Simplify DIPjavaio build by including a Bio-Formats "stub" jar file in the repo.

.github/workflows/deploy.yml

@@ -31,7 +31,7 @@ jobs:
         #     export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1
         #     brew update
         run: |
-          brew install libomp glfw wget
+          brew install libomp glfw
 
       - name: Deploy
         run: bash tools/build/deploy_macos.sh
@@ -54,7 +54,7 @@ jobs:
         #     export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1
         #     brew update
         run: |
-          brew install libomp glfw wget
+          brew install libomp glfw
 
       - name: Deploy
         run: bash tools/build/deploy_macos.sh

CMakeLists.txt

@@ -86,21 +86,14 @@ if(JAVA_FOUND)
    if(JNI_FOUND)
       set(DIP_BUILD_JAVAIO ON CACHE BOOL "Build the javaio module")
       include(UseJava)
-      find_jar(BIOFORMATS_JAR bioformats_package DOC "Location of the Bio-Formats package JAR-file")
-      if(BIOFORMATS_JAR)
-         list(APPEND DIP_JAVAIO_INTERFACES "Bio-Formats")
-      endif()
+      list(APPEND DIP_JAVAIO_INTERFACES "Bio-Formats")
    endif()
-   set(DIP_JAVA_VERSION "1.8" CACHE BOOL "Java version to target when building DIPviewer Java bindings and DIPjavaio.")
+   set(DIP_JAVA_VERSION "1.8" CACHE STRING "Java version to target when building DIPviewer Java bindings and DIPjavaio.")
    # MATLAB R2013b--R2017a use Java SDK 1.7, R2017b-- use SDK 1.8.
    set(CMAKE_JAVA_COMPILE_FLAGS -target ${DIP_JAVA_VERSION} -source ${DIP_JAVA_VERSION})
 endif()
 
 if(DIP_BUILD_JAVAIO)
-   if(NOT DEFINED DIP_JAVAIO_INTERFACES)
-      message(WARNING "No interfaces for DIPjavaio were found -- disabling DIPjavaio")
-      set(DIP_BUILD_JAVAIO OFF CACHE BOOL "Build the javaio module" FORCE)
-   endif()
    add_subdirectory(javaio)
 endif()
 

README.md

@@ -172,6 +172,13 @@ limitations under the License.
   see [`dipimage/private/bf*.m`](dipimage/private/bfGetReader.m)  
   (the full *Bio-Formats* library needs to be installed for these to be useful)
 
+- A few Java files from *OME Bio-Formats* (used only to resolve references during the build
+  process of *DIPjavaio*, not used otherwise)  
+  Copyright (C) 2005 - 2017 Open Microscopy Environment  
+  2-Clause BSD License  
+  see [`javaio/java/bioformats/readme.md`](javaio/java/bioformats/readme.md)  
+  (the full *Bio-Formats* library needs to be installed to use *DIPjavaio*)
+
 - Modified CSS files from *dox++*, which originally came from *m.css* (for documentation)  
   Copyright 2017, 2018, 2019 Vladimír Vondruš  
   MIT License

doc/release_procedure/DIPimage_on_Linux.md

@@ -4,7 +4,7 @@ Few things to keep in mind:
 
