Initial beta release version of melview

.gitignore

+*.pyc
+*.pyo
+build/
+dist/
+*.egg-info
+MANIFEST

.project

+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>melview</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.python.pydev.PyDevBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.python.pydev.pythonNature</nature>
+	</natures>
+</projectDescription>

.pydevproject

+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<?eclipse-pydev version="1.0"?>
+
+<pydev_project>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">EPD Python</pydev_property>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.7</pydev_property>
+<pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
+<path>/melview</path>
+</pydev_pathproperty>
+</pydev_project>

INSTALL

+This program is intended to be installed using setuptools:
+
+python ./setup.py install

README

+Copyright (c) 2012, University of Oxford
+
+Dave Flitney <dave.flitney@ndcn.ox.ac.uk>
+FMRIB Centre
+University of Oxford
+John Radcliffe Hospital
+Headington
+Oxford
+OX3 9DU

ez_setup.py

+#!python
+"""Bootstrap setuptools installation
+
+If you want to use setuptools in your package's setup.py, just include this
+file in the same directory with it, and add this to the top of your setup.py::
+
+    from ez_setup import use_setuptools
+    use_setuptools()
+
+If you want to require a specific version of setuptools, set a download
+mirror, or use an alternate download directory, you can do so by supplying
+the appropriate options to ``use_setuptools()``.
+
+This file can also be run as a script to install or upgrade setuptools.
+"""
+import sys
+DEFAULT_VERSION = "0.6c11"
+DEFAULT_URL     = "http://pypi.python.org/packages/%s/s/setuptools/" % sys.version[:3]
+
+md5_data = {
+    'setuptools-0.6b1-py2.3.egg': '8822caf901250d848b996b7f25c6e6ca',
+    'setuptools-0.6b1-py2.4.egg': 'b79a8a403e4502fbb85ee3f1941735cb',
+    'setuptools-0.6b2-py2.3.egg': '5657759d8a6d8fc44070a9d07272d99b',
+    'setuptools-0.6b2-py2.4.egg': '4996a8d169d2be661fa32a6e52e4f82a',
+    'setuptools-0.6b3-py2.3.egg': 'bb31c0fc7399a63579975cad9f5a0618',
+    'setuptools-0.6b3-py2.4.egg': '38a8c6b3d6ecd22247f179f7da669fac',
+    'setuptools-0.6b4-py2.3.egg': '62045a24ed4e1ebc77fe039aa4e6f7e5',
+    'setuptools-0.6b4-py2.4.egg': '4cb2a185d228dacffb2d17f103b3b1c4',
+    'setuptools-0.6c1-py2.3.egg': 'b3f2b5539d65cb7f74ad79127f1a908c',
+    'setuptools-0.6c1-py2.4.egg': 'b45adeda0667d2d2ffe14009364f2a4b',
+    'setuptools-0.6c10-py2.3.egg': 'ce1e2ab5d3a0256456d9fc13800a7090',
+    'setuptools-0.6c10-py2.4.egg': '57d6d9d6e9b80772c59a53a8433a5dd4',
+    'setuptools-0.6c10-py2.5.egg': 'de46ac8b1c97c895572e5e8596aeb8c7',
+    'setuptools-0.6c10-py2.6.egg': '58ea40aef06da02ce641495523a0b7f5',
+    'setuptools-0.6c11-py2.3.egg': '2baeac6e13d414a9d28e7ba5b5a596de',
+    'setuptools-0.6c11-py2.4.egg': 'bd639f9b0eac4c42497034dec2ec0c2b',
+    'setuptools-0.6c11-py2.5.egg': '64c94f3bf7a72a13ec83e0b24f2749b2',
+    'setuptools-0.6c11-py2.6.egg': 'bfa92100bd772d5a213eedd356d64086',
+    'setuptools-0.6c2-py2.3.egg': 'f0064bf6aa2b7d0f3ba0b43f20817c27',
+    'setuptools-0.6c2-py2.4.egg': '616192eec35f47e8ea16cd6a122b7277',
+    'setuptools-0.6c3-py2.3.egg': 'f181fa125dfe85a259c9cd6f1d7b78fa',
+    'setuptools-0.6c3-py2.4.egg': 'e0ed74682c998bfb73bf803a50e7b71e',
+    'setuptools-0.6c3-py2.5.egg': 'abef16fdd61955514841c7c6bd98965e',
+    'setuptools-0.6c4-py2.3.egg': 'b0b9131acab32022bfac7f44c5d7971f',
+    'setuptools-0.6c4-py2.4.egg': '2a1f9656d4fbf3c97bf946c0a124e6e2',
+    'setuptools-0.6c4-py2.5.egg': '8f5a052e32cdb9c72bcf4b5526f28afc',
+    'setuptools-0.6c5-py2.3.egg': 'ee9fd80965da04f2f3e6b3576e9d8167',
+    'setuptools-0.6c5-py2.4.egg': 'afe2adf1c01701ee841761f5bcd8aa64',
+    'setuptools-0.6c5-py2.5.egg': 'a8d3f61494ccaa8714dfed37bccd3d5d',
