Merge pull request #1201 from thewtex/native-pixi

native pixi

.gitattributes

@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

.gitignore

@@ -97,3 +97,9 @@ CMakePresets.json
 
 packages/core/typescript/itk-wasm/test/data/cow.iwm
 packages/transform-io/typescript/demo-app/
+# pixi environments
+.pixi
+*.egg-info
+
+native/
+

docs/development/hacking_itk_wasm.md

@@ -36,66 +36,12 @@ ITK-Wasm's [C++ core](../introduction/parts.md#cxx-core) can be developed with n
 2. Build the `WebAssemblyInterface` module from this module against ITK
 3. Run the tests
 
-We recommend using the scripts provided in [dev-utils](../../dev-utils/) folder
-to [grab the source code](../../dev-utils/itk-wasm-native-get-source.sh) and run [native build commands](../../dev-utils/itk-wasm-native-build.sh).
-Note that you will need to include certain CXX compiler flags for the native windows build as shown in the script.
-The build script also demonstrates how to native build sub-packages such as @itk-wasm/dicom with additional ITK dependencies turned on.
+We recommend using [pixi](https://pixi.sh) with a bash shell (including on Windows).
+The steps to build and test the C++ core with a native toolchain are:
 
-From a command line, these steps in brief are:
-
-```sh
-# For Windows build (with mingw-bash or git-bash terminal)
-export CXXFLAGS="/Zc:__cplusplus /DNOMINMAX"
-
-# Build ITK
-git clone https://github.com/InsightSoftwareConsortium/ITK --branch=itkwasm-main-mutable
-# cmake -BITK-build -SITK -DBUILD_TESTING=OFF -DModule_MeshToPolyData=ON -DITK_MSVC_STATIC_RUNTIME_LIBRARY=ON
-cmake -BITK-build -SITK \
-    -DBUILD_TESTING=OFF \
-    -DCMAKE_CXX_STANDARD:STRING=17 \
-    -DCMAKE_BUILD_TYPE:STRING=Debug \
-    -DCMAKE_CONFIGURATION_TYPES:STRING=Debug \
-    -DBUILD_EXAMPLES:BOOL=OFF \
-    -DBUILD_TESTING:BOOL=OFF \
-    -DBUILD_SHARED_LIBS=OFF \
-    -DBUILD_STATIC_LIBS=ON \
-    -DDCMTK_LINK_STATIC=ON \
-    -DITK_LEGACY_REMOVE:BOOL=ON \
-    -DITK_BUILD_DEFAULT_MODULES:BOOL=ON \
-    -DModule_MeshToPolyData=ON \
-    -DDO_NOT_BUILD_ITK_TEST_DRIVER:BOOL=ON \
-    -DOPJ_USE_THREAD:BOOL=OFF \
-    -DDCMTK_WITH_THREADS:BOOL=OFF \
-    -DDCMTK_BUILD_APPS:BOOL=OFF \
-    -DNO_FLOAT_EXCEPTIONS:BOOL=ON \
-    -DITK_MSVC_STATIC_RUNTIME_LIBRARY=ON
-cmake --build ITK-build --config Debug -j16
-
-# Build the WebAssemblyInterface module from this module against ITK
-git clone https://github.com/InsightSoftwareConsortium/ITK-Wasm
-cmake -BITK-Wasm-build \
-    -SITK-Wasm \
-    -DBUILD_TESTING=ON \
-    -DCMAKE_CXX_STANDARD:STRING=20 \
-    -DCMAKE_BUILD_TYPE:STRING=Debug \
-    -DCMAKE_CONFIGURATION_TYPES:STRING=Debug \
-    -DBUILD_SHARED_LIBS=OFF \
-    -DITK_DIR=$PWD/ITK-build
-cmake --build ITK-Wasm-build --config Debug -j16
-
-# Run the tests
-ctest --test-dir itk-wasm-build
-
-cmake -Bpackages-dicom \
-    -SITK-Wasm/packages/dicom \
-    -DBUILD_TESTING=ON \
-    -DCMAKE_CXX_STANDARD:STRING=20 \
-    -DCMAKE_BUILD_TYPE:STRING=Debug \
-    -DCMAKE_CONFIGURATION_TYPES:STRING=Debug \
-    -DITK_DIR=$PWD/ITK-build
-
-cmake --build packages-dicom --config Debug -j16
-```
+1. Install pixi: `curl -fsSL https://pixi.sh/install.sh | bash`
+2. Clone [the ITK-Wasm GitHub repository](https://github.com/InsightSoftwareConsortium/ITK-Wasm)
+3. Run `pixi run test-itk-wasm`
 
 For additional guidance on C++ development, see the [ITK Software Guide].
 