 * No documentation
 * No Python interface
-* Build with BioFormats
+* No DIPjavaio
 * Build with Matlab R2018b
 * Matlab R2021b install has problems with root rights in display, use `xhost` line
 * Matlab R2018b requires g++-8
@@ -37,7 +37,6 @@ export CC=gcc-8
 export CXX=g++-8
 mkdir ~/diplib
 cd ~/diplib
-wget https://downloads.openmicroscopy.org/bio-formats/7.0.0/artifacts/bioformats_package.jar
 mkdir download source repository
 cd download
 wget http://www.fftw.org/fftw-3.3.10.tar.gz
@@ -69,17 +68,16 @@ git clone https://github.com/DIPlib/diplib.git
 cd diplib
 cmake .. -DCMAKE_INSTALL_PREFIX=~/diplib/diplib \
     -DDIP_BUILD_PYDIP=Off \
+    -DDIP_BUILD_JAVAIO=Off \
     -DDIP_ENABLE_FFTW=On \
     -DDIP_ENABLE_FREETYPE=On \
     -DFFTW3_LIBRARY_FFTW3=~/diplib/fftw/lib/libfftw3.so \
     -DFFTW3_LIBRARY_FFTW3F=~/diplib/fftw/lib/libfftw3f.so \
     -DFFTW3_LIBRARY_FFTW3_THREADS=~/diplib/fftw/lib/libfftw3_threads.so \
     -DFFTW3_LIBRARY_FFTW3F_THREADS=~/diplib/fftw/lib/libfftw3f_threads.so \
-    -DFFTW3_INCLUDE_DIR=~/diplib/fftw/include \
-    -DBIOFORMATS_JAR=~/diplib/bioformats_package.jar
+    -DFFTW3_INCLUDE_DIR=~/diplib/fftw/include
 make -j
 make -j check
 make install
-cp ~/diplib/bioformats_package.jar ~/diplib/diplib/share/DIPimage/private
 matlab
 ```

doc/release_procedure/DIPimage_on_Windows.md

@@ -81,7 +81,6 @@ Also the following dependencies have been downloaded:
 - FFTW, version 3.3.10 <https://fftw.org/download.html>. Download the source as we will build our own static library (see [FFTW static library](#fftw-static-library))
 - GLFW, version 3.3.6 <https://www.glfw.org/download.html>. Download the 64-bit Windows binaries as they contain a prebuild static library
 - Freetype, version 2.11.1 <https://github.com/ubawurinna/freetype-windows-binaries/releases>. Download the `Source code (zip)` as is it contains a prebuild static library
-- Bio-Formats package, version 7.0.0 <https://www.openmicroscopy.org/bio-formats/downloads/>. Download `bioformats_package.jar`
 
 For testing the *DIPlib* images are used:
 
@@ -147,9 +146,9 @@ FFTW comes with the GNU General Public License, Version 2 which is not compatibl
    - `Matlab_ROOT_DIR` `C:/Program Files/MATLAB/R2021b`
 1. press the <kbd>Generate</kbd> button
 1. continue setting the variables:
-   - `BIOFORMATS_JAR` `C:/diplib/bioformats_package.jar`
    - `DIP_ENABLE_FFTW` set
    - `DIP_ENABLE_FREETYPE` set
+   - `DIP_BUILD_JAVAIO` unset
 1. press the <kbd>Generate</kbd> button
 1. press the <kbd>Open Project</kbd> button
 1. in Visual Studio check if Solution Configuration is set to `Release`

doc/src/Build/Linux.md

@@ -113,23 +113,20 @@ correctly.
 If building only *DIPimage* (the *MATLAB* toolbox), skip this section and instead follow the directions
 you can read when you do `help readim` in *MATLAB* after installation.
 
-First, make sure you have the *Java 8 SDK* (*JDK 8*) installed, you can obtain it from the
-[Oracle website](http://www.oracle.com/technetwork/java/javase/downloads/index.html) for commercial
-purposes, or from [jdk.java.net](https://jdk.java.net) for an open-source build. Next, download
-`bioformats_package.jar` from the [*Bio-Formats* website](https://www.openmicroscopy.org/bio-formats/).
-You need to add the location of this file to the `cmake` command line using the `-DBIOFORMATS_JAR=<path>`
-flag.
+First, make sure you have the *Java 8 SDK* (*JDK 8*) or later installed,
+you can obtain it from the [Oracle website](http://www.oracle.com/technetwork/java/javase/downloads/index.html)
+for commercial purposes, or from [jdk.java.net](https://jdk.java.net) for an open-source build.
 
 When running *CMake* with the proper *JDK* installed, the *DIPjavaio* module becomes available.
 
 Check the *CMake* output to see which *JNI* was found. It should match the version of Java found.
-These two should be listed together, but the *JNI* output is only produced on first run. Delete the
-`CMakeCache.txt` file to run `cmake` fresh and see all its output.
