Getting geo-tagged information from photos for blogging

| categories: emacs, orgmode, geotag | tags: | View Comments

I am kind of late to this game, but recently I turned on location services for the camera on my phone. That means the location of the photo is stored in the photo, and we can use that to create urls to the photo location in a map for example. While traveling, I thought this would be a good application for org-mode to add functionality to documents with photos in them, e.g. to be able to click on them to see where they are from, or to automate creation of html pages with links to maps, etc. In this post I explore some ways to achieve those ideas. What I would like is a custom org link that shows me a thumbnail of the image, and which exports to show the image in an html file with a link to a pin on Google maps.

So, let's dig in. Imagemagick provides an identify command that can extract the information stored in the images. Here we consider just the GPS information. I some pictures on a recent vacation, and one is unimaginatively named IMG_1759.JPG. Let's see where it was taken.

identify -verbose IMG_1759.JPG | grep GPS
exif:GPSAltitude: 14426/387    
exif:GPSAltitudeRef: 0    
exif:GPSDateStamp: 2018:06:30    
exif:GPSDestBearing: 11767/80    
exif:GPSDestBearingRef: T    
exif:GPSImgDirection: 11767/80    
exif:GPSImgDirectionRef: T    
exif:GPSInfo: 1632    
exif:GPSLatitude: 22/1, 11/1, 614/100
exif:GPSLatitudeRef: N    
exif:GPSLongitude: 159/1, 40/1, 4512/100
exif:GPSLongitudeRef: W    
exif:GPSSpeed: 401/100    
exif:GPSSpeedRef: K    
exif:GPSTimeStamp: 3/1, 44/1, 3900/100

The interpretation here is that I took that photo at latitude 22° 11' 6.14" N, and longitude 159° 40' 45.12" W. Evidently I was moving at 4.01 in some unit; I can confirm that I was at least moving, I was on a ship when I took that picture, and it was moving.

According to this you can make a url to a Google maps pin in satellite picture mode that looks like this: http://maps.google.com/maps?q=22 11 6.14N,159 40 45.12W&t=k. It doesn't seem possible to set the zoom in this url (at least setting the zoom doesn't do anything, and I didn't feel like trying all the other variations that are reported to sometimes work). I guess that is ok for now, it adds some suspense that you have to zoom out to see where the image is in some cases.

We need a little function to take an image file and generate that link. We have to do some algebra on the latitude and longitude which are stored as integers with a division operator. I am going to pipe this through an old unix utility called bc mostly because it is simple, and I won't have to parse it much. bc is a little archaic, you have to set the scale first, which tells it how many decimal places to output. The degrees and minutes are integers, so we will have to deal with that later.

echo "scale=2; 614/100" | bc
6.14

Here is our function. I filter out the lines with GPS in them into an a-list. Then, I grab out the specific quantities I want and construct the url. There is a little hackery since it appears the degrees and minutes should be integers in the url formulation used here, so I convert them to numbers and then take the floor. The function is a little longer than I thought, but it isn't too bad I guess. It is a little repetitious, but not enough to justify refactoring.

(defun iphoto-map-url (fname)
  (let* ((gps-lines (-keep (lambda (line)
                             (when (s-contains? "GPS" line) (s-trim line)))
                           (process-lines "identify" "-verbose" fname)))
         (gps-alist (mapcar (lambda (s) (s-split ": " s t))  gps-lines))
         (latitude (mapcar
                    (lambda (s)
                      (s-trim (shell-command-to-string
                               (format "echo \"scale=2;%s\" | bc" s))))
                    (s-split "," (cadr (assoc "exif:GPSLatitude" gps-alist)))))
         (latitude-ref (cadr (assoc "exif:GPSLatitudeRef" gps-alist)))
         (longitude (mapcar
                     (lambda (s)
                       (s-trim
                        (shell-command-to-string
                         (format "echo \"scale=2;%s\" | bc" s))))
                     (s-split "," (cadr (assoc "exif:GPSLongitude" gps-alist)))))
         (longitude-ref (cadr (assoc "exif:GPSLongitudeRef" gps-alist))))
    (s-format "http://maps.google.com/maps?q=$0 $1 $2$3,$4 $5 $6$7&t=k"
              'elt
              (list
               (floor (string-to-number (nth 0 latitude)))
               (floor (string-to-number (nth 1 latitude)))
               (nth 2 latitude)
               latitude-ref
               (floor (string-to-number (nth 0 longitude)))
               (floor (string-to-number (nth 1 longitude)))
               (nth 2 longitude)
               longitude-ref))))
iphoto-map-url

