Medical imaging tutorial (#172)

* made dataloader work for dicom

* tutorial working

* made xray training work

* made tutorial work correctly

* fastai2 update

* added SIIM_SMALL dataset

* restored vision/core

* fixed ImageBlock import

* integrated SIIM dataset into medical tutorial

* implemented DICOM import in vision.core

* added SIIM folder structure image and updated medical imaging tutorial

* completed medical imaging tutorial

* cleaned repository for pull request

* implemented PILDicom and updated medical tutorial

* removed pydicom from vision.core

* created variable to store tta output

* reverted dcmread function

fastai2/data/checks.txt

@@ -210,5 +210,9 @@
   "http://files.grouplens.org/datasets/movielens/ml-100k.zip": [
     4924029,
     "39f6af2d7ea4e117f8838e4a302fec70"
+  ],
+  "http://files.vedavimedical.com/siim_small.tgz": [
+    33277183,
+    "bb55c5ba9aa9eb9dcac9e0f29581b52c"
   ]
 }

fastai2/data/external.py

@@ -119,6 +119,9 @@ class URLs():
     PASCAL_2007        = f'{S3_IMAGELOC}pascal_2007.tgz'
     PASCAL_2012        = f'{S3_IMAGELOC}pascal_2012.tgz'
 
+    # Medical Imaging datasets
+    SIIM_SMALL     = 'http://files.vedavimedical.com/siim_small.tgz'
+
     #Pretrained models
     OPENAI_TRANSFORMER = f'{S3_MODEL}transformer.tgz'
     WT103_FWD          = f'{S3_MODEL}wt103-fwd.tgz'

fastai2/medical/imaging.py

@@ -1,8 +1,8 @@
 # AUTOGENERATED! DO NOT EDIT! File to edit: nbs/60_medical.imaging.ipynb (unless otherwise specified).
 
-__all__ = ['DcmDataset', 'DcmTag', 'DcmMultiValue', 'dcmread', 'get_dicom_files', 'get_dicom_files', 'pixels',
-           'scaled_px', 'array_freqhist_bins', 'dicom_windows', 'TensorCTScan', 'PILCTScan', 'show', 'uniform_blur2d',
-           'gauss_blur2d', 'mask2bbox', 'crop_resize', 'shape']
+__all__ = ['DcmDataset', 'DcmTag', 'DcmMultiValue', 'dcmread', 'get_dicom_files', 'get_dicom_files', 'dcmread',
+           'TensorDicom', 'PILDicom', 'pixels', 'scaled_px', 'array_freqhist_bins', 'dicom_windows', 'TensorCTScan',
+           'PILCTScan', 'show', 'uniform_blur2d', 'gauss_blur2d', 'mask2bbox', 'crop_resize', 'shape']
 
 # Cell
 from ..basics import *
@@ -26,9 +26,25 @@ def get_dicom_files(path, recurse=True, folders=None):
     return get_files(path, extensions=[".dcm"], recurse=recurse, folders=folders)
 
 # Cell
-@patch
-def dcmread(self:Path, force = False):
-    return pydicom.dcmread(str(self), force)
+def dcmread(fn:(Path,str), force = False):
+    "Open a `DICOM` file"
+    return pydicom.dcmread(str(fn), force)
+
+# Cell
+class TensorDicom(TensorImage): _show_args = {'cmap':'gray'}
+
+# Cell
+class PILDicom(PILBase):
+    _open_args,_tensor_cls,_show_args = {},TensorDicom,TensorDicom._show_args
+    @classmethod
+    def create(cls, fn:(Path,str), mode=None)->None:
+        "Open a `DICOM file` from path `fn` and load it as a `PIL Image`"
+        im = Image.fromarray(dcmread(fn).pixel_array)
+        im.load()
+        im = im._new(im.im)
+        return cls(im.convert(mode) if mode else im)
+
+PILDicom._tensor_cls = TensorDicom
 
 # Cell
 @patch_property

nbs/04_data.external.ipynb

@@ -213,6 +213,9 @@
     "    LSUN_BEDROOMS      = f'{S3_IMAGE}bedroom.tgz'\n",
     "    PASCAL_2007        = f'{S3_IMAGELOC}pascal_2007.tgz'\n",
     "    PASCAL_2012        = f'{S3_IMAGELOC}pascal_2012.tgz'\n",
+    "    \n",
+    "    # Medical Imaging datasets\n",
+    "    SIIM_SMALL     = 'http://files.vedavimedical.com/siim_small.tgz'\n",
     "\n",
     "    #Pretrained models\n",
     "    OPENAI_TRANSFORMER = f'{S3_MODEL}transformer.tgz'\n",
@@ -624,7 +627,18 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [],
+      "text/plain": [
+       "<IPython.core.display.HTML object>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "#hide\n",
     "# url = URLs.IMAGEWANG_160\n",

nbs/60_medical.imaging.ipynb

@@ -87,9 +87,39 @@
    "outputs": [],
    "source": [
     "#export\n",
-    "@patch\n",
-    "def dcmread(self:Path, force = False):\n",
-    "    return pydicom.dcmread(str(self), force)"
+    "def dcmread(fn:(Path,str), force = False):\n",
+    "    \"Open a `DICOM` file\"\n",
+    "    return pydicom.dcmread(str(fn), force)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#export\n",
+    "class TensorDicom(TensorImage): _show_args = {'cmap':'gray'}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#export\n",
+    "class PILDicom(PILBase):\n",
+    "    _open_args,_tensor_cls,_show_args = {},TensorDicom,TensorDicom._show_args\n",
+    "    @classmethod\n",
+    "    def create(cls, fn:(Path,str), mode=None)->None:\n",
+    "        \"Open a `DICOM file` from path `fn` and load it as a `PIL Image`\"\n",
+    "        im = Image.fromarray(dcmread(fn).pixel_array) \n",
+    "        im.load()\n",
+    "        im = im._new(im.im)\n",
+    "        return cls(im.convert(mode) if mode else im)\n",
+    "\n",
+    "PILDicom._tensor_cls = TensorDicom"
    ]
   },
   {