Add ability to resample subject while reading (#363)

* Enable diffdrr.data.Subject to be resampled

* Fix docs

diffdrr/data.py

@@ -50,6 +50,7 @@ def read(
     fiducials: torch.Tensor = None,  # 3D fiducials in world coordinates
     transform: RigidTransform = None,  # RigidTransform to apply to the volume's affine
     center_volume: bool = True,  # Move the volume's isocenter to the world origin
+    resample_target=None,  # Resampling resolution argument passed to torchio.transforms.Resample
     **kwargs,  # Any additional information to be stored in the torchio.Subject
 ) -> Subject:
     """
@@ -172,6 +173,11 @@ def read(
         except:
             subject.density.data = subject.density.data * mask
 
+    # Apply resample
+    if resample_target is not None:
+        resample = Resample(resample_target)
+        subject = resample(subject)
+
     return subject
 
 # %% ../notebooks/api/03_data.ipynb 7

notebooks/api/03_data.ipynb

@@ -63,6 +63,7 @@
     "from a variety of formats and orientations. We canonicalize all volumes to \n",
     "the RAS+ coordinate space. In addition to reading an input volume, you can also pass\n",
     "the following to `diffdrr.data.read` when loading a subject:\n",
+    "\n",
     "- `labelmap` : a 3D segmentation of the input volume\n",
     "- `labels` : a subset of structures from the labelmap that you want to render\n",
     "- `orientation` : a frame-of-reference change for the C-arm (currently, \"AP\" and \"PA\" are supported)\n",
@@ -121,6 +122,7 @@
     "    fiducials: torch.Tensor = None,  # 3D fiducials in world coordinates\n",
     "    transform: RigidTransform = None,  # RigidTransform to apply to the volume's affine\n",
     "    center_volume: bool = True,  # Move the volume's isocenter to the world origin\n",
+    "    resample_target=None,  # Resampling resolution argument passed to torchio.transforms.Resample\n",
     "    **kwargs,  # Any additional information to be stored in the torchio.Subject\n",
     ") -> Subject:\n",
     "    \"\"\"\n",
@@ -243,6 +245,11 @@
     "        except:\n",
     "            subject.density.data = subject.density.data * mask\n",
     "\n",
+    "    # Apply resample\n",
+    "    if resample_target is not None:\n",
+    "        resample = Resample(resample_target)\n",
+    "        subject = resample(subject)\n",
+    "\n",
     "    return subject"
    ]
   },

notebooks/index.ipynb

@@ -58,7 +58,8 @@
     "\n",
     "```zsh\n",
     "git clone https://github.com/eigenvivek/DiffDRR.git --depth 1\n",
-    "pip install -e 'DiffDRR/[dev]'"
+    "pip install -e 'DiffDRR/[dev]'\n",
+    "```"
    ]
   },
   {