def export(user, directory=None, warnings=True):
"""
Build a temporary directory with the visualization.
Returns the local path where files have been written.
Examples
--------
>>> bandicoot.visualization.export(U)
Successfully exported the visualization to /tmp/tmpsIyncS
"""
# Get dashboard directory
current_file = os.path.realpath(__file__)
current_path = os.path.dirname(current_file)
dashboard_path = os.path.join(current_path, '../dashboard_src')
# Create a temporary directory if needed and copy all files
if directory:
dirpath = directory
else:
dirpath = tempfile.mkdtemp()
# Copy all files except source code
copy_tree(dashboard_path + '/public', dirpath, update=1)
# Export indicators
data = user_data(user)
bc.io.to_json(data, dirpath + '/data/bc_export.json', warnings=False)
if warnings:
print("Successfully exported the visualization to %s" % dirpath)
return dirpath
def copyHtml(self):
htmlDir = os.path.join(self.LOCALEDIR, "html")
try:
copy_tree(self.HTMLDIR, htmlDir)
except Exception, e:
self.raiseError("Unable to copy html from '%s': %s." % (self.HTMLDIR, e))
def install():
autotools.rawInstall("INSTALL_PREFIX=%s MANDIR=/usr/share/man" % get.installDIR())
# Rename conflicting manpages
pisitools.rename("/usr/share/man/man1/passwd.1", "ssl-passwd.1")
pisitools.rename("/usr/share/man/man3/rand.3", "ssl-rand.3")
pisitools.rename("/usr/share/man/man3/err.3", "ssl-err.3")
if get.buildTYPE() == "_emul32":
from distutils.dir_util import copy_tree
copy_tree("%s/_emul32/lib32/" % get.installDIR(), "%s/usr/lib32" % get.installDIR())
pisitools.removeDir("/_emul32")
pisitools.remove("/usr/lib32/*.a")
path = "%s/usr/lib32/pkgconfig" % get.installDIR()
for f in shelltools.ls(path): pisitools.dosed("%s/%s" % (path, f), "^(prefix=\/)_emul32", r"\1usr")
return
# Move engines to /usr/lib/openssl/engines
pisitools.dodir("/usr/lib/openssl")
pisitools.domove("/usr/lib/engines", "/usr/lib/openssl")
# Certificate stuff
pisitools.dobin("tools/c_rehash")
pisitools.dosym("/etc/pki/tls/certs/ca-bundle.crt","/etc/pki/tls/cert.pem")
# Create CA dirs
for cadir in ["CA", "CA/private", "CA/certs", "CA/crl", "CA/newcerts"]:
pisitools.dodir("/etc/pki/%s" % cadir)
# No static libs
pisitools.remove("/usr/lib/*.a")
pisitools.dohtml("doc/*")
pisitools.dodoc("CHANGES*", "FAQ", "LICENSE", "NEWS", "README", "doc/*.txt")
def _copy_sdk_template(self, gen_api_root, package_type):
""" Copy sdk template to gen_api_root directory.
Args:
gen_api_root (str): Root directory for generated APIs.
package_type (str): Sdk template to copied from.
Valid options are: core, packages.
"""
target_dir = os.path.join(self.ydk_root, 'sdk', self.language)
if self.language == 'python':
if package_type == 'service':
service_name = gen_api_root.split('-')[-1]
target_dir = os.path.join(target_dir, service_name)
else:
target_dir = os.path.join(target_dir, package_type)
elif self.language == 'cpp':
if package_type == 'packages':
target_dir = os.path.join(target_dir, package_type)
elif package_type == 'core':
target_dir = os.path.join(target_dir, 'core')
elif package_type == 'service':
service_name = gen_api_root.split('-')[-1]
target_dir = os.path.join(target_dir, service_name)
elif self.language == 'go':
if package_type == 'service':
service_name = gen_api_root.split('-')[-1]
target_dir = os.path.join(target_dir, service_name)
else:
target_dir = os.path.join(target_dir, package_type)
shutil.rmtree(gen_api_root)
logger.debug('Copying %s to %s' % (target_dir, gen_api_root))
dir_util.copy_tree(target_dir, gen_api_root)
def install():
pisitools.dodir("/usr/share")
wanteddirs = []
for file_ in shelltools.ls(get.workDIR()):
if shelltools.isDirectory(file_) and not "texmf" in file_:
wanteddirs.append(file_)
for folder in wanteddirs:
pisitools.insinto("/usr/share/texmf-dist", folder)
if shelltools.can_access_directory("texmf-dist"):
# Recursively copy on directory on top of another, overwrite duplicate files too
copy_tree("texmf-dist", "%s/usr/share/texmf-dist" % get.installDIR())
## chmod of script files
script_dir = get.installDIR() + "/usr/share/texmf-dist/scripts"
if shelltools.can_access_directory(script_dir):
for root, dirs, files in os.walk(script_dir):
for name in files:
shelltools.chmod(os.path.join(root, name), 0755)
# copy config file to texmf-config
pisitools.dodir("/etc/texmf/tex/context/config")
shelltools.copy("%s/usr/share/texmf-dist/tex/context/config/cont-usr.tex" % get.installDIR(), \
"%s/etc/texmf/tex/context/config/cont-usr.tex" % get.installDIR())
# old packages, we will not provide them
pisitools.remove("/usr/share/texmf-dist/tex/plain/config/omega.ini")
pisitools.remove("/usr/share/texmf-dist/tex/plain/config/aleph.ini")
pisitools.removeDir("/usr/share/texmf-dist/scripts/context/stubs/mswin/")
def fetch(in_base, in_id, out_base='/var/tmp/repositorg/', in_id_is_file=False, in_path='', ): """Fetch data and reposit verbatim inside repositorg temporal directory Parameters ---------- in_base : str Base input directory from which to copy files. in_id : str UUID of the source device. This string will be added as a subidrectory under the `out_base` directory. out_base : str, optional Output base directory. A subdirectory named according to the value of `in_id` will be created under this directory to contain the output files. in_id_is_file : bool, optional Whether the value passed to `in_id` is a file name or path. If `True`, the `in_id` will be stripped of the extension and its basename will be extracted. in_path : str, optional An additional subpath to be added under the `in_base` directory. """ if in_id_is_file: in_id = os.path.basename(in_id) in_id = os.path.splitext(in_id)[0] in_path = os.path.join(in_base,in_path) out_path = os.path.join(out_base,in_id) if not os.path.isdir(in_path): return False dir_util.copy_tree(in_path, out_path, preserve_mode=0 )
def constructPreBuiltHTMITFakeroot(self):
"""
Construct fakeroot from prebuilt htm-it
:returns: SHA of the products repo in the fakeroot
:rtype: tuple
"""
config = self.config
logger = self.logger
productsDirectory = self.productsDirectory
logger.debug("Creating %s", productsDirectory)
mkpath(productsDirectory)
copy_tree(config.productsDir, productsDirectory)
iteration = git.getCommitCount(productsDirectory, logger=logger)
with changeToWorkingDir(productsDirectory):
actualSHA = git.getCurrentSha(logger=logger)
# Set extra python path
self.setPythonPath()
# Clean HTM-IT Scripts
self.cleanScripts()
# Purge anything not whitelisted
self.purgeBlacklistedStuff()
return (iteration, actualSHA)
def openTestProject(name):
orgPath = os.path.join(os.path.dirname(__file__), "data", "projects", name)
destPath = tempFolderInTempFolder()
copy_tree(orgPath, destPath)
projectFile = os.path.join(destPath, name + ".qgs")
if projectFile != QgsProject.instance().fileName():
iface.addProject(projectFile)
def copy_folder_from(self, source, incremental=False):
"""
Copies the given source directory to this directory. If incremental is True
only newer objects are overwritten.
"""
# There is a bug in dir_util that makes copy_tree crash if a folder in the
# tree has been deleted before and readded now. To workaround the bug, we first
# walk the tree and create directories that are needed.
#
# pylint: disable-msg=C0111,W0232
target_root = self
class _DirCreator:
@staticmethod
def visit_folder(folder):
target = folder.get_mirror_folder(
source.parent, target_root, ignore_root=True)
target.make()
source.walk(_DirCreator)
dir_util.copy_tree(str(source),
self.child(source.name),
preserve_symlinks=True,
update=incremental)
def updateIWSPlugin(self):
self.logger.info(u"Performing update of DomoPad" "s IWS plugin...")
