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pbi-code.lisp
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;;;
;;; pbi-code.cl
;;;
;;; contains all the function and macro definitions from Principles of
;;; Biomedical Informatics by Ira J. Kalet. This code is available for
;;; use without restrictions. I only ask that you cite the book in any
;;; written documents that report on the use of the code or actually
;;; include the code.
;;;
;;;-----------------------------------------------------
;;; only the function and macro definitions are here, not the example
;;; dialogs with the Lisp read-eval-print loop. They are in order by chapter.
;;;-----------------------------------------------------
;;; Chapter 1
;;;-----------------------------------------------------
(defun hypotenuse (x y)
"returns the hypotenuse of the triangle
whose sides are x and y"
(sqrt (+ (* x x) (* y y))))
(defun factorial (n)
(if (= n 0) 1
(* n (factorial (- n 1)))))
(defun all-pos (item seq start)
(let ((pos (position item seq :start start)))
(if pos
(cons pos
(all-pos item seq (+ 1 pos)))
nil)))
;;;-----------------------------------------------------
;;; there are three versions of all-positions. Here I name them
;;;differently so the load function does not complain
;;;-----------------------------------------------------
(defun all-positions-1 (item seq)
(all-pos item seq 0))
(defun all-positions-2 (item seq)
(labels
((all-pos-aux (item seq start)
(let ((pos (position item seq :start start)))
(if pos (cons pos
(all-pos-aux item seq (+ 1 pos)))
nil))))
(all-pos-aux item seq 0)))
(defun all-positions-3 (item seq)
(labels
((all-pos-aux (item seq start accum)
(let ((pos (position item seq :start start)))
(if pos
(all-pos-aux item seq (+ 1 pos)
(cons pos accum))
(reverse accum)))))
(all-pos-aux item seq 0 nil)))
;;;-----------------------------------------------------
(defun count-g (dna)
(if (null dna) 0
(if (eql (first dna) 'g)
(+ 1 (count-g (rest dna)))
(count-g (rest dna)))))
(defun dna-count-simple (seq)
"does an explicit count of the G A C and T in seq"
(let ((ng 0)
(na 0)
(nc 0)
(nt 0))
(dolist (base seq)
(case base
(g (incf ng))
(a (incf na))
(c (incf nc))
(t (incf nt))))
(list ng na nc nt)))
(defun gc-ratio-broken (freq-table)
(/ (+ (first freq-table) (third freq-table))
(+ freq-table)))
(defun gc-ratio (freq-table)
(/ (+ (first freq-table) (third freq-table))
(apply #'+ freq-table)))
(defun gc-ratio-from-file (filename)
(gc-ratio (dna-count-simple (get-data filename))))
(defun item-count (seq)
"returns a frequency table of all the items in seq, a list
of items, tagging the count by the item itself"
(let ((results nil))
(dolist (item seq results)
(let ((tmp (find item results :key #'first)))
(if tmp (incf (second tmp))
(push (list item 1) results))))))
(defun naive-read-from-file (strm)
(let ((char (read-char strm nil :eof)))
(if (eql char :eof) nil
(cons (intern (string char))
(naive-read-from-file strm)))))
(defun read-from-file (strm accum)
(let ((char (read-char strm nil :eof)))
(if (eql char :eof) (reverse accum)
(read-from-file strm (cons (intern (string char))
accum)))))
(defun get-data (filename)
(with-open-file (strm filename)
(read-from-file strm nil)))
(defun read-from-file (strm accum)
(let ((char (read-char strm nil :eof)))
(cond ((eql char :eof) (reverse accum))
((member char (list #\g #\c #\a #\t #\G #\C #\A #\T))
(read-from-file strm
(cons (intern (string-upcase
(string char)))
accum)))
(t (read-from-file strm accum)))))
(defun parse-line (line)
"parses tab delimited text, assumes no other whitespace between
objects"
(labels ((read-items (str accum pos tab)
(if (>= pos (length str))
(reverse (if tab (cons "" accum) accum))
(let ((first (char str pos)))
(if (eql first #\Tab)
(read-item str
(if tab (cons "" accum) accum)
(1+ pos) t)
(multiple-value-bind (item next)
(read-from-string str nil :eof :start pos
:preserve-whitespace t)
(if (eql item :eof)
(reverse (if tab (cons "" accum) accum))
(read-items str (cons item accum)
next nil))))))))
(read-items line nil 0 t)))
(defun parse-loinc (filename)
(let ((n 0))
