Merge pull request #93 from arcadelab/dev

Dev

Author: benjamindkilleen

deepdrr/annotations/line_annotation.py

@@ -7,6 +7,7 @@
 import json
 import pyvista as pv
 
+from .fiducials import FiducialList
 from .. import geo, utils
 from ..vol import Volume
 
@@ -50,18 +51,16 @@ def __init__(
         self.endpoint = geo.point(endpoint)
         self.volume = volume
         if volume is None:
-            assert (
-                world_from_anatomical is not None
-                and anatomical_coordinate_system.upper() in ["RAS", "LPS"]
-            )
+            assert world_from_anatomical is not None and anatomical_coordinate_system.upper() in [
+                "RAS",
+                "LPS",
+            ]
             self._anatomical_coordinate_system = anatomical_coordinate_system.upper()
             self._world_from_anatomical = geo.frame_transform(world_from_anatomical)
         else:
             self.volume = volume
 
-        assert (
-            self.startpoint.dim == self.endpoint.dim
-        ), "annotation points must have matching dim"
+        assert self.startpoint.dim == self.endpoint.dim, "annotation points must have matching dim"
 
     def __str__(self):
         return f"LineAnnotation({self.startpoint}, {self.endpoint})"
@@ -93,8 +92,7 @@ def from_json(
 
         if volume is None:
             assert (
-                world_from_anatomical is not None
-                and anatomical_coordinate_system is not None
+                world_from_anatomical is not None and anatomical_coordinate_system is not None
             ), "must supply the anatomical transform"
         else:
             anatomical_coordinate_system = volume.anatomical_coordinate_system
@@ -140,6 +138,25 @@ def from_json(
     def from_markup(cls, *args, **kwargs):
         return cls.from_json(*args, **kwargs)
 
+    @classmethod
+    def from_fcsv(cls, path: Path, **kwargs) -> LineAnnotation:
+        """Load a LineAnnotation from a .fcsv file.
+
+        Args:
+            path (Path): Path to the .fcsv file.
+            world_from_anatomical (Optional[geo.FrameTransform], optional): The pose of the volume in world coordinates. Defaults to None.
+
+        Returns:
+            LineAnnotation: The loaded annotation.
+        """
+        fiducial_list = FiducialList.from_fcsv(path)
+        assert len(fiducial_list) == 2, "fcsv file must contain exactly two points"
+        return cls(
+            fiducial_list[0],
+            fiducial_list[1],
+            **kwargs,
+        )
+
     def save(
         self,
         path: str,
@@ -287,6 +304,9 @@ def trajectory_in_world(self) -> geo.Vector3D:
     def direction_in_world(self) -> geo.Vector3D:
         return self.trajectory_in_world.normalized()
 
+    def get_direction(self) -> geo.Vector3D:
+        return self.direction_in_world
+
     def get_mesh(self):
         """Get the mesh in anatomical coordinates."""
         u = self.startpoint
@@ -297,9 +317,7 @@ def get_mesh(self):
         mesh += pv.Sphere(2.5, v)
         return mesh
 
-    def get_mesh_in_world(
-        self, full: bool = True, use_cached: bool = False
-    ) -> pv.PolyData:
+    def get_mesh_in_world(self, full: bool = True, use_cached: bool = False) -> pv.PolyData:
         u = self.startpoint_in_world
         v = self.endpoint_in_world
 

deepdrr/device/device.py

@@ -188,8 +188,8 @@ def get_mesh_in_world(self, full=False, use_cached=True):
             + pv.Line(s, ur)
             + pv.Line(s, bl)
             + pv.Line(s, br)
-            + pv.Line(c, s)
-            + pv.Sphere(5, c)
+            # + pv.Line(c, s) # Line along principle ray
+            # + pv.Sphere(5, c) # Sphere in center of image.
         )
         mesh.transform(geo.get_data(self.world_from_camera3d), inplace=True)
         return mesh

deepdrr/projector/projector.py

@@ -34,10 +34,14 @@
 
     # import pycuda.autoinit # causes problems when running with pytorch concurrently
     import pycuda.driver as cuda
-    from pycuda.autoinit import context
+
+    # from pycuda.autoinit import context # also causes problems
+    from pycuda.autoprimaryctx import context  # retains context across multiple calls
     from pycuda.compiler import SourceModule
 except ImportError:
     log.warning(f"Running without pycuda: projector operations will fail.")
+except RuntimeError as e:
+    log.warning(f"Running without pycuda, possibly in subprocess: {e}")
 
 
 def import_pycuda():

deepdrr/utils/mesh_utils.py

@@ -147,11 +147,12 @@ def voxelize(
     ijk_from_world = world_from_ijk.inv
 
     data = np.zeros((x, y, z), dtype=np.uint8)
-    for p in track(voxels.points, "Rasterizing..."):
-        p = geo.point(p)
-        ijk = ijk_from_world @ p
-        i, j, k = np.array(ijk).astype(int)
-        data[i, j, k] = 1
+    vectors = np.array(voxels.points)
+    A_h = np.hstack((vectors, np.ones((vectors.shape[0], 1))))
+    transform = np.array(ijk_from_world)
+    B = (transform @ A_h.T).T[:, :3]
+    B = np.round(B).astype(int)
+    data[B[:, 0], B[:, 1], B[:, 2]] = 1
 
     return data, world_from_ijk
 

deepdrr/vol/kwire.py

@@ -11,7 +11,7 @@
 
 
 class KWire(Volume):
-    _mesh_material = "titanium"
+    _mesh_material = "iron"
 
     diameter = 2.0  # mm
     tip_in_IJK: geo.Point3D
@@ -54,7 +54,7 @@ def from_example(
         Returns:
             KWire: The example KWire built into DeepDRR.
         """
-        url = "https://livejohnshopkins-my.sharepoint.com/:u:/g/personal/bkillee1_jh_edu/Ec2XGMXg_ItGtYWR_FfqHmUBwXJ1LmLBbbs4J_-3rJJQZg?e=fFWq6f&download=1"
+        url = "https://livejohnshopkins-my.sharepoint.com/:u:/g/personal/bkillee1_jh_edu/ERoEsDbaFj9InktoRKnrT-MBSF2oCOrZ9uyOeWViRx4-Qg?e=s5fofv&download=1"
         md5 = "83ba7b63ebc0912d34ed5880460f81bd"
         filename = "Kwire2.nii.gz"
         path = data_utils.download(url, filename, md5=md5)