# determine the IWS server directory
indigoInstallPath = indigo.server.getInstallFolderPath()
pluginBasePath = os.getcwd()
mainPluginHome = os.path.join(pluginBasePath, "AndroidClientHelper")
iwsPluginHome = os.path.join(indigoInstallPath, "IndigoWebServer/plugins/AndroidClientHelper")
self.logger.info(u"Source IWS directory: " + mainPluginHome)
self.logger.info(u"Target IWS directory: " + iwsPluginHome)
# ensure that we have the correct source directory...
if os.path.exists(mainPluginHome) == False:
self.logger.error(
u"ERROR: Source directory not found! AndroidClientHelper IWS plugin install could not complete."
)
return
# execute the directory copy now...
try:
copy_tree(mainPluginHome, iwsPluginHome, preserve_mode=1)
self.logger.info(
u"AndroidClientHelper successfully installed/updated. Restarting Indigo IWS server to complete install."
)
self.restartIWS()
except:
self.logger.error(
u"Error copying AndroidClientHelper, AndroidClientHelper IWS plugin install could not complete."
)
def bookmarkCurrentPage(self, dimdimID, newResourceID):
meeting = self.getMeeting(dimdimID)
resourceList = meeting.get('resources')
currentResourceID = meeting.get('currentResource')
currentResourceCopy = self.getCurrentResource(dimdimID)
currentResourceType = self.getResourceType(dimdimID, currentResourceID)
currentPageNum = currentResourceCopy.get('currentPage')
currentPageCopy = self.getCurrentPage(dimdimID)
newResource = {'currentPage':0, 'lastPage':0, 'pages': {0:currentPageCopy}}
sourcePath = os.path.join(os.path.join(os.path.join(os.path.join(osconfig.cobArchive(), dimdimID), \
currentResourceType), currentResourceID), str(currentPageNum))
destPath = os.path.join(os.path.join(os.path.join(os.path.join(osconfig.cobArchive(), dimdimID), \
currentResourceType), newResourceID), '0')
try:
shutil.rmtree(destPath)
except:
pass
dir_util.copy_tree(sourcePath, destPath)
typeList = resourceList.get(currentResourceType)
self.stateLock.acquire()
typeList.update({newResourceID : newResource})
self.exportStateMachine(dimdimID)
self.stateLock.release()
return
def handle(self, dump_path, **options):
if dump_path == "-":
arc = tarfile.open(fileobj=sys.stdin, mode="r:gz")
else:
arc = tarfile.open(dump_path, mode="r:gz")
base_path = tempfile.mkdtemp()
arc.extractall(path=base_path)
path = glob(os.path.join(base_path, "*"))[0]
# media files
# shutil.copytree(os.path.join(path, 'media'), settings.MEDIA_ROOT)
dir_util.copy_tree(os.path.join(path, "media"), settings.MEDIA_ROOT)
# load db fields
old_stdout = sys.stdout
sys.stdout = open(os.path.join(path, "backup_db_dump.json"), "w")
call_command("dumpdata", indent=4)
sys.stdout.close()
sys.stdout = old_stdout
call_command("flush", noinput=True, interactive=False)
call_command("reset", "contenttypes", "auth", noinput=True, interactive=False)
call_command("loaddata", os.path.join(path, "db_dump.json"))
# rebase FilepathFields
call_command("rebase_filepathfields", os.path.join(path, "fpf_bases_dump.json"))
def install():
pisitools.dodir("/usr/share")
wanteddirs = []
for file_ in shelltools.ls('.'):
if shelltools.isDirectory(file_) and not "texmf" in file_:
wanteddirs.append(file_)
for folder in wanteddirs:
pisitools.insinto("/usr/share/texmf-dist", folder)
if shelltools.can_access_directory("texmf-dist"):
# Recursively copy on directory on top of another, overwrite duplicate files too
copy_tree("texmf-dist", "%s/usr/share/texmf-dist" % get.installDIR())
## chmod of script files
script_dir = get.installDIR() + "/usr/share/texmf-dist/scripts"
if shelltools.can_access_directory(script_dir):
for root, dirs, files in os.walk(script_dir):
for name in files:
shelltools.chmod(os.path.join(root, name), 0755)
pisitools.remove("/usr/share/texmf-dist/scripts/m-tx/m-tx.lua")
pisitools.remove("/usr/share/texmf-dist/scripts/musixtex/musixtex.lua")
pisitools.remove("/usr/share/texmf-dist/scripts/musixtex/musixflx.lua")
pisitools.remove("/usr/share/texmf-dist/scripts/pmx/pmx2pdf.lua")
def extract_rpclib(args):
"""
THE extraction function
"""
workdir = tempfile.mkdtemp()
rpclib_root = args.rpclib_root
new_rpclib_root = tempfile.mkdtemp()
copy_tree(rpclib_root, new_rpclib_root)
patch_rpclib(new_rpclib_root)
copy_important_files(workdir, new_rpclib_root)
version = extract_rpclib_version(new_rpclib_root)
shutil.rmtree(new_rpclib_root)
cmake_template = Template(
filename=os.path.join(os.path.dirname(os.path.realpath(__file__)), "rpc_CMakeLists.txt"))
real_cmake_file = cmake_template.render(
rpclib_major_version=version[0],
rpclib_minor_version=version[1],
rpclib_patch_version=version[2]
)
with open(os.path.join(workdir, "CMakeLists.txt"), "w") as cmake_file:
cmake_file.write(real_cmake_file)
cmake_file.truncate()
fix_naming(workdir)
copy_tree(workdir, args.rpclib_target, update=True)
shutil.rmtree(workdir)
def run(self):
if sys.platform not in ("linux2", "win32"):
msg = "**Error: Can't install on this platform: %s" % sys.platform
print msg
sys.exit(1)
if not self.single_version_externally_managed:
self.do_egg_install()
else:
_install.run(self)
# check if someone else is copying the files to the destination
# if self.single_version_externally_managed:# and not self.root:
# return
# install bauble.desktop and icons
if sys.platform == "linux2":
# install everything in share
dir_util.copy_tree(os.path.join(self.build_base, "share"), os.path.join(self.install_data, "share"))
elif sys.platform == "win32":
# install only i18n files
locales = os.path.dirname(locale_path)
install_cmd = self.get_finalized_command("install")
build_base = install_cmd.build_base
src = os.path.join(build_base, locales)
dir_util.copy_tree(src, os.path.join(self.install_data, locales))
def windows_package(args):
pkgfile = 'windows_package.7z'
pkgdir = os.path.abspath('windows_package')
logging.info("Packaging libraries and headers in package: %s", pkgfile)
j = os.path.join
pkgdir_lib = os.path.abspath(j(pkgdir, 'lib'))
with remember_cwd():
os.chdir(args.output)
logging.info("Looking for static libraries and dlls in: \"%s", os.getcwd())
libs = list(glob.iglob('**/*.lib', recursive=True))
dlls = list(glob.iglob('**/*.dll', recursive=True))
os.makedirs(pkgdir_lib, exist_ok=True)
for lib in libs:
logging.info("packing lib: %s", lib)
shutil.copy(lib, pkgdir_lib)
for dll in dlls:
logging.info("packing dll: %s", dll)
shutil.copy(dll, pkgdir_lib)
os.chdir(get_mxnet_root())
logging.info('packing python bindings')
copy_tree('python', j(pkgdir, 'python'))
logging.info('packing headers')
copy_tree('include', j(pkgdir, 'include'))
logging.info("Compressing package: %s", pkgfile)
check_call(['7z', 'a', pkgfile, pkgdir])
def add_local_binaries_to_stage(self):
progress("Adding local binaries to staging directory")
safe_make_directory("appleseed/bin")
dir_util.copy_tree(os.path.join(self.settings.appleseed_path, "sandbox/bin", self.settings.configuration), "appleseed/bin/")
shutil.copy(os.path.join(self.settings.appleseed_path, "sandbox/bin", exe("maketx")), "appleseed/bin/")
shutil.copy(os.path.join(self.settings.appleseed_path, "sandbox/bin", exe("oslc")), "appleseed/bin/")
shutil.copy(os.path.join(self.settings.appleseed_path, "sandbox/bin", exe("oslinfo")), "appleseed/bin/")
def run(self):
# TODO: make sure we have everything installed that we need to
# bundle e.g. sqlite, psycopg2, others...
_py2exe_cmd.run(self)
# install locale files
locales = os.path.dirname(locale_path)
build_base = self.get_finalized_command("build").build_base
# print build_base
src = os.path.join(build_base, locales)
dir_util.copy_tree(src, os.path.join(self.dist_dir, locales))
# copy GTK to the dist directory, assuming PyGTK
# all-in-one installer
gtk_root = "c:\\python27\\lib\\site-packages\\gtk-2.0\\runtime"
dist_gtk = os.path.join(self.dist_dir, "gtk")
import shutil
if not os.path.exists(dist_gtk):
ignore = shutil.ignore_patterns("src", "gtk-doc", "icons", "man", "demo", "aclocal", "doc", "include")
shutil.copytree(gtk_root, dist_gtk, ignore=ignore)
# register the pixbuf loaders
exe = "%s\\bin\\gdk-pixbuf-query-loaders.exe" % dist_gtk
dest = "%s\\etc\\gtk-2.0\\gdk-pixbuf.loaders" % dist_gtk
cmd = 'call "%s" > "%s"' % (exe, dest)
print cmd
os.system(cmd)
# copy the the MS-Windows gtkrc to make it the default theme
rc = "%s\\share\\themes\\MS-Windows\\gtk-2.0\\gtkrc" % dist_gtk
dest = "%s\\etc\\gtk-2.0" % dist_gtk
file_util.copy_file(rc, dest)
def copy_sources():
"""Copy the C sources into the source directory.
