Problem with runPipelineNode then writeImageLocalFile

[yh3ds]

Hello,
I try to adapt BinShrink example to write the ShrinkImage on the hard drive (using writeImageLocalFile).

If I just load the image and write it, I don t have any problem.
If I load the image, runPipelineNode with hello.cxx (the code from the sample) and then try to write the outputs on the disk. I have nothing written.... is there a bug or am I doing something wrong ?

Thanks a lot

---

Here are the sources used

---

index.js

const path = require('path')
const runPipelineNode = require('itk/runPipelineNode.js')

const readImageLocalFile = require('itk/readImageLocalFile.js')
const writeImageLocalFile = require('itk/writeImageLocalFile.js')

const IOTypes = require('itk/IOTypes.js')

const pipelinePath = path.resolve(__dirname, 'web-build', 'hello' )

const testInputFilePath = path.resolve(__dirname, 'cthead1.png')
const testOutputFilePath = path.resolve(__dirname, 'cthead1Shrink.png')

/* * /
// Working piece of code
readImageLocalFile(testInputFilePath)
.then(function (image) {
const useCompression = false
return writeImageLocalFile(useCompression, image, testOutputFilePath)
})
/* */
// Piece of code not with bug
readImageLocalFile(testInputFilePath)
.then(function (image) {
const args = ['cthead1.png.json', 'cthead1Shrink.png.json', '4']
const desiredOutputs = [
{ path: args[1], type: IOTypes.Image }
]
const inputs = [
{ path: args[0], type: IOTypes.Image, data: image }
]

  return runPipelineNode(pipelinePath, args, desiredOutputs, inputs)
}).then(function ({stdout, stderr, outputs}) {

    const useCompression = false
    return writeImageLocalFile(useCompression, outputs[0].data, testOutputFilePath)
}).then(function () {
    console.log("DEBUG - Script runned - Output written on disk")
})

/* */

---

hello.cxx

#include

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"

#include "itkBinShrinkImageFilter.h"

int main( int argc, char *argv[] ) {

// Test from website
if( argc < 4 )
{
std::cerr << "Usage: " << argv[0] << " " << std::endl;
return EXIT_FAILURE;
}

std::cout << "Inside js coming from cxx" << std::endl;

const char * inputImageFile = argv[1];
const char * outputImageFile = argv[2];
unsigned int shrinkFactor = atoi( argv[3] );

using PixelType = unsigned char;
constexpr unsigned int Dimension = 2;
using ImageType = itk::Image< PixelType, Dimension >;

using ReaderType = itk::ImageFileReader< ImageType >;
auto reader = ReaderType::New();
reader->SetFileName( inputImageFile );

using ShrinkFilterType = itk::BinShrinkImageFilter< ImageType, ImageType >;
auto shrinker = ShrinkFilterType::New();
shrinker->SetInput( reader->GetOutput() );
shrinker->SetShrinkFactors( shrinkFactor );

using WriterType = itk::ImageFileWriter< ImageType >;
auto writer = WriterType::New();
writer->SetInput( shrinker->GetOutput() );
writer->SetFileName( outputImageFile );

try
{
writer->Update();
}
catch( itk::ExceptionObject & error )
{
std::cerr << "Error: " << error << std::endl;
return EXIT_FAILURE;
}

return EXIT_SUCCESS;

}

---

CMakeLists.txt

cmake_minimum_required(VERSION 3.10)
project(HelloWorld)

FIND_PACKAGE ( ITK )

IF ( ITK_FOUND )
INCLUDE( ${ITK_USE_FILE} )
ELSE (ITK_FOUND)
MESSAGE (FATAL ERROR
"itk not found. Il est ou?")
ENDIF( ITK_FOUND )

set(io_components ITKImageIO)
if(EMSCRIPTEN)
set(io_components BridgeJavaScript)
endif()
find_package(ITK REQUIRED
COMPONENTS ${io_components}
ITKImageGrid
)
include(${ITK_USE_FILE})

if(EMSCRIPTEN)
include(ITKBridgeJavaScript)
web_add_executable(hello hello.cxx)
web_target_link_libraries(hello ${ITK_LIBRARIES})
else()
add_executable(hello hello.cxx)
target_link_libraries(hello ${ITK_LIBRARIES})
endif()

[thewtex]

Hi @yh3ds ,

I think we are running into Node behavior where the process is exiting before the promises have resolved.

[yh3ds]

Hi @thewtex ,
maybe but I m not sure. At least, it looks strange when I write logs to follow the process.
Indeed I get :

DEBUG - Script runned - Before read image
DEBUG - Script runned - Image read, before run pipeline
Inside js coming from cxx - START
Inside js coming from cxx - END
DEBUG - Script runned - Pipeline runned, before write output on disk

Which looks like expected.
Nonetheless, there is one last log missing (I put on when writing output on disk is over. I tested when I just read and write directly and it is printed correctly)

I can imagine two possibilities for the problem :

---

Question 1

Would it be possible that image coming from run node is corrupted or different than expected ?

Indeed if I log what I m going to write in case of working case (just read / write), I got :

DEBUG - Write output on disk - image : Image {
imageType:
ImageType {
dimension: 2,
componentType: 'uint8_t',
pixelType: 2,
components: 3 },
name: 'Image',
origin: [ 0, 0 ],
spacing: [ 1, 1 ],
direction: Matrix { rows: 2, columns: 2, data: [ 1, 0, 0, 1 ] },
size: [ 256, 256 ],
data:
Uint8Array [
0,
0,
0,
0,
...

But with the 'failing' pipeline, I got :

DEBUG - Write output on disk - outputs[0].data : { imageType:
{ dimension: 2,
componentType: 'uint8_t',
pixelType: 1,
components: 1 },
origin: [ 1.5, 1.5 ],
spacing: [ 4, 4 ],
direction: [ 1, 0, 0, 1 ],
size: [ 64, 64 ],
data: ArrayBuffer { byteLength: 4096 } }

But this second image looks strange isn t it ?
So maybe it is a problem with the cxx ?

---

Question 2

In the .cxx converted in js, we finish the script with writer->Update(); I guess we don't wait for this Update method to be finished and then we return.
So maybe the problem is just coming from this ?
We need (in a way or another) to force or cxx (converted in js) to wait the end of this Update before exiting ?

Thanks a lot,
Yves

[thewtex]

Re: Question 1: that looks OK to me.

Re: Question 2: the executable will run synchronously and it should not return until your .cxx calls return from main.

I recently added a synchronous API for running in Node. Once it has been released, I will ping you so we can see if that fixed your problem.

[thewtex]

@yh3ds itk.js 9.2.0 has been released. Could you please try the synchronous API? i.e.

const image = readImageLocalFileSync(testInputFilePath)
const result = runPipelineNodeSync(pipelinePath, args, outputs, inputs) 
[....]

[thewtex]

@yh3ds I assume the *Sync functions solved your issue. If there are still problems, please re-open.