;; ;; NineML network level descriptions. ;; ;; ;; Copyright 2015 Ivan Raikov ;; ;; This program is free software: you can redistribute it and/or ;; modify it under the terms of the GNU General Public License as ;; published by the Free Software Foundation, either version 3 of the ;; License, or (at your option) any later version. ;; ;; This program is distributed in the hope that it will be useful, but ;; WITHOUT ANY WARRANTY; without even the implied warranty of ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU ;; General Public License for more details. ;; ;; A full copy of the GPL license can be found at ;; . ;; (require-extension extras posix utils files data-structures tcp srfi-1 srfi-13 irregex) (require-extension datatype matchable make ssax sxml-transforms sxpath sxpath-lolevel object-graph ersatz-lib unitconv uri-generic getopt-long ) (require-extension 9ML-types 9ML-parse 9ML-ivp-mlton) (require-library ersatz-lib salt) (import (prefix ersatz-lib ersatz: ) (prefix salt salt: )) (define (string-match rx str) (and-let* ((m (irregex-match rx str))) (let loop ((i (irregex-match-num-submatches m)) (res '())) (if (fx<= i 0) (cons str res) (loop (fx- i 1) (cons (irregex-match-substring m i) res)))))) (define lookup-def (lambda (k lst . rest) (let-optionals rest ((default #f)) (alist-ref k lst eq? default)))) (define (safe-car x) (and (pair? x) (car x))) (define (sxml-singleton x) (and (pair? x) (car x))) (define $ string->symbol) (define (s+ . rest) (string-concatenate (map ->string rest))) (define (alist->tenv xs) (map (lambda (x) (cons (car x) (ersatz:sexpr->tvalue (cdr x)))) xs)) (define (string->bool x) (cond ((string=? x "true") #t) ((string=? x "false") #f) (else (error 'string->bool "invalid boolean string" x)))) (define (warn port message . specialising-msgs) (print-error-message message (current-output-port) "Warning") (print (string-concatenate (map ->string specialising-msgs)))) (include "SXML.scm") (include "SXML-to-XML.scm") (include "stx-engine.scm") (define ivp-simulation-platform (make-parameter 'mlton)) (define alsys-simulation-platform (make-parameter 'mlton)) (define ivp-simulation-method (make-parameter 'rkfe)) (define opt-defaults `( (platform . mlton) (method . rkdp) (duration . 100.0) (timestep . 0.1) )) (define (defopt x) (lookup-def x opt-defaults)) (define opt-grammar `( (platform "simulation platform (one of mlton, chicken, chicken/cvode)" (value (required PLATFORM) (predicate ,(lambda (x) (let ((s (string->symbol (string-downcase x)))) (case s ((chicken chicken/cvode mlton octave/mlton) s) (else (error '9ML-network "unrecognized platform" x)))))) (transformer ,string->symbol) )) (method "integration method (one of rkfe, rk3, rk4a, rk4b, rkoz, rkdp)" (value (required PLATFORM) (predicate ,(lambda (x) (let ((s (string->symbol (string-downcase x)))) (case s ((rkfe rk3 rk4a rk4b rkoz rkdp) s) (else (error '9ML-network "unrecognized method" x)))))) (transformer ,string->symbol) ) (single-char #\m) ) (duration "simulation duration in milliseconds" (value (required VALUE) (predicate ,(lambda (x) (let ((n (string->number x))) (if (> n 0) n (error '9ML-network "duration must be a positive number" x))))) (transformer ,string->number) ) (single-char #\d) ) (timestep "simulation timestep milliseconds" (value (required VALUE) (predicate ,(lambda (x) (let ((n (string->number x))) (if (> n 0) n (error '9ML-network "timestep must be a positive number" x))))) (transformer ,string->number) ) ) (spikerecord "name of population for spike recording" (value (required POPULATION)) (single-char #\s) ) (statesample "sample size of neurons for state recording" (value (required VALUE) (predicate ,(lambda (x) (let ((n (string->number x))) (if (> n 0) n (error '9ML-network "sample size must be a positive number" x))))) (transformer ,string->number) ) ) (extsample "sample size of neurons for external input recording" (value (required VALUE) (predicate ,(lambda (x) (let ((n (string->number x))) (if (> n 0) n (error '9ML-network "sample size must be a positive number" x))))) (transformer ,string->number) ) ) (verbose "print commands as they are executed" (single-char #\v)) (help "Print help" (single-char #\h)) )) ;; Use args:usage to generate a formatted list of options (from OPTS), ;; suitable for embedding into help text. (define (network:usage) (print "Usage: " (car (argv)) " file1... [options...] ") (newline) (print "Where operands are NineML user layer files") (newline) (print "The following options are recognized: ") (newline) (width 45) (print (parameterize ((indent 5)) (usage opt-grammar))) (exit 1)) ;; Process arguments and collate options and arguments into OPTIONS ;; alist, and operands (filenames) into OPERANDS. You can handle ;; options as they are processed, or afterwards. (define opts (getopt-long (command-line-arguments) opt-grammar)) (define opt (make-option-dispatch opts opt-grammar)) (define network-verbose (make-parameter 0)) (define data-dir (make-parameter #f)) (define simulation-platform (make-parameter #f)) (define simulation-method (make-parameter 'rk3)) (define (d fstr . args) (let ([port (current-error-port)]) (if (positive? (network-verbose)) (begin (apply fprintf port fstr args) (flush-output port) ) ))) (define (sxml-string->uri s) (let ((ss (string-trim-both s))) (uri-reference ss))) (define (get-data-dir) (or (opt 'data-dir) (or (data-dir) (let ([dir (create-temporary-directory)]) (data-dir dir) dir ) ) )) (define (run:execute explist) (define (smooth lst) (let ((slst (map ->string lst))) (string-intersperse (cons (car slst) (cdr slst)) " "))) (for-each (lambda (cmd) (system (->string cmd))) (map smooth explist))) (define (run:execute* explist) (define (smooth lst) (let ((slst (map ->string lst))) (string-intersperse (cons (car slst) (cdr slst)) " "))) (for-each (lambda (cmd) (system* "~a" cmd)) (map smooth explist))) (define-syntax run (syntax-rules () ((_ exp ...) (begin (d "running ~A ...~%" (list `exp ...)) (run:execute* (list `exp ...)))))) (define-syntax run- (syntax-rules () ((_ exp ...) (begin (d "running ~A ...~%" (list `exp ...)) (run:execute (list `exp ...)))))) (define (create-temporary-directory) (let ((dir (or (get-environment-variable "TMPDIR") (get-environment-variable "TEMP") (get-environment-variable "TMP") "/tmp"))) (let loop () (let* ((n (current-milliseconds)) (pn (make-pathname dir (string-append "9ML-network-" (number->string n 16)) "tmp"))) (cond ((file-exists? pn) (loop)) (else (mkdir pn) pn)))))) (define (network-failure msg . args) (signal (make-composite-condition (make-property-condition 'exn 'message "invalid response from server" 'arguments args) (make-property-condition 'http-fetch))) ) (define (make-HTTP-GET/1.1 location user-agent host #!key (port 80) (connection "close") (accept "*") (content-length 0)) (conc "GET " location " HTTP/1.1" "\r\n" "Connection: " connection "\r\n" "User-Agent: " user-agent "\r\n" "Accept: " accept "\r\n" "Host: " host #\: port "\r\n" "Content-length: " content-length "\r\n" "\r\n") ) (define (match-http-response rsp) (and (string? rsp) (string-match "HTTP/[0-9.]+\\s+([0-9]+)\\s+.*" rsp)) ) (define (response-match-code? mrsp code) (and mrsp (string=? (number->string code) (cadr mrsp))) ) (define (match-chunked-transfer-encoding ln) (string-match "[Tt]ransfer-[Ee]ncoding:\\s*chunked.*" ln) ) (define (http-fetch uri dest) (d "fetching ~s ...~%" (uri->string uri)) (match-let (((_ ((_ host port) ('/ . path) query) _) (uri->list uri))) (let* ((port (or port 80)) (locn (uri->string (update-uri (update-uri uri scheme: #f) host: #f))) (query (and query (not (string-null? query)) query)) (filedir (uri-decode-string (string-concatenate (intersperse (if query path (drop-right path 1)) "/")))) (filename (uri-decode-string (or (and query (cadr (string-split query "="))) (last path)))) (dest (make-pathname dest filedir)) (filepath (make-pathname dest filename))) (if (file-exists? filepath) filepath (begin (d "connecting to host ~s, port ~a ...~%" host port) (let-values ([(in out) (tcp-connect host port)]) (d "requesting ~s ...~%" locn) (display (make-HTTP-GET/1.1 locn "NineML" host port: port accept: "*/*") out) (flush-output out) (d "reading response ...~%") (let ([chunked #f] [ok-response #f]) (let* ([h1 (read-line in)] [response-match (match-http-response h1)]) (d "~a~%" h1) ;;*** handle redirects here (cond ((response-match-code? response-match 200) (set! ok-response #t)) ((response-match-code? response-match 404) (d "file not found on server: ~s~%" locn)) (else (network-failure "invalid response from server" h1) )) (and ok-response (begin (let loop () (let ([ln (read-line in)]) (unless (string-null? ln) (when (match-chunked-transfer-encoding ln) (set! chunked #t)) (d "~a~%" ln) (loop) ) ) ) (if chunked (begin (d "reading chunks ...~%") (let ([data (read-chunks in)]) (close-input-port in) (close-output-port out) (if (not (file-exists? dest)) (mkdir dest)) (d "writing to ~s~%" filepath) (with-output-to-file filepath (cut display data) ) filepath)) (begin (d "reading data ...~%") (let ([data (read-string #f in)]) (close-input-port in) (close-output-port out) (if (not (file-exists? dest)) (mkdir dest)) (d "writing to ~s~%" filepath) (with-output-to-file filepath (cut display data) binary:) filepath))))) ) ))))))) (define (read-chunks in) (let get-chunks ([data '()]) (let ([size (string->number (read-line in) 16)]) (if (zero? size) (string-concatenate-reverse data) (let ([chunk (read-string size in)]) (read-line in) (get-chunks (cons chunk data)) ) ) ) ) ) (define (fetch uri) (case (uri-scheme uri) ((http) (let-values (((fd temp-path) (file-mkstemp "/tmp/9ML.XXXXXX"))) (let ((data (and (http-fetch uri temp-path) (read-all temp-path)))) (file-close fd) data))) ((file #f) (let ((data (read-all (string-concatenate (intersperse (map ->string (uri-path uri)) "/"))))) data)) (else (error 'fetch "unknown scheme" (uri-scheme uri))) )) (define (parse-xml str) (call-with-input-string str (lambda (in) (ssax:xml->sxml in `((nml . ,(string-append nineml-xmlns-base "1.0")) ))) )) (define default-units `( (current . nA) )) (define (eval-sxml-units dimensions-sxml units-sxml) (let* ((dimensions (map parse-sxml-dimension dimensions-sxml)) (dimensions-env (map (lambda (x) (cons (quantity-name x) x)) dimensions)) (units (map (lambda (x) (parse-sxml-unit x dimensions-env)) units-sxml)) (units-env (map (lambda (x) (cons (unit-name x) x)) units))) (salt:model-quantities (append dimensions-env (salt:model-quantities))) (salt:model-units (append units-env (salt:model-units))) )) (define (eval-ul-component x) (let ( (node-name (sxml:attr x 'name)) (definition ((sxpath `(// (*or* nml:Definition nml:definition))) x)) (propns ((sxpath `(// (*or* nml:Property nml:property) @ name)) x)) (propvs ((sxpath `(// (*or* nml:Property nml:property) nml:SingleValue)) x)) (propunits ((sxpath `(// (*or* nml:Property nml:property) @ units)) x)) (fieldns ((sxpath `(// (*or* nml:Field nml:field) @ name)) x)) (fieldvs ((sxpath `(// (*or* nml:Field nml:field) nml:SingleValue)) x)) (initialns ((sxpath `(// (*or* nml:Initial nml:initial) @ name)) x)) (initialvs ((sxpath `(// (*or* nml:Initial nml:initial) nml:SingleValue)) x)) (initialunits ((sxpath `(// (*or* nml:Initial nml:initial) @ units)) x)) (ivp (safe-car ((sxpath `(// nml:IVP)) x))) ) (if (null? definition) (error 'eval-ul-component "component without definition" x)) (let ((al-definition-name (string->symbol (sxml:text (safe-car definition)))) (uri (sxml-string->uri (sxml:attr (safe-car definition) 'url)))) (d "NineML abstraction layer URI: ~A~%" (uri->string uri)) (d "NineML abstraction layer definition name: ~A~%" al-definition-name) (d "NineML component propns: ~A~%" propns) (d "NineML component propvs: ~A~%" propvs) (d "NineML component propunits: ~A~%" propunits) (d "NineML component initialns: ~A~%" initialns) (d "NineML component initialvs: ~A~%" initialvs) (d "NineML component initialunits: ~A~%" initialunits) (d "NineML component fieldns: ~A~%" fieldns) (d "NineML component fieldvs: ~A~%" fieldvs) (let* ( (model-src (fetch uri)) (model-sxml (if (not model-src) (error 'eval-ul-component "resource not found" (uri->string uri)) (parse-xml model-src))) (model-decls (parse-al-sxml model-sxml)) (dd (d "NineML abstraction layer model declarations: ~A~%" model-decls)) (model-dimensions-sxml ((sxpath `(// nml:NineML nml:Dimension)) model-sxml)) (model-units-sxml ((sxpath `(// nml:NineML nml:Unit)) model-sxml)) (units-env (eval-sxml-units model-dimensions-sxml model-units-sxml)) (model-env (map (match-lambda (($ dynamics-node model-name model-formals model-decls) (cons model-name (make-dynamics-node model-name model-formals (salt:parse model-decls)))) ((and ($ alsys-node model-name model-formals model-decls) node) (cons model-name node)) ((and ($ connection-rule-node model-name model-formals model-decls) node) (cons model-name node)) (node (error 'eval-ul-component "unknown node type" node))) model-decls)) (dd (d "NineML abstraction layer models: ~A~%" model-env)) (model (alist-ref al-definition-name model-env)) (dd (d "NineML abstraction layer model intermediate form: ~A~%" model)) (model-parameters (map (lambda (x) (let ((name (string->symbol (sxml:attr x 'name))) (dim (sxml:attr x 'dimension))) (if dim `(,name . ,(string->symbol dim)) `(,name . Unity)))) ((sxpath `(// nml:Parameter)) model-sxml))) (model-variables (map (lambda (x) (let ((name (string->symbol (sxml:attr x 'name))) (dim (sxml:attr x 'dimension))) (if dim `(,name . ,(string->symbol dim)) `(,name . Unity)))) ((sxpath `(// nml:StateVariable)) model-sxml))) (model-event-receive-ports (map (lambda (x) (let ((name (string->symbol (sxml:attr x 'name))) (dim (sxml:attr x 'dimension))) (if dim `(,name . ,(string->symbol dim)) `(,name . Unity)))) ((sxpath `(// nml:EventReceivePort)) model-sxml))) (model-analog-receive-ports (map (lambda (x) (let ((name (string->symbol (sxml:attr x 'name))) (dim (sxml:attr x 'dimension))) (if dim `(,name . ,(string->symbol dim)) `(,name . Unity)))) ((sxpath `(// nml:AnalogReceivePort)) model-sxml))) (model-reduce-ports (map (lambda (x) (let ((name (string->symbol (sxml:attr x 'name))) (dim (sxml:attr x 'dimension))) (if dim `(,name . ,(string->symbol dim)) `(,name . Unity)))) ((sxpath `(// nml:AnalogReducePort)) model-sxml))) ) (if (not model) (error 'eval-ul-component "cannot find definition named" al-definition-name)) (let* ( (parameter-decls (map (lambda (n v u) (let* ((vtext (sxml:text v)) (name (string->symbol (sxml:text n))) (unit (string->symbol (sxml:text u))) (dim (alist-ref name model-parameters))) (if unit `(define ,name = parameter (dim ,dim) (,(parse-string-expr vtext) * ,unit)) `(define ,name = parameter ,(parse-string-expr vtext))) )) propns propvs propunits)) (field-decls (map (lambda (n v) (let ((vtext (sxml:text v)) (name (sxml:text n))) (cons ($ name) `(signal.realfield ,(make-signal-expr (parse-string-expr vtext) '())) ))) fieldns fieldvs)) (state-decls (map (lambda (n v u) (let* ((name (string->symbol (sxml:text n))) (vtext (sxml:text v)) (unit (string->symbol (sxml:text u))) (dim (alist-ref name model-variables))) (if unit `(define ,name = unknown (dim ,dim) (,(parse-string-expr vtext) * ,unit)) `(define ,name = unknown ,(parse-string-expr vtext))) )) initialns initialvs initialunits)) (ext-decls (map (match-lambda ((name . dim) (case dim ((Unity) `(define ,name = external 0.0)) (else (let ((unit (alist-ref dim default-units ))) (if (not unit) (error 'eval-ul-component "cannot find default unit for dimension in receive port definition" dim name)) `(define ,name = external (dim ,dim) (0.0 * ,unit))))))) model-analog-receive-ports)) (extev-decls (map (match-lambda ((name . dim) (case dim ((Unity) `(define ,name = external-event -1.0)) (else (let ((unit (alist-ref dim default-units ))) (if (not unit) (error 'eval-ul-component "cannot find default unit for dimension in receive port definition" dim name)) `(define ,name = external-event (dim ,dim) (0.0 * ,unit))))))) model-event-receive-ports)) (reduce-decls (map (match-lambda ((name . dim) (let ((unit (alist-ref dim default-units ))) (if (not unit) (error 'eval-ul-component "cannot find default unit for dimension in reduce port definition" dim name)) `(define ,name = unknown (dim ,dim) (0.0 * ,unit))))) model-reduce-ports)) ) (match model (($ dynamics-node model-name model-formals model-decls) (let ((decls (append parameter-decls state-decls ext-decls extev-decls reduce-decls (list model-decls)))) (pp `(model-decls = ,decls) (current-error-port)) (cons (string->symbol node-name) (make-dynamics-node model-name model-formals (salt:parse decls) )) )) ((and ($ alsys-node model-name model-formals model-decls) node) (cons (string->symbol node-name) node)) ((and ($ connection-rule-node model-name model-formals model-stdlib) node) (let ((parameters (map (lambda (n v) (let* ((vtext (sxml:text v)) (name (string->symbol (sxml:text n)))) `(,name . ,vtext))) propns propvs))) (cons (string->symbol node-name) (make-connection-rule-node model-name model-formals (cons model-stdlib parameters))) )) ) )) )) ) (define (parse-ul-properties prefix sxml-properties) (let ( (prop-env (reverse (map (lambda (node lst) (d "parse-ul-properties: node = ~A~%" node) (let ((name (sxml:attr node 'name)) (sxml-value (car ((sxpath `(// nml:SingleValue)) (list node))))) (d "parse-ul-properties: name = ~A sxml-value = ~A~%" name sxml-value) (let ((n (string->number vtext))) (or (and n (make-real-signal name n)) (and (sxml:kidn 'nml:MathInline sxml-value) (make-signal-expr (parse-string-expr (->string (sxml:kidn-cadr 'nml:MathInline sxml-value ))) '())) )) )) '() sxml-properties))) ) (map (lambda (entry) (d "parse-ul-properties: entry = ~A~%" entry) (let* ((name ($ (ident-name (car entry)))) (val (definition-apply prefix (car entry) (list (current-scope) (current-type-env) (list entry)) value-hook: parse-property-hook))) (d "parse-ul-properties: name = ~A val = ~A~%" name val) `(,name (expr . ,(->string val)) (exprML . ,(mlton-value val)) ))) prop-env) )) (define (eval-ul-property prefix node) (d "eval-ul-property: node = ~A~%" node) (let* ( (sxml-single-value (sxml:kidn 'nml:SingleValue node)) (sxml-math-expr (sxml:kidn 'nml:MathInline node)) (name (gensym 'prop)) ) `(,name . ,(let* ((vtext (sxml:text node)) (n (string->number vtext))) (cond (n n) (sxml-single-value (make-signal-expr (string->number (sxml:text sxml-single-value)))) (sxml-math-expr (parse-string-expr (sxml:text sxml-math-expr))) (else (error 'eval-ul-property "unknown property format" node)) )) )) ) (define (make-population-tenv name prototype size order) (alist->tenv `((name . ,name) (prototype . ,prototype) (size . ,size) (start . ,order)) )) (define (population= x y) (equal? (car x) (car y))) (define (make-population-set node populations) (let* ( (concatenate-template (sxml:match 'nml:Concatenate (lambda (node bindings root env) (let ((kids (sxml:kids node))) (fold (lambda (x ax) (lset-union population= (make-population-set x populations) ax)) '() kids) )) )) (union-template (sxml:match 'nml:Union (lambda (node bindings root env) (let ((left (sxml:kidn* 'nml:Left node)) (right (sxml:kidn* 'nml:Right node))) (lset-union population= (make-population-set (sxml:kid left) populations) (make-population-set (sxml:kid right) populations)) )) )) (intersection-template (sxml:match 'nml:Intersection (lambda (node bindings root env) (let ((left (sxml:kidn* 'nml:Left node)) (right (sxml:kidn* 'nml:Right node))) (lset-intersection population= (make-population-set (sxml:kid left) populations) (make-population-set (sxml:kid right) populations)) )) )) (difference-template (sxml:match 'nml:Difference (lambda (node bindings root env) (let ((left (sxml:kidn* 'nml:Left node)) (right (sxml:kidn* 'nml:Right node))) (lset-difference population= (make-population-set (sxml:kid left) populations) (make-population-set (sxml:kid right) populations)) )) )) (singleton-template (sxml:match 'nml:Item (lambda (node bindings root env) (let* ((ref (sxml:kidn* 'nml:Reference node)) (name ($ (sxml:text ref)))) (d "Item: node = ~A name = ~A~%" node name) (let ((population (lookup-def name populations))) (if population `((,name . ,population)) (error 'make-population-set "unknown population" name)) )) ))) ) (stx:apply-templates node (sxml:make-null-ss union-template intersection-template difference-template singleton-template concatenate-template) node (list)) )) (define (make-population-set-tenv name populations) (alist->tenv `((name . ,name) (populations . ,(map cdr populations)) (size . ,(fold + 0 (map (lambda (x) (ersatz:tvalue->sexpr (alist-ref 'size (cdr x)))) populations))) ))) (define (make-projection-tenv name type source destination connectivity response response-ports plasticity del properties) (d "make-projection-tenv: source = ~A~%" source) (d "make-projection-tenv: destination = ~A~%" destination) (d "make-projection-tenv: connectivity = ~A~%" connectivity) (d "make-projection-tenv: delay = ~A~%" del) (d "make-projection-tenv: properties = ~A~%" properties) (alist->tenv `((name . ,name) (type . ,type) (source . ,source) (destination . ,destination) (connectivity . ,connectivity) (response . ,response) (responsePorts . ,response-ports) (plasticity . ,plasticity) (delay . ,del) (properties . ,properties) ) )) (define (make-connection-tenv prefix name node-env) (let ((sys-name ($ (->string name)))) (cond ((lookup-def sys-name node-env) => (match-lambda (($ connection-rule-node name connection-formals connection-rule) (alist->tenv (append `((name . ,sys-name) (stdlib . ,(car connection-rule))) (cdr connection-rule)))) (else (error 'make-connection-tenv "unknown stdlib connection")))) ((lookup-def sys-name node-env) => (lambda (sdinfo) (let ((dvars (lookup-def 'dvars sdinfo)) (ic (lookup-def 'initial-conditions sdinfo)) (params (lookup-def 'params sdinfo)) (sysFn (lookup-def 'sys-id sdinfo))) (let* ( (states dvars) (icstates (filter (lambda (x) (member (car x) states)) ic)) (initialExpr/ML (mlton-initial (append ic params))) (initialStateExpr/ML (and (not (null? icstates)) (mlton-initial icstates))) ) (d "NineML make-connection-tenv: states = ~A ics = ~A~%" states (map car ic)) (alist->tenv `((name . ,name) (sysFn . ,sysFn) (states . ,states) )) )) )) (else (error 'make-connection-tenv "unknown connection equation system" name)) )) ) (define (make-group-tenv name order populations sets projections psr-types plas-types connection-types projection-ports spikepoplst statesample extsample properties) (let ((alst `((group . ((name . ,name) (order . ,order) (sets . ,sets) (populations . ,populations) (projections . ,projections) (projectionPorts . ,projection-ports) (psrtypes . ,(if (null? psr-types) #f psr-types)) (plastypes . ,(if (null? plas-types) #f plas-types)) (conntypes . ,(if (null? connection-types) #f connection-types)) (properties . ,(if (null? properties) (ersatz:sexpr->tvalue '()) properties)) (spikepoplst . ,spikepoplst) (statesample . ,statesample) (extsample . ,extsample) )) )) ) (alist->tenv alst))) (define (eval-ul-group operand ul-properties node ul-node-env) (define (update-population-prototype-env population-prototype-env population-names response) (let recur ((prototypes (population-prototype-env)) (new-prototypes '())) (if (null? prototypes) (population-prototype-env new-prototypes) (let ((prototype (car prototypes))) (if (member (car prototype) population-names) (recur (cdr prototypes) (cons (cons (car prototype) (cons (cadr prototype) (append (cddr prototype) (list response)))) new-prototypes)) (recur (cdr prototypes) (cons prototype new-prototypes))) )) )) (define (projections-range projections) (let ((destination-union (fold (lambda (x ax) (let* ((props (cdr x)) (destination (ersatz:tvalue->sexpr (alist-ref 'destination props)))) (lset-union population= (alist-ref 'populations destination) ax))) '() projections))) (fold (lambda (x ax) (+ (alist-ref 'size x) ax)) 0 destination-union) )) (pp `("UL node" . ,node) (current-error-port)) (let* ( (source-directory (pathname-directory operand)) (prefix (pathname-file operand)) (group-name (or (sxml:attr node 'name) (string->symbol prefix))) (populations-sxml (sxml:kidsn 'nml:Population node)) (selections-sxml (sxml:kidsn 'nml:Selection node)) (projections-sxml ((sxpath `(// nml:Projection)) node)) (properties-sxml ((sxpath `(// nml:Property)) node)) ) (d "UL group: ~A properties: ~A populations: ~A selections: ~A projections: ~A~%" group-name properties-sxml populations-sxml selections-sxml projections-sxml) (if (null? populations-sxml) (error 'eval-ul-group "group without populations" node)) (let* ((properties (parse-ul-properties group-name properties-sxml)) (populations+order (fold (lambda (node ax) (let ((populations (car ax)) (order (cadr ax))) (let* ((name (sxml:attr node 'name)) (prototype-name ($ (sprintf "~A_~A" name (sxml:text (sxml:kidn* 'nml:Reference (sxml:kidn* 'nml:Cell node)))))) (size (eval-ul-property group-name (sxml:kidn* 'nml:Number node))) (size-val (inexact->exact (cdr size)))) (list (cons `(,($ name) . ,(make-population-tenv ($ name) `((name . ,prototype-name)) size-val order)) populations) (+ size-val order) )) )) (list '() 0) populations-sxml)) (populations (reverse (car populations+order))) (order (cadr populations+order)) (population-prototype-env (make-parameter (map (lambda (node) (let* ((name ($ (sxml:attr node 'name))) (prototype-name ($ (sxml:text (sxml:kidn* 'nml:Reference (sxml:kidn* 'nml:Cell node)))))) (list name prototype-name) )) populations-sxml))) (sets (append (map (lambda (x) (let ((name (car x))) `(,name . ((name . ,name) (populations ,(string->symbol (->string (alist-ref 'name (cdr x)))))))) ) populations) (map (lambda (node) (let* ((name (sxml:attr node 'name)) (set (make-population-set (sxml:kid node) populations))) `(,($ name) . ((name . ,name) (populations . ,(map (lambda (x) (string->symbol (->string (alist-ref 'name (cdr x))))) set)))) )) selections-sxml))) (sets-tenv (append (map (lambda (x) (let ((name (car x))) `(,name . ((name . ,name) (populations . ,(ersatz:sexpr->tvalue (list (cdr x)))) (size . ,(alist-ref 'size (cdr x)))) ) )) populations) (map (lambda (node) (let* ((name (sxml:attr node 'name)) (set (make-population-set (sxml:kid node) populations))) `(,($ name) . ,(make-population-set-tenv ($ name) set)))) selections-sxml))) (projection-port (make-parameter 0)) (projections+types (map (lambda (node) (let* ( (name (sxml:attr node 'name)) (type ($ (or (sxml:attr node 'type) "event"))) (source-node (sxml:kidn* 'nml:Source node)) (source-name ($ (sxml:text (sxml:kidn* 'nml:Reference source-node)))) (destination-node (sxml:kidn* 'nml:Destination node)) (destination-name ($ (sxml:text (sxml:kidn* 'nml:Reference destination-node)))) (destination-response-ports (let ((from-response (sxml:kidn* 'nml:FromResponse destination-node))) (list ($ (sxml:attr from-response 'send_port)) ($ (sxml:attr from-response 'receive_port))) )) (response-node (sxml:kidn* 'nml:Response node)) (response-name (and response-node (sxml:text (sxml:kidn* 'nml:Reference response-node )))) (response-plasticity-ports (and response-node (let ((from-plasticity (sxml:kidn* 'nml:FromPlasticity response-node ))) (d "response-node: response-node = ~A from-plasticity = ~A~%" response-node from-plasticity) (list ($ (sxml:attr from-plasticity 'send_port)) ($ (sxml:attr from-plasticity 'receive_port))) ))) (response-ports `( (projection-port . ,(projection-port)) (plasticity-ports . ,response-plasticity-ports) (destination-ports . ,destination-response-ports) )) (plasticity-node (sxml:kidn* 'nml:Plasticity node)) (plasticity-name (sxml:text (sxml:kidn* 'nml:Reference plasticity-node))) (connectivity (sxml:kidn* 'nml:Connectivity node)) (connectivity-name (let ((ref (sxml:kidn* 'nml:Reference connectivity))) (and ref (sxml:text ref)))) (connectivity-port (let ((st (sxml:kidn* 'nml:Port connectivity))) (and st (sxml:text st)))) (del (salt:codegen-const-expr (cdr (eval-ul-property name (sxml:kidn* 'nml:Delay node))))) (properties (parse-ul-properties name (append (sxml:kidsn 'nml:property connectivity) (sxml:kidsn 'nml:Property connectivity)))) ) (d "group-ul-eval: projection node = ~A~%" node) (d "group-ul-eval: response = ~A response-name = ~A~%" response-node response-name) (d "group-ul-eval: delay = ~A~%" del) (d "group-ul-eval: type = ~A ~%" type) (d "group-ul-eval: plasticity = ~A plasticity-name = ~A~%" plasticity-node plasticity-name) (d "group-ul-eval: properties = ~A ~%" properties) (d "group-ul-eval: connectivity-name = ~A ~%" connectivity-name) (d "group-ul-eval: connectivity-port = ~A ~%" connectivity-port) (projection-port (+ 1 (projection-port))) (let* ( (source (lookup-def source-name sets-tenv)) (destination (lookup-def destination-name sets-tenv)) (connection (and connectivity-name (make-connection-tenv prefix connectivity-name ul-node-env))) ) (if (not source) (error 'eval-ul-group "invalid projection source" source)) (if (not destination) (error 'eval-ul-group "invalid projection destination" destination)) (update-population-prototype-env population-prototype-env (alist-ref 'populations (alist-ref destination-name sets)) (cons source-name (cons response-name response-ports))) (list `(,($ name) . ,(make-projection-tenv ($ name) type source destination `( (name . ,connectivity-name) (port . ,connectivity-port) (type . ,connection) ) response-name response-ports plasticity-name `((exprML . ,(salt:value->ML del))) properties)) `( ,(and response-name ($ response-name)) (type . ,type) (response . ,response-name) (ports . ,response-ports) (projection . ,name) ) `(,(and plasticity-name ($ plasticity-name)) (plasticity . ,plasticity-name) ) `(,($ connectivity-name) (connection . ,connection) ) ) )) ) projections-sxml)) (projections (map car projections+types )) (psr-types (let* ((psrs0 (filter car (map cadr projections+types))) (psr-projections (fold (lambda (x ax) (let* ((psr-name (car x)) (projection (alist-ref 'projection (cdr x))) (type (alist-ref 'type (cdr x))) (psr-projections (alist-ref psr-name ax))) (if psr-projections (alist-update psr-name (cons `(,projection ,type) psr-projections) ax) (alist-update psr-name (list `(,projection ,type)) ax)))) '() psrs0)) ) (map (lambda (x) (let* ( (name (car x)) (response (alist-ref 'response (cdr x))) (projection-names (map car (alist-ref name psr-projections))) (projection-types (delete-duplicates (map cadr (alist-ref name psr-projections)))) (ports (alist-ref 'ports (cdr x))) ) (if (> (length projection-types) 1) (error 'eval-ul-group "different projection types for synapse model" name)) `(,name . ((response . ,response) (projections . ,projection-names) (type . ,(car projection-types)) (range . ,(projections-range (map (lambda (x) (alist-ref ($ x) projections)) projection-names))) (ports . ,ports) )) )) (delete-duplicates psrs0 (lambda (x y) (eq? (car x) (car y))) )) )) (plas-types (let ((plas-types0 (filter car (map caddr projections+types)))) (map (lambda (x) (let* ((name (car x)) (plasticity (alist-ref 'plasticity (cdr x)))) `(,name . ,plasticity) )) (delete-duplicates plas-types0 (lambda (x y) (eq? (car x) (car y))) plas-types0)) )) (connection-types (let ((connection-types0 (filter car (map cadddr projections+types)))) (map (lambda (x) (let* ((name (car x)) (connection (alist-ref 'connection (cdr x)))) `(,name . ,connection) )) (delete-duplicates connection-types0 (lambda (x y) (eq? (car x) (car y))) connection-types0)) )) ) (d "group-ul-eval: order = ~A~%" order) (d "group-ul-eval: projections = ~A~%" projections) (d "group-ul-eval: psr-types = ~A~%" psr-types) (d "group-ul-eval: plas-types = ~A~%" plas-types) (let* ( (shared-dir (chicken-home)) (template-dir (make-pathname (make-pathname shared-dir "9ML") "templates")) (network-tmpl (case (ivp-simulation-method) ((rkoz rkdp) "Network.sml.adaptive.tmpl") (else "Network.sml.tmpl"))) (sim-tmpl (case (ivp-simulation-method) ((rkoz rkdp) "Sim.sml.adaptive.tmpl") (else "Sim.sml.tmpl"))) (mlb-tmpl (case (ivp-simulation-method) ((rkoz rkdp) "Sim.mlb.adaptive.tmpl") (else "Sim.mlb.tmpl"))) (makefile-tmpl "Makefile.tmpl") (group-path (make-pathname source-directory (conc group-name ".sml"))) (sim-path (make-pathname source-directory (conc "Sim_" group-name ".sml"))) (mlb-path (make-pathname source-directory (conc "Sim_" group-name ".mlb"))) (exec-path (make-pathname source-directory (conc "Sim_" group-name))) (makefile-path (make-pathname source-directory (conc "Makefile." group-name))) (spikelst (fold (lambda (name ax) (let ((set (alist-ref ($ name) sets-tenv))) (if (not set) (error '9ML-network "Population set not found" name)) (let ((populations (let ((poplst (alist-ref 'populations set))) (ersatz:tvalue->sexpr poplst)))) (append (map (lambda (x) (->string (alist-ref 'name x))) populations) ax)))) '() (filter identity (list (opt 'spikerecord))))) (projection-ports (ersatz:sexpr->tvalue (map (match-lambda ((population node-name . responses) (let ((ports (filter-map (lambda (x) (alist-ref 'projection-port (cddr x))) responses))) `(,population . ,ports)))) (population-prototype-env)))) (group-tenv (make-group-tenv group-name order populations sets-tenv projections psr-types plas-types connection-types projection-ports spikelst (or (opt 'statesample) 0) (or (opt 'extsample) 0) (append properties ul-properties) )) (simcontrol-tenv (alist->tenv `((duration . ,(or (opt 'duration) (defopt 'duration))) (timestep . ,(or (opt 'timestep) (defopt 'timestep)))))) ) (d "projection-ports = ~A~%" (ersatz:tvalue->sexpr projection-ports)) (d "group-path = ~A~%" group-path) (d "group-tenv = ~A~%" (map (lambda (x) (cons (car x) (ersatz:tvalue->sexpr (cdr x)))) group-tenv)) (d "population-prototype-env = ~A~%" (population-prototype-env)) (for-each (match-lambda ((population node-name . responses) (match-let ( (($ dynamics-node model-name model-formals model-eqset) (alist-ref node-name ul-node-env)) ) (d "node name = ~A model-eqset = ~A responses = ~A~%" node-name model-eqset responses) (let* ((response-dynamics (map (match-lambda ((source-population response-node . ports) (match-let ( (($ dynamics-node model-name model-formals model-eqset) (alist-ref (string->symbol response-node) ul-node-env)) ) model-eqset))) responses)) (prototype-decls (salt:make-astdecls (append (salt:astdecls-decls model-eqset) response-dynamics)))) (d "prototype-decls = ~A~%" prototype-decls) (let* ((sim (salt:simcreate (salt:elaborate prototype-decls)))) (let ((port (open-output-file (make-pathname source-directory (sprintf "~A_~A.sml" population node-name))))) (salt:codegen-ODE/ML sim out: port solver: (ivp-simulation-method) libs: '(random)) (close-output-port port)) )) )) ) (population-prototype-env)) (for-each (match-lambda ((node-name . plas-type) (match-let ( (($ dynamics-node model-name model-formals model-eqset) (alist-ref node-name ul-node-env)) ) (d "plasticity node name = ~A model-eqset = ~A~%" node-name model-eqset) (let* ((sim (salt:simcreate (salt:elaborate model-eqset)))) (let ((port (open-output-file (make-pathname source-directory (sprintf "~A.sml" node-name))))) (salt:codegen-ODE/ML sim out: port solver: (ivp-simulation-method) libs: '(random)) (close-output-port port)) )) )) plas-types) (let ((node-files (map (match-lambda ((population node-name . responses) (make-pathname source-directory (sprintf "~A_~A.sml" population node-name)))) (population-prototype-env)))) (make/proc `((,group-path ,node-files ,(lambda () (with-output-to-file group-path (lambda () (print (ersatz:from-file network-tmpl env: (template-std-env search-path: `(,template-dir)) models: (append simcontrol-tenv group-tenv)))))) )) (list group-path)) ) (make ( (sim-path (group-path) (with-output-to-file sim-path (lambda () (print (ersatz:from-file sim-tmpl env: (template-std-env search-path: `(,template-dir)) models: (append simcontrol-tenv