Add: CXR support

inst/extdata/config/concept-dict.R

@@ -3322,6 +3322,175 @@ cfg <- list(
       )
     ),
     class = c("unt_cncpt", "num_cncpt")
+  ),
+  viewposition = list(
+    levels = c("frontal", "lateral", "decubitus", "oblique", "special", "unknown"),
+    class = "fct_cncpt",
+    description = "Grouped X-ray view positions",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(
+          table = "cxrmetadata",
+          val_var = "viewposition",
+          callback = "apply_map(
+            c(
+              'PA' = 'frontal', 'AP' = 'frontal', 'AP AXIAL' = 'frontal',
+              'LATERAL' = 'lateral', 'LL' = 'lateral', 'XTABLE LATERAL' = 'lateral',
+              'PA LLD' = 'decubitus', 'AP LLD' = 'decubitus', 'AP RLD' = 'decubitus', 'PA RLD' = 'decubitus',
+              'LAO' = 'oblique', 'RAO' = 'oblique', 'LPO' = 'oblique',
+              'SWIMMERS' = 'special'
+            )
+          )",
+          class = "col_itm"
+        )
+      )
+    )
+  ),
+  study_id = list(
+    description = "unique identifier for the subject",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrmetadata", val_var = "study_id", class = "col_itm")
+      )
+    )
+  ),
+  dicom_id = list(
+    description = "unique identifier for the image",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrmetadata", sub_var = "dicom_id", regex = "^.*$",
+          class = "rgx_itm")
+      )
+    )
+  ),
+  atelectasis = list(
+    description = "Atelectasis",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "atelectasis", class = "col_itm")
+      )
+    )
+  ),
+  cardiomegaly = list(
+    description = "Cardiomegaly",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "cardiomegaly", class = "col_itm")
+      )
+    )
+  ),
+  consolidation = list(
+    description = "Consolidation",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "consolidation", class = "col_itm")
+      )
+    )
+  ),
+  edema = list(
+    description = "Edema",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "edema", class = "col_itm")
+      )
+    )
+  ),
+  enlarged_cardiomediastinum = list(
+    description = "Enlarged Cardiomediastinum",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "enlarged_cardiomediastinum", class = "col_itm")
+      )
+    )
+  ),
+  fracture = list(
+    description = "Fracture",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "fracture", class = "col_itm")
+      )
+    )
+  ),
+  lung_lesion = list(
+    description = "Lung Lesion",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "lung_lesion", class = "col_itm")
+      )
+    )
+  ),
+  lung_opacity = list(
+    description = "Lung Opacity",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "lung_opacity", class = "col_itm")
+      )
+    )
+  ),
+  no_finding = list(
+    description = "If all other chexpert labels are 0 or -1, no finding is 1",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "no_finding", class = "col_itm")
+      )
+    )
+  ),
+  pleural_effusion = list(
+    description = "Pleural Effusion",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "pleural_effusion", class = "col_itm")
+      )
+    )
+  ),
+  pleural_other = list(
+    description = "Pleural Other",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "pleural_other", class = "col_itm")
+      )
+    )
+  ),
+  pneumonia = list(
+    description = "Pneumonia",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "pneumonia", class = "col_itm")
+      )
+    )
+  ),
+  pneumothorax = list(
+    description = "Pneumothorax",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "pneumothorax", class = "col_itm")
+      )
+    )
+  ),
+  support_devices = list(
+    description = "Support Devices",
+    category = "imaging",
+    sources = list(
+      miiv = list(
+        list(table = "cxrchexpert", val_var = "support_devices", class = "col_itm")
+      )
+    )
   )
 )