(labels ((read-loinc-records (strm accum)
(let ((line (read-line strm nil :eof)))
(format t "Reading record ~A~%" (incf n))
(if (eql line :eof) (reverse accum)
(read-loinc-records strm
(cons (parse-line line)
accum))))))
(with-open-file (strm filename)
(list (parse-line (read-line strm))
(read-loinc-records strm nil))))))
(defun print-loinc-record (headers record)
(mapcar #'(lambda (hdr item)
(format nil "~A = ~A" hdr item))
headers record))
(defun make-sagittal-image (image-list)
(let ((new-img (make-array '(512 512)))
(image-num 0))
(dolist (image image-list)
(dotimes (i 512)
(setf (aref new-img i image-num)
(aref image i 256)))
(incf image-num))
new-img))
(defun make-graymap (window level range-top)
(let* ((map (make-array (1+ range-top)))
(low-end (- level (truncate (/ window 2))))
(high-end (+ low-end window)))
(do ((i 0 (1+ i)))
((= i low-end))
(setf (aref map i) 0)) ;; black
(do ((i low-end (1+ i)))
((= i high-end))
(setf (aref map i)
(round (/ (* 255 (- i low-end)) window))))
(do ((i high-end (1+ i)))
((> i range-top))
(setf (aref map i) 255))
map))
(defun map-image (raw-image window level range)
(let* ((x-dim (array-dimension raw-image 1))
(y-dim (array-dimension raw-image 0))
(new-image (make-array (list y-dim x-dim)))
(map (make-graymap window level range)))
(dotimes (i y-dim)
(dotimes (j x-dim)
(setf (aref new-image i j)
(aref map (aref raw-image i j)))))
new-image))
(defun diagnosis (patient-data)
(find 'diagnosis (rest patient-data) :key #'first))
(defstruct person ()
name birthdate telephone email)
(defstruct (patient (:include person))
diagnosis appointments)
(defstruct (provider (:include person))
specialty title office patients)
(defvar *patients*)
(defvar *providers*)
(defun add-provider (name specialty title)
(push (make-provider :name name
:specialty specialty
:title title)
*providers*))
(defun lookup-specialty (name)
(provider-specialty (find name *providers*
:key #'person-name
:test #'string-equal)))
(defun update-patient-phone (name phone)
(let ((record (find name *patients*
:key #'person-name
:test #'string-equal)))
(setf (person-telephone record) phone)))
(defstruct heart ()
size beat-rate x y z)
(defstruct kidney ()
side x y z)
(defstruct tumor ()
size grade tissue-type x y z)
(defmethod draw ((obj t) (v t))
"DRAW (obj t) (v t)
This is a default or stub method so we can build and use the various
functions without crashing on not yet implemented draw calls."
(format t "No DRAW method for class ~A in ~A~%"
(class-name (class-of obj))
(class-name (class-of v))))
(defclass heart ()
((size :accessor size)
(beat-rate :accessor beat-rate)
(x :accessor x)
(y :accessor y)
(z :accessor z)
))
(defclass kidney ()
((side :accessor side)
(x :accessor x)
(y :accessor y)
(z :accessor z)
))
(defclass tumor ()
((size :accessor size)
(grade :accessor grade)
(tissue-type :accessor tissue-type)
(x :accessor x)
(y :accessor y)
(z :accessor z)
))
(defclass patient ()
((name :accessor name :initarg :name)
(hospital-id :accessor hospital-id :initarg :hospital-id)
(age :accessor age :initarg :age)
(address :accessor address :initarg :address)
(diagnosis :accessor diagnosis :initarg :diagnosis)
(lab-tests :accessor lab-tests :initarg :lab-tests)
))
(defclass address ()
((number :accessor number :initarg :number)
(street :accessor street :initarg :street)
(city :accessor city :initarg :city)
(zip-code :accessor zip-code :initarg :zip-code)))
(defclass diagnosis ()
((name :accessor name :initarg :name)
(evidence :accessor evidence :initarg :evidence)
))
(defmethod print-object ((obj patient) strm)
(format strm "(Patient ~%")
(format strm " :name ~S~%" (name obj))
(format strm " :hospital-id ~S~%" (hospital-id obj))
(format strm " ...etc. ) ~%"))
(defun read-object (stream)
(apply #'make-instance (read stream)))
(defun read-object (stream)
(eval (read stream)))
(defun slot-names (obj)
(mapcar #'slot-definition-name
(class-slots (class-of obj))))
(defun get-object-basic (in-stream)
(let* ((current-key (read in-stream))
(object (make-instance current-key)))
(loop
(setq current-key (read in-stream))
(if (eq current-key :end) ;; no more slots?