This rearranges the source files under the python distribution
directory.
"""
src = []
try:
dir_util.remove_tree("src/")
except (IOError, OSError):
pass
dir_util.copy_tree("../../arch", "src/arch/")
dir_util.copy_tree("../../include", "src/include/")
src.extend(glob.glob("../../*.[ch]"))
src.extend(glob.glob("../../*.mk"))
src.extend(glob.glob("../../Makefile"))
src.extend(glob.glob("../../LICENSE*"))
src.extend(glob.glob("../../README"))
src.extend(glob.glob("../../*.TXT"))
src.extend(glob.glob("../../RELEASE_NOTES"))
src.extend(glob.glob("../../make.sh"))
src.extend(glob.glob("../../CMakeLists.txt"))
for filename in src:
outpath = os.path.join("./src/", os.path.basename(filename))
log.info("%s -> %s" % (filename, outpath))
shutil.copy(filename, outpath)
def install():
"""Install MLTSP config file and create data folders.
Copies mltsp.yaml.example to ~/.config/mltsp/mltsp.yaml and creates data
directories as described in `mltsp.config.cfg['paths']`
"""
import os
import shutil
from distutils.dir_util import copy_tree
data_src = os.path.join(os.path.dirname(__file__), "data")
data_dst = os.path.expanduser('~/.local/mltsp/')
copy_tree(data_src, data_dst, update=1)
print("Created data directory at {} and copied sample data.".format(
os.path.expanduser('~/.local/mltsp/')))
cfg = os.path.expanduser('~/.config/mltsp/mltsp.yaml')
cfg_dir = os.path.dirname(cfg)
if os.path.exists(cfg):
print('Existing configuration at {} -- not overwriting.'.format(cfg))
return
if not os.path.exists(cfg_dir):
os.makedirs(cfg_dir)
shutil.copyfile(os.path.join(os.path.dirname(__file__),
'mltsp.yaml.example'),
cfg)
print('Installed {}'.format(cfg))
print('Please customize this file with authentication tokens, etc.')
def copy_static(args):
if '../' in args['html_folder']:
dir_util.copy_tree(os.path.join(os.path.dirname(__file__), 'static'),
os.path.join(os.path.abspath(args['html_folder']), 'static'))
else:
dir_util.copy_tree(os.path.join(os.path.dirname(__file__), 'static'),
os.path.join(os.path.abspath(args['html_folder']), 'static'))
def __deploy_app(self):
"""
Deploy the local SO bundle
assumption here
- a git repo is returned
- the bundle is not managed by git
"""
# create temp dir...and clone the remote repo provided by OpS
tmp_dir = tempfile.mkdtemp()
LOG.debug('Cloning git repository: ' + self.repo_uri + ' to: ' + tmp_dir)
cmd = ' '.join(['git', 'clone', self.repo_uri, tmp_dir])
os.system(cmd)
# Get the SO bundle
bundle_loc = CONFIG.get('service_manager', 'bundle_location', '')
if bundle_loc == '':
raise Exception('No bundle_location parameter supplied in sm.cfg')
LOG.debug('Bundle to add to repo: ' + bundle_loc)
dir_util.copy_tree(bundle_loc, tmp_dir)
self.__add_openshift_files(bundle_loc, tmp_dir)
# add & push to OpenShift
os.system(' '.join(['cd', tmp_dir, '&&', 'git', 'add', '-A']))
os.system(' '.join(['cd', tmp_dir, '&&', 'git', 'commit', '-m', '"deployment of SO for tenant ' +
self.extras['tenant_name'] + '"', '-a']))
LOG.debug('Pushing new code to remote repository...')
os.system(' '.join(['cd', tmp_dir, '&&', 'git', 'push']))
shutil.rmtree(tmp_dir)
def _copy_resources(template, instance, resource, dir=False):
if dir:
src = path.join(template, resource)
dst = path.join(instance, resource)
copy_tree(src, dst)
else:
raise NotImplementedError()
def mergeDir(self, path, dest):
"""
We don't want to delete the old dir, since it might contain third
party plugin content from previous installations; we simply want to
merge the existing directory with the new one.
"""
copy_tree(path, os.path.join(dest, path), preserve_symlinks=True)
def copy_base_course(self):
""" Create all the base files needed to restore the course. """
print ' > Creating course base files... ',
if not os.path.exists(self.course_dir):
os.makedirs(self.course_dir)
copy_tree(settings.BASE_COURSE, self.course_dir)
print 'Done.'
def pyinstall(source_folder):
pyinstaller_path = os.path.join(os.path.curdir, 'pyinstaller')
_install_pyintaller(pyinstaller_path)
try:
shutil.rmtree(os.path.join(pyinstaller_path, 'conan'))
except Exception as e:
print("Unable to remove old folder", e)
try:
shutil.rmtree(os.path.join(pyinstaller_path, 'conan_server'))
except Exception as e:
print("Unable to remove old server folder", e)
conan_path = os.path.join(source_folder, 'conans', 'conan.py')
conan_server_path = os.path.join(source_folder, 'conans', 'conan_server.py')
subprocess.call('python pyinstaller.py -y -p %s --console %s' % (source_folder, conan_path),
cwd=pyinstaller_path, shell=True)
_run_bin(pyinstaller_path)
subprocess.call('python pyinstaller.py -y -p %s --console %s'
% (source_folder, conan_server_path),
cwd=pyinstaller_path, shell=True)
conan_bin = os.path.join(pyinstaller_path, 'conan', 'dist', 'conan')
conan_server_folder = os.path.join(pyinstaller_path, 'conan_server', 'dist', 'conan_server')
dir_util.copy_tree(conan_server_folder, conan_bin)
_run_bin(pyinstaller_path)
return os.path.abspath(os.path.join(pyinstaller_path, 'conan', 'dist', 'conan'))
def deploy(config, host):
# add -H command to set home directory of target user
new_sudo_command = "sudo -H -S -p '%(sudo_prompt)s'"
print colors.green('change sudo_prefix from "%s" to "%s"' % (env['sudo_prefix'], new_sudo_command))
with settings(sudo_prefix=new_sudo_command):
fixtures_dir = tempfile.mkdtemp()
print colors.green('create fixtures directory: "%s"' % fixtures_dir)
try:
print colors.green('merge fixtures')
for source_fixtures_dir in reversed(config.fixtures):
dir_util.copy_tree(source_fixtures_dir, fixtures_dir)
config.fixtures_path = fixtures_dir
host.prepair()
host.check()
host.setup()
except Exception, e:
traceback.print_exc()
print colors.red('Exception while deploing: "%s"' % e)
finally:
def aggregate(outputdir=OUTPUT_DIR, buildname=DEFAULT_BUILD_NAME):
"""
Aggregates the captures from various campaigns to the 'default'
:return:
"""
if not os.path.exists(outputdir):
raise ValueError("outputdir does not exist at %s!" % outputdir)
# Aggregate all the capture job data
outputdir = str(outputdir).rstrip('/')
buildpaths = glob.glob(outputdir + '/*/')
aggregate_path = os.path.join(outputdir, buildname)
if not os.path.exists(aggregate_path):
LOGGER.debug("Creating path for aggregates at %s", aggregate_path)
os.makedirs(aggregate_path)
LOGGER.info("Aggregating build data to %s", aggregate_path)
# Workaround bug with dir_util
# See http://stackoverflow.com/questions/9160227/
dir_util._path_created = {}
for buildpath in buildpaths:
if str(buildpath).endswith(DEFAULT_BUILD_NAME + "/"):
# Don't do this for the default build
LOGGER.debug("Skipping default path: %s", buildpath)
continue
sourcepath = os.path.join(outputdir, buildpath)
LOGGER.debug("Copying from %s to %s", buildpath,
aggregate_path)
dir_util.copy_tree(sourcepath, aggregate_path, update=1)
return aggregate_path
def cp(source, target, force=True):
