added resample

bioMONAI/_modidx.py

@@ -7,6 +7,7 @@
                 'lib_path': 'bioMONAI'},
   'syms': { 'bioMONAI.callbacks': {'bioMONAI.callbacks.foo': ('callbacks.html#foo', 'bioMONAI/callbacks.py')},
             'bioMONAI.core': { 'bioMONAI.core.attributesFromDict': ('core.html#attributesfromdict', 'bioMONAI/core.py'),
+                               'bioMONAI.core.img2Tensor': ('core.html#img2tensor', 'bioMONAI/core.py'),
                                'bioMONAI.core.img2float': ('core.html#img2float', 'bioMONAI/core.py')},
             'bioMONAI.data': { 'bioMONAI.data.BioImage': ('data.html#bioimage', 'bioMONAI/data.py'),
                                'bioMONAI.data.BioImage.__repr__': ('data.html#bioimage.__repr__', 'bioMONAI/data.py'),

bioMONAI/core.py

@@ -1,7 +1,7 @@
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/00_core.ipynb.
 
 # %% auto 0
-__all__ = ['attributesFromDict', 'img2float']
+__all__ = ['attributesFromDict', 'img2float', 'img2Tensor']
 
 # %% ../nbs/00_core.ipynb 4
 from torch import Tensor as torchTensor
@@ -34,3 +34,7 @@ def attributesFromDict(d):
 # %% ../nbs/00_core.ipynb 9
 def img2float(image, force_copy=False):
     return util.img_as_float(image, force_copy=force_copy)
+
+# %% ../nbs/00_core.ipynb 10
+def img2Tensor(image):
+    return torchTensor(img2float(image))

bioMONAI/transforms.py

@@ -6,10 +6,10 @@
 # %% ../nbs/05_transforms.ipynb 3
 from fastai.vision.all import *
 from fastai.data.all import *
-from monai.transforms import SpatialCrop, Flip, Rotate90
+from monai.transforms import SpatialCrop, Flip, Rotate90, Spacing
 from numpy import percentile, isscalar, float32 as np_float32
 
-# %% ../nbs/05_transforms.ipynb 11
+# %% ../nbs/05_transforms.ipynb 13
 def _process_sz(size, ndim=3):
     if isinstance(size,int): 
         size=(size,)*ndim
@@ -20,7 +20,7 @@ def _get_sz(x):
     if not isinstance(x, Tensor): return fastuple(x.size)
     return fastuple(getattr(x, 'img_size', getattr(x, 'sz', (x.shape[1:])))) # maybe it should swap x and y axes 
 
-# %% ../nbs/05_transforms.ipynb 14
+# %% ../nbs/05_transforms.ipynb 16
 class RandCrop2D(RandTransform):
     "Randomly crop an image to `size`"
     split_idx,order = None,1
@@ -50,7 +50,7 @@ def before_call(self,
     def encodes(self, x):
         return SpatialCrop(roi_center=self.ctr, roi_size=self.size, lazy=self.lazy)(x)
 
-# %% ../nbs/05_transforms.ipynb 15
+# %% ../nbs/05_transforms.ipynb 17
 class RandCropND(RandTransform):
     """
     Randomly crops an ND image to a specified size.
@@ -103,7 +103,7 @@ def encodes(self, x):
         return SpatialCrop(roi_start=self.tl, roi_end=self.br, lazy=self.lazy)(x)
 
 
-# %% ../nbs/05_transforms.ipynb 17
+# %% ../nbs/05_transforms.ipynb 19
 class RandCropND_T(RandTransform):
     """
     Randomly crops an ND image to a specified size.
@@ -166,7 +166,7 @@ def encodes(self, x):
         return cropped_img
 
 
-# %% ../nbs/05_transforms.ipynb 19
+# %% ../nbs/05_transforms.ipynb 21
 class RandFlip(RandTransform):
     """
     Randomly flips an ND image over a specified axis.
@@ -199,7 +199,7 @@ def encodes(self, x):
         else:
             return x
 
-# %% ../nbs/05_transforms.ipynb 21
+# %% ../nbs/05_transforms.ipynb 23
 class RandRot90(RandTransform):
     """
     Randomly rotate an ND image by 90 degrees in the plane specified by axes.

nbs/00_core.ipynb

@@ -109,6 +109,17 @@
     "    return util.img_as_float(image, force_copy=force_copy)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#| export\n",
+    "def img2Tensor(image):\n",
+    "    return torchTensor(img2float(image))"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -118,7 +129,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 25,
    "metadata": {},
    "outputs": [],
    "source": [