(return object)
(setf (slot-value object current-key)
(read in-stream))))))
(defun put-object-basic (object out-stream &optional (tab 0))
(tab-print (class-name (class-of object)) out-stream tab t)
(dolist (slotname (slot-names object))
(when (slot-boundp object slotname)
(tab-print slotname out-stream (+ 2 tab))
(tab-print (slot-value object slotname)
out-stream 0 t)))
(tab-print :end out-stream tab t))
(defun tab-print (item stream tab &optional (new-line nil))
(format stream "~A~S "
(make-string tab :initial-element #\space)
item)
(when new-line (format stream "~%")))
(defun get-object (in-stream)
(let* ((current-key (read in-stream))
(object (if (eq current-key :end)
nil ;; end of object list
(make-instance current-key))))
(loop
(setq current-key (read in-stream))
(if (eq current-key :end) ;; no more slots?
(return object)
(setf (slot-value object current-key)
(case (slot-type object current-key)
(:simple (read in-stream))
(:object (get-object in-stream))
(:object-list
(let ((slotlist '())
(next-object nil))
(loop
(setq next-object
(get-object in-stream :parent object))
(if next-object
(push next-object slotlist)
(return (nreverse slotlist))))))))))))
(defun put-object (object out-stream &optional (tab 0))
(tab-print (class-name (class-of object)) out-stream tab t)
(dolist (slotname (slot-names object))
(when (slot-boundp object slotname)
(tab-print slotname out-stream (+ 2 tab))
(case (slot-type object slotname)
(:simple
(tab-print (slot-value object slotname)
out-stream 0 t))
(:object
(fresh-line out-stream)
(put-object (slot-value object slotname)
out-stream (+ 4 tab)))
(:object-list
(fresh-line out-stream)
(dolist (obj (slot-value object slotname))
(put-object obj out-stream (+ 4 tab)))
(tab-print :end out-stream (+ 2 tab) t)))))
(tab-print :end out-stream tab t))
(defmethod slot-type ((object t) slotname)
:simple)
(defmethod slot-type ((object patient) slotname)
(case slotname
((address diagnosis) :object)
(otherwise :simple)))
(defmethod slot-type ((object patient) slotname)
(case slotname
((address diagnosis) :object)
(otherwise (call-next-method))))
(defun get-all-objects (filename)
(with-open-file (stream filename
:direction :input
:if-does-not-exist nil)
(when (streamp stream)
(let ((object-list '()))
(loop
(cond ((eq (peek-char t stream nil :eof) :eof)
(return object-list))
(t (push (get-object stream) object-list))))))))
(defun put-all-objects (object-list filename)
(with-open-file (stream filename
:direction :output
:if-exists :new-version)
(dolist (obj object-list)
(put-object obj stream))))
(defclass image ()
((uid :type string :accessor uid :initarg :uid)
(patient-id :accessor patient-id :initarg :patient-id
:documentation "The patient id of the
patient this image belongs to.")
(image-set-id :accessor image-set-id :initarg :image-set-id
:documentation "The image set id of the
primary image set the image belongs to.")
(position :type string
:accessor position :initarg :position
:documentation "String, one of HFP, HFS,
FFP, FFS, etc. describing patient position as
scanned (Head/Feet-First Prone/Supine, etc).")
(description :type string
:accessor description :initarg :description)
(origin :type (vector single-float 3)
:accessor origin :initarg :origin
:documentation "Origin refers to the location in
patient space of the corner of the image as defined
by the point at pixel array reference 0 0 or voxel
array reference 0 0 0.")
(size :type list ;; of two or three elements, x y z
:accessor size :initarg :size
:documentation "The size slot refers to the physical
size of the image in each dimension, measured in
centimeters in patient space.")
;; ...other slots
)
(:default-initargs :id 0 :uid "" :patient-id 0
:image-set-id 0 :position "HFS"
:description "")
(:documentation "The basic information common to all types of
images, including 2-D images, 3-D images."))
