fastMONAI 0.5.1__py3-none-any.whl → 0.5.2__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (9) hide show
  1. fastMONAI/__init__.py +1 -1
  2. fastMONAI/_modidx.py +13 -1
  3. fastMONAI/vision_augmentation.py +102 -18
  4. {fastmonai-0.5.1.dist-info → fastmonai-0.5.2.dist-info}/METADATA +7 -7
  5. {fastmonai-0.5.1.dist-info → fastmonai-0.5.2.dist-info}/RECORD +9 -9
  6. {fastmonai-0.5.1.dist-info → fastmonai-0.5.2.dist-info}/WHEEL +0 -0
  7. {fastmonai-0.5.1.dist-info → fastmonai-0.5.2.dist-info}/entry_points.txt +0 -0
  8. {fastmonai-0.5.1.dist-info → fastmonai-0.5.2.dist-info}/licenses/LICENSE +0 -0
  9. {fastmonai-0.5.1.dist-info → fastmonai-0.5.2.dist-info}/top_level.txt +0 -0
fastMONAI/__init__.py CHANGED
@@ -1 +1 @@
1
- __version__ = "0.5.1"
1
+ __version__ = "0.5.2"
fastMONAI/_modidx.py CHANGED
@@ -1,6 +1,6 @@
1
1
  # Autogenerated by nbdev
2
2
 
3
- d = { 'settings': { 'branch': 'master',
3
+ d = { 'settings': { 'branch': 'main',
4
4
  'doc_baseurl': '/',
5
5
  'doc_host': 'https://fastmonai.no',
6
6
  'git_url': 'https://github.com/MMIV-ML/fastMONAI',
@@ -99,6 +99,12 @@ d = { 'settings': { 'branch': 'master',
99
99
  'fastMONAI/vision_augmentation.py'),
100
100
  'fastMONAI.vision_augmentation.CustomDictTransform.encodes': ( 'vision_augment.html#customdicttransform.encodes',
101
101
  'fastMONAI/vision_augmentation.py'),
102
+ 'fastMONAI.vision_augmentation.NormalizeIntensity': ( 'vision_augment.html#normalizeintensity',
103
+ 'fastMONAI/vision_augmentation.py'),
104
+ 'fastMONAI.vision_augmentation.NormalizeIntensity.__init__': ( 'vision_augment.html#normalizeintensity.__init__',
105
+ 'fastMONAI/vision_augmentation.py'),
106
+ 'fastMONAI.vision_augmentation.NormalizeIntensity.encodes': ( 'vision_augment.html#normalizeintensity.encodes',
107
+ 'fastMONAI/vision_augmentation.py'),
102
108
  'fastMONAI.vision_augmentation.OneOf': ( 'vision_augment.html#oneof',
103
109
  'fastMONAI/vision_augmentation.py'),
104
110
  'fastMONAI.vision_augmentation.OneOf.__init__': ( 'vision_augment.html#oneof.__init__',
@@ -163,6 +169,12 @@ d = { 'settings': { 'branch': 'master',
163
169
  'fastMONAI/vision_augmentation.py'),
164
170
  'fastMONAI.vision_augmentation.RandomSpike.encodes': ( 'vision_augment.html#randomspike.encodes',
165
171
  'fastMONAI/vision_augmentation.py'),
172
+ 'fastMONAI.vision_augmentation.RescaleIntensity': ( 'vision_augment.html#rescaleintensity',
173
+ 'fastMONAI/vision_augmentation.py'),
174
+ 'fastMONAI.vision_augmentation.RescaleIntensity.__init__': ( 'vision_augment.html#rescaleintensity.__init__',
175
+ 'fastMONAI/vision_augmentation.py'),
176
+ 'fastMONAI.vision_augmentation.RescaleIntensity.encodes': ( 'vision_augment.html#rescaleintensity.encodes',
177
+ 'fastMONAI/vision_augmentation.py'),
166
178
  'fastMONAI.vision_augmentation.ZNormalization': ( 'vision_augment.html#znormalization',
167
179
  'fastMONAI/vision_augmentation.py'),
168
180
  'fastMONAI.vision_augmentation.ZNormalization.__init__': ( 'vision_augment.html#znormalization.__init__',
fastMONAI/vision_augmentation.py CHANGED
@@ -1,14 +1,16 @@
1
1
  # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/03_vision_augment.ipynb.
2
2
 
