Restructure repo

AIM-Harvard · Sep 22, 2022 · 7b9d97f · 7b9d97f
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diff --git a/__init__.py b/__init__.py
@@ -1 +1 @@
-from .aime import *
+from .aimi import *
diff --git a/aimi/totalsegmentator/config/dicomseg_metadata.json b/aimi/totalsegmentator/config/dicomseg_metadata.json
@@ -1 +1,221 @@
-{"ContentCreatorName": "Reader1", "ClinicalTrialSeriesID": "Session1", "ClinicalTrialTimePointID": "1", "SeriesDescription": "Segmentation", "SeriesNumber": "300", "InstanceNumber": "1", "segmentAttributes": [[{"labelID": 1, "SegmentAlgorithmType": "AUTOMATIC", "SegmentedPropertyCategoryCodeSequence": {"CodeValue": "123037004", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Anatomical Structure"}, "SegmentDescription": "A_Aorta", "SegmentAlgorithmName": "TotalSegmentator", "SegmentedPropertyTypeCodeSequence": {"CodeValue": "15825003", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Aorta"}, "recommendedDisplayRGBValue": [224, 97, 76]}], [{"labelID": 1, "SegmentAlgorithmType": "AUTOMATIC", "SegmentedPropertyCategoryCodeSequence": {"CodeValue": "123037004", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Anatomical Structure"}, "SegmentDescription": "A_Pulmonary", "SegmentAlgorithmName": "TotalSegmentator", "SegmentedPropertyTypeCodeSequence": {"CodeValue": "81040000", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Pulmonary artery"}, "recommendedDisplayRGBValue": [0, 122, 171]}], [{"labelID": 1, "SegmentAlgorithmType": "AUTOMATIC", "SegmentedPropertyCategoryCodeSequence": {"CodeValue": "123037004", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Anatomical Structure"}, "SegmentDescription": "Atrium_L", "SegmentAlgorithmName": "TotalSegmentator", "SegmentedPropertyTypeCodeSequence": {"CodeValue": "82471001", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Left atrium"}, "recommendedDisplayRGBValue": [203, 108, 81]}], [{"labelID": 1, "SegmentAlgorithmType": "AUTOMATIC", "SegmentedPropertyCategoryCodeSequence": {"CodeValue": "123037004", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Anatomical Structure"}, "SegmentDescription": "Atrium_R", "SegmentAlgorithmName": "TotalSegmentator", "SegmentedPropertyTypeCodeSequence": {"CodeValue": "73829009", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Right atrium"}, "recommendedDisplayRGBValue": [210, 155, 89]}], [{"labelID": 1, "SegmentAlgorithmType": "AUTOMATIC", "SegmentedPropertyCategoryCodeSequence": {"CodeValue": "123037004", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Anatomical Structure"}, "SegmentDescription": "Ventricle_L", "SegmentAlgorithmName": "TotalSegmentator", "SegmentedPropertyTypeCodeSequence": {"CodeValue": "87878005", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Left ventricle"}, "recommendedDisplayRGBValue": [152, 55, 13]}], [{"labelID": 1, "SegmentAlgorithmType": "AUTOMATIC", "SegmentedPropertyCategoryCodeSequence": {"CodeValue": "123037004", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Anatomical Structure"}, "SegmentDescription": "Ventricle_L_Chamber", "SegmentAlgorithmName": "TotalSegmentator", "SegmentedPropertyTypeCodeSequence": {"CodeValue": "87878006", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Left ventricle chamber without myocardium"}, "recommendedDisplayRGBValue": [152, 55, 13]}], [{"labelID": 1, "SegmentAlgorithmType": "AUTOMATIC", "SegmentedPropertyCategoryCodeSequence": {"CodeValue": "123037004", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Anatomical Structure"}, "SegmentDescription": "Ventricle_L_Myocardium", "SegmentAlgorithmName": "TotalSegmentator", "SegmentedPropertyTypeCodeSequence": {"CodeValue": "87878007", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Myocardium around left ventricle"}, "recommendedDisplayRGBValue": [223, 150, 119]}], [{"labelID": 1, "SegmentAlgorithmType": "AUTOMATIC", "SegmentedPropertyCategoryCodeSequence": {"CodeValue": "123037004", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Anatomical Structure"}, "SegmentDescription": "Ventricle_R", "SegmentAlgorithmName": "TotalSegmentator", "SegmentedPropertyTypeCodeSequence": {"CodeValue": "53085002", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Right ventricle"}, "recommendedDisplayRGBValue": [181, 85, 57]}], [{"labelID": 1, "SegmentAlgorithmType": "AUTOMATIC", "SegmentedPropertyCategoryCodeSequence": {"CodeValue": "123037004", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Anatomical Structure"}, "SegmentDescription": "V_Venacava_I", "SegmentAlgorithmName": "TotalSegmentator", "SegmentedPropertyTypeCodeSequence": {"CodeValue": "64131007", "CodingSchemeDesignator": "SCT", "CodeMeaning": "Inferior vena cava"}, "recommendedDisplayRGBValue": [57, 109, 169]}]], "ContentLabel": "SEGMENTATION", "ContentDescription": "Image segmentation", "ClinicalTrialCoordinatingCenterName": "dcmqi", "BodyPartExamined": ""}
+{
+  "ContentCreatorName": "IDC",
+  "ClinicalTrialSeriesID": "0",
+  "ClinicalTrialTimePointID": "1",
+  "SeriesDescription": "Segmentation",
+  "SeriesNumber": "42",
+  "InstanceNumber": "1",
+  "BodyPartExamined": "Chest",
+  "segmentAttributes": [
+    [
+      {
+        "labelID": 1,
+        "SegmentAlgorithmType": "AUTOMATIC",
+        "SegmentedPropertyCategoryCodeSequence": {
+          "CodeValue": "123037004",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Anatomical Structure"
+        },
+        "SegmentDescription": "A_Aorta",
+        "SegmentAlgorithmName": "TotalSegmentator",
+        "SegmentedPropertyTypeCodeSequence": {
