sitk::ERROR: No ImageJ/Fiji application found.
目录
sitk::ERROR: No ImageJ/Fiji application found.
问题：
执行simpleITK框架进行图像配准时候发生如下错误：
sitk::ERROR: No ImageJ/Fiji application found.
执行命令如下，可以使用不同的变换器。
python dalign.py 1703801.jpg 1703801_1.jpg composite.tfm
python dalign.py 1703801.jpg 1703801_1.jpg euler2D.tfm
python dalign.py 1703801.jpg 1703801_1.jpg RIRE_training_001_CT_2_mr_T1.tfm
python dalign.py 1703801.jpg 1703801_1.jpg composescaleskewversor.tfm
python dalign.py 1703801.jpg 1703801_1.jpg affine.tfm
import SimpleITK as sitk
import sys
import os
def command_iteration(filter):
print(f"{filter.GetElapsedIterations():3} = {filter.GetMetric():10.5f}")
if len(sys.argv) < 4:
print(
f"Usage: {sys.argv[0]}"
+ " <fixedImageFilter> <movingImageFile> <outputTransformFile>"
)
sys.exit(1)
fixed = sitk.ReadImage(sys.argv[1], sitk.sitkFloat32)
moving = sitk.ReadImage(sys.argv[2], sitk.sitkFloat32)
matcher = sitk.HistogramMatchingImageFilter()
matcher.SetNumberOfHistogramLevels(1024)
matcher.SetNumberOfMatchPoints(7)
matcher.ThresholdAtMeanIntensityOn()
moving = matcher.Execute(moving, fixed)
# The basic Demons Registration Filter
# Note there is a whole family of Demons Registration algorithms included in
# SimpleITK
demons = sitk.DemonsRegistrationFilter()
demons.SetNumberOfIterations(50)
# Standard deviation for Gaussian smoothing of displacement field
demons.SetStandardDeviations(1.0)
demons.AddCommand(sitk.sitkIterationEvent, lambda: command_iteration(demons))
displacementField = demons.Execute(fixed, moving)
print("-------")
print(f"Number Of Iterations: {demons.GetElapsedIterations()}")
print(f" RMS: {demons.GetRMSChange()}")
outTx = sitk.DisplacementFieldTransform(displacementField)
sitk.WriteTransform(outTx, sys.argv[3])
if "SITK_NOSHOW" not in os.environ:
resampler = sitk.ResampleImageFilter()
resampler.SetReferenceImage(fixed)
resampler.SetInterpolator(sitk.sitkLinear)
resampler.SetDefaultPixelValue(100)
resampler.SetTransform(outTx)
out = resampler.Execute(moving)
simg1 = sitk.Cast(sitk.RescaleIntensity(fixed), sitk.sitkUInt8)
simg2 = sitk.Cast(sitk.RescaleIntensity(out), sitk.sitkUInt8)
# Use the // floor division operator so that the pixel type is
# the same for all three images which is the expectation for
# the compose filter.
cimg = sitk.Compose(simg1, simg2, simg1 // 2.0 + simg2 // 2.0)
sitk.Show(cimg, "DeformableRegistration1 Composition")解决：
注意：fiji软件包的底层环境是java，所以需要提前安装好java哦。
可以再cmd中输入java命令测试，你的系统是否已经安装好了java.
下载fiji软件包：笔者选择windows64位
下载完成之后，解压，会得到一个叫做Fiji.app的文件夹。
将Fiji.app的文件夹拷贝包笔者使用的anaconda主环境的Scripts文件夹中。
D:\anaconda\Scripts\Fiji.app
OK了
完整错误：
(base) C:\Users\users>python align.py 1703801.jpg 1703801_1.jpg euler2D.tfm
1 = 316.08310
2 = 309.61603
3 = 305.84348
4 = 303.55265
5 = 301.97677
6 = 300.83932
7 = 299.98187
8 = 299.30239
9 = 298.74999
10 = 298.26859
11 = 297.87110
12 = 297.51645
13 = 297.20165
14 = 296.92658
15 = 296.66421
16 = 296.44000
17 = 296.22853
18 = 296.03984
19 = 295.86223
20 = 295.70708
21 = 295.54896
22 = 295.39734
23 = 295.27245
24 = 295.14585
25 = 295.02095
26 = 294.90249
27 = 294.78907
28 = 294.69944
29 = 294.59759
30 = 294.51432
31 = 294.42624
32 = 294.35778
33 = 294.27413
34 = 294.21444
35 = 294.13871
36 = 294.07736
37 = 294.01093
38 = 293.96671
39 = 293.89736
40 = 293.85241
41 = 293.79037
42 = 293.75224
43 = 293.69498
44 = 293.66584
45 = 293.60078
46 = 293.57719
47 = 293.52466
48 = 293.49716
49 = 293.45349
50 = 293.41868
-------
Number Of Iterations: 50
RMS: 0.25455084462799155
Traceback (most recent call last):
File "align.py", line 61, in <module>
sitk.Show(cimg, "DeformableRegistration1 Composition")
File "D:\anaconda\lib\site-packages\SimpleITK\SimpleITK.py", line 7768, in Show
return _SimpleITK.Show(*args, **kwargs)
RuntimeError: Exception thrown in SimpleITK Show: D:\a\1\sitk\Code\IO\src\sitkImageViewer.cxx:620:
sitk::ERROR: No ImageJ/Fiji application found.
(base) C:\Users\users>
参考：simpleITK
参考：https://blog.csdn.net/weixin_44727457/article/details/109661412
参考：https://blog.csdn.net/Magician0619/article/details/124046418