Here is the function in action, making the url.

(iphoto-map-url "IMG_1759.JPG")
http://maps.google.com/maps?q=22 11 6.14N,159 40 45.12W&t=k

It is kind of slow, but that is because the identify shell command is kind of slow when you run it with the -verbose tag. Now, I would like the following things to happen when I publish it to html:

  1. I want the image wrapped in an img tag inside a figure environment.
  2. I want the image to by hyperlinked to its location in Google maps.

In the org file, I want a thumbnail overlay on it, so I can see the image while writing, and I want it to toggle like other images. I use an iPhone to take the photos, so we will call it an iphoto link.

Here is the html export function I will use. It is a little hacky that I hard code the width in at 300 pixels, but I didn't feel like figuring out how to get it from an #+attr_html line right now. It probably requires a filter function where you have access to the actual org-elements. I put the url to the image location in a figure caption here.

(defun iphoto-export (path desc backend)
  (cond
   ((eq 'html backend)
    (format "<figure>
<img src=\"%s\" width=\"300\">
%s
</figure>"
            path
            (format "<figcaption>%s <a href=\"%s\">map</a></figcaption>"
                    (or desc "")
                    (iphoto-map-url path))))))
iphoto-export

Ok, the last detail I want is to put an image overlay on my new link so I can see it. I want this to work with org-toggle-inline-images so I can turn the images on and off like regular image links with C-c C-x C-v. This function creates overlays as needed, and ties into the org-inline-image-overlays so they get deleted on toggling. We have to advise the display function to redraw these, which we clumsily do by restarting the org font-lock machinery which will redraw the thumbnails from the activate-func property of the links. I also hard code the thumbnail width in this function, when it could be moved out to a variable or attribute.

(defun iphoto-thumbnails (start end imgfile bracketp)
  (unless bracketp
    (when (and
           ;; it is an image
           (org-string-match-p (image-file-name-regexp) imgfile)
           ;; and it exists
           (f-exists? imgfile)
           ;; and there is no overlay here.
           (not (ov-at start)))
      (setq img (create-image (expand-file-name imgfile)
                              'imagemagick nil :width 300
                              :background "lightgray"))
      (setq ov (make-overlay start end))
      (overlay-put ov 'display img)
      (overlay-put ov 'face 'default)
      (overlay-put ov 'org-image-overlay t)
      (overlay-put ov 'modification-hooks
                   (list
                    `(lambda (&rest args)
                       (org-display-inline-remove-overlay ,ov t ,start ,end))))
      (push ov org-inline-image-overlays))))

(defun iphoto-redraw-thumbnails (&rest args)
  (org-restart-font-lock))

;; this redisplays these thumbnails on image toggling
(advice-add 'org-display-inline-images :after 'iphoto-redraw-thumbnails)

Next, we define the link with a follow, export, tooltip and activate-func (which puts the overlay on).

