From ceeea7bcc2786e9dfb1c4e5ab7d6592e789d323c Mon Sep 17 00:00:00 2001
From: "Robert L. Read" <read.robert@gmail.com>
Date: Sun, 14 Mar 2021 13:33:54 -0500
Subject: [PATCH] incoporationg respiration_math.js into the main file so that
it can be served from a local file system. Also, more accuratly renamed
server.js to serialserver.js
---
breath_plot.html | 721 +++++++++++++++++-
js/respiration_math.js => respiration_math.js | 0
server.js => serialserver.js | 0
3 files changed, 719 insertions(+), 2 deletions(-)
rename js/respiration_math.js => respiration_math.js (100%)
rename server.js => serialserver.js (100%)
diff --git a/breath_plot.html b/breath_plot.html
index 0773b0c..990fbec 100644
--- a/breath_plot.html
+++ b/breath_plot.html
@@ -26,9 +26,16 @@ Breath Plot: COVID-19 Respiration Analysis Software
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/css/bootstrap.min.css" integrity="sha384-Vkoo8x4CGsO3+Hhxv8T/Q5PaXtkKtu6ug5TOeNV6gBiFeWPGFN9MuhOf23Q9Ifjh" crossorigin="anonymous">
<!-- Load plotly.js into the DOM -->
- <script src='https://cdn.plot.ly/plotly-latest.min.js'></script>
+ <script src='https://cdn.plot.ly/plotly-latest.min.js'></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
+
+ <!-- NOTE: I have included respiration_math.js wholesale below.
+This allows breath_plot to be used locally, which may be valuable
+for some purposes, without a browser pointing at the file, instead
+of served with python -m http.server, Apache, etc.
<script src='/respiration_math.js'></script>
+-->
<title>Public Invention Respiration Analysis</title>
@@ -518,7 +525,717 @@ an interactive or static analysis of a respiration. It's primary purpose is
</div>
</body>
- <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
+
+
+ <!-- NOTE: This is respiration_math.js.
+I HOPE it is separately valuable to anyone doing breath calculations
+in Javascript. For that reason it is also separately in the repo,
+or you can cut this out.
+-->
+
+ <script>
+const CONVERT_PIRDS_TO_SLM = 1/1000;
+
+function unpack(rows, key) {
+ return rows.map(function(row) { return row[key]; });
+}
+
+
+function compute_transitions(vm,flows) {
+ var transitions = [];
+ var state = 0; // Let 1 mean inspiration, -1 mean expiration, 0 neither
+ for(var i = 0; i < flows.length; i++) {
+ var f = flows[i].val * CONVERT_PIRDS_TO_SLM;
+ // var ms = flows[i].ms-first_time;
+ var ms = flows[i].ms;
+ if (state == 0) {
+ if (f > vm) {
+ state = 1;
+ transitions.push({ state: 1, sample: i, ms: ms})
+ } else if (f < -vm) {
+ state = -1;
+ transitions.push({ state: -1, sample: i, ms: ms})
+ }
+ } else if (state == 1) {
+ if (f < -vm) {
+ state = -1;
+ transitions.push({ state: -1, sample: i, ms: ms})
+ } else if (f < vm) {
+ state = 0;
+ transitions.push({ state: 0, sample: i, ms: ms})
+ }
+ } else if (state == -1) {
+ if (f > vm) {
+ state = 1;
+ transitions.push({ state: 1, sample: i, ms: ms})
+ } else if (f > 0) {
+ state = 0;
+ transitions.push({ state: 0, sample: i, ms: ms})
+ }
+ }
+ }
+ return transitions;
+}
+
+// Return, [min,avg,max] pressures (no smoothing)!
