Recent blog entries for crhodes

naive vs proper code-walking

I said in my discussion about backquote representations that some utilities had defects made manifest by SBCL 1.2.2’s new internal representation for backquote and related operators, and that those defects could have been avoided by using a code-walker. I’m going to look at let-over-lambda code here, to try to demonstrate what I meant by that, and show how a proper code-walker can quite straightforwardly be used for the code transformations that have been implemented using a naïve walker (typically walking over a tree of conses), removing whole classes of defects in the process.

The let-over-lambda code I’m discussing is from https://github.com/thephoeron/let-over-lambda, specifically this version. This isn’t intended to be a hatchet job on the utility – clearly, it is of use to its users – but to show up potential problems and offer solutions for how to fix them. I should also state up front that I haven’t read the Let over Lambda book, but it’s entirely possible that discussing and using a full code-walker would have been out of scope (as it explicitly was for On Lisp).

Firstly, let’s deal with how the maintainer of the let-over-lambda code is dealing with the change in backquote representations, since it’s still topical:

  ;; package definition here just in case someone decides to paste
;; things into a Lisp session, and for private namespacing
(defpackage "LOL" (:use "CL"))
(in-package "LOL")
;; actual excerpts from let-over-lambda code from
;; <https://github.com/thephoeron/let-over-lambda/blob/a202167629cb421cbc2139cfce1db22a84278f9f/let-over-lambda.lisp>
;; begins here:
#+sbcl
(if (string-lessp (lisp-implementation-version) "1.2.2")
    (pushnew :safe-sbcl *features*)
    (setq *features* (remove :safe-sbcl *features*)))
(defun flatten (x)
  (labels ((rec (x acc)
             (cond ((null x) acc)
                   #+(and sbcl (not safe-sbcl))
                   ((typep x 'sb-impl::comma) (rec (sb-impl::comma-expr x) acc))
                   ((atom x) (cons x acc))
                   (t (rec (car x) (rec (cdr x) acc))))))
    (rec x nil)))

The issues around the (*features*) handling here have been reported at github; for the purpose of this blog entry, I will just say that I wrote about them in Maintaining Portable Lisp Programs, a long time ago, and that a better version might look a bit like this:

  #+sbcl
(eval-when (:compile-toplevel :execute)
  (defun comma-implementation ()
    (typecase '`,x
      (symbol 'old)
      ((cons symbol (cons structure-object)) 'new)))
  (if (eql (comma-implementation) 'old)
      (pushnew 'cons-walkable-backquote *features*)
      (setq *features* (remove 'cons-walkable-backquote *features*))))
(defun flatten (x)
  (labels ((rec (x acc)
             (cond ((null x) acc)
                   #+lol::cons-walkable-backquote
                   ((typep x 'sb-impl::comma) (rec (sb-impl::comma-expr x) acc))
                   ((atom x) (cons x acc))
                   (t (rec (car x) (rec (cdr x) acc))))))
    (rec x nil)))

With these changes, the code is (relatively) robustly testing for the particular feature it needs to know about at the time that it needs to know, and recording it in a way that doesn’t risk confusion or contention with any other body of code. What is the let-over-lambda library using flatten for?

  (defun g!-symbol-p (thing)
  (and (symbolp thing)
       (eql (mismatch (symbol-name thing) "G!") 2)))
(defmacro defmacro/g! (name args &rest body)
  (let ((syms (remove-duplicates
               (remove-if-not #'g!-symbol-p (flatten body)))))
    `(defmacro ,name ,args
       (let ,(mapcar
              (lambda (s)
                `(,s (gensym ,(subseq (symbol-name s) 2))))
              syms)
         ,@body))))

The intent behind this macro-defining macro, defmacro/g!, appears to be automatic gensym generation: being able to write

  (defmacro/g! with-foo ((foo) &body body)
  `(let ((,g!foo (activate-foo ,foo)))
     (unwind-protect
         (progn ,@body)
       (deactivate-foo ,g!foo))))

without any explicit calls to gensym but retaining the protection that gensyms give against name capture:

  (macroexpand-1 '(with-foo (3) 4))
; => (let ((#1=#:FOO1 (activate-foo 3)))
;      (unwind-protect
;          (progn 4)
;        (deactivate-foo #1#)))

That's fine; it’s reasonable to want something like this. Are there any issues with this, apart from the one exposed by SBCL’s new backquote implementation? In its conventional use, probably not – essentially, all uses of g! symbols are unquoted (i.e. behind commas) – but there are a couple of more theoretical points. One issue is that flatten as it currently stands will look for all symbols beginning with g! in the macroexpander function source, whether or not they are actually variable evaluations:

  (defmacro/g! with-bar ((bar) &body body)
  `(block g!block
     (let ((,g!bar ,bar)) ,@body)))
; unused variable G!BLOCK
(macroexpand-1 '(with-bar (3) 4))
; => (block g!block (let ((#:BAR1 3)) 4))

In this example, that’s fair enough: it’s probably user error to have those g! symbols not be unquoted; this probably only becomes a real problem if there are macro-defining macros, with both the definer and the definition using g! symbols. It's not totally straightforward to demonstrate other problems with this simple approach to Lisp code transformation using just this macro; the transformation is sufficiently minimal, and the symptoms of problems relatively innocuous, that existing programming conventions are strong enough to prevent anything seriously untoward going wrong.

Before getting on to another example where the problems with this approach become more apparent, how could this transformation be done properly? By “properly” here I mean that the defmacro/g! should arrange to bind gensyms only for those g! symbols which are to be evaluated by the macroexpander, and not for those which are used for any other purpose. This is a task for a code-walker: a piece of code which exploits the fact that Lisp code is made up of Lisp data structures, all of which are introspectable, and the semantics of which in terms of effect on environment and execution are known. It is tedious, though possible, to write a mostly-portable code-walker (there needs to be some hook into the implementation’s representation of environments); I’m not going to do that here, but instead will use SBCL’s built-in code-walker.

The sb-walker:walk-form function takes three arguments: a form to walk, an initial environment to walk it in, and a walker function to perform whatever action is necessary on the walk. That walker function itself takes three arguments, a form, context and environment, and the walker arranges for it to be called on every macroexpanded or evaluated subform in the original form. The walker function should return a replacement form for the subform it is given (or the subform itself if it doesn’t want to take any action), and a secondary value of t if no further walking of that form should take place.

To do g! symbol detection and binding is fairly straightforward. If a symbol is in a context for evaluation, we collect it, and here we can take the first benefit from a proper code walk: we only collect g! symbols if the code-walker deems that they will be evaluated and there isn't an already-existing lexical binding for it:

  (defmacro defmacro/g!-walked (name args &body body)
  (let* (g!symbols)
    (flet ((g!-walker (subform context env)
             (declare (ignore context))
             (typecase subform
               (symbol
                (when (and (g!-symbol-p subform)
                           (not (sb-walker:var-lexical-p subform env)))
                  (pushnew subform g!symbols))
                subform)
               (t subform))))
      (sb-walker:walk-form `(progn ,@body) nil #'g!-walker)
      `(defmacro ,name ,args
         (let ,(mapcar (lambda (s) (list s `(gensym ,(subseq (symbol-name s) 2))))
                       g!symbols)
           ,@body)))))

The fact that we only collect symbols which will be evaluated deals with the problem exhibited by with-bar, above:

  (defmacro/g!-walked with-bar/walked ((bar) &body body)
  `(block g!block
     (let ((,g!bar ,bar)) ,@body)))
(macroexpand-1 '(with-bar/walked (3) 4))
; => (block g!block (let ((#:BAR1 3)) 4))

Only gathering symbols which don’t have lexical bindings (testing sb-walker:var-lexical-p) deals with another minor problem:

  (defmacro/g!-walked with-baz ((baz) &body body)
  (let ((g!sym 'sym))
    `(let ((,g!sym ,baz)) ,@body)))
(macroexpand-1 '(with-baz (3) 4))
; => (let ((sym 3)) 4)

(the cons-walker – flatten – would not be able to detect that there is already a binding for g!sym, and would introduce another one, again leading to an unused variable warning.)

