Add some Visible Human datasets (#679)

* Add some Visible Human datasets

* Rename module

* Fix URL formatting

* Fix module name

docs/source/datasets.rst

@@ -99,16 +99,16 @@ MNI
 :class:`Pediatric`
 ~~~~~~~~~~~~~~~~~~
 
-.. autoclass:: Pediatric
-    :members:
-    :show-inheritance:
-
 .. plot::
 
     import torchio as tio
     subject = tio.datasets.Pediatric((4.5, 8.5))
     subject.plot()
 
+.. autoclass:: Pediatric
+    :members:
+    :show-inheritance:
+
 
 :class:`Sheep`
 ~~~~~~~~~~~~~~
@@ -134,6 +134,46 @@ MNI
     :show-inheritance:
 
 
+.. currentmodule:: torchio.datasets.visible_human
+
+
+Visible Human Project
+---------------------
+
+The `Visible Human Project <https://www.nlm.nih.gov/research/visible/visible_human.html>`_
+is an effort to create a detailed data set of cross-sectional photographs of
+the human body, in order to facilitate anatomy visualization applications.
+It is used as a tool for the progression of medical findings, in which these
+findings link anatomy to its audiences.
+A male and a female cadaver were cut into thin slices which were then
+photographed and digitized (from `Wikipedia <https://en.wikipedia.org/wiki/Visible_Human_Project>`_).
+
+:class:`VisibleMale`
+~~~~~~~~~~~~~~~~~~~~
+
+.. plot::
+
+    import torchio as tio
+    tio.datasets.VisibleMale('Shoulder').plot()
+
+.. autoclass:: VisibleMale
+    :members:
+    :show-inheritance:
+
+
+:class:`VisibleFemale`
+~~~~~~~~~~~~~~~~~~~~~~
+
+.. plot::
+
+    import torchio as tio
+    tio.datasets.VisibleFemale('Shoulder').plot()
+
+.. autoclass:: VisibleFemale
+    :members:
+    :show-inheritance:
+
+
 ITK-SNAP
 --------
 
@@ -144,6 +184,11 @@ ITK-SNAP
 :class:`BrainTumor`
 ~~~~~~~~~~~~~~~~~~~
 
+.. plot::
+
+    import torchio as tio
+    tio.datasets.BrainTumor().plot()
+
 .. autoclass:: BrainTumor
     :members:
     :show-inheritance:

torchio/datasets/__init__.py

@@ -5,6 +5,7 @@
 from .ixi import IXI, IXITiny
 from .rsna_miccai import RSNAMICCAI
 from .itk_snap import BrainTumor, T1T2, AorticValve
+from .visible_human import VisibleFemale, VisibleMale
 from .mni import Colin27, Sheep, Pediatric, ICBM2009CNonlinearSymmetric
 
 
@@ -23,4 +24,6 @@
     'Sheep',
     'Pediatric',
     'ICBM2009CNonlinearSymmetric',
+    'VisibleFemale',
+    'VisibleMale',
 ]

torchio/datasets/visible_human.py

@@ -0,0 +1,75 @@
+import abc
+import tempfile
+
+from .. import Subject, ScalarImage
+from ..utils import get_torchio_cache_dir
+from ..download import download_and_extract_archive
+
+
+class VisibleHuman(abc.ABC, Subject):
+
+    URL = 'https://mri.radiology.uiowa.edu/website_documents/visible_human_tar_files/{}{}.tar.gz'  # noqa: E501, FS003
+
+    def __init__(self, part: str):
+        self.part = self._parse_part(part)
+        if not self.cache_part_dir.is_dir():
+            tempdir = tempfile.gettempdir()
+            filename = f'{self.__class__.__name__}-{self.part}.tar.gz'
+            download_and_extract_archive(
+                self.url,
+                tempdir,
+                filename=filename,
+                extract_root=self.cache_class_dir,
+                remove_finished=True,
+            )
+        super().__init__({self.part.lower(): ScalarImage(self.cache_part_dir)})
+
+    @property
+    def cache_class_dir(self):
+        return get_torchio_cache_dir() / self.__class__.__name__
+
+    @property
+    def cache_part_dir(self):
+        return self.cache_class_dir / self.part
+
+    @property
+    def url(self):
+        return self.URL.format(self.PREFIX, self.part)
+
+    def _parse_part(self, part: str) -> None:
+        part_capital = part.capitalize()
+        if part_capital not in self.PARTS:
+            message = f'Part "{part}" not in available parts: {self.PARTS}'
+            raise ValueError(message)
+        return part_capital
+
+
+class VisibleMale(VisibleHuman):
+    """Visible Male CT Datasets.
+
+    Args:
+        part: Can be ``'Head'``, ``'Hip'``, ``'Pelvis'`` or ``'Shoulder'``.
+    """
+
+    PREFIX = 'VHMCT1mm_'
+    PARTS = (
+        'Head',
+        'Hip',
+        'Pelvis',
+        'Shoulder',
+    )
+
+
+class VisibleFemale(VisibleHuman):
+    """Visible Female CT Datasets.
+
+    Args:
+        part: Can be ``'Ankle'``, ``'Head'``, ``'Hip'``, ``'Knee'``,
+            ``'Pelvis'`` or ``'Shoulder'``.
+    """
+
+    PREFIX = 'VHF-'
+    PARTS = VisibleMale.PARTS + (
+        'Ankle',
+        'Knee',
+    )