fastMONAI 0.3.2__tar.gz → 0.3.3__tar.gz

{fastMONAI-0.3.2/fastMONAI.egg-info → fastMONAI-0.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fastMONAI
-Version: 0.3.2
+Version: 0.3.3
 Summary: fastMONAI library
 Home-page: https://github.com/MMIV-ML/fastMONAI
 Author: Satheshkumar Kaliyugarasan

fastMONAI-0.3.3/fastMONAI/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.3.3"

{fastMONAI-0.3.2 → fastMONAI-0.3.3}/fastMONAI/external_data.py

@@ -257,6 +257,7 @@ def download_medmnist3d_dataset(study: str, path: (str, Path) = '../data',
     dataset_file_path = path / f'{study}.npz'
 
     try:
+        #todo: check if dataset is downloaded
         download_url(url=MURLs.MEDMNIST_DICT[study], filepath=dataset_file_path)
     except:
         raise ValueError(f"Dataset '{study}' does not exist.")

{fastMONAI-0.3.2 → fastMONAI-0.3.3}/fastMONAI/vision_data.py

@@ -110,19 +110,19 @@ class MedImageDataLoaders(DataLoaders):
 # %% ../nbs/02_vision_data.ipynb 16
 @typedispatch
 def show_batch(x: MedImage, y, samples, ctxs=None, max_n=6, nrows=None, 
-               ncols=None, figsize=None, channel: int = 0, indices=None, 
-               anatomical_plane: int = 0, **kwargs):
-    """Showing a batch of samples for classification and regression tasks."""
-    
+               ncols=None, figsize=None, channel=0, indices=None,
+               anatomical_plane=0, **kwargs):
+    '''Showing a batch of samples for classification and regression tasks.'''
+
     if ctxs is None: 
         ctxs = get_grid(min(len(samples), max_n), nrows=nrows, ncols=ncols, figsize=figsize)
-    
+        
     n = 1 if y is None else 2
     
     for i in range(n):
         ctxs = [
-            b.show(ctx=c, channel=channel, indices=indices, anatomical_plane=anatomical_plane, **kwargs) 
-            for b, c, _ in zip(samples.itemgot(i), ctxs, range(max_n))
+            b.show(ctx=c, channel=channel, indices=indices, anatomical_plane=anatomical_plane, **kwargs)
+            for b,c,_ in zip(samples.itemgot(i),ctxs,range(max_n))
         ]
 
     plt.tight_layout()
@@ -131,9 +131,9 @@ def show_batch(x: MedImage, y, samples, ctxs=None, max_n=6, nrows=None,
 
 # %% ../nbs/02_vision_data.ipynb 17
 @typedispatch
-def show_batch(x: MedImage, y: MedMask, samples, ctxs=None, max_n=6, nrows: int = None,
-               ncols: int = None, figsize=None, channel: int = 0, indices: int = None,
-               anatomical_plane: int = 0, **kwargs):
+def show_batch(x: MedImage, y: MedMask, samples, ctxs=None, max_n=6, nrows=None,
+               ncols=None, figsize=None, channel=0, indices=None,
+               anatomical_plane=0, **kwargs):
     """Showing a batch of decoded segmentation samples."""
 
     nrows, ncols = min(len(samples), max_n), x.shape[1] + 1
@@ -226,7 +226,7 @@ def show_results(x: MedImage, y: MedMask, samples, outs, ctxs=None, max_n: int =
 
 # %% ../nbs/02_vision_data.ipynb 23
 @typedispatch
-def plot_top_losses(x: MedImage, y, samples, outs, raws, losses, nrows: int = None, 
+def plot_top_losses(x: MedImage, y: TensorCategory, samples, outs, raws, losses, nrows: int = None, 
                     ncols: int = None, figsize=None, channel: int = 0, indices: int = None, 
                     anatomical_plane: int = 0, **kwargs):
     """Show images in top_losses along with their prediction, actual, loss, and probability of actual class."""

{fastMONAI-0.3.2 → fastMONAI-0.3.3}/fastMONAI/vision_inference.py

@@ -4,15 +4,16 @@
 __all__ = ['inference', 'refine_binary_pred_mask']
 
 # %% ../nbs/06_vision_inference.ipynb 1
-import numpy as np
+from copy import copy
 from pathlib import Path
-from torchio import Resize
+import torch
+import numpy as np
 from scipy.ndimage import label
-from .vision_core import *
-from .vision_augmentation import do_pad_or_crop
 from skimage.morphology import remove_small_objects
 from SimpleITK import DICOMOrient, GetArrayFromImage
-from copy import copy
+from torchio import Resize
+from .vision_core import *
+from .vision_augmentation import do_pad_or_crop
 
 # %% ../nbs/06_vision_inference.ipynb 3
 def _to_original_orientation(input_img, org_orientation):
@@ -74,7 +75,7 @@ def inference(learn_inf, reorder, resample, fn: (str, Path) = '',
 def refine_binary_pred_mask(pred_mask, 
                             remove_size: (int, float) = None,
                             percentage: float = 0.2,
-                            verbose: bool = False) -> np.ndarray:
+                            verbose: bool = False) -> torch.Tensor:
     """Removes small objects from the predicted binary mask.
 
     Args:
@@ -102,4 +103,4 @@ def refine_binary_pred_mask(pred_mask,
     processed_mask = remove_small_objects(
         labeled_mask, min_size=small_objects_threshold)
 
-    return np.where(processed_mask > 0, 1., 0.)
+    return torch.Tensor(processed_mask > 0).float()                          

{fastMONAI-0.3.2 → fastMONAI-0.3.3/fastMONAI.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fastMONAI
-Version: 0.3.2
+Version: 0.3.3
 Summary: fastMONAI library
 Home-page: https://github.com/MMIV-ML/fastMONAI
 Author: Satheshkumar Kaliyugarasan

{fastMONAI-0.3.2 → fastMONAI-0.3.3}/settings.ini

@@ -5,7 +5,7 @@
 ### Python Library ###
 lib_name = fastMONAI
 min_python = 3.7
-version = 0.3.2
+version = 0.3.3
 ### OPTIONAL ###
 
 requirements = fastai==2.7.12 monai==1.2.0 torchio==0.18.91 xlrd>=1.2.0 scikit-image==0.19.3 huggingface-hub gdown

fastMONAI-0.3.2/fastMONAI/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.3.2"