OK, time to recap. So far, we’ve corrected the code that tests for particular backquote implementations, which was used in flatten, which itself was used to perform a code-walk; we’ve also seen some low-impact or theoretical problems with that simple code-walking technique, and have used a proper code-walker instead of flatten to deal with those problems. If the odd extra unused variable binding were the worst thing that could happen, there wouldn’t be much benefit from using a code-walker (other than the assurance that the walker is dealing with forms for execution); however, let us now turn our attention to the other macro in let-over-lambda’s code which does significant codewalking:

  (defun dollar-symbol-p (thing)
  (and (symbolp thing)
       (char= (char (symbol-name thing) 0) #\$)
       (ignore-errors (parse-integer (subseq (symbol-name thing) 1)))))
(defun prune-if-match-bodies-from-sub-lexical-scope (tree)
  (if (consp tree)
      (if (or (eq (car tree) 'if-match)
              (eq (car tree) 'when-match))
          (cddr tree)
          (cons (prune-if-match-bodies-from-sub-lexical-scope (car tree))
                (prune-if-match-bodies-from-sub-lexical-scope (cdr tree))))
      tree))
;; WARNING: Not %100 correct. Removes forms like (... if-match ...) from the
;; sub-lexical scope even though this isn't an invocation of the macro.
#+cl-ppcre
(defmacro! if-match ((test str) conseq &optional altern)
  (let ((dollars (remove-duplicates
                  (remove-if-not #'dollar-symbol-p
                                 (flatten (prune-if-match-bodies-from-sub-lexical-scope conseq))))))
    (let ((top (or (car (sort (mapcar #'dollar-symbol-p dollars) #'>)) 0)))
      `(let ((,g!str ,str))
         (multiple-value-bind (,g!s ,g!e ,g!ms ,g!me) (,test ,g!str)
           (declare (ignorable ,g!e ,g!me))
           (if ,g!s
               (if (< (length ,g!ms) ,top)
                   (error "ifmatch: too few matches")
                   ;; lightly edited here to remove irrelevant use of #`
                   (let ,(mapcar (lambda (a1) `(,(symb "$" a1)
                                                (subseq ,g!str (aref ,g!ms ,(1- a1))
                                                               (aref ,g!me ,(1- a1)))))
                                 (loop for i from 1 to top collect i))
                     ,conseq))
               ,altern))))))
(defmacro when-match ((test str) conseq &rest more-conseq)
  `(if-match (,test ,str)
     (progn ,conseq ,@more-conseq)))

What’s going on here? We have a prune-if-match-bodies-from-sub-lexical-scope function which, again, performs some kind of cons-based tree walk, removing some conses whose car is if-match or when-match. We have a trivial macro when-match which transforms into an if-match; the if-match macro is more involved. Any symbols named as a $ sign followed by an integer (in base 10) are treated specially; the intent is that they will be bound to capture groups of the cl-ppcre match. So it would be used in something like something like

  (defun key-value (line)
  (if-match ((lambda (s) (scan "^\\(.*\\): \\(.*\\)$" s)) line)
      (list $1 $2)
      (error "not actually a key-value line: ~S" line)))

and that would macroexpand to, roughly,

  (defun key-value (line)
  (multiple-value-bind (s e ms me)
      ((lambda (s) (scan "^\\(.*\\): \\(.*\\)$" s)) line)
    (if s
        (if (< (length ms) 2)
            (error "if-match: not enough matches)
            (let (($1 (subseq line (aref ms 0) (aref me 0)))
                  ($2 (subseq line (aref ms 1) (aref me 1))))
              (list $1 $2)))
        (error "not actually a key-value line: ~S" line))))

(there's additional reader macrology in let-over-lambda to make that lambda form unnecessary, but we can ignore that for our purposes).

Now, if-match has a similar problem that defmacro/g! had: since the tree walker doesn’t make a distinction between symbols present for evaluation and symbols for any other purpose, it is possible to confuse the walker. For example:

  (if-match (scanner string)
    (if (> (length $1) 6)
        '|$1000000|
        'less-than-$1000000))

This form, if macroexpanded, will attempt to bind one million variables to matched groups; even if the compiler doesn’t choke on that, evaluation will go wrong, as the matcher is unlikely to match one million groups (so the “not enough matches” error branch will be taken) – whereas of course the quoted one million dollar symbol is not intended for evaluation.

But the nesting problems are more obvious in this case than for defmacro/g!. Firstly, take the simple case:

  (if-match (scanner string)
    (list $1
          (if-match (scanner2 string)
              $2
              nil))
    nil)

Here, the $2 is in the scope of the inner if-match, and so mustn’t be included for the macroexpansion of the outer if-match. This case is handled in let-over-lambda’s implementation by the prune-if-match-bodies-from-sub-lexical-scope: the consequent of the inner if-match is pruned from the dollar-symbol accumulator. However, there are several issues with this; the first is that the test is pruned:

  (if-match (scanner string)
    (if-match (scanner2 $2)
        $1
        nil)
    nil)

In this example, the $2 is ‘invisible’ to the outer if-match, and so won’t get a binding. That’s straightforwardly fixable, along with the mishandling of when-let’s syntax (the entire body of when-let should be pruned, not just the first form), and what I think is an error in the pruning of if-match (it should recurse on the cdddr, not the cddr; github issue).

Not fixable at all while still using naïve code-walking are two other problems, one of which is noted in the comment present in the let-over-lambda code: the pruner doesn’t distinguish between if-match forms for evaluation and other conses whose car is if-match. Triggering this problem does involve some contortions – in order for it to matter, we need an if-match not for evaluation followed by a dollar symbol which is to be evaluated; but, for example:

  (defmacro list$/q (&rest args)
  `(list ,@(mapcar (lambda (x) (if (dollar-symbol-p x) x `',x)) args)))
(if-match (scanner string)
    (list$/q foo if-match $2)
    nil)

Here, although the $2 is in a position for evaluation (after macroexpansion), it will have no binding because it will have been pruned when naïvely walking the outer if-match macro. The if-match symbol argument to `list$/q ends up quoted, and should not be treated as a macro call.

Also, the pruner function must have special knowledge not just about the semantics of if-match, but also of any macro which can expand to if-match – see the attempt to handle when-match in the pruner. If a user were to have the temerity to define case-match

  (defmacro case-match (string &rest clauses)
  (if (null clauses)
      nil
      `(if-match (,(caar clauses) ,string)
           (progn ,@(cdar clauses))
           (case-match string ,@(cdr clauses)))))

any attempt to nest a case-match inside an outer if-match is liable to fail, as the pruner has no knowledge of how to handle the case-match form.

All of these problems are solvable by using a proper code-walker. The code-walker should collect up all dollar symbols to be evaluated in the consequent of an if-match form, so that bindings for them can be generated, except for those with already existing lexical bindings within the if-match (not those from outside, otherwise nesting won’t work). For testing purposes, we’ll also signal a diagnostic condition within the macroexpander to indicate which dollar symbols we’ve found.

  (define-condition if-match/walked-diagnostic (condition)
  ((symbols :initarg :symbols :reader if-match-symbols)))
(defmacro if-match/walked ((test string) consequent &optional alternative)
  (let* (dollar-symbols)
    (flet ((dollar-walker (subform context env)
             (declare (ignore context))
             (typecase subform
               (symbol
                (when (and (dollar-symbol-p subform)
                           (not (sb-walker:var-lexical-p subform env)))
                  (pushnew subform dollar-symbols))
                subform)
               (t subform))))
      (handler-bind ((if-match/walked-diagnostic #'continue))
        (sb-walker:walk-form consequent nil #'dollar-walker))
      (let* ((dollar-symbols (sort dollar-symbols #'> :key #'dollar-symbol-p))
             (top (dollar-symbol-p (car dollar-symbols))))
        (with-simple-restart (continue "Ignore diagnostic condition")
          (signal 'if-match/walked-diagnostic :symbols dollar-symbols))
        (sb-int:with-unique-names (start end match-start match-end)
          (sb-int:once-only ((string string))
            `(multiple-value-bind (,start ,end ,match-start ,match-end)
                 (,test ,string)
               (declare (ignore ,end) (ignorable ,match-end))
               (if ,start
                   (if (< (length ,match-start) ,top)
                       (error "~S: too few matches: needed ~D, got ~D." 'if-match
                              ,top (length ,match-start))
                       (let ,(mapcar (lambda (s)
                                       (let ((i (1- (dollar-symbol-p s))))
                                         `(,s (subseq ,string (aref ,match-start ,i) (aref ,match-end ,i)))))
                                     (reverse dollar-symbols))
                         ,consequent))
                   ,alternative))))))))

(I'm using sb-int:once-only and sb-int:with-unique-names to avoid having to include their definitions in this post, which is getting a bit lengthy). Testing this looks like

  (defmacro test-if-match (form expected-symbols)
  `(handler-case (macroexpand-1 ',form)
     (if-match/walked-diagnostic (c)
       (assert (equal (if-match-symbols c) ',expected-symbols)))
     (:no-error (&rest values) (declare (ignore values)) (error "no diagnostic"))))
(test-if-match (if-match/walked (test string) (list $1 $2) 'foo) ($2 $1))
(test-if-match (if-match/walked (test string) (if (> (length $1) 6) '$10 '$8) nil) ($1))
(test-if-match (if-match/walked (scanner string)
                   (list $1
                         (if-match/walked (scanner2 string)
                             $2
                             nil))
                   nil)
               ($1))
(test-if-match (if-match/walked (scanner string) (list$/q foo if-match/walked $3) nil) ($3))
(defmacro case-match/walked (string &rest clauses)
  (if (null clauses)
      nil
      `(if-match/walked (,(caar clauses) ,string)
           (progn ,@(cdar clauses))
           (case-match/walked string ,@(cdr clauses)))))
(test-if-match (if-match/walked (scanner string)
                   (case-match/walked $1
                     (foo $2)
                     (bar $3)))
               ($1))

To summarize: I’ve shown here how to make use of a full code-walker to make a couple of code transforming macros more robust. Full code-walkers can do more than just what I've shown here: the sb-walker:walk-form interface can also inhibit macroexpansion, transform function calls into calls to other functions, while respecting the semantics of the Lisp operators in the code that is being walked and allowing some introspection of the lexical environment. Here, we have called sb-walker:walk-form for side effects from the walker function we’ve provided; it is also possible to use its value (that’s how sb-cltl2:macroexpand-all is implemented, for example). I hope that this can help users affected by the change in internal representation of backquote, as well as others who want to write advanced code-transforming macros. If the thought of using an SBCL-internal code-walker makes you a bit queasy (as well it might), you could instead start by looking at one or two other more explicitly-portable code-walkers out there, for example John Fremlin’s macroexpand-dammit, the walker in Alex Plotnick's CLWEB literate programming system (github link), or the code walker in iterate.

