ITK ERROR: CenteredTransformInitializer: Fixed Image has not been set #437

amirreza1998 · 2023-03-12T04:27:32Z

hi

i have problem with registration with ants. i install ants with pip in windows os but when I try this code below for registration I get error that is mentioned:
my code:

  registration_path = r"E:\python_venv/medvispy/mri_skull_plugin/savepath"
  input_sample_path = "E:\python_venv\input_sample2/MR_N1.nii"
  database_path = r"E:\python_venv/medvispy/mri_skull_plugin/plugin"

  fname1 = ants.image_read(str(input_sample_path))
   for i in range(1, 8):
       print(f"image {i} out of 8")
       fname2 = ants.image_read(str(database_path / "MR_N{}.nii".format(i)))
       print("error here")
       mytx4 = ants.registration(fixed=fname1, moving=fname2,
                                 type_of_transform="SyN",
                                 outprefix=str(registration_path / "diffToMR_N{}_".format(i)),
                                 reg_iterations=[100, 70, 50, 10],  # -m 100x70x50x10 \
                                 )
       print(mytx4)
       result1 = mytx4["warpedmovout"].to_nibabel()
       result2 = mytx4["warpedfixout"].to_nibabel()
       nib.save(result2, str(registration_path / "N{}_invToMRN1.nii".format(i)))
       nib.save(result1, str(registration_path / "N{}_diffToMRN1.nii".format(i)))

but the result is for each one of registration some thing like below:

 file 0000018600E3C1C0 does not exist . 
Exception Object caught: 

itk::ExceptionObject (0000000A275EBBC0)
Location: "unknown" 
File: D:\a\ANTsPy\ANTsPy\itksource\Modules\Registration\Common\include\itkCenteredTransformInitializer.hxx
Line: 31
Description: ITK ERROR: CenteredTransformInitializer(000001867F47D310): Fixed Image has not been set

{'warpedmovout': ANTsImage (LPI)
	 Pixel Type : float (float32)
	 Components : 1
	 Dimensions : (116, 142, 102)
	 Spacing    : (0.94, 0.94, 0.94)
	 Origin     : (54.05, 66.27, -47.47)
	 Direction  : [-1.  0.  0.  0. -1.  0.  0.  0.  1.]
, 'warpedfixout': ANTsImage (LPI)
	 Pixel Type : float (float32)
	 Components : 1
	 Dimensions : (116, 142, 102)
	 Spacing    : (0.94, 0.94, 0.94)
	 Origin     : (54.05, 66.27, -47.47)
	 Direction  : [-1.  0.  0.  0. -1.  0.  0.  0.  1.]
, 'fwdtransforms': [], 'invtransforms': []}

and in no one of them save fwdtransforms and invtransforms
I use same code ,library and python distribution in linux and every thing was alright but I need it in windows actually

The text was updated successfully, but these errors were encountered:

cookpa · 2023-03-16T17:59:09Z

Unfortunately, the pointer representation of the image doesn't work on Windows (see #345).

Looking at this it occurs to me, is the whole problem that the pointer address is incorrectly formatted on Windows? If "0000018600E3C1C0" was "0x000018600E3C1C0", would it work?

cookpa · 2023-03-16T19:19:08Z

I see this has already been considered

ANTsPy/ants/lib/LOCAL_antsImageWin.cxx

Lines 52 to 58 in ac6c264

    
           std::string ptrstr(py::capsule c) 
        
           { 
        
           	char buffer[50]; 
        
           	int n = sprintf(buffer, "0x%p", (void const *)c); 
        
           	std::string s(buffer, n); 
        
           	return s; 
        
           }

EDIT: this looks like it should work, because %p should format the pointer with the correct number of leading zeros.

cookpa · 2023-03-16T19:23:41Z

Related, #28

Perhaps #435 could be changed to edit string pointer representations?

cookpa · 2023-03-21T15:22:59Z

@amirreza1998 can you try installing a wheel from here?

https://github.com/ANTsX/ANTsPy/actions/runs/4478997465

cookpa · 2023-03-21T15:50:52Z

Actually I made a mistake, hold on

cookpa · 2023-03-21T17:36:59Z

OK fixed, this will hopefully read the pointer on Windows

https://github.com/ANTsX/ANTsPy/actions/runs/4481220355

stnava · 2023-03-21T19:01:06Z

Can’t we just run a test? automatically on each platform?

