Commit 50ecf905 authored by CD's avatar CD
Browse files

Added some helper functions to physio module file

parent e547b3e6
# Port settings for ACT-R server started at 06:58:20 11/03/2020
set actr_port 2671
set actr_address ""
# Port settings for ACT-R server started at 12:06:06 11/15/2020
set actr_port 2650
set actr_address ""
......@@ -85,7 +85,7 @@
(setf noise-val (/ (+ (* arous-dm-noise (AA-nom-dm-noise aa)) (* (- arous-mid arous-dm-noise) (AA-max-dm-noise aa))) arous-mid))
;We only record every 5 seconds
(when (eq (mod (mp-time) 5) 0)
(when (eq (mod (mp-time) 2) 0)
(n-stream (format nil "Phys-data/ans-log~a.txt" (phys-module-pipeID (get-module physio))) :direction :output :if-exists :append :if-does-not-exist :create)
(format n-stream "~5$,~10$~&" (mp-time-ms) noise-val)))
......@@ -94,7 +94,7 @@
(setf noise-val (/ (+ (* (- (AA-max-arous aa) arous-dm-noise) (AA-nom-dm-noise aa)) (* (- arous-dm-noise arous-mid) (AA-max-dm-noise aa))) arous-mid))
;(when (and (>= (mod (mp-time) 5) 0) (<= (mod (mp-time) 5) 1))
(when (eq (mod (mp-time) 5) 0)
(when (eq (mod (mp-time) 2) 0)
(n-stream (format nil "Phys-data/ans-log~a.txt" (phys-module-pipeID (get-module physio))) :direction :output :if-exists :append :if-does-not-exist :create)
(format n-stream "~5$,~10$~&" (mp-time-ms) noise-val)))
......@@ -255,8 +255,8 @@
(msgStream (concatenate 'string "Phys-data/CEC-Arous" (phys-module-pipeID phys) ".txt")
:direction :output :if-exists :append :if-does-not-exist :create)
(format msgStream "~$,~5$,~5$,~5$,~5$~&"
(mp-time-ms) (compute-cort test) (compute-epi-arousal test) (compute-crh-arousal test)
(format msgStream "~$,~5$,~5$,~5$,~5$,~5$~&"
(mp-time-ms) (compute-homeostatic-arousal-factor) (compute-cort test) (compute-epi-arousal test) (compute-crh-arousal test)
(* (compute-homeostatic-arousal-factor)
(compute-cort test)
(+ (* (AA-epi-arous-ratio aa)
......@@ -265,7 +265,7 @@
(msgStream (concatenate 'string "Phys-data/CEC-Arous" (phys-module-pipeID phys) ".txt")
:direction :output :if-exists :overwrite :if-does-not-exist :create)
(format msgStream "time (ms),f(Cortisol),g(Epinephrine),h(CRH),Arousal~&"))))
(format msgStream "time (ms),Homeostatic-Arousal-Factor,f(Cortisol),g(Epinephrine),h(CRH),Arousal~&"))))
(* (compute-homeostatic-arousal-factor) (compute-cort)
(if (and (get-module physio) (phys-module-enabled phys))
#| Copyright 2017 Christopher L. Dancy II
#| Copyright 2020 Christopher L. Dancy II
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
......@@ -13,9 +13,9 @@
along with this program. If not, see <>.
;;;By Christopher L. Dancy II
;;;By Christopher L. Dancy
;;;Dept of Computer Science, Bucknell University
;;;Made to be used with HumMod v1.6.2 - Modular
;;;Made to be used with ModelSolver v1.0.16 (which comes with HumMod v3.1)
;;; ---For any nerve activity related to heart-rate, HR shouldn't go above : 208-(0.7*age) : (from H Tanaka, KD Monahan 2001).
......@@ -23,6 +23,10 @@
;;; Should theoretically work with sbcl
;;; (*features* stil need to be tested for all implementation specific functions)
;;; Consider getting baseline by moving ahead ~1 day with larger step & averaging those values output from that day
;;Thread library
;(eval-when (:compile-toplevel :load-toplevel :execute)
......@@ -248,7 +252,7 @@ t)
;(format t "Changing the following physiology: ~a~&" varValList)
(let ((phys (get-module physio))
(setPhysMessage "<solverin>")
(timeOut 6)
(timeOut 12)
(num-param-changes 0))
;;Construct message to be sent to new HumMod Solver Process
;; -We must find the chunk in the hash-table because the request to HumMod is case sensitive
......@@ -640,6 +644,74 @@ t)
(setf (phys-module-vars-baseLine-init phys) t))))
(defun update-phys-baseline (&optional (phys-module nil) (timeout 120))
"Allows us to update baseline (e.g., after moving ahead in time at beginning of experiment)
@param phys-module: [ACT-R Module] should be the Physio ACT-R module (which is what is defined within the physiology_thread.lisp file!