+    'setuptools-0.6c6-py2.3.egg': '35686b78116a668847237b69d549ec20',
+    'setuptools-0.6c6-py2.4.egg': '3c56af57be3225019260a644430065ab',
+    'setuptools-0.6c6-py2.5.egg': 'b2f8a7520709a5b34f80946de5f02f53',
+    'setuptools-0.6c7-py2.3.egg': '209fdf9adc3a615e5115b725658e13e2',
+    'setuptools-0.6c7-py2.4.egg': '5a8f954807d46a0fb67cf1f26c55a82e',
+    'setuptools-0.6c7-py2.5.egg': '45d2ad28f9750e7434111fde831e8372',
+    'setuptools-0.6c8-py2.3.egg': '50759d29b349db8cfd807ba8303f1902',
+    'setuptools-0.6c8-py2.4.egg': 'cba38d74f7d483c06e9daa6070cce6de',
+    'setuptools-0.6c8-py2.5.egg': '1721747ee329dc150590a58b3e1ac95b',
+    'setuptools-0.6c9-py2.3.egg': 'a83c4020414807b496e4cfbe08507c03',
+    'setuptools-0.6c9-py2.4.egg': '260a2be2e5388d66bdaee06abec6342a',
+    'setuptools-0.6c9-py2.5.egg': 'fe67c3e5a17b12c0e7c541b7ea43a8e6',
+    'setuptools-0.6c9-py2.6.egg': 'ca37b1ff16fa2ede6e19383e7b59245a',
+}
+
+import sys, os
+try: from hashlib import md5
+except ImportError: from md5 import md5
+
+def _validate_md5(egg_name, data):
+    if egg_name in md5_data:
+        digest = md5(data).hexdigest()
+        if digest != md5_data[egg_name]:
+            print >>sys.stderr, (
+                "md5 validation of %s failed!  (Possible download problem?)"
+                % egg_name
+            )
+            sys.exit(2)
+    return data
+
+def use_setuptools(
+    version=DEFAULT_VERSION, download_base=DEFAULT_URL, to_dir=os.curdir,
+    download_delay=15
+):
+    """Automatically find/download setuptools and make it available on sys.path
+
+    `version` should be a valid setuptools version number that is available
+    as an egg for download under the `download_base` URL (which should end with
+    a '/').  `to_dir` is the directory where setuptools will be downloaded, if
+    it is not already available.  If `download_delay` is specified, it should
+    be the number of seconds that will be paused before initiating a download,
+    should one be required.  If an older version of setuptools is installed,
+    this routine will print a message to ``sys.stderr`` and raise SystemExit in
+    an attempt to abort the calling script.
+    """
+    was_imported = 'pkg_resources' in sys.modules or 'setuptools' in sys.modules
+    def do_download():
+        egg = download_setuptools(version, download_base, to_dir, download_delay)
+        sys.path.insert(0, egg)
+        import setuptools; setuptools.bootstrap_install_from = egg
+    try:
+        import pkg_resources
+    except ImportError:
+        return do_download()       
+    try:
+        pkg_resources.require("setuptools>="+version); return
+    except pkg_resources.VersionConflict, e:
+        if was_imported:
+            print >>sys.stderr, (
+            "The required version of setuptools (>=%s) is not available, and\n"
+            "can't be installed while this script is running. Please install\n"
+            " a more recent version first, using 'easy_install -U setuptools'."
+            "\n\n(Currently using %r)"
+            ) % (version, e.args[0])
+            sys.exit(2)
+    except pkg_resources.DistributionNotFound:
+        pass
+
+    del pkg_resources, sys.modules['pkg_resources']    # reload ok
+    return do_download()
+
+def download_setuptools(
+    version=DEFAULT_VERSION, download_base=DEFAULT_URL, to_dir=os.curdir,
+    delay = 15
+):
+    """Download setuptools from a specified location and return its filename
+
+    `version` should be a valid setuptools version number that is available
+    as an egg for download under the `download_base` URL (which should end
+    with a '/'). `to_dir` is the directory where the egg will be downloaded.
+    `delay` is the number of seconds to pause before an actual download attempt.
+    """
+    import urllib2, shutil
+    egg_name = "setuptools-%s-py%s.egg" % (version,sys.version[:3])
