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dcmjs is a javascript cross-compile of dcmtk (dcmtk.org).

Home Page: http://dcmjs.org

License: Other

CMake 99.64% JavaScript 0.25% Shell 0.11%

dicom javascript imaging open-science reproducible-science webassembly asmjs wasm emscripten dcmtk

dcmjs's People

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pieper jcfr matthiasg ming-hai 151706061 swederik lynch829 nagyistge simonbiggs felepeg rickryo ihelpsoft fedorov empeywong willyci yjsyyyjszf amol-t mystlive ljp006 vitgou jackyshaw2017

dcmjs's Issues

conflict with dcmtk in /usr/local/lib - can't find libc.h

On a mac with dcmtk installed via homebrew the emscripten build of dcmtk was finding ofstd headers from /usr/local/lib rather than the ones in DCMTK-build. Uninstalling dcmtk from brew fixes this.

Link to www.dcmjs.org in README.md is broken

Link to www.dcmjs.org in README.md is broken: there is no "www".dcmjs.org (only dcmjs.org).

Build errors with libxml2

While building the project, I am getting a failure

LibXml2 build seems to have completed without errors, although there seems to be an error in PNG.

Is this project still maintained? Can someone help?

second invocation of make causes new things to build

It's happened on two fresh builds now that I'll run make once and only the selected apps get built.

But then I'll run make again and a bunch of other apps, like the dicom networking apps, get built.

I suspect there's something wrong with the cmake code that enables and disables app building (BUILD_dcm*_APP).

Re-factor demos onto a single page using boostrap

I have a problem: when I build it and the dcmj2pnm app is in the build, the build is faild with this error:
In file included from /work/dcmjs-build/DCMTK/dcmjpeg/apps/dcmj2pnm.cc:27:
/work/dcmjs-build/DCMTK/dcmjpeg/apps/../../dcmimage/apps/dcm2pnm.cc:121:10: fatal error: 'dcmtk/config/dcm2pnm_app.h' file not found
#include "dcmtk/config/dcm2pnm_app.h"
If I am right the problem is in the dcmtk source code, my question is that is there any option to change the version of the used dcmtk source? (If I am right You forked the dcmtk git repo and You use your own version of it. ) Can You give me a little description how can I use an other version of the dcmtk? (On my machine I currently using the native c++ 3.6.2 and it is working well.)
thx

Fix build with BUILD_dsr2xml_APP set to ON

[ 80%] Building CXX object src/CMakeFiles/dcmjs.dir/dcmjs.cpp.o
WARNING:root:not all asm.js optimizations are possible with ALLOW_MEMORY_GROWTH, disabling those. [-Walmost-asm]
[100%] Linking CXX executable ../bin/dcmjs.js
WARNING:root:emcc: cannot find library "nsl"
WARNING:root:emcc: cannot find library "socket"
WARNING:root:not all asm.js optimizations are possible with ALLOW_MEMORY_GROWTH, disabling those. [-Walmost-asm]
error: Linking globals named 'xmlParserMaxDepth': symbol multiply defined!
ERROR:root:Failed to run llvm optimizations: 
src/CMakeFiles/dcmjs.dir/build.make:102: recipe for target 'bin/dcmjs.js' failed

dcmsend can not open tcp connection

I build a dcm.js by myself, using Your description, I added the dcmsend during the build. But it is not working neither from cli and neither from browser. (If I am using the dcmsend from the installed dcmtk it works like charm)
Other dcmtk apps are working well (I tried dcmodify and dcmdump and both are working in the browser and in the cli too...).

command:
node dcmjs.js dcmsend localhost 6666 /working/1.dcm

This is the error message what I got for the above command :

Calling stub instead of signal()
F: cannot negotiate network association: Failed to establish association
F: 0006:0317 Peer aborted Association (or never connected)
F: 0006:031c TCP Initialization Error: Host is unreachable

Can You please give some hint about it?
My main goal is to make the dcmsend work in the browser.

Fix the unresolved symbols warnings

[...]
[100%] Building CXX object dcmpstat/apps/CMakeFiles/dcmpsmk.dir/dcmpsmk.cc.o
Linking CXX executable ../../bin/dcmpsmk.js
warning: unresolved symbol: syslog
warning: unresolved symbol: openlog
warning: unresolved symbol: gethostbyaddr_r
warning: unresolved symbol: closelog
warning: unresolved symbol: getsockopt
[...]

emscripten FS doc does not mention readdir

Need to edit the documentation and issue a pull request

dcmjs.js compiled by myself seems doesn't work on client side.