+function compute_pressures(secs,samples,alarms,limits) {
+ var pressures = samples.filter(s => s.event == 'M' && s.type == 'D' && (s.loc == 'I' || s.loc == 'A'));
+
+ if (pressures.length == 0) {
+ return [0,0,0,[]];
+ } else {
+ const recent_ms = pressures[pressures.length - 1].ms;
+ var cur_ms = recent_ms;
+ var cnt = 0.0;
+ var i = pressures.length - 1;
+ var cur_sample = pressures[i];
+
+ var min = Number.MAX_VALUE;
+ var max = Number.MIN_VALUE;
+ var sum = 0;
+ var alarms = [];
+ while((i >=0) && (pressures[i].ms > (cur_ms - secs*1000))) {
+ var p = pressures[i].val / 10.0; // this is now cm H2O
+ if (p < min ) {
+ min = p;
+ }
+ if (p > max) {
+ max = p;
+ }
+ sum += p;
+ cnt++;
+ alarms = alarms.concat(check_alarms(limits,"max","h",p,(a,b) =>(a > b),pressures[i].ms));
+ alarms = alarms.concat(check_alarms(limits,"max","l",p,(a,b) =>(a < b),pressures[i].ms));
+ i--;
+ }
+ return [min,sum/cnt,max,alarms];
+ }
+}
+
+
+function compute_fio2_mean(secs,samples) {
+ var oxygens = samples.filter(s => s.event == 'M' && s.type == 'O' && (s.loc == 'I' || s.loc == 'A'));
+
+ if (oxygens.length == 0) {
+ return null;
+ } else {
+ const recent_ms = oxygens[oxygens.length - 1].ms;
+ var cur_ms = recent_ms;
+ var cnt = 0.0;
+ var i = oxygens.length - 1;
+
+ var sum = 0;
+ var alarms = [];
+ while((i >=0) && (oxygens[i].ms > (cur_ms - secs*1000))) {
+ var oxy = oxygens[i].val; // oxygen concentration as a percentage
+ sum += oxy;
+ cnt++;
+ i--;
+ }
+
+ var fio2_avg = sum / cnt;
+
+ return fio2_avg;
+ }
+}
+
+// WARNING! With a low number of breaths, this may be wrong.
+function compute_respiration_rate(secs,samples,transitions,breaths) {
+ // In order to compute the number of breaths
+ // in the last s seconds, I compute those breaths
+ // whose time stamp is s seconds from the most recent sample
+
+ // We will compute respiration rate by counting breaths
+ // and dividing (cnt - 1) by time the first and last inhalation
+ var first_inhale_ms = -1;
+ var last_inhale_ms = -1;
+ if (breaths.length == 0) {
+ return [0,0,0,"NA","NA"];
+ } else {
+ const recent_ms = samples[samples.length - 1].ms;
+ var cur_ms = recent_ms;
+ var cnt = 0.0;
+ var vol_i = 0.0;
+ var vol_e = 0.0;
+ var i = breaths.length - 1;
+ var time_inh = 0;
+ var time_exh = 0;
+ // fully completed inhalation volume does not include the
+ // most recent breath; we need it to be able to accurately
+ // divide by the inhlation_duration.
+ var vol_ci = 0.0;
+
+ var wob = 0.0;
+ var wob_cnt = 0;
+
+ while((i >=0) && (breaths[i].ms > (cur_ms - secs*1000))) {
+ cnt++;
+ vol_i += breaths[i].vol_i;
+ if (i < (breaths.length -1)) {
+ vol_ci += breaths[i].vol_i;
+ }
+ vol_e += breaths[i].vol_e;
+
+ const inh_ms = transitions[breaths[i].trans_begin_inhale].ms;
+ // note i is counting down in this loop...
+ if (last_inhale_ms < 0) last_inhale_ms = inh_ms;
+ first_inhale_ms = inh_ms;
+ const exh_ms = transitions[breaths[i].trans_end_exhale].ms;
+ const zero_ms = transitions[breaths[i].trans_cross_zero].ms;
+ time_inh += (zero_ms - inh_ms);
+ time_exh += (exh_ms - zero_ms);
+
+ if (breaths[i].work != null) {
+ wob += breaths[i].work / breaths[i].vol_i;
+ wob_cnt++;
+ }
+ i--;
+ }
+ if ((cnt > 1) && (first_inhale_ms != last_inhale_ms)) {
+ // I now think this math is specious!!
+ var inhalation_duration = last_inhale_ms - first_inhale_ms;
+ var inhalation_duration_min = inhalation_duration / (60.0 * 1000.0);
+ var rr = (cnt - 1) / inhalation_duration_min;
+ var duration_minutes = secs / 60.0;
+
+ // This is liters per minute. vol_ci is in liters.