@param timeout: [int] The maximum amount of time in which the function should wait for the ModelSolver to output the file we need"
(let* ((phys
(if phys-module phys-module (get-module physio)))
(pipeID (phys-module-pipeID phys))
;;Set the name of the files used to input to model solver stream and to which solver outputs results
(solverInputFile (concatenate 'string *SolverPipeFileDir* "SolverIn" pipeID))
(solverOutputFile (concatenate 'string *SolverPipeFileDir* "SolverOut" pipeID))
(initial-advance-time (format nil "~10,$" (phys-module-initial-advance phys)))
(concatenate 'string
"<solverin><gofor><solutionint>" initial-advance-time
"</solutionint><displayint>" initial-advance-time
(physValueList nil))
(tagbody startGetVals
;;Get new value list output by the ModelSolver
(messageStream solverInputFile
:direction :output :if-exists :overwrite :if-does-not-exist :create)
(format messageStream getValsMessage))
#+:ccl ccl::simple-file-error
#+:sbcl sb-impl::simple-file-error
simple-error) ()
(progn (delete-file solverInputFile) (delete-file solverOutputFile))
(error () nil))
(go startGetVals))))
(while (probe-file solverInputFile)) ;Wait for input file to be digested
(let ((currTime (get-universal-time)))
;;We only wait so long for the file to be created
(while (and (not (probe-file solverOutputFile)) (< (- (get-universal-time) currTime) timeout)))
(error () nil)))
;;When we ran out of time, start this section of the code over
(when (not (probe-file solverOutputFile)) (go startGetVals))
;;Parse the list of values output by ModelSolver
(let ((parseStart (get-universal-time)))
(tagbody parseValList
;If we've been stuck in this block for 4 secs or more, go back to the beginning of the function
(when (> (- (get-universal-time) parseStart) 4) (go startGetVals))
(setf physValueList (s-xml:parse-xml-file solverOutputFile))
((or file-error s-xml::xml-parser-error type-error) () (go parseValList)))
;;If parsing the output file didn't error, but physValList is still nil
;; (Can this actually happen?
;; May want to explore in the future to see if I need to do this)
(when (not physValueList)
(go parseValList))
;;If the modelsolver happens to give us a variable roster
;; instead of list, delete and redo this section of code
(when (equal (caadr physValueList) ':|varroster|)
(while (not (handler-case (delete-file solverOutputFile)
(error () nil))))
(go parseValList)))))
(while (not (handler-case (delete-file solverOutputFile) (error () nil))))
;;Set our current values
(setf (phys-module-physValList-baseline phys) physValueList)
(setf (phys-module-vars-baseLine-init phys) t)))
;;Record values for variables specified by model
(defun record-phys-vals (recVarList allValList savedValList)
(let ((valNumbers nil)
......@@ -946,6 +1018,37 @@ t)
"Move to spontaneous breath"
(set-phys-vals (list (list "ControlledBreathing.ControlledBreathing" 0))))
(defun start-sleep-dep ()
"Make all changes needed for sleep deprivation (and full enactment of circadian rhythms)"
;;Turn on daily planner so that sleep schedule and sleep homeostasis can cause deprivation
(schedule-event-relative 0.023 'set-phys-vals :module 'physio
:params (list (list (list "DailyPlannerControl.Switch" 1) ;Start daily planner
(list "DailyPlannerSchedule.Hour12AM-1AM" 1) ;Rest
(list "DailyPlannerSchedule.Hour1AM-2AM" 4) ;Eat
(list "DailyPlannerSchedule.Hour2AM-3AM" 1) ;Rest
(list "DailyPlannerSchedule.Hour3AM-4AM" 1) ;Rest
(list "DailyPlannerSchedule.Hour4AM-5AM" 1) ;Rest
(list "DailyPlannerSchedule.Hour5AM-6AM" 1) ;Rest
(list "DailyPlannerSchedule.Hour6AM-7AM" 1) ;Rest
(list "DailyPlannerSchedule.Hour7AM-8AM" 4) ;Eat
(list "DailyPlannerSchedule.Hour8AM-9AM" 1) ;Rest
(list "DailyPlannerSchedule.Hour9AM-10AM" 1) ;Rest
(list "DailyPlannerSchedule.Hour10AM-11AM" 1) ;Rest
(list "DailyPlannerSchedule.Hour11AM-12PM" 1) ;Rest
(list "DailyPlannerSchedule.Hour12PM-1PM" 1) ;Rest
(list "DailyPlannerSchedule.Hour1PM-2PM" 4) ;Eat
(list "DailyPlannerSchedule.Hour2PM-3PM" 1) ;Rest
(list "DailyPlannerSchedule.Hour3PM-4PM" 1) ;Rest
(list "DailyPlannerSchedule.Hour4PM-5PM" 1) ;Rest
(list "DailyPlannerSchedule.Hour5PM-6PM" 1) ;Rest
(list "DailyPlannerSchedule.Hour6PM-7PM" 1) ;Rest
(list "DailyPlannerSchedule.Hour7PM-8PM" 4) ;Eat
(list "DailyPlannerSchedule.Hour8PM-9PM" 1) ;Rest
(list "DailyPlannerSchedule.Hour9PM-10PM" 1) ;Rest
(list "DailyPlannerSchedule.Hour10PM-11PM" 1) ;Rest
(list "DailyPlannerSchedule.Hour11PM-12AM" 1))) ;Rest
:priority :max :details "Start Daily Control Cycle & change daily planner"))
;;;Set food intake (eating) variable to a value
(defun set-food-intake (value)
(set-phys-vals (list (list "DietIntakeNutrition.Fixed?" 1) (list "DietIntakeNutrition.FixedIntake(xGoal)" value)))
\ No newline at end of file
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