Skip to content

Commit 234c9b7

Browse files
zivyzivy
committed
Update R to current SimpleITK API.
1 parent 5374f1d commit 234c9b7

File tree

5 files changed

+13
-78
lines changed

5 files changed

+13
-78
lines changed

‎R/22_Transforms.ipynb‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -986,7 +986,7 @@
986986
"displacement$SetFixedParameters(c(field_size, field_origin, field_spacing, field_direction))\n",
987987
"displacement$SetParameters(runif(length(displacement$GetParameters())))\n",
988988
"\n",
989-
"composite_transform <- Transform(basic_transform)\n",
989+
"composite_transform <- CompositeTransform(basic_transform)\n",
990990
"composite_transform$AddTransform(displacement)\n",
991991
"\n",
992992
"full_file_name <- file.path(OUTPUT_DIR, \"composite.tfm\")\n",

‎R/300_Segmentation_Overview.ipynb‎

Lines changed: 3 additions & 48 deletions
Original file line numberDiff line numberDiff line change
@@ -38,10 +38,6 @@
3838
"cell_type": "code",
3939
"execution_count": null,
4040
"metadata": {
41-
"collapsed": true,
42-
"jupyter": {
43-
"outputs_hidden": true
44-
},
4541
"simpleitk_error_allowed": "Exception in SITK"
4642
},
4743
"outputs": [],
@@ -67,10 +63,6 @@
6763
"cell_type": "code",
6864
"execution_count": null,
6965
"metadata": {
70-
"collapsed": true,
71-
"jupyter": {
72-
"outputs_hidden": true
73-
},
7466
"simpleitk_error_allowed": "Exception in SITK"
7567
},
7668
"outputs": [],
@@ -85,10 +77,6 @@
8577
"cell_type": "code",
8678
"execution_count": null,
8779
"metadata": {
88-
"collapsed": true,
89-
"jupyter": {
90-
"outputs_hidden": true
91-
},
9280
"simpleitk_error_allowed": "Exception in SITK"
9381
},
9482
"outputs": [],
@@ -166,7 +154,7 @@
166154
"seg <- Image(img_T1$GetSize(), \"sitkUInt8\")\n",
167155
"seg$CopyInformation(img_T1)\n",
168156
"seg$SetPixel(seed,1)\n",
169-
"seg <- BinaryDilate(seg, 3)\n",
157+
"seg <- BinaryDilate(seg, c(3,3,3))\n",
170158
"\n",
171159
"Show(LabelOverlay(img_T1_255, seg))"
172160
]
@@ -182,10 +170,6 @@
182170
"cell_type": "code",
183171
"execution_count": null,
184172
"metadata": {
185-
"collapsed": true,
186-
"jupyter": {
187-
"outputs_hidden": true
188-
},
189173
"simpleitk_error_allowed": "Exception in SITK"
190174
},
191175
"outputs": [],
@@ -208,10 +192,6 @@
208192
"cell_type": "code",
209193
"execution_count": null,
210194
"metadata": {
211-
"collapsed": true,
212-
"jupyter": {
213-
"outputs_hidden": true
214-
},
215195
"simpleitk_error_allowed": "Exception in SITK"
216196
},
217197
"outputs": [],
@@ -236,10 +216,6 @@
236216
"cell_type": "code",
237217
"execution_count": null,
238218
"metadata": {
239-
"collapsed": true,
240-
"jupyter": {
241-
"outputs_hidden": true
242-
},
243219
"simpleitk_error_allowed": "Exception in SITK"
244220
},
245221
"outputs": [],
@@ -268,10 +244,6 @@
268244
"cell_type": "code",
269245
"execution_count": null,
270246
"metadata": {
271-
"collapsed": true,
272-
"jupyter": {
273-
"outputs_hidden": true
274-
},
275247
"simpleitk_error_allowed": "Exception in SITK"
276248
},
277249
"outputs": [],
@@ -294,10 +266,6 @@
294266
"cell_type": "code",
295267
"execution_count": null,
296268
"metadata": {
297-
"collapsed": true,
298-
"jupyter": {
299-
"outputs_hidden": true
300-
},
301269
"simpleitk_error_allowed": "Exception in SITK"
302270
},
303271
"outputs": [],
@@ -324,10 +292,6 @@
324292
"cell_type": "code",
325293
"execution_count": null,
326294
"metadata": {
327-
"collapsed": true,
328-
"jupyter": {
329-
"outputs_hidden": true
330-
},
331295
"simpleitk_error_allowed": "Exception in SITK"
332296
},
333297
"outputs": [],
@@ -359,20 +323,15 @@
359323
{
360324
"cell_type": "code",
361325
"execution_count": null,
362-
"metadata": {
363-
"collapsed": true,
364-
"jupyter": {
365-
"outputs_hidden": true
366-
}
367-
},
326+
"metadata": {},
368327
"outputs": [],
369328
"source": [
370329
"seed <- c(132,142,96)\n",
371330
"\n",
372331
"seg <- Image(img_T1$GetSize(), \"sitkUInt8\")\n",
373332
"seg$CopyInformation(img_T1)\n",
374333
"seg$SetPixel(seed, 1)\n",
375-
"seg <- BinaryDilate(seg, 3)"
334+
"seg <- BinaryDilate(seg, c(3,3,3))"
376335
]
377336
},
378337
{
@@ -444,10 +403,6 @@
444403
"cell_type": "code",
445404
"execution_count": null,
446405
"metadata": {
447-
"collapsed": true,
448-
"jupyter": {
449-
"outputs_hidden": true
450-
},
451406
"simpleitk_error_allowed": "Exception in SITK"
452407
},
453408
"outputs": [],