I download dcmjs project and run the below command then get the dcmjs.js file.
dockcross-browser-asmjs cmake -Bdcmjs-build -H. -GNinja
dockcross-browser-asmjs ninja -Cdcmjs-build
I run command node ./dcmjs.js dcmdump /working/test.dcm, it works very well.
But when I replace the same file with the dcmjs.js file in dcmjs.org website project. It seems doesn't work on client side.
Is there any wrong what I do or is it a bug？
I tried it on macOS High Sierra 10.13.6 and Ubuntu 16.04 and Ubuntu 18.04, It has the same problem.
When I test dump dicom, Chrome DevTools Terminal console warning and error information on the below:
Assertion failed: undefined
exception thrown: abort("Assertion failed: undefined") at Error
abort @ dcmjs.js:23
assert @ dcmjs.js:1
mount @ dcmjs.js:1
mount @ dcmjs.js:1
(anonymous) @ dcmjs.js:1
_emscripten_asm_const_i @ dcmjs.js:1
Yc @ dcmjs.js:8
(anonymous) @ dcmjs.js:23
callMain @ dcmjs.js:23
dcmjs.utils.execute @ utils.js:97
dcmdump @ dump.js:24
(anonymous) @ utils.js:110
load (async)
dcmjs.utils.readFile @ utils.js:109
readSelectedFiles @ dump.js:38
handleFileDrop @ dump.js:67

gzip invalid option

Gzip'ing dcmdspfn.js
/usr/bin/gzip: invalid option -- k
Try `gzip --help' for more information.
make[2]: *** [bin/dcmdspfn.js] Error 1
make[1]: *** [dcmimgle/apps/CMakeFiles/dcmdspfn.dir/all] Error 2
make: *** [all] Error 2

How to use this in NodeJS? Using `require('./dcmjs/dcmjs')` is failing

If I try:

const dcm = require('./dcmjs/dcmjs')

I get

Usage: /Users/dbousamra/Code/Projects/functor/src/dcm.js <appname> [options]

Is there a recommended approach to using from NodejS?

Fix CMP0074 policy warning

CMake Warning (dev) at /usr/share/cmake-3.13/Modules/FindPNG.cmake:51 (find_package):
  Policy CMP0074 is not set: find_package uses <PackageName>_ROOT variables.
  Run "cmake --help-policy CMP0074" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  CMake variable ZLIB_ROOT is set to:

    /work/dcmjs-build/ZLIB-install

  For compatibility, CMake is ignoring the variable.
Call Stack (most recent call first):
  CMake/3rdparty.cmake:178 (find_package)
  CMake/dcmtkPrepare.cmake:426 (include)
  CMakeLists.txt:17 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.

Build fails on M1 Mac

Hello,
I tried building dcmjs with a M1 Mac, but it did not succeed. I did the following:

docker run --rm --platform=linux/amd64 dockcross/web-wasm > ./dockcross-web-wasm
chmod +x dockcross-web-wasm
./dockcross-web-wasm -a "--platform=linux/amd64" cmake -Bdcmjs-build -H. -GNinja -Ddcmjs_USE_GIT_PROTOCOL=OFF
./dockcross-web-wasm -a "--platform=linux/amd64" ninja -Cdcmjs-build

The last command has the following output (slightly shortened):

WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
ninja: Entering directory `dcmjs-build'
[1/41] Performing download step (git clone) for 'ZLIB'
Cloning into 'ZLIB'...
HEAD is now at 66a7530 Add option ZLIB_MANGLE_PREFIX
[3/41] Performing download step (download, verify and extract) for 'LibXml2'
-- verifying file...
       file='/work/dcmjs-build/../dcmjs-download-cache/libxml2-2.9.8.tar.gz'
-- File already exists and hash match (skip download):
  file='/work/dcmjs-build/../dcmjs-download-cache/libxml2-2.9.8.tar.gz'
  MD5='b786e353e2aa1b872d70d5d1ca0c740d'
-- extracting...
     src='/work/dcmjs-download-cache/libxml2-2.9.8.tar.gz'
     dst='/work/dcmjs-build/LibXml2'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[4/41] Performing update step for 'ZLIB'
[5/41] No update step for 'LibXml2'
[7/41] Performing configure step for 'ZLIB'
loading initial cache file /work/dcmjs-build/ZLIB-prefix/tmp/ZLIB-cache-Release.cmake
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