(org-link-set-parameters
 "iphoto"
 :follow (lambda (path) (browse-url (iphoto-map-url path)))
 :export 'iphoto-export
 :help-echo "Click me to see where this photo is on a map."
 :activate-func 'iphoto-thumbnails)

So finally, here is the mysterious image.

map

Now, in org-mode, I see the image in an overlay, and I can toggle it on and off. If I click on the image, it opens a browser to Google maps with a pin at the spot I took it. When I export it, it wraps the image in a <figure> tag, and puts a url in the caption to the map. If you click on it, and zoom out, you will see this is a picture of the Nāpali Coast on Kauai in Hawaii, and I was in fact out at sea when I took the picture. It was spectacular. Here is another one. This one is a little more obvious with the zoom. Here, I was on land. Since this link is bracketed, it does not show the overlay however in the org-file.

Another vacation picture, this time with a caption. map

Overall, this was easier than I expected. It might be faster to outsource reading the exif data to some dedicate library, perhaps in python that would return everything you want in an easy to parse json data structure. The speed of computing the url is only annoying when you export or click on the links though.

I didn't build in any error handling, e.g. if you do this on a photo with no GPS data it will probably not handle it gracefully. I also haven't tested this on any other images, e.g. south of the equator, from other cameras, etc. I assume this exif data is pretty standard, but it is a wild world out there… It would still be nice to find a way to get a string representing the nearest known location somehow, that would help the caption be more useful.

There is one little footnote to speak of, and that is I had to do a little hackery to get this to work with my blog machinery. You can see what it is in the org-source, I buried it in a noexport subheading, because it isn't that interesting in the grand scheme of things. It was just necessary because I export these org-files to blogofile, which then builds the html pages, instead of just exporting them. The images have to be copied to a source directory, and paths changed in the html to point to them. See, boring stuff. Otherwise, the code above should be fine for regular org and html files! Now, my vacation is over so it is time to get back to work.

Copyright (C) 2018 by John Kitchin. See the License for information about copying.

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Literate programming with python doctests

| categories: python, noweb, orgmode | tags: | View Comments

On the org-mode mailing list we had a nice discussion about using noweb and org-mode in literate programming. The results of that discussion were blogged about here. I thought of a different application of this for making doctests in Python functions. I have to confess I have never liked these because I have always thought they were a pain to write since you basically have to put code and results into a docstring. The ideas developed in the discussion above led me to think of a new way to write these that seems totally reasonable.

The idea is just to put noweb placeholders in the function docstring for the doctests. The placeholders will be expanded when you tangle the file, and they will get their contents from other src-blocks where you have written and run examples to test them.

This video might make the rest of this post easier to follow:

I will illustrate the idea using org-mode and the ob-ipython I have in scimax. The defaults of my ob-ipython setup are not useful for this example because it puts the execution count and mime types of output in the output. These are not observed in a REPL, and so we turn this off by setting these variables.

(setq ob-ipython-suppress-execution-count t
      ob-ipython-show-mime-types nil)

Now, we make an example function that takes a single argument and returns one divided by that argument. This block is runnable, and the function is then defined in the jupyter kernel. The docstring contains several noweb references to doctest blocks we define later. For now, they don't do anything. See The noweb doctest block section for the block that is used to expand these. This block also has a tangle header which indicates the file to tangle the results to. When I run this block, it is sent to a Jupyter kernel and saved in memory for use in subsequent blocks.

Here is the block with no noweb expansion. Note that this is easier to read in the original org source than it is to read in the published blog format.

def func(a):
    """A function to divide one by a.

    <<doctest("doctest-1")>>

    <<doctest("doctest-2")>>

    <<doctest("doctest-3")>>

    Returns: 1 / a.
    """
    return 1 / a

Now, we can write a series of named blocks that define various tests we might want to use as doctests. You can run these blocks here, and verify they are correct. Later, when we tangle the document, these will be incorporated into the tangled file in the docstring we defined above.

func(5) == 0.2
True

This next test will raise an Exception, and we just run it to make sure it does.

func(0)

ZeroDivisionErrorTraceback (most recent call last)
<ipython-input-6-ba0cd5a88f0a> in <module>()
----> 1 func(0)

<ipython-input-1-eafd354a3163> in func(a)
     18     Returns: 1 / a.
     19     """
---> 20     return 1 / a

ZeroDivisionError: division by zero

This is just a doctest with indentation to show how it is used.

for i in range(1, 4):
    print(func(i))
1.0
0.5
0.3333333333333333


That concludes the examples I want incorporated into the doctests. Each one of these blocks has a name, which is used as an argument to the noweb references in the function docstring.