Syndicated 2014-09-08 20:13:38 from notes

31 Jul 2014 (updated 31 Jul 2014 at 18:14 UTC) »

london employment visualization part 2

Previously, I did all the hard work to obtain and transform some data related to London, including borough and MSOA shapes, population counts, and employment figures, and used them to generate some subjectively pretty pictures. I promised a followup on the gridSVG approach to generating visualizations with more potential for interactivity than a simple picture; this is the beginning of that.

Having done all the heavy lifting in the last post, including being able to generate ggplot objects (whose printing results in the pictures), it is relatively simple to wrap output to SVG instead of output to PNG around it all. In fact it is extremely simple to output to SVG; simply use an SVG output device

  svg("/tmp/london.svg", width=16, height=10)

rather than a PNG one

  png("/tmp/london.png", width=1536, height=960)

(which brings back for me memories of McCLIM, and my implementation of an SVG backend, about a decade ago). So what does that look like? Well, if you’ve entered those forms at the R repl, close the png device

  dev.off()

and then (the currently active device being the SVG one)

  print(ggplot.london(fulltime/(allages-younger-older)))
dev.off()

default (cairo) SVG device

That produces an SVG file, and if SVG in and of itself is the goal, that’s great. But I would expect that the main reason for producing SVG isn’t so much for the format itself (though it is nice that it is a vector image format rather than rasterized, so that zooming in principle doesn’t cause artifacts) but for the ability to add scripting to it: and since the output SVG doesn’t retain any information about the underlying data that was used to generate it, it is very difficult to do anything meaningful with it.

I write “very difficult” rather than “impossible”, because in fact the SVGAnnotation package aimed to do just that: specifically, read the SVG output produced by the R SVG output device, and (with a bit of user assistance and a liberal sprinkling of heuristics) attempt to identify the regions of the plot corresponding to particular slices of datasets. Then, using a standard XML library, the user could decorate the SVG with extra information, add links or scripts, and essentially do whatever they needed to do; this was all wrapped up in an svgPlot function. The problem with this approach is that it is fragile: for example, one heuristic used to identify a lattice plot area was that there should be no text in it, which fails for custom panel functions with labelled guidlines. It is possible to override the default heuristic, but it’s difficult to build a robust system this way (and in fact when I tried to run some two-year old analysis routines recently, the custom SVG annotation that I wrote broke into multiple pieces given new data).

gridSVG’s approach is a little bit different. Instead of writing SVG out and reading it back in, it relies on the grid graphics engine (so does not work with so-called base graphics, the default graphics system in R), and on manipulating the grid object which represents the current scene. The gridsvg pseudo-graphics-device does the behind-the-scenes rendering for us, with some cost related to yet more wacky interactions with R’s argument evaluation semantics which we will pay later.

  gridsvg("/tmp/gridsvg-london.svg", width=16, height=10)
print(ggplot.london(fulltime/(allages-younger-older)))
dev.off()

Because ggplot uses grid graphics, this just works, and generates a much more structured svg file, which should render identically to the previous one:

SVG from gridSVG device

If it renders identically, why bother? Well, because now we have something that writes out the current grid scene, we can alter that scene before writing out the document (at dev.off() time). For example, we might want to add tooltips to the MSOAs so that their name and the quantity value can be read off by a human. Wrapping it all up into a function, we get

  gridsvg.london <- function(expr, subsetexpr=TRUE, filename="/tmp/london.svg") {

We need to compute the subset in this function, even though we’re going to be using the full dataset in ggplot.london when we call it, in order to get the values and zone labels.

      london.data <- droplevels(do.call(subset, list(london$msoa.fortified, substitute(subsetexpr))))

Then we need to map (pun mostly intended) the values in the fortified data frame to the polygons drawn; without delving into the format, my intuition is that the fortified data frame contains vertex information, whereas the grid (and hence SVG) data is organized by polygons, and there may be more than one polygon for a region (for example if there are islands in the Thames). Here we simply generate an index from a group identifier to the first row in the dataframe in that group, and use it to pull out the appropriate value and label.

      is <- match(levels(london.data$group), london.data$group)
    vals <- eval(substitute(expr), london.data)[is]
    labels <- levels(london.data$zonelabel)[london.data$zonelabel[is]]

Then we pay the cost of the argument evaluation semantics. My first try at this line was gridsvg(filename, width=16, height=10), which I would have (perhaps naïvely) expected to work, but which in fact gave me an odd error suggesting that the environment filename was being evaluated in was the wrong one. Calling gridsvg like this forces evaluation of filename before the call, so there should be less that can go wrong.

      do.call(gridsvg, list(filename, width=16, height=10))

And, as before, we have to do substitutions rather than evaluations to get the argument expressions evaluated in the right place:

      print(do.call(ggplot.london, list(substitute(expr), substitute(subsetexpr))))

Now comes the payoff. At this point, we have a grid scene, which we can investigate using grid.ls(). Doing so suggests that the map data is in a grid object named like GRID.polygon followed by an integer, presumably in an attempt to make names unique. We can “garnish” that object with attributes that we want: some javascript callbacks, and the values and labels that we previously calculated.

      grid.garnish("GRID.polygon.*",
                 onmouseover=rep("showTooltip(evt)", length(is)),
                 onmouseout=rep("hideTooltip()", length(is)),
                 zonelabel=labels, value=vals,
                 group=FALSE, grep=TRUE)

We need also to provide implementations of those callbacks. It is possible to do that inline, but for simplicity here we simply link to an external resource.

      grid.script(filename="tooltip.js")

Then close the gridsvg device, and we’re done!

      dev.off()
}

Then gridsvg.london(fulltime/(allages-younger-older)) produces:

proportion employed full-time

which is some kind of improvement over a static image for data of this complexity.

And yet... the perfectionist in me is not quite satisfied. At issue is a minor graphical glitch, but it’s enough to make me not quite content; the border of each MSOA is stroked in a slightly lighter colour than the fill colour, but that stroke extends beyond the border of the MSOA region (the stroke’s centre is along the polygon edge). This means that the strokes from adjacent MSOAs overlie each other, so that the most recently drawn obliterates any drawn previously. This also causes some odd artifacts around the edges of London (and into the Thames, and pretty much obscures the river Lea).

This can be fixed by clipping; I think the trick to clip a path to itself counts as well-known. But clipping in SVG is slightly hard, and the gridSVG facilities for doing it work on a grob-by-grob basis, while the map is all one big polygon grid object. So to get the output I want, I am going to have to perform surgery on the SVG document itself after all; we are still in a better position than before, because we will start with a sensible hierarchical arrangement of graphical objects in the SVG XML structure, and gridSVG furthermore provides some introspective capabilities to give XML ids or XPath query strings for particular grobs.

grid.export exports the current grid scene to SVG, returning a list with the SVG XML itself along with this mapping information. We have in the SVG output an arbitrary number of polygon objects; our task is to arrange such that each of those polygons has a clip mask which is itself. In order to do that, we need for each polygon a clipPath entry with a unique id in a defs section somewhere, where each clipPath contains a use pointing to the original polygon’s ID; then each polygon needs to have a clip-path style property pointing to the corresponding clipPath object. Clear?

  addClipPaths <- function(gridsvg, id) {

given the return value of grid.export and the identifier of the map grob, we want to get the set of XML nodes corresponding to the polygons within that grob.

      ns <- getNodeSet(gridsvg$svg, sprintf("%s/*", gridsvg$mappings$grobs[[id]]$xpath))

Then for each of those nodes, we want to set a clip path.

      for (i in 1:length(ns)) {
        addAttributes(ns[[i]], style=sprintf("clip-path: url(#clipPath%s)", i))
    }