+These two should be listed together, but the *JNI* output is only produced on first run.
+Delete the `CMakeCache.txt` file to run `cmake` fresh and see all its output.
 
 If the version of *JNI* found is not the one in the *JDK*, or if it is not found at all, add `-DJAVA_HOME=<path>`
 to the `cmake` command line:
 ```bash
-cmake .. -DBIOFORMATS_JAR=$HOME/java/bioformats_package.jar -DJAVA_HOME=/opt/jvm/java-8-oracle
+cmake .. -DJAVA_HOME=/opt/jvm/java-8-oracle
 ```
 Note that these arguments to `cmake` must be combined with the arguments mentioned earlier, into a single,
 long command line argument.

doc/src/Build/Windows.md

@@ -121,9 +121,8 @@ directory for the first parameter, and "lib-vc2015\glfw3.lib" for the second.
 don't have *MATLAB* installed, you are building 32-bit binaries, or the *Java SDK* could not
 be found. This is only necessary if you want to use the `viewslice` command from *DIPimage*.
 
-- If `BIOFORMATS_JAR` is not on the list, the *Java SDK* could not be found. If it is,
-point it to the "bioformats_package.jar" you downloaded earlier. This is only necessary if
-you want to import image formats that are not directly supported by *DIPlib*, and only
+- If `DIP_BUILD_JAVAIO` is not on the list, the *Java SDK* could not be found. This is only
+necessary if you want to import image formats that are not directly supported by *DIPlib*, and only
 for *Python* and C++ (*MATLAB* uses the *Bio-Formats* package differently, see `help readim`
 after installation).
 

doc/src/Build/build.md

@@ -160,7 +160,6 @@ Controlling the build of *DIPjavaio*:
     if its dependencies are available.
 - `JAVA_HOME`: Set the path to the JDK to use.
 - `DIP_JAVA_VERSION`: Set the version of Java to target. Defaults to "1.8".
-- `BIOFORMATS_JAR`: Set the path to the Bio-Formats JAR file (`bioformats_package.jar`).
 - Note that for the *MATLAB* toolbox, *DIPjavaio* is not used; build this only if you work in C++ or Python.
 
 Controlling the build of *DIPimage*:
@@ -170,9 +169,9 @@ Controlling the build of *DIPimage*:
 - `Matlab_ROOT_DIR`: Set the path of the *MATLAB* installation to compile *DIPimage* against.
 - `JAVA_HOME`: Set the path to the JDK to use. Java is used by *DIPimage* to interface with *DIPviewer*.
 - `DIP_JAVA_VERSION`: Set the version of Java to target. Defaults to "1.8". For MATLAB versions prior to R2017b
-  use "1.7" (and set `JAVA_HOME` to a release of the JDK that supports 1.7). You should not target a Java version
-  later than the one used by your MATLAB. Check the version of Java used by MATLAB by running `version -java`
-  on the MATLAB command prompt.
+    use "1.7" (and set `JAVA_HOME` to a release of the JDK that supports 1.7). You should not target a Java version
+    later than the one used by your MATLAB. Check the version of Java used by MATLAB by running `version -java`
+    on the MATLAB command prompt.
 
 Controlling the build of *PyDIP*:
 

doc/src/Build/macOS.md

@@ -212,11 +212,9 @@ This will change over time, as new versions of *GCC* are adopted by *HomeBrew*.
 If building only *DIPimage* (the *MATLAB* toolbox), skip this section and instead follow the directions
 you can read when you do `help readim` in *MATLAB* after installation.
 
-First, make sure you have the *Java 8 SDK* (*JDK 8*) installed,
+First, make sure you have the *Java 8 SDK* (*JDK 8*) or later installed,
 you can obtain it from the [Oracle website](http://www.oracle.com/technetwork/java/javase/downloads/index.html)
 for commercial purposes, or from [jdk.java.net](https://jdk.java.net) for an open-source build.
-Next, download `bioformats_package.jar` from the [*Bio-Formats* website](https://www.openmicroscopy.org/bio-formats/).
-You need to add the location of this file to the `cmake` command line using the `-DBIOFORMATS_JAR=<path>` flag.
 
 When running *CMake* with the proper *JDK* installed, the *DIPjavaio* module becomes available.
 
@@ -229,8 +227,7 @@ For example, on my Mac it might find the *JNI* that belongs to *Java 6*.
 In this case, add `-DJAVA_HOME=<path>` to the `cmake` command line:
 