CMake Warning (dev) at CMakeLists.txt:51 (ADD_LIBRARY):
  ADD_LIBRARY called with SHARED option but the target platform does not
  support dynamic linking.  Building a STATIC library instead.  This may lead
  to problems.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Configuring done
-- Generating done
-- Build files have been written to: /work/dcmjs-build/ZLIB-build
[9/41] Performing configure step for 'LibXml2'
loading initial cache file /work/dcmjs-build/LibXml2-prefix/tmp/LibXml2-cache-Release.cmake
CMake Warning (dev) at CMakeLists.txt:82 (add_library):
  ADD_LIBRARY called with SHARED option but the target platform does not
  support dynamic linking.  Building a STATIC library instead.  This may lead
  to problems.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Configuring done
-- Generating done
-- Build files have been written to: /work/dcmjs-build/LibXml2-build
[10/41] Performing build step for 'ZLIB'
[1/12] Building C object CMakeFiles/zlib.dir/compress.c.o
emcc: warning: linker setting ignored during compilation: 'ALLOW_MEMORY_GROWTH' [-Wunused-command-line-argument]
emcc: warning: linker setting ignored during compilation: 'ASSERTIONS' [-Wunused-command-line-argument]
emcc: warning: linker flag ignored during compilation: '--memory-init-file' [-Wunused-command-line-argument]
[2/12] Building C object CMakeFiles/zlib.dir/zutil.c.o
...
emcc: warning: linker setting ignored during compilation: 'ALLOW_MEMORY_GROWTH' [-Wunused-command-line-argument]
emcc: warning: linker setting ignored during compilation: 'ASSERTIONS' [-Wunused-command-line-argument]
emcc: warning: linker flag ignored during compilation: '--memory-init-file' [-Wunused-command-line-argument]
[12/12] Linking C static library libzlib.a
[11/41] Performing build step for 'LibXml2'
[1/45] Building C object CMakeFiles/xml2.dir/DOCBparser.c.o
emcc: warning: linker setting ignored during compilation: 'ALLOW_MEMORY_GROWTH' [-Wunused-command-line-argument]
emcc: warning: linker setting ignored during compilation: 'ASSERTIONS' [-Wunused-command-line-argument]
emcc: warning: linker flag ignored during compilation: '--memory-init-file' [-Wunused-command-line-argument]
...
emcc: warning: linker setting ignored during compilation: 'ALLOW_MEMORY_GROWTH' [-Wunused-command-line-argument]
emcc: warning: linker setting ignored during compilation: 'ASSERTIONS' [-Wunused-command-line-argument]
emcc: warning: linker flag ignored during compilation: '--memory-init-file' [-Wunused-command-line-argument]
/work/dcmjs-build/LibXml2/xmlmodule.c:32:14: warning: function 'xmlModulePlatformOpen' has internal linkage but is not defined [-Wundefined-internal]
static void *xmlModulePlatformOpen(const char *name);
             ^
/work/dcmjs-build/LibXml2/xmlmodule.c:90:22: note: used here
    module->handle = xmlModulePlatformOpen(name);
                     ^
/work/dcmjs-build/LibXml2/xmlmodule.c:34:12: warning: function 'xmlModulePlatformSymbol' has internal linkage but is not defined [-Wundefined-internal]
static int xmlModulePlatformSymbol(void *handle, const char *name, void **result);
           ^
/work/dcmjs-build/LibXml2/xmlmodule.c:130:10: note: used here
    rc = xmlModulePlatformSymbol(module->handle, name, symbol);
         ^
/work/dcmjs-build/LibXml2/xmlmodule.c:33:12: warning: function 'xmlModulePlatformClose' has internal linkage but is not defined [-Wundefined-internal]
static int xmlModulePlatformClose(void *handle);
           ^
/work/dcmjs-build/LibXml2/xmlmodule.c:166:10: note: used here
    rc = xmlModulePlatformClose(module->handle);
         ^
3 warnings generated.
[25/45] Building C object CMakeFiles/xml2.dir/uri.c.o
emcc: warning: linker setting ignored during compilation: 'ALLOW_MEMORY_GROWTH' [-Wunused-command-line-argument]
emcc: warning: linker setting ignored during compilation: 'ASSERTIONS' [-Wunused-command-line-argument]
emcc: warning: linker flag ignored during compilation: '--memory-init-file' [-Wunused-command-line-argument]
...
emcc: warning: linker setting ignored during compilation: 'ALLOW_MEMORY_GROWTH' [-Wunused-command-line-argument]
emcc: warning: linker setting ignored during compilation: 'ASSERTIONS' [-Wunused-command-line-argument]
emcc: warning: linker flag ignored during compilation: '--memory-init-file' [-Wunused-command-line-argument]
[45/45] Linking C static library libxml2.a
[12/41] Performing install step for 'ZLIB'
[0/1] Install the project...
-- Install configuration: "Release"
-- Installing: /work/dcmjs-build/ZLIB-install/lib/libzlib.a
-- Installing: /work/dcmjs-build/ZLIB-install/include/zlib.h
-- Installing: /work/dcmjs-build/ZLIB-install/include/zconf.h
-- Installing: /work/dcmjs-build/ZLIB-install/include/zlib_mangle.h
-- Installing: /work/dcmjs-build/ZLIB-install/include/zlibDllConfig.h
-- Installing: /work/dcmjs-build/ZLIB-install/doc/zlib-1.2.3/Copyright.txt
[13/41] No install step for 'LibXml2'
[17/41] Performing download step (download, verify and extract) for 'PNG'
-- Downloading...
   dst='/work/dcmjs-build/../dcmjs-download-cache/libpng-1.6.36.tar.xz'
   timeout='none'
   inactivity timeout='none'
-- Using src='http://download.sourceforge.net/libpng/libpng-1.6.36.tar.xz'
-- verifying file...
       file='/work/dcmjs-build/../dcmjs-download-cache/libpng-1.6.36.tar.xz'
-- Downloading... done
-- extracting...
     src='/work/dcmjs-download-cache/libpng-1.6.36.tar.xz'
     dst='/work/dcmjs-build/PNG'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[18/41] No update step for 'PNG'
[20/41] Performing configure step for 'PNG'
loading initial cache file /work/dcmjs-build/PNG-prefix/tmp/PNG-cache-Release.cmake
-- The ASM compiler identification is unknown
-- Found assembler: /emsdk/upstream/emscripten/emcc
-- Warning: Did not find file Compiler/-ASM
CMake Warning (dev) at CMakeLists.txt:42 (find_package):
  Policy CMP0074 is not set: find_package uses <PackageName>_ROOT variables.
  Run "cmake --help-policy CMP0074" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  CMake variable ZLIB_ROOT is set to:

    /work/dcmjs-build/ZLIB-install

  For compatibility, CMake is ignoring the variable.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found ZLIB: /work/dcmjs-build/ZLIB-install/lib/libzlib.so (found version "1.2.3") 
-- Performing Test HAVE_LD_VERSION_SCRIPT
-- Performing Test HAVE_LD_VERSION_SCRIPT - Success
-- Symbol prefix: 
CMake Warning (dev) at CMakeLists.txt:530 (add_library):
  ADD_LIBRARY called with SHARED option but the target platform does not
  support dynamic linking.  Building a STATIC library instead.  This may lead
  to problems.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Configuring done
-- Generating done
-- Build files have been written to: /work/dcmjs-build/PNG-build
[21/41] Performing build step for 'PNG'
ninja: error: '/work/dcmjs-build/ZLIB-install/lib/libzlib.so', needed by 'pngfix.js', missing and no known rule to make it
FAILED: PNG-prefix/src/PNG-stamp/PNG-build /work/dcmjs-build/PNG-prefix/src/PNG-stamp/PNG-build 
cd /work/dcmjs-build/PNG-build && /usr/bin/cmake --build . && /usr/bin/cmake -E touch /work/dcmjs-build/PNG-prefix/src/PNG-stamp/PNG-build
ninja: build stopped: subcommand failed.

How can I fix this?
Best regards
Niclas

Can't build on ubuntu 14.04

I installed the last version emscripten and did make -j5 like the given tutorial in the building section , but I'm ending up with a lot of errors in my CMakeFiles/CMakeError.log"

CMakeError.log.txt

Please any help would very appreciated.

Suppress warning - Disabling asm.js validation for memory growth

While commit e5881ec added support for dynamic memory allocation, it also generates a warnings that we may want to suppress.

WARNING  root: Disabling asm.js validation for memory growth (memory can grow, but you lose some amount of speed)

can't build on mac - missing 'python2' executable

Build fails by default because the executable is missing.

A workaround is:

$ ln -s /usr/bin/python2.7 /usr/local/bin/python2

File not found in node environment.

Hey guys this is more a question than an issue. I am trying to use this solution in node.js server side application. I was able to build dcmjs.js but when I try to execute it with node dcmjs.js dcmj2pnm x.dcm it fails with an error "F: No such file or directory: reading file: x.dcm".

I've tried multiple variations like using absolute path, prefixing a path with './', moving file to file system root, executing in git-bash environment. But with no success.

In READEME.md there is a clause:

Note that node executables do not have access to the local file system. To use dcmjs on a browser see the demos in the gh-pages branch.

But I did not found out how to pass the file to the environment where is the dcmjs.js executed.

Do you have any hints?

Thank you.

compilation error on mac 10.8.5

Any idea what's wrong?