+ // inhalation_duration is in ms.
+ var minute_volume = vol_ci / inhalation_duration_min;
+
+ var tidal_volume = 1000.0 * vol_i / cnt;
+
+ var EIratio = (time_inh == 0) ? null : time_exh / time_inh;
+ var WorkOfBreathing_J_per_L = wob / wob_cnt;
+ return [
+ rr,
+ tidal_volume,
+ minute_volume,
+ EIratio,
+ WorkOfBreathing_J_per_L];
+ } else {
+ return [0,0,0,"NA","NA"];
+ }
+ }
+}
+
+
+// produces a set of rising signals, time in ms of the leading edge of the rise and the trailing edge of the rise
+// an array of 2-tuple
+// taip == true implies compute TAIP, else compute TRIP
+// Possibly this routine should be generalized to a general rise-time routine.
+function compute_TAIP_or_TRIP_signals(min,max,pressures,taip) {
+ var pressures = pressures.filter(s => s.event == 'M' && s.type == 'D' && (s.loc == 'I' || s.loc == 'A'));
+ const responseBegin = 0.1;
+ const responseEnd = 0.9;
+
+ var signals = [];
+ var foundMinSignal = false;
+
+ const highFence = (min + (responseEnd * (max - min)))*10;
+ const lowFence = (min + (responseBegin * (max - min)))*10;
+
+ var cur_signal_start;
+ var state = -1; // Let 1 mean rising, -1 mean fallen, 0 risen, but not fallen
+ var first_sample_index = taip ? 0 : pressures.length-1 ;
+ var last_sample_index = taip ? pressures.length-1 : 0;
+ var increment = taip ? 1 : -1;
+ for(var i = first_sample_index; i != last_sample_index; i+=increment) {
+ var p = pressures[i].val;
+ var ms = pressures[i].ms;
+ if (state == -1) {
+ if (p >= lowFence) {
+ state = 1;
+ cur_signal_start = pressures[i];
+ }
+ if (p >= highFence){
+ signals.push([ms,ms]);
+ }
+ } else if (state == 1) {
+ //console.log("state = 1",cur_signal_start); for debugging
+ if (p >= highFence) {
+ signals.push(taip ? [cur_signal_start.ms,ms] : [ms,cur_signal_start.ms])
+ state = 0;
+ } else if (p <= lowFence) {
+ state = -1;
+ cur_signal_start = null;
+ }
+ } else if (state == 0) {
+ if (p <= lowFence) {
+ state = -1;
+ }
+ }
+ }
+ return signals;
+}
+
+function compute_mean_TRIP_or_TAIP_sigs(sigs,min,max,pressures,taip){
+ if (sigs.length == 0){
+ return "NA";
+ } else {
+ var sum = 0;
+ for(var i = 0; i < sigs.length; i++) {
+ sum += sigs[i][1] - sigs[i][0]; // time in ms
+ }
+ return sum / sigs.length;
+ }
+}
+
+function testdata(){
+ //0 (not good enough), 10 (rising), 20 (above threshold) all 10 ms apart
+ //saw tooth function
+ var data = []; // pushing 50 things into it
+ for(var i = 0; i < 10; i++) {
+ var ms = i*5*10;
+ data[i*5+0] = {event:'M',loc:'I',ms:ms + 0,type:'D',val: 0};
+ data[i*5+1] = {event:'M',loc:'I',ms:ms + 10,type:'D',val: 100};
+ data[i*5+2] = {event:'M',loc:'I',ms:ms + 20,type:'D',val: 200};
+ data[i*5+3] = {event:'M',loc:'I',ms:ms + 30,type:'D',val: 100};
+ data[i*5+4] = {event:'M',loc:'I',ms:ms + 40,type:'D',val: 0};
+ }
+ return data;
+}
+
+function testdataSine(period_sm){ // period expressed in # of samples, each sample 10 ms
+ //0 (not good enough), 10 (rising), 20 (above threshold) all 10 ms apart
+ //sine tooth function
+ var data = []; // pushing 50 things into it
+ for(var i = 0; i < 1000; i++) {
+ var ms = i*10;