1 Add a way to run the tests

This is a common idiom to enable easy running of the doctests. This will get tangled out to the file.

if __name__ == "__main__":
    import doctest
    doctest.testmod()

2 Tangle the file

So far, the Python code we have written only exists in the org-file, and in memory. Tangling is the extraction of the code into a code file.

We run this command, which extracts the code blocks marked for tangling, and expands the noweb references in them.

(org-babel-tangle)
test.py

Here is what we get:

def func(a):
    """A function to divide one by a.

    >>> func(5) == 0.2
    True

    >>> func(0)
    Traceback (most recent call last):
    ZeroDivisionError: division by zero

    >>> for i in range(1, 4):
    ...     print(func(i))
    1.0
    0.5
    0.3333333333333333


    Returns: 1 / a.
    """
    return 1 / a

if __name__ == "__main__":
    import doctest
    doctest.testmod()

That looks like a reasonable python file. You can see the doctest blocks have been inserted into the docstring, as desired. The proof of course is that we can run these doctests, and use the python module. We show that next.

3 Run the tests

Now, we can check if the tests pass in a fresh run (i.e. not using the version stored in the jupyter kernel.) The standard way to run the doctests is like this:

python test.py -v

Well, that's it! It worked fine. Now we have a python file we can import and reuse, with some doctests that show how it works. For example, here it is in a small Python script.

from test import func
print(func(3))
0.3333333333333333

There are surely some caveats to keep in mind here. This was just a simple proof of concept idea that isn't tested beyond this example. I don't know how many complexities would arise from more complex doctests. But, it seems like a good idea to continue pursuing if you like using doctests, and like using org-mode and interactive/literate programming techniques.

It is definitely an interesting way to use noweb to build up better code files in my opinion.

4 The noweb doctest block

These blocks are used in the noweb expansions. Each block takes a variable which is the name of a block. This block grabs the body of the named src block and formats it as if it was in a REPL.

We also grab the results of the named block and format it for the doctest. We use a heuristic to detect Tracebacks and modify the output to be consistent with it. In that case we assume the relevant Traceback is on the last line.

Admittedly, this does some fragile feeling things, like trimming whitespace here and there to remove blank lines, and quoting quotes (which was not actually used in this example), and removing the ": " pieces of ob-ipython results. Probably other ways of running the src-blocks would not be that suitable for this.

(org-babel-goto-named-src-block name)
(let* ((src (s-trim-right (org-element-property :value (org-element-context))))
       (src-lines (split-string src "\n"))
       body result)
  (setq body
        (s-trim-right
         (s-concat ">>> " (car src-lines) "\n"
                   (s-join "\n" (mapcar (lambda (s)
                                          (concat "... " s))
                                        (cdr src-lines))))))
  ;; now the results
  (org-babel-goto-named-result name)
  (let ((result (org-element-context)))
    (setq result
          (thread-last
              (buffer-substring (org-element-property :contents-begin result)
                                (org-element-property :contents-end result))
            (s-trim)
            ;; remove ": " from beginning of lines
            (replace-regexp-in-string "^: *" "")
            ;; quote quotes
            (replace-regexp-in-string "\\\"" "\\\\\"")))
    (when (string-match "Traceback" result)
      (setq result (format
                    "Traceback (most recent call last):\n%s"
                    (car (last (split-string result "\n"))))))
    (concat body "\n" result)))

Copyright (C) 2018 by John Kitchin. See the License for information about copying.

