Libtiff Install For Mac
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I have given it to a colleague to run on a Mac (OS X 10.9.2). I have never used a Mac and am having trouble helping them to get started. I have downloaded and installed Anaconda 1.9.2 on the Mac. According to the continuum documentation, libtiff is included, but when I run my python file using the Spyder IDE I get the following error when it tries to import libtiff:
These pages describe how to install PROJ on your computer without compiling ityourself. Below are guides for installing on Windows, Linux and Mac OS X. Thisis a good place to get started if this is your first time using PROJ. Moreadvanced users may want to compile the software themselves.
The simplest way to install PROJ on Windows is to use the OSGeo4W softwaredistribution. OSGeo4W provides easy access to many popular open source geospatialsoftware packages. After installation you can use PROJ from the OSGeo4W shell.To install PROJ do the following:
If you have already installed software via OSGeo4W on your computer, or ifyou have already installed QGIS on your computer, it is likely that PROJ isalready installed. Type "OSGeo4W Shell" in your start menu and check whetherthat gives a match.
The use of projsync requires that network support is enabled (thedefault option). If the resource files are not installed usingprojsync PROJ will attempt to fetch them automatically when atransformation needs a specific data file. This requires thatPROJ_NETWORK is set to ON.
Path to a shared or static library file, such as tiff.dll,libtiff.so, tiff.lib, or other name. A similar variableTIFF_LIBRARY_DEBUG can also be specified to a similar library forbuilding Debug releases.
relion has an installation procedure which relies on cmake.You will need to have this program installed, but most UNIX-systems have this by default.You will need to make a build-directory in which the code will be compiled.This can be placed inside the repository:
The output will notify you of what was detected and what type of build will be installed.Because relion is rich in terms of the possible configurations, it is important to check this output.For instance:
Wherever you install relion, make sure your PATH environmental variable points to the directory containing relion binaries.Launching relion with a path like /path/to/relion is not the right way;this starts the right GUI, but the GUI might invoke other versions of relion in the PATH.
CMake allows configuration of many aspects of the installation, some of which are outlined here.Most options can be set by adding options to the cmake configuration.Under the below subheadings, some example replacement commands are given to substitute the original configuration command.It is also recommended to clean or purge your build-directory between builds, since CMake caches some of previous configurations:
This will use FFT library from Intel MKL.In contrast to the FFTW options above, this will not download MKL automatically.You have to install MKL and set relevants paths (usually by sourcing the mkl_vars.sh script).
This will download, verify and install FLTK during the installation process.If any of these are not detected during configuration, this will happen automatically anyway, and you should not have to specify the below options manually.
Do not specify the build directory itself as CMAKE_INSTALL_PREFIX.This does not work!If you are happy with binaries in the build directory, leave CMAKE_INSTALL_PREFIX as default and omit the make install step.
The template job submission script may be saved in any location.By default, the one used at the LMB is present as gui/qsub.csh in the relion tar-ball.Upon installation this file is copied to the bin directory.It is convenient for the user if he does not have to select this file each time he opens the relion GUI in a new directory.Therefore, one may set the environment variable RELION_QSUB_TEMPLATE to point to the location of the script for the system at hand.This value will be pre-set as default in the GUI.(Note the user still has the liberty to define and use his own template!)
We provide binaries for Linux for each of the supported Pythonversions in the manylinux wheel format. These include support for alloptional libraries except libimagequant. Raqm support requiresFriBiDi to be installed separately:
We provide binaries for macOS for each of the supported Pythonversions in the wheel format. These include support for all optionallibraries except libimagequant. Raqm support requiresFriBiDi to be installed separately:
We provide Pillow binaries for Windows compiled for the matrix ofsupported Pythons in both 32 and 64-bit versions in the wheel format.These binaries include support for all optional libraries exceptlibimagequant and libxcb. Raqm support requiresFriBiDi to be installed separately:
Pillow wheels since version 8.2.0 include a modified version of libraqm thatloads libfribidi at runtime if it is installed.On Windows this requires compiling FriBiDi and installing fribidi.dllinto a directory listed in the Dynamic-Link Library Search Order (Microsoft Docs)(fribidi-0.dll or libfribidi-0.dll are also detected).See Build Options to see how to build this version.