On Tue, Mar 21, 2023 at 1:37 PM Philip Cook ***@***.***> wrote: OK fixed, this will hopefully read the pointer on Windows https://github.com/ANTsX/ANTsPy/actions/runs/4481220355 — Reply to this email directly, view it on GitHub <#437 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACPE7VDYNDQ66JDWLDELJLW5HRMNANCNFSM6AAAAAAVX4EGBY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- brian

cookpa · 2023-03-21T19:15:09Z

Yes, I'm trying to run run_tests.sh and run_tests.bat now. But I don't know if run_tests.bat itself has been tested.

I'll make the tests part of the automated builds going forward.

cookpa · 2023-03-21T23:34:10Z

@stnava I think I'm making progress on my fork - readimage looks fixed, now working on writeimage. Will update later

cookpa · 2023-03-22T04:17:53Z

I think #442 has done it - tests run on all platforms

amirreza1998 · 2023-03-22T08:25:28Z

hi
thanks for your responses

I actually created python 3.7 venv and tried this version: pip install https://github.com/SGotla/ANTsPy/releases/download/0.1.7Win64/antspy-0.1.7-cp37-cp37m-win_amd64.whl that has been mentioned in #435 and every think become alright I enthusiasm to use https://github.com/ANTsX/ANTsPy/actions/runs/4478997465 and try it in windows

thanks a lot

amirreza1998 · 2023-03-23T09:40:03Z

I try this version [antspyx-0.3.8-cp39-win_amd64] and everything is smoothly and alright

cookpa · 2023-03-23T11:41:07Z

Thanks for the update!

amirreza1998 · 2023-03-26T15:00:29Z

i want to try to create template by ants.build_template and get this error :

Exception Object caught: 

itk::ImageFileWriterException (000000E7179EB068)
Location: "unknown" 
File: D:\a\ANTsPy\ANTsPy\itksource\Modules\IO\ImageBase\include\itkImageFileWriter.hxx
Line: 117
Description:  Could not create IO object for writing file 000002462225CAD0
  Tried to create one of the following:
    BMPImageIO
    BioRadImageIO
    Bruker2dseqImageIO
    GDCMImageIO
    GE4ImageIO
    GE5ImageIO
    GiplImageIO
    HDF5ImageIO
    JPEGImageIO
    JPEG2000ImageIO
    LSMImageIO
    MGHImageIO
    MINCImageIO
    MRCImageIO
    MetaImageIO
    NiftiImageIO
    NrrdImageIO
    PNGImageIO
    StimulateImageIO
    TIFFImageIO
    VTKImageIO
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

ntustison · 2023-03-26T19:54:04Z

This appears to be unrelated to the original posting. Please open a separate issue.

amirreza1998 · 2023-03-26T20:39:46Z

I think it's related. still have a problem with the pointer because I inspected the source code of create a template and it has registration on it but the issue of saving the warp file of transition has been solved
and also in registration show this message but doesn't cause any error and stops in the code

ntustison · 2023-03-26T20:44:13Z

Are you able to run the code that you originally posted?

amirreza1998 · 2023-03-26T21:11:53Z

this is the result of original code above:

Exception Object caught: 

itk::ImageFileWriterException (0000007E8ABEBD08)
Location: unknown
File: D:\a\ANTsPy\ANTsPy\itksource\Modules\IO\ImageBase\include\itkImageFileWriter.hxx
Line: 117
Description:  Could not create IO object for writing file 000001CF1AE8FE30
  Tried to create one of the following:
    BMPImageIO
    BioRadImageIO
    Bruker2dseqImageIO
    GDCMImageIO
    GE4ImageIO
    GE5ImageIO
    GiplImageIO
    HDF5ImageIO
    JPEGImageIO
    JPEG2000ImageIO
    LSMImageIO
    MGHImageIO
    MINCImageIO
    MRCImageIO
    MetaImageIO
    NiftiImageIO
    NrrdImageIO
    PNGImageIO
    StimulateImageIO
    TIFFImageIO
    VTKImageIO
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.


{"warpedmovout": ANTsImage (LPI)
         Pixel Type : float (float32)
         Components : 1
         Dimensions : (116, 142, 102)
         Spacing    : (0.94, 0.94, 0.94)
         Origin     : (54.05, 66.27, -47.47)
         Direction  : [-1.  0.  0.  0. -1.  0.  0.  0.  1.]
, "warpedfixout": ANTsImage (LPI)
         Pixel Type : float (float32)
         Components : 1
         Dimensions : (116, 142, 102)
         Spacing    : (0.94, 0.94, 0.94)
         Origin     : (54.05, 66.27, -47.47)
         Direction  : [-1.  0.  0.  0. -1.  0.  0.  0.  1.]
, 'fwdtransforms': ['C:\\Users\\amirreza\\Desktop\\result_reg\\diffToMR_N2_1Warp.nii.gz', 'C:\\Users\\amirreza\\Desktop\\result_reg\\diffToMR_N2_0GenericAffine.mat'], 'invtransforms': 
['C:\\Users\\amirreza\\Desktop\\result_reg\\diffToMR_N2_0GenericAffine.mat', 'C:\\Users\\amirreza\\Desktop\\result_reg\\diffToMR_N2_1InverseWarp.nii.gz']}

it's working ok but still, give exceptions at the beginning
but when I run to create a temple, it gets stuck after the first iteration and doesn't start the second iteration.
my code:

xavg,return_list = ants.build_template(
                iterations=2	#  -i 4 \
                ,gradient_step = 0.25	#  -g 0.25 \
                ,initial_template=fname1	#  -z GRAMFC_Template39404142_N7.nii\
                ,image_list = list_of_fnames	#	${inputPath}/N*_NLAff_diff.nii
                ,warp_path = warp_path
                ,**kwargs
                )

ntustison · 2023-03-26T21:16:32Z

This is the result when you run the original code? Ie

  registration_path = r"E:\python_venv/medvispy/mri_skull_plugin/savepath"
  input_sample_path = "E:\python_venv\input_sample2/MR_N1.nii"
  database_path = r"E:\python_venv/medvispy/mri_skull_plugin/plugin"

  fname1 = ants.image_read(str(input_sample_path))
   for i in range(1, 8):
       print(f"image {i} out of 8")
       fname2 = ants.image_read(str(database_path / "MR_N{}.nii".format(i)))
       print("error here")
       mytx4 = ants.registration(fixed=fname1, moving=fname2,
                                 type_of_transform="SyN",
                                 outprefix=str(registration_path / "diffToMR_N{}_".format(i)),
                                 reg_iterations=[100, 70, 50, 10],  # -m 100x70x50x10 \
                                 )
       print(mytx4)
       result1 = mytx4["warpedmovout"].to_nibabel()
       result2 = mytx4["warpedfixout"].to_nibabel()
       nib.save(result2, str(registration_path / "N{}_invToMRN1.nii".format(i)))
       nib.save(result1, str(registration_path / "N{}_diffToMRN1.nii".format(i)))

amirreza1998 · 2023-03-26T21:17:47Z

yes

ntustison · 2023-03-26T21:19:36Z

Okay, heavily simplify the code to a single ants.registration call and repost.