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Org-mode version = 9.1.13

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f-strings in emacs-lisp

| categories: emacs, elisp | tags: | View Comments

I am a big fan of f-strings in Python 3. They let you put variable names and expressions in a string template that get expanded to create new strings. Here is a simple example of using those:

username = 'John Kitchin'
somevar = 5**0.5
print(f'{username:30s}{somevar:1.2f}')
John Kitchin                  2.24


String formatting in emacs-lisp is by comparison not as fun and easy. Out of the box we have:

(let ((username "John Kitchin")
      (somevar (sqrt 5)))
  (format "%-30s%1.2f" username somevar))
John Kitchin                  2.24

That is still three lines of code, but it is ugly and hard to read like the old python code:

print('%-30s%1.2f' % (username, somevar))
John Kitchin                  2.24


My experience has shown that this gets harder to figure out as the strings get larger, and f-strings are easier to read.

The wonderful 's library provides some salvation for emacs-lisp, if you don't want the format fields. You can refer to variables in a lexical environment like this.

(let ((username "John Kitchin")
      (somevar (sqrt 5)))
  (s-lex-format "${username}${somevar}"))
John Kitchin2.23606797749979

Today, I decided to do something about this, and wrote this little macro. It is a variation on s-lex-format that introduces a slightly new syntax. You can now add an optional format field separated from the variable name by a space.

(defmacro f-string (fmt)
  "Like `s-format' but with format fields in it.
FMT is a string to be expanded against the current lexical
environment. It is like what is used in `s-lex-format', but has
an expanded syntax to allow format-strings. For example:
${user-full-name 20s} will be expanded to the current value of
the variable `user-full-name' in a field 20 characters wide.
  (let ((f (sqrt 5)))  (f-string \"${f 1.2f}\"))
  will render as: 2.24
This function is inspired by the f-strings in Python 3.6, which I
enjoy using a lot.
"
  (let* ((matches (s-match-strings-all"${\\(?3:\\(?1:[^} ]+\\) *\\(?2:[^}]*\\)\\)}" fmt))
         (agetter (cl-loop for (m0 m1 m2 m3) in matches
                        collect `(cons ,m3  (format (format "%%%s" (if (string= ,m2 "")
                                                                      (if s-lex-value-as-lisp "S" "s")
                                                                   ,m2))
                                                  (symbol-value (intern ,m1)))))))

    `(s-format ,fmt 'aget (list ,@agetter))))
f-string

Here it is in action.

(let ((username "John Kitchin")
      (somevar (sqrt 5)))
  (f-string "${username -30s}${somevar 1.2f}"))
John Kitchin                  2.24

It still lacks some of the capability of f-strings in python, e.g. in Python, arguments inside the template to be expanded get evaluated. The solution used above is too simple for that, since it just used a regexp and is limited to the value of variables in the lexical environment.

print(f'{5**0.5:1.3f}')
2.236


Nevertheless, this simple solution matches what I do most of the time anyway, so I still consider it an improvement!

Copyright (C) 2018 by John Kitchin. See the License for information about copying.

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Org-mode version = 9.1.13

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Making it easier to extend the export of org-mode links with generic functions

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I am a big fan of org-mode links. Lately, I have had a need to modify how some links are exported, e.g. defining new exports for different backends, or fine-tuning a particular backend. This can be difficult, depending on how the link was set up. Here is a typical setup I am used to using, where the different options for the backends are handled in a conditional statement in a single function. I will just use a link that just serves to illustrate the issues here. These links are just sytactic sugar for markup, they don't do anything else. We start with an example that just converts text to italic text for different backends like html or latex.

(defun italic-link-export (path desc backend)
  (cond
   ((eq 'html backend)
    (format "<em>%s</em>" path))
   ((eq 'latex backend)
    (format "\\textit{%s}" path))
   ;; fall-through case for everything else
   (t
    path)))

(org-link-set-parameters "italic" :export 'italic-link-export)
:export italic-link-export
(org-export-string-as "italic:text" 'html t)
<p>
<em>text</em></p>

(org-export-string-as "italic:text" 'latex t)
\textit{text}

This falls through though to the default case.

