Micromanager - microscope hardware control

7 files changed, 263 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..d29cf7029dcb
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,27 @@
+pkgbase = micromanager-git
+	pkgdesc = Software package for microscopy hardware devices control. CMMCore and python2 bindings only.
+	pkgver = 1.4.13.r2326.g5117eb9
+	pkgrel = 1
+	url = http://www.micro-manager.org
+	install = mm.install
+	arch = x86_64
+	arch = i686
+	license = LGPL-2.1 BSD GPL-3
+	makedepends = git
+	makedepends = swig
+	depends = zlib
+	depends = boost
+	depends = libdc1394
+	depends = python2
+	depends = python2-numpy
+	source = micromanager-git::git+https://github.com/mdcurtis/micromanager-upstream.git
+	source = python_makefile.diff
+	source = python_setup.diff
+	source = micromanager-lib.conf
+	md5sums = SKIP
+	md5sums = 76a9fb824728a8397e3b5245ffe4ddaf
+	md5sums = e14361cc344c2fb0d03f3458d53eb152
+	md5sums = b7b6a68ce53d8ea1a4a29d187174ee4c
+
+pkgname = micromanager-git
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..d9d43a8072ae
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,83 @@
+# Maintainer: radioxoma <radioxoma from gmail com>
+# Last successful build with 1.4.13.r2306.gf5e50bd 22.01.2014 on x86_64.
+pkgname=micromanager-git
+pkgver=1.4.13.r2326.g5117eb9
+pkgrel=1
+epoch=
+pkgdesc="Software package for microscopy hardware devices control. CMMCore and python2 bindings only."
+arch=('x86_64' 'i686')
+url="http://www.micro-manager.org"
+license=('LGPL-2.1 BSD GPL-3')
+groups=()
+depends=('zlib' 'boost' 'libdc1394' 'python2' 'python2-numpy')
+makedepends=('git' 'swig')
+checkdepends=()
+optdepends=()
+provides=()
+conflicts=()
+replaces=()
+backup=()
+options=()
+install=mm.install
+changelog=
+source=($pkgname::git+https://github.com/mdcurtis/micromanager-upstream.git
+        'python_makefile.diff'
+        'python_setup.diff'
+        'micromanager-lib.conf')
+noextract=()
+md5sums=('SKIP'
+         '76a9fb824728a8397e3b5245ffe4ddaf'
+         'e14361cc344c2fb0d03f3458d53eb152'
+         'b7b6a68ce53d8ea1a4a29d187174ee4c') #generate with 'makepkg -g'
+
+pkgver() {
+  cd "$srcdir/$pkgname"
+  git describe --long | sed -E 's/([^-]*-g)/r\1/;s/-/./g'
+}
+
+prepare() {
+        cd "$srcdir/$pkgname"
+        
+        # Change python to python2.
+        # Remove installing commands form makefile and use setuptools instead.
+        # See PKGBUILD package() function.
+        patch -p0 < "$srcdir/python_makefile.diff"
+        
+        # Patching setup.py to prevent
+        # >>> import MMCorePy
+        # ...
+        # ImportError: ./_MMCorePy.so: undefined symbol: _ZTI8CMMError
+        # ... etc
+        patch -p0 < "$srcdir/python_setup.diff"
+
+        sh mmUnixBuild.sh
+}
+
+build() {
+        cd "$srcdir/$pkgname"
+        # Without Java-based GUI too.
+        # Feel free to improve package to work with ImageJ or FIJI.
+        ./configure --prefix=/usr --without-imagej --enable-python
+        make
+}
+
+# check() {
+#         cd "$srcdir/$pkgname"
+#         make -k check
+# }
+
+package() {
+        cd "$srcdir/$pkgname"
+        make DESTDIR="$pkgdir/" install
+
+        # Micro-manager devs plan use autotools without setuptools for python.
+        cd "$srcdir/$pkgname/MMCorePy_wrap/"
+        python2 setup.py install --root="$pkgdir"
+
+        # We need to update ldconfig cache with new libs.
+        install -D -m644 "$srcdir/micromanager-lib.conf" "$pkgdir/etc/ld.so.conf.d/micromanager-lib.conf"
+}
+
+# This script print 'DemoCamera' property list if CMMCore and python bindings
+# was installed well.
