id int32 0 252k | repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
value | code stringlengths 75 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 |
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237,100 | angr/pyvex | pyvex/block.py | IRSB.operations | def operations(self):
"""
A list of all operations done by the IRSB, as libVEX enum names
"""
ops = []
for e in self.expressions:
if hasattr(e, 'op'):
ops.append(e.op)
return ops | python | def operations(self):
"""
A list of all operations done by the IRSB, as libVEX enum names
"""
ops = []
for e in self.expressions:
if hasattr(e, 'op'):
ops.append(e.op)
return ops | [
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237,101 | angr/pyvex | pyvex/block.py | IRSB.constant_jump_targets | def constant_jump_targets(self):
"""
A set of the static jump targets of the basic block.
"""
exits = set()
if self.exit_statements:
for _, _, stmt_ in self.exit_statements:
exits.add(stmt_.dst.value)
default_target = self.default_exit_target... | python | def constant_jump_targets(self):
"""
A set of the static jump targets of the basic block.
"""
exits = set()
if self.exit_statements:
for _, _, stmt_ in self.exit_statements:
exits.add(stmt_.dst.value)
default_target = self.default_exit_target... | [
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237,102 | angr/pyvex | pyvex/block.py | IRSB.constant_jump_targets_and_jumpkinds | def constant_jump_targets_and_jumpkinds(self):
"""
A dict of the static jump targets of the basic block to their jumpkind.
"""
exits = dict()
if self.exit_statements:
for _, _, stmt_ in self.exit_statements:
exits[stmt_.dst.value] = stmt_.jumpkind
... | python | def constant_jump_targets_and_jumpkinds(self):
"""
A dict of the static jump targets of the basic block to their jumpkind.
"""
exits = dict()
if self.exit_statements:
for _, _, stmt_ in self.exit_statements:
exits[stmt_.dst.value] = stmt_.jumpkind
... | [
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237,103 | angr/pyvex | pyvex/block.py | IRSB._pp_str | def _pp_str(self):
"""
Return the pretty-printed IRSB.
:rtype: str
"""
sa = []
sa.append("IRSB {")
if self.statements is not None:
sa.append(" %s" % self.tyenv)
sa.append("")
if self.statements is not None:
for i, s in en... | python | def _pp_str(self):
"""
Return the pretty-printed IRSB.
:rtype: str
"""
sa = []
sa.append("IRSB {")
if self.statements is not None:
sa.append(" %s" % self.tyenv)
sa.append("")
if self.statements is not None:
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237,104 | angr/pyvex | pyvex/block.py | IRSB._is_defaultexit_direct_jump | def _is_defaultexit_direct_jump(self):
"""
Checks if the default of this IRSB a direct jump or not.
"""
if not (self.jumpkind == 'Ijk_InvalICache' or self.jumpkind == 'Ijk_Boring' or self.jumpkind == 'Ijk_Call'):
return False
target = self.default_exit_target
... | python | def _is_defaultexit_direct_jump(self):
"""
Checks if the default of this IRSB a direct jump or not.
"""
if not (self.jumpkind == 'Ijk_InvalICache' or self.jumpkind == 'Ijk_Boring' or self.jumpkind == 'Ijk_Call'):
return False
target = self.default_exit_target
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237,105 | angr/pyvex | pyvex/block.py | IRTypeEnv.lookup | def lookup(self, tmp):
"""
Return the type of temporary variable `tmp` as an enum string
"""
if tmp < 0 or tmp > self.types_used:
l.debug("Invalid temporary number %d", tmp)
raise IndexError(tmp)
return self.types[tmp] | python | def lookup(self, tmp):
"""
Return the type of temporary variable `tmp` as an enum string
"""
if tmp < 0 or tmp > self.types_used:
l.debug("Invalid temporary number %d", tmp)
raise IndexError(tmp)
return self.types[tmp] | [
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237,106 | angr/pyvex | pyvex/lifting/lifter.py | Lifter._lift | def _lift(self,
data,
bytes_offset=None,
max_bytes=None,
max_inst=None,
opt_level=1,
traceflags=None,
allow_arch_optimizations=None,
strict_block_end=None,
skip_stmts=False,
collec... | python | def _lift(self,
data,
bytes_offset=None,
max_bytes=None,
max_inst=None,
opt_level=1,
traceflags=None,
allow_arch_optimizations=None,
strict_block_end=None,
skip_stmts=False,
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:param bytes_offset: The offset into `data` to start lifting at.
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237,107 | TeamHG-Memex/scrapy-rotating-proxies | rotating_proxies/expire.py | exp_backoff | def exp_backoff(attempt, cap=3600, base=300):
""" Exponential backoff time """
# this is a numerically stable version of
# min(cap, base * 2 ** attempt)
max_attempts = math.log(cap / base, 2)
if attempt <= max_attempts:
return base * 2 ** attempt
return cap | python | def exp_backoff(attempt, cap=3600, base=300):
""" Exponential backoff time """
# this is a numerically stable version of
# min(cap, base * 2 ** attempt)
max_attempts = math.log(cap / base, 2)
if attempt <= max_attempts:
return base * 2 ** attempt
return cap | [
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237,108 | TeamHG-Memex/scrapy-rotating-proxies | rotating_proxies/expire.py | Proxies.get_proxy | def get_proxy(self, proxy_address):
"""
Return complete proxy name associated with a hostport of a given
``proxy_address``. If ``proxy_address`` is unkonwn or empty,
return None.
"""
if not proxy_address:
return None
hostport = extract_proxy_hostport(p... | python | def get_proxy(self, proxy_address):
"""
Return complete proxy name associated with a hostport of a given
``proxy_address``. If ``proxy_address`` is unkonwn or empty,
return None.
