• In the Swift Playgrounds app on your Mac, go to the More Playgrounds screen. If you’re on the My Playgrounds screen, click See All near the bottom right. Click Customize at the top right, then do any of the following: Remove a subscription: Click next to a subscription you want to remove, then click Delete.
  • In the Finder search box, type Playground. Locate the Playground app, which will have an icon with a white note on a blue background and double click to open it. Once you've located Playground in your Finder, you'll then have the option of clicking and dragging it to your dock, creating a shortcut for accessing it.
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Author

Bob Savage <bobsavage@mac.com>

Python on a Macintosh running Mac OS X is in principle very similar to Python onany other Unix platform, but there are a number of additional features such asthe IDE and the Package Manager that are worth pointing out.

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4.1. Getting and Installing MacPython¶

Mac OS X 10.8 comes with Python 2.7 pre-installed by Apple. If you wish, youare invited to install the most recent version of Python 3 from the Pythonwebsite (https://www.python.org). A current “universal binary” build of Python,which runs natively on the Mac’s new Intel and legacy PPC CPU’s, is availablethere.

What you get after installing is a number of things:

  • A Python3.9 folder in your Applications folder. In hereyou find IDLE, the development environment that is a standard part of officialPython distributions; and PythonLauncher, which handles double-clicking Pythonscripts from the Finder.

  • A framework /Library/Frameworks/Python.framework, which includes thePython executable and libraries. The installer adds this location to your shellpath. To uninstall MacPython, you can simply remove these three things. Asymlink to the Python executable is placed in /usr/local/bin/.

The Apple-provided build of Python is installed in/System/Library/Frameworks/Python.framework and /usr/bin/python,respectively. You should never modify or delete these, as they areApple-controlled and are used by Apple- or third-party software. Remember thatif you choose to install a newer Python version from python.org, you will havetwo different but functional Python installations on your computer, so it willbe important that your paths and usages are consistent with what you want to do.

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IDLE includes a help menu that allows you to access Python documentation. If youare completely new to Python you should start reading the tutorial introductionin that document.

If you are familiar with Python on other Unix platforms you should read thesection on running Python scripts from the Unix shell.

4.1.1. How to run a Python script¶

Your best way to get started with Python on Mac OS X is through the IDLEintegrated development environment, see section The IDE and use the Help menuwhen the IDE is running.

If you want to run Python scripts from the Terminal window command line or fromthe Finder you first need an editor to create your script. Mac OS X comes with anumber of standard Unix command line editors, vim andemacs among them. If you want a more Mac-like editor,BBEdit or TextWrangler from Bare Bones Software (seehttp://www.barebones.com/products/bbedit/index.html) are good choices, as isTextMate (see https://macromates.com/). Other editors includeGvim (http://macvim-dev.github.io/macvim/) and Aquamacs(http://aquamacs.org/).

To run your script from the Terminal window you must make sure that/usr/local/bin is in your shell search path.

To run your script from the Finder you have two options:

  • Drag it to PythonLauncher

  • Select PythonLauncher as the default application to open yourscript (or any .py script) through the finder Info window and double-click it.PythonLauncher has various preferences to control how your script islaunched. Option-dragging allows you to change these for one invocation, or useits Preferences menu to change things globally.

4.1.2. Running scripts with a GUI¶

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With older versions of Python, there is one Mac OS X quirk that you need to beaware of: programs that talk to the Aqua window manager (in other words,anything that has a GUI) need to be run in a special way. Use pythonwinstead of python to start such scripts.

With Python 3.9, you can use either python or pythonw.

4.1.3. Configuration¶

Python on OS X honors all standard Unix environment variables such asPYTHONPATH, but setting these variables for programs started from theFinder is non-standard as the Finder does not read your .profile or.cshrc at startup. You need to create a file~/.MacOSX/environment.plist. See Apple’s Technical Document QA1067 fordetails.

For more information on installation Python packages in MacPython, see sectionInstalling Additional Python Packages.

4.2. The IDE¶

MacPython ships with the standard IDLE development environment. A goodintroduction to using IDLE can be found athttp://www.hashcollision.org/hkn/python/idle_intro/index.html.

4.3. Installing Additional Python Packages¶

There are several methods to install additional Python packages:

  • Packages can be installed via the standard Python distutils mode (pythonsetup.pyinstall).

  • Many packages can also be installed via the setuptools extensionor pip wrapper, see https://pip.pypa.io/.

4.4. GUI Programming on the Mac¶

There are several options for building GUI applications on the Mac with Python.

PyObjC is a Python binding to Apple’s Objective-C/Cocoa framework, which isthe foundation of most modern Mac development. Information on PyObjC isavailable from https://pypi.org/project/pyobjc/.