if isinstance(source, list): # list
# copy files to dir
targets = []
for s in source:
t = cp(s, target, force)
targets.append(t)
return targets
assert_exists(source) # assert exists
if not force and os.path.exists(target):
return
if source == target:
return target
if os.path.isfile(source) and os.path.isdir(target):
# target is DIR
target = os.path.join(target, os.path.basename(source))
if os.path.isfile(source) or os.path.islink(source):
if (os.path.exists(target) or os.path.lexists(target)):
if os.path.isfile(source) != os.path.isfile(target):
os.unlink(target)
shutil.copy(source, target)
if os.path.isdir(source):
# first create dirs
if not os.path.exists(target):
os.makedirs(target)
dir_util.copy_tree(source, target)
return target
def handle(self, *args, **options):
app_name = args[0]
module = importlib.import_module(app_name)
path = os.path.dirname(module.__file__) + os.sep
project_path = os.path.dirname(os.path.normpath(os.sys.modules[settings.SETTINGS_MODULE].__file__))
install_app('social_auth')
copy_tree(os.path.dirname(djangobp.__file__) + os.sep + 'scaffold/socialauth/templates/accounts', path + '/templates/accounts', update=True)
copy_file(os.path.dirname(djangobp.__file__) + os.sep + 'scaffold/socialauth/controllers/accounts.py', path + '/controllers', update=True)
copy_file(os.path.dirname(djangobp.__file__) + os.sep + 'scaffold/scaffold/socialauthsettings.py', project_path, update=True)
urls_edit = CodeEditor(path + 'urls.py')
urls_edit.insert_line("url(r'', include('social_auth.urls')),", 'urlpatterns')
urls_edit.commit()
settings_edit = CodeEditor(project_path + os.sep + 'settings.py')
settings_edit.append_line("from socialauthsettings import *")
settings_edit.commit()
# TODO copy controllers/accounts.py
# TODO copy templates/accounts/login.html
# TODO urls social auth
# TODO django-social-auth settings
def copy_directory(src, dst, clear_dst=False):
ensure_directory(dst)
if clear_dst:
clear_directory(dst)
from distutils.dir_util import copy_tree
copy_tree(src, dst)
def main(self):
begin = time.time()
source_language = "en"
total_char = 0
labs = [f.path for f in os.scandir(self.src_dir) if f.is_dir()]
for lab in labs:
print("Translating lab manual: {}".format(lab))
start_time = time.time()
for target_language_code in self.codes:
start_time_lab = time.time()
print(
"##########################################################"
)
print("Translating content from {} to {}".format(
source_language, target_language_code))
with open(str(lab) + '/content.xml') as f:
tree = ET.parse(f)
root = tree.getroot()
len_of_text = 0
for elem in root.getiterator():
text_translate = elem.text
tag = elem.tag
if text_translate is None or text_translate.isspace():
continue
else:
self.logger.info(
"---------------------Start of text----------------------------------"
)
self.logger.info(
"-----------------------translating text-----------------------------"
)
curr_len = len(text_translate.encode('utf-8'))
total_char += curr_len
if tag == 'name' or tag == 'dataFormat':
continue
if tag == 'defaultLanguageCode':
elem.text = str(target_language_code)
continue
result = self.language_translation(
text=text_translate,
source_language="en",
target_language=target_language_code,
model=self.modelType)
if self.modelType == 'custom':
self.logger.info(result)
elem.text = str(result)
else:
self.logger.info(result['translatedText'])
elem.text = str(result['translatedText'])
len_of_text += curr_len
self.logger.info(
"-----------------------translation complete-----------------------------"
)
self.logger.info(
"---------------------End of text----------------------------------"
)
self.logger.info("")
if not os.path.isdir(self.dst_dir + '/' + str(lab[7:-2]) +
target_language_code):
os.mkdir(self.dst_dir + '/' + str(lab[7:-2]) +
target_language_code)
os.mkdir(self.dst_dir + '/' + str(lab[7:-2]) +
target_language_code + '/images')
tree.write(self.dst_dir + '/' + str(lab[7:-2]) +
target_language_code + '/content.xml',
encoding="UTF-8")
copy_tree(
str(lab) + '/images', self.dst_dir + '/' + str(lab[7:-2]) +
target_language_code + '/images')
end_time = time.time()
print(
"Total elapsed time to translate the xml document is: {} minutes"
.format((end_time - start_time_lab) / 60))
is_upload = self.upload_s3(
self.dst_dir + '/' + str(lab[7:-2]) +
target_language_code + '.zip', self.dst_dir,
self.bucket_name,
str(lab[7:-2]) + "all_translations",
str(lab[7:-2]) + target_language_code)
if not is_upload:
print("Upload failed....Exiting!!")
exit(0)
final_end_time = time.time()
print(
"Total characters processed in this translating lab {} are {} chars"
.format(lab, total_char))
print("Total Translation time {} minutes".format(
(final_end_time - start_time) / 60))
end = time.time()
print("Total execution time for all labs: {} hrs".format(
(end - begin) / 3600))
def main():
if len(sys.argv) < 2 or sys.argv[1].startswith('-'):
print usage % (aliases, ets_package_names)
return
arg1 = sys.argv[1]
# Update the gh-pages branch
if arg1 == 'update':
if 2 < len(sys.argv):
ets_packages = sys.argv[2:]
else:
ets_packages = ets_package_names.split()
for ets_pkg_name in ets_packages:
print "Updating documentation branch for {0}...".format(
ets_pkg_name)
# Find the current branch, so that we may return to it
branches = subprocess.check_output(['git', 'branch'],
cwd=ets_pkg_name)
current_branch = [
line.split()[1] for line in branches.splitlines()
if line.startswith('*')
]
current_branch = current_branch[0]
# Checkout the gh-pages branch
try:
subprocess.check_call(['git', 'checkout', 'gh-pages'],
cwd=ets_pkg_name)
except (OSError, subprocess.CalledProcessError), detail:
print " Error running command in package %s:\n %s" % (
ets_pkg_name, detail)
raw_input(" Press enter to process remaining packages.")
continue
# Copy the files over
print "Copying files for {0}".format(ets_pkg_name)
if ets_pkg_name == 'mayavi':
copy_tree(ets_pkg_name + '/docs/build/tvtk/html/',
ets_pkg_name + '/tvtk/')
copy_tree(ets_pkg_name + '/docs/build/mayavi/html/',
ets_pkg_name + '/mayavi/')
else:
copy_tree(ets_pkg_name + '/docs/build/html/', ets_pkg_name)
# Add everything to the repository
try:
subprocess.check_call(['git', 'add', '.'], cwd=ets_pkg_name)
except (OSError, subprocess.CalledProcessError), detail:
print " Error running command in package %s:\n %s" % (
ets_pkg_name, detail)
raw_input(" Press enter to process remaining packages.")
continue
# Commit to the repo.
try:
subprocess.check_call(
['git', 'commit', '-a', '-m', '"Updated docs."'],
cwd=ets_pkg_name)
except (OSError, subprocess.CalledProcessError), detail:
print " Error running command in package %s:\n %s" % (
ets_pkg_name, detail)
raw_input(" Press enter to process remaining packages.")
continue
def _compare_baseline(self):
with self._test_status:
if int(self._case.get_value("RESUBMIT")) > 0:
# This is here because the comparison is run for each submission
# and we only want to compare once the whole run is finished. We
# need to return a pass here to continue the submission process.
self._test_status.set_status(CIME.test_status.BASELINE_PHASE,
CIME.test_status.TEST_PASS_STATUS)
return
self._test_status.set_status(CIME.test_status.BASELINE_PHASE,
CIME.test_status.TEST_FAIL_STATUS)
run_dir = self._case.get_value("RUNDIR")
case_name = self._case.get_value("CASE")
base_dir = os.path.join(
self._case.get_value("BASELINE_ROOT"),
self._case.get_value("BASECMP_CASE"),
)
test_name = "{}".format(case_name.split(".")[-1])
evv_config = {
test_name: {
"module": os.path.join(evv_lib_dir, "extensions", "ks.py"),
"test-case": "Test",
"test-dir": run_dir,
"ref-case": "Baseline",
"ref-dir": base_dir,
"var-set": "default",
"ninst": NINST,
"critical": 13,
"component": self.component,
}
}
json_file = os.path.join(run_dir, ".".join([case_name, "json"]))
with open(json_file, "w") as config_file:
json.dump(evv_config, config_file, indent=4)
evv_out_dir = os.path.join(run_dir, ".".join([case_name, "evv"]))
evv(["-e", json_file, "-o", evv_out_dir])
with open(os.path.join(evv_out_dir, "index.json")) as evv_f:
evv_status = json.load(evv_f)
comments = ""
for evv_elem in evv_status["Data"]["Elements"]:
if (evv_elem["Type"] == "ValSummary" and evv_elem["TableTitle"]
== "Kolmogorov-Smirnov test"):
comments = "; ".join("{}: {}".format(key, val)
for key, val in evv_elem["Data"]
[test_name][""].items())
if evv_elem["Data"][test_name][""]["Test status"].lower(
) == "pass":
self._test_status.set_status(
CIME.test_status.BASELINE_PHASE,
CIME.test_status.TEST_PASS_STATUS,
)
break
status = self._test_status.get_status(
CIME.test_status.BASELINE_PHASE)
mach_name = self._case.get_value("MACH")
mach_obj = Machines(machine=mach_name)
htmlroot = CIME.utils.get_htmlroot(mach_obj)
urlroot = CIME.utils.get_urlroot(mach_obj)
if htmlroot is not None:
with CIME.utils.SharedArea():
dir_util.copy_tree(
evv_out_dir,
os.path.join(htmlroot, "evv", case_name),
preserve_mode=False,
)
if urlroot is None:
urlroot = "[{}_URL]".format(mach_name.capitalize())
viewing = "{}/evv/{}/index.html".format(urlroot, case_name)
else:
viewing = (
"{}\n"
" EVV viewing instructions can be found at: "
" https://github.com/E3SM-Project/E3SM/blob/master/cime/scripts/"
"climate_reproducibility/README.md#test-passfail-and-extended-output"
"".format(evv_out_dir))
comments = ("{} {} for test '{}'.\n"
" {}\n"
" EVV results can be viewed at:\n"
" {}".format(
CIME.test_status.BASELINE_PHASE,
status,
test_name,
comments,
viewing,
))
CIME.utils.append_testlog(comments, self._orig_caseroot)
with open(logfile, 'w') as ff:
ff.write(WORK_DIR)
ff.write('\n\n\n')
# main directory to be used when running the knife:
KNIFE_DIR = "/srv/software/knife/circularRNApipeline_Standalone"
# place files in appropriate locations; fix code in future to
# avoid this step
anly_src = (KNIFE_DIR + "/analysis")
anly_dst = (RESOURCE_DIR + "/analysis")
anly_dst2 = (WORK_DIR + "/analysis")
if not os.path.exists(anly_dst):
copy_tree(anly_src, anly_dst)
if not os.path.exists(anly_dst2):
os.symlink(anly_dst, anly_dst2)
comprun_src = (KNIFE_DIR + "/completeRun.sh")
comprun_dst = (RESOURCE_DIR + "/completeRun.sh")
comprun_dst2 = (WORK_DIR + "/completeRun.sh")
if not os.path.exists(comprun_dst):
copyfile(comprun_src, comprun_dst)
if not os.path.exists(comprun_dst2):
os.symlink(comprun_dst, comprun_dst2)
findcirc_src = (KNIFE_DIR + "/findCircularRNA.sh")
findcirc_dst = (RESOURCE_DIR + "/findCircularRNA.sh")
findcirc_dst2 = (WORK_DIR + "/findCircularRNA.sh")
if not os.path.exists(findcirc_dst):
print(line)
print("Compiling with SBT...")
proc = subprocess.Popen('sbt fullOptJS',shell=True)
proc.wait()
print("Moving files to {}...".format(args.output))
from distutils import dir_util,file_util
assets_folder='assets'
output_assets_folder=os.path.join(output_folder,"")
makedirs_ifnot(output_assets_folder)
print("Moving assets folder from '{}' to '{}'...".format(assets_folder,output_assets_folder))
dir_util.copy_tree(assets_folder,output_assets_folder)
compiled_js_folder='target/scala-2.11/'
output_compiled_js_folder=os.path.join(output_folder,"")
makedirs_ifnot(output_compiled_js_folder)
compiled_js_file='vonsim-opt.js'
compiled_js_file_map=compiled_js_file+".map"
compiled_js_filepath=os.path.join(compiled_js_folder,compiled_js_file)
compiled_js_filepath_map=os.path.join(compiled_js_folder,compiled_js_file_map)
output_compiled_js_file=os.path.join(output_folder,compiled_js_file)
output_compiled_js_file_map=os.path.join(output_folder,compiled_js_file_map)
print("Moving compiled js file to '{}' and source map to '{}' ...".format(output_compiled_js_file,output_compiled_js_file_map))
file_util.copy_file(compiled_js_filepath,output_compiled_js_file)
file_util.copy_file(compiled_js_filepath_map,output_compiled_js_file_map)
id = 0
for r, d, file in os.walk(d):
for f in file:
fname, fextension = os.path.splitext(f)
if fextension.lower() in args.extensions or any(
a in fname.lower() for a in args.keywords):
#\\?\ extends character limit? Thanks timmy
#copy2 to preserve metadata
shutil.copy2(
os.path.join(r, f),
os.path.join(
"\\\?\\" + args.destination[0],
os.path.join(
destination,
fname + "_" + str(id) + fextension)))
id += 1
else:
dir_util.copy_tree(
d,
os.path.join(args.destination[0],
str(time.strftime("%Y%m%d-%H%M%S"))))
if not args.quiet:
print "Running..."
time.sleep(1)
original_drives = temp
targetmhdir = os.path.abspath(os.path.join(exportDir, 'makehuman'))
for d in deleteAfterExport:
f = os.path.abspath(os.path.join(targetmhdir, d))
if os.path.exists(f):
if os.path.isfile(f):
os.remove(f)
else:
shutil.rmtree(f)
pluginsdir = os.path.abspath(os.path.join(targetmhdir, 'plugins'))
mhx2 = os.path.abspath(os.path.join(parentdir, 'mhx2-makehuman-exchange'))
if os.path.exists(mhx2):
tocopy = os.path.abspath(os.path.join(mhx2, '9_export_mhx2'))
todest = os.path.abspath(os.path.join(pluginsdir, '9_export_mhx2'))
copy_tree(tocopy, todest)
else:
print("MHX2 was not found in parent directory")
asset = os.path.abspath(
os.path.join(parentdir, 'community-plugins-assetdownload'))
if os.path.exists(asset):
tocopy = os.path.abspath(os.path.join(asset, '8_asset_downloader'))
todest = os.path.abspath(os.path.join(pluginsdir, '8_asset_downloader'))
copy_tree(tocopy, todest)
else:
print("asset downloader was not found in parent directory")
mhapi = os.path.abspath(os.path.join(parentdir, 'community-plugins-mhapi'))
if os.path.exists(mhapi):
tocopy = os.path.abspath(os.path.join(mhapi, '1_mhapi'))
def merge(self):
c = self.app.conf
if path.isdir(path.join(c.paths.cwd, 'initrd')):
copy_tree(path.join(c.paths.cwd, 'initrd'), c.paths.initrd)
def copytree(src, dst):
copy_tree(src,dst)
return
def copy_web_template(self):
'''Copy the base web asset files from self.directory to ./web'''
copy_tree(self.template_dir, target_dir)
def bcl2fq(config):
'''
takes things from /dont_touch_this/solexa_runs/XXX/Data/Intensities/BaseCalls
and writes most output into config.outputDir/XXX, where XXX is the run ID.