For each of those nodes, we also need to define a clip path

      clippaths <- list()
    for (i in 1:length(ns)) {
        clippaths[[i]] <- newXMLNode("clipPath", attrs=c(id=sprintf("clipPath%s", i)))
        use <- newXMLNode("use", attrs = c("xlink:href"=sprintf("#%s", xmlAttrs(ns[[i]])[["id"]])))
        addChildren(clippaths[[i]], kids=list(use))
    }

And hook it into the existing XML

      defs <- newXMLNode("defs")
    addChildren(defs, kids=clippaths)
    top <- getNodeSet(gridsvg$svg, "//*[@id='gridSVG']")[[1]]
    addChildren(top, kids=list(defs))
}

Then our driver function needs some slight modifications:

  gridsvg.london2 <- function(expr, subsetexpr=TRUE, filename="/tmp/london.svg") {
    london.data <- droplevels(do.call(subset, list(london$msoa.fortified, substitute(subsetexpr))))
    is <- match(levels(london.data$group), london.data$group)
    vals <- eval(substitute(expr), london.data)[is]
    labels <- levels(london.data$zonelabel)[london.data$zonelabel[is]]

Until here, everything is the same, but we can’t use the gridsvg pseudo-graphics device any more, so we need to do graphics device handling ourselves:

      pdf(width=16, height=10)
    print(do.call(ggplot.london, list(substitute(expr), substitute(subsetexpr))))
    grid.garnish("GRID.polygon.*",
                 onmouseover=rep("showTooltip(evt)", length(is)),
                 onmouseout=rep("hideTooltip()", length(is)),
                 zonelabel=labels, value=vals,
                 group=FALSE, grep=TRUE)
    grid.script(filename="tooltip.js")

Now we export the scene to SVG,

      gridsvg <- grid.export()

find the grob containing all the map polygons,

      grobnames <- grid.ls(flatten=TRUE, print=FALSE)$name
    grobid <- grobnames[[grep("GRID.polygon", grobnames)[1]]]

add the clip paths,

      addClipPaths(gridsvg, grobid)
    saveXML(gridsvg$svg, file=filename)

and we’re done!

      dev.off()
}

Then gridsvg.london2(fulltime/(allages-younger-older)) produces:

proportion employed full-time (with polygon clipping)

and I leave whether the graphical output is worth the effort to the beholder’s judgment.

As before, these images contain National Statistics and Ordnance Survey data © Crown copyright and database right 2012.

Syndicated 2014-07-31 17:07:34 (Updated 2014-07-31 17:14:34) from notes

19 Jul 2014 (updated 19 Jul 2014 at 21:12 UTC) »

london employment visualization

I went to londonR a month or so ago, and the talk whose content stayed with me most was the one given by Simon Hailstone on map-making and data visualisation with ggplot2. The take-home message for me from that talk was that it was likely to be fairly straightforward to come up with interesting visualisations and data mashups, if you already know what you are doing.

Not unrelatedly, in the Goldsmiths Data Science MSc programme which we are running from October, it is quite likely that I will be teaching a module in Open Data, where the students will be expected to produce visualisations and mashups of publically-accessible open data sets.

So, it is then important for me to know what I am doing, in order that I can help the students to learn to know what they are doing. My first, gentle steps are to look at life in London; motivated at least partly by the expectation that I encounter when dropping off or picking up children from school that I need more things to do with my time (invitations to come and be trained in IT at a childrens' centre at 11:00 are particularly misdirected, I feel) I was interested to try to find out how local employment varies. This blog serves at least partly as a stream-of-exploration of not just the data but also ggplot and gridsvg; as a (mostly satisfied) user of lattice and SVGAnnotation in a previous life, I'm interested to see how the R graphing tools have evolved.

Onwards! Using R 3.1 or later: first, we load in the libraries we will need.

  library(ggplot2)
library(extremevalues)
library(maps)
library(rgeos)
library(maptools)
library(munsell)
library(gridSVG)

Then, let's define a couple of placeholder lists to accumulate related data structures.

  london <- list()
tmp <- list()

Firstly, let's get hold of some data. I want to look at employment; that means getting hold of counts of employed people, broken down by area, and also counts of people living in that area in the first place. I found some Excel spreadsheets published by London datastore and the Office for National Statistics, with data from the 2011 census, and extracted from them some useful data in CSV format. (See the bottom of this post for more detail about the data sources).

  london$labour <- read.csv("2011-labour.csv", header=TRUE, skip=1)
london$population <- read.csv("mid-2011-lsoa-quinary-estimates.csv", header=TRUE, skip=3)

The labour information here does include working population counts by area – specifically by Middle Layer Super Output Area (MSOA), a unit of area holding roughly eight thousand people. Without going into too much detail, these units of area are formed by aggregating Lower Layer Super Output Areas (LSOAs), which themselves are formed by aggregating census Output Areas. In order to get the level of granularity we want, we have to do some of that aggregation ourselves.

The labour data is published in one sheet by borough (administrative area), ward (local electoral area) and LSOA. The zone IDs for these areas begin E09, E05 and E01; we need to manipulate the data frame we have to include just the LSOA entries

  london$labour.lsoa <- droplevels(subset(london$labour, grepl("^E01", ZONEID)))

and then aggregate LSOAs into MSOAs “by hand”, by using the fact that LSOAs are named such that the name of their corresponding MSOA is all but the last letter of the LSOA name (e.g. “Newham 001A” and “Newham 001B” LSOAs both have “Newham 001” as their parent MSOA). In doing the aggregation, all the numeric columns are count data, so the correct aggregation is to sum corresponding entries of numerical data (and discard non-numeric ones)

  tmp$nonNumericNames <- c("DISTLABEL", "X", "X.1", "ZONEID", "ZONELABEL")
tmp$msoaNames <- sub(".$", "", london$labour.lsoa$ZONELABEL)
tmp$data <- london$labour.lsoa[,!names(london$labour.lsoa) %in% tmp$nonNumericNames]

london$labour.msoa <- aggregate(tmp$data, list(tmp$msoaNames), sum)
tmp <- list()

The population data is also at LSOA granularity; it is in fact for all LSOAs in England and Wales, rather than just London, and includes some aggregate data at a higher level. We can restrict our attention to London LSOAs by reusing the zone IDs from the labour data, and then performing the same aggregation of LSOAs into MSOAs.

  london$population.lsoa <- droplevels(subset(london$population, Area.Codes %in% levels(london$labour.lsoa$ZONEID)))
tmp$nonNumericNames <- c("Area.Codes", "Area.Names", "X")
tmp$msoaNames <- sub(".$", "", london$population.lsoa$X)
tmp$data <- london$population.lsoa[,!(names(london$population.lsoa) %in% tmp$nonNumericNames)]
london$population.msoa <- aggregate(tmp$data, list(tmp$msoaNames), sum)
tmp <- list()

This is enough data to be getting on with; it only remains to join the data frames up. The MSOA name column is common between the two tables; we can therefore reorder one of them so that it lines up with the other before simply binding columns together:

  london$employment.msoa <- cbind(london$labour.msoa, london$population.msoa[match(london$labour.msoa$Group.1, london$population.msoa$Group.1)])

(In practice in this case, the order of the two datasets is the same, so the careful reordering is in fact the identity transformation)

  tmp$notequals <- london$population.msoa$Group.1 != london$labour.msoa$Group.1
stopifnot(!sum(tmp$notequals))
tmp <- list()

Now, finally, we are in a position to look at some of the data. The population data contains a count of all people in the MSOA, along with counts broken down into 5-year age bands (so 0-5 years old, 5-10, and so on, up to 90+). We can take a look at the proportion of each MSOA's population in each age band:

  ggplot(reshape(london$population.msoa, varying=list(3:21),
               direction="long", idvar="Group.1")) +
    geom_line(aes(x=5*time-2.5, y=X0.4/All.Ages, group=Group.1),
              alpha=0.03, show_guide=FALSE) +
    scale_x_continuous(name="age / years") +
    scale_y_continuous(name="fraction") +
    theme_bw()

age distributions in London MSOAs

This isn't a perfect visualisation; it does show the broad overall shape of the London population, along with some interesting deviations (some MSOAs having a substantial peak in population in the 20-25 year band, while rather more peak in the 25-30 band; a concentration around 7% of 0-5 year olds, with some significant outliers; and a tail of older people with some interesting high outliers in the 45-50 and 60-65 year bands, as well as one outlier in the 75-80 and 80-85).