(defclass image-2d (image)
((thickness :type single-float
:accessor thickness :initarg :thickness)
(x-orient :type (vector single-float 3)
:accessor x-orient :initarg :x-orient
:documentation "A vector in patient space defining
the orientation of the X axis of the image in the
patient coordinate system.")
(y-orient :type (vector single-float 3)
:accessor y-orient :initarg :y-orient
:documentation "See x-orient.")
(pix-per-cm :type single-float
:accessor pix-per-cm :initarg :pix-per-cm)
(pixels :type (simple-array (unsigned-byte 16) 2)
:accessor pixels :initarg :pixels
:documentation "The array of image data itself.")))
(defclass image-3d (image)
((voxels :type (simple-array (unsigned-byte 16) 3)
:accessor voxels
:initarg :voxels
:documentation "a 3-D array of image data values"))
(:documentation "An image-3D depicts some 3-D rectangular
solid region of a patient's anatomy."))
(defun read-bin-array (filename size)
(let ((bin-array (make-array (list size)
:element-type '(unsigned-byte 16))))
(with-open-file (infile filename :direction :input
:element-type
'(unsigned-byte 16))
(read-sequence bin-array infile))
bin-array))
(defun read-bin-array (filename bin-array)
(with-open-file (infile filename :direction :input
:element-type
'(unsigned-byte 16))
(read-sequence bin-array infile)))
(defun read-bin-array (filename dimensions)
(let* ((bin-array (make-array dimensions
:element-type '(unsigned-byte 16)))
(disp-array (make-array (array-total-size bin-array)
:element-type '(unsigned-byte 16)
:displaced-to bin-array)))
(with-open-file (infile filename :direction :input
:element-type '(unsigned-byte 16))
(read-sequence disp-array infile))
bin-array))
(defun read-bin-array (filename bin-array)
(let ((disp-array (make-array (array-total-size bin-array)
:element-type '(unsigned-byte 16)
:displaced-to bin-array)))
(with-open-file (infile filename :direction :input
:element-type '(unsigned-byte 16))
(read-sequence disp-array infile))))
(defun get-object (in-stream)
(let* ((current-key (read in-stream))
(object (if (eq current-key :end)
nil ;; end of object list
(make-instance current-key))))
(loop
(setq current-key (read in-stream))
(if (eq current-key :end) ;; no more slots?
(return object)
(setf (slot-value object current-key)
(case (slot-type object current-key)
(:simple (read in-stream))
(:object (get-object in-stream))
(:object-list
(let ((slotlist '())
(next-object nil))
(loop
(let ((obj (get-object in-stream
:parent object)))
(if obj (push obj slotlist)
(return (nreverse slotlist)))))))
(:bin-array
(let ((bin-info (read in-stream)))
(read-bin-array (first bin-info)
(rest bin-info))))
))))))
(defun put-object-xml (object out-stream &optional (tab 0))
(let ((tag (class-name (class-of object))))
(print-xml-tag tag out-stream tab)
(mapc #'(lambda (slotname)
(when (slot-boundp object slotname)
(print-xml-tag slotname out-stream (+ 2 tab))
(case (slot-type object slotname)
(:simple (tab-print (slot-value object slotname)
out-stream 0 t))
(:object (fresh-line out-stream)
(put-object-xml
(slot-value object slotname)
out-stream (+ 4 tab)))
(:object-list
(fresh-line out-stream)
(mapc #'(lambda (obj)
(put-object-xml obj out-stream
(+ 4 tab)))
(slot-value object slotname))))
;; closing tag for each slot regardless of content
(print-xml-end-tag slotname out-stream (+ 2 tab))
))
(set-difference (slot-names object) (not-saved object)))
(print-xml-end-tag tag out-stream tab))) ; terminates object
(defun print-xml-tag (tag stream tab)
(format stream "~a<~a>~%"
(make-string tab :initial-element #\space)
tag))
(defun print-xml-end-tag (tag stream tab)
(format stream "~a</~a>~%"
(make-string tab :initial-element #\space)
tag))
(defun make-xml-tag (tag stream tab &optional close)
(format stream (if close "~a</~a>~%"
"~a<~a>~%")
(make-string tab :initial-element #\space)
tag))