 ```bash
-cmake .. -DBIOFORMATS_JAR=$HOME/java/bioformats_package.jar \
-         -DJAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_121.jdk/Contents/Home/
+cmake .. -DJAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_121.jdk/Contents/Home/
 ```
 
 Note that these arguments to `cmake` must be combined with the arguments mentioned earlier,

javaio/CMakeLists.txt

@@ -58,10 +58,9 @@ install(DIRECTORY "${PROJECT_SOURCE_DIR}/include/diplib/javaio" DESTINATION incl
 
 ### Java part
 
-if (BIOFORMATS_JAR)
-   set(DIP_JAVAIO_JAVA ${DIP_JAVAIO_JAVA} ${DIP_JAVAIO_BIOFORMATS_JAVA})
-   set(DIP_JAVAIO_CLASSPATH ${DIP_JAVAIO_CLASSPATH} ${BIOFORMATS_JAR})
-endif()
+# Bio-Formats interface
+set(DIP_JAVAIO_JAVA ${DIP_JAVAIO_JAVA} ${DIP_JAVAIO_BIOFORMATS_JAVA})
+set(DIP_JAVAIO_CLASSPATH ${DIP_JAVAIO_CLASSPATH} "${CMAKE_CURRENT_LIST_DIR}/java/bioformats/bio-formats-stripped.jar")
 
 configure_file("${CMAKE_CURRENT_LIST_DIR}/Manifest.txt.in" "${CMAKE_CURRENT_BINARY_DIR}/Manifest.txt" @ONLY)
 

javaio/Manifest.txt.in

@@ -1 +1 @@
-Class-Path: bioformats_package.jar file:///@BIOFORMATS_JAR@ file:///@CMAKE_INSTALL_PREFIX@/@LIBRARY_DESTINATION@/bioformats_package.jar
+Class-Path: bioformats_package.jar file:///@CMAKE_INSTALL_PREFIX@/@LIBRARY_DESTINATION@/bioformats_package.jar

javaio/java/bioformats/readme.md

@@ -0,0 +1,52 @@
+`bio-formats-stripped.jar` is a stripped-down version of `bioformats_package.jar`
+We simply removed all the files that weren't necessary to build our `BioFormatsInterface.java`
+source file into `DIPjavaio.jar`. This left a small amount of compiled Java that we
+could include into our repository, to simplify the build process. Note that this
+Java package is only used to resolve references when building `DIPjavaio.jar`, none
+of the code actually ands up in there. When using *DIPjavaio*, one must fetch the
+original `bioformats_package.jar`.
+
+The files in `bio-formats-stripped.jar` come from these repositories:
+
+ - https://github.com/ome/bioformats
+ - https://github.com/ome/ome-common-java
+ - https://github.com/ome/ome-model
+
+The original sources for these files are distributed under a 2-clause BSD licence.
+Below we reproduce the copyright statement for these files and the associated license
+text.
+
+```none
+Copyright (C) 2005 - 2017 Open Microscopy Environment:
+  - Board of Regents of the University of Wisconsin-Madison
+  - Glencoe Software, Inc.
+  - University of Dundee
+
+Copyright (C) 2006 - 2016 Open Microscopy Environment:
+  - Massachusetts Institute of Technology
+  - National Institutes of Health
+  - University of Dundee
+  - Board of Regents of the University of Wisconsin-Madison
+  - Glencoe Software, Inc.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+```

tools/build/cmake_windows_2017a.bat

@@ -11,7 +11,6 @@ cmake ^
 -DJava_JAVAC_EXECUTABLE:FILEPATH=D:/local/jdk-12.0.2/bin/javac.exe ^
 -DJava_JAVADOC_EXECUTABLE:FILEPATH=D:/local/jdk-12.0.2/bin/javadoc.exe ^
 -DJava_JAVA_EXECUTABLE:FILEPATH=D:/local/jdk-12.0.2/bin/java.exe ^
--DBIOFORMATS_JAR:FILEPATH=D:/local/bioformats_package.jar ^
 -DMatlab_ROOT_DIR:PATH="C:/Program Files/MATLAB/R2017a" ^
 -DDIP_PYDIP_RELATIVE_LOCATION:BOOL=ON ^