group-tenv))))) ) (mlb-path (group-path) (with-output-to-file mlb-path (lambda () (print (ersatz:from-file mlb-tmpl env: (template-std-env search-path: `(,template-dir)) models: group-tenv)))) ) (makefile-path () (with-output-to-file makefile-path (lambda () (print (ersatz:from-file makefile-tmpl env: (template-std-env search-path: `(,template-dir)) models: (append group-tenv `((sml_lib_home . ,(Tstr (make-pathname (make-pathname shared-dir "salt") "sml-lib"))) (nineml_lib_home . ,(Tstr (make-pathname (make-pathname shared-dir "9ML") "sml-lib"))) )) )) )) ) (exec-path (group-path sim-path mlb-path makefile-path) (run (make -f ,makefile-path))) ) (list exec-path) ) )) )) (define (resolve-ul-components node) (let ((components-list (make-parameter '()))) (let ( (population-template (sxml:match 'nml:Population (lambda (node bindings root env) (let ((name (sxml:attr node 'name)) (number (sxml:kidn 'nml:Number node)) (cell-component ((sxpath `(// nml:Cell nml:Component)) node))) (if (null? cell-component) node (let ((component-name (sxml:attr (sxml-singleton cell-component) 'name))) (components-list (cons (sxml-singleton cell-component) (components-list))) `(nml:Population (@ (name ,name)) ,number (nml:Cell (nml:Reference ,component-name))) )) )) )) (projection-template (sxml:match 'nml:Projection (lambda (node bindings root env) (let* ( (name (sxml:attr node 'name)) (src ((sxpath `(// nml:Source)) node)) (dest ((sxpath `(// nml:Destination)) node)) (del ((sxpath `(// nml:Delay)) node)) (connectivity ((sxpath `(// nml:Connectivity)) node)) (connectivity-component ((sxpath `(// nml:Connectivity nml:Component)) node)) (response ((sxpath `(// nml:Response)) node)) (response-component ((sxpath `(// nml:Response nml:Component)) node)) (plasticity ((sxpath `(// nml:Plasticity)) node)) (plasticity-component ((sxpath `(// nml:Plasticity nml:Component)) node)) ) (if (not (null? connectivity-component)) (components-list (cons (sxml-singleton connectivity-component) (components-list)))) (if (not (null? response-component)) (components-list (cons (sxml-singleton response-component) (components-list)))) (if (not (null? plasticity-component)) (components-list (cons (sxml-singleton plasticity-component) (components-list)))) `(nml:Projection (@ (name ,name)) ,(sxml-singleton src) ,(sxml-singleton dest) ,(sxml-singleton del) ,(if (null? connectivity-component) (sxml-singleton connectivity) (let ((component-name (sxml:attr (sxml-singleton connectivity-component) 'name))) `(nml:Connectivity (nml:Reference ,component-name) . ,((select-kids (lambda (x) (not (eq? (car x) 'nml:Component)))) connectivity)))) ,(if (null? response-component) (sxml-singleton response) (let ((component-name (sxml:attr (sxml-singleton response-component) 'name))) `(nml:Response (nml:Reference ,component-name) . ,((select-kids (lambda (x) (not (eq? (car x) 'nml:Component)))) response)) )) ,(if (null? plasticity-component) (sxml-singleton plasticity) (let ((component-name (sxml:attr (sxml-singleton plasticity-component) 'name))) `(nml:Plasticity (nml:Reference ,component-name) . ,((select-kids (lambda (x) (not (eq? (car x) 'nml:Component)))) plasticity)))) ) )) )) ) (let ((result (stx:apply-templates node (sxml:make-identity-ss population-template projection-template ) node (list)))) (values (components-list) result) )) )) (define (main options operands) (if (options 'help) (network:usage)) (if (null? operands) (network:usage)) (if (options 'verbose) (begin (salt:verbose 1) (network-verbose 1))) (simulation-platform (or (options 'platform) (defopt 'platform) )) (simulation-method (or (options 'method) (defopt 'method) )) (ivp-simulation-platform (simulation-platform)) (alsys-simulation-platform (simulation-platform)) (ivp-simulation-method (simulation-method)) (for-each (lambda (operand) (let* ( (nineml-sxml ((sxpath `(// nml:NineML)) (parse-xml (read-all operand)))) (model-sxml (sxml:kids nineml-sxml)) (ul-imports ((sxpath `(// (*or* nml:Import nml:import))) model-sxml)) (ul-import-sxmls (map (lambda (x) (parse-xml (fetch (sxml-string->uri (sxml:text x))))) ul-imports)) (all-sxml (fold append model-sxml ul-import-sxmls)) ) (let-values (((component-env ul-sxml) (resolve-ul-components all-sxml))) (pp `(all-sxml . ,all-sxml) (current-error-port)) (pp `(component-env . ,component-env) (current-error-port)) (let ((dimensions-sxml (sxml:kidsn 'nml:Dimension `(nml:NineML . ,all-sxml))) (units-sxml (sxml:kidsn 'nml:Unit `(nml:NineML . ,all-sxml)))) (eval-sxml-units dimensions-sxml units-sxml)) (let* ( (ul-properties (parse-ul-properties operand ((sxpath `(// (*or* nml:Property nml:property))) ul-sxml))) (dd (d "ul-properties = ~A~%" ul-properties)) (ul-components (append ((sxpath `(// (*or* nml:Component nml:component))) model-sxml) component-env)) (dd (begin (d "ul-components = ~%") (pp ul-components (current-error-port)))) (ul-component-eval-env (map eval-ul-component ul-components)) ) (d "ul-component-eval-env = ~%") (pp ul-component-eval-env (current-error-port)) (eval-ul-group operand ul-properties `(nml:Group . ,ul-sxml) ul-component-eval-env) )) )) operands)) (main opt (opt '@))