That was just population; what about the employment statistics? Here's a visualisation of the fraction of people in full-time employment, treated as a distribution

  ggplot(london$employment.msoa, aes(x=Full.time/All.Ages)) +
    geom_density() + theme_bw()

fraction in full-time employment in London MSOAs

showing an overal concentration of full-time employment level around 35%. But this of course includes in the population estimate people of non-working ages; it may be more relevant to view the distribution of full-time employment as a fraction of those of “working age”, which here we will define as those between 15 and 65 (not quite right but close enough):

  london$employment.msoa$younger = rowSums(london$employment.msoa[,62:64])
london$employment.msoa$older = rowSums(london$employment.msoa[,75:80])
ggplot(london$employment.msoa, aes(x=Full.time/(All.Ages-younger-older))) +
    geom_density() + theme_bw()

fraction of those of working age in full-time employment in London MSOAs

That's quite a different picture: we've lost the bump of outliers of high employment around 60%, and instead there's substantial structure at lower employment rates (plateaus in the density function around 50% and 35% of the working age population). What's going on? The proportions of people not of working age must not be evenly distributed between MSOAs; what does it look like?

  ggplot(london$employment.msoa, aes(x=older/All.Ages, y=younger/All.Ages)) +
    geom_point(alpha=0.1) + geom_density2d() + coord_equal() + theme_bw()

distribution of younger vs older people in London MSOAs

So here we see that a high proportion of older people in an MSOA (around 20%) is a strong predictor of the proportion of younger people (around 17%); similarly, if the younger population is 25% or so of the total population, there are likely to be less than 10% of people of older non-working ages. But at intermediate values of either older or younger proportions, 10% of older or 15% of younger, the observed variation of the other proportion is very high: what this says is that the proportion of people of working age in an MSOA varies quite strongly, and for a given proportion of people of working age, some MSOAs have more older people and some more younger people. Not a world-shattering discovery, but important to note.

So, going back to employment: what are the interesting cases? One way of trying to characterize them is to fit the central portion of the observations to some parameterized distribution, and then examining cases where the observation is of a sufficiently low probability. The extremevalues R package does some of this for us; it offers the option to fit a variety of distributions to a set of observations with associated quantiles. Unfortunately, the natural distribution to use for proportions, the Beta distribution, is not one of the options (fitting involves messing around with derivatives of the inverse of the incomplete Beta function, which is a bit of a pain), but we can cheat: instead of doing the reasonable thing and fitting a beta distribution, we can transform the proportion using the logit transform and fit a Normal distribution instead, because everything is secretly a Normal distribution. Right? Right? Anyway.

  tmp$outliers <- with(london$employment.msoa, getOutliers(log(Full.time/All.Ages/(1-Full.time/All.Ages))))
tmp$high <- london$employment.msoa$Group.1[tmp$outliers$iRight]
tmp$low <-london$employment.msoa$Group.1[tmp$outliers$iLeft]
print(tmp[c("high", "low")])
tmp <- list()

This shows up 9 MSOAs as having a surprisingly high full employment rate, and one (poor old Hackney 001) as having a surprisingly low rate (where “surprising” is defined relative to our not-well-motivated-at-all Normal distribution of logit-transformed full employment rates, and so shouldn't be taken too seriously). Where are these things? Clearly the next step is to put these MSOAs on a map. Firstly, let's parse some shape files (again, see the bottom of this post for details of where to get them from).

  london$borough <- readShapePoly("London_Borough_Excluding_MHW")
london$msoa <- readShapePoly("MSOA_2011_London_gen_MHW")

In order to plot these shape files using ggplot, we need to convert the shape file into a “fortified” form:

  london$borough.fortified <- fortify(london$borough)
london$msoa.fortified <- fortify(london$msoa)

and we will also need to make sure that we have the MSOA (and borough) information as well as the shapes:

  london$msoa.fortified$borough <- london$msoa@data[as.character(london$msoa.fortified$id), "LAD11NM"]
london$msoa.fortified$zonelabel <- london$msoa@data[as.character(london$msoa.fortified$id), "MSOA11NM"]

For convenience, let's add to the “fortified” MSOA data frame the columns that we've been investigating so far:

  tmp$is <- match(london$msoa.fortified$zonelabel, london$employment.msoa$Group.1)
london$msoa.fortified$fulltime <- london$employment.msoa$Full.time[tmp$is]
london$msoa.fortified$allages <- london$employment.msoa$All.Ages[tmp$is]
london$msoa.fortified$older <- london$employment.msoa$older[tmp$is]
london$msoa.fortified$younger <- london$employment.msoa$younger[tmp$is]

And now, a side note about R and its evaluation semantics. R has... odd semantics. The basic evaluation model is that function arguments are evaluated lazily, when the callee needs them, but in the caller's environment – except if the argument is a defaulted one (when no argument was actually passed), in which ase it's in the callee's environment active at the time of evaluation, except that these rules can be subverted using various mechanisms, such as simply looking at the call object that is currently being evaluated. There's significant complexity lurking, and libraries like ggplot (and lattice, and pretty much anything you could mention) make use of that complexity to give a convenient surface interface to their functions. Which is great, until the time comes for someone to write a function that calls these libraries, such as the one I'm about to present which draws pictures of London. I have to know about the evaluation semantics of the functions that I'm calling – which I suppose would be reasonable if there weren't quite so many possible options – and necessary workarounds that I need to install so that my function has the right, convenient evaluation semantics while still being able to call the library functions that I need to. I can cope with this because I have substantial experience with programming languages with customizeable evaluation semantics; I wonder how to present this to Data Science students.

With all that said, I present a fairly flexible function for drawing bits of London. This presentation of the finished object of course obscures all my exploration of things that didn't work, some for obvious reasons and some which remain a mystery to me.

  ggplot.london <- function(expr, subsetexpr=TRUE) {

We will call this function with an (unevaluated) expression to be displayed on a choropleth, to be evaluated in the data frame london$msoa.fortified, and an optional subsetting expression to restrict the plotting. We compute the range of the expression, independent of any data subsetting, so that we have a consistent scale between calls

      expr.limits <- range(eval(substitute(expr), london$msoa.fortified))

and compute a suitable default aesthetic structure for ggplot

      expr.aes <- do.call(aes, list(fill=substitute(expr), colour=substitute(expr)))

where substitute is used to propagate the convenience of an expression interface in our function to the same expression interface in the ggplot functions, and do.call is necessary because aes does not evaluate its arguments, while we do need to perform the substitution before the call.

      london.data <- droplevels(do.call(subset, list(london$msoa.fortified, substitute(subsetexpr))))

This is another somewhat complicated set of calls to make sure that the subset expression is evaluated when we need it, in the environment of the data frame. london.data at this point contains the subset of the MSOAs that we will be drawing.

      (ggplot(london$borough.fortified) + coord_equal() +

Then, we set up the plot, specify that we want a 1:1 aspect ratio,

       (theme_minimal() %+replace%
      theme(panel.background = element_rect(fill="black"),
            panel.grid.major = element_blank(),
            panel.grid.minor = element_blank())) +

a black background with no grid lines,

       geom_map(map=london.data, data=london.data, modifyList(aes(map_id=id, x=long, y=lat), expr.aes), label="map") +

and plot the map.

       scale_fill_gradient(limits=expr.limits, low=mnsl2hex(darker(rgb2mnsl(coords(hex2RGB("#13432B", TRUE))))), high=mnsl2hex(darker(rgb2mnsl(coords(hex2RGB("#56F7B1", TRUE)))))) +
     scale_colour_gradient(limits=expr.limits, low="#13432B", high="#56F7B1", guide=FALSE) +

We specify a greenish colour scale, with the fill colour being slightly darker than the outline colour for prettiness, and

       geom_map(map=london$borough.fortified, aes(map_id=id, x=long, y=lat), colour="white", fill=NA, size=0.1)

also draw a superposition of borough boundaries to help guide the eye.

       )
}

So, now, we can draw a map of full time employment:

  ggplot.london(fulltime/(allages-younger-older))

proportion employed full-time

or the same, but just the outlier MSOAs:

  ggplot.london(fulltime/(allages-younger-older), zonelabel %in% london$outliers)

proportion employed full-time (outlier MSOAs)

or the same again, plotting only those MSOAs which are within 0.1 of the extremal values:

  ggplot.london(fulltime/(allages-younger-older), pmin(fulltime/(allages-younger-older) - min(fulltime/(allages-younger-older)), max(fulltime/(allages-younger-older)) - fulltime/(allages-younger-older)) < 0.1)

proportion employed full-time (near-extremal MSOAs)

Are there take-home messages from this? On the data analysis itself, probably not; it's not really a surprise to discover that there's substantial underemployment in the North and East of London, and relatively full employment in areas not too far from the City of London; it is not unreasonable for nursery staff to ask whether parents dropping children off might want training; it might be that they have the balance of probabilities on their side.

From the tools side, it seems that they can be made to work; I've only really been kicking the tyres rather than pushing them hard, and the number of times I had to rewrite a call to ggplot, aes or one of the helper functions as a response to an error message, presumably because of some evaluation not happening at quite the right time, is high – but the flexibility and interactivity they offer for exploration feels to me as if the benefits outweigh the costs.