"""
if not proxy_address:
return None
hostport = extract_proxy_hostport(p... | [
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237,109 | TeamHG-Memex/scrapy-rotating-proxies | rotating_proxies/expire.py | Proxies.mark_dead | def mark_dead(self, proxy, _time=None):
""" Mark a proxy as dead """
if proxy not in self.proxies:
logger.warn("Proxy <%s> was not found in proxies list" % proxy)
return
if proxy in self.good:
logger.debug("GOOD proxy became DEAD: <%s>" % proxy)
else:... | python | def mark_dead(self, proxy, _time=None):
""" Mark a proxy as dead """
if proxy not in self.proxies:
logger.warn("Proxy <%s> was not found in proxies list" % proxy)
return
if proxy in self.good:
logger.debug("GOOD proxy became DEAD: <%s>" % proxy)
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237,110 | TeamHG-Memex/scrapy-rotating-proxies | rotating_proxies/expire.py | Proxies.mark_good | def mark_good(self, proxy):
""" Mark a proxy as good """
if proxy not in self.proxies:
logger.warn("Proxy <%s> was not found in proxies list" % proxy)
return
if proxy not in self.good:
logger.debug("Proxy <%s> is GOOD" % proxy)
self.unchecked.discard... | python | def mark_good(self, proxy):
""" Mark a proxy as good """
if proxy not in self.proxies:
logger.warn("Proxy <%s> was not found in proxies list" % proxy)
return
if proxy not in self.good:
logger.debug("Proxy <%s> is GOOD" % proxy)
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237,111 | TeamHG-Memex/scrapy-rotating-proxies | rotating_proxies/expire.py | Proxies.reanimate | def reanimate(self, _time=None):
""" Move dead proxies to unchecked if a backoff timeout passes """
n_reanimated = 0
now = _time or time.time()
for proxy in list(self.dead):
state = self.proxies[proxy]
assert state.next_check is not None
if state.next_... | python | def reanimate(self, _time=None):
""" Move dead proxies to unchecked if a backoff timeout passes """
n_reanimated = 0
now = _time or time.time()
for proxy in list(self.dead):
state = self.proxies[proxy]
assert state.next_check is not None
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237,112 | TeamHG-Memex/scrapy-rotating-proxies | rotating_proxies/expire.py | Proxies.reset | def reset(self):
""" Mark all dead proxies as unchecked """
for proxy in list(self.dead):
self.dead.remove(proxy)
self.unchecked.add(proxy) | python | def reset(self):
""" Mark all dead proxies as unchecked """
for proxy in list(self.dead):
self.dead.remove(proxy)
self.unchecked.add(proxy) | [
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237,113 | boakley/robotframework-hub | rfhub/kwdb.py | KeywordTable.on_change | def on_change(self, path, event_type):
"""Respond to changes in the file system
This method will be given the path to a file that
has changed on disk. We need to reload the keywords
from that file
"""
# I can do all this work in a sql statement, but
# for debuggi... | python | def on_change(self, path, event_type):
"""Respond to changes in the file system
This method will be given the path to a file that
has changed on disk. We need to reload the keywords
from that file
"""
# I can do all this work in a sql statement, but
# for debuggi... | [
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237,114 | boakley/robotframework-hub | rfhub/kwdb.py | KeywordTable._load_keywords | def _load_keywords(self, collection_id, path=None, libdoc=None):
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One of path or libdoc needs to be passed in...
"""
if libdoc is None and path is None:
raise(Exception("You must provide either a path or libdoc argument"))
if libdo... | python | def _load_keywords(self, collection_id, path=None, libdoc=None):
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"""
if libdoc is None and path is None:
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237,115 | boakley/robotframework-hub | rfhub/kwdb.py | KeywordTable.add_file | def add_file(self, path):
"""Add a resource file or library file to the database"""
libdoc = LibraryDocumentation(path)
if len(libdoc.keywords) > 0:
if libdoc.doc.startswith("Documentation for resource file"):
# bah! The file doesn't have an file-level documentation
... | python | def add_file(self, path):
"""Add a resource file or library file to the database"""
libdoc = LibraryDocumentation(path)
if len(libdoc.keywords) > 0:
if libdoc.doc.startswith("Documentation for resource file"):
# bah! The file doesn't have an file-level documentation
... | [
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237,116 | boakley/robotframework-hub | rfhub/kwdb.py | KeywordTable.add_library | def add_library(self, name):
"""Add a library to the database
This method is for adding a library by name (eg: "BuiltIn")
rather than by a file.
"""
libdoc = LibraryDocumentation(name)
if len(libdoc.keywords) > 0:
# FIXME: figure out the path to the library f... | python | def add_library(self, name):
"""Add a library to the database
This method is for adding a library by name (eg: "BuiltIn")
rather than by a file.
"""
libdoc = LibraryDocumentation(name)
if len(libdoc.keywords) > 0:
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237,117 | boakley/robotframework-hub | rfhub/kwdb.py | KeywordTable.add_folder | def add_folder(self, dirname, watch=True):
"""Recursively add all files in a folder to the database
By "all files" I mean, "all files that are resource files
or library files". It will silently ignore files that don't
look like they belong in the database. Pity the fool who
uses... | python | def add_folder(self, dirname, watch=True):
"""Recursively add all files in a folder to the database
By "all files" I mean, "all files that are resource files
or library files". It will silently ignore files that don't
look like they belong in the database. Pity the fool who
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237,118 | boakley/robotframework-hub | rfhub/kwdb.py | KeywordTable.add_installed_libraries | def add_installed_libraries(self, extra_libs = ["Selenium2Library",
"SudsLibrary",
"RequestsLibrary"]):
"""Add any installed libraries that we can find
We do this by looking in the `libraries` folder... | python | def add_installed_libraries(self, extra_libs = ["Selenium2Library",
"SudsLibrary",
"RequestsLibrary"]):
"""Add any installed libraries that we can find
We do this by looking in the `libraries` folder... | [
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We do this by looking in the `libraries` folder where
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237,119 | boakley/robotframework-hub | rfhub/kwdb.py | KeywordTable.get_collection | def get_collection(self, collection_id):
"""Get a specific collection"""
sql = """SELECT collection.collection_id, collection.type,
collection.name, collection.path,
collection.doc,
collection.version, collection.scope,
... | python | def get_collection(self, collection_id):
"""Get a specific collection"""
sql = """SELECT collection.collection_id, collection.type,
collection.name, collection.path,
collection.doc,
collection.version, collection.scope,
... | [
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237,120 | boakley/robotframework-hub | rfhub/kwdb.py | KeywordTable.get_keyword | def get_keyword(self, collection_id, name):
"""Get a specific keyword from a library"""
sql = """SELECT keyword.name, keyword.args, keyword.doc
FROM keyword_table as keyword
WHERE keyword.collection_id == ?
AND keyword.name like ?
"""
... | python | def get_keyword(self, collection_id, name):
"""Get a specific keyword from a library"""
sql = """SELECT keyword.name, keyword.args, keyword.doc
FROM keyword_table as keyword
WHERE keyword.collection_id == ?
