Merge 91700cf into a5aae08

README.md

@@ -72,6 +72,17 @@ for volume_file in ashs.HippocampalSubfieldsVolumeFile.find('/my/ashs/subjects')
     print(volume_file.read_volumes_dataframe())
 ```
 
+#### Intracranial Volume
+
+```python
+from freesurfer_volume_reader import ashs
+
+for volume_file in ashs.IntracranialVolumeFile.find('/my/ashs/subjects'):
+    print(volume_file.subject)
+    print(volume_file.read_volume_mm3())
+    print(volume_file.read_volume_series())
+```
+
 ### Freesurfer & ASHS
 
 ```sh

examples/ashs.ipynb

@@ -17,10 +17,45 @@
     "SUBJECT = 'bert'"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Intracranial Volume"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "1234560.0 mm^3\n"
+     ]
+    }
+   ],
+   "source": [
+    "from freesurfer_volume_reader.ashs import IntracranialVolumeFile\n",
+    "\n",
+    "for volume_file in IntracranialVolumeFile.find(SUBJECTS_DIR):\n",
+    "    if volume_file.subject == SUBJECT:\n",
+    "        print(volume_file.read_volume_mm3(), 'mm^3')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Subfield Volumes"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -31,7 +66,7 @@
        " 'bert_left_corr_nogray_volumes.txt']"
       ]
      },
-     "execution_count": 2,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -47,7 +82,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -132,7 +167,7 @@
        "4      PHC     2345.878    bert      right     nogray"
       ]
      },
-     "execution_count": 3,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -145,7 +180,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -157,7 +192,7 @@
        "Name: correction, dtype: int64"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -169,7 +204,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -282,7 +317,7 @@
        "SUB          457.789   457.781   457.780   457.781"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -295,7 +330,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -1093,10 +1128,10 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.axes._subplots.AxesSubplot at 0x7ff6715a74e0>"
+       "<matplotlib.axes._subplots.AxesSubplot at 0x7fb6ca200208>"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 7,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1133,7 +1168,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

examples/compare_ashs_freesurfer_hipposf.ipynb

@@ -115,9 +115,9 @@
    ],
    "source": [
     "import os, pandas\n",
-    "from freesurfer_volume_reader import VolumeFile, ashs, freesurfer\n",
+    "from freesurfer_volume_reader import SubfieldVolumeFile, ashs, freesurfer\n",
     "\n",
-    "def read_volume_file(volume_file: VolumeFile) -> pandas.DataFrame:\n",
+    "def read_volume_file(volume_file: SubfieldVolumeFile) -> pandas.DataFrame:\n",
     "    volume_frame = volume_file.read_volumes_dataframe()\n",
     "    volume_frame['source_basename'] = os.path.basename(volume_file.absolute_path)\n",
     "    return volume_frame\n",

freesurfer_volume_reader/__init__.py

@@ -45,20 +45,23 @@ class VolumeFile(metaclass=abc.ABCMeta):
     def absolute_path(self):
         raise NotImplementedError()
 
-    @abc.abstractmethod
-    def read_volumes_mm3(self) -> typing.Dict[str, float]:
-        raise NotImplementedError()
-
-    @abc.abstractmethod
-    def read_volumes_dataframe(self) -> pandas.DataFrame:
-        raise NotImplementedError()
-
     @classmethod
     def find(cls, root_dir_path: str,
              filename_regex: typing.Optional[typing.Pattern] = None,
-             ) -> typing.Iterator['VolumeFile']:
+             ) -> typing.Iterator['SubfieldVolumeFile']:
         if not filename_regex:
             filename_regex = cls.FILENAME_REGEX
         for dirpath, _, filenames in os.walk(root_dir_path):
             for filename in filter(filename_regex.search, filenames):
                 yield cls(path=os.path.join(dirpath, filename))
+
+
+class SubfieldVolumeFile(VolumeFile):
+
+    @abc.abstractmethod
+    def read_volumes_mm3(self) -> typing.Dict[str, float]:
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def read_volumes_dataframe(self) -> pandas.DataFrame:
+        raise NotImplementedError()

freesurfer_volume_reader/ashs.py

@@ -9,6 +9,13 @@
 >>>     print(volume_file.subject, volume_file.hemisphere, volume_file.correction)
 >>>     print(volume_file.read_volumes_mm3())
 >>>     print(volume_file.read_volumes_dataframe())
+
+>>> from freesurfer_volume_reader.ashs import IntracranialVolumeFile
+>>>
+>>> for volume_file in IntracranialVolumeFile('/my/ashs/subjects'):
+>>>     print(volume_file.subject)
+>>>     print(volume_file.read_volume_mm3())
+>>>     print(volume_file.read_volume_series())
 """
 
 import os
@@ -20,7 +27,38 @@
 import freesurfer_volume_reader
 
 
-class HippocampalSubfieldsVolumeFile(freesurfer_volume_reader.VolumeFile):
+class IntracranialVolumeFile(freesurfer_volume_reader.VolumeFile):
+
+    FILENAME_REGEX = re.compile(r'^(?P<s>\w+)_icv.txt$')
+
+    def __init__(self, path: str):
+        self._absolute_path = os.path.abspath(path)
+        filename_match = self.FILENAME_REGEX.match(os.path.basename(path))
+        assert filename_match, self._absolute_path
+        self.subject = filename_match.groupdict()['s']
+
+    @property
+    def absolute_path(self):
+        return self._absolute_path
+
+    def read_volume_mm3(self) -> float:
+        with open(self.absolute_path, 'r') as volume_file:
+            subject, icv = volume_file.read().rstrip().split(' ')
+            assert subject == self.subject, (subject, self.subject)
+            return float(icv)
+
+    def read_volume_series(self) -> pandas.Series:
+        return pandas.Series(
+            data=[self.read_volume_mm3()],
+            name='volume_mm^3',
+            index=pandas.Index(
+                data=[self.subject],
+                name='subject',
+            ),
+        )
+
+
+class HippocampalSubfieldsVolumeFile(freesurfer_volume_reader.SubfieldVolumeFile):
 
     # https://sites.google.com/site/hipposubfields/tutorial#TOC-Viewing-ASHS-Segmentation-Results
     FILENAME_PATTERN = r'^(?P<s>\w+)_(?P<h>left|right)' \

freesurfer_volume_reader/freesurfer.py

@@ -20,7 +20,7 @@
 import freesurfer_volume_reader
 
 
-class HippocampalSubfieldsVolumeFile(freesurfer_volume_reader.VolumeFile):
+class HippocampalSubfieldsVolumeFile(freesurfer_volume_reader.SubfieldVolumeFile):
 
     # https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
     FILENAME_PATTERN = r'^(?P<h>[lr])h\.hippoSfVolumes' \