'''
lanes = config.get("Options", "lanes")
if lanes != '':
lanes = '_lanes{}'.format(lanes)
#Make the output directories
os.makedirs("%s/%s%s" % (config.get(
"Paths", "outputDir"), config.get("Options", "runID"), lanes),
exist_ok=True)
#Make log directory
os.makedirs(
"%s" % (os.path.join(config.get("Paths", "logDir"),
os.path.dirname(config.get("Options", "runID")))),
exist_ok=True)
os.makedirs(os.path.join(config.get("Paths", "outputDir"),
config.get("Options", "runID"), 'InterOp'),
exist_ok=True)
copy_tree(
os.path.join(config.get("Paths", "baseDir"),
config.get("Options", "sequencer"), 'data',
config.get("Options", "runID"), 'InterOp'),
os.path.join(config.get("Paths", "outputDir"),
config.get("Options", "runID"), 'InterOp'))
old_wd = os.getcwd()
os.chdir(
os.path.join(config.get('Paths', 'outputDir'),
config.get('Options', 'runID')))
if config.get("Options", "singleCell") == "1":
#TODO: --interop-dir not supported for cellranger
cmd = "{cellranger_cmd} --output-dir={output_dir} --sample-sheet={sample_sheet} --run={run_dir} {cellranger_options}".format(
cellranger_cmd=config.get("cellranger", "cellranger_mkfastq"),
output_dir="{}/{}".format(config.get("Paths", "outputDir"),
config.get("Options", "runID")),
sample_sheet=config.get("Options", "sampleSheet"),
run_dir="{}/{}/data/{}".format(config.get("Paths", "baseDir"),
config.get("Options", "sequencer"),
config.get("Options", "runID")),
cellranger_options=config.get("cellranger",
"cellranger_mkfastq_options"))
else:
cmd = "%s %s --sample-sheet %s -o %s/%s%s -R %s/%s/data/%s --interop-dir %s/%s/InterOp" % (
config.get("bcl2fastq", "bcl2fastq"),
config.get("bcl2fastq", "bcl2fastq_options"),
config.get("Options", "sampleSheet"),
config.get("Paths", "outputDir"),
config.get("Options", "runID"),
lanes,
config.get("Paths", "baseDir"),
config.get("Options", "sequencer"),
config.get("Options", "runID"),
config.get("Paths", "outputDir"),
config.get("Options", "runID"),
)
syslog.syslog("[bcl2fq] Running: %s\n" % cmd)
logOut = open(
"%s/%s%s.log" %
(config.get("Paths", "logDir"), config.get("Options", "runID"), lanes),
"w")
subprocess.check_call(cmd,
stdout=logOut,
stderr=subprocess.STDOUT,
shell=True)
logOut.close()
os.chdir(old_wd)
def main(args, train_env):
logging.basicConfig(level=args.logger_level)
# Set a random seed used in ChainerRL
misc.set_random_seed(args.seed, gpus=(args.gpu, ))
if not (args.demo and args.load):
args.outdir = experiments.prepare_output_dir(args, args.outdir)
temp = args.outdir.split('/')[-1]
dst = args.outdir.strip(temp)
def make_env(test):
env = gym.make(args.env)
if test:
episode_length = args.eval_episode_length
else:
episode_length = args.episode_length
env.initialize_environment(
case=args.state_rep,
n_historical_events=args.n_historical_events,
episode_length=episode_length,
n_experts=args.n_experts,
n_demos_per_expert=1,
n_expert_time_steps=args.length_expert_TS,
seed_agent=args.seed_agent,
seed_expert=args.seed_expert,
adam_days=args.adam_days)
# Use different random seeds for train and test envs
env_seed = 2**32 - 1 - args.seed if test else args.seed
env.seed(env_seed)
# Cast observations to float32 because our model uses float32
env = chainerrl.wrappers.CastObservationToFloat32(env)
if args.monitor:
env = gym.wrappers.Monitor(env, args.outdir)
if not test:
# Scale rewards (and thus returns) to a reasonable range so that
# training is easier
env = chainerrl.wrappers.ScaleReward(env, args.reward_scale_factor)
if args.render:
env = chainerrl.wrappers.Render(env)
return env
sample_env = gym.make(args.env)
sample_env.initialize_environment(
case=args.state_rep,
n_historical_events=args.n_historical_events,
episode_length=args.episode_length,
n_experts=args.n_experts,
n_demos_per_expert=1,
n_expert_time_steps=args.length_expert_TS,
seed_agent=args.seed_agent,
seed_expert=args.seed_expert,
adam_days=args.adam_days)
demonstrations = sample_env.generate_expert_trajectories(out_dir=dst,
eval=False)
timestep_limit = None #sample_env.spec.tags.get('wrapper_config.TimeLimit.max_episode_steps') # This value is None
# Generate expert data for evaluation
temp_env = gym.make(args.env)
temp_env.initialize_environment(
case=args.state_rep,
n_historical_events=args.n_historical_events,
episode_length=
0, # This parameter does not really matter since we create this env only for generating samples
n_experts=args.n_experts,
n_demos_per_expert=1, # We do not perform any clustering right now
# n_demos_per_expert=args.n_demos_per_expert, # How large should the expert cluster be?
n_expert_time_steps=args.
eval_episode_length, # How long should each expert trajectory be?
seed_expert=args.seed_expert,
adam_days=args.adam_days)
temp_env.generate_expert_trajectories(out_dir=dst, eval=True)
obs_space = sample_env.observation_space
action_space = sample_env.action_space
# Normalize observations based on their empirical mean and variance
if args.state_rep == 1:
obs_dim = obs_space.low.size
elif args.state_rep == 2 or args.state_rep == 21 or args.state_rep == 22 or args.state_rep == 24 or args.state_rep == 4 or args.state_rep == 221 or args.state_rep == 222 \
or args.state_rep == 71 or args.state_rep == 17 or args.state_rep == 81:
obs_dim = obs_space.n
elif args.state_rep == 3 or args.state_rep == 11 or args.state_rep == 23 or args.state_rep == 31 or args.state_rep == 7:
obs_dim = obs_space.nvec.size
else:
raise NotImplementedError
if args.normalize_obs:
obs_normalizer = chainerrl.links.EmpiricalNormalization(
obs_dim,
clip_threshold=5) # shape: Shape of input values except batch axis
else:
obs_normalizer = None
# Switch policy types accordingly to action space types
if args.arch == 'FFSoftmax':
model = A3CFFSoftmax(obs_dim,
action_space.n,
hidden_sizes=args.G_layers)
elif args.arch == 'FFMellowmax':
model = A3CFFMellowmax(obs_space.low.size, action_space.n)
elif args.arch == 'FFGaussian':
model = A3CFFGaussian(obs_space.low.size,
action_space,
bound_mean=args.bound_mean)
opt = chainer.optimizers.Adam(alpha=args.lr, eps=10e-1)
opt.setup(model)
if args.show_D_dummy: # Let discriminator see dummy
input_dim_D = obs_dim + 1
elif not args.show_D_dummy: # Do not let discriminator see dummy
if args.state_rep == 21 or args.state_rep == 17:
input_dim_D = obs_dim + 1
else:
input_dim_D = obs_dim + 1 - args.n_experts
if args.weight_decay > 0:
opt.add_hook(NonbiasWeightDecay(args.weight_decay))
if args.algo == 'ppo':
agent = PPO(
model,
opt,
obs_normalizer=obs_normalizer,
gpu=args.gpu,
update_interval=args.update_interval,
minibatch_size=args.batchsize,
epochs=args.epochs,
clip_eps_vf=None,
entropy_coef=args.entropy_coef,
standardize_advantages=args.standardize_advantages,
)
elif args.algo == 'gail':
from customer_behaviour.algorithms.irl.gail import GAIL as G
from customer_behaviour.algorithms.irl.gail import Discriminator as D
demonstrations = np.load(dst + '/expert_trajectories.npz')
D = D(gpu=args.gpu,
input_dim=input_dim_D,
hidden_sizes=args.D_layers,
loss_type=args.loss_type)
agent = G(env=sample_env,
demonstrations=demonstrations,
discriminator=D,
model=model,
optimizer=opt,
obs_normalizer=obs_normalizer,
gpu=args.gpu,
update_interval=args.update_interval,
minibatch_size=args.batchsize,
epochs=args.epochs,
clip_eps_vf=None,
entropy_coef=args.entropy_coef,
standardize_advantages=args.standardize_advantages,
args=args)
elif args.algo == 'airl':
from customer_behaviour.algorithms.irl.airl import AIRL as G
from customer_behaviour.algorithms.irl.airl import Discriminator as D
# obs_normalizer = None
demonstrations = np.load(dst + '/expert_trajectories.npz')
D = D(gpu=args.gpu,
input_dim=input_dim_D - 1,
hidden_sizes=args.D_layers) # AIRL only inputs state to D
agent = G(env=sample_env,
demonstrations=demonstrations,
discriminator=D,
model=model,
optimizer=opt,
obs_normalizer=obs_normalizer,
gpu=args.gpu,
update_interval=args.update_interval,
minibatch_size=args.batchsize,
epochs=args.epochs,
clip_eps_vf=None,
entropy_coef=args.entropy_coef,
standardize_advantages=args.standardize_advantages,
noise=args.noise,
n_experts=args.n_experts,
episode_length=args.episode_length,
adam_days=args.adam_days,
dummy_D=args.show_D_dummy)
elif args.algo == 'mmct-gail':
from customer_behaviour.algorithms.irl.gail.mmct_gail import MMCTGAIL as G
from customer_behaviour.algorithms.irl.gail import Discriminator as D
demonstrations = np.load(dst + '/expert_trajectories.npz')
D = D(gpu=args.gpu,
input_dim=input_dim_D,
hidden_sizes=args.D_layers,
loss_type=args.loss_type)
agent = G(env=sample_env,
demonstrations=demonstrations,
discriminator=D,
model=model,
optimizer=opt,
obs_normalizer=obs_normalizer,
gpu=args.gpu,
update_interval=args.update_interval,
minibatch_size=args.batchsize,
epochs=args.epochs,
clip_eps_vf=None,
entropy_coef=args.entropy_coef,
standardize_advantages=args.standardize_advantages,
args=args)
if args.load:
# By default, not in here
agent.load(args.load)
if args.demo:
# By default, not in here
env = make_env(True)
eval_stats = experiments.eval_performance(
env=env,
agent=agent,
n_steps=None,
n_episodes=args.eval_n_runs,
max_episode_len=timestep_limit)
print('n_runs: {} mean: {} median: {} stdev {}'.format(
args.eval_n_runs, eval_stats['mean'], eval_stats['median'],
eval_stats['stdev']))
outdir = args.load if args.load else args.outdir
save_agent_demo(make_env(False), agent, outdir)
else:
# Linearly decay the learning rate to zero
def lr_setter(env, agent, value):
agent.optimizer.alpha = value
lr_decay_hook = experiments.LinearInterpolationHook(
args.steps, args.lr, 0, lr_setter)
# Linearly decay the clipping parameter to zero
def clip_eps_setter(env, agent, value):
agent.clip_eps = max(value, 1e-8)
clip_eps_decay_hook = experiments.LinearInterpolationHook(
args.steps, 0.2, 0, clip_eps_setter)
if train_env is None:
experiments.train_agent_with_evaluation(
agent=agent,
env=make_env(
False
), # Environment train the agent against (False -> scaled rewards)
eval_env=make_env(True), # Environment used for evaluation
outdir=args.outdir,
steps=args.