The standard Python GUI toolkit is tkinter, based on the cross-platformTk toolkit (https://www.tcl.tk). An Aqua-native version of Tk is bundled with OSX by Apple, and the latest version can be downloaded and installed fromhttps://www.activestate.com; it can also be built from source.

wxPython is another popular cross-platform GUI toolkit that runs natively onMac OS X. Packages and documentation are available from https://www.wxpython.org.

PyQt is another popular cross-platform GUI toolkit that runs natively on MacOS X. More information can be found athttps://riverbankcomputing.com/software/pyqt/intro.

4.5. Distributing Python Applications on the Mac¶

The standard tool for deploying standalone Python applications on the Mac ispy2app. More information on installing and using py2app can be foundat http://undefined.org/python/#py2app.

4.6. Other Resources¶

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The MacPython mailing list is an excellent support resource for Python users anddevelopers on the Mac:

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Another useful resource is the MacPython wiki:

Note that BDP requires the use of MATLAB Compiler Runtime (MCR) R2015b (9.0) to execute its binaries, available here. The BDP scripts assume that the MCR is installed in a default location; if this is not the case, open the script (bdp.sh) in a text editor and change the BrainSuiteMCR variable to point to the correct installation. Users may also need to download and install C/C++ runtime libraries which can be found here for Windows (64-bit), via Xcode for Mac and by installing libstdc++6 & its dependencies for your corresponding Linux distribution.

Running BDP

The BDP is a command-line tool that takes diffusion images and a bias-field corrected MPRAGE image (fileprefix.bfc.nii.gz file generated by BrainSuite) as input, performs distortion correction and co-registration, and writes out the estimated diffusion tensors and ODFs and various other output files. BDP can read diffusion images in NIfTI-1 format. Please see supported file-formats for more details. It is recommended, but not required, to copy all of the required files to a separate directory for diffusion processing. The output files are written to the directory where the bias-field corrected MPRAGE image is located.

  1. Check this list of requirement details to verify that your diffusion data is appropriate for BDP processing.
  2. If you have not already done so, download and install MATLAB Compiler Runtime (MCR) release R2015b (9.0) for your operating system using links below.

    (The BDP scripts assume that the MCR is installed in a default location; if this is not the case, open the script (bdp.sh) in a text editor and change the BrainSuiteMCR variable to point to the correct installation.)

  3. If you have not already done so, download and install C/C++ runtime libraries for your operating system:
    • Windows: Visual C++ runtime package from Microsoft website (64-bit only).
    • Mac: Install Xcode to get all runtime libraries.
    • Linux:(Usually pre-installed) Install libstdc++6 & its dependencies for your distribution.
  4. Open Terminal (or Command Prompt)
    In Windows, the Command Prompt is found by clicking the Start Menu, All Programs, and then the Accessories folder. The Terminal application in Mac OS X is found in the Utilities directory in the Applications menu. How to open a terminal in Linux is distribution-specific, so search online for your distribution and how to open a terminal (often it is located in an “Accessories” or “System Tools” folder in the application menu).

    Windows Command Prompt showing a sample BDP command

  5. Run BDP
    Depending on the format of your diffusion images and type of distortion correction required, the BDP script can be run in different ways as explained below. For details, please check exhaustive list of all the available flags and their descriptions on the BDP flags page.
    Please replace bdp.exe with full path of BDP executable in examples below. E.g. On Windows, replace bdp.exe with C:UsersnameBrainSuite16a1bdpbdp.exe.

    Using NIfTI input:
    BDP can read 4D NIfTI files as diffusion data input, which can be specified with the --nii flag. In this mode, the following files are required:

    1. fileprefix.bfc.nii.gz – bias-field corrected MRI image, saved by BrainSuite extraction sequence with .bfc.nii.gz extension.
    2. Diffusion images in 4D NIfTI format – saved as .nii or .nii.gz extension
    3. Gradient file – usually saved as plain text files with .bvec extension which contains diffusion gradient directions (example here). BDP assumes that the gradient directions are specified in voxel coordinates of the diffusion image. If not, the resulting tensors and ODFs produced may not be properly aligned to the anatomy of the subject.
    4. b-values file – usually saved as plain text files with .bval extension which contains b-values of diffusion scan.
    Windows:
    Linux and Macintosh:

    Where <BFC File> is the filename of the .bfc.nii.gz file, <4D DWI NIfTI> is the filename of the diffusion weighted image in NIfTI format, <Gradient File> is the filename of the gradient (bvec) file, and <B-Value File> is the filename of the b-value file or the value in s/mm2 if you do not have this file.

    Example
    Assume all required files are in the directory C:Usersnamesubjectdiffusion_processing as such:

    To run BDP with default settings, run the script as (all on a single line):

    Or to estimate both ODF and tensor data, run:

    Optional flags

    A list of all the available flags and their detailed description are available on the BDP flags page.