QOL updates (#21)

* Reorient CT to be PA

* Update environment.yml

* Bump version

* Fix savepath

* Make downloads verbose

* Update DiffDRR version

Author: eigenvivek

diffdrrdata/__init__.py

@@ -1 +1 @@
-__version__ = "0.0.5"
+__version__ = "0.0.6"

diffdrrdata/deepfluoro.py

@@ -97,6 +97,7 @@ def __getitem__(self, idx):
             .compose(self.world2camera.inverse())
             .compose(pose)
             .compose(self.anatomical2world)
+            .compose(self.rot_180)
         )
         if self.rot_180_for_up(idx):
             img = torch.rot90(img, k=2)
@@ -118,11 +119,11 @@ def parse_volume(subject, bone_attenuation_multiplier, labels):
     # Get all parts of the volume
     volume = subject["vol/pixels"][:]
     volume = np.swapaxes(volume, 0, 2).copy()
-    volume = torch.from_numpy(volume).unsqueeze(0)  # .flip(1).flip(2)
+    volume = torch.from_numpy(volume).unsqueeze(0).flip(1).flip(2)
 
     mask = subject["vol-seg/image/pixels"][:]
     mask = np.swapaxes(mask, 0, 2).copy()
-    mask = torch.from_numpy(mask).unsqueeze(0)  # .flip(1).flip(2)
+    mask = torch.from_numpy(mask).unsqueeze(0).flip(1).flip(2)
 
     affine = np.eye(4)
     affine[:3, :3] = subject["vol/dir-mat"][:]
@@ -166,6 +167,8 @@ def parse_volume(subject, bone_attenuation_multiplier, labels):
         label_def=defns,
         fiducials=fiducials,
     )
+    reorient = RigidTransform(torch.diag(torch.tensor([-1.0, -1.0, 1.0, 1.0])))
+    subject.fiducials = reorient(subject.fiducials)
 
     return subject, anatomical2world
 

diffdrrdata/utils.py

@@ -11,8 +11,8 @@
 
 # %% ../notebooks/02_utils.ipynb 4
 def get_data_home() -> Path:
-    """By default, datasets are saved in `~/diffdrr_data`."""
-    data_home = Path("~/diffdrr_data").expanduser()
+    """By default, datasets are saved in `~/user/diffdrr_data`."""
+    data_home = data_home = Path("~/user/diffdrr_data").expanduser()
     data_home.mkdir(exist_ok=True)
     return data_home
 
@@ -33,7 +33,7 @@ def load_file(filename: str):
         try:
             f = h5py.File(file_path)
         except FileNotFoundError:
-            print(f"Downloading DeepFluoro dataset (~2.5 GB) to {file_path}")
+            print(f"Downloading Ljubljana dataset (~1.0 GB) to {file_path}")
             download_ljubljana()
             f = h5py.File(file_path)
     else:
@@ -47,7 +47,7 @@ def download_deepfluoro():
     download_link = "http://archive.data.jhu.edu/api/access/datafile/:persistentId/?persistentId=doi:10.7281/T1/IFSXNV/EAN9GH"
     download_path = data_home / "ipcai_2020_full_res_data.zip"
     subprocess.run(
-        f"wget -q --no-check-certificate -O {download_path} {download_link}".split(" ")
+        f"wget --no-check-certificate -O {download_path} {download_link}".split(" ")
     )
     subprocess.run(f"unzip -o {download_path} -d {data_home}".split(" "))
     subprocess.run(f"rm {download_path}".split(" "))
@@ -58,7 +58,7 @@ def download_ljubljana():
     download_link = "https://drive.usercontent.google.com/download?id=1x585pGLI8QGk21qZ2oGwwQ9LMJ09Tqrx&confirm=xxx"
     download_path = data_home / "ljubljana.zip"
     subprocess.run(
-        f"curl -s {download_link} -o {download_path} ".split(" ")
+        f"curl {download_link} -o {download_path} ".split(" ")
     )
     subprocess.run(f"unzip -o {download_path} -d {data_home}".split(" "))
     subprocess.run(f"rm {download_path}".split(" "))