+ data[i] = {event:'M',loc:'I',ms:ms + 20,type:'D',val: 200*Math.sin(2*Math.PI*i/period_sm)};
+ }
+ return data;
+}
+
+function compute_mean_TRIP_or_TAIP(min,max,samples,taip) {
+ return compute_mean_TRIP_or_TAIP_sigs(
+ compute_TAIP_or_TRIP_signals(min,max,samples,taip),
+ min,max,samples,taip);
+}
+
+function test_compute_TAIP() {
+ var samples = testdata();
+ const TAIP_min = 0; // cm of H2O
+ const TAIP_max = 20; // cm of H2O
+ var TAIP_m = compute_mean_TRIP_or_TAIP(min,max,samples,true);
+ console.assert(TAIP_m == 10);
+ for (i = 50; i<150; i+=10) {
+ var sinewave = testdataSine(i);
+ var TAIP_m = compute_mean_TRIP_or_TAIP(min,max,sinewave,true);
+ }
+}
+
+function compute_current_TAIP(TAIP_min,TAIP_max){ //uses samples from a global var
+ var TAIP_m = compute_mean_TRIP_or_TAIP(TAIP_min,TAIP_max,samples,true);
+ return TAIP_m;
+}
+
+// Because TAIP and TRIP are symmetric when viewed from
+// from the direction of the samples; this tests that
+// as a prelude to computing a single way.
+
+function reverseArray(arr) {
+ var newArray = [];
+ for (var i = arr.length - 1; i >= 0; i--) {
+ newArray.push(arr[i]);
+ }
+ return newArray;
+}
+function test_TRIP_and_TAIP_are_symmetric() {
+ var samples = testdata();
+ var rsamples = reverseArray(samples);
+ const min = 0;
+ const max = 20;
+ var TRIP_m = compute_mean_TRIP_or_TAIP(min,max,samples,false);
+ var TRIP_m_r = -compute_mean_TRIP_or_TAIP(min,max,rsamples,true);
+ console.assert(TRIP_m == TRIP_m_r);
+ console.assert(TRIP_m == 10);
+ for (i = 50; i<150; i+=10) {
+ var sinewave = testdataSine(i);
+ var rsinewave = reverseArray(sinewave);
+ var TRIP_m = compute_mean_TRIP_or_TAIP(min,max,samples,false);
+ var TRIP_m_r = -compute_mean_TRIP_or_TAIP(min,max,rsamples,true);
+ console.assert(TRIP_m == TRIP_m_r);
+ var TAIP_m = compute_mean_TRIP_or_TAIP(min,max,samples,true);
+ var TAIP_m_r = -compute_mean_TRIP_or_TAIP(min,max,rsamples,false);
+ console.assert(TAIP_m == TAIP_m_r);
+ }
+}
+
+function compute_current_TRIP(TRIP_min,TRIP_max, samples)
+{ //uses samples from a global var
+ if (samples.length == 0){
+ return "NA";
+ }
+ else {
+ var TRIP_m = compute_mean_TAIP_or_TRIP(TRIP_min,TRIP_max,false);
+ return TRIP_m;
+ }
+}
+
+
+
+
+ // A routine to calculate work per breath
+function PressureVolumeWork(breath, transitions, samples) {
+ // -1 for quadilateral approximation
+ if (breath.vol_i == 0) {
+ return null;
+ } else {
+ var beginTransition = transitions[breath.trans_begin_inhale];
+ var beginTime_ms = beginTransition.ms;
+ var endTransition = transitions[breath.trans_cross_zero];
+ var endTime_ms = endTransition.ms;
+ var flows = samples.filter(s => s.event == 'M' && s.type == 'F' &&
+ s.ms >= beginTime_ms && s.ms <= endTime_ms);
+ var pressures = samples.filter(s => s.event == 'M' && s.type == 'D' &&
+ (s.loc == 'I' || s.loc == 'A') && s.ms >= beginTime_ms && s.ms <= endTime_ms);
+
+ // Note: The algorithm below relies on the fact that there is
+ // only one flow or pressure with a single ms value; and that
+ // increvementing an index necessarily incremenst the .ms value.
+
+ // Without two samples, we have no duration and can't define
+ // work.