 -DPYDIP_INSTALL_PATH:PATH=D:/local/DIPlib_2017a/lib ^

tools/build/cmake_windows_2018b.bat

@@ -11,7 +11,6 @@ cmake ^
 -DJava_JAVAC_EXECUTABLE:FILEPATH=D:/local/jdk-12.0.2/bin/javac.exe ^
 -DJava_JAVADOC_EXECUTABLE:FILEPATH=D:/local/jdk-12.0.2/bin/javadoc.exe ^
 -DJava_JAVA_EXECUTABLE:FILEPATH=D:/local/jdk-12.0.2/bin/java.exe ^
--DBIOFORMATS_JAR:FILEPATH=D:/local/bioformats_package.jar ^
 -DMatlab_ROOT_DIR:PATH="D:\MATLAB\R2018b" ^
 -DDIP_PYDIP_RELATIVE_LOCATION:BOOL=ON ^
 -DPYDIP_INSTALL_PATH:PATH=D:/local/DIPlib_2018b/lib ^

tools/build/deploy_macos.sh

@@ -12,10 +12,9 @@ python3 -m pip install -U twine delocate
 
 mkdir build
 cd build
-wget -nv https://downloads.openmicroscopy.org/bio-formats/7.0.0/artifacts/bioformats_package.jar
 
 # Basic configuration
-cmake .. -DDIP_PYDIP_WHEEL_INCLUDE_LIBS=On -DBIOFORMATS_JAR=`pwd`/bioformats_package.jar -DDIP_BUILD_DIPIMAGE=Off -DCMAKE_CXX_FLAGS="-I$HOMEBREW_DIR/opt/libomp/include -L$HOMEBREW_DIR/opt/libomp/lib"
+cmake .. -DDIP_PYDIP_WHEEL_INCLUDE_LIBS=On -DDIP_BUILD_DIPIMAGE=Off -DCMAKE_CXX_FLAGS="-I$HOMEBREW_DIR/opt/libomp/include -L$HOMEBREW_DIR/opt/libomp/lib"
 
 # Build all wheels
 for v in ${PYTHON_VERSIONS[@]}; do

tools/build/deploy_windows.bat

@@ -13,7 +13,6 @@ mkdir build
 cd build
 mkdir wheelhouse
 
-python -m wget https://downloads.openmicroscopy.org/bio-formats/7.0.0/artifacts/bioformats_package.jar
 python -m wget https://sourceforge.net/projects/freeglut/files/freeglut/3.0.0/freeglut-3.0.0.tar.gz/download
 python -c "import tarfile; tar = tarfile.open('download'); tar.extractall()"
 cd freeglut-3.0.0
@@ -25,7 +24,7 @@ cd ..
 cd ..
 
 REM Basic configuration
-cmake .. -A x64 -DBIOFORMATS_JAR=%CD%\bioformats_package.jar -DFREEGLUT_INCLUDE_DIR=%CD%\freeglut-3.0.0\include -DFREEGLUT_LIBRARY=%CD%\freeglut-3.0.0\build\lib\Release\freeglut_static.lib -DFREEGLUT_STATIC=On -DDIP_BUILD_DIPIMAGE=Off -DDIP_PYDIP_WHEEL_INCLUDE_LIBS=On -DDIP_ENABLE_UNICODE=Off
+cmake .. -A x64 -DFREEGLUT_INCLUDE_DIR=%CD%\freeglut-3.0.0\include -DFREEGLUT_LIBRARY=%CD%\freeglut-3.0.0\build\lib\Release\freeglut_static.lib -DFREEGLUT_STATIC=On -DDIP_BUILD_DIPIMAGE=Off -DDIP_PYDIP_WHEEL_INCLUDE_LIBS=On -DDIP_ENABLE_UNICODE=Off
 
 REM Python 3.8
 C:\hostedtoolcache\windows\Python\%PYTHON38%\x64\python.exe -m pip install setuptools wheel build

tools/build/manylinux.sh

@@ -2,7 +2,7 @@
 # Run this in a manylinux2014 docker container with /io mounted to some local directory
 
 # Setup
-yum -y install wget freeglut-devel java-1.8.0-openjdk-devel.x86_64
+yum -y install freeglut-devel java-1.8.0-openjdk-devel.x86_64
 /opt/python/cp39-cp39/bin/python -m pip install cmake auditwheel
 CMAKE=/opt/python/cp39-cp39/lib/python3.9/site-packages/cmake/data/bin/cmake
 BUILD_THREADS=4
@@ -14,10 +14,9 @@ git clone https://github.com/diplib/diplib
 cd diplib
 mkdir build
 cd build
-wget -nv https://downloads.openmicroscopy.org/bio-formats/7.0.0/artifacts/bioformats_package.jar
 
 # Basic configuration
-$CMAKE .. -DDIP_PYDIP_WHEEL_INCLUDE_LIBS=On -DBIOFORMATS_JAR=`pwd`/bioformats_package.jar
+$CMAKE .. -DDIP_PYDIP_WHEEL_INCLUDE_LIBS=On
 
 # Build wheels
 for v in ${PYTHON_VERSIONS[@]}; do