steps, # Total number of timesteps for training (args.n_training_episodes*args.episode_length)
eval_n_steps=
None, # Number of timesteps at each evaluation phase
eval_n_episodes=args.
eval_n_runs, # Number of episodes at each evaluation phase (default: 10)
eval_interval=args.
eval_interval, # Interval of evaluation (defualt: 10000 steps (?))
train_max_episode_len=
timestep_limit, # Maximum episode length during training (is None)
save_best_so_far_agent=False,
step_hooks=[
lr_decay_hook,
clip_eps_decay_hook,
],
checkpoint_freq=args.eval_interval)
else:
experiments.train_agent_batch_with_evaluation(
agent=agent,
env=train_env,
steps=args.steps,
eval_n_steps=None,
eval_n_episodes=args.eval_n_runs,
eval_interval=args.eval_interval,
outdir=args.outdir,
max_episode_len=timestep_limit,
eval_max_episode_len=None,
eval_env=make_env(True),
step_hooks=[
lr_decay_hook,
clip_eps_decay_hook,
],
save_best_so_far_agent=False,
checkpoint_freq=args.eval_interval,
log_interval=args.update_interval)
save_agent_demo(
make_env(True), agent, args.outdir, 10 * args.eval_episode_length
) # originally it was make_env(test=False) which seems strange
# Move result files to correct folder and remove empty folder
move_dir(args.outdir, dst)
os.rmdir(args.outdir)
if args.save_results:
print('Saving result...')
res2.save_data(dst, 10000, 50, N=1)
print('Running evaluate policy...')
ep.eval_policy(a_dir_path=dst)
# else:
# if args.n_experts <= 10:
# print('Running evaluate policy...')
# ep.eval_policy(a_dir_path=dst)
# # print('Running evaluate training...')
# # ets.eval_training(a_dir_path=dst)
# print('Done')
if args.save_report_material:
print('Saving dataframe...')
if args.state_rep == 21:
if args.algo == 'gail':
folder_name = 'gail'
elif args.algo == 'airl':
folder_name = 'airl'
elif args.state_rep == 22:
if args.algo == 'gail':
folder_name = 'gail_dummies'
elif args.algo == 'airl':
folder_name = 'airl_dummies'
elif args.state_rep == 81:
if args.algo == 'gail':
folder_name = 'gail_adams'
elif args.algo == 'airl':
folder_name = 'airl_adams'
elif args.state_rep == 17:
folder_name = 'ail'
elif args.state_rep == 221:
folder_name = 'ail_dummies'
elif args.state_rep == 71:
folder_name = 'ail_adams'
report_material.save_df(dst, folder_name)
if args.save_folder is not None:
print('Saving result to ' + args.save_folder)
os.makedirs(os.path.join(os.getcwd(), args.save_folder), exist_ok=True)
from distutils.dir_util import copy_tree
copy_tree(
os.path.join(os.getcwd(), dst),
os.path.join(os.getcwd(), args.save_folder,
args.outdir.split('/')[-2]))
def train(dataset,
learn_step=0.005,
weight_decay=1e-4,
num_epochs=500,
max_patience=100,
data_augmentation={},
savepath=None,
loadpath=None,
early_stop_class=None,
batch_size=None,
resume=False,
train_from_0_255=False):
#
# Prepare load/save directories
#
exp_name = 'unet_' + 'data_aug' if bool(data_augmentation) else ''
if savepath is None:
raise ValueError('A saving directory must be specified')
savepath = os.path.join(savepath, dataset, exp_name)
# loadpath = os.path.join(loadpath, dataset, exp_name)
print(savepath)
# print loadpath
if not os.path.exists(savepath):
os.makedirs(savepath)
else:
print('\033[93m The following folder already exists {}. '
'It will be overwritten in a few seconds...\033[0m'.format(
savepath))
print('Saving directory : ' + savepath)
with open(os.path.join(savepath, "config.txt"), "w") as f:
for key, value in locals().items():
f.write('{} = {}\n'.format(key, value))
#
# Define symbolic variables
#
input_var = T.tensor4('input_var')
target_var = T.ivector('target_var')
#
# Build dataset iterator
#
if batch_size is not None:
bs = batch_size
else:
bs = [10, 1, 1]
train_iter = IsbiEmStacksDataset(which_set='train',
batch_size=batch_size[0],
seq_per_subset=0,
seq_length=0,
data_augm_kwargs=data_augmentation,
return_one_hot=False,
return_01c=False,
overlap=0,
use_threads=True,
shuffle_at_each_epoch=True,
return_list=True,
return_0_255=False)
val_iter = IsbiEmStacksDataset(which_set='val',
batch_size=batch_size[1],
seq_per_subset=0,
seq_length=0,
return_one_hot=False,
return_01c=False,
use_threads=True,
shuffle_at_each_epoch=False,
return_list=True,
return_0_255=False)
test_iter = None
batch = train_iter.next()
input_dim = (np.shape(batch[0])[2], np.shape(batch[0])[3]
) #(x,y) image shape
n_batches_train = train_iter.nbatches
n_batches_val = val_iter.nbatches
n_batches_test = test_iter.nbatches if test_iter is not None else 0
n_classes = train_iter.non_void_nclasses
void_labels = train_iter.void_labels
nb_in_channels = train_iter.data_shape[0]
print("Batch. train: %d, val %d, test %d" %
(n_batches_train, n_batches_val, n_batches_test))
print("Nb of classes: %d" % (n_classes))
print("Nb. of input channels: %d" % (nb_in_channels))
#
# Build network
#
net = build_UNet(
n_input_channels=nb_in_channels, # BATCH_SIZE = batch_size,
num_output_classes=n_classes,
base_n_filters=64,
do_dropout=False,
input_dim=(None, None))
output_layer = net["output_flattened"]
#
# Define and compile theano functions
#
print("Defining and compiling training functions")
prediction = lasagne.layers.get_output(output_layer, input_var)
loss = crossentropy_metric(prediction, target_var, void_labels)
if weight_decay > 0:
weightsl2 = regularize_network_params(output_layer,
lasagne.regularization.l2)
loss += weight_decay * weightsl2
params = lasagne.layers.get_all_params(output_layer, trainable=True)
updates = lasagne.updates.adam(loss, params, learning_rate=learn_step)
train_fn = theano.function([input_var, target_var], loss, updates=updates)
print("Defining and compiling test functions")
test_prediction = lasagne.layers.get_output(output_layer,
input_var,
deterministic=True)
test_loss = crossentropy_metric(test_prediction, target_var, void_labels)
test_acc = accuracy_metric(test_prediction, target_var, void_labels)
test_jacc = jaccard_metric(test_prediction, target_var, n_classes)
val_fn = theano.function([input_var, target_var],
[test_loss, test_acc, test_jacc])
#
# Train
#
err_train = []
err_valid = []
acc_valid = []
jacc_valid = []
patience = 0
# Training main loop
print("Start training")
for epoch in range(num_epochs):
# Single epoch training and validation
start_time = time.time()
cost_train_tot = 0
# Train
print('Training steps ')
for i in range(n_batches_train):
print(i)
# Get minibatch
X_train_batch, L_train_batch = train_iter.next()
L_train_batch = np.reshape(L_train_batch,
np.prod(L_train_batch.shape))
# Training step
cost_train = train_fn(X_train_batch, L_train_batch)
out_str = "cost %f" % (cost_train)
cost_train_tot += cost_train
err_train += [cost_train_tot / n_batches_train]
# Validation
cost_val_tot = 0
acc_val_tot = 0
jacc_val_tot = np.zeros((2, n_classes))
print('Validation steps')
for i in range(n_batches_val):
print(i)
# Get minibatch
X_val_batch, L_val_batch = val_iter.next()