AND keyword.name like ?
"""
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237,121 | boakley/robotframework-hub | rfhub/kwdb.py | KeywordTable._looks_like_libdoc_file | def _looks_like_libdoc_file(self, name):
"""Return true if an xml file looks like a libdoc file"""
# inefficient since we end up reading the file twice,
# but it's fast enough for our purposes, and prevents
# us from doing a full parse of files that are obviously
# not libdoc fil... | python | def _looks_like_libdoc_file(self, name):
"""Return true if an xml file looks like a libdoc file"""
# inefficient since we end up reading the file twice,
# but it's fast enough for our purposes, and prevents
# us from doing a full parse of files that are obviously
# not libdoc fil... | [
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237,122 | boakley/robotframework-hub | rfhub/kwdb.py | KeywordTable._looks_like_resource_file | def _looks_like_resource_file(self, name):
"""Return true if the file has a keyword table but not a testcase table"""
# inefficient since we end up reading the file twice,
# but it's fast enough for our purposes, and prevents
# us from doing a full parse of files that are obviously
... | python | def _looks_like_resource_file(self, name):
"""Return true if the file has a keyword table but not a testcase table"""
# inefficient since we end up reading the file twice,
# but it's fast enough for our purposes, and prevents
# us from doing a full parse of files that are obviously
... | [
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237,123 | boakley/robotframework-hub | rfhub/kwdb.py | KeywordTable._should_ignore | def _should_ignore(self, name):
"""Return True if a given library name should be ignored
This is necessary because not all files we find in the library
folder are libraries. I wish there was a public robot API
for "give me a list of installed libraries"...
"""
_name = na... | python | def _should_ignore(self, name):
"""Return True if a given library name should be ignored
This is necessary because not all files we find in the library
folder are libraries. I wish there was a public robot API
for "give me a list of installed libraries"...
"""
_name = na... | [
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237,124 | boakley/robotframework-hub | rfhub/kwdb.py | KeywordTable._execute | def _execute(self, *args):
"""Execute an SQL query
This exists because I think it's tedious to get a cursor and
then use a cursor.
"""
cursor = self.db.cursor()
cursor.execute(*args)
return cursor | python | def _execute(self, *args):
"""Execute an SQL query
This exists because I think it's tedious to get a cursor and
then use a cursor.
"""
cursor = self.db.cursor()
cursor.execute(*args)
return cursor | [
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237,125 | boakley/robotframework-hub | rfhub/kwdb.py | KeywordTable._glob_to_sql | def _glob_to_sql(self, string):
"""Convert glob-like wildcards to SQL wildcards
* becomes %
? becomes _
% becomes \%
\\ remains \\
\* remains \*
\? remains \?
This also adds a leading and trailing %, unless the pattern begins with
^ or ends with ... | python | def _glob_to_sql(self, string):
"""Convert glob-like wildcards to SQL wildcards
* becomes %
? becomes _
% becomes \%
\\ remains \\
\* remains \*
\? remains \?
This also adds a leading and trailing %, unless the pattern begins with
^ or ends with ... | [
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237,126 | boakley/robotframework-hub | rfhub/blueprints/doc/__init__.py | doc | def doc():
"""Show a list of libraries, along with the nav panel on the left"""
kwdb = current_app.kwdb
libraries = get_collections(kwdb, libtype="library")
resource_files = get_collections(kwdb, libtype="resource")
hierarchy = get_navpanel_data(kwdb)
return flask.render_template("home.html",
... | python | def doc():
"""Show a list of libraries, along with the nav panel on the left"""
kwdb = current_app.kwdb
libraries = get_collections(kwdb, libtype="library")
resource_files = get_collections(kwdb, libtype="resource")
hierarchy = get_navpanel_data(kwdb)
return flask.render_template("home.html",
... | [
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237,127 | boakley/robotframework-hub | rfhub/blueprints/doc/__init__.py | index | def index():
"""Show a list of available libraries, and resource files"""
kwdb = current_app.kwdb
libraries = get_collections(kwdb, libtype="library")
resource_files = get_collections(kwdb, libtype="resource")
return flask.render_template("libraryNames.html",
data=... | python | def index():
"""Show a list of available libraries, and resource files"""
kwdb = current_app.kwdb
libraries = get_collections(kwdb, libtype="library")
resource_files = get_collections(kwdb, libtype="resource")
return flask.render_template("libraryNames.html",
data=... | [
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237,128 | boakley/robotframework-hub | rfhub/blueprints/doc/__init__.py | search | def search():
"""Show all keywords that match a pattern"""
pattern = flask.request.args.get('pattern', "*").strip().lower()
# if the pattern contains "in:<collection>" (eg: in:builtin),
# filter results to only that (or those) collections
# This was kind-of hacked together, but seems to work well e... | python | def search():
"""Show all keywords that match a pattern"""
pattern = flask.request.args.get('pattern', "*").strip().lower()
# if the pattern contains "in:<collection>" (eg: in:builtin),
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237,129 | boakley/robotframework-hub | rfhub/blueprints/doc/__init__.py | get_collections | def get_collections(kwdb, libtype="*"):
"""Get list of collections from kwdb, then add urls necessary for hyperlinks"""
collections = kwdb.get_collections(libtype=libtype)
for result in collections:
url = flask.url_for(".doc_for_library", collection_id=result["collection_id"])
result["url"] ... | python | def get_collections(kwdb, libtype="*"):
"""Get list of collections from kwdb, then add urls necessary for hyperlinks"""
collections = kwdb.get_collections(libtype=libtype)
for result in collections:
url = flask.url_for(".doc_for_library", collection_id=result["collection_id"])
result["url"] ... | [
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237,130 | boakley/robotframework-hub | rfhub/blueprints/doc/__init__.py | get_navpanel_data | def get_navpanel_data(kwdb):
"""Get navpanel data from kwdb, and add urls necessary for hyperlinks"""
data = kwdb.get_keyword_hierarchy()
for library in data:
library["url"] = flask.url_for(".doc_for_library", collection_id=library["collection_id"])
for keyword in library["keywords"]:
... | python | def get_navpanel_data(kwdb):
"""Get navpanel data from kwdb, and add urls necessary for hyperlinks"""
data = kwdb.get_keyword_hierarchy()
for library in data:
library["url"] = flask.url_for(".doc_for_library", collection_id=library["collection_id"])
for keyword in library["keywords"]:
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237,131 | boakley/robotframework-hub | rfhub/blueprints/doc/__init__.py | doc_to_html | def doc_to_html(doc, doc_format="ROBOT"):
"""Convert documentation to HTML"""
from robot.libdocpkg.htmlwriter import DocToHtml
return DocToHtml(doc_format)(doc) | python | def doc_to_html(doc, doc_format="ROBOT"):
"""Convert documentation to HTML"""
from robot.libdocpkg.htmlwriter import DocToHtml
return DocToHtml(doc_format)(doc) | [
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237,132 | boakley/robotframework-hub | rfhub/app.py | RobotHub.start | def start(self):
"""Start the app"""
if self.args.debug:
self.app.run(port=self.args.port, debug=self.args.debug, host=self.args.interface)
else:
root = "http://%s:%s" % (self.args.interface, self.args.port)
print("tornado web server running on " + root)
... | python | def start(self):
"""Start the app"""
if self.args.debug:
self.app.run(port=self.args.port, debug=self.args.debug, host=self.args.interface)
else:
root = "http://%s:%s" % (self.args.interface, self.args.port)
print("tornado web server running on " + root)
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237,133 | boakley/robotframework-hub | rfhub/app.py | RobotHub.check_shutdown_flag | def check_shutdown_flag(self):
"""Shutdown the server if the flag has been set"""
if self.shutdown_requested:
tornado.ioloop.IOLoop.instance().stop()
print("web server stopped.") | python | def check_shutdown_flag(self):
"""Shutdown the server if the flag has been set"""
if self.shutdown_requested:
tornado.ioloop.IOLoop.instance().stop()
print("web server stopped.") | [
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237,134 | jazzband/python-geojson | geojson/utils.py | coords | def coords(obj):
"""
Yields the coordinates from a Feature or Geometry.