The R commands in this post are here; the shape files are extracted from Statistical GIS Boundary Files for London and redistributed here under the terms of the Open Government Licence; they contain National Statistics and Ordnance Survey data © Crown copyright and database right 2012. The CSV data file for population counts is derived from an ONS publication, distributed here under the terms of the Open Government Licence, and contains National Statistics data © Crown copyright and database right 2013; the CSV data file for labour statistics is derived from a spreadsheet published by the London datastore, distributed here under the terms of the Open Government Licence, and contains National Statistics data © Crown copyright and database right 2013.

Still here after all that licence information? I know I promised some gridSVG evaluation too, but it's getting late and I've been drafting this post for long enough already. I will come back to it, though, because it was the more fun bit, and it makes some nifty interactive visualizations fairly straightforward. Watch this space.

Syndicated 2014-07-19 20:12:00 (Updated 2014-07-19 20:18:42) from notes

off to tours

I’m on a train. And, more than usually, I don’t know what I’m doing.

Because of my involvement with Transforming Musicology, I’ve been invited to participate in a seminar on Renaissance musicat the Centre d'Études Supérieurs de la Renaissance at Tours. This is a real privilege, and the guest list is a bit intimidating – I went through a French Baroque phase 20 years ago, and it’s therefore nice to be able to bring the book on Marc-Antoine Charpentier to get it autographed by the author.

But if the guest list is intimidating, that’s nothing compared to the format. It has been made very clear that this is not a conference – we don’t have to present research we've already done, but rather our plans for future research that might be of interest to the assembled community. And it will be really interesting for me to hear that, of course, but I will of course be called on to justify my own presence there.

I think I might have two stories to tell. The first is about tools for directly improving the musicologist’s life, with the exemplar I would use being the Gombert/Josquin case study that, depressingly, remains aspirational rather than actual. Here, although more of the pieces are in place than previously, and I do have a complete workflow for examining individual fragments, the thing that is holding up the investigation is that aggregation of search results for those individual fragments into a useful summary suitable for digestion is more challenging and involves more time for concentrated thought than I currently have available.

The second story involves Bernardino de Ribera, and would aim to tell the musicological story from as near as possible to the start – Bruno Turner’s discovery of manuscripts at Toledo and Valencia – to finish, a professional-quality recording. The hope here is that by making the intermediate “data” available (electronic versions of manuscripts, critical editions, recording sessions) as well as links to the commercial performing editions and recording release, we enable a wider community of researchers and enthusiasts to engage with the material, enriching the commons. I should make clear that this story, too, is aspirational; I do not yet have clearance for releasing /any/ of this, and there are many hurdles to overcome before that clearance is given – but here this is intended as a case study of how musicologists and associated parties can publish their work and make them accessible to allow more people to engage with their work. This might address the fears of some that archive-based musicology is a dying art, by making the fruits of the labour much more visible.

The common theme underlying these two stories is, for me, the validation of new knowledge. I am not one who has completely bought in to the “impact” agenda currently driving a fair amount of the evaluation of academic utility in the UK, but I do perhaps take a harder line about the creation of knowledge than some of my colleagues at Goldsmiths, where I strongly feel that new knowledge itself should be communicable to others and not just used in the context of artistic practice. (I should say that my own line has softened quite substantially in the last decade; it is entirely possible that given a few more I will be as arty as the next Goldsmiths academic). The validation of the new knowledge does not have to be fully quantitative or “scientific” – I have certainly mellowed enough to allow that – but there has to be some kind of proof of the pudding, and I strongly think that that proof should be able to be entered into the permanent record and made as accessible as possible, and that this is orthogonal to making a value judgment on individuals or fields of research.

[ update: I’ve arrived. The weather is horrible, but the natives are friendly ]

Syndicated 2014-05-27 08:33:38 from notes

15 May 2014 (updated 17 May 2014 at 20:13 UTC) »

languages for teaching programming

There’s seems to be something about rainy weekends in May that stimulates academics in Computing departments to have e-mail discussions about programming languages and teaching. The key ingredients probably include houseboundness, the lull between the end of formal teaching and the start of exams, the beginning of contemplation of next year’s workload, and enthusiasm; of course, the academic administrative timescale is such that any changes that we contemplate now, in May 2014, can only be put in place for the intake in September 2015... if you’ve ever wondered why University programmes in fashionable subjects seem to lag about two years behind the fashion (e.g. the high growth of Masters programmes in “Financial Engineering” or similar around 2007 – I suspect that demand for paying surprisingly high tuition fees for a degree in Synthetic Derivative Construction weakened shortly after those programmes came on stream, but I don’t actually have the data to be certain).

Meanwhile, I was at the European Lisp Symposium in Paris last week, where there was a presentation of a very apposite nature: the Computing Department at Middlesex university has implemented an integrated first-year of undergraduate teaching, covering a broad range of the computing curriculum (possibly not as broad as at Goldsmiths, though) through an Arduino and Raspberry Pi robot with a Racket-based programmer interface. Students’ progress is evaluated not through formal tests, courseworks or exams, but through around 100 binary judgments in the natural context of “student observable behaviours” at three levels (‘threshold’, which students must exhibit to progress to the second year; ‘typical’, and ‘excellent’).

This approach has a number of advantages, I think, over a more traditional division of the year into four thirty-credit modules (e.g. Maths, Java, Systems, and Profession): for one, it pretty much guarantees a coherent approach to the year, where in the divided modules case it is surprisingly easy for one module to be updated in syllabus or course content without adjustments to the others, leaving for example some programming material insufficiently supported by the maths (and some maths taught without motivation). The assessment method is in principle transparent to the students, who know what they have to do to progress (and to get better marks); I'm not convinced that this is always a good thing, but for an introductory and core course I think the benefits substantially outweigh the disadvantages. The use of Racket as the teaching language has an equalising effect – it’s unlikely that students will have prior experience with it, so everyone starts off at the same point at least with respect to the language – and the use of a robot provides visceral feedback and a sense of achievement when it is made to do something in a way that text and even pixels on a screen might not. (This feedback and tangible sense of achievement is perhaps why the third-year option of Physical Computing at Goldsmiths is so popular: often oversubscribed by a huge margin).

With these thoughts bubbling around in my head, then, when the annual discussion kicked off at the weekend I decided to try to articulate my thoughts in a less ephemeral way than in the middle of a hydra-like discussion: so I wrote a wiki page, and circulated that. One of the points of having a personal wiki is that the content on it can evolve, but before I eradicate the evidence of what was there before, and since it got at least one response (beyond “why don’t you allow comments on your wiki?”) it's worth trying to continue the dialogue.

Firstly, Chris Cannam pulls me up on not including an Understand goal, or one like it: teaching students to understand and act on their understanding of computing artifacts, hardware and software. I could make the argument that this lives at the intersection of my Think and Experiment goals, but I think that would be retrospective justification and that there is a distinct aim there. I’m not sure why I left it out; possibly, I am slightly hamstrung in this discussion about pedagogy by a total absence of formal computing education; one course in fundamentals of computing as a 17-year-old, and one short course on Fortran and numerical methods as an undergraduate, and that’s it. It's in some ways ironic that I left out Understand, given that in my use of computers as a hobby it’s largely what I do: Lisp software maintenance is often a cross between debugger-oriented programming and software archaeology. But maybe that irony is not as strong as it might seem; I learnt software and computing as a craft, apprenticed to a master; I learnt the shibboleths (“OAOO! OAOO! OAOO!”) and read the training manuals, but I learnt by doing, and I’m sure I’m far from alone, even in academic Computing let alone among programmers or computing professionals more generally.

Maybe the Middlesex approach gets closer, in the University setting, to the apprenticeship (or pre-apprenticeship) period; certainly, there are clear echoes in their approach of the switch by MIT from the SICP- and Scheme-based 6.001 to the Robotics- and Python-based introduction to programming – and Sussman’s argument from the time of the switch points to a qualitative difference in the role of programmers, which happens to dovetail with current research on active learning. In my conversation with the lecturers involved after their presentation, they said that the students take a more usual set of languages in their second-years (Java, C++); obviously, since this is the first year of their approach, they don’t yet know how the transition will go.

And then there was the slightly cynical Job vs Career distinction that I drew, being the difference between a graduate-level job six months after graduation as distinct from a fulfilling career. One can of course lead to the other, but it’s by no means guaranteed, and I would guess that if asked most people would idealistically say we as teachers in Universities should be attempting to optimize for the latter. Unfortunately, we are measured in our performance in the former; one of the “Key Information Sets” collected by higher-education agencies and presented to prospective undergraduates is the set of student ‘destinations’. Aiming to optimize this statistic is somewhat akin to schools optimizing their GCSE results with respect to the proportion of pupils gaining at least 5 passes: ideally, the measurement should be a reflection of the pedagogical practice, but the foreknowledge of the measurement has the potential to distort the allocation of effort and resources. In the case of the school statistic, there’s evidence that extra effort is concentrated on borderline pupils, at the expense of both the less able and potential high-fliers; the distortion isn’t so stark in the case of programming languages, because the students have significant agency between teaching and measurement, but there is certainly pressure to ensure that we teach the most common language used in assessment centres.

