moved tiff2torch

bmandracchia · Aug 28, 2024 · edada14 · edada14
1 parent 5abe59e
commit edada14
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Showing 6 changed files with 3,795 additions and 70 deletions.
diff --git a/bioMONAI/_modidx.py b/bioMONAI/_modidx.py
@@ -46,6 +46,7 @@
                              'bioMONAI.io.h5_reader': ('io.html#h5_reader', 'bioMONAI/io.py'),
                              'bioMONAI.io.img_reader': ('io.html#img_reader', 'bioMONAI/io.py'),
                              'bioMONAI.io.lif_reader': ('io.html#lif_reader', 'bioMONAI/io.py'),
+                             'bioMONAI.io.tiff2torch': ('io.html#tiff2torch', 'bioMONAI/io.py'),
                              'bioMONAI.io.tiff_reader': ('io.html#tiff_reader', 'bioMONAI/io.py')},
             'bioMONAI.losses': { 'bioMONAI.losses.CombinedLoss': ('losses.html#combinedloss', 'bioMONAI/losses.py'),
                                  'bioMONAI.losses.CombinedLoss.__call__': ('losses.html#combinedloss.__call__', 'bioMONAI/losses.py'),
@@ -113,5 +114,4 @@
                                     'bioMONAI.visualize.mosaic_image_3d': ('visualize.html#mosaic_image_3d', 'bioMONAI/visualize.py'),
                                     'bioMONAI.visualize.show_images_grid': ('visualize.html#show_images_grid', 'bioMONAI/visualize.py'),
                                     'bioMONAI.visualize.show_plane': ('visualize.html#show_plane', 'bioMONAI/visualize.py'),
-                                    'bioMONAI.visualize.tiff2torch': ('visualize.html#tiff2torch', 'bioMONAI/visualize.py'),
                                     'bioMONAI.visualize.visualize_slices': ('visualize.html#visualize_slices', 'bioMONAI/visualize.py')}}}
diff --git a/bioMONAI/io.py b/bioMONAI/io.py
@@ -1,17 +1,27 @@
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/02_io.ipynb.
 
 # %% auto 0
-__all__ = ['tiff_reader', 'lif_reader', 'czi_reader', 'h5_reader', 'img_reader']
+__all__ = ['tiff2torch', 'tiff_reader', 'lif_reader', 'czi_reader', 'h5_reader', 'img_reader']
 
 # %% ../nbs/02_io.ipynb 3
 from fastai.vision.all import *
 from fastai.data.all import *
 from torchio import ScalarImage, ToCanonical, Resample
 import multipagetiff as mtif
 
-from .core import torchTensor
+from .core import torchTensor, torch_from_numpy
 
 # %% ../nbs/02_io.ipynb 6
+def tiff2torch(file_path: str):
+    '''
+    Load tiff into pytorch tensor
+    '''
+    import tifffile as tiff
+
+    img = np.array(tiff.imread(file_path))
+    return torch_from_numpy(img)
+
+# %% ../nbs/02_io.ipynb 7
 def tiff_reader(path,  # The path to the TIFF file to be read
                 units='um',  # The units for the image data.
                ):
@@ -44,7 +54,7 @@ def tiff_reader(path,  # The path to the TIFF file to be read
     # Return the image data and the affine matrix
     return data, affine
 
-# %% ../nbs/02_io.ipynb 9
+# %% ../nbs/02_io.ipynb 10
 from aicsimageio import AICSImage
 
 def lif_reader(path, # The path to the LIF file to be read
@@ -82,7 +92,7 @@ def lif_reader(path, # The path to the LIF file to be read
     # Return the image data and the affine matrix
     return data, affine
 
-# %% ../nbs/02_io.ipynb 12
+# %% ../nbs/02_io.ipynb 13
 from aicsimageio.readers import CziReader
 
 def czi_reader(path, # The path to the CZI file to be read
@@ -112,7 +122,7 @@ def czi_reader(path, # The path to the CZI file to be read
     # Return the image data and the affine matrix
     return data, affine
 
-# %% ../nbs/02_io.ipynb 15
+# %% ../nbs/02_io.ipynb 16
 def _image_reader(path, # The file path to the image             
                  ):
 