:param obj: A geometry or feature to extract the coordinates from.
:type obj: Feature, Geometry
:return: A generator with coordinate tuples from the geometry or feature.
:rtype: generator
"""
# Handle recursive case... | python | def coords(obj):
"""
Yields the coordinates from a Feature or Geometry.
:param obj: A geometry or feature to extract the coordinates from.
:type obj: Feature, Geometry
:return: A generator with coordinate tuples from the geometry or feature.
:rtype: generator
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237,135 | jazzband/python-geojson | geojson/utils.py | map_tuples | def map_tuples(func, obj):
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:param func: Function to apply to tuples
:type func: function
:param obj: A geometry or feature to extract the coordinates from.
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"""
Returns the mapped coordinates from a Geometry after applying the provided
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237,136 | jazzband/python-geojson | geojson/utils.py | map_geometries | def map_geometries(func, obj):
"""
Returns the result of passing every geometry in the given geojson object
through func.
:param func: Function to apply to tuples
:type func: function
:param obj: A geometry or feature to extract the coordinates from.
:type obj: GeoJSON
:return: The resu... | python | def map_geometries(func, obj):
"""
Returns the result of passing every geometry in the given geojson object
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:type func: function
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237,137 | jazzband/python-geojson | geojson/base.py | GeoJSON.to_instance | def to_instance(cls, ob, default=None, strict=False):
"""Encode a GeoJSON dict into an GeoJSON object.
Assumes the caller knows that the dict should satisfy a GeoJSON type.
:param cls: Dict containing the elements to be encoded into a GeoJSON
object.
:type cls: dict
:par... | python | def to_instance(cls, ob, default=None, strict=False):
"""Encode a GeoJSON dict into an GeoJSON object.
Assumes the caller knows that the dict should satisfy a GeoJSON type.
:param cls: Dict containing the elements to be encoded into a GeoJSON
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:type cls: dict
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237,138 | jazzband/python-geojson | geojson/base.py | GeoJSON.check_list_errors | def check_list_errors(self, checkFunc, lst):
"""Validation helper function."""
# check for errors on each subitem, filter only subitems with errors
results = (checkFunc(i) for i in lst)
return [err for err in results if err] | python | def check_list_errors(self, checkFunc, lst):
"""Validation helper function."""
# check for errors on each subitem, filter only subitems with errors
results = (checkFunc(i) for i in lst)
return [err for err in results if err] | [
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237,139 | mkorpela/pabot | pabot/pabotlib.py | PabotLib.run_only_once | def run_only_once(self, keyword):
"""
Runs a keyword only once in one of the parallel processes.
As the keyword will be called
only in one process and the return value could basically be anything.
The "Run Only Once" can't return the actual return value.
If the keyword fa... | python | def run_only_once(self, keyword):
"""
Runs a keyword only once in one of the parallel processes.
As the keyword will be called
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237,140 | mkorpela/pabot | pabot/pabotlib.py | PabotLib.set_parallel_value_for_key | def set_parallel_value_for_key(self, key, value):
"""
Set a globally available key and value that can be accessed
from all the pabot processes.
"""
if self._remotelib:
self._remotelib.run_keyword('set_parallel_value_for_key',
[k... | python | def set_parallel_value_for_key(self, key, value):
"""
Set a globally available key and value that can be accessed
from all the pabot processes.
"""
if self._remotelib:
self._remotelib.run_keyword('set_parallel_value_for_key',
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237,141 | mkorpela/pabot | pabot/pabotlib.py | PabotLib.get_parallel_value_for_key | def get_parallel_value_for_key(self, key):
"""
Get the value for a key. If there is no value for the key then empty
string is returned.
"""
if self._remotelib:
return self._remotelib.run_keyword('get_parallel_value_for_key',
... | python | def get_parallel_value_for_key(self, key):
"""
Get the value for a key. If there is no value for the key then empty
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"""
if self._remotelib:
return self._remotelib.run_keyword('get_parallel_value_for_key',
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237,142 | mkorpela/pabot | pabot/pabotlib.py | PabotLib.acquire_lock | def acquire_lock(self, name):
"""
Wait for a lock with name.
This will prevent other processes from acquiring the lock with
the name while it is held. Thus they will wait in the position
where they are acquiring the lock until the process that has it
releases it.
... | python | def acquire_lock(self, name):
"""
Wait for a lock with name.
This will prevent other processes from acquiring the lock with
the name while it is held. Thus they will wait in the position
where they are acquiring the lock until the process that has it
releases it.