+          "CodeValue": "15825003",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Aorta"
+        },
+        "recommendedDisplayRGBValue": [
+          224,
+          97,
+          76
+        ]
+      }
+    ],
+    [
+      {
+        "labelID": 1,
+        "SegmentAlgorithmType": "AUTOMATIC",
+        "SegmentedPropertyCategoryCodeSequence": {
+          "CodeValue": "123037004",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Anatomical Structure"
+        },
+        "SegmentDescription": "A_Pulmonary",
+        "SegmentAlgorithmName": "TotalSegmentator",
+        "SegmentedPropertyTypeCodeSequence": {
+          "CodeValue": "81040000",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Pulmonary artery"
+        },
+        "recommendedDisplayRGBValue": [
+          0,
+          122,
+          171
+        ]
+      }
+    ],
+    [
+      {
+        "labelID": 1,
+        "SegmentAlgorithmType": "AUTOMATIC",
+        "SegmentedPropertyCategoryCodeSequence": {
+          "CodeValue": "123037004",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Anatomical Structure"
+        },
+        "SegmentDescription": "Atrium_L",
+        "SegmentAlgorithmName": "TotalSegmentator",
+        "SegmentedPropertyTypeCodeSequence": {
+          "CodeValue": "82471001",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Left atrium"
+        },
+        "recommendedDisplayRGBValue": [
+          203,
+          108,
+          81
+        ]
+      }
+    ],
+    [
+      {
+        "labelID": 1,
+        "SegmentAlgorithmType": "AUTOMATIC",
+        "SegmentedPropertyCategoryCodeSequence": {
+          "CodeValue": "123037004",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Anatomical Structure"
+        },
+        "SegmentDescription": "Atrium_R",
+        "SegmentAlgorithmName": "TotalSegmentator",
+        "SegmentedPropertyTypeCodeSequence": {
+          "CodeValue": "73829009",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Right atrium"
+        },
+        "recommendedDisplayRGBValue": [
+          210,
+          155,
+          89
+        ]
+      }
+    ],
+    [
+      {
+        "labelID": 1,
+        "SegmentAlgorithmType": "AUTOMATIC",
+        "SegmentedPropertyCategoryCodeSequence": {
+          "CodeValue": "123037004",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Anatomical Structure"
+        },
+        "SegmentDescription": "Ventricle_L",
+        "SegmentAlgorithmName": "TotalSegmentator",
+        "SegmentedPropertyTypeCodeSequence": {
+          "CodeValue": "87878005",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Left ventricle"
+        },
+        "recommendedDisplayRGBValue": [
+          152,
+          55,
+          13
+        ]
+      }
+    ],
+    [
+      {
+        "labelID": 1,
+        "SegmentAlgorithmType": "AUTOMATIC",
+        "SegmentedPropertyCategoryCodeSequence": {
+          "CodeValue": "123037004",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Anatomical Structure"
+        },
+        "SegmentDescription": "Ventricle_L_Chamber",
+        "SegmentAlgorithmName": "TotalSegmentator",
+        "SegmentedPropertyTypeCodeSequence": {
+          "CodeValue": "87878006",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Left ventricle chamber without myocardium"
+        },
+        "recommendedDisplayRGBValue": [
+          152,
+          55,
+          13
+        ]
+      }
+    ],
+    [
+      {
+        "labelID": 1,
+        "SegmentAlgorithmType": "AUTOMATIC",
+        "SegmentedPropertyCategoryCodeSequence": {
+          "CodeValue": "123037004",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Anatomical Structure"
+        },
+        "SegmentDescription": "Ventricle_L_Myocardium",
+        "SegmentAlgorithmName": "TotalSegmentator",
+        "SegmentedPropertyTypeCodeSequence": {
+          "CodeValue": "87878007",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Myocardium around left ventricle"
+        },
+        "recommendedDisplayRGBValue": [
+          223,
+          150,
+          119
+        ]
+      }
+    ],
+    [
+      {
+        "labelID": 1,
+        "SegmentAlgorithmType": "AUTOMATIC",
+        "SegmentedPropertyCategoryCodeSequence": {
+          "CodeValue": "123037004",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Anatomical Structure"
+        },
+        "SegmentDescription": "Ventricle_R",
+        "SegmentAlgorithmName": "TotalSegmentator",
+        "SegmentedPropertyTypeCodeSequence": {
+          "CodeValue": "53085002",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Right ventricle"
+        },
+        "recommendedDisplayRGBValue": [
+          181,
+          85,
+          57
+        ]
+      }
+    ],
+    [
+      {
+        "labelID": 1,
+        "SegmentAlgorithmType": "AUTOMATIC",
+        "SegmentedPropertyCategoryCodeSequence": {
+          "CodeValue": "123037004",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Anatomical Structure"
+        },
+        "SegmentDescription": "V_Venacava_I",
+        "SegmentAlgorithmName": "TotalSegmentator",
+        "SegmentedPropertyTypeCodeSequence": {
+          "CodeValue": "64131007",
+          "CodingSchemeDesignator": "SCT",
+          "CodeMeaning": "Inferior vena cava"
+        },
+        "recommendedDisplayRGBValue": [
+          57,
+          109,
+          169
+        ]
+      }
+    ]
+  ],
+  "ContentLabel": "SEGMENTATION",
+  "ContentDescription": "Image segmentation",
+  "ClinicalTrialCoordinatingCenterName": "dcmqi",
+}