@@ -165,7 +175,7 @@ def _image_reader(path, # The file path to the image
     return data, affine
 
 
-# %% ../nbs/02_io.ipynb 18
+# %% ../nbs/02_io.ipynb 19
 import h5py
 
 def h5_reader(path, dataset):
@@ -179,7 +189,7 @@ def h5_reader(path, dataset):
     return dataset1
 
 
-# %% ../nbs/02_io.ipynb 21
+# %% ../nbs/02_io.ipynb 22
 def _preprocess(obj, # The object to preprocess
                 reorder, # Whether to reorder the object
                 resample # Whether to resample the object
@@ -213,7 +223,7 @@ def _preprocess(obj, # The object to preprocess
     return obj, original_size
 
 
-# %% ../nbs/02_io.ipynb 23
+# %% ../nbs/02_io.ipynb 24
 def _load_and_preprocess(file_path, # Image file path
                          reorder=False, # Whether to reorder data for canonical (RAS+) orientation
                          resample=False, # Whether to resample image to different voxel sizes and dimensions
@@ -237,7 +247,7 @@ def _load_and_preprocess(file_path, # Image file path
     return org_img, input_img, org_size
 
 
-# %% ../nbs/02_io.ipynb 26
+# %% ../nbs/02_io.ipynb 27
 def _multi_channel(image_paths: (L, list), # List of image paths (e.g., T1, T2, T1CE, DWI)
                    reorder: bool = False, # Whether to reorder data for canonical (RAS+) orientation
                    resample: list = None, # Whether to resample image to different voxel sizes and dimensions
@@ -273,7 +283,7 @@ def _multi_channel(image_paths: (L, list), # List of image paths (e.g., T1, T2,
     input_img.set_data(tensor)
     return org_img, input_img, org_size
 
-# %% ../nbs/02_io.ipynb 29
+# %% ../nbs/02_io.ipynb 30
 def img_reader(file_path: (str, Path, L, list), # Path to the image
                dtype=torchTensor, # Datatype for the return value. Defaults to torchTensor
                reorder: bool = False, # Whether to reorder to canonical orientation

diff --git a/bioMONAI/visualize.py b/bioMONAI/visualize.py
@@ -1,7 +1,7 @@
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/09_visualize.ipynb.
 
 # %% auto 0
-__all__ = ['mosaic_image_3d', 'tiff2torch', 'show_images_grid', 'show_plane', 'visualize_slices']
+__all__ = ['mosaic_image_3d', 'show_images_grid', 'show_plane', 'visualize_slices']
 
 # %% ../nbs/09_visualize.ipynb 3
 import numpy as np
@@ -16,14 +16,15 @@
 from fastai.vision.all import plt, ifnone
 
 from .core import torchTensor, tensor, delegates, torch_from_numpy, hasattrs
+from .io import tiff2torch
 
-# %% ../nbs/09_visualize.ipynb 5
+# %% ../nbs/09_visualize.ipynb 6
 # Utility function for determining figure bounds
 def _fig_bounds(x):
     r = x//8
     return min(15, max(1,r))
 
-# %% ../nbs/09_visualize.ipynb 6
+# %% ../nbs/09_visualize.ipynb 7
 def mosaic_image_3d(t: (np.ndarray, torchTensor),
                   axis: int = 0,
                   figsize: tuple = (15,15),
@@ -77,17 +78,6 @@ def mosaic_image_3d(t: (np.ndarray, torchTensor),
     plt.imshow(grid[0,:,:], cmap=cmap, alpha=alpha)
     plt.axis('off')
 
-# %% ../nbs/09_visualize.ipynb 7
-def tiff2torch(file_path: str):
-    '''
-    Load tiff into pytorch tensor
-    '''
-    import tifffile as tiff
-
-    img = np.array(tiff.imread(file_path))
-    return torch_from_numpy(img)
-
-
 # %% ../nbs/09_visualize.ipynb 8
 @delegates(plt.Axes.imshow, keep=True, but=['shape', 'imlim'])
 def show_images_grid(images, ax=None, ncols=10, figsize=None, title=None, spacing=0.02, max_slices=3, ctx=None, **kwargs):