patch-neural-representation update + bug fix related to differences in image and patch spacing (#52)

Author: Lena235711

example-data/patch-neural-representation.json

@@ -1,33 +1,69 @@
 [
-    {
-        "meta": {
-            "spacing": [0.5, 0.5, 1],
-            "patch-size": [224, 224, 3]
-        },
-        "patches": [
-            {
-                "features": [
-                    0.345,
-                    0.234
-                ],
-                "coordinates": [
-                    1,
-                    2,
-                    3
-                ]
-            },
-            {
-                "features": [
-                    0.234,
-                    0.623
-                ],
-                "coordinates": [
-                    1,
-                    2,
-                    3
-                ]
-            }
+  {
+    "meta": {
+      "image-size": [
+        640,
+        640,
+        31
+      ],
+      "patch-size": [
+        224,
+        224,
+        16
+      ],
+      "image-origin": [
+        -109.22891616821,
+        -76.614260508237,
+        -84.293114437337
+      ],
+      "image-spacing": [
+        0.28125,
+        0.28125,
+        3.2999999825580133
+      ],
+      "patch-spacing": [
+        0.5,
+        0.5,
+        1.0
+      ],
+      "image-direction": [
+        1.0,
+        0.0,
+        0.0,
+        0.0,
+        0.9198214989417033,
+        0.3923371128056057,
+        0.0,
+        -0.3923371128056057,
+        0.9198214989417033
+      ]
+    },
+    "title": "transverse-t2-prostate-mri",
+    "patches": [
+      {
+        "features": [
+          318.71170479910717,
+          230.66145469236733,
+          345.0
         ],
-        "title": "generic-medical-image"
-    }
+        "coordinates": [
+          -113.72891616821,
+          -80.75345725347466,
+          -82.52759742971178
+        ]
+      },
+      {
+        "features": [
+          246.62460887675383,
+          200.84204573309574,
+          265.0
+        ],
+        "coordinates": [
+          -113.72891616821,
+          -60.0380578068289,
+          -33.961022542286074
+        ]
+      }
+    ]
+  }
 ]

src/unicorn_baseline/vision/radiology/main.py

@@ -88,7 +88,7 @@ def extract_features_segmentation(
         image = sitk.DICOMOrient(image, desiredCoordinateOrientation="LPS")
 
     print(f"Extracting patches from image")
-    patches, coordinates = extract_patches(
+    patches, coordinates, image = extract_patches(
         image=image,
         patch_size=patch_size,
         spacing=patch_spacing,

src/unicorn_baseline/vision/radiology/patch_extraction.py

@@ -87,4 +87,4 @@ def extract_patches(
         )
         coordinates.append(world_coordinates)
 
-    return patches, coordinates
+    return patches, coordinates, image