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237,143 | mkorpela/pabot | pabot/pabotlib.py | PabotLib.release_lock | def release_lock(self, name):
"""
Release a lock with name.
This will enable others to acquire the lock.
"""
if self._remotelib:
self._remotelib.run_keyword('release_lock',
[name, self._my_id], {})
else:
_Pab... | python | def release_lock(self, name):
"""
Release a lock with name.
This will enable others to acquire the lock.
"""
if self._remotelib:
self._remotelib.run_keyword('release_lock',
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237,144 | mkorpela/pabot | pabot/pabotlib.py | PabotLib.release_locks | def release_locks(self):
"""
Release all locks called by instance.
"""
if self._remotelib:
self._remotelib.run_keyword('release_locks',
[self._my_id], {})
else:
_PabotLib.release_locks(self, self._my_id) | python | def release_locks(self):
"""
Release all locks called by instance.
"""
if self._remotelib:
self._remotelib.run_keyword('release_locks',
[self._my_id], {})
else:
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237,145 | mkorpela/pabot | pabot/pabotlib.py | PabotLib.acquire_value_set | def acquire_value_set(self, *tags):
"""
Reserve a set of values for this execution.
No other process can reserve the same set of values while the set is
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other processes to access it.
Add tags to limit th... | python | def acquire_value_set(self, *tags):
"""
Reserve a set of values for this execution.
No other process can reserve the same set of values while the set is
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No other process can reserve the same set of values while the set is
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237,146 | mkorpela/pabot | pabot/pabotlib.py | PabotLib.get_value_from_set | def get_value_from_set(self, key):
"""
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"""
#TODO: This should be done locally.
# We do not really need to call centralised server if the set is already
# reserved as the data there is immutable during execution
key ... | python | def get_value_from_set(self, key):
"""
Get a value from previously reserved value set.
"""
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237,147 | mkorpela/pabot | pabot/pabotlib.py | PabotLib.release_value_set | def release_value_set(self):
"""
Release a reserved value set so that other executions can use it also.
"""
if self._remotelib:
self._remotelib.run_keyword('release_value_set', [self._my_id], {})
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"""
Release a reserved value set so that other executions can use it also.
"""
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237,148 | uber-common/opentracing-python-instrumentation | opentracing_instrumentation/client_hooks/__init__.py | install_all_patches | def install_all_patches():
"""
A convenience method that installs all available hooks.
If a specific module is not available on the path, it is ignored.
"""
from . import mysqldb
from . import psycopg2
from . import strict_redis
from . import sqlalchemy
from . import tornado_http
... | python | def install_all_patches():
"""
A convenience method that installs all available hooks.
If a specific module is not available on the path, it is ignored.
"""
from . import mysqldb
from . import psycopg2
from . import strict_redis
from . import sqlalchemy
from . import tornado_http
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237,149 | uber-common/opentracing-python-instrumentation | opentracing_instrumentation/client_hooks/__init__.py | install_patches | def install_patches(patchers='all'):
"""
Usually called from middleware to install client hooks
specified in the client_hooks section of the configuration.
:param patchers: a list of patchers to run. Acceptable values include:
* None - installs all client patches
* 'all' - installs all clie... | python | def install_patches(patchers='all'):
"""
Usually called from middleware to install client hooks
specified in the client_hooks section of the configuration.
:param patchers: a list of patchers to run. Acceptable values include:
* None - installs all client patches
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237,150 | uber-common/opentracing-python-instrumentation | opentracing_instrumentation/client_hooks/__init__.py | install_client_interceptors | def install_client_interceptors(client_interceptors=()):
"""
Install client interceptors for the patchers.
:param client_interceptors: a list of client interceptors to install.
Should be a list of classes
"""
if not _valid_args(client_interceptors):
raise ValueError('client_intercep... | python | def install_client_interceptors(client_interceptors=()):
"""
Install client interceptors for the patchers.
:param client_interceptors: a list of client interceptors to install.
Should be a list of classes
"""
if not _valid_args(client_interceptors):
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237,151 | uber-common/opentracing-python-instrumentation | opentracing_instrumentation/client_hooks/__init__.py | _load_symbol | def _load_symbol(name):
"""Load a symbol by name.
:param str name: The name to load, specified by `module.attr`.
:returns: The attribute value. If the specified module does not contain
the requested attribute then `None` is returned.
"""
module_name, key = name.rsplit('.', 1)
try:... | python | def _load_symbol(name):
"""Load a symbol by name.
:param str name: The name to load, specified by `module.attr`.
:returns: The attribute value. If the specified module does not contain
the requested attribute then `None` is returned.
"""
module_name, key = name.rsplit('.', 1)
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237,152 | uber-common/opentracing-python-instrumentation | opentracing_instrumentation/request_context.py | span_in_stack_context | def span_in_stack_context(span):
"""
Create Tornado's StackContext that stores the given span in the
thread-local request context. This function is intended for use
in Tornado applications based on IOLoop, although will work fine
in single-threaded apps like Flask, albeit with more overhead.
##... | python | def span_in_stack_context(span):
"""
Create Tornado's StackContext that stores the given span in the
thread-local request context. This function is intended for use
in Tornado applications based on IOLoop, although will work fine
in single-threaded apps like Flask, albeit with more overhead.
##... | [
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237,153 | uber-common/opentracing-python-instrumentation | opentracing_instrumentation/local_span.py | traced_function | def traced_function(func=None, name=None, on_start=None,
require_active_trace=False):
"""
A decorator that enables tracing of the wrapped function or
Tornado co-routine provided there is a parent span already established.
.. code-block:: python
@traced_function
def ... | python | def traced_function(func=None, name=None, on_start=None,
require_active_trace=False):
"""
A decorator that enables tracing of the wrapped function or
Tornado co-routine provided there is a parent span already established.
.. code-block:: python
@traced_function
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237,154 | uber-common/opentracing-python-instrumentation | opentracing_instrumentation/utils.py | start_child_span | def start_child_span(operation_name, tracer=None, parent=None, tags=None):
"""
Start a new span as a child of parent_span. If parent_span is None,
start a new root span.
:param operation_name: operation name
:param tracer: Tracer or None (defaults to opentracing.tracer)
:param parent: parent Sp... | python | def start_child_span(operation_name, tracer=None, parent=None, tags=None):
"""
Start a new span as a child of parent_span. If parent_span is None,
start a new root span.