(defun put-objects-xml (object-list filename)
(with-open-file (stream filename
:direction :output
:if-exists :new-version)
(dolist (obj object-list)
(put-object-xml obj stream))))
(defmethod print-dom-node ((node dom1-text))
(format t "Value: ~A~%" (dom-node-value node)))
(defmethod print-dom-node ((node dom1-element))
(let ((name (dom-node-name node)))
(format t "Element name: ~A~%" name)
(mapcar #'print-dom-node
(dom-child-node-list node))
(format t "End of ~A~%" name)))
(defmethod print-dom-node ((node dom1-document))
(format t "DOCUMENT ")
(print-dom-node (dom-document-element node)))
;;;-----------------------------------------------------
;;; Chapter 2
;;;-----------------------------------------------------
(defvar *rules* (make-hash-table) "The so-called knowledge base")
(defun <-fn (consequent &optional antecedent)
(push antecedent (gethash consequent *rules*)))
(defmacro <- (consequent &optional antecedent)
(list 'push antecedent (list 'gethash consequent '*rules*)))
(defmacro <- (consequent &optional antecedent)
(list 'push (list 'quote antecedent)
(list 'gethash (list 'quote consequent) '*rules*)))
(defmacro <- (consequent &optional antecedent)
`(push ',antecedent (gethash ',consequent *rules*)))
(defmacro <- (consequent &optional antecedent)
"adds antecedent to the hash table entry for consequent, even if
antecedent is nil"
`(length (push ',antecedent (gethash ',consequent *rules*))))
(defun prove-simple (pred)
"checks if an entry is present, and succeeds if there is a nil for
simple assertion, or an expression that itself can be proved"
(multiple-value-bind (ants found) (gethash pred *rules*)
(cond ((not found) nil)
((member nil ants) t) ;; find won't work here!
(t (some #'prove ants)))))
(defun prove (expr)
(if (listp expr)
(case (first expr)
(and (every #'prove (reverse (rest expr))))
(or (some #'prove (rest expr)))
(not (not (prove (second expr)))))
(prove-simple expr)))
(defun printhash (hashtable)
"prints out the contents of hashtable"
(maphash #'(lambda (key val)
(format t "Key: ~S Value: ~S~%" key val))
hashtable))
(defvar *clauses* nil
"The cumulative list of clauses, aka knowledge base.")
(defstruct clause
ants con count)
(defmacro -> (antecedents consequent)
`(let* ((ants ',antecedents) ;; to avoid multiple eval
(con ',consequent)
(clause (make-clause :ants ants
:con con
:count (length ants))))
(dolist (pred ants)
(push clause (get pred 'on-clauses)))
(push clause *clauses*)
clause))
(defun init-stack (clauses)
(let (stack)
(dolist (clause clauses)
(if (zerop (clause-count clause))
(push (clause-con clause) stack)))
stack))
(defun forward-chain (clauses)
(labels ((fc-aux (stack results)
(if (null stack) results
(let ((prop (first stack))
(newprops nil))
(format t "Current prop: ~A~%" prop)
(dolist (clause (get prop 'on-clauses))
(format t "Clause: ~S~%" clause)
(if (zerop (decf (clause-count clause)))
(let ((concl (clause-con clause)))
(format t "Concl: ~A~%" concl)
(if (null concl) (return-from fc-aux 'fail)
(unless (find concl results)
(push concl newprops))))))
(fc-aux (append newprops (rest stack))
(cons prop results))))))
(fc-aux (init-stack clauses) nil)))
(defmacro <- (con &optional ant)
"adds ant to the hash table entry for con, even if ant is nil"
`(length (push (cons (rest ',con) ',ant)
(gethash (first ',con) *rules*))))
(defun prove (expr &optional binds)
(case (first expr)
(and (prove-and (reverse (rest expr)) binds))
(or (prove-or (rest expr) binds))
(not (prove-not (first (rest expr)) binds))
(t (prove-simple (first expr) (rest expr) binds))))
(defun prove-simple (pred args binds)
(mapcan #'(lambda (r)
(multiple-value-bind (b2 yes)
(match args (first r) binds)
(when yes
(if (rest r) (prove (rest r) b2)
(list b2)))))
(mapcar #'change-vars
(gethash pred *rules*))))
(defun change-vars (r)
(sublis (mapcar #'(lambda (v) (cons v (gensym "?")))