/Users/arnaud/GITROOT/dcmjs/build/DCMTK/ofstd/include/dcmtk/ofstd/ofstream.h:43:2: error:
DCMTK needs stringstream or strstream type

error DCMTK needs stringstream or strstream type

^
/Users/arnaud/GITROOT/dcmjs/build/DCMTK/ofstd/include/dcmtk/ofstd/ofstream.h:118:23: error:
no type named 'strstream' in namespace 'std'
typedef STD_NAMESPACE strstream OFStringStream;
~~~~~~~~~~~~~ ^
/Users/arnaud/GITROOT/dcmjs/build/DCMTK/ofstd/include/dcmtk/ofstd/ofstream.h:119:23: error:
no type named 'ostrstream' in namespace 'std'
typedef STD_NAMESPACE ostrstream OFOStringStream;
~~~~~~~~~~~~~ ^
/Users/arnaud/GITROOT/dcmjs/build/DCMTK/ofstd/include/dcmtk/ofstd/ofstream.h:120:23: error:
no type named 'istrstream' in namespace 'std'
typedef STD_NAMESPACE istrstream OFIStringStream;
~~~~~~~~~~~~~ ^
4 errors generated.
ERROR root: compiler frontend failed to generate LLVM bitcode, halting

Any on going work on this project?

Dear Team,
You are amazing team and doing greate for medical imaging through this project. My concern is there is no recent activities updates in the project. I request you all to do active development with need of the current scenario.
Great projects are done with small incremental improvement.

libxml2 error on macOS

Hello

I followed instructions from the wiki but I get an error when executing the following command :

dockcross-browser-asmjs ninja -Cdcmjs-build

I get the following message :

ninja: error: '/work/dcmjs-build/LibXml2/.libs/libxml2.so', needed by 'lib/libxml2dcm.so.3.6.1', missing and no known rule to make it
FAILED: DCMTK-prefix/src/DCMTK-stamp/DCMTK-build
cd /work/dcmjs-build/DCMTK-build && /usr/bin/cmake --build . && /usr/bin/cmake -E touch /work/dcmjs-build/DCMTK-prefix/src/DCMTK-stamp/DCMTK-build
ninja: build stopped: subcommand failed.

What can I do to fix it ?

NB: I'm using macOS 10.13.6

Thx for your help.

Build wasm module

@thewtex Based on your experience with itk-js, could you point us to relevant documentation/example to make this happen.

Here are the emscripten options we currently use:

dcmjs/CMakeLists.txt

Lines 85 to 99 in fea79b9

 set(CMAKE_C_COMPILER "${EMSCRIPTEN_ROOT_PATH}/emcc") 

 set(CMAKE_CXX_COMPILER "${EMSCRIPTEN_ROOT_PATH}/em++") 

 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-warn-absolute-paths -s ALLOW_MEMORY_GROWTH=1 -s ASSERTIONS=1 --memory-init-file 0") 

 set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-warn-absolute-paths -s ALLOW_MEMORY_GROWTH=1 -s ASSERTIONS=1 --memory-init-file 0") 

 # Emscripten toolchain options 

 set(EMSCRIPTEN_TOOLCHAIN_OPTIONS 

 -DCMAKE_MODULE_PATH:PATH=${EMSCRIPTEN_ROOT_PATH}/cmake/Modules 

 -DCMAKE_TOOLCHAIN_FILE:FILEPATH=${EMSCRIPTEN_ROOT_PATH}/cmake/Modules/Platform/Emscripten.cmake 

 -DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER} 

 -DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS} 

 -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER} 

 -DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS} 

 -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE} 

 )

	set(CMAKE_C_COMPILER "${EMSCRIPTEN_ROOT_PATH}/emcc")
	set(CMAKE_CXX_COMPILER "${EMSCRIPTEN_ROOT_PATH}/em++")
	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-warn-absolute-paths -s ALLOW_MEMORY_GROWTH=1 -s ASSERTIONS=1 --memory-init-file 0")
	set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-warn-absolute-paths -s ALLOW_MEMORY_GROWTH=1 -s ASSERTIONS=1 --memory-init-file 0")

	# Emscripten toolchain options
	set(EMSCRIPTEN_TOOLCHAIN_OPTIONS
	-DCMAKE_MODULE_PATH:PATH=${EMSCRIPTEN_ROOT_PATH}/cmake/Modules
	-DCMAKE_TOOLCHAIN_FILE:FILEPATH=${EMSCRIPTEN_ROOT_PATH}/cmake/Modules/Platform/Emscripten.cmake
	-DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER}
	-DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS}
	-DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER}
	-DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS}
	-DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
	)