Completely new wasm build

README.md

@@ -53,6 +53,14 @@ cd niimath/src
 make
 ```
 
+You can also compile this project to Web Assembly so it can be embedded in a web page, as shown in the [live demo](https://niivue.github.io/niivue-niimath/).
+
+```
+git clone https://github.com/rordenlab/niimath.git
+cd niimath/src
+make wasm
+```
+
 Advanced users may want to run `CF=1 OMP=1 make -j` to make a version that uses OpenMP (parallel processing) and the CloudFlare accelerated compression library. You may need to edit the `Makefile` for your compiler name. On MacOS, the default C compiler is Clang, which has [poor OpenMP](https://github.com/neurolabusc/simd) support. Therefore, MacOS users may want to install the gcc compiler `brew install gcc@9`.
 
 For Windows, using the cmake method described above is highly recommended. However, you can also compile the project directly from the command line (here without the `-DHAVE_ZLIB` directive, so gz files will not be supported) :

SuperBuild/SuperBuild.cmake

@@ -20,8 +20,14 @@ if(FSLSTYLE)
    ADD_DEFINITIONS(-DPIGZ)
 endif()
 
+ADD_DEFINITIONS(-DHAVE_64BITS)
+ADD_DEFINITIONS(-DHAVE_BUTTERWORTH)
+ADD_DEFINITIONS(-DHAVE_FORMATS)
+ADD_DEFINITIONS(-DHAVE_TENSOR)
+ADD_DEFINITIONS(-DHAVE_ZLIB)
 ADD_DEFINITIONS(-DNII2MESH)
 
+
 # Basic CMake build settings
 if(NOT CMAKE_BUILD_TYPE)
     set(CMAKE_BUILD_TYPE "Release" CACHE STRING

src/Makefile

@@ -1,12 +1,22 @@
 # Regular use, set compiler name, compiler flags, openmp flags zlib flags
 CNAME=gcc
-#linker flags
-LFLAGS=-lm -lz
-#c flags
-CFLAGS=-O3 -DHAVE_ZLIB -DFSLSTYLE -DPIGZ -DREJECT_COMPLEX
-#CFLAGS=-O3 -ffast-math -DHAVE_ZLIB -DFSLSTYLE -DPIGZ -DREJECT_COMPLEX -DNII2MESH
-# Westmere required for fast gz https://github.com/tikv/tikv/issues/4843
-#CFLAGS=-O3 -DHAVE_ZLIB -march=westmere
+#universal flags always included
+UFLAGS= niimath.c core.c core32.c niftilib/nifti2_io.c znzlib/znzlib.c -I./niftilib -I./znzlib -DFSLSTYLE -DPIGZ -DREJECT_COMPLEX -lm
+UFLAGS64= -DHAVE_64BITS core64.c
+#Zlib flags
+ZFLAGS= -DHAVE_ZLIB -lz
+#compiler flags
+CFLAGS= -O3
+# CFLAGS= -O0 -Wall
+# GIfTI, obj, vtk, stl, etc support
+GFILES= -DHAVE_FORMATS base64.c
+#Butterworth bandpass flags
+BFLAGS= -DHAVE_BUTTERWORTH bw.c
+#Tensor decomposition
+TFILES= -DHAVE_TENSOR tensor.c
+#Marching Cubes flag
+#MFLAGS= -DNII2MESH meshify.c quadric.c bwlabel.c MarchingCubes.c
+MFLAGS= -DNII2MESH meshify.c quadric.c bwlabel.c radixsort.c fdr.c -DUSE_CLASSIC_CUBES oldcubes.c
 
 ifeq ($(CXX),g++)
 	CFLAGS += -std=gnu99
@@ -15,19 +25,30 @@ endif
 #run "OMP=1 make -j" for both OpenMP and CloudFlare
 ifeq "$(OMP)" "1"
 	CNAME= gcc-9
-	CFLAGS+=-fopenmp -flto
-	#to get full file path:
-	#gcc-9 --print-file-name=libgomp.a
-	#LFLAGS+= /usr/local/Cellar/gcc/9.2.0_3/lib/gcc/9/gcc/x86_64-apple-darwin18/9.2.0/../../../libgomp.a
-	LFLAGS+= -static-libgcc -static-libstdc++ -L.
+	CFLAGS+=-fopenmp -flto -static-libgcc -static-libstdc++ -L.
 endif
 
-MFLAGS= -DNII2MESH MarchingCubes.c meshify.c quadric.c
 #run "MESH=0 make" for minimal compile without nii2mesh functions
 ifeq "$(MESH)" "0"
 	MFLAGS=
 endif
 
 all:
-	$(CNAME) $(CFLAGS) $(MFLAGS) niimath.c base64.c radixsort.c fdr.c bwlabel.c bw.c core.c tensor.c core32.c core64.c niftilib/nifti2_io.c znzlib/znzlib.c -I./niftilib -I./znzlib $(LFLAGS) -o niimath
-
+	$(CNAME) $(CFLAGS) $(BFLAGS) $(TFILES) $(GFILES) $(MFLAGS) $(UFLAGS) $(UFLAGS64) $(ZFLAGS) -o niimath
+
+# tiny: terminal executable to emulate WASM
+tiny:
+	$(CNAME) $(CFLAGS) $(MFLAGS) $(UFLAGS) -o niimath
+
+# tiny without nii2mesh
+nano:
+	$(CNAME) $(CFLAGS) $(UFLAGS) -o niimath
+
+# sanitize checks memory errors - similar to tiny/wasm
+sanitize:
+	g++ -O1 -g -Wno-deprecated -fsanitize=address -fno-omit-frame-pointer $(MFLAGS) $(UFLAGS) -o niimath
+
+wasm:
+	em++ -O3 -Wno-deprecated $(MFLAGS) $(UFLAGS) -s DEMANGLE_SUPPORT=1 -s EXPORTED_RUNTIME_METHODS='["ccall", "cwrap", "FS_createDataFile", "FS_readFile", "FS_unlink"]' -s ALLOW_MEMORY_GROWTH=1 -s WASM=1 -s EXPORTED_FUNCTIONS='["_simplify"]' -o niimath.js
+	# hint: consider further optimizations:
+	#   wasm-opt -O3 -o output.wasm niimath.wasm; rm niimath.wasm; mv output.wasm niimath.wasm