+ if (pressures.length < 2 || flows.length < 2) return null;
+
+ var ct = Math.min(flows[0].ms,pressures[0].ms);
+ var lfp = { val : flows[0].val, ms: flows[0].ms } ; // last flow point
+ var lpp = { val : pressures[0].val, ms: pressures[0].ms }; // last pressure_point
+ var fi = increment_past(flows,flows[0].ms,0); // Index of next flow sample
+ var pi = increment_past(pressures,pressures[0].ms,0); // Index of next pressure sample
+ var w = 0; // current work
+
+ // compute flow at time ms give index and last point
+ // This is just a simple linear interpolation
+ function f(ms,cur,last) {
+ var ms0 = last.ms;
+ var ms1 = cur.ms;
+ return last.val + (cur.val - last.val)*(ms - ms0)/(ms1 - ms0);
+ }
+ function increment_past(array,ms,index) {
+ var begin = index;
+ while(index < array.length && array[index].ms <= ms)
+ index++;
+ if (index == begin) debugger;
+ if (index >= array.length)
+ return null;
+ else
+ return index;
+ }
+
+ // A fundamental invariant:
+ // pressures[pi].ms > lpp.ms
+ // flows[pi].ms > lfp.ms
+ while ((fi + pi) < (flows.length + pressures.length)) {
+ // Invariant always increment fi or pi
+ // fi and pi point to unprocessed value
+ console.assert(pressures[pi].ms > lpp.ms);
+ console.assert(flows[fi].ms > lfp.ms);
+ var ms;
+ if (pressures[pi].ms <= flows[fi].ms) { // process pressure
+ ms = pressures[pi].ms;
+ pi = increment_past(pressures,ms,pi);
+ if (flows[fi].ms <= ms) {
+ fi = increment_past(flows,ms,fi);
+ }
+ } else {
+ ms = flows[fi].ms;
+ fi = increment_past(flows,ms,fi);
+ if (pressures[pi].ms <= ms) {
+ pi = increment_past(pressures,ms,pi);
+ }
+ }
+ if ((fi === null) || (pi === null))
+ break;
+ var dur_s = (ms - ct) / 1000;
+ console.assert(pressures[pi].ms > lpp.ms);
+ console.assert(flows[fi].ms > lfp.ms);
+ var nf = f(ms,flows[fi],lfp);
+ var np = f(ms,pressures[pi],lpp);
+ var f1 = (lfp.val + nf)/2;
+ var p1 = (lpp.val + np)/2;
+ // convert 10ths of cm H2O to pascals..
+ var p1_pa = (p1 * 98.0665) / 10;
+
+ // convert flows in lpm to cubic meters per seconds
+ var f1_m_cubed_per_s = f1 / (1000 * 1000 * 60);
+
+ // work is now in Joules!
+ w += dur_s * p1_pa * f1_m_cubed_per_s;
+ lfp = { val : f1, ms: ms };
+ lpp = { val : p1, ms: ms };
+ ct = ms;
+ }
+ return w;
+ }
+}
+
+// Let's first set up a perfectly square 1-second
+function generate_synthetic_trace() {
+ const SAMPLES_PER_PHASE = 1000;
+ const SAMPLES_MS_PER_SAMPLE = 1;
+ var trace = [];
+ var cur = 0;
+ // p is a probability of occuring.
+ function push_samples(start,num,d,f,pd,pf) {
+ for(var i = start; i < start+num; i++) {
+ if (Math.random() < pd) {
+ trace.push(
+ {
+ event: "M",
+ loc: "A",
+ ms: i,
+ num: 0,
+ type: "D",
+ val: d
+ });
+ }
+ if (Math.random() < pf) {
+ trace.push(
+ {
+ event: "M",
+ loc: "A",
+ ms: i,
+ num: 0,
+ type: "F",
+ val: f
+ });
+ }
+ }
+ }
+ const P1 = 1/2;
+ const P2 = 1/2;
+ push_samples(SAMPLES_PER_PHASE,SAMPLES_PER_PHASE,200,50000,P1,P2);
+ push_samples(0,SAMPLES_PER_PHASE,-200,-50000,P1,P2);
+ push_samples(SAMPLES_PER_PHASE,SAMPLES_PER_PHASE,200,50000,P1,P2);
+ push_samples(SAMPLES_PER_PHASE*2,SAMPLES_PER_PHASE,-200,-50000,P1,P2);
+ push_samples(SAMPLES_PER_PHASE*3,SAMPLES_PER_PHASE,200,50000,P1,P2);
+ return trace;
+}
+
+function nearp(x,y,d) {
+ return Math.abs(x - y) <= d;
+}
+
+function testWorkSynthetic(){ // breaths give us inspiration transition points
+ var samples = generate_synthetic_trace();
+
+ const JOULES_IN_BREATH = 1 * 1961.33 * 50000 / (60e+6);
+
+ var flows = samples.filter(s => s.event == 'M' && s.type == 'F');
+ var first_time = flows[0].ms;
+ var last_time = flows[flows.length - 1].ms;
+ var duration = last_time - first_time;
+ console.log(flows);
+
+
+ const vm = 10;
+ // There is a problem here that this does not create a transition at the beginning.
+ var transitions = compute_transitions(vm,flows);
+ var breaths = compute_breaths_based_without_negative_flow(transitions,flows);
+ console.log(breaths);
+ for(i = 0; i<breaths.length; i++) {
+ var w = PressureVolumeWork(breaths[i], transitions, samples);
+ console.assert((w == null) || (nearp(w,JOULES_IN_BREATH),0.1));
+ console.log("final (Joules) = ",w);
+ }
+ return true;
+}
+
+
+ function testWork(samples){ // breaths give us inspiration transition points
+ var flows = samples.filter(s => s.event == 'M' && s.type == 'F');
+ var first_time = flows[0].ms;
+ var last_time = flows[flows.length - 1].ms;
+ var duration = last_time - first_time;
+ console.log(flows);
+
+ const vm = 10;
+ var transitions = compute_transitions(vm,flows);
+ var breaths = compute_breaths_based_without_negative_flow(transitions,flows);
+ console.log(breaths);
+ for(i = 0; i<breaths.length; i++) {
+ var w = PressureVolumeWork(breaths[i], transitions, samples);
+ console.log(w);
+ }
+ }
+
+
+
+ // This should be in liters...
+ function integrateSamples(a,z,flows) {
+ // -1 for quadilateral approximation
+ var vol = 0;
+ for(var j = a; j < z-1; j++) {
+ // I'll use qadrilateral approximation.
+ // We'll form each quadrilateral between two samples.
+ var ms = flows[j+1].ms - flows[j].ms;
+ var ht = ((flows[j+1].val + flows[j].val )/2) * CONVERT_PIRDS_TO_SLM;
+ // Flow is actually in standard liters per minute,
+ // so to get liters we divide by 60 to it l/s,
+ // and and divde by 1000 to convert ms to seconds.
+ // We could do that here, but will move constants
+ // to end...
+ vol += ms * ht;
+ if (isNaN(vol)) {
+ debugger;
+ }
+ }
+ return vol/(60*1000);
+ }
+
+ // This is based only on inhalations, and
+ // is therefore functional when there is a check valve
+ // in place. Such a system will rarely
+ // have negative flows, and we must mark
+ // the beginning of a breath from a transition to a "1"
+ // state from any other state.
+ // This algorithm is simple: A breath begins on a trasition
+ // to 1 from a not 1 state. This algorithm is susceptible
+ // to "stutter" near the boundary point, but if necessary
+ // a digital filter would sove that; we have not yet found
+ // that level of sophistication needed.
+ // We still want to track zeros, but now must strack them
+ // as a falling signal.
+
+ function compute_breaths_based_without_negative_flow(transitions,flows) {
+ var beg = 0;
+ var zero = 0;
+ var last = 0;
+ var voli = 0;
+ var vole = 0;
+
+ var breaths = [];
+ var expiring = false;
+
+ for(var i = 0; i < transitions.length; i++) {
+ // We're looking for the end of the inhalation here!!