(vars-in r))
r))
(defun var? (x)
(and (symbolp x)
(eql (char (symbol-name x) 0) #\?)))
(defun vars-in (expr)
(if (atom expr)
(if (var? expr) (list expr))
(union (vars-in (first expr))
(vars-in (rest expr)))))
(defun match (x y &optional binds)
(cond
((eql x y) (values binds t))
((assoc x binds) (match (binding x binds) y binds))
((assoc y binds) (match x (binding y binds) binds))
((var? x) (values (cons (cons x y) binds) t))
((var? y) (values (cons (cons y x) binds) t))
(t
(when (and (consp x) (consp y))
(multiple-value-bind (b2 yes)
(match (first x) (first y) binds)
(and yes (match (rest x) (rest y) b2)))))))
(defun binding (x binds)
(let ((b (assoc x binds)))
(if b
(or (binding (rest b) binds)
(rest b)))))
(defun prove-and (clauses binds)
(if (null clauses)
(list binds)
(mapcan #'(lambda (b)
(prove (first clauses) b))
(prove-and (rest clauses) binds))))
(defun prove-or (clauses binds)
(mapcan #'(lambda (c) (prove c binds))
clauses))
(defun prove-not (clause binds)
(unless (prove clause binds)
(list binds)))
(defmacro with-answer (query &body body)
(let ((binds (gensym)))
`(dolist (,binds (prove ',query))
(let ,(mapcar #'(lambda (v)
`(,v (binding ',v ,binds)))
(vars-in query))
,@body))))
(defclass frame ()
((id :reader id
:initform (gentemp "frame-"))
(name :accessor name
:initarg :name
:initform nil)
(instance-of :accessor instance-of
:initarg :instance-of
:initform nil)
(superclasses :accessor superclasses
:initarg :superclasses
:initform nil)
(template-slots :accessor template-slots
:initarg :template-slots
:initform nil)
(own-slots :accessor own-slots
:initarg :own-slots
:initform nil)
(instances :accessor instances
:initform nil)
))
(defvar *frames* nil "The global list of all frames")
(defun find-frame-by-id (frm-id)
(find frm-id *frames* :key #'id))
(defun find-frame-by-name (frm-name)
(find frm-name *frames* :key #'name :test #'equal))
(defun add-frame (frm)
(push fr *frames*))
(defun remove-frame (frm)
(setf *frames* (remove frm *frames*)))
(defun save-frame-kb (filename)
(put-all-objects *frames* filename))
(defun restore-frame-kb (filename)
(setq *frames* (get-all-objects filename)))
(defun slot-name (slot) (first slot))
(defun contents (slot) (second slot))
(defun (setf contents) (newval slot)
(setf (second slot) newval))
(defun get-slot (fr name)
(find name (own-slots fr) :key #'slot-name))
(defun slot-list (fr)
(mapcar #'slot-name (own-slots fr)))
(defun slot-data (fr slot-name)
(contents (get-slot fr slot-name)))
(defun (setf slot-data) (newval fr slot-name)
(setf (contents (get-slot fr slot-name))
newval))
(defun frame-type (fr)
(let ((parent (instance-of fr)))
(if parent (name (find-frame-by-id parent)))))
(defun all-superclasses (fr)
"returns the frame-ids of all the frames that are superclasses of
frame fr all the way up the class hierarchy"
(let ((direct-sup-ids (superclasses fr)))
(apply #'append
direct-sup-ids
(mapcar #'(lambda (frm-id)
(all-superclasses
(find-frame-by-id frm-id)))
direct-sup-ids))))
(defun all-template-slots (fr)
(remove-duplicates
(apply #'append
(template-slots fr)
(mapcar #'(lambda (id)
(template-slots (find-frame-by-id id)))
(all-superclasses fr)))))
(defun make-pairs (x)
(if (oddp (length x)) (error "list length not even")
(if x (cons (list (first x) (second x))
(make-pairs (rest (rest x)))))))
(defun initialize-slot (slotname inits)
(or (assoc slotname inits)
(list slotname nil)))
(defun make-frame (name &key class superclasses template-slots
&rest slot-inits)
(let* ((parent (if class (find-frame-by-name class)))
(super-ids (mapcar #'(lambda (x)
(id (find-frame-by-name x)))
superclasses))
(fr (make-instance 'frame
:name name
:instance-of (if parent (id parent))
:superclasses super-ids