In Chris’ case, C++ might have had a positive effect on both; the programming language snob in me, though, wants to believe that there are hordes of dissatisfied programmers out there, having got a job using their competence in some “industry-standard” language, desperately wanting to know about a better way of doing things. I might be overprojecting the relationship of a professional programmer with their tools, of course: for many a career in programming and development is just that, rather than a love-hate relationship with their compiler and linker. (Also, there’s the danger of showing the students that there is a better way, but that the market doesn’t let them use it...)

Is it possible to conclude anything from all of this? Well, as I said in my initial thoughts, this is an underspecified problem; I think that a sensible decision can only be taken in practice once the priorities for teaching programming at all have been established, in combination with the resources available for delivering teaching. I’m also not enough of a polyglot in practice to offer a mature judgment on many fashionable languages; I know enough of plenty of languages to modify and maintain code, but am comfortable writing from scratch in far fewer.

So with all those caveats, an ideal programming curriculum (reflecting my personal preferences and priorities) might include in its first two years: something in the Lisp family, for Think and Experiment; ARM Assembler, for Think and Understand; C++, for Job and Career (and all three together for Society). Study should probably be handled in individual third-year electives, and I would probably also include a course hybrid between programming, database and system administration to cover a Web programming stack for more Job purposes. Flame on (but not here, because system administration is hard).

Syndicated 2014-05-15 19:50:23 (Updated 2014-05-17 19:45:54) from notes

just like old times

Sometimes, it feels like old times, rolling back the years, and so on. One of the things I did while avoiding work on my PhD (on observational tests of exotic cosmologies inspired by then-fashionable high-energy physics theories, since you ask) was to assist in resurrecting old and new CMUCL backends for SBCL, and to do some additional backend hacking. I learnt a lot! (To be fair, I learnt a lot about General Relativity too). And I even wrote about some of the funny bits when porting, such as getting to a working REPL with a completely broken integer multiply on SPARC, or highly broken bignums when working on a proper 64-bit backend for alpha.

On the #sbcl IRC channel over the last few days, the ARM porting crew (not me! I've just been kibitzing) has made substantial progress, to the point that it's now possible to boot a mostly-working REPL. Some of the highlights of the non-workingness:

  (truncate (expt 2 32) 10)
21074691228794313799883120286105
6

(fib 50)
6277101738309684039858724727853387073209631205623600462197

(expt 2.0 3)
2.0

(sb-ext:run-program "uname" '() :search t :output *standard-output*)
Linux
Memory fault at 3c

Meanwhile, given that most ARM cores don't have an integer division instruction, it's a nice bit of synchronicity that one of this year's Summer of Code projects for SBCL is to improve division by constant integers; I'm very much looking forward to getting involved with that, and hopefully also bringing some of the next generation of SBCL hackers into the community. Maybe my writing a while back about a self-sustaining system wasn't totally specious.

Syndicated 2014-04-25 16:43:10 from notes

http-content-negotiation-and-generalized-specializers

I promised a non-trivial example of a use for generalized specializers a while ago. Here it is: automatic handling of HTTP (RFC 2616) Content-Type negotiation in computed responses.

In RESTful services and things of that ilk, a client indicates that it wants to apply a verb (GET, for example) to a particular resource (named by a URN, or possibly identified by a URI). This resource is a conceptual object; it will have zero or more concrete manifestations, and content negotiation provides a way for the client to indicate which of those manifestations it would prefer to receive.

That's all a bit abstract. To take a concrete example, consider the woefully incomplete list of books in my living room at openlibrary. A user operating a graphical web browser to access that resource is presumed to want to retrieve HTML and associated resources, in order to view a shiny representation of the information associated with that resource (a “web page”, if you will). But the human-oriented representation of the information is not the only possible one, and it is common practice in some circles to provide machine-readable representations as well as human-oriented ones, at the same URL; for example, try:

  curl -H 'Accept: application/json' https://openlibrary.org/people/csrhodes/lists

and observe the difference between that and visiting the same URL in a graphical browser.

How does the web server know which representation to send? Well, the example has given away the punchline (if the links above to RFC sections haven't already). The graphical web browser will send an Accept header indicating that it prefers to receive objects with presentational content types – text/html, image/* and so on; the browser I have to hand sends text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8 as its Accept header, meaning “please give me text/html or application/xhtml+xml, or failing that application/xml, or failing that anything else”. If the server has more than one representation for a given resource, it can use this client-supplied information to provide the best possible content; if the client has particular requirements – for example, attempting to find machine-readable content for further processing – it can declare this by specifying particular acceptable content-types in its Accept header.

For a resource for which more than one representation exists, then, the server must dispatch between them based on the client Accept header. And this is exactly a non-standard dispatch of the kind I've been discussing. Consider a resource http://foo.example/ which is implemented by sending the return value of the generic function foo back to the client:

  (defgeneric foo (request)
  (:generic-function-class accept-generic-function))

The default behaviour is somewhat a matter of taste, but one reasonable choice is that if no content-type matches we should use the defined HTTP status code to indicate that the responses we could generate are not acceptable to the client:

  (defmethod foo ((request t))
  (http:406 request))

Maybe we have a couple of presentational representations for the resource:

  (defmethod foo ((request (accept "text/plain")))
  "Foo")

(defmethod foo ((request (accept "text/html")))
  "<!DOCTYPE html>
<html>
 <head><title>Foo</title></head>
 <body><p>Foo</p></body>
</html>")

And we might have some machine-readable representations:

  (defmethod foo ((request (accept "text/turtle")))
  "@prefix foo: <http://example.org/ns#> .
@prefix : <http://other.example.org/ns#> .
foo:bar foo: : .")

(defmethod foo ((request (accept "application/rdf+xml")))
  "<?xml version=\"1.0\"?>
<rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"
         xmlns:foo=\"http://example.org/ns#\">
  <rdf:Description about=\"http://example.org/ns#bar\">
    <foo:>
      <rdf:Description about=\"http://other.example.org/ns#\"/>
    </foo:>
  </rdf:Description>
</rdf:RDF>")

(I apologize to any fans of XML/RDF if I have mangled that).

Now a graphical web browser sending an accept header of text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8 as above will cause the server to send the HTML version, as that is the most specific applicable method to that accept string. Given this, it is perfectly possible to construct specialized clients with alternative preferences expressed in the accept header. A terminal-based client might prioritize text/plain over text/html (though in fact neither w3m nor lynx does that, at least in the versions I have installed). A client for the Semantic Web might instead accept data in serialized RDF, preferring more modern serializations, by sending an accept string of text/turtle,application/rdf+xml;q=0.9. All these clients could each be served the resource in their preferred format.

The case of serving one of a set of alternative files hosted on the filesystem in response to a request with an arbitrary accept string is different; in this case, it doesn't make sense to do the dispatch through methods. If we were to try to do so, it would look something like

  (defmethod filesystem-handler (url (content-type (accept "text/html")))
  (let ((prospect (pathname-for-url url "html")))
    (if (probe-file prospect)
        (serve-file prospect "text/html")
        (call-next-method))))

but we would need to define one such method per possible mime-type we might want to serve: doable, but unnecessary compared with the alternative strategy of finding all content-types servable for a given url, then choosing the one with the highest score:

  (defun filesystem-handler (url accept)
  (do* ((prospects (files-for url) (cdr prospects))
        (mime-types (mapcar #'mime-type prospects) (cdr mime-types))
        result mime-type (q 0))
       ((null prospects) (serve-file result mime-type))
     (when (> (q (car mime-types) accept) q)
       (setf result (car prospects) 
             mime-type (car mime-types) 
             q (q (car mime-types))))))

(the set of files on the filesystem effectively already define a set of methods for a given url; it doesn't make sense to try to mirror that as a set of reified methods on a generic function. Also, I've written this out using do* largely to keep the do*-is-not-that-bad society alive.)

Anyway. There's an interesting detail I've elided so far; not only do response-generating functions have to generate the content they wish to send in the response; they also have to indicate what content-type they are actually sending. Our accept-generic-function already handles dispatching on content-type; can it also take responsibility for setting the content-type of the response?