+# $ python2 -c 'import MMCorePy; DEVICE = ["Camera", "DemoCamera", "DCam"]; mmc = MMCorePy.CMMCore(); mmc.loadDevice(*DEVICE); mmc.initializeDevice(DEVICE[0]); mmc.setCameraDevice(DEVICE[0]); print mmc.getDevicePropertyNames(DEVICE[0])'
diff --git a/info.txt b/info.txt
new file mode 100644
index 000000000000..95d9a7cf0eb1
--- /dev/null
+++ b/info.txt
@@ -0,0 +1,90 @@
+# extra/libraw1394            Provides an API to the Linux IEEE1394 (FireWire) driver
+#     extra/libavc1394 0.5.4-2    A library to control A/V devices using the 1394ta AV/C commands.
+#     extra/libdc1394 2.2.1-2     High level programming interface to control IEEE 1394 based cameras
+#     extra/libiec61883 1.2.0-4   A higher level API for streaming DV, MPEG-2 and audio over Linux IEEE 1394
+
+# git clone https://github.com/mdcurtis/micromanager-upstream.git
+# git checkout tags/1.4.13
+wget -c http://github.com/mdcurtis/micromanager-upstream/archive/1.4.13.tar.gz
+Версия 1.4.13 вышла 
+    16.11.2012 21:05:26 Смена текстовой версии
+    30.11.2012 11:49:07 На сайте и GitHub
+
+    05.07.2013 1.4.13 ebuild python
+    22.09.2013 1.4.13 ebuild zlib
+Версия 1.4.14
+    20.03.2013 На сайте
+Версия 1.4.15
+    23.09.2013 на сайте, коммит svn 10680
+    23.09.2013 12:35:02 исключили адаптер камеры svn 11822
+    
+    16.10.2013 собирают под Ubuntu 13.10 x64
+    21.10.2013 Открыт тикет [MMCorePy Unix build is missing libraries](https://valelab.ucsf.edu/trac/micromanager/ticket/685)
+    27.10.2013 добавил boost_system in setup.py, но это сломало сборку в других местах.
+
+    # The error should be fixed in r11990 (i.e. there should no longer be
+    # any need for -fpermissive).
+
+    # Turns out the code causing the error wasn't actually ever being called
+    # -- although it may have crashed if called, so the compiler was doing
+    # its job right by making it an error.
+
+    # I've also addressed the include path issue you raised (r11991).
+
+    # Having looked at this code, I'd have to characterize MMCorePy
+    # (especially its Unix build system) as an unfinished project (which
+    # hasn't received much attention for a few years). Hopefully the basic
+    # functionality is there, though, once it's built.
+
+    # You are also right about the boost.system symbols missing (there are
+    # actually more symbols missing on Mac OS X; it looks like the Mac build
+    # has been broken for quite a while). There was also a source file
+    # missing, which I added in r11992.
+
+    # I think the best way to address the missing libraries issue is to
+    # remove the setup.py and compile the module from Makefile.am (this
+    # should allow it to use the same Boost as the other parts of MM,
+    # determined by the configure script). I'm going to leave this as an
+    # open ticket for now: 
+
+prepare()
+
+# Needed
+# SWIG может для python2.
+# Используется сборка при помощи distutils
+$ sed -i -e 's/python setup.py build_ext --inplace/python2 setup.py build_ext --inplace/g' MMCorePy_wrap/Makefile.am
+$ sed -i -e 's: $(DEVICEADAPTERPATH): $(DESTDIR)\/$(DEVICEADAPTERPATH):' MMCorePy_wrap/Makefile.am
+
+# Z Вроде не обязательно.
+libraries = ['boost_system', 'z'],
+
+$ sh mmUnixBuild.sh
+build()
+$ ./configure --prefix=/usr --without-imagej --enable-python
+
+
+# Fixed
+# /usr/include/python2.7/numpy/
+# include_dirs=numpy.distutils.misc_util.get_numpy_include_dirs(),
+# $ sed -i -e "/include_dirs/s~=.*~= \[\/usr/include/python2.7/numpy/"\]~" MMCorePy_wrap/setup.py
+
+# Fixed
+# DeviceUtils.cpp add `include <unistd.h>`
+
+
+$ make -j9
+# cp MMCorePy.py ../bin
+# cp _MMCorePy.so ../bin
+
+package()
+# make DESTDIR="/home/radioxoma/build/mm/pkg/" install
+$ make DESTDIR="$pkgdir" install
+
+
+# This particular error should be fixed in r11992, but let me know if it
+# > still results in other undefined symbols (other than Boost.System).
+
+# https://stackoverflow.com/questions/11643666/python-importerror-undefined-symbol-for-custom-c-module
+
+g++ -fPIC -shared -o mymodule.so mymodule.cpp `pkg-config --cflags --libs python` `pkg-config --cflags --libs opencv` -I/usr/local/include/opencv2/legacy 
+g++ -fPIC -shared -o mymodule.so mymodule.cpp `pkg-config --cflags --libs python` `pkg-config --cflags --libs opencv` -I/usr/local/include/opencv2/legacy
\ No newline at end of file
diff --git a/micromanager-lib.conf b/micromanager-lib.conf
new file mode 100644
index 000000000000..9e5934ca167c
--- /dev/null
+++ b/micromanager-lib.conf
@@ -0,0 +1 @@
+/usr/lib/micro-manager
diff --git a/mm.install b/mm.install
new file mode 100644
index 000000000000..7a0e5d40fefb
--- /dev/null
+++ b/mm.install
@@ -0,0 +1,15 @@
+# arg 1:  the new package version
+post_install() {
+	ldconfig
+}
+
+# arg 1:  the new package version
+# arg 2:  the old package version
+post_upgrade() {
+	post_install
+}
+
+# arg 1:  the old package version
+post_remove() {
+	post_install
+}
diff --git a/python_makefile.diff b/python_makefile.diff
new file mode 100644
index 000000000000..00c06e191108
--- /dev/null
+++ b/python_makefile.diff
@@ -0,0 +1,22 @@
+--- MMCorePy_wrap/Makefile.am	2014-01-21 05:25:37.000000000 +0300
++++ MMCorePy_wrap/Makefile_new.am	2014-01-24 17:14:15.904157691 +0300
+@@ -34,18 +34,14 @@
+ 	$(top_srcdir)/MMCore/LoadableModules/LoadedDeviceAdapter.cpp
+ 
+ _MMCorePy.so: MMCorePy_wrap.cxx $(MMCOREPYSOURCES)
+-	python setup.py build_ext --inplace
++	python2 setup.py build
+ 
+ all:
+ 	make MMCorePy_wrap.cxx
+ 	make MMCorePy.py
+ 	make _MMCorePy.so
+-	cp MMCorePy.py ../bin
+-	cp _MMCorePy.so ../bin
+ 
+ install:
+-	cp MMCorePy.py $(DEVICEADAPTERPATH)
+-	cp _MMCorePy.so $(DEVICEADAPTERPATH)
+ 
+ clean:
+ 	rm MMCorePy_wrap.cxx || echo "Not found, no problem"
diff --git a/python_setup.diff b/python_setup.diff
new file mode 100644
index 000000000000..17df60da04aa
--- /dev/null
+++ b/python_setup.diff
@@ -0,0 +1,25 @@
+--- MMCorePy_wrap/setup.py	2014-01-21 05:25:37.000000000 +0300
++++ MMCorePy_wrap/setup_new.py	2014-01-23 04:06:20.676996837 +0300
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python2
+ 
+ """
+ This setup.py is intended for use from the Autoconf/Automake build system.
+@@ -27,10 +27,16 @@
+                                      '../MMCore/Host.cpp',
+                                      '../MMCore/MMCore.cpp',
+                                      '../MMCore/PluginManager.cpp',
++                                     '../MMCore/Error.cpp',
++                                     '../MMCore/LoadableModules/LoadedDeviceAdapter.cpp',
++                                     '../MMCore/LoadableModules/LoadedModule.cpp',
++                                     '../MMCore/LoadableModules/LoadedModuleImpl.cpp',
++                                     '../MMCore/LoadableModules/LoadedModuleImplUnix.cpp',
+                                      '../MMDevice/DeviceUtils.cpp',
+                                      '../MMDevice/ImgBuffer.cpp',
+                                     ],
+                             language="c++",
++                            libraries=['boost_system', 'z'],
+                             include_dirs=numpy.distutils.misc_util.get_numpy_include_dirs(),
+                            )
+