:template-slots template-slots
:own-slots
(if parent
(mapcar #'(lambda (name)
(initialize-slot name
(make-pairs slot-inits)))
(all-template-slots parent)))
)))
(if parent (push fr (instances parent)))
(add-frame fr)
fr))
(defun disease-lookup (drug-inst)
(let ((drug-type (find-frame-by-id (slot-data drug-inst
'instance-of))))
(append (slot-data drug-inst 'diseases)
(slot-data drug-type 'diseases)
(mapcar #'(lambda (x) (slot-data
(find-frame-by-id x)
'diseases))
(all-superclasses drug-type)))))
(defun subsumed-by (fr1 fr2)
(let ((id-list (superclasses fr1)))
(cond ((null id-list) nil)
((find (frame-id fr2) id-list) t)
(some #'(lambda (x)
(subsumed-by (find-frame-by-id x) fr2))
id-list))))
(defun part-of (fr)
(slot-data fr 'part-of))
(defun is-part-of (fr1 fr2)
(let ((id-list (part-of fr1)))
(cond ((null id-list) nil)
((find (frame-id fr2) id-list) t)
(some #'(lambda (x)
(is-part-of (find-frame-by-id x) fr2))
id-list))))
(defun connected-upward (fr1 fr2 link-fn)
(let ((id-list (funcall link-fn fr1)))
(cond ((null id-list) nil)
((find (frame-id fr2) id-list) t)
((some #'(lambda (x)
(connected-upward
(find-frame-by-id x) fr2 link-fn))
id-list)))))
(defun get-all-children (fr frame-kb)
"searches the entire frame knowledge base to collect all the
subclass-of descendants of frame fr."
(let ((children nil))
(dolist (entry frame-kb children)
(if (subsumed-by entry fr)
(push entry children)))))
(defun get-all-parts (fr frame-kb)
"searches for items in the part-of subtree"
(let ((parts nil))
(dolist (entry frame-kb parts)
(if (is-part-of entry fr)
(push entry parts)))))
(defun slot-data (fr slot)
"returns the contents of slot slot-name in frame fr, after
executing any :if-needed function that might be present"
(let* ((the-slot (get-slot fr slot))
(if-needed-fn (second (member :if-needed the-slot))))
(if if-needed-fn (funcall if-needed-fn fr slot))
(second (get-slot fr slot))))
(defun (setf slot-data) (newval fr slot)
"updates the contents of slot slot-name in frame fr, after
executing any :if-added function that might be present"
(let* ((the-slot (get-slot fr slot))
(if-added-fn (second (member :if-added the-slot))))
(if if-added-fn (funcall if-added-fn fr slot newval))
(setf (second (get-slot fr slot)) newval)))
(defun set-attached-fn (fr slot fn key)
"puts function fn in the slot named slot in frame fr, using key as
a tag, e.g., :if-needed or :if-added or possibly other types of
attached functions"
(let* ((the-slot (get-slot fr slot))
(length (length the-slot))
(location (position key the-slot)))
(if location (setf (elt the-slot (+ location 1)) fn)
(setf (rest (last the-slot)) (list key fn)))))
(defun remove-attached-fn (fr slot key)
"replaces any attached function for key to nil"
(set-attached-fn fr slot nil key))
(defun simple-search (initial-state goal)
(labels
((search-inner (queue)
(if (null queue) 'fail
(let ((current (first queue)))
(if (eql current goal)
'success
(search-inner (append (successors current)
(rest queue))))))))
(search-inner (list initial-state))))
(defun better-search (initial-state goal? successors)
(labels
((search-inner (queue)
(if (null queue) 'fail
(let ((current (first queue)))
(if (funcall goal? current) 'success
(search-inner (append (funcall successors
current)
(rest queue))))))))
(search-inner (list initial-state))))
(defun multi-search (initial-state goal? enough? successors)
(labels
((search-inner (queue wins)
(if (null queue) wins
(let ((current (first queue))
(remains (rest queue)))
(cond ((funcall goal? current)
(setq wins (cons current wins))
(if (or (eq enough? t)
(and (null enough?)
(null remains))
(and enough?
(funcall enough? wins)))
wins
(search-inner remains wins)))
(t (search-inner (append (funcall successors
current)