+    url = download_base + egg_name
+    saveto = os.path.join(to_dir, egg_name)
+    src = dst = None
+    if not os.path.exists(saveto):  # Avoid repeated downloads
+        try:
+            from distutils import log
+            if delay:
+                log.warn("""
+---------------------------------------------------------------------------
+This script requires setuptools version %s to run (even to display
+help).  I will attempt to download it for you (from
+%s), but
+you may need to enable firewall access for this script first.
+I will start the download in %d seconds.
+
+(Note: if this machine does not have network access, please obtain the file
+
+   %s
+
+and place it in this directory before rerunning this script.)
+---------------------------------------------------------------------------""",
+                    version, download_base, delay, url
+                ); from time import sleep; sleep(delay)
+            log.warn("Downloading %s", url)
+            src = urllib2.urlopen(url)
+            # Read/write all in one block, so we don't create a corrupt file
+            # if the download is interrupted.
+            data = _validate_md5(egg_name, src.read())
+            dst = open(saveto,"wb"); dst.write(data)
+        finally:
+            if src: src.close()
+            if dst: dst.close()
+    return os.path.realpath(saveto)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+def main(argv, version=DEFAULT_VERSION):
+    """Install or upgrade setuptools and EasyInstall"""
+    try:
+        import setuptools
+    except ImportError:
+        egg = None
+        try:
+            egg = download_setuptools(version, delay=0)
+            sys.path.insert(0,egg)
+            from setuptools.command.easy_install import main
+            return main(list(argv)+[egg])   # we're done here
+        finally:
+            if egg and os.path.exists(egg):
+                os.unlink(egg)
+    else:
+        if setuptools.__version__ == '0.0.1':
+            print >>sys.stderr, (
+            "You have an obsolete version of setuptools installed.  Please\n"
+            "remove it from your system entirely before rerunning this script."
+            )
+            sys.exit(2)
+
+    req = "setuptools>="+version
+    import pkg_resources
+    try:
+        pkg_resources.require(req)
+    except pkg_resources.VersionConflict:
+        try:
+            from setuptools.command.easy_install import main
+        except ImportError:
+            from easy_install import main
+        main(list(argv)+[download_setuptools(delay=0)])
+        sys.exit(0) # try to force an exit
+    else:
+        if argv:
+            from setuptools.command.easy_install import main
+            main(argv)
+        else:
+            print "Setuptools version",version,"or greater has been installed."
+            print '(Run "ez_setup.py -U setuptools" to reinstall or upgrade.)'
+
+def update_md5(filenames):
+    """Update our built-in md5 registry"""
+
+    import re
+
+    for name in filenames:
+        base = os.path.basename(name)
+        f = open(name,'rb')
+        md5_data[base] = md5(f.read()).hexdigest()
+        f.close()
+
+    data = ["    %r: %r,\n" % it for it in md5_data.items()]
+    data.sort()
+    repl = "".join(data)
+
+    import inspect
+    srcfile = inspect.getsourcefile(sys.modules[__name__])
+    f = open(srcfile, 'rb'); src = f.read(); f.close()
+
+    match = re.search("\nmd5_data = {\n([^}]+)}", src)
+    if not match:
+        print >>sys.stderr, "Internal error!"
+        sys.exit(2)
+
+    src = src[:match.start(1)] + repl + src[match.end(1):]
+    f = open(srcfile,'w')
+    f.write(src)
+    f.close()
+
+
+if __name__=='__main__':
+    if len(sys.argv)>2 and sys.argv[1]=='--md5update':
+        update_md5(sys.argv[2:])
+    else:
+        main(sys.argv[1:])
+
+
+
+
+

