CODEWITHSUNDEEP
pythonpython-3.xsimpleitk
ananass
ananass

Reputation: 93

SimpleITK for image registration. Writing issue

I've installed from sources the SimpleITK package on Python3. When I perform the provided registration example : 

#!/usr/bin/env python    
#=========================================================================
#
#  Copyright NumFOCUS
#
#  Licensed under the Apache License, Version 2.0 (the "License");
#  you may not use this file except in compliance with the License.
#  You may obtain a copy of the License at
#
#         http://www.apache.org/licenses/LICENSE-2.0.txt
#
#  Unless required by applicable law or agreed to in writing, software
#  distributed under the License is distributed on an "AS IS" BASIS,
#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#  See the License for the specific language governing permissions and
#  limitations under the License.
#
#=========================================================================

from __future__ import print_function

import SimpleITK as sitk
import sys
import os


def command_iteration(method) :
    print("{0:3} = {1:10.5f} : {2}".format(method.GetOptimizerIteration(),
                               method.GetMetricValue(),
                               method.GetOptimizerPosition()))

if len ( sys.argv ) < 4:
    print( "Usage: {0} <fixedImageFilter> <movingImageFile>             
    <outputTransformFile>".format(sys.argv[0]))
    sys.exit ( 1 )


fixed = sitk.ReadImage(sys.argv[1], sitk.sitkFloat32)

moving = sitk.ReadImage(sys.argv[2], sitk.sitkFloat32)

R = sitk.ImageRegistrationMethod()
R.SetMetricAsMeanSquares()
R.SetOptimizerAsRegularStepGradientDescent(4.0, .01, 200 )
R.SetInitialTransform(sitk.TranslationTransform(fixed.GetDimension()))
R.SetInterpolator(sitk.sitkLinear)

R.AddCommand( sitk.sitkIterationEvent, lambda: command_iteration(R) )

outTx = R.Execute(fixed, moving)

print("-------")
print(outTx)
print("Optimizer stop condition: 
{0}".format(R.GetOptimizerStopConditionDescription()))
print(" Iteration: {0}".format(R.GetOptimizerIteration()))
print(" Metric value: {0}".format(R.GetMetricValue()))

sitk.WriteTransform(outTx,  sys.argv[3])

if ( not "SITK_NOSHOW" 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)
cimg = sitk.Compose(simg1, simg2, simg1//2.+simg2//2.)
sitk.Show( cimg, "ImageRegistration1 Composition" )

The execution with Python ImageRegistrationMethod1.py image_ref.tif image_moving.tif res.tif seems to work well until it comes to write the res.tif image and triggers the following error : 

TIFFReadDirectory: Warning, Unknown field with tag 50838 (0xc696)         
encountered.
TIFFReadDirectory: Warning, Unknown field with tag 50839 (0xc697)     
encountered.
TIFFReadDirectory: Warning, Unknown field with tag 50838 (0xc696) 
encountered.
TIFFReadDirectory: Warning, Unknown field with tag 50839 (0xc697)     
encountered.
-------
itk::simple::Transform
TranslationTransform (0x7fb2a54ec0f0)
RTTI typeinfo:   itk::TranslationTransform<double, 3u>
Reference Count: 2
Modified Time: 2196
Debug: Off
Object Name: 
Observers: 
none
Offset: [14.774, 10.57, 18.0612]

Optimizer stop condition: RegularStepGradientDescentOptimizerv4: Step 
too small after 22 iterations. Current step (0.0078125) is less than 
minimum step (0.01).
Iteration: 23
Metric value: 2631.5128202930223

Traceback (most recent call last):
File "ImageRegistrationMethod1.py", line 57, in <module>
sitk.WriteTransform(outTx,  sys.argv[3])
File "/usr/local/lib/python3.7/site- 
packages/SimpleITK/SimpleITK.py", line 5298, in 
WriteTransform
return _SimpleITK.WriteTransform(transform, filename)
RuntimeError: Exception thrown in SimpleITK WriteTransform: 


itk::ERROR: TransformFileWriterTemplate(0x7faa4fcfce70): Could not 
create Transform IO 
object for writing file /Users/anass/Desktop/res.tif
Tried to create one of the following:
HDF5TransformIOTemplate
HDF5TransformIOTemplate
MatlabTransformIOTemplate
MatlabTransformIOTemplate
TxtTransformIOTemplate
TxtTransformIOTemplate
You probably failed to set a file suffix, or
set the suffix to an unsupported type.

I really don't know why I'm getting this error since the code was built from source. Any help please?

Upvotes: 1

Views: 1924

Answers (2)

Elliot
Elliot

Reputation: 13

if you want to write dicom as file output, please try this one.

writer.SetFileName(os.path.join('transformed.dcm'))
writer.Execute(cimg)

Upvotes: 0

Dave Chen
Dave Chen

Reputation: 2085

The result of running the ImageRegistrationMethod1 example is a transform. SimpleITK supports a number of file formats for transformations, including a text file (.txt), a Matlab file (.mat) and a HDF5Tranform (.hdf5). That does not include a .tif file, which is an image file, not a transform.

You can read more about it on the Transform section of the SimpleITK IO page:

https://simpleitk.readthedocs.io/en/master/IO.html#transformations

In the case of this example, the transform produced is a 3-d translation. So if you've chosen a .txt file output, you can see the X, Y and Z translations on the Parameters line.

Upvotes: 1

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