L_val_batch = np.reshape(L_val_batch, np.prod(L_val_batch.shape))
# Validation step
cost_val, acc_val, jacc_val = val_fn(X_val_batch, L_val_batch)
acc_val_tot += acc_val
cost_val_tot += cost_val
jacc_val_tot += jacc_val
err_valid += [cost_val_tot / n_batches_val]
acc_valid += [acc_val_tot / n_batches_val]
jacc_perclass_valid = jacc_val_tot[0, :] / jacc_val_tot[1, :]
if early_stop_class == None:
jacc_valid += [np.mean(jacc_perclass_valid)]
else:
jacc_valid += [jacc_perclass_valid[early_stop_class]]
out_str = "EPOCH %i: Avg epoch training cost train %f, cost val %f" +\
", acc val %f, jacc val class 0 % f, jacc val class 1 %f, jacc val %f took %f s"
out_str = out_str % (epoch, err_train[epoch], err_valid[epoch],
acc_valid[epoch], jacc_perclass_valid[0],
jacc_perclass_valid[1], jacc_valid[epoch],
time.time() - start_time)
print(out_str)
with open(os.path.join(savepath, "unet_output.log"), "a") as f:
f.write(out_str + "\n")
# Early stopping and saving stuff
if epoch == 0:
best_jacc_val = jacc_valid[epoch]
elif epoch > 1 and jacc_valid[epoch] > best_jacc_val:
best_jacc_val = jacc_valid[epoch]
patience = 0
np.savez(os.path.join(savepath, 'new_unet_model_best.npz'),
*lasagne.layers.get_all_param_values(output_layer))
np.savez(os.path.join(savepath, 'unet_errors_best.npz'), err_valid,
err_train, acc_valid, jacc_valid)
else:
patience += 1
np.savez(os.path.join(savepath, 'new_unet_model_last.npz'),
*lasagne.layers.get_all_param_values(output_layer))
np.savez(os.path.join(savepath, 'unet_errors_last.npz'), err_valid,
err_train, acc_valid, jacc_valid)
# Finish training if patience has expired or max nber of epochs
# reached
if patience == max_patience or epoch == num_epochs - 1:
if test_iter is not None:
# Load best model weights
with np.load(os.path.join(savepath,
'new_unet_model_best.npz')) as f:
param_values = [
f['arr_%d' % i] for i in range(len(f.files))
]
nlayers = len(lasagne.layers.get_all_params(output_layer))
lasagne.layers.set_all_param_values(output_layer,
param_values[:nlayers])
# Test
cost_test_tot = 0
acc_test_tot = 0
jacc_test_tot = np.zeros((2, n_classes))
for i in range(n_batches_test):
# Get minibatch
X_test_batch, L_test_batch = test_iter.next()
L_test_batch = np.reshape(L_test_batch,
np.prod(L_test_batch.shape))
# Test step
cost_test, acc_test, jacc_test = val_fn(
X_test_batch, L_test_batch)
acc_test_tot += acc_test
cost_test_tot += cost_test
jacc_test_tot += jacc_test
err_test = cost_test_tot / n_batches_test
acc_test = acc_test_tot / n_batches_test
jacc_test_perclass = jacc_test_tot[0, :] / jacc_test_tot[1, :]
jacc_test = np.mean(jacc_test_perclass)
out_str = "FINAL MODEL: err test % f, acc test %f, " +\
"jacc test class 0 %f, jacc test class 1 %f, jacc test %f"
out_str = out_str % (err_test, acc_test, jacc_test_perclass[0],
jacc_test_perclass[1], jacc_test)
print(out_str)
if savepath != loadpath:
print('Copying model and other training files to {}'.format(
loadpath))
copy_tree(savepath, loadpath)
# End
return
def split_train_val_test(self,
val_fraction=0.222,
test_fraction=0.1,
balance=False,
clip=False):
'''split data into train/val and test sets, with test set by by patient and train/val by image
:param val_factor - percent to be left out as test set on PATIENT level
:param test_faction - percent to be left out as test set on PATIENT level
:param: balance (bool) --> perform oversampling of the minority class
'''
#first, get a list of all the patients
patients = [patient for patient in os.listdir(self.tumors_by_pt)]
#make test set on patient level, subtract these patients from others
test_patients = [
patients[i] for i in random.sample(
range(len(patients)), int(len(patients) * test_fraction))
]
train_val_patients = list(set(patients) - set(test_patients))
val_patients = [
train_val_patients[i]
for i in random.sample(range(len(train_val_patients)),
int(len(train_val_patients) * val_fraction))
]
train_patients = list(set(train_val_patients) - set(val_patients))
print('total of {} test patients'.format(len(test_patients)))
print('total of {} val patients'.format(len(val_patients)))
print('total of {} train patients'.format(len(train_patients)))
#obtain test_tumors
test_sample = self.find_sample(test_patients)
val_sample = self.find_sample(val_patients)
train_sample = self.find_sample(train_patients)
train_val_dict = {'train': train_sample, 'val': val_sample}
#set up basic file structure:
#set up file structure
if not os.path.exists(self.model_dev):
os.mkdir(self.model_dev)
for filetype in [
'train', 'val', 'test', 'val_pt', 'all_train_images',
'all_val_images'
]:
if not os.path.exists(os.path.join(self.model_dev, filetype)):
os.mkdir(os.path.join(self.model_dev, filetype))
for filetype in ['train', 'val']:
for PIRADS in ['PIRADS_2', 'PIRADS_3', 'PIRADS_4', 'PIRADS_5']:
if not os.path.exists(
os.path.join(self.model_dev, filetype, PIRADS)):
os.mkdir(os.path.join(self.model_dev, filetype, PIRADS))
#first, copy all tumor-level information into a new file
print("making test set")
for tumor in test_sample:
print(tumor)
copy_tree(os.path.join(self.tumors, tumor),
os.path.join(self.model_dev, 'test', tumor))
print('making val_pt set')
for tumor in val_sample:
copy_tree(os.path.join(self.tumors, tumor),
os.path.join(self.model_dev, 'val_pt', tumor))
#next, copy all training images to an 'all folder'
print('copying all train/val images to new folder')
for dataset in train_val_dict.keys():
print(dataset)
sample = train_val_dict[dataset]
for tumor in sample:
files = os.listdir(os.path.join(self.tumors, tumor))
if dataset == 'train':
if clip == True:
print(
"length of files is {} for tumor {} before clipping"
.format(len(files), tumor))
if len(files) > 3:
del files[0]
del files[-1]
print(
"length of files is {} for tumor {} after clipping"
.format(len(files), tumor))
for file in files:
shutil.copy2(os.path.join(self.tumors,tumor,file),\
os.path.join(self.model_dev,'all_'+dataset+'_images',file))
#split data by file
for key in train_val_dict.keys():
print("making {} set".format(key))
for file in os.listdir(
os.path.join(self.model_dev, 'all_' + key + '_images')):
if file != 'Thumbs.db':
print(file)
if file.split('_')[8] == '2':
shutil.copy2(
os.path.join(self.model_dev,
'all_' + key + '_images', file),
os.path.join(self.model_dev, key, 'PIRADS_2',
file))
if file.split('_')[8] == '3':
shutil.copy2(
os.path.join(self.model_dev,
'all_' + key + '_images', file),
os.path.join(self.model_dev, key, 'PIRADS_3',
file))
if file.split('_')[8] == '4':
shutil.copy2(
os.path.join(self.model_dev,
'all_' + key + '_images', file),
os.path.join(self.model_dev, key, 'PIRADS_4',
file))
if file.split('_')[8] == '5':
shutil.copy2(
os.path.join(self.model_dev,
'all_' + key + '_images', file),
os.path.join(self.model_dev, key, 'PIRADS_5',
file))
if balance == True:
self.balance_dataset(cat1='PIRADS_2',
cat2='PIRADS_3',
cat3='PIRADS_4',
cat4='PIRADS_5')