fsl/caches.py

+import collections
+import functools
+from itertools import ifilterfalse
+from heapq import nsmallest
+from operator import itemgetter
+
+class Counter(dict):
+    'Mapping where default values are zero'
+    def __missing__(self, key):
+        return 0
+
+def lru_cache(maxsize=100):
+    '''Least-recently-used cache decorator.
+
+    Arguments to the cached function must be hashable.
+    Cache performance statistics stored in f.hits and f.misses.
+    Clear the cache with f.clear().
+    http://en.wikipedia.org/wiki/Cache_algorithms#Least_Recently_Used
+
+    '''
+    maxqueue = maxsize * 10
+    def decorating_function(user_function,
+            len=len, iter=iter, tuple=tuple, sorted=sorted, KeyError=KeyError):
+        cache = {}                  # mapping of args to results
+        queue = collections.deque() # order that keys have been used
+        refcount = Counter()        # times each key is in the queue
+        sentinel = object()         # marker for looping around the queue
+        kwd_mark = object()         # separate positional and keyword args
+
+        # lookup optimizations (ugly but fast)
+        queue_append, queue_popleft = queue.append, queue.popleft
+        queue_appendleft, queue_pop = queue.appendleft, queue.pop
+
+        @functools.wraps(user_function)
+        def wrapper(*args, **kwds):
+            # cache key records both positional and keyword args
+            key = args
+            if kwds:
+                key += (kwd_mark,) + tuple(sorted(kwds.items()))
+
+            # record recent use of this key
+            queue_append(key)
+            refcount[key] += 1
+
+            # get cache entry or compute if not found
+            try:
+                result = cache[key]
+                wrapper.hits += 1
+            except KeyError:
+                result = user_function(*args, **kwds)
+                cache[key] = result
+                wrapper.misses += 1
+
+                # purge least recently used cache entry
+                if len(cache) > maxsize:
+                    key = queue_popleft()
+                    refcount[key] -= 1
+                    while refcount[key]:
+                        key = queue_popleft()
+                        refcount[key] -= 1
+                    del cache[key], refcount[key]
+
+            # periodically compact the queue by eliminating duplicate keys
+            # while preserving order of most recent access
+            if len(queue) > maxqueue:
+                refcount.clear()
+                queue_appendleft(sentinel)
+                for key in ifilterfalse(refcount.__contains__,
+                                        iter(queue_pop, sentinel)):
+                    queue_appendleft(key)
+                    refcount[key] = 1
+
+
+            return result
+
+        def clear():
+            cache.clear()
+            queue.clear()
+            refcount.clear()
+            wrapper.hits = wrapper.misses = 0
+
+        wrapper.hits = wrapper.misses = 0
+        wrapper.clear = clear
+        return wrapper
+    return decorating_function
+
+
+def lfu_cache(maxsize=100):
+    '''Least-frequenty-used cache decorator.
+
+    Arguments to the cached function must be hashable.
+    Cache performance statistics stored in f.hits and f.misses.
+    Clear the cache with f.clear().
+    http://en.wikipedia.org/wiki/Least_Frequently_Used
+
+    '''
+    def decorating_function(user_function):
+        cache = {}                      # mapping of args to results
+        use_count = Counter()           # times each key has been accessed
+        kwd_mark = object()             # separate positional and keyword args
+
+        @functools.wraps(user_function)
+        def wrapper(*args, **kwds):
+            key = args
+            if kwds:
+                key += (kwd_mark,) + tuple(sorted(kwds.items()))
+            use_count[key] += 1
+
+            # get cache entry or compute if not found
+            try:
+                result = cache[key]
+                wrapper.hits += 1
+            except KeyError:
+                result = user_function(*args, **kwds)
+                cache[key] = result
+                wrapper.misses += 1
+
+                # purge least frequently used cache entry
+                if len(cache) > maxsize:
+                    for key, _ in nsmallest(maxsize // 10,
+                                            use_count.iteritems(),
+                                            key=itemgetter(1)):
+                        del cache[key], use_count[key]
+
+            return result
+
+        def clear():
+            cache.clear()
+            use_count.clear()
+            wrapper.hits = wrapper.misses = 0
+
+        wrapper.hits = wrapper.misses = 0
+        wrapper.clear = clear
+        return wrapper
+    return decorating_function
+
+
+if __name__ == '__main__':
+
+    @lru_cache(maxsize=20)
+    def f(x, y):
+        return 3*x+y
+
+    domain = range(5)
+    from random import choice
+    for i in range(1000):
+        r = f(choice(domain), choice(domain))
+
+    print(f.hits, f.misses)
+
+    @lfu_cache(maxsize=20)
+    def f(x, y):
+        return 3*x+y
+
+    domain = range(5)
+    from random import choice
+    for i in range(1000):
+        r = f(choice(domain), choice(domain))
+
+    print(f.hits, f.misses)

