Thaar50 commited on
Commit
e1da286
·
1 Parent(s): b5e5fe8

restructuring for use in gui

Browse files
fold_2/dataset.json DELETED
@@ -1,11 +0,0 @@
1
- {
2
- "channel_names": {
3
- "0": "T1"
4
- },
5
- "labels": {
6
- "background": 0,
7
- "epilepsy_lesion": 1
8
- },
9
- "numTraining": 531,
10
- "file_ending": ".nii.gz"
11
- }
 
 
 
 
 
 
 
 
 
 
 
 
fold_2/plans.json DELETED
@@ -1,345 +0,0 @@
1
- {
2
- "dataset_name": "Dataset001_BrainEpilepsy",
3
- "plans_name": "nnUNetPlans",
4
- "original_median_spacing_after_transp": [
5
- 1.0998936891555786,
6
- 0.9375,
7
- 0.9375
8
- ],
9
- "original_median_shape_after_transp": [
10
- 170,
11
- 176,
12
- 159
13
- ],
14
- "image_reader_writer": "SimpleITKIO",
15
- "transpose_forward": [
16
- 1,
17
- 0,
18
- 2
19
- ],
20
- "transpose_backward": [
21
- 1,
22
- 0,
23
- 2
24
- ],
25
- "configurations": {
26
- "2d": {
27
- "data_identifier": "nnUNetPlans_2d",
28
- "preprocessor_name": "DefaultPreprocessor",
29
- "batch_size": 88,
30
- "patch_size": [
31
- 192,
32
- 192
33
- ],
34
- "median_image_size_in_voxels": [
35
- 179.0,
36
- 162.0
37
- ],
38
- "spacing": [
39
- 0.9375,
40
- 0.9375
41
- ],
42
- "normalization_schemes": [
43
- "ZScoreNormalization"
44
- ],
45
- "use_mask_for_norm": [
46
- true
47
- ],
48
- "resampling_fn_data": "resample_data_or_seg_to_shape",
49
- "resampling_fn_seg": "resample_data_or_seg_to_shape",
50
- "resampling_fn_data_kwargs": {
51
- "is_seg": false,
52
- "order": 3,
53
- "order_z": 0,
54
- "force_separate_z": null
55
- },
56
- "resampling_fn_seg_kwargs": {
57
- "is_seg": true,
58
- "order": 1,
59
- "order_z": 0,
60
- "force_separate_z": null
61
- },
62
- "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
63
- "resampling_fn_probabilities_kwargs": {
64
- "is_seg": false,
65
- "order": 1,
66
- "order_z": 0,
67
- "force_separate_z": null
68
- },
69
- "architecture": {
70
- "network_class_name": "dynamic_network_architectures.architectures.unet.PlainConvUNet",
71
- "arch_kwargs": {
72
- "n_stages": 6,
73
- "features_per_stage": [
74
- 32,
75
- 64,
76
- 128,
77
- 256,
78
- 512,
79
- 512
80
- ],
81
- "conv_op": "torch.nn.modules.conv.Conv2d",
82
- "kernel_sizes": [
83
- [
84
- 3,
85
- 3
86
- ],
87
- [
88
- 3,
89
- 3
90
- ],
91
- [
92
- 3,
93
- 3
94
- ],
95
- [
96
- 3,
97
- 3
98
- ],
99
- [
100
- 3,
101
- 3
102
- ],
103
- [
104
- 3,
105
- 3
106
- ]
107
- ],
108
- "strides": [
109
- [
110
- 1,
111
- 1
112
- ],
113
- [
114
- 2,
115
- 2
116
- ],
117
- [
118
- 2,
119
- 2
120
- ],
121
- [
122
- 2,
123
- 2
124
- ],
125
- [
126
- 2,
127
- 2
128
- ],
129
- [
130
- 2,
131
- 2
132
- ]
133
- ],
134
- "n_conv_per_stage": [
135
- 2,
136
- 2,
137
- 2,
138
- 2,
139
- 2,
140
- 2
141
- ],
142
- "n_conv_per_stage_decoder": [
143
- 2,
144
- 2,
145
- 2,
146
- 2,
147
- 2
148
- ],
149
- "conv_bias": true,
150
- "norm_op": "torch.nn.modules.instancenorm.InstanceNorm2d",
151
- "norm_op_kwargs": {
152
- "eps": 1e-05,
153
- "affine": true
154
- },
155
- "dropout_op": null,
156
- "dropout_op_kwargs": null,
157
- "nonlin": "torch.nn.LeakyReLU",
158
- "nonlin_kwargs": {
159
- "inplace": true
160
- }
161
- },
162
- "_kw_requires_import": [
163
- "conv_op",
164
- "norm_op",
165
- "dropout_op",
166
- "nonlin"
167
- ]
168
- },
169
- "batch_dice": true
170
- },
171
- "3d_fullres": {
172
- "data_identifier": "nnUNetPlans_3d_fullres",
173
- "preprocessor_name": "DefaultPreprocessor",
174
- "batch_size": 2,
175
- "patch_size": [
176
- 128,
177
- 128,
178
- 128
179
- ],
180
- "median_image_size_in_voxels": [
181
- 168.0,
182
- 179.0,
183
- 162.0
184
- ],
185
- "spacing": [
186
- 1.0998936891555786,
187
- 0.9375,
188
- 0.9375
189
- ],
190
- "normalization_schemes": [
191
- "ZScoreNormalization"
192
- ],
193
- "use_mask_for_norm": [
194
- true
195
- ],
196
- "resampling_fn_data": "resample_data_or_seg_to_shape",
197
- "resampling_fn_seg": "resample_data_or_seg_to_shape",
198
- "resampling_fn_data_kwargs": {
199
- "is_seg": false,
200
- "order": 3,
201
- "order_z": 0,
202
- "force_separate_z": null
203
- },
204
- "resampling_fn_seg_kwargs": {
205
- "is_seg": true,
206
- "order": 1,
207
- "order_z": 0,
208
- "force_separate_z": null
209
- },
210
- "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
211
- "resampling_fn_probabilities_kwargs": {
212
- "is_seg": false,
213
- "order": 1,
214
- "order_z": 0,
215
- "force_separate_z": null
216
- },
217
- "architecture": {
218
- "network_class_name": "dynamic_network_architectures.architectures.unet.PlainConvUNet",
219
- "arch_kwargs": {
220
- "n_stages": 6,
221
- "features_per_stage": [
222
- 32,
223
- 64,
224
- 128,
225
- 256,
226
- 320,
227
- 320
228
- ],
229
- "conv_op": "torch.nn.modules.conv.Conv3d",
230
- "kernel_sizes": [
231
- [
232
- 3,
233
- 3,
234
- 3
235
- ],
236
- [
237
- 3,
238
- 3,
239
- 3
240
- ],
241
- [
242
- 3,
243
- 3,
244
- 3
245
- ],
246
- [
247
- 3,
248
- 3,
249
- 3
250
- ],
251
- [
252
- 3,
253
- 3,
254
- 3
255
- ],
256
- [
257
- 3,
258
- 3,
259
- 3
260
- ]
261
- ],
262
- "strides": [
263
- [
264
- 1,
265
- 1,
266
- 1
267
- ],
268
- [
269
- 2,
270
- 2,
271
- 2
272
- ],
273
- [
274
- 2,
275
- 2,
276
- 2
277
- ],
278
- [
279
- 2,
280
- 2,
281
- 2
282
- ],
283
- [
284
- 2,
285
- 2,
286
- 2
287
- ],
288
- [
289
- 2,
290
- 2,
291
- 2
292
- ]
293
- ],
294
- "n_conv_per_stage": [
295
- 2,
296
- 2,
297
- 2,
298
- 2,
299
- 2,
300
- 2
301
- ],
302
- "n_conv_per_stage_decoder": [
303
- 2,
304
- 2,
305
- 2,
306
- 2,
307
- 2
308
- ],
309
- "conv_bias": true,
310
- "norm_op": "torch.nn.modules.instancenorm.InstanceNorm3d",
311
- "norm_op_kwargs": {
312
- "eps": 1e-05,
313
- "affine": true
314
- },
315
- "dropout_op": null,
316
- "dropout_op_kwargs": null,
317
- "nonlin": "torch.nn.LeakyReLU",
318
- "nonlin_kwargs": {
319
- "inplace": true
320
- }
321
- },
322
- "_kw_requires_import": [
323
- "conv_op",
324
- "norm_op",
325
- "dropout_op",
326
- "nonlin"
327
- ]
328
- },
329
- "batch_dice": false
330
- }
331
- },
332
- "experiment_planner_used": "ExperimentPlanner",
333
- "label_manager": "LabelManager",
334
- "foreground_intensity_properties_per_channel": {
335
- "0": {
336
- "max": 19552.0,
337
- "mean": 1597.0310440128085,
338
- "median": 1536.0,
339
- "min": 0.0,
340
- "percentile_00_5": 101.0,
341
- "percentile_99_5": 5622.0,
342
- "std": 1032.1604166567174
343
- }
344
- }
345
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
{fold_2 → nnUNetTrainer__nnUNetPlans__3d_fullres}/dataset_fingerprint.json RENAMED
File without changes
nnUNetTrainer__nnUNetPlans__3d_fullres/fold_1/checkpoint_latest.pth DELETED
@@ -1,3 +0,0 @@
1
- version https://git-lfs.github.com/spec/v1
2
- oid sha256:9594c2e2f68bc8386d2301fc3e6c2e91b7e3ee0514d6fe4f926ec19d2d7f7d66
3
- size 249701978
 
 
 
 
{fold_2 → nnUNetTrainer__nnUNetPlans__3d_fullres/fold_2}/checkpoint_final.pth RENAMED
File without changes
nnUNetTrainer__nnUNetPlans__3d_fullres/plans.json CHANGED
@@ -2,14 +2,14 @@
2
  "dataset_name": "Dataset001_BrainEpilepsy",
3
  "plans_name": "nnUNetPlans",
4
  "original_median_spacing_after_transp": [
5
- 1.100000023841858,
6
  0.9375,
7
  0.9375
8
  ],
9
  "original_median_shape_after_transp": [
10
  170,
11
- 179,
12
- 160
13
  ],
14
  "image_reader_writer": "SimpleITKIO",
15
  "transpose_forward": [
@@ -32,7 +32,7 @@
32
  192
33
  ],
34
  "median_image_size_in_voxels": [
35
- 180.0,
36
  162.0
37
  ],
38
  "spacing": [
@@ -179,11 +179,11 @@
179
  ],
180
  "median_image_size_in_voxels": [
181
  168.0,
182
- 180.0,
183
  162.0
184
  ],
185
  "spacing": [
186
- 1.100000023841858,
187
  0.9375,
188
  0.9375
189
  ],
@@ -334,12 +334,12 @@
334
  "foreground_intensity_properties_per_channel": {
335
  "0": {
336
  "max": 19552.0,
337
- "mean": 1599.6502685546875,
338
  "median": 1536.0,
339
  "min": 0.0,
340
  "percentile_00_5": 101.0,
341
- "percentile_99_5": 5626.0,
342
- "std": 1039.716796875
343
  }
344
  }
345
  }
 
2
  "dataset_name": "Dataset001_BrainEpilepsy",
3
  "plans_name": "nnUNetPlans",
4
  "original_median_spacing_after_transp": [
5
+ 1.0998936891555786,
6
  0.9375,
7
  0.9375
8
  ],
9
  "original_median_shape_after_transp": [
10
  170,
11
+ 176,
12
+ 159
13
  ],
14
  "image_reader_writer": "SimpleITKIO",
15
  "transpose_forward": [
 
32
  192
33
  ],
34
  "median_image_size_in_voxels": [
35
+ 179.0,
36
  162.0
37
  ],
38
  "spacing": [
 
179
  ],
180
  "median_image_size_in_voxels": [
181
  168.0,
182
+ 179.0,
183
  162.0
184
  ],
185
  "spacing": [
186
+ 1.0998936891555786,
187
  0.9375,
188
  0.9375
189
  ],
 
334
  "foreground_intensity_properties_per_channel": {
335
  "0": {
336
  "max": 19552.0,
337
+ "mean": 1597.0310440128085,
338
  "median": 1536.0,
339
  "min": 0.0,
340
  "percentile_00_5": 101.0,
341
+ "percentile_99_5": 5622.0,
342
+ "std": 1032.1604166567174
343
  }
344
  }
345
  }