(require 'ox-md)
(org-export-string-as "italic:text" 'md t)

# Table of Contents



text


The point I want to make here is that this is not easy to extend as a user. You have to either modify the italic-link-export function, advise it, or monkey-patch it. None of these are especially nice.

I could define italic-link-export in a way that it retrieves the function to use from an alist or hash-table using the backend, but then you have to do two things to modify the behavior: define a backend specific function and register it in the lookup variable. It is also possible to just look up a function by a derived symbol, e.g. using fboundp, and then using funcall to execute it. This looks something like this:

;; a user definable function for exporting to latex
(defun italic-link-export-latex (path desc backend)
  (format "\\textit{%s}" path))

;; generic export function that looks up functions or defaults to
(defun italic-link-exporter (path desc backend)
  "Run `italic-link-export-BACKEND' if it exists, or return path."
  (let ((func (intern-soft (format "italic-link-export-%s" backend))))
    (if (fboundp func)
        (funcall func path desc backend)
      path)))

This has some indirection, but allows you to just define new functions to add new export backends, or replace single backend exports. It isn't bad, but there is room for improvement.

In this comment in org-ref, I saw a new opportunity to address this issue using generic functions in elisp! The idea is to define a generic function that handles the general export case, and then define additional functions for each specific backend based on the signature of the export function. I will switch to bold markup for this.

(cl-defgeneric bold-link-export (path desc backend)
 "Generic function to export a bold link."
 path)

;; this one runs when the backend is equal to html
(cl-defmethod bold-link-export ((path t) (desc t) (backend (eql html)))
 (format "<b>%s</b>" path))

;; this one runs when the backend is equal to latex
(cl-defmethod bold-link-export ((path t) (desc t) (backend (eql latex)))
 (format "\\textit{%s}" path))

(org-link-set-parameters "bold" :export 'bold-link-export)
:export bold-link-export

Here it is in action:

(org-export-string-as "some bold:text" 'html t)
<p>
some <b>text</b></p>

(org-export-string-as "some bold:text" 'latex t)

This uses the generic function.

(require 'ox-md)
(org-export-string-as "some bold:text" 'md t)

# Table of Contents



some text


The syntax for defining the generic function is pretty similar to a regular function. The specific methods are a little different since they have to provide the specific "signature" that triggers each method. Here we only differentiate on the type of the backend. It is nice these are all separate functions though. It makes it trivial to add new ones, and less intrusive to replace in my opinion.

Generic functions have many other potential applications to replace functions that use lots of conditions to control flow, with a fall-through option at the end. You can learn more about them here: https://www.gnu.org/software/emacs/manual/html_node/elisp/Generic-Functions.html. There is a lot more to them than I have illustrated here.

Copyright (C) 2018 by John Kitchin. See the License for information about copying.

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Org-mode version = 9.1.13

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New publication in Nature Catalysis

| categories: publication, news | tags: | View Comments

Machine learning (ML) is impacting many fields, including catalysis. In this comment, I briefly discuss the major directions that ML is influencing the field of catalysis, along with some outlook on future directions. There were strict word and reference limits, so apologies in advance if I left out your work!

@article{kitchin-2018-machin-learn-catal,
  author =       {John R. Kitchin},
  title =        {Machine Learning in Catalysis},
  journal =      {Nature Catalysis},
  volume =       1,
  number =       4,
  pages =        {230-232},
  year =         2018,
  doi =          {10.1038/s41929-018-0056-y},
  url =          {https://doi.org/10.1038/s41929-018-0056-y},
  DATE_ADDED =   {Mon Apr 16 12:50:43 2018},
}

You can see a read-only version of the paper here: https://rdcu.be/LGrM

Copyright (C) 2018 by John Kitchin. See the License for information about copying.

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Org-mode version = 9.1.6

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