itk_wasm_env.bash

@@ -0,0 +1,30 @@
+#!/usr/bin/env bash
+
+function die() {
+    echo "$1"
+    exit 1
+}
+
+if [$OSTYPE == "cygwin"] || [$OSTYPE == "msys"] || [$OSTYPE =="win32"]; then
+    echo "Windows platform detected ... adding \"/Zc:__cplusplus /DNOMINMAX\" to \$CXXFLAGS"
+    export CXXFLAGS="/Zc:__cplusplus /DNOMINMAX"
+fi
+
+export ITK_WASM_DCMTK_REPOSITORY=${ITK_WASM_DCMTK_REPOSITORY:-"https://github.com/InsightSoftwareConsortium/DCMTK"}
+export ITK_WASM_DCMTK_GIT_TAG=${ITK_WASM_DCMTK_GIT_TAG:-"fe7cff5de40b67ae0490d476ddf17689c06bcaf4"}
+
+export ITK_WASM_ITK_REPOSITORY=${ITK_WASM_ITK_REPOSITORY:-"https://github.com/KitwareMedical/ITK"}
+export ITK_WASM_ITK_BRANCH=${ITK_WASM_ITK_BRANCH:-"itkwasm-2024-05-20-5db055d7ad3b-1"}
+
+export ITK_WASM_NATIVE_WORKSPACE=${ITK_WASM_NATIVE_WORKSPACE:-$(pwd)/native}
+
+export ITK_WASM_ITK_SOURCE_DIR=${ITK_WASM_ITK_SOURCE_DIR:-${ITK_WASM_NATIVE_WORKSPACE}/ITK}
+export ITK_WASM_ITK_BUILD_DIR=${ITK_WASM_ITK_BUILD_DIR:-${ITK_WASM_NATIVE_WORKSPACE}/ITK-build}
+mkdir -p ${ITK_WASM_ITK_BUILD_DIR} || die "Could not create ITK build directory"
+
+
+export ITK_WASM_DICOM_TEST_DATA_HASH=${ITK_WASM_DICOM_TEST_DATA_HASH:-$(cat packages/dicom/package.json | jq -e -r '."itk-wasm"."test-data-hash"')}
+export ITK_WASM_DICOM_TEST_DATA_URLS=${ITK_WASM_DICOM_TEST_DATA_URLS:-$(cat packages/dicom/package.json | jq -e -r '."itk-wasm"."test-data-urls" | join(" ")')}
+
+export ITK_WASM_MESH_IO_TEST_DATA_HASH=${ITK_WASM_MESH_IO_TEST_DATA_HASH:-$(cat packages/mesh-io/package.json | jq -e -r '."itk-wasm"."test-data-hash"')}
+export ITK_WASM_MESH_IO_TEST_DATA_URLS=${ITK_WASM_MESH_IO_TEST_DATA_URLS:-$(cat packages/mesh-io/package.json | jq -e -r '."itk-wasm"."test-data-urls" | join(" ")')}

packages/dicom/dcmtk/CMakeLists.txt

@@ -8,7 +8,8 @@ include(${ITK_USE_FILE})
 add_executable(structured-report-to-text structured-report-to-text.cxx)
 target_link_libraries(structured-report-to-text PUBLIC ${ITK_LIBRARIES})
 
-add_executable(apply-presentation-state-to-image apply-presentation-state-to-image.cxx)
+add_executable(apply-presentation-state-to-image
+  apply-presentation-state-to-image.cxx dcostrmb.cc)
 target_link_libraries(apply-presentation-state-to-image PUBLIC cpp-base64 ${ITK_LIBRARIES})
 #add_test(NAME apply-presentation-state-to-image-test
   #COMMAND apply-presentation-state-to-image

