Add transform to apply orientation to guidance: Updated (#1853)

* Add transform to apply orientation to guidance

Signed-off-by: Andres <[email protected]>

* Remove log sentence

Signed-off-by: Andres <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Remove unnecessary flag

Signed-off-by: Andres <[email protected]>

* Update for loop and affine argument

Signed-off-by: Andres <[email protected]>

* Add ref_image arg

Signed-off-by: Andres <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Fix pre-commit code formatting

Signed-off-by: José Frias <[email protected]>

---------

Signed-off-by: Andres <[email protected]>
Signed-off-by: José Frias <[email protected]>
Co-authored-by: Andres <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: 3 people

sample-apps/radiology/lib/infers/deepedit.py

@@ -11,7 +11,7 @@
 import logging
 from typing import Callable, Sequence, Union
 
-from lib.transforms.transforms import GetCentroidsd
+from lib.transforms.transforms import GetCentroidsd, OrientationGuidanceMultipleLabelDeepEditd
 from monai.apps.deepedit.transforms import (
     AddGuidanceFromPointsDeepEditd,
     AddGuidanceSignalDeepEditd,
@@ -88,6 +88,7 @@ def pre_transforms(self, data=None):
         if self.type == InferType.DEEPEDIT:
             t.extend(
                 [
+                    OrientationGuidanceMultipleLabelDeepEditd(ref_image="image", label_names=self.labels),
                     AddGuidanceFromPointsDeepEditd(ref_image="image", guidance="guidance", label_names=self.labels),
                     Resized(keys="image", spatial_size=self.spatial_size, mode="area"),
                     ResizeGuidanceMultipleLabelDeepEditd(guidance="guidance", ref_image="image"),

sample-apps/radiology/lib/transforms/transforms.py

@@ -14,6 +14,7 @@
 
 import numpy as np
 import torch
+from einops import rearrange
 from monai.config import KeysCollection, NdarrayOrTensor
 from monai.data import MetaTensor
 from monai.networks.layers import GaussianFilter
@@ -511,6 +512,39 @@ def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> Dict[Hashable, N
         return d
 
 
+class OrientationGuidanceMultipleLabelDeepEditd(Transform):
+    def __init__(self, ref_image: str, label_names=None):
+        """
+        Convert the guidance to the RAS orientation
+        """
+        self.ref_image = ref_image
+        self.label_names = label_names
+
+    def transform_points(self, point, affine):
+        """transform point to the coordinates of the transformed image
+        point: numpy array [bs, N, 3]
+        """
+        bs, N = point.shape[:2]
+        point = np.concatenate((point, np.ones((bs, N, 1))), axis=-1)
+        point = rearrange(point, "b n d -> d (b n)")
+        point = affine @ point
+        point = rearrange(point, "d (b n)-> b n d", b=bs)[:, :, :3]
+        return point
+
+    def __call__(self, data):
+        d: Dict = dict(data)
+        for key_label in self.label_names.keys():
+            points = d.get(key_label, [])
+            if len(points) < 1:
+                continue
+            reoriented_points = self.transform_points(
+                np.array(points)[None],
+                np.linalg.inv(d[self.ref_image].meta["affine"].numpy()) @ d[self.ref_image].meta["original_affine"],
+            )
+            d[key_label] = reoriented_points[0]
+        return d
+
+
 def get_guidance_tensor_for_key_label(data, key_label, device) -> torch.Tensor:
     """Makes sure the guidance is in a tensor format."""
     tmp_gui = data.get(key_label, torch.tensor([], dtype=torch.int32, device=device))