:param operation_name: operation name
:param tracer: Tracer or None (defaults to opentracing.tracer)
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237,155 | uber-common/opentracing-python-instrumentation | opentracing_instrumentation/http_server.py | before_request | def before_request(request, tracer=None):
"""
Attempts to extract a tracing span from incoming request.
If no tracing context is passed in the headers, or the data
cannot be parsed, a new root span is started.
:param request: HTTP request with `.headers` property exposed
that satisfies a re... | python | def before_request(request, tracer=None):
"""
Attempts to extract a tracing span from incoming request.
If no tracing context is passed in the headers, or the data
cannot be parsed, a new root span is started.
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237,156 | uber-common/opentracing-python-instrumentation | opentracing_instrumentation/http_server.py | WSGIRequestWrapper._parse_wsgi_headers | def _parse_wsgi_headers(wsgi_environ):
"""
HTTP headers are presented in WSGI environment with 'HTTP_' prefix.
This method finds those headers, removes the prefix, converts
underscores to dashes, and converts to lower case.
:param wsgi_environ:
:return: returns a diction... | python | def _parse_wsgi_headers(wsgi_environ):
"""
HTTP headers are presented in WSGI environment with 'HTTP_' prefix.
This method finds those headers, removes the prefix, converts
underscores to dashes, and converts to lower case.
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237,157 | uber-common/opentracing-python-instrumentation | opentracing_instrumentation/interceptors.py | ClientInterceptors.append | def append(cls, interceptor):
"""
Add interceptor to the end of the internal list.
Note: Raises ``ValueError`` if interceptor
does not extend ``OpenTracingInterceptor``
"""
cls._check(interceptor)
cls._interceptors.append(interceptor) | python | def append(cls, interceptor):
"""
Add interceptor to the end of the internal list.
Note: Raises ``ValueError`` if interceptor
does not extend ``OpenTracingInterceptor``
"""
cls._check(interceptor)
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237,158 | uber-common/opentracing-python-instrumentation | opentracing_instrumentation/interceptors.py | ClientInterceptors.insert | def insert(cls, index, interceptor):
"""
Add interceptor to the given index in the internal list.
Note: Raises ``ValueError`` if interceptor
does not extend ``OpenTracingInterceptor``
"""
cls._check(interceptor)
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"""
Add interceptor to the given index in the internal list.
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237,159 | uber-common/opentracing-python-instrumentation | opentracing_instrumentation/client_hooks/_singleton.py | singleton | def singleton(func):
"""
This decorator allows you to make sure that a function is called once and
only once. Note that recursive functions will still work.
WARNING: Not thread-safe!!!
"""
@functools.wraps(func)
def wrapper(*args, **kwargs):
if wrapper.__call_state__ == CALLED:
... | python | def singleton(func):
"""
This decorator allows you to make sure that a function is called once and
only once. Note that recursive functions will still work.
WARNING: Not thread-safe!!!
"""
@functools.wraps(func)
def wrapper(*args, **kwargs):
if wrapper.__call_state__ == CALLED:
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237,160 | ANTsX/ANTsPy | ants/utils/smooth_image.py | smooth_image | def smooth_image(image, sigma, sigma_in_physical_coordinates=True, FWHM=False, max_kernel_width=32):
"""
Smooth an image
ANTsR function: `smoothImage`
Arguments
---------
image
Image to smooth
sigma
Smoothing factor. Can be scalar, in which case the same sigma is... | python | def smooth_image(image, sigma, sigma_in_physical_coordinates=True, FWHM=False, max_kernel_width=32):
"""
Smooth an image
ANTsR function: `smoothImage`
Arguments
---------
image
Image to smooth
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Smoothing factor. Can be scalar, in which case the same sigma is... | [
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237,161 | ANTsX/ANTsPy | ants/registration/build_template.py | build_template | def build_template(
initial_template=None,
image_list=None,
iterations = 3,
gradient_step = 0.2,
**kwargs ):
"""
Estimate an optimal template from an input image_list
ANTsR function: N/A
Arguments
---------
initial_template : ANTsImage
initialization for the templat... | python | def build_template(
initial_template=None,
image_list=None,
iterations = 3,
gradient_step = 0.2,
**kwargs ):
"""
Estimate an optimal template from an input image_list
ANTsR function: N/A
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---------
initial_template : ANTsImage
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237,162 | ANTsX/ANTsPy | ants/registration/resample_image.py | resample_image | def resample_image(image, resample_params, use_voxels=False, interp_type=1):
"""
Resample image by spacing or number of voxels with
various interpolators. Works with multi-channel images.
ANTsR function: `resampleImage`
Arguments
---------
image : ANTsImage
input image
re... | python | def resample_image(image, resample_params, use_voxels=False, interp_type=1):
"""
Resample image by spacing or number of voxels with
various interpolators. Works with multi-channel images.
ANTsR function: `resampleImage`
Arguments
---------
image : ANTsImage
input image
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237,163 | ANTsX/ANTsPy | ants/core/ants_transform.py | apply_ants_transform | def apply_ants_transform(transform, data, data_type="point", reference=None, **kwargs):
"""
Apply ANTsTransform to data
ANTsR function: `applyAntsrTransform`
Arguments
---------
transform : ANTsTransform
transform to apply to image
data : ndarray/list/tuple
data to which t... | python | def apply_ants_transform(transform, data, data_type="point", reference=None, **kwargs):
"""
Apply ANTsTransform to data
ANTsR function: `applyAntsrTransform`
Arguments
---------
transform : ANTsTransform
transform to apply to image
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237,164 | ANTsX/ANTsPy | ants/core/ants_transform.py | compose_ants_transforms | def compose_ants_transforms(transform_list):
"""
Compose multiple ANTsTransform's together
ANTsR function: `composeAntsrTransforms`
Arguments
---------
transform_list : list/tuple of ANTsTransform object
list of transforms to compose together
Returns
-------
ANTsTransform
... | python | def compose_ants_transforms(transform_list):
"""
Compose multiple ANTsTransform's together
ANTsR function: `composeAntsrTransforms`
Arguments
---------
transform_list : list/tuple of ANTsTransform object
list of transforms to compose together
Returns
-------
ANTsTransform
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237,165 | ANTsX/ANTsPy | ants/core/ants_transform.py | transform_index_to_physical_point | def transform_index_to_physical_point(image, index):
"""
Get spatial point from index of an image.