amirreza1998 · 2023-03-26T21:25:08Z

for more information the error that happend in create template is :


  File "E:\python_venv\medvispy\mri_skull_plugin\ants_override\build_template.py", line 161, in build_template
    xavg = xavg * blending_weight + utils.iMath(xavg, "Sharpen") * (
  File "E:\python_venv\medvispy\venv\lib\site-packages\ants\utils\iMath.py", line 106, in iMath
    libfn(processed_args)
untimeError: D:\a\ANTsPy\ANTsPy\itksource\Modules\IO\ImageBase\include\itkImageFileWriter.hxx:117:
 Could not create IO object for writing file 0000020D4F604CD0
    MRCImageIO
    VTKImageIO
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

ntustison · 2023-03-26T21:30:21Z

Again, I think there's a misunderstanding because you keep referring to "template building" but there was no template building in your original post. Rather, you just iterated a bunch of ants.registration calls

Tell me, does the following work:

import ants

r16 = ants.image_read(ants.get_ants_data("r16"))
r64 = ants.image_read(ants.get_ants_data("r64"))
reg = ants.registration(r16, r64, type_of_transform="SyN", verbose=True)

amirreza1998 · 2023-03-26T22:03:22Z

this is the result and it doesn't work :

itk::ImageFileWriterException (000000F10CBEBBA0)
Location: "unknown"
File: D:\a\ANTsPy\ANTsPy\itksource\Modules\IO\ImageBase\include\itkImageFileWriter.hxx
Line: 117
Description:  Could not create IO object for writing file 0000022DF5626DC0
  Tried to create one of the following:
    BMPImageIO
    BioRadImageIO
    Bruker2dseqImageIO
    GDCMImageIO
    GE4ImageIO
    GE5ImageIO
    GiplImageIO
    HDF5ImageIO
    JPEGImageIO
    JPEG2000ImageIO
    LSMImageIO
    MGHImageIO
    MINCImageIO
    MRCImageIO
    MetaImageIO
    NiftiImageIO
    NrrdImageIO
    PNGImageIO
    StimulateImageIO
    TIFFImageIO
    VTKImageIO
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.



Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "E:\python_venv\medvispy\venv\lib\site-packages\ants\registration\interface.py", line 1390, in registration
    raise RuntimeError(f"Registration failed with error code {reg_exit}")
RuntimeError: Registration failed with error code 1

stnava · 2023-03-26T22:31:27Z

May need to install latest version - make sure other versions are purged ….

On Sun, Mar 26, 2023 at 6:03 PM amirreza ***@***.***> wrote: this is result and it don't work : itk::ImageFileWriterException (000000F10CBEBBA0) Location: "unknown" File: D:\a\ANTsPy\ANTsPy\itksource\Modules\IO\ImageBase\include\itkImageFileWriter.hxx Line: 117 Description: Could not create IO object for writing file 0000022DF5626DC0 Tried to create one of the following: BMPImageIO BioRadImageIO Bruker2dseqImageIO GDCMImageIO GE4ImageIO GE5ImageIO GiplImageIO HDF5ImageIO JPEGImageIO JPEG2000ImageIO LSMImageIO MGHImageIO MINCImageIO MRCImageIO MetaImageIO NiftiImageIO NrrdImageIO PNGImageIO StimulateImageIO TIFFImageIO VTKImageIO You probably failed to set a file suffix, or set the suffix to an unsupported type. Traceback (most recent call last): File "<stdin>", line 1, in <module> File "E:\python_venv\medvispy\venv\lib\site-packages\ants\registration\interface.py", line 1390, in registration raise RuntimeError(f"Registration failed with error code {reg_exit}") RuntimeError: Registration failed with error code 1 — Reply to this email directly, view it on GitHub <#437 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACPE7QUFD2JUNT6RSVR4ODW6C4LLANCNFSM6AAAAAAVX4EGBY> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- brian

cookpa · 2023-03-27T00:34:53Z

Windows tests all look good here

https://github.com/ANTsX/ANTsPy/actions/runs/4524955037

amirreza1998 · 2023-04-11T07:13:31Z

yes it solved thanks alot

This was referenced Mar 16, 2023

Added ANTsSerializer to replace previous _int_antsProcessArguments and get_pointer_string #435