packages/dicom/dcmtk/dcostrmb.cc

@@ -0,0 +1,118 @@
+/*
+ *
+ *  Copyright (C) 2002-2023, OFFIS e.V.
+ *  All rights reserved.  See COPYRIGHT file for details.
+ *
+ *  This software and supporting documentation were developed by
+ *
+ *    OFFIS e.V.
+ *    R&D Division Health
+ *    Escherweg 2
+ *    D-26121 Oldenburg, Germany
+ *
+ *
+ *  Module:  dcmdata
+ *
+ *  Author:  Marco Eichelberg
+ *
+ *  Purpose: DcmOutputBufferStream and related classes,
+ *    implements output to blocks of memory as needed in the dcmnet module.
+ *
+ */
+
+#include "dcmtk/config/osconfig.h"
+#include "dcmtk/dcmdata/dcostrmb.h"
+#include "dcmtk/dcmdata/dcerror.h"
+
+
+DcmBufferConsumer::DcmBufferConsumer(void *buf, offile_off_t bufLen)
+: DcmConsumer()
+, buffer_(OFstatic_cast(unsigned char *, buf))
+, bufSize_(bufLen)
+, filled_(0)
+, status_(EC_Normal)
+{
+  if (buffer_ == NULL) status_ = EC_IllegalCall;
+}
+
+DcmBufferConsumer::~DcmBufferConsumer()
+{
+}
+
+OFBool DcmBufferConsumer::good() const
+{
+  return status_.good();
+}
+
+OFCondition DcmBufferConsumer::status() const
+{
+  return status_;
+}
+
+OFBool DcmBufferConsumer::isFlushed() const
+{
+  return (filled_ == 0);
+}
+
+offile_off_t DcmBufferConsumer::avail() const
+{
+  return bufSize_ - filled_;
+}
+
+offile_off_t DcmBufferConsumer::write(const void *buf, offile_off_t buflen)
+{
+  offile_off_t result = 0;
+  if (buflen && buf && status_.good())
+  {
+    result = bufSize_ - filled_;
+    if (result > buflen) result = buflen;
+    memcpy(buffer_+ filled_, buf, OFstatic_cast(size_t, result));
+    filled_ += result;
+  }
+  return result;
+}
+
+void DcmBufferConsumer::flush()
+{
+  // nothing to flush
+}
+
+void DcmBufferConsumer::flushBuffer(void *& buffer, offile_off_t& length)
+{
+  buffer = buffer_;
+  length = filled_;
+  filled_ = 0;
+}
+
+offile_off_t DcmBufferConsumer::filled()
+{
+  return filled_;
+}
+
+/* ======================================================================= */
+
+DcmOutputBufferStream::DcmOutputBufferStream(void *buf, offile_off_t bufLen)
+: DcmOutputStream(&consumer_) // safe because DcmOutputStream only stores pointer
+, consumer_(buf, bufLen)
+{
+}
+
+DcmOutputBufferStream::~DcmOutputBufferStream()
+{
+#ifdef DEBUG
+  if (! isFlushed())
+  {
+    DCMDATA_WARN("DcmOutputBufferStream: Closing unflushed DcmOutputBufferStream, loss of data!");
+  }
+#endif
+}
+
+void DcmOutputBufferStream::flushBuffer(void *& buffer, offile_off_t& length)
+{
+  consumer_.flushBuffer(buffer, length);
+}
+
+offile_off_t DcmOutputBufferStream::filled()
+{
+  return consumer_.filled();
+}

packages/dicom/gdcm/CMakeLists.txt

@@ -43,6 +43,13 @@ else()
   set(Iconv_BUILD_COMMAND make)
 endif()
 
+if(${CMAKE_VERSION} VERSION_LESS 3.24)
+  set(download_extract_timestamp_flag)
+else()
+  set(download_extract_timestamp_flag
+    DOWNLOAD_EXTRACT_TIMESTAMP TRUE)
+ endif()
+
 ExternalProject_Add(${Iconv_LIBRARY}
   PREFIX ${Iconv_DIR}
   URL "https://bafybeid2yl6aeunciy5rynjmaoxkhhau3jgjpv7x25pylby7hq6n23c57i.ipfs.dweb.link/libiconv-1.16.tar.gz"
@@ -52,6 +59,7 @@ ExternalProject_Add(${Iconv_LIBRARY}
   BUILD_COMMAND ${Iconv_BUILD_COMMAND}
   # needed for ninja generator
   BUILD_BYPRODUCTS ${Iconv_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}iconv${CMAKE_STATIC_LIBRARY_SUFFIX}
+  ${download_extract_timestamp_flag}
 )
 
 add_library(${Iconv} STATIC IMPORTED)

packages/dicom/package.json

@@ -6,6 +6,11 @@
   "description": "scripts to generate @itk-wasm/dicom itk-wasm artifacts.",
   "type": "module",
   "itk-wasm": {
+    "test-data-hash": "bafybeicskxufnvuem6342pkfwgeo3siiozgzmfo5f34woge6aptuzuwzzu ",
+    "test-data-urls": [
+      "https://github.com/InsightSoftwareConsortium/ITK-Wasm/releases/download/itk-wasm-v1.0.0-b.119/dicom-test-data.tar.gz",
+      "https://w3s.link/ipfs/bafybeiby67winzvozowf4moqthwunuxxscssitnb6wahxv4ugvfxhu2vki/data.tar.gz"
+    ],
     "emscripten-docker-image": "itkwasm/emscripten:latest",
     "wasi-docker-image": "itkwasm/wasi:latest",
     "typescript-package-name": "@itk-wasm/dicom",