Merge pull request #21 from camicroscope/develop

For 3.11.0

Author: birm

.gitignore

@@ -80,3 +80,6 @@ Makefile.in
 /ltmain.sh
 /m4/
 /missing
+
+# BioFormats either copied by Docker of copied manually and locally
+BFBridge/

Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:focal
+FROM camicroscope/image-decoders:latest
 
 ### update
 ARG DEBIAN_FRONTEND=noninteractive
@@ -8,11 +8,10 @@ RUN apt-get -q -y dist-upgrade
 RUN apt-get clean
 RUN apt-get -q update
 
-RUN apt-get -q -y install git autoconf automake make libtool pkg-config cmake apache2 libapache2-mod-fcgid libfcgi0ldbl zlib1g-dev libpng-dev libjpeg-dev libtiff5-dev libgdk-pixbuf2.0-dev libxml2-dev libsqlite3-dev libcairo2-dev libglib2.0-dev g++ libmemcached-dev libjpeg-turbo8-dev
+RUN apt-get -q -y install git autoconf automake make libtool pkg-config apache2 libapache2-mod-fcgid libfcgi0ldbl g++ libmemcached-dev libjpeg-turbo8-dev
 RUN a2enmod rewrite
 RUN a2enmod fcgid
 
-RUN mkdir /root/src
 COPY . /root/src
 WORKDIR /root/src
 
@@ -29,31 +28,8 @@ RUN ln -s /etc/apache2/mods-available/proxy.conf /etc/apache2/mods-enabled/proxy
 COPY apache2.conf /etc/apache2/apache2.conf
 COPY ports.conf /etc/apache2/ports.conf
 
-WORKDIR /root/src
-
-### openjpeg version in ubuntu 14.04 is 1.3, too old and does not have openslide required chroma subsampled images support.  download 2.1.0 from source and build
-RUN git clone https://github.com/uclouvain/openjpeg.git --branch=v2.3.0
-RUN mkdir /root/src/openjpeg/build
-WORKDIR /root/src/openjpeg/build
-RUN cmake -DBUILD_JPIP=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=Release -DBUILD_CODEC=ON -DBUILD_PKGCONFIG_FILES=ON ../
-RUN make
-RUN make install
-
-### Openslide
-WORKDIR /root/src
-## get my fork from openslide source cdoe
-RUN git clone https://github.com/openslide/openslide.git
-
-## build openslide
-WORKDIR /root/src/openslide
-RUN git checkout tags/v3.4.1
-RUN autoreconf -i
-#RUN ./configure --enable-static --enable-shared=no
-# may need to set OPENJPEG_CFLAGS='-I/usr/local/include' and OPENJPEG_LIBS='-L/usr/local/lib -lopenjp2'
-# and the corresponding TIFF flags and libs to where bigtiff lib is installed.
-RUN ./configure
-RUN make
-RUN make install
+## Print BioFormats errors, etc. to Docker console (stderr)
+#RUN ln -sf /proc/self/fd/1 /var/log/apache2/error.log
 
 ###  iipsrv
 WORKDIR /root/src/iipsrv

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2019, caMicroscope
+Copyright (c) 2018-2023, caMicroscope
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -3,6 +3,8 @@ Containerized IIP
 
 ## building and running
 
+Unless using caMicroscope Distro Docker, [BFBridge](https://github.com/camicroscope/BFBridge) needs to be cloned and placed next to iipsrv/, so that this project's root iipimage/ has subfolders iipimage/ and BFBridge/
+
 docker build . -t iipsrv
 
 docker run iipsrv -d -p 4010:80

apache2-iipsrv-fcgid.conf

@@ -27,6 +27,9 @@ FcgidInitialEnv MAX_CVT "5000"
 #FcgidInitialEnv FILESYSTEM_PREFIX "/mnt/images/"
 FcgidInitialEnv LD_LIBRARY_PATH "/usr/local/lib"
 FcgidInitialEnv MAX_TILE_CACHE_SIZE "64"
+FcgidInitialEnv BFBRIDGE_CACHEDIR "/tmp/"
+FcgidInitialEnv BFBRIDGE_CLASSPATH "/usr/lib/java"
+FcgidInitialEnv BFBRIDGE_LOGLEVEL "WARN"
 
 # Define the idle timeout as unlimited and the number of
 # processes we want

fcgid.conf

@@ -27,6 +27,9 @@ FcgidInitialEnv MAX_CVT "5000"
 FcgidInitialEnv LD_LIBRARY_PATH "/usr/local/lib"
 FcgidInitialEnv MAX_TILE_CACHE_SIZE "64"
 FcgidInitialEnv CORS "*"
+FcgidInitialEnv BFBRIDGE_CACHEDIR "/tmp/"
+FcgidInitialEnv BFBRIDGE_CLASSPATH "/usr/lib/java"
+FcgidInitialEnv BFBRIDGE_LOGLEVEL "WARN"
 
 # Define the idle timeout as unlimited and the number of
 # processes we want

iip_httpd.conf

@@ -28,5 +28,8 @@ FastCgiServer /var/www/localhost/fcgi-bin/iipsrv.fcgi \
 -initial-env JPEG_QUALITY=50 \
 -initial-env MAX_CVT=3000 \
 -initial-env CORS=* \
+-initial-env BFBRIDGE_CACHEDIR=/tmp/ \
+-initial-env BFBRIDGE_CLASSPATH=/usr/lib/java \
+-initial-env BFBRIDGE_LOGLEVEL=WARN \
 -listen-queue-depth 2048 \
 -processes 1