‎R/61_Registration_Introduction_Continued.ipynb‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -406,7 +406,7 @@
406406
" Cast(moving_image, \"sitkFloat32\"))\n",
407407
"\n",
408408
"# Need to compose the transformations after registration.\n",
409-
"final_transform_v11 <- Transform(optimized_transform)\n",
409+
"final_transform_v11 <- CompositeTransform(optimized_transform)\n",
410410
"dev_null <- final_transform_v11$AddTransform(initial_transform)"
411411
]
412412
},

‎R/70_Data_Augmentation.ipynb‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -382,7 +382,7 @@
382382
" # Augmentation is done in the reference image space, so we first map the points from \n",
383383
" # the reference image space back onto itself T_aug (e.g. rotate the reference image)\n",
384384
" # and then we map to the original image space T0.\n",
385-
" T_all <- Transform(T0)\n",
385+
" T_all <- CompositeTransform(T0)\n",
386386
" T_all$AddTransform(T_aug)\n",
387387
" aug_image <- Resample(original_image, reference_image, T_all,\n",
388388
" interpolator, default_intensity_value)\n",
@@ -449,7 +449,7 @@
449449
" img_center <- img$TransformContinuousIndexToPhysicalPoint(img$GetSize()/2.0)\n",
450450
" centering_transform$SetOffset(transform$GetInverse()$TransformPoint(img_center) - \n",
451451
" reference_center)\n",
452-
" centered_transform <- Transform(transform)\n",
452+
" centered_transform <- CompositeTransform(transform)\n",
453453
" centered_transform$AddTransform(centering_transform)\n",
454454
"\n",
455455
" # Set the augmenting transform's center so that rotation is around the image center.\n",
@@ -508,7 +508,7 @@
508508
" centering_transform <- TranslationTransform(dimension)\n",
509509
" img_center <- img$TransformContinuousIndexToPhysicalPoint(img$GetSize()/2.0)\n",
510510
" centering_transform$SetOffset(transform$GetInverse()$TransformPoint(img_center) - reference_center)\n",
511-
" centered_transform <- Transform(transform)\n",
511+
" centered_transform <- CompositeTransform(transform)\n",
512512
" centered_transform$AddTransform(centering_transform)\n",
513513
" \n",
514514
" flipped_transform <- AffineTransform(dimension) \n",

‎R/R_style_image.ipynb‎

Lines changed: 5 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -277,12 +277,7 @@
277277
{
278278
"cell_type": "code",
279279
"execution_count": null,
280-
"metadata": {
281-
"collapsed": true,
282-
"jupyter": {
283-
"outputs_hidden": true
284-
}
285-
},
280+
"metadata": {},
286281
"outputs": [],
287282
"source": [
288283
"img3d = GaborSource(\"sitkFloat32\", size=rep(64,3), sigma=rep(16, 3), mean=rep(32,3), frequency=.05)"
@@ -423,7 +418,7 @@
423418
"jupyter": {
424419
"outputs_hidden": false
425420
},
426-
"simpleitk_error_expected": "Exception in SITK"
421+
"simpleitk_error_expected": "Exception thrown in SimpleITK Add"
427422
},
428423
"outputs": [],
429424
"source": [
@@ -491,12 +486,7 @@
491486
{
492487
"cell_type": "code",
493488
"execution_count": null,
494-
"metadata": {
495-
"collapsed": true,
496-
"jupyter": {
497-
"outputs_hidden": true
498-
}
499-
},
489+
"metadata": {},
500490
"outputs": [],
501491
"source": [
502492
"m <- (img > 90) != (img > 150)"
@@ -535,12 +525,7 @@
535525
{
536526
"cell_type": "code",
537527
"execution_count": null,
538-
"metadata": {
539-
"collapsed": true,
540-
"jupyter": {
541-
"outputs_hidden": true
542-
}
543-
},
528+
"metadata": {},
544529
"outputs": [],
545530
"source": [
546531
"sz <- 512\n",
@@ -572,12 +557,7 @@
572557
{
573558
"cell_type": "code",
574559
"execution_count": null,
575-
"metadata": {
576-
"collapsed": true,
577-
"jupyter": {
578-
"outputs_hidden": true
579-
}
580-
},
560+
"metadata": {},
581561
"outputs": [],
582562
"source": [
583563
"system.time(((im1 * im2) / im3) > 24)\n",

0 commit comments

Comments
 (0)