The Xcode command line tools are required to compile portions ofPillow. The tools are installed by running xcode-select --installfrom the command line. The command line tools are required even if youhave the full Xcode package installed. It may be necessary to runsudo xcodebuild -license to accept the license prior to using thetools.
If the prerequisites are installed in the standard library locationsfor your machine (e.g. /usr or /usr/local), noadditional configuration should be required. If they are installed ina non-standard location, you may need to configure setuptools to usethose locations by editing setup.py orsetup.cfg, or by adding environment variables on the commandline:
If Pillow has been previously built without the requiredprerequisites, it may be necessary to manually clear the pip cache orbuild without cache using the --no-cache-dir option to force abuild with newly installed external libraries.
The library will usually be installed under the /usr/local/lib/ directory.To avoid run-time errors, make sure that your LD_LIBRARY_PATH environmentvariable includes this location. The C headers are typically installed under/usr/local/include/webp.
dyld: Library not loaded: /usr/local/opt/libtiff/lib/libtiff.5.dylibReferenced from: /usr/local/Cellar/mrtrix3/bin/mrviewReason: Incompatible library version: mrview requires version 9.0.0 or later, but libtiff.5.dylib provides version 6.0.0Abort trap: 6
Assuming libtiff was installed via homebrew, you have an up to date installation (brew upgrade libtiff), and that version is linked: brew switch libtiff 4.0.9_3, please check that the dylib version is what it should be:
/usr/local/opt/libtiff/lib/libtiff.5.dylib:/usr/local/opt/libtiff/lib/libtiff.5.dylib (compatibility version 9.0.0, current version 9.0.0)/usr/local/opt/jpeg/lib/libjpeg.9.dylib (compatibility version 13.0.0, current version 13.0.0)/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.50.4)
I ran brew unlink libtiff && brew link --verbose libtiff (without error messages), which did not work. I then uninstalled and reinstalled both libtiff and mrtrix and it still does not work. However, the unlinked kegs in your Cellar for matrix3 message went away. The output from brew doctor was otherwise the same as before.
Ghostscript (release 7.0 and later) may optionally install a library(libgs) under Linux. If this library is installed, GraphicsMagick maybe configured to use it. We do NOT recommend using this libraryunder Unix type systems. The Ghostscript library does not supportconcurrency since only one instance of the interpreter is available.Unix systems will obtain better performance from executing Ghostscript asan external process since then multiple interpreters may execute atonce on multiple CPU cores.
If the Ghostscript library is used, then please be aware thatGhostscript provides its own modified version of libjpeg andlibJasper while GraphicsMagick will be using these libraries asprovided with the system. If Ghostscript is not using the samelibraries, then identically named symbols may be used from the wrongcode, causing confusion or a program crash. If conflicts cause JPEGto fail (JPEG returns an error regarding expected structure sizes),it may be necessary to use Ghostscript's copy of libjpeg forGraphicsMagick, and all delegate libraries which depend on libjpeg,or convince Ghostscript to build against an unmodified installedJPEG library (and lose compatibility with some Postscript files).
GraphicsMagick requires an X server for the 'display', 'animate', and'import' functions to work properly. Unix systems usually provide an Xserver as part of their standard installation. For MacOS-X, X11 is asystem install time option.
AlternaTIFF is free to use for any purpose; however, you willbe required to register it before it can be used to view images.You will be told how to register when you install it, or when you firstuse it to view an image.(You do not need to search this web site looking for a way to register.If you are not asked to register, it means your computer hasalready been registered.)
To run YajHFC, download one of the files below. It is recommended to use the one most specific to your platform (i.e. if you run Windows, download one of the Windows installers). The JAR file should run on all platforms where Java is available, so you can download this if you do not want to use an installer or there is no download for your operating system. 2b1af7f3a8