB onto the DNA to restart replication. Single-stranded DNA–binding protein (SSB) is typically present at the abandoned forks, but it is unclear how SSB and PriA interact, although it has been shown that the two proteins interact both physically and functionally. Here, we used atomic force microscopy to visualize the interaction of PriA with DNA substrates with or without SSB. These experiments were done in the absence of ATP to delineate the substrate recognition pattern of PriA before its ATP-catalyzed DNA-unwinding reaction. These analyses revealed that in the absence of SSB, PriA binds preferentially to a fork substrate with a gap in the leading strand. Such a preference has not been observed for 5'- and 3'-tailed duplexes, suggesting that it is the fork structure that plays an essential role in PriA's selection of DNA substrates. Furthermore, we found that in the absence of SSB, PriA binds exclusively to the fork regions of the DNA substrates. In contrast, fork-bound SSB loads PriA onto the duplex DNA arms of forks, suggesting a remodeling of PriA by SSB. We also demonstrate that the remodeling of PriA requires a functional C-terminal domain of SSB. In summary, our atomic force microscopy analyses reveal key details in the interactions between PriA and stalled DNA replication forks with or without SSB.

Jordi Pau and Antti Perälä
Trans. Amer. Math. Soc. 373 (2020), 3031-3062.
Abstract, references and article information

petrapetruta posted a reply:

Corrado Carlini:

It's not a like/dislike thing.It's all about colors.Just take a look at the pool.
We want specific kind of photos.Otherwise this group won't be named Catchy Colors.

Jeniverse Photography posted a reply:

Yellow