Why yes! The way to do this is using a method combination; it might look something like this:

  (defvar *actual-content-type*)

(defgeneric handle-content-type (request))

(define-method-combination content-negotiation/or ()
  ((around (:around))
   (primary () :required t))
  (:arguments request)
  (labels ((transform/1 (method)
             `(make-method
               (progn
                 (let ((s (car (sb-mop:method-specializers ,method))))
                   (when (typep s 'accept-specializer)
                     (setf *actual-content-type* (media-type s))))
                 (call-method ,method))))
           (transform (primaries)
             (mapcar #'(lambda (x) `(call-method ,(transform/1 x)))
                     primaries))
           (wrap (form)
             `(let ((*actual-content-type*))
                (multiple-value-prog1
                    ,form
                  (handle-content-type ,request)))))
    (let ((form (if (rest primary)
                    `(or ,@(transform primary))
                    `(call-method ,(transform/1 (car primary))))))
      (if around
          (wrap `(call-method ,(first around)
                              (,@(rest around) (make-method ,form))))
          (wrap form)))))

This behaves just like the or built-in method-combination, except that when calling a primary method whose specializer for the first argument is one of our accept-specializers, the content-type of the specializer is stored in a special variable; the last thing the effective method does is to call the new handle-content-type generic function, passing it the original generic function's first argument.

Now let's redefine our foo generic function to have the new method combination, and a method on handle-content-type:

  (defgeneric foo (request)
  (:generic-function-class accept-generic-function)
  (:method-combination content-negotiation/or))

(defmethod handle-content-type ((x string))
  (format t "Content-Type: ~A~%" *actual-content-type*))

and now, finally, we can try it all out:

  SPECIALIZABLE> (foo "text/plain,text/html;q=0.9,*/*;q=0.8")
Content-Type: text/plain
"Foo"

SPECIALIZABLE> (foo "text/turtle,application/rdf+xml;q=0.9")
Content-Type: text/turtle
"@prefix foo: <http://example.org/ns#> .
@prefix : <http://other.example.org/ns#> .
foo:bar foo: : ."

SPECIALIZABLE> (foo "audio/mp3")
406

OK, but by what magic do these accept-specializer objects exist and function? I wrote a paper about that, with Jan Moringen and David Lichteblau: as part of my ongoing open access experimentation, the version we submitted to the European Lisp Symposium is viewable at Goldsmiths' e-prints repository or on arXiv. The ELS Chairs have just announced a deadline extension, so there's still time (until March 23) for anyone to submit technical papers or abstracts for tutorials and demonstration sessions: please do, and I hope to see many of my readers there.

Syndicated 2014-03-13 12:22:26 from notes

sbcl release management in the air

Just because I'm attending mobile world congress doesn't mean that everything else stops. It's the end of the month, so it must be time to release sbcl. This month's is a little unsatisfying, because we've only achieved one of the two things I'd hoped for: we've been cautious and conservative after last month's landing of the new register allocator, but we haven't sorted out what's going on to cause the less active architectures to fail to build. There are some workarounds that have been mooted; for one reason and another no-one has had the time to check whether they actually work, and while there's partial progress on identifying the root cause of the build failure on sparc it is only partial.

Nevertheless, minor architectures have been broken before, and no-one particularly benefits from not releasing, so 1.1.16 it is. Actually making the release is a little more challenging than usual: I aim to release by the end of the month, and in practice that means it must be done today, 28th February. However, this is the day that I am returning from Barcelona, so I am less in control of laptop power and connectivity than usual for a release day. And to add to the challenge, I am trying this time to address the valid complaints that the binaries built on my laptop don't actually run on released versions of Linux, thanks to the change in the semantics of memcpy (glibc changed the implementation in its version 2.14 to exploit the freedom given to return undefined results if the source and destination overlap) and the behaviour of the linker and versioned symbols.

So over breakfast I dusted off my squeeze chroot (that doesn't sound dodgy at all), and tried to work out how to get a runnable version of SBCL in there at all (answer: build using clisp and link to the chroot's libc). At lunchtime, I used the café's wireless to check for any last-minute changes, and in the airport I found a power socket, so I started the release build. Of course it didn't finish before the gate opened, and in any case I wasn't going to chance uploading sbcl binaries over the free airport wifi (15 minutes, woo!)

I've performed some release stunts before. SBCL 0.9 was released by William Harold Newman and simultaneously announced by me at the first European Common Lisp Meeting in Amsterdam in 2005. Last year, I released SBCL 1.1.8 “live” as part of a lightning talk at the European Lisp Symposium in Madrid. But I think this is the first time that an SBCL release was even partially effected from the air. Next stop, space?

Syndicated 2014-02-28 22:10:21 from notes

sbcl summer of code 2014 participation

I received notification yesterday that SBCL was accepted as a “mentoring organization” to Google's Summer of Code 2014 programme. What this means is that eligible students can think about applying to be mentored by members of the SBCL team to work on a development project – and to be paid a stipend for that work.

The next steps for students are:

  • get involved with the community: join #lisp and #sbcl on the freenode IRC network; read the sbcl-devel mailing list (e.g. at gmane.lisp.steel-bank.devel; have a go at some of the bugs marked as ‘easy’
  • look at the existing list of project ideas, and see if any of those ideas would form a good basis for a project that would sustain your interest for three months or so.
  • read Paul Khuong's essay on getting started with SBCL from last year: it is still absolutely applicable to this year's programme, or indeed getting into SBCL hacking independently.

The period for student applications to be mentored as part of SBCL's participation is from 10th March until 21st March 2014; for best results, get engaged with the community and potential mentors well before the cutoff point.

Last year two projects were funded, and both completed successfully, even if merging them into the mainline is/was slower than one might like. I'm looking forward to seeing what this year brings!

Syndicated 2014-02-25 12:01:20 (Updated 2014-02-25 12:02:33) from notes

3 Feb 2014 (updated 5 Mar 2014 at 15:13 UTC) »

generic function precompilation

Once upon a time, I wrote two blog entries about precompiling the dispatch for generic functions in order to improve the responsiveness at application startup, and obviously planned a third but didn't get around to writing it. Some time later, I asked the lazyweb about it, and unfortunately this time didn't get anything much back. On further reflection, I think I was going to discuss a couple of additional technical points.

First of all, there's the question about having this kind of precompilation on all the time; wouldn't it be nice if generic functions were always at their most efficient, ready to be called? Well, yes, but what we actually want is for functions to be at their most efficient when we want to call them, and we don't particularly care at other times. Why draw that distinction? Well, when we write code that uses generic functions, it is usually of the form:

  (defgeneric foo (x y))
(defmethod foo ((x t) (y t)) ...)
(defmethod foo ((x integer) (y integer)) ...)
(defmethod foo ((x rational) (y float)) ...)

a sequence of method definitions; sometimes contiguous, as above; often distributed among various files. loading such code will execute the defmethod forms in series. And each of those executions will call add-method, changing the generic function's methods, so any aggressive dispatch precompilation scheme will kick in at every defmethod. That would be bad enough, being O(N) in the number of methods, but it's actually worse than that: the amount of work involved in precompilation will tend to be O(N) in the number of methods, or in the number of concrete classes applicable to those methods, so there's O(N2) or worse behaviour from having precompilation active all the time. SBCL is routinely mocked for having slow-loading FASL files (originally, FASL probably stood for FASt Load; we don't advertise that much); expensive and poorly-scaling computations at load-time probably won't win us any extra friends. (Though having written that, I now wonder if recording changed generic functions using the dependent-update protocol, and hooking load or asdf:load-system to precompile after loading a whole file or system, might be a tasteful compromise).

Secondly, there's the detail of exactly how to pre-fill the cache for a given generic function (given that its specializers are mostly or entirely classes). The simplest strategy, of filling the cache with exactly those classes used as specializers, fails as soon as abstract or protocol classes are used to organize the implementation of the generic function. The next simplest, which is to fill the cache with all possible subclasses of specializers at all argument positions, well, just reading that should set alarm bells ringing – it might not be too problematic for generic functions with one argument, but the cross-product effect of multiple arguments will probably cause the implementation to collapse under its own weight into a virtual black hole. It might be that the best approach is to allow the user to specify an exact set of classes: and to allow the user to introspect a running system to find out which class combinations have actually been seen and hence cached in a given session.

In fact, SBCL itself depends on a particular, specific version of this. The generic function print-object is used for printing almost everything; even without user specialization, it is called whenever a structure-object or standard-object needs to be output to any stream. Users can write methods on it, though, and that then invalidates any previous precomputed dispatch information. But there are times when it's really important that print-object just work, without any kind of extra computation to go on: in particular, when the debugger needs to inform the user that the Lisp is running out of storage space (heap or stack), it's pretty important that that reporting can happen without using more heap or stack than necessary. So for print-object, we never reset the cache state to empty; it is always prefilled with entries for control-stack-exhausted, binding-stack-exhausted, alien-stack-exhausted, heap-exhausted-error and restart for its first argument. (This strategy only works if there are no specializations of the second argument to print-object anywhere in the system; there's no good reason for a user to try to specialize the second argument in any case, so we emit a warning if they do that and hope that they read and learn from it.)

Syndicated 2014-02-03 09:56:36 (Updated 2014-03-05 14:36:05) from notes

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