enhancements

synthetichealth · May 31, 2024 · a6cd0f9 · a6cd0f9
1 parent 4c7ad1c
commit a6cd0f9
Show file tree

Hide file tree

Showing 8 changed files with 229 additions and 17 deletions.
diff --git a/keep_diabetes_no_dr.json b/keep_diabetes_no_dr.json
@@ -0,0 +1,54 @@
+{
+  "name": "keep_diabetes_no_dr",
+  "remarks": [
+    "A blank module"
+  ],
+  "states": {
+    "Initial": {
+      "type": "Initial",
+      "conditional_transition": [
+        {
+          "transition": "Keep",
+          "condition": {
+            "condition_type": "And",
+            "conditions": [
+              {
+                "condition_type": "Active Condition",
+                "codes": [
+                  {
+                    "system": "SNOMED-CT",
+                    "code": 44054006,
+                    "display": "Diabetes mellitus type 2 (disorder)"
+                  }
+                ]
+              },
+              {
+                "condition_type": "Not",
+                "condition": {
+                  "condition_type": "Active Condition",
+                  "codes": [
+                    {
+                      "system": "SNOMED-CT",
+                      "code": "1551000119108",
+                      "display": "Nonproliferative diabetic retinopathy due to type 2 diabetes mellitus (disorder)"
+                    }
+                  ]
+                }
+              }
+            ]
+          }
+        },
+        {
+          "transition": "Terminal"
+        }
+      ]
+    },
+    "Terminal": {
+      "type": "Terminal"
+    },
+    "Keep": {
+      "type": "Terminal"
+    }
+  },
+  "gmf_version": 2
+}
diff --git a/keep_npdr.json b/keep_npdr.json
@@ -0,0 +1,36 @@
+{
+  "name": "Generated Keep Module",
+  "states": {
+    "Initial": {
+      "type": "Initial",
+      "name": "Initial",
+      "conditional_transition": [
+        {
+          "transition": "Keep",
+          "condition": {
+            "condition_type": "Active Condition",
+            "codes": [
+              {
+                "system": "SNOMED-CT",
+                "code": "1551000119108",
+                "display": "Nonproliferative diabetic retinopathy due to type 2 diabetes mellitus (disorder)"
+              }
+            ]
+          }
+        },
+        {
+          "transition": "Terminal"
+        }
+      ]
+    },
+    "Terminal": {
+      "type": "Terminal",
+      "name": "Terminal"
+    },
+    "Keep": {
+      "type": "Terminal",
+      "name": "Keep"
+    }
+  },
+  "gmf_version": 2
+}
diff --git a/keep_npdr_no_pdr.json b/keep_npdr_no_pdr.json
@@ -0,0 +1,54 @@
+{
+  "name": "keep_npdr_no_pdr",
+  "remarks": [
+    "A blank module"
+  ],
+  "states": {
+    "Initial": {
+      "type": "Initial",
+      "conditional_transition": [
+        {
+          "transition": "Keep",
+          "condition": {
+            "condition_type": "And",
+            "conditions": [
+              {
+                "condition_type": "Active Condition",
+                "codes": [
+                  {
+                    "system": "SNOMED-CT",
+                    "code": "1551000119108",
+                    "display": "Nonproliferative diabetic retinopathy due to type 2 diabetes mellitus (disorder)"
+                  }
+                ]
+              },
+              {
+                "condition_type": "Not",
+                "condition": {
+                  "condition_type": "Active Condition",
+                  "codes": [
+                    {
+                      "system": "SNOMED-CT",
+                      "code": "1501000119109",
+                      "display": "Proliferative diabetic retinopathy due to type II diabetes mellitus (disorder)"
+                    }
+                  ]
+                }
+              }
+            ]
+          }
+        },
+        {
+          "transition": "Terminal"
+        }
+      ]
+    },
+    "Terminal": {
+      "type": "Terminal"
+    },
+    "Keep": {
+      "type": "Terminal"
+    }
+  },
+  "gmf_version": 2
+}
diff --git a/keep_pdr.json b/keep_pdr.json
@@ -0,0 +1,36 @@
+{
+  "name": "Generated Keep Module",
+  "states": {
+    "Initial": {
+      "type": "Initial",
+      "name": "Initial",
+      "conditional_transition": [
+        {
+          "transition": "Keep",
+          "condition": {
+            "condition_type": "Active Condition",
+            "codes": [
+              {
+                "system": "SNOMED-CT",
+                "code": "1501000119109",
+                "display": "Proliferative diabetic retinopathy due to type II diabetes mellitus (disorder)"
+              }
+            ]
+          }
+        },
+        {
+          "transition": "Terminal"
+        }
+      ]
+    },
+    "Terminal": {
+      "type": "Terminal",
+      "name": "Terminal"
+    },
+    "Keep": {
+      "type": "Terminal",
+      "name": "Keep"
+    }
+  },
+  "gmf_version": 2
+}
diff --git a/run_coherent_eyes.sh b/run_coherent_eyes.sh
@@ -0,0 +1,11 @@
+#!/bin/sh
+
+basedir=`pwd`
+
+#./run_synthea -p 10 -a 55-70 -k keep_diabetes.json -fm src/test/resources/flexporter/eyes_on_fhir.yaml
+# pre-processed files are now in ./output
+
+cd src/main/python/coherent-data/
+source ./venv/bin/activate
+
+./venv/bin/python associate_images.py ${basedir}/images/fundus_index.csv ${basedir}/images/oct_index.csv ${basedir}/output/fhir --clean --output ${basedir}/coherent_eyes
diff --git a/src/main/java/org/mitre/synthea/modules/OphthalmicNoteModule.java b/src/main/java/org/mitre/synthea/modules/OphthalmicNoteModule.java
@@ -126,12 +126,17 @@ public boolean process(Person person, long time) {
     boolean edema = (boolean) person.attributes.getOrDefault("macular_edema", false);
 
     if (edema) {
-    	// TODO encounterNote.append("Macula: Flat, no edema or exudates OU\n");
+    	encounterNote.append("Macula: edema present OU\n");
     } else {
     	encounterNote.append("Macula: Flat, no edema or exudates OU\n");
     }
 