3
3
  # %% auto 0
4
- __all__ = ['CustomDictTransform', 'do_pad_or_crop', 'PadOrCrop', 'ZNormalization', 'BraTSMaskConverter', 'BinaryConverter',
5
- 'RandomGhosting', 'RandomSpike', 'RandomNoise', 'RandomBiasField', 'RandomBlur', 'RandomGamma',
6
- 'RandomMotion', 'RandomElasticDeformation', 'RandomAffine', 'RandomFlip', 'OneOf']
4
+ __all__ = ['CustomDictTransform', 'do_pad_or_crop', 'PadOrCrop', 'ZNormalization', 'RescaleIntensity', 'NormalizeIntensity',
5
+ 'BraTSMaskConverter', 'BinaryConverter', 'RandomGhosting', 'RandomSpike', 'RandomNoise', 'RandomBiasField',
6
+ 'RandomBlur', 'RandomGamma', 'RandomMotion', 'RandomElasticDeformation', 'RandomAffine', 'RandomFlip',
7
+ 'OneOf']
7
8
 
8
9
  # %% ../nbs/03_vision_augment.ipynb 2
9
10
  from fastai.data.all import *
10
11
  from .vision_core import *
11
12
  import torchio as tio
13
+ from monai.transforms import NormalizeIntensity as MonaiNormalizeIntensity
12
14
 
13
15
  # %% ../nbs/03_vision_augment.ipynb 5
14
16
  class CustomDictTransform(ItemTransform):
@@ -84,9 +86,29 @@ class ZNormalization(DisplayedTransform):
84
86
  self.channel_wise = channel_wise
85
87
 
86
88
  def encodes(self, o: MedImage):
87
- if self.channel_wise:
88
- o = torch.stack([self.z_normalization(c[None])[0] for c in o])
89
- else: o = self.z_normalization(o)
89
+ try:
90
+ if self.channel_wise:
91
+ o = torch.stack([self.z_normalization(c[None])[0] for c in o])
92
+ else:
93
+ o = self.z_normalization(o)
94
+ except RuntimeError as e:
95
+ if "Standard deviation is 0" in str(e):
96
+ # Calculate mean for debugging information
97
+ mean = float(o.mean())
98
+
99
+ error_msg = (
100
+ f"Standard deviation is 0 for image (mean={mean:.3f}).\n"
101
+ f"This indicates uniform pixel values.\n\n"
102
+ f"Possible causes:\n"
103
+ f"• Corrupted or blank image\n"
104
+ f"• Oversaturated regions\n"
105
+ f"• Background-only regions\n"
106
+ f"• All-zero mask being processed as image\n\n"
107
+ f"Suggested solutions:\n"
108
+ f"• Check image quality and acquisition\n"
109
+ f"• Verify image vs mask data loading"
110
+ )
111
+ raise RuntimeError(error_msg) from e
90
112
 
91
113
  return MedImage.create(o)
92
114
 
@@ -94,6 +116,68 @@ class ZNormalization(DisplayedTransform):
94
116
  return o
95
117
 
96
118
  # %% ../nbs/03_vision_augment.ipynb 10
119
+ class RescaleIntensity(DisplayedTransform):
120
+ """Apply TorchIO RescaleIntensity for robust intensity scaling.
121
+
122
+ Args:
123
+ out_min_max (tuple[float, float]): Output intensity range (min, max)
124
+ in_min_max (tuple[float, float]): Input intensity range (min, max)
125
+
126
+ Example for CT images:
127
+ # Normalize CT from air (-1000 HU) to bone (1000 HU) into range (-1, 1)
128
+ transform = RescaleIntensity(out_min_max=(-1, 1), in_min_max=(-1000, 1000))
129
+ """
130
+
131
+ order = 0
132
+
133
+ def __init__(self, out_min_max: tuple[float, float], in_min_max: tuple[float, float]):
134
+ self.rescale = tio.RescaleIntensity(out_min_max=out_min_max, in_min_max=in_min_max)
135
+
136
+ def encodes(self, o: MedImage):
137
+ return MedImage.create(self.rescale(o))
138
+
139
+ def encodes(self, o: MedMask):
140
+ return o
141
+
142
+ # %% ../nbs/03_vision_augment.ipynb 11
143
+ class NormalizeIntensity(DisplayedTransform):
144
+ """Apply MONAI NormalizeIntensity.
145
+
146
+ Args:
147
+ nonzero (bool): Only normalize non-zero values (default: True)
148
+ channel_wise (bool): Apply normalization per channel (default: True)
149
+ subtrahend (float, optional): Value to subtract
150
+ divisor (float, optional): Value to divide by
151
+ """
152
+
153
+ order = 0
154
+
155
+ def __init__(self, nonzero: bool = True, channel_wise: bool = True,
156
+ subtrahend: float = None, divisor: float = None):
157
+ self.nonzero = nonzero
158
+ self.channel_wise = channel_wise
159
+ self.subtrahend = subtrahend
160
+ self.divisor = divisor
161
+
162
+ self.transform = MonaiNormalizeIntensity(
163
+ nonzero=nonzero,
164
+ channel_wise=False, # Always 'False', we handle channel-wise manually
165
+ subtrahend=subtrahend,
166
+ divisor=divisor
167
+ )
168
+
169
+ def encodes(self, o: MedImage):
170
+ if self.channel_wise:
171
+ result = torch.stack([self.transform(c[None])[0] for c in o])
172
+ else:
173
+ result = torch.Tensor(self.transform(o))
174
+
175
+ return MedImage.create(result)
176
+
177
+ def encodes(self, o: MedMask):
178
+ return o
179
+
180
+ # %% ../nbs/03_vision_augment.ipynb 12
97
181
  class BraTSMaskConverter(DisplayedTransform):
98
182
  '''Convert BraTS masks.'''
99
183
 
@@ -105,7 +189,7 @@ class BraTSMaskConverter(DisplayedTransform):
105
189
  o = torch.where(o==4, 3., o)
106
190
  return MedMask.create(o)
107
191
 
108
- # %% ../nbs/03_vision_augment.ipynb 11
192
+ # %% ../nbs/03_vision_augment.ipynb 13
109
193
  class BinaryConverter(DisplayedTransform):
110
194
  '''Convert to binary mask.'''
111
195
 
@@ -118,7 +202,7 @@ class BinaryConverter(DisplayedTransform):
118
202
  o = torch.where(o>0, 1., 0)
119
203
  return MedMask.create(o)
120
204
 
121
- # %% ../nbs/03_vision_augment.ipynb 12
205
+ # %% ../nbs/03_vision_augment.ipynb 14
122
206
  class RandomGhosting(DisplayedTransform):
123
207
  """Apply TorchIO `RandomGhosting`."""
124
208
 
@@ -133,7 +217,7 @@ class RandomGhosting(DisplayedTransform):
133
217
  def encodes(self, o: MedMask):
134
218
  return o
135
219
 
136
- # %% ../nbs/03_vision_augment.ipynb 13
220
+ # %% ../nbs/03_vision_augment.ipynb 15
137
221
  class RandomSpike(DisplayedTransform):
138
222
  '''Apply TorchIO `RandomSpike`.'''
139
223
 
@@ -148,7 +232,7 @@ class RandomSpike(DisplayedTransform):
148
232
  def encodes(self, o:MedMask):
149
233
  return o
150
234
 
151
- # %% ../nbs/03_vision_augment.ipynb 14
235
+ # %% ../nbs/03_vision_augment.ipynb 16
152
236
  class RandomNoise(DisplayedTransform):
153
237
  '''Apply TorchIO `RandomNoise`.'''
154
238
 
@@ -163,7 +247,7 @@ class RandomNoise(DisplayedTransform):
163
247
  def encodes(self, o: MedMask):
164
248
  return o
165
249
 
166
- # %% ../nbs/03_vision_augment.ipynb 15
250
+ # %% ../nbs/03_vision_augment.ipynb 17
167
251
  class RandomBiasField(DisplayedTransform):
168
252
  '''Apply TorchIO `RandomBiasField`.'''
169
253
 
@@ -178,7 +262,7 @@ class RandomBiasField(DisplayedTransform):
178
262
  def encodes(self, o: MedMask):
179
263
  return o
180
264
 
181
- # %% ../nbs/03_vision_augment.ipynb 16
265
+ # %% ../nbs/03_vision_augment.ipynb 18
182
266
  class RandomBlur(DisplayedTransform):
183
267
  '''Apply TorchIO `RandomBiasField`.'''
184
268
 
@@ -193,7 +277,7 @@ class RandomBlur(DisplayedTransform):
193
277
  def encodes(self, o: MedMask):
194
278
  return o
195
279
 
196
- # %% ../nbs/03_vision_augment.ipynb 17
280
+ # %% ../nbs/03_vision_augment.ipynb 19
197
281
  class RandomGamma(DisplayedTransform):
198
282
  '''Apply TorchIO `RandomGamma`.'''
199
283
 
@@ -209,7 +293,7 @@ class RandomGamma(DisplayedTransform):
209
293
  def encodes(self, o: MedMask):
210
294
  return o
211
295
 
212
- # %% ../nbs/03_vision_augment.ipynb 18
296
+ # %% ../nbs/03_vision_augment.ipynb 20
213
297
  class RandomMotion(DisplayedTransform):
214
298
  """Apply TorchIO `RandomMotion`."""
215
299
 
@@ -237,7 +321,7 @@ class RandomMotion(DisplayedTransform):
237
321
  def encodes(self, o: MedMask):
238
322
  return o
239
323
 
240
- # %% ../nbs/03_vision_augment.ipynb 20
324
+ # %% ../nbs/03_vision_augment.ipynb 22
241
325
  class RandomElasticDeformation(CustomDictTransform):
242
326
  """Apply TorchIO `RandomElasticDeformation`."""
243
327
 
@@ -250,7 +334,7 @@ class RandomElasticDeformation(CustomDictTransform):
250
334
  image_interpolation=image_interpolation,
251
335
  p=p))
252
336
 
253
- # %% ../nbs/03_vision_augment.ipynb 21
337
+ # %% ../nbs/03_vision_augment.ipynb 23
254
338
  class RandomAffine(CustomDictTransform):
255
339
  """Apply TorchIO `RandomAffine`."""
256
340
 
@@ -266,14 +350,14 @@ class RandomAffine(CustomDictTransform):
266
350
  default_pad_value=default_pad_value,
267
351
  p=p))
268
352
 
269
- # %% ../nbs/03_vision_augment.ipynb 22
353
+ # %% ../nbs/03_vision_augment.ipynb 24
270
354
  class RandomFlip(CustomDictTransform):
271
355
  """Apply TorchIO `RandomFlip`."""
272
356
 
273
357
  def __init__(self, axes='LR', p=0.5):
274
358
  super().__init__(tio.RandomFlip(axes=axes, flip_probability=p))
275
359
 
276
- # %% ../nbs/03_vision_augment.ipynb 23
360
+ # %% ../nbs/03_vision_augment.ipynb 25
277
361
  class OneOf(CustomDictTransform):
278
362
  """Apply only one of the given transforms using TorchIO `OneOf`."""
279
363
 
{fastmonai-0.5.1.dist-info → fastmonai-0.5.2.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: fastMONAI
3
- Version: 0.5.1
3
+ Version: 0.5.2
4
4
  Summary: fastMONAI library
5
5
  Home-page: https://github.com/MMIV-ML/fastMONAI
6
6
  Author: Satheshkumar Kaliyugarasan
@@ -53,7 +53,7 @@ Dynamic: summary
53
53
 
54
54
  <!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
55
55
 
56
- ![](https://raw.githubusercontent.com/skaliy/skaliy.github.io/master/assets/fastmonai_v1.png)
56
+ ![](https://raw.githubusercontent.com/skaliy/skaliy.github.io/main/assets/fastmonai_v1.png)
57
57
 
58
58
  ![CI](https://github.com/MMIV-ML/fastMONAI/workflows/CI/badge.svg)
59
59
  [![Docs](https://github.com/MMIV-ML/fastMONAI/actions/workflows/deploy.yaml/badge.svg)](https://fastmonai.no)
@@ -120,15 +120,15 @@ https://fastmonai.no for more information.
120
120
 
121
121
  | Notebook | 1-Click Notebook |
122
122
  |:---|----|
123
- | [10a_tutorial_classification.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/master/nbs/10a_tutorial_classification.ipynb) <br>shows how to construct a binary classification model based on MRI data. | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/master/nbs/10a_tutorial_classification.ipynb) |
124
- | [10b_tutorial_regression.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/master/nbs/10b_tutorial_regression.ipynb) <br>shows how to construct a model to predict the age of a subject from MRI scans (“brain age”). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/master/nbs/10b_tutorial_regression.ipynb) |
125
- | [10c_tutorial_binary_segmentation.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/master/nbs/10c_tutorial_binary_segmentation.ipynb) <br>shows how to do binary segmentation (extract the left atrium from monomodal cardiac MRI). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/master/nbs/10c_tutorial_binary_segmentation.ipynb) |
126
- | [10d_tutorial_multiclass_segmentation.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/master/nbs/10d_tutorial_multiclass_segmentation.ipynb) <br>shows how to perform segmentation from multimodal MRI (brain tumor segmentation). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/master/nbs/10d_tutorial_multiclass_segmentation.ipynb) |
123
+ | [10a_tutorial_classification.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/10a_tutorial_classification.ipynb) <br>shows how to construct a binary classification model based on MRI data. | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/10a_tutorial_classification.ipynb) |
124
+ | [10b_tutorial_regression.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/10b_tutorial_regression.ipynb) <br>shows how to construct a model to predict the age of a subject from MRI scans (“brain age”). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/10b_tutorial_regression.ipynb) |
125
+ | [10c_tutorial_binary_segmentation.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/10c_tutorial_binary_segmentation.ipynb) <br>shows how to do binary segmentation (extract the left atrium from monomodal cardiac MRI). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/10c_tutorial_binary_segmentation.ipynb) |
126
+ | [10d_tutorial_multiclass_segmentation.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/10d_tutorial_multiclass_segmentation.ipynb) <br>shows how to perform segmentation from multimodal MRI (brain tumor segmentation). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/10d_tutorial_multiclass_segmentation.ipynb) |
127
127
 
128
128
  # How to contribute
129
129
 
130
130
  We welcome contributions! See
131
- [CONTRIBUTING.md](https://github.com/MMIV-ML/fastMONAI/blob/master/CONTRIBUTING.md)
131
+ [CONTRIBUTING.md](https://github.com/MMIV-ML/fastMONAI/blob/main/CONTRIBUTING.md)
132
132
 
133
133
  # Citing fastMONAI
134
134
 
{fastmonai-0.5.1.dist-info → fastmonai-0.5.2.dist-info}/RECORD RENAMED
@@ -1,20 +1,20 @@
1
- fastMONAI/__init__.py,sha256=eZ1bOun1DDVV0YLOBW4wj2FP1ajReLjbIrGmzN7ASBw,22
2
- fastMONAI/_modidx.py,sha256=iuYWVoaM3bmpb_Dv6lMQU8zOVPA76hYfnyFxVgKyuBg,37759
1
+ fastMONAI/__init__.py,sha256=isJrmDBLRag7Zc2UK9ZovWGOv7ji1Oh-zJtJMNJFkXw,22
2
+ fastMONAI/_modidx.py,sha256=pV36J9-oryTjfV9gL-lXJqoCH9SCQFGsa_NIRdkUlYI,39527
3
3
  fastMONAI/dataset_info.py,sha256=aJ-utYZ1OrA32RIQbF7jHxcDE8SgOZE3Vt1AojxnvZc,5026
4
4
  fastMONAI/external_data.py,sha256=IVj9GbIRFh9bTFkIa2wySUObSnNfZiaVtuzFxOFAi0Q,12219
5
5
  fastMONAI/research_utils.py,sha256=LZu62g8BQAVYS4dD7qDsKHJXZnDd1uLkJ6LoaMDhUhk,590
6
6
  fastMONAI/utils.py,sha256=jG8SiYebcrPJsmnmMZh4SokWRj7McdJ_gftINnfcE1A,16590
7
7
  fastMONAI/vision_all.py,sha256=_l6F8ZlUaPYcplNG6mg1-1xssYforByEe4zECbPzTck,359
8
- fastMONAI/vision_augmentation.py,sha256=lAlrLm8jbXRmk9a6e8_o_CNTS6Pyp-KKNXwjpelUUJc,9070
8
+ fastMONAI/vision_augmentation.py,sha256=-4LsLuPi55bh0KduB6EPTzudG63japebszdtN5FtFC0,12281
9
9
  fastMONAI/vision_core.py,sha256=k4RUBzZuh9W8J4zbcVzXCKfJxkKCsBDG0oSRMwiCNp0,13848
10
10
  fastMONAI/vision_data.py,sha256=VCB3hyBN7dYuLiYGSGeuWlBTMvb2cLVo_sbENrRWe5Q,11510
11
11
  fastMONAI/vision_inference.py,sha256=3SaJbKGbgaf9ON9PH5DtvfNlhAurov_Idnrlp4jyU9w,6625
12
12
  fastMONAI/vision_loss.py,sha256=NrHnk1yD4EBKsp6aippppXU4l-mwmsZOqE_bsZP3ZNI,3591
13
13
  fastMONAI/vision_metrics.py,sha256=CVxdOBPaMJT6Mo5jF3WoQj6a3C-_FsnBicMAU_ZrFS8,3549
14
14
  fastMONAI/vision_plot.py,sha256=-X_nNBXx7lYCZSFBIN1587ZTA3T_-2ASBM4K31wU660,3792
15
- fastmonai-0.5.1.dist-info/licenses/LICENSE,sha256=xV8xoN4VOL0uw9X8RSs2IMuD_Ss_a9yAbtGNeBWZwnw,11337
16
- fastmonai-0.5.1.dist-info/METADATA,sha256=VZcJOlNQR7g3mJZkMnnoukPPJZ0yt_B5T9r5yPdCLBk,7094
17
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