Merge pull request #66 from CGDogan/patch-4

Build libvips ALSO without openslide

Dockerfile

@@ -4,14 +4,64 @@ WORKDIR /var/www
 RUN apt-get update
 RUN apt-get -q update --fix-missing
 RUN apt-get -q install -y openslide-tools python3-openslide vim openssl
-RUN apt-get -q install -y libvips libvips-dev
+
+# Tony has a future use case where we may adapt caMic to GIS visualization
+# install libvips-dev for pyvips. No need for libvips.
+RUN apt-get -q install -y libvips-dev
+
+# But, build libvips instead of using libvips-dev from apt
+# Build without OpenSlide to open images with rather ImageMagick to handle
+# images without pyramids. Otherwise opens e.g. DICOM with OpenSlide so conversion
+# of files OpenSlide cannot open does not help at all.
+# So, we'll have two copies on openslide on the system.
+# By changing LD_LIBRARY_PATH before we launch python
+# we can choose which openslide to run
+# TODO: replace libjpeg-dev with libjpeg-turbo8-dev when current apt repo has it; for performance
+RUN apt-get -q install -y meson libjpeg-dev libexif-dev libgsf-1-dev libtiff-dev libfftw3-dev liblcms2-dev libpng-dev libmagickcore-dev libmagickwand-dev liborc-0.4-dev libopenjp2-7 libgirepository1.0-dev
+WORKDIR /root/src
+RUN git clone https://github.com/libvips/libvips.git --depth=1 --branch=8.14
+RUN mkdir /root/src/libvips/build
+WORKDIR /root/src/libvips
+RUN mkdir /usr/local/vips-no-openslide/
+# normally --prefix=/usr/local/ --libdir=lib build
+RUN meson setup -Dopenslide=disabled --buildtype=release --prefix=/usr/local/vips-no-openslide/ --libdir=lib build
+RUN meson compile -C build
+RUN meson test -C build
+RUN meson install -C build
 
 RUN pip install pyvips
 RUN pip install flask
 RUN pip install gunicorn
 RUN pip install greenlet
 RUN pip install gunicorn[eventlet]
 
+# verify pyvips can call libvips
+RUN python3 -c "import pyvips"
+
+# verify that the apt libvips has openslide
+ADD test_imgs/CMU-1-Small-Region.svs .
+RUN python3 -c "import pyvips; pyvips.Image.openslideload(('CMU-1-Small-Region.svs'))"
+
+# back up previous ld_library_path
+ENV LD_LIBRARY_PATH_ORIG="${LD_LIBRARY_PATH}"
+
+# now, prioritize openslideless libvips
+# the path shown in output lines of "meson install" where .so.42 are installed
+# normally /usr/local/lib/:
+ENV LD_LIBRARY_PATH="/usr/local/vips-no-openslide/lib/:${LD_LIBRARY_PATH}"
+
+# verify that this libvips has no openslide
+RUN ! python3 -c "import pyvips; pyvips.Image.openslideload(('CMU-1-Small-Region.svs'))"
+
+# ok, so to recap,
+# there are two libvips are installed and which one pyvips connects to
+# is chosen when "import pyvips" is run.
+# at this point in this dockerfile,
+# ld_library_path is set so that no-openslide version is run
+# but if you do LD_LIBRARY_PATH="${LD_LIBRARY_PATH_ORIG}" python a.py
+# or likewise using docker ENV command or os.environ in python before
+# importing, this will remove the no-openslide libvips from path.
+
 run openssl version -a
 
 ENV FLASK_ENV development