fsl/melodic.py

+from pylab import *
+from fsl.caches import *
+from commands import getoutput
+import nibabel as nb
+
+class MelodicIOError(IOError):
+    pass
+
+def trace_call(fn):
+
+    from itertools import chain
+    import traceback
+
+    def wrapped(*v, **k):
+        name = fn.__name__
+        print "{0}({1})".format(name, ", ".join(map(repr, chain(v, k.values()))))
+        traceback.print_stack(limit=2)
+        return fn(*v, **k)
+    return wrapped
+
+class melodic:
+    def __init__(self, path="", ic=1):
+        self.set_directory(path)
+        self.select_component(ic)
+
+    def set_directory(self, path=""):
+        self.dir = path
+        self.ic = 1
+
+        mfname = "{0}/melodic_mix".format(self.dir)
+        ffname = "{0}/melodic_FTmix".format(self.dir)
+        bfname = "{0}/mean.nii.gz".format(self.dir)
+        vfname = "{0}/melodic_ICstats".format(self.dir)
+        zfname = "{0}/melodic_IC.nii.gz".format(self.dir)
+
+        self.mix = genfromtxt(mfname)
+        self.FTmix = genfromtxt(ffname)
+        self.exp_var_stats = genfromtxt(vfname)
+        self.background_image = bfname
+        self.zstat_data = nb.load(zfname).get_data()
+        self.select_component(self.ic)
+
+    def select_component(self, ic=1):
+        self.ic = ic
+
+        self.stat = self.zstat_data[:,:,:,self.ic-1]
+   
+    def get_tr(self):
+        tr = 1
+        for line in open("{0}/log.txt".format(self.dir)):
+            if "--tr" in line:
+                print line
+                for arg in line.split():
+                    if "--tr" in arg:
+                        tr = float(arg.split("=")[1])
+                break
+        return tr
+
+    def get_bg_image(self):
+        return self.background_image
+
+    def get_mix_shape(self):
+        return self.mix.shape
+
+    def get_stat_data(self):
+        return self.stat
+
+    def get_mix_data(self):
+        return self.mix[:,self.ic-1]
+
+    def get_FTmix_data(self):
+        return self.FTmix[:,self.ic-1]
+
+    def get_variance_stats(self):
+        return (self.exp_var_stats[self.ic-1, 0], self.exp_var_stats[self.ic-1, 1])

melview.ini

+
+path = /vols/Data/steve/FIX/HCP_hp100/CP10051_v3.ica/filtered_func_data.ica
+bgpath = /vols/Data/steve/FIX/HCP_hp100/CP10051_v3.ica/filtered_func_data.ica/mean.nii.gz
+    

melview/mv2fix.py

+import os
+import logging
+
+from fsl.melodic import *
+from optparse import OptionParser
+
+class Classification():
+    class_name = ""
+    ic_number = 0
+    filter = bool(False)
+    
+    def __init__(self, class_name, ic_number, filter):
+        self.class_name = class_name
+        self.ic_number = ic_number
+        self.filter = filter
+        
+    def __str__(self):
+        return "{0}, {1}, {2}".format(self.ic_number, self.class_name, self.filter)
+        
+class ClassificationFile():
+    
+    def __init__(self, filename, **kwargs):
+        self.path = os.path.join('.', filename)
+        
+    def write(self, class_list, dirpath):
+        try:
+            f = open(self.path, 'w')
+    
+            f.write(dirpath + '\n')
+#            for c in [ c for c in class_list if c.class_name != 'Unknown' ]:
+            for c in class_list:
+                f.write( '{0}\n'.format(c) )    
+            f.write( str([ int(ic.ic_number) for ic in class_list if ic.filter == True]) + '\n')
+    
+            f.close()
+
+        except Exception, e: