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rijobrorijobro
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Meta tensor orientation (#722)
* spleen_segmentation_3d * spleen_segmentation_3d_lightning.ipynb * brats_segmentation_3d.ipynb * fixes
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-60
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7 files changed

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-60
lines changed

‎3d_segmentation/brats_segmentation_3d.ipynb

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -266,9 +266,9 @@
266266
" # load 4 Nifti images and stack them together\n",
267267
" LoadImaged(keys=[\"image\", \"label\"]),\n",
268268
" EnsureChannelFirstd(keys=\"image\"),\n",
269+
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
269270
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
270271
" ConvertToMultiChannelBasedOnBratsClassesd(keys=\"label\"),\n",
271-
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
272272
" Spacingd(\n",
273273
" keys=[\"image\", \"label\"],\n",
274274
" pixdim=(1.0, 1.0, 1.0),\n",
@@ -288,9 +288,9 @@
288288
" [\n",
289289
" LoadImaged(keys=[\"image\", \"label\"]),\n",
290290
" EnsureChannelFirstd(keys=\"image\"),\n",
291+
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
291292
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
292293
" ConvertToMultiChannelBasedOnBratsClassesd(keys=\"label\"),\n",
293-
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
294294
" Spacingd(\n",
295295
" keys=[\"image\", \"label\"],\n",
296296
" pixdim=(1.0, 1.0, 1.0),\n",
@@ -787,9 +787,9 @@
787787
" [\n",
788788
" LoadImaged(keys=[\"image\", \"label\"]),\n",
789789
" EnsureChannelFirstd(keys=[\"image\"]),\n",
790+
" Orientationd(keys=[\"image\"], axcodes=\"RAS\"),\n",
790791
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
791792
" ConvertToMultiChannelBasedOnBratsClassesd(keys=\"label\"),\n",
792-
" Orientationd(keys=[\"image\"], axcodes=\"RAS\"),\n",
793793
" Spacingd(keys=[\"image\"], pixdim=(1.0, 1.0, 1.0), mode=\"bilinear\"),\n",
794794
" NormalizeIntensityd(keys=\"image\", nonzero=True, channel_wise=True),\n",
795795
" EnsureTyped(keys=[\"image\", \"label\"]),\n",

‎3d_segmentation/spleen_segmentation_3d.ipynb

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -281,8 +281,8 @@
281281
" [\n",
282282
" LoadImaged(keys=[\"image\", \"label\"]),\n",
283283
" EnsureChannelFirstd(keys=[\"image\", \"label\"]),\n",
284-
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
285284
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
285+
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
286286
" Spacingd(keys=[\"image\", \"label\"], pixdim=(\n",
287287
" 1.5, 1.5, 2.0), mode=(\"bilinear\", \"nearest\")),\n",
288288
" ScaleIntensityRanged(\n",
@@ -314,8 +314,8 @@
314314
" [\n",
315315
" LoadImaged(keys=[\"image\", \"label\"]),\n",
316316
" EnsureChannelFirstd(keys=[\"image\", \"label\"]),\n",
317-
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
318317
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
318+
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
319319
" Spacingd(keys=[\"image\", \"label\"], pixdim=(\n",
320320
" 1.5, 1.5, 2.0), mode=(\"bilinear\", \"nearest\")),\n",
321321
" ScaleIntensityRanged(\n",
@@ -696,8 +696,8 @@
696696
" [\n",
697697
" LoadImaged(keys=[\"image\", \"label\"]),\n",
698698
" EnsureChannelFirstd(keys=[\"image\", \"label\"]),\n",
699-
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
700699
" Orientationd(keys=[\"image\"], axcodes=\"RAS\"),\n",
700+
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
701701
" Spacingd(keys=[\"image\"], pixdim=(\n",
702702
" 1.5, 1.5, 2.0), mode=\"bilinear\"),\n",
703703
" ScaleIntensityRanged(\n",
@@ -791,8 +791,8 @@
791791
" [\n",
792792
" LoadImaged(keys=\"image\"),\n",
793793
" EnsureChannelFirstd(keys=\"image\"),\n",
794-
" FromMetaTensord(keys=\"image\"),\n",
795794
" Orientationd(keys=[\"image\"], axcodes=\"RAS\"),\n",
795+
" FromMetaTensord(keys=\"image\"),\n",
796796
" Spacingd(keys=[\"image\"], pixdim=(\n",
797797
" 1.5, 1.5, 2.0), mode=\"bilinear\"),\n",
798798
" ScaleIntensityRanged(\n",

‎3d_segmentation/spleen_segmentation_3d_lightning.ipynb

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -271,8 +271,8 @@
271271
" [\n",
272272
" LoadImaged(keys=[\"image\", \"label\"]),\n",
273273
" AddChanneld(keys=[\"image\", \"label\"]),\n",
274-
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
275274
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
275+
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
276276
" Spacingd(\n",
277277
" keys=[\"image\", \"label\"],\n",
278278
" pixdim=(1.5, 1.5, 2.0),\n",
@@ -312,8 +312,8 @@
312312
" [\n",
313313
" LoadImaged(keys=[\"image\", \"label\"]),\n",
314314
" AddChanneld(keys=[\"image\", \"label\"]),\n",
315-
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
316315
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
316+
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
317317
" Spacingd(\n",
318318
" keys=[\"image\", \"label\"],\n",
319319
" pixdim=(1.5, 1.5, 2.0),\n",

‎modules/decollate_batch.ipynb

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -246,8 +246,8 @@
246246
" [\n",
247247
" LoadImaged(keys=[\"img\", \"seg\"]),\n",
248248
" EnsureChannelFirstd(keys=[\"img\", \"seg\"]),\n",
249-
" FromMetaTensord(keys=[\"img\", \"seg\"]),\n",
250249
" Orientationd(keys=\"img\", axcodes=\"RAS\"),\n",
250+
" FromMetaTensord(keys=[\"img\", \"seg\"]),\n",
251251
" Resized(keys=\"img\", spatial_size=(96, 96, 96), mode=\"trilinear\", align_corners=True),\n",
252252
" ScaleIntensityd(keys=\"img\"),\n",
253253
" EnsureTyped(keys=[\"img\", \"seg\"]),\n",

‎modules/integrate_3rd_party_transforms.ipynb

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -267,10 +267,10 @@
267267
"source": [
268268
"monai_transforms = [\n",
269269
" LoadImaged(keys=[\"image\", \"label\"]),\n",
270-
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
271-
" ToNumpyd(keys=[\"image\", \"label\", \"image_meta_dict\", \"label_meta_dict\"]),\n",
272270
" AddChanneld(keys=[\"image\", \"label\"]),\n",
273271
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
272+
" FromMetaTensord(keys=[\"image\", \"label\"]),\n",
273+
" ToNumpyd(keys=[\"image\", \"label\", \"image_meta_dict\", \"label_meta_dict\"]),\n",
274274
" Spacingd(keys=[\"image\", \"label\"], pixdim=(\n",
275275
" 1.5, 1.5, 2.0), mode=(\"bilinear\", \"nearest\")),\n",
276276
" ScaleIntensityRanged(keys=[\"image\"], a_min=-57,\n",

‎modules/interpretability/cats_and_dogs.ipynb

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -165,8 +165,8 @@
165165
"divisible_factor = 20\n",
166166
"transforms = Compose([\n",
167167
" LoadImaged(\"image\"),\n",
168-
" FromMetaTensord(\"image\"),\n",
169168
" AsChannelFirstd(\"image\"),\n",
169+
" FromMetaTensord(\"image\"),\n",
170170
" ScaleIntensityd(\"image\"),\n",
171171
" Rotate90d(\"image\", k=3),\n",
172172
" DivisiblePadd(\"image\", k=divisible_factor),\n",
@@ -202,7 +202,7 @@
202202
" axes = np.asarray(axes) if nims == 1 else axes\n",
203203
" for d, ax in zip(data, axes.ravel()):\n",
204204
" # channel last for matplotlib\n",
205-
" im = np.moveaxis(d[\"image\"], 0, -1)\n",
205+
" im = np.moveaxis(d[\"image\"].cpu().numpy(), 0, -1)\n",
206206
" ax.imshow(im, cmap='gray')\n",
207207
" ax.set_title(Animals(d['label']).name, fontsize=25)\n",
208208
" ax.axis(\"off\")\n",

‎modules/nifti_read_example.ipynb

Lines changed: 3 additions & 46 deletions
Original file line numberDiff line numberDiff line change
@@ -89,7 +89,6 @@
8989
"\n",
9090
"import glob\n",
9191
"import os\n",
92-
"import shutil\n",
9392
"import tempfile\n",
9493
"\n",
9594
"import nibabel as nib\n",
@@ -113,30 +112,6 @@
113112
"print_config()"
114113
]
115114
},
116-
{
117-
"cell_type": "markdown",
118-
"metadata": {},
119-
"source": [
120-
"## Setup data directory\n",
121-
"\n",
122-
"You can specify a directory with the `MONAI_DATA_DIRECTORY` environment variable. \n",
123-
"This allows you to save results and reuse downloads. \n",
124-
"If not specified a temporary directory will be used."
125-
]
126-
},
127-
{
128-
"cell_type": "code",
129-
"execution_count": null,
130-
"metadata": {
131-
"tags": []
132-
},
133-
"outputs": [],
134-
"source": [
135-
"directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
136-
"root_dir = tempfile.mkdtemp() if directory is None else directory\n",
137-
"print(root_dir)"
138-
]
139-
},
140115
{
141116
"cell_type": "markdown",
142117
"metadata": {},
@@ -150,6 +125,7 @@
150125
"metadata": {},
151126
"outputs": [],
152127
"source": [
128+
"root_dir = tempfile.mkdtemp()\n",
153129
"for i in range(5):\n",
154130
" im, seg = create_test_image_3d(128, 128, 128)\n",
155131
"\n",
@@ -189,9 +165,9 @@
189165
"imtrans = Compose(\n",
190166
" [\n",
191167
" LoadImage(),\n",
168+
" AddChannel(),\n",
192169
" ToNumpy(),\n",
193170
" ScaleIntensity(),\n",
194-
" AddChannel(),\n",
195171
" RandSpatialCrop((64, 64, 64), random_size=False),\n",
196172
" EnsureType(),\n",
197173
" ]\n",
@@ -200,8 +176,8 @@
200176
"segtrans = Compose(\n",
201177
" [\n",
202178
" LoadImage(),\n",
203-
" ToNumpy(),\n",
204179
" AddChannel(),\n",
180+
" ToNumpy(),\n",
205181
" RandSpatialCrop((64, 64, 64), random_size=False),\n",
206182
" EnsureType(),\n",
207183
" ]\n",
@@ -263,25 +239,6 @@
263239
"im, seg = first(loader)\n",
264240
"print(\"image shapes:\", im.shape, seg.shape)"
265241
]
266-
},
267-
{
268-
"cell_type": "markdown",
269-
"metadata": {},
270-
"source": [
271-
"## Cleanup data directory\n",
272-
"\n",
273-
"Remove directory if a temporary was used."
274-
]
275-
},
276-
{
277-
"cell_type": "code",
278-
"execution_count": 7,
279-
"metadata": {},
280-
"outputs": [],
281-
"source": [
282-
"if directory is None:\n",
283-
" shutil.rmtree(root_dir)"
284-
]
285242
}
286243
],
287244
"metadata": {

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