Closed

ENH: Read Windows pointers ANTsX/ANTs#1513

Merged

cookpa closed this as completed Mar 23, 2023

ntustison reopened this Mar 26, 2023

amirreza1998 closed this as completed Apr 11, 2023

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

ITK ERROR: CenteredTransformInitializer: Fixed Image has not been set #437

ITK ERROR: CenteredTransformInitializer: Fixed Image has not been set #437

amirreza1998 commented Mar 12, 2023 •

edited

Loading

cookpa commented Mar 16, 2023

cookpa commented Mar 16, 2023 •

edited

Loading

cookpa commented Mar 16, 2023

cookpa commented Mar 21, 2023

cookpa commented Mar 21, 2023

cookpa commented Mar 21, 2023

stnava commented Mar 21, 2023 via email

cookpa commented Mar 21, 2023

cookpa commented Mar 21, 2023

cookpa commented Mar 22, 2023

amirreza1998 commented Mar 22, 2023

amirreza1998 commented Mar 23, 2023

cookpa commented Mar 23, 2023

amirreza1998 commented Mar 26, 2023 •

edited

Loading

ntustison commented Mar 26, 2023

amirreza1998 commented Mar 26, 2023

ntustison commented Mar 26, 2023

amirreza1998 commented Mar 26, 2023 •

edited

Loading

ntustison commented Mar 26, 2023

amirreza1998 commented Mar 26, 2023

ntustison commented Mar 26, 2023

amirreza1998 commented Mar 26, 2023

ntustison commented Mar 26, 2023

amirreza1998 commented Mar 26, 2023 •

edited

Loading

stnava commented Mar 26, 2023 via email

cookpa commented Mar 27, 2023

amirreza1998 commented Apr 11, 2023

ITK ERROR: CenteredTransformInitializer: Fixed Image has not been set #437

ITK ERROR: CenteredTransformInitializer: Fixed Image has not been set #437

Comments

amirreza1998 commented Mar 12, 2023 • edited Loading

cookpa commented Mar 16, 2023

cookpa commented Mar 16, 2023 • edited Loading

cookpa commented Mar 16, 2023

cookpa commented Mar 21, 2023

cookpa commented Mar 21, 2023

cookpa commented Mar 21, 2023

stnava commented Mar 21, 2023 via email

cookpa commented Mar 21, 2023

cookpa commented Mar 21, 2023

cookpa commented Mar 22, 2023

amirreza1998 commented Mar 22, 2023

amirreza1998 commented Mar 23, 2023

cookpa commented Mar 23, 2023

amirreza1998 commented Mar 26, 2023 • edited Loading

ntustison commented Mar 26, 2023

amirreza1998 commented Mar 26, 2023

ntustison commented Mar 26, 2023

amirreza1998 commented Mar 26, 2023 • edited Loading

ntustison commented Mar 26, 2023

amirreza1998 commented Mar 26, 2023

ntustison commented Mar 26, 2023

amirreza1998 commented Mar 26, 2023

ntustison commented Mar 26, 2023

amirreza1998 commented Mar 26, 2023 • edited Loading

stnava commented Mar 26, 2023 via email

cookpa commented Mar 27, 2023

amirreza1998 commented Apr 11, 2023

amirreza1998 commented Mar 12, 2023 •

edited

Loading

cookpa commented Mar 16, 2023 •

edited

Loading

amirreza1998 commented Mar 26, 2023 •

edited

Loading

amirreza1998 commented Mar 26, 2023 •

edited

Loading

amirreza1998 commented Mar 26, 2023 •

edited

Loading