environment.yml

@@ -3,6 +3,21 @@ channels:
   - conda-forge
 dependencies:
   - pip
+  - pytorch>=2.2
+  - einops
+  - torchvision
+  - torchio
+  - kornia
+  - timm
+  - numpy
+  - matplotlib
+  - seaborn
+  - imageio
+  - fastcore
+  - scipy
+  - tqdm
+  - pyvista
+  - vtk
   - h5py
   - pip:
     - diffdrr

notebooks/00_deepfluoro.ipynb

@@ -56,8 +56,8 @@
    "source": [
     "#| export\n",
     "def get_data_home() -> Path:\n",
-    "    \"\"\"By default, datasets are saved in `~/diffdrr_data`.\"\"\"\n",
-    "    data_home = Path(\"~/diffdrr_data\").expanduser()\n",
+    "    \"\"\"By default, datasets are saved in `~/user/diffdrr_data`.\"\"\"\n",
+    "    data_home = data_home = Path(\"~/user/diffdrr_data\").expanduser()\n",
     "    data_home.mkdir(exist_ok=True)\n",
     "    return data_home"
    ]
@@ -86,7 +86,7 @@
     "        try:\n",
     "            f = h5py.File(file_path)\n",
     "        except FileNotFoundError:\n",
-    "            print(f\"Downloading DeepFluoro dataset (~2.5 GB) to {file_path}\")\n",
+    "            print(f\"Downloading Ljubljana dataset (~1.0 GB) to {file_path}\")\n",
     "            download_ljubljana()\n",
     "            f = h5py.File(file_path)\n",
     "    else:\n",
@@ -108,7 +108,7 @@
     "    download_link = \"http://archive.data.jhu.edu/api/access/datafile/:persistentId/?persistentId=doi:10.7281/T1/IFSXNV/EAN9GH\"\n",
     "    download_path = data_home / \"ipcai_2020_full_res_data.zip\"\n",
     "    subprocess.run(\n",
-    "        f\"wget -q --no-check-certificate -O {download_path} {download_link}\".split(\" \")\n",
+    "        f\"wget --no-check-certificate -O {download_path} {download_link}\".split(\" \")\n",
     "    )\n",
     "    subprocess.run(f\"unzip -o {download_path} -d {data_home}\".split(\" \"))\n",
     "    subprocess.run(f\"rm {download_path}\".split(\" \"))"
@@ -127,7 +127,7 @@
     "    download_link = \"https://drive.usercontent.google.com/download?id=1x585pGLI8QGk21qZ2oGwwQ9LMJ09Tqrx&confirm=xxx\"\n",
     "    download_path = data_home / \"ljubljana.zip\"\n",
     "    subprocess.run(\n",
-    "        f\"curl -s {download_link} -o {download_path} \".split(\" \")\n",
+    "        f\"curl {download_link} -o {download_path} \".split(\" \")\n",
     "    )\n",
     "    subprocess.run(f\"unzip -o {download_path} -d {data_home}\".split(\" \"))\n",
     "    subprocess.run(f\"rm {download_path}\".split(\" \"))"

notebooks/02_utils.ipynb

@@ -1,7 +1,7 @@
 [DEFAULT]
 repo = DiffDRR-Datasets
 lib_name = diffdrrdata
-version = 0.0.5
+version = 0.0.6
 min_python = 3.7
 license = apache2
 black_formatting = False
@@ -26,7 +26,7 @@ keywords = nbdev jupyter notebook python
 language = English
 status = 3
 user = eigenvivek
-requirements = diffdrr>=0.4.6 h5py
+requirements = diffdrr>=0.5.0 h5py
 readme_nb = index.ipynb
 allowed_metadata_keys = 
 allowed_cell_metadata_keys =