ANTsR function: `antsTransformIndexToPhysicalPoint`
Arguments
---------
img : ANTsImage
image to get values from
index : list or tuple or numpy.ndarray
location in image
... | python | def transform_index_to_physical_point(image, index):
"""
Get spatial point from index of an image.
ANTsR function: `antsTransformIndexToPhysicalPoint`
Arguments
---------
img : ANTsImage
image to get values from
index : list or tuple or numpy.ndarray
location in image
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237,166 | ANTsX/ANTsPy | ants/core/ants_transform.py | ANTsTransform.invert | def invert(self):
""" Invert the transform """
libfn = utils.get_lib_fn('inverseTransform%s' % (self._libsuffix))
inv_tx_ptr = libfn(self.pointer)
new_tx = ANTsTransform(precision=self.precision, dimension=self.dimension,
transform_type=self.transform_typ... | python | def invert(self):
""" Invert the transform """
libfn = utils.get_lib_fn('inverseTransform%s' % (self._libsuffix))
inv_tx_ptr = libfn(self.pointer)
new_tx = ANTsTransform(precision=self.precision, dimension=self.dimension,
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237,167 | ANTsX/ANTsPy | ants/core/ants_transform.py | ANTsTransform.apply | def apply(self, data, data_type='point', reference=None, **kwargs):
"""
Apply transform to data
"""
if data_type == 'point':
return self.apply_to_point(data)
elif data_type == 'vector':
return self.apply_to_vector(data)
elif data_type == 'image':
... | python | def apply(self, data, data_type='point', reference=None, **kwargs):
"""
Apply transform to data
"""
if data_type == 'point':
return self.apply_to_point(data)
elif data_type == 'vector':
return self.apply_to_vector(data)
elif data_type == 'image':
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237,168 | ANTsX/ANTsPy | ants/core/ants_transform.py | ANTsTransform.apply_to_point | def apply_to_point(self, point):
"""
Apply transform to a point
Arguments
---------
point : list/tuple
point to which the transform will be applied
Returns
-------
list : transformed point
Example
-------
>>> import a... | python | def apply_to_point(self, point):
"""
Apply transform to a point
Arguments
---------
point : list/tuple
point to which the transform will be applied
Returns
-------
list : transformed point
Example
-------
>>> import a... | [
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237,169 | ANTsX/ANTsPy | ants/core/ants_transform.py | ANTsTransform.apply_to_vector | def apply_to_vector(self, vector):
"""
Apply transform to a vector
Arguments
---------
vector : list/tuple
vector to which the transform will be applied
Returns
-------
list : transformed vector
"""
if isinstance(vector, np.nd... | python | def apply_to_vector(self, vector):
"""
Apply transform to a vector
Arguments
---------
vector : list/tuple
vector to which the transform will be applied
Returns
-------
list : transformed vector
"""
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237,170 | ANTsX/ANTsPy | ants/viz/plot.py | plot_hist | def plot_hist(image, threshold=0., fit_line=False, normfreq=True,
## plot label arguments
title=None, grid=True, xlabel=None, ylabel=None,
## other plot arguments
facecolor='green', alpha=0.75):
"""
Plot a histogram from an ANTsImage
Arguments
---------
image : ANTsImage
ima... | python | def plot_hist(image, threshold=0., fit_line=False, normfreq=True,
## plot label arguments
title=None, grid=True, xlabel=None, ylabel=None,
## other plot arguments
facecolor='green', alpha=0.75):
"""
Plot a histogram from an ANTsImage
Arguments
---------
image : ANTsImage
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237,171 | ANTsX/ANTsPy | ants/utils/morphology.py | morphology | def morphology(image, operation, radius, mtype='binary', value=1,
shape='ball', radius_is_parametric=False, thickness=1,
lines=3, include_center=False):
"""
Apply morphological operations to an image
ANTsR function: `morphology`
Arguments
---------
input : ANTsIma... | python | def morphology(image, operation, radius, mtype='binary', value=1,
shape='ball', radius_is_parametric=False, thickness=1,
lines=3, include_center=False):
"""
Apply morphological operations to an image
ANTsR function: `morphology`
Arguments
---------
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237,172 | ANTsX/ANTsPy | ants/utils/scalar_rgb_vector.py | rgb_to_vector | def rgb_to_vector(image):
"""
Convert an RGB ANTsImage to a Vector ANTsImage
Arguments
---------
image : ANTsImage
RGB image to be converted
Returns
-------
ANTsImage
Example
-------
>>> import ants
>>> mni = ants.image_read(ants.get_data('mni'))
>>> mni_rg... | python | def rgb_to_vector(image):
"""
Convert an RGB ANTsImage to a Vector ANTsImage
Arguments
---------
image : ANTsImage
RGB image to be converted
Returns
-------
ANTsImage
Example
-------
>>> import ants
>>> mni = ants.image_read(ants.get_data('mni'))
>>> mni_rg... | [
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237,173 | ANTsX/ANTsPy | ants/utils/scalar_rgb_vector.py | vector_to_rgb | def vector_to_rgb(image):
"""
Convert an Vector ANTsImage to a RGB ANTsImage
Arguments
---------
image : ANTsImage
RGB image to be converted
Returns
-------
ANTsImage
Example
-------
>>> import ants
>>> img = ants.image_read(ants.get_data('r16'), pixeltype='uns... | python | def vector_to_rgb(image):
"""
Convert an Vector ANTsImage to a RGB ANTsImage
Arguments
---------
image : ANTsImage
RGB image to be converted
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237,174 | ANTsX/ANTsPy | ants/utils/quantile.py | quantile | def quantile(image, q, nonzero=True):
"""
Get the quantile values from an ANTsImage
"""
img_arr = image.numpy()
if isinstance(q, (list,tuple)):
q = [qq*100. if qq <= 1. else qq for qq in q]
if nonzero:
img_arr = img_arr[img_arr>0]
vals = [np.percentile(img_arr, qq... | python | def quantile(image, q, nonzero=True):
"""
Get the quantile values from an ANTsImage
"""
img_arr = image.numpy()
if isinstance(q, (list,tuple)):
q = [qq*100. if qq <= 1. else qq for qq in q]
if nonzero:
img_arr = img_arr[img_arr>0]
vals = [np.percentile(img_arr, qq... | [
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237,175 | ANTsX/ANTsPy | ants/utils/quantile.py | bandpass_filter_matrix | def bandpass_filter_matrix( matrix,
tr=1, lowf=0.01, highf=0.1, order = 3):
"""
Bandpass filter the input time series image
ANTsR function: `frequencyFilterfMRI`
Arguments
---------
image: input time series image
