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improvements based on review feedback
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@dehall
dehall committed Aug 8, 2024
1 parent a099464 commit 49f16a0
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Showing 9 changed files with 700 additions and 225 deletions.
2 changes: 1 addition & 1 deletion src/main/java/org/mitre/synthea/engine/State.java
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Expand Up @@ -2065,7 +2065,7 @@ private void duplicateInstances(RandomNumberGenerator random, long time,

// Create the new instances
for (int j = 0; j < s.instances.size(); j++) {
instanceClones.add(s.instances.get(i).clone());
instanceClones.add(s.instances.get(j).clone());
}
s.instances = instanceClones;
}
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2 changes: 1 addition & 1 deletion src/main/java/org/mitre/synthea/helpers/RandomNumberGenerator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@ public default double rand(double[] range) {
* @param choices The options to be returned.
* @return One of the options randomly selected.
*/
public default String rand(String[] choices) {
public default String rand(String... choices) {
int value = randInt(choices.length);
return choices[value];
}
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243 changes: 204 additions & 39 deletions src/main/java/org/mitre/synthea/modules/OphthalmicNoteModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,12 @@
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import org.mitre.synthea.engine.Module;
import org.mitre.synthea.export.ExportHelper;
import org.mitre.synthea.world.agents.Person;
import org.mitre.synthea.world.concepts.HealthRecord;
import org.mitre.synthea.world.concepts.HealthRecord.Encounter;
import org.mitre.synthea.world.concepts.HealthRecord.Observation;
import org.mitre.synthea.world.concepts.HealthRecord.Procedure;
Expand Down Expand Up @@ -70,9 +72,11 @@ public boolean process(Person person, long time) {
stable = false;
}

if (drStage == 0) {
encounterNote.append("No current signs of diabetic retinopathy, both eyes\n");
} else {
long currentStageFirstObserved = drStageFirstObservedDate.get(drStage);


if (drStage > 0) {
encounterNote.append("\nDiagnosis History:");
boolean first = true;
for (int i = 1 ; i <= 4 ; i++) {
Long observed = drStageFirstObservedDate.get(i);
Expand All @@ -85,61 +89,65 @@ public boolean process(Person person, long time) {
}
}
}
encounterNote.append('\n');
}

Procedure panRetinalLaser = (Procedure) person.attributes.get("panretinal_laser");
List<Procedure> gridLaserHistory = (List<Procedure>)person.attributes.get("grid_laser_history");
Procedure firstAntiVEGF = (Procedure)person.attributes.get("first_anti_vegf");

if (gridLaserHistory == null) {
gridLaserHistory = new ArrayList<>();
person.attributes.put("grid_laser_history", gridLaserHistory);
}

if (panRetinalLaser != null || !gridLaserHistory.isEmpty()) {
encounterNote.append("Procedure History:\n");
if (panRetinalLaser != null || !gridLaserHistory.isEmpty() || firstAntiVEGF != null) {
encounterNote.append(person.rand("\nProcedure History:\n", "\nPast Surgical History:\n"));
if (panRetinalLaser != null) {
encounterNote.append("Panretinal laser ").append(ExportHelper.dateFromTimestamp(panRetinalLaser.start)).append('\n');
} else {
}
if (!gridLaserHistory.isEmpty()) {
encounterNote.append("Grid laser");
for (Procedure g : gridLaserHistory) {
encounterNote.append(", ").append(ExportHelper.dateFromTimestamp(g.start));
}
encounterNote.append('\n');
}
if (firstAntiVEGF != null) {
encounterNote.append("Anti-VEGF first performed ").append(ExportHelper.dateFromTimestamp(firstAntiVEGF.start)).append('\n');
}
}
encounterNote.append('\n');

double va = (double) person.attributes.get("visual_acuity_logmar");
// logmar to 20/x = 20*10^(logmar)
long denom = Math.round(20 * Math.pow(10, va));
encounterNote.append("Visual Acuity: 20/").append(denom).append(" OD, 20/").append(denom).append(" OS\n");
recordVA(person, encounterNote);
recordIOP(person, encounterNote);
encounterNote.append('\n');

int iop = (int) person.attributes.get("intraocular_pressure");
encounterNote.append("Intraocular Pressure (IOP): ").append(iop).append(" mmHg OD, ").append(iop).append(" mmHg OS\n");

// an example from chatGPT
encounterNote.append("Pupils: Equal, round, reactive to light and accommodation\n");
encounterNote.append("Pupils: Equal, round, reactive to light\n");
encounterNote.append("Extraocular Movements: Full and smooth\n");
encounterNote.append("Confrontation Visual Fields: Full to finger count OU\n");
encounterNote.append("Anterior Segment: Normal lids, lashes, and conjunctiva OU. Cornea clear OU. Anterior chamber deep and quiet OU. Iris normal architecture OU. Lens clear OU.\n");
encounterNote.append("Dilated Fundus Examination:\n");
encounterNote.append("Optic Disc: Pink, well-defined margins, cup-to-disc ratio 0.3 OU\n");

boolean edema = (boolean) person.attributes.getOrDefault("macular_edema", false);

if (edema) {
encounterNote.append("Macula: edema present OU\n");
encounterNote.append("Anterior Segment: Normal lids, lashes, and conjunctiva OU.\n Cornea clear OU. Anterior chamber deep and quiet OU. Iris normal OU. ");
int age = person.ageInYears(time);
if (age > 70) {
encounterNote.append("Moderate nuclear sclerosis observed OU.");
} else if (age > 50) {
encounterNote.append("Early nuclear sclerosis bilaterally.");
} else {
encounterNote.append("Macula: Flat, no edema or exudates OU\n");
encounterNote.append("Lens clear OU.");
}
encounterNote.append('\n');

if (drStage >= 3) {
encounterNote.append("Vessels: Attenuated arterioles with some copper wiring changes OU. Neovascularization present.\n");
} else {
encounterNote.append("Vessels: Attenuated arterioles with some copper wiring changes OU. No neovascularization noted.\n");
encounterNote.append(person.rand("Dilated Fundus Examination:\n", "Posterior Segment:\n"));

Map<String, String> drSymptoms = (Map<String, String>) person.attributes.get("diabetic_retinopathy_symptoms");
if (drSymptoms == null) {
drSymptoms = new HashMap<>();
}

encounterNote.append("Periphery: No tears, holes, or detachments OU");

Procedure firstAntiVEGF = (Procedure)person.attributes.get("first_anti_vegf");
recordOpticDisc(person, encounterNote, drStage, stable, drSymptoms);
recordMacula(person, encounterNote, drStage, stable, drSymptoms, gridLaserHistory, currentStageFirstObserved);
recordVessels(person, encounterNote, drStage, stable, drSymptoms);
recordPeriphery(person, encounterNote, drStage, stable, drSymptoms, panRetinalLaser, currentStageFirstObserved);

for (Procedure p : currEncounter.procedures) {
switch (p.type) {
Expand Down Expand Up @@ -191,32 +199,39 @@ public boolean process(Person person, long time) {
person.attributes.put("first_anti_vegf", firstAntiVEGF);
}
break;

}
}

encounterNote.append("\nAssessment: \n");
if (currEncounter.conditions != null && !currEncounter.conditions.isEmpty()) {
for (HealthRecord.Entry c : currEncounter.conditions) {
encounterNote.append(" - ").append(c.codes.get(0).display).append('\n');
}
} else if (drStage == 0) {
encounterNote.append("No current signs of diabetic retinopathy, both eyes\n");
} else {
encounterNote.append(" - ").append(STAGES[drStage]);
}


Observation hba1c = person.record.getLatestObservation("4548-4");

if (((Double)hba1c.value) > 6.5 && person.rand() > .7) {
if (drStage == 0) {
encounterNote.append("Discussed the nature of DM and its potential effects on the eye in detail with the patient. Discussed the importance of maintaining strict glycemic control to avoid developing retinopathy.\n");
encounterNote.append("\nDiscussed the nature of DM and its potential effects on the eye in detail with the patient. \nDiscussed the importance of maintaining strict glycemic control to avoid developing retinopathy.\n");
} else {
encounterNote.append("I discussed the effects of elevated glucose on the eye, and the importance of strict control in preventing progression of retinopathy.\n");
encounterNote.append("\nI discussed the effects of elevated glucose on the eye, \nand the importance of strict control in preventing progression of retinopathy.\n");
}
}

if (prevEncounter == null) {
encounterNote.append("Discussed the signs of vision changes that require immediate medical attention.\n");
encounterNote.append("\nDiscussed the signs of vision changes that require immediate medical attention.\n");
}

// TODO: line about follow-up

currEncounter.note = encounterNote.toString();

// System.out.println(currEncounter.note);
// System.out.println("\n");


person.attributes.put("previous_ophthalmic_encounter", currEncounter);

// note return options here, see State$CallSubmodule
Expand All @@ -225,4 +240,154 @@ public boolean process(Person person, long time) {
// and will re-process the next timestep.
return true;
}

private static void recordVA(Person person, StringBuilder encounterNote) {
double va = (double) person.attributes.get("visual_acuity_logmar");
// logmar to 20/x = 20*10^(logmar)
long denom = Math.round(20 * Math.pow(10, va));
encounterNote.append("Visual Acuity: 20/").append(denom).append(" OD, 20/").append(denom).append(" OS\n");
}

private static void recordIOP(Person person, StringBuilder encounterNote) {
int iop = (int) person.attributes.get("intraocular_pressure");
encounterNote.append("Intraocular Pressure (IOP): ").append(iop).append(" mmHg OD, ").append(iop).append(" mmHg OS\n");
}



private static void recordOpticDisc(Person person, StringBuilder encounterNote, int drStage, boolean stable, Map<String, String> drSymptoms) {

String opticDiscSymptom = drSymptoms.get("optic_disc");

if (opticDiscSymptom == null || !stable) {
switch(drStage) {
case 0:
opticDiscSymptom = "Normal, no edema or pallor";
break;
case 1:
opticDiscSymptom = person.rand("Pink, well-defined margins, cup-to-disc ratio 0.3 OU", "Normal, no edema or pallor");
break;
case 2:
case 3:
opticDiscSymptom = "Normal in color and contour, no signs of neovascularization or optic disc edema.";
break;
case 4:
opticDiscSymptom = "NVD extending from the disc margins into the adjacent retina";
break;

}
drSymptoms.put("optic_disc", opticDiscSymptom);
}

encounterNote.append("Optic Disc: ").append(opticDiscSymptom).append('\n');

}


private static void recordMacula(Person person, StringBuilder encounterNote, int drStage, boolean stable,
Map<String, String> drSymptoms, List<Procedure> gridLaserHistory, long currentStageFirstObserved) {
boolean edema = (boolean) person.attributes.getOrDefault("macular_edema", false);

String maculaSymptom = drSymptoms.get("macula");

if (stable && !gridLaserHistory.isEmpty()
&& gridLaserHistory.get(gridLaserHistory.size() - 1).start > currentStageFirstObserved) {
maculaSymptom = "Evidence of grid laser scars, no active edema, no exudates";
} else if (maculaSymptom == null || !stable) {

if (edema) {
switch(drStage) {
// 0 and 1 can't get edema in this model
case 2:
maculaSymptom = "Mild edema noted OU.";
break;
case 3:
case 4:
maculaSymptom = "Severe edema noted OU, with hard exudates present.";
}

} else {
switch(drStage) {
case 0:
case 1:
case 2:
maculaSymptom = person.rand("Flat, no edema or exudates OU.", "No edema or exudates OU.", "Clear, no edema or exudates OU");
break;
case 3:
case 4:
maculaSymptom = "No CSME, but presence of microaneurysms near the macula.";
break;
}
}

if (!gridLaserHistory.isEmpty()) {
maculaSymptom += " Evidence of prior grid laser scars.";
}


drSymptoms.put("macula", maculaSymptom);
}

encounterNote.append("Macula: ").append(maculaSymptom).append('\n');
}

private static void recordVessels(Person person, StringBuilder encounterNote, int drStage, boolean stable, Map<String, String> drSymptoms) {
String vesselsSymptom = drSymptoms.get("vessels");

if (vesselsSymptom == null || !stable) {
switch(drStage) {
case 0:
vesselsSymptom = "Normal, no microaneurysms, hemorrhages, or venous beading observed.";
break;
case 1:
vesselsSymptom = person.rand("Mild microaneurysms noted in both eyes.", "Microaneurysms OU.") + " No neovascularization noted.";
break;
case 2:
vesselsSymptom = "Presence of microaneurysms and mild venous beading.";
break;
case 3:
vesselsSymptom = "Presence of microaneurysms, intraretinal hemorrhages, IRMA, and mild venous beading.";
break;
case 4:
vesselsSymptom = "Numerous microaneurysms, intraretinal hemorrhages, IRMA, and venous beading OU";
break;
}
drSymptoms.put("vessels", vesselsSymptom);
}

encounterNote.append("Vessels: ").append(vesselsSymptom).append('\n');
}

private static void recordPeriphery(Person person, StringBuilder encounterNote, int drStage, boolean stable, Map<String, String> drSymptoms, Procedure panRetinalLaser, long currentStageFirstObserved) {
String peripherySymptom = drSymptoms.get("periphery");

if (stable && panRetinalLaser != null && panRetinalLaser.start > currentStageFirstObserved) {
peripherySymptom = "Evidence of scattered laser scars from previous PRP, no new hemorrhages or microaneurysms, no neovascularization";
} else if (peripherySymptom == null || !stable) {
switch(drStage) {
case 0:
case 1:
peripherySymptom = person.rand("No signs of retinal neovascularization, microaneurysms, or areas of non-perfusion.", "No tears, holes, or detachments OU");
break;
case 2:
case 3:
peripherySymptom = "Scattered microaneurysms and dot-blot hemorrhages, no signs of neovascularization.";
break;
case 4:
peripherySymptom = "Neovascularization OU, no retinal detachment.";
break;
}

if (panRetinalLaser != null) {
peripherySymptom += " Evidence of scattered laser scars from prior PRP.";
}


drSymptoms.put("periphery", peripherySymptom);
}



encounterNote.append("Periphery: ").append(peripherySymptom).append('\n');
}
}
32 changes: 28 additions & 4 deletions src/main/java/org/mitre/synthea/modules/OphthalmicProgressionModule.java
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Expand Up @@ -50,12 +50,36 @@ public boolean process(Person person, long time) {
// 20/40 0.30
// 20/20 0.00
// 20/16 −0.10
if (edema) {
person.attributes.put("visual_acuity_logmar", 0.30);
} else {
person.attributes.put("visual_acuity_logmar", 0.0);

// pick a "baseline" VA for this individual.
// real VA is distributed roughly normally/poisson
// "Modelling visual acuity distributions to inform a simplified cost effectiveness analysis",
// Hirst A, Perera C, Hughes R
// https://www.ispor.org/docs/default-source/euro2023/ee758---modelling-visual-acuity-distributions-to-inform-a-simplified-cost-effectiveness-analysis-v10131936-pdf.pdf
// for simplicity we'll stick to a uniform distribution -0.1 to 0.1 (20/16 to 20/24)

Double baselineVA = (Double)person.attributes.get("visual_acuity_baseline");
if (baselineVA == null) {
baselineVA = person.rand(-0.1, 0.1);
}

// eyes are usually at their best around age 25-30 then very slowly worsen
// (~ 0.05 / 10 yrs)
// https://www.researchgate.net/figure/The-distribution-of-visual-acuity-among-eyes-of-223-normal-healthy-subjects-ranging-from_fig4_50289760
double ageAdjustment = ((person.ageInYears(time) - 30.0) / 10.0) * 0.05;

double edemaAdjustment = edema && drStage == 4 ? 0.20 : 0.0;

double finalVA = baselineVA + ageAdjustment + edemaAdjustment;

// round to 1 decimal place
finalVA = Math.round(finalVA / 10.0) * 10.0;

// limit to max of 1.0, though it shouldn't get that high anyway
finalVA = Math.min(finalVA, 1.0);

person.attributes.put("visual_acuity_logmar", finalVA);

// set intraocular pressure in mmHG

boolean highIop = (boolean) person.attributes.getOrDefault("high_iop", false);
Expand Down
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