-    encounterNote.append("Vessels: Attenuated arterioles with some copper wiring changes OU. No neovascularization noted.\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("Periphery: No tears, holes, or detachments OU");
 
     Procedure firstAntiVEGF = (Procedure)person.attributes.get("first_anti_vegf");

diff --git a/src/main/java/org/mitre/synthea/modules/OphthalmicProgressionModule.java b/src/main/java/org/mitre/synthea/modules/OphthalmicProgressionModule.java
@@ -15,6 +15,12 @@ public OphthalmicProgressionModule() {
   public Module clone() {
     return this;
   }
+
+  /**
+   * Constant factor to represent impact of Diabetic Retinopathy stage on Macular thickness.
+   * Based on https://pubmed.ncbi.nlm.nih.gov/12510717/
+   */
+  public static final double DR_THICKNESS_FACTOR = 1;
 
   @Override
   public boolean process(Person person, long time) {
@@ -23,7 +29,7 @@ public boolean process(Person person, long time) {
     boolean edema = (boolean) person.attributes.getOrDefault("macular_edema", false);
 
     // set visual acuity in LogMAR
-    
+
     // some examples (ref: https://en.wikipedia.org/wiki/LogMAR_chart)
     // Foot LogMAR
     // 20/200 1.00
@@ -45,6 +51,8 @@ public boolean process(Person person, long time) {
 
     // "Pressures of between 11 and 21 mmHg are considered normal"
     // https://www.ncbi.nlm.nih.gov/books/NBK532237/
+    //
+    // https://www.mdpi.com/2077-0383/13/3/676
     if (highIop || (drStage == 4 && person.rand() < 0.001)) {
       // very small chance of this happening
       person.attributes.getOrDefault("high_iop", true);
@@ -83,7 +91,8 @@ public boolean process(Person person, long time) {
      */
 
     // https://iovs.arvojournals.org/article.aspx?articleid=2165526
-    Integer octOffset = (Integer) person.attributes.get("oct_offset");
+    // another source (not used) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1941772/
+    Integer octOffset = (Integer) person.attributes.get("base_oct_offset");
     if (octOffset == null) {
       octOffset = (int) person.rand(-10, 10);
       if (person.attributes.get(Person.GENDER).equals("M")) {
@@ -92,22 +101,28 @@ public boolean process(Person person, long time) {
         // with a mean of 278 ± 23 μm in males and 263 ± 22 μm in females.
         octOffset += 10;
       }
-
-      person.attributes.put("oct_center_point_thickness", 227 + octOffset);
-      person.attributes.put("oct_center_subfield_thickness", 270 + octOffset);
-      person.attributes.put("oct_inner_superior_subfield_thickness", 335 + octOffset);
-      person.attributes.put("oct_inner_nasal_subfield_thickness", 338 + octOffset);
-      person.attributes.put("oct_inner_inferior_subfield_thickness", 332 + octOffset);
-      person.attributes.put("oct_inner_temporal_subfield_thickness", 324 + octOffset);
-      person.attributes.put("oct_outer_superior_subfield_thickness", 290 + octOffset);
-      person.attributes.put("oct_outer_nasal_subfield_thickness", 305 + octOffset);
-      person.attributes.put("oct_outer_inferior_subfield_thickness", 280 + octOffset);
-      person.attributes.put("oct_outer_temporal_subfield_thickness", 279 + octOffset);
-      person.attributes.put("oct_total_volume", 8.4);
+
+      person.attributes.put("base_oct_offset", octOffset);
     }
+
+    //
+    octOffset += (int)(drStage * DR_THICKNESS_FACTOR);
+
+    person.attributes.put("oct_center_point_thickness", 227 + octOffset);
+    person.attributes.put("oct_center_subfield_thickness", 270 + octOffset);
+    person.attributes.put("oct_inner_superior_subfield_thickness", 335 + octOffset);
+    person.attributes.put("oct_inner_nasal_subfield_thickness", 338 + octOffset);
+    person.attributes.put("oct_inner_inferior_subfield_thickness", 332 + octOffset);
+    person.attributes.put("oct_inner_temporal_subfield_thickness", 324 + octOffset);
+    person.attributes.put("oct_outer_superior_subfield_thickness", 290 + octOffset);
+    person.attributes.put("oct_outer_nasal_subfield_thickness", 305 + octOffset);
+    person.attributes.put("oct_outer_inferior_subfield_thickness", 280 + octOffset);
+    person.attributes.put("oct_outer_temporal_subfield_thickness", 279 + octOffset);
+    person.attributes.put("oct_total_volume", 8.4);
 
     // note return options here, see State$CallSubmodule
-    // if we return true, the submodule completed and processing continues to the next state
+    // if we return true, the submodule completed and processing continues to the
+    // next state
     // if we return false, the submodule did not complete (like with a Delay)
     // and will re-process the next timestep.
     return true;

diff --git a/src/main/python/coherent-data b/src/main/python/coherent-data