+ if (((i -1) >= 0) && transitions[i-1].state == 1 &&
+ (transitions[i].state == 0 || transitions[i].state == -1 )) {
+ zero = i;
+ }
+ if (expiring && transitions[i].state == 1) {
+ breaths.push({ ms: transitions[i].ms,
+ sample: transitions[i].sample,
+ vol_e: vole,
+ vol_i: voli,
+ trans_begin_inhale: beg,
+ trans_cross_zero: zero,
+ trans_end_exhale: i,
+ }
+ );
+ var w = PressureVolumeWork(breaths[breaths.length-1], transitions, samples);
+ breaths[breaths.length-1].work = w;
+ beg = i;
+ expiring = false;
+ vole = integrateSamples(last,transitions[i].sample,flows);
+
+ last = transitions[i].sample;
+ }
+ if (!expiring && ((transitions[i].state == -1) || (transitions[i].state == 0))) {
+ expiring = true;
+ voli = integrateSamples(last,transitions[i].sample,flows);
+ last = transitions[i].sample;
+ }
+ }
+ return breaths;
+ }
+
+
+// A simple computation of a moving window trace
+// computing [A + -B], where A is volume to left
+// of sample int time window t, and B is volume to right
+// t is in milliseconds
+function computeMovingWindowTrace(samples,t,v) {
+
+ var flows = samples.filter(s => s.event == 'M' && s.type == 'F');
+
+ if (flows.length == 0) {
+ return [[],[]];
+ }
+ var first_time = flows[0].ms;
+ var last_time = flows[flows.length - 1].ms;
+ var duration = last_time - first_time;
+
+ // Here is an idea...
+ // We define you to be in one of three states:
+ // Inspiring, expiring, or neither.
+ // Every transition between these states is logged.
+ // Having two inspirations between an expiration is
+ // weird but could happen.
+ // We record transitions.
+ // When the time series crossed a fixed threshold
+ // or zero, it causes a transition. If you are inspiring,
+ // you have to cross zero to transition to neither,
+ // and you start expiring when you cross the treshold.
+
+ // This is measured in standard liters per minute.
+ const vm = 10; // previously used 4
+
+ // We will model this as a list of transitions.
+ // A breath is any number of inspirations followed by
+ // any number of expirations. (I+)(E+)
+
+ var transitions = compute_transitions(vm,flows);
+
+ // Now that we have transitions, we can apply a
+ // diferrent algorithm to try to define "breaths".
+ // Because a breath is defined as an inspiration
+ // and then an expiration, we will define a breath
+ // as from the first inspiration, until there has
+ // been one expiration, until the next inspiration.
+ var breaths = [];
+ var expiring = false;
+
+ function compute_breaths_based_on_exhalations(transitions) {
+ var beg = 0;
+ var zero = 0;
+ var last = 0;
+ var voli = 0;
+ var vole = 0;
+
+ // This code was robust when I breathed through a mask,
+ // but on clean simulations with negative flow, seemes to
+ // go awry...
+ // It think really it makes more sense to find the first
+ // transition from a non-inspiring state to an inspiring state
+ // and start there.
+ for(var i = 0; i < transitions.length; i++) {
+ // We're looking for the end of the inhalation here!!
+ if (((i -1) >= 0) && transitions[i-1].state == 1 && (transitions[i].state == 0 || transitions[i].state == -1 )) {
+ zero = i;
+ }
+ if (expiring && transitions[i].state == 1) {
+ breaths.push({ ms: transitions[i].ms,
+ sample: transitions[i].sample,
+ vol_e: vole,
+ vol_i: voli,
+ trans_begin_inhale: beg,
+ trans_cross_zero: zero,
+ trans_end_exhale: i,
+ }
+ );
+ var w = PressureVolumeWork(breaths[0], transitions, samples);
+ breaths[0].work = w;
+ beg = i;
+ expiring = false;
+ vole = integrateSamples(last,transitions[i].sample,flows);
+ last = transitions[i].sample;
+ }
+ if (!expiring && (transitions[i].state == -1)) {
+ expiring = true;
+ voli = integrateSamples(last,transitions[i].sample,flows);
+ last = transitions[i].sample;
+ }
+ }
+ }
+
+ breaths = compute_breaths_based_without_negative_flow(transitions,flows);
+
+ return [transitions,breaths];
+}
+ </script>
+
<script>
diff --git a/js/respiration_math.js b/respiration_math.js
similarity index 100%
rename from js/respiration_math.js
rename to respiration_math.js
diff --git a/server.js b/serialserver.js
similarity index 100%
rename from server.js
rename to serialserver.js
--
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