tr: sampling time interval (inverse of sampling rate)
lowf: lo... | python | def bandpass_filter_matrix( matrix,
tr=1, lowf=0.01, highf=0.1, order = 3):
"""
Bandpass filter the input time series image
ANTsR function: `frequencyFilterfMRI`
Arguments
---------
image: input time series image
tr: sampling time interval (inverse of sampling rate)
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ANTsR function: `frequencyFilterfMRI`
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237,176 | ANTsX/ANTsPy | ants/utils/quantile.py | compcor | def compcor( boldImage, ncompcor=4, quantile=0.975, mask=None, filter_type=False, degree=2 ):
"""
Compute noise components from the input image
ANTsR function: `compcor`
this is adapted from nipy code https://github.com/nipy/nipype/blob/e29ac95fc0fc00fedbcaa0adaf29d5878408ca7c/nipype/algorithms/confou... | python | def compcor( boldImage, ncompcor=4, quantile=0.975, mask=None, filter_type=False, degree=2 ):
"""
Compute noise components from the input image
ANTsR function: `compcor`
this is adapted from nipy code https://github.com/nipy/nipype/blob/e29ac95fc0fc00fedbcaa0adaf29d5878408ca7c/nipype/algorithms/confou... | [
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ANTsR function: `compcor`
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237,177 | ANTsX/ANTsPy | ants/utils/bias_correction.py | n3_bias_field_correction | def n3_bias_field_correction(image, downsample_factor=3):
"""
N3 Bias Field Correction
ANTsR function: `n3BiasFieldCorrection`
Arguments
---------
image : ANTsImage
image to be bias corrected
downsample_factor : scalar
how much to downsample image before performing bias co... | python | def n3_bias_field_correction(image, downsample_factor=3):
"""
N3 Bias Field Correction
ANTsR function: `n3BiasFieldCorrection`
Arguments
---------
image : ANTsImage
image to be bias corrected
downsample_factor : scalar
how much to downsample image before performing bias co... | [
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ANTsR function: `n3BiasFieldCorrection`
Arguments
---------
image : ANTsImage
image to be bias corrected
downsample_factor : scalar
how much to downsample image before performing bias correction
Returns
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Example
-----... | [
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237,178 | ANTsX/ANTsPy | ants/utils/bias_correction.py | n4_bias_field_correction | def n4_bias_field_correction(image, mask=None, shrink_factor=4,
convergence={'iters':[50,50,50,50], 'tol':1e-07},
spline_param=200, verbose=False, weight_mask=None):
"""
N4 Bias Field Correction
ANTsR function: `n4BiasFieldCorrection`
Arguments... | python | def n4_bias_field_correction(image, mask=None, shrink_factor=4,
convergence={'iters':[50,50,50,50], 'tol':1e-07},
spline_param=200, verbose=False, weight_mask=None):
"""
N4 Bias Field Correction
ANTsR function: `n4BiasFieldCorrection`
Arguments... | [
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ANTsR function: `n4BiasFieldCorrection`
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237,179 | ANTsX/ANTsPy | ants/utils/bias_correction.py | abp_n4 | def abp_n4(image, intensity_truncation=(0.025,0.975,256), mask=None, usen3=False):
"""
Truncate outlier intensities and bias correct with the N4 algorithm.
ANTsR function: `abpN4`
Arguments
---------
image : ANTsImage
image to correct and truncate
intensity_truncation : 3-tuple
... | python | def abp_n4(image, intensity_truncation=(0.025,0.975,256), mask=None, usen3=False):
"""
Truncate outlier intensities and bias correct with the N4 algorithm.
ANTsR function: `abpN4`
Arguments
---------
image : ANTsImage
image to correct and truncate
intensity_truncation : 3-tuple
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237,180 | ANTsX/ANTsPy | ants/registration/metrics.py | image_mutual_information | def image_mutual_information(image1, image2):
"""
Compute mutual information between two ANTsImage types
ANTsR function: `antsImageMutualInformation`
Arguments
---------
image1 : ANTsImage
image 1
image2 : ANTsImage
image 2
Returns
-------
scalar
Exam... | python | def image_mutual_information(image1, image2):
"""
Compute mutual information between two ANTsImage types
ANTsR function: `antsImageMutualInformation`
Arguments
---------
image1 : ANTsImage
image 1
image2 : ANTsImage
image 2
Returns
-------
scalar
Exam... | [
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ANTsR function: `antsImageMutualInformation`
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Returns
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Example
-------
>>> import ants
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237,181 | ANTsX/ANTsPy | ants/utils/get_mask.py | get_mask | def get_mask(image, low_thresh=None, high_thresh=None, cleanup=2):
"""
Get a binary mask image from the given image after thresholding
ANTsR function: `getMask`
Arguments
---------
image : ANTsImage
image from which mask will be computed. Can be an antsImage of 2, 3 or 4 dimensions.
... | python | def get_mask(image, low_thresh=None, high_thresh=None, cleanup=2):
"""
Get a binary mask image from the given image after thresholding
ANTsR function: `getMask`
Arguments
---------
image : ANTsImage
image from which mask will be computed. Can be an antsImage of 2, 3 or 4 dimensions.
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237,182 | ANTsX/ANTsPy | ants/utils/label_image_centroids.py | label_image_centroids | def label_image_centroids(image, physical=False, convex=True, verbose=False):
"""
Converts a label image to coordinates summarizing their positions
ANTsR function: `labelImageCentroids`
Arguments
---------
image : ANTsImage
image of integer labels
physical : boolean
wh... | python | def label_image_centroids(image, physical=False, convex=True, verbose=False):
"""
Converts a label image to coordinates summarizing their positions
ANTsR function: `labelImageCentroids`
Arguments
---------
image : ANTsImage
image of integer labels
physical : boolean
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ANTsR function: `labelImageCentroids`
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237,183 | ANTsX/ANTsPy | ants/contrib/sampling/transforms.py | MultiResolutionImage.transform | def transform(self, X, y=None):
"""
Generate a set of multi-resolution ANTsImage types
Arguments
---------
X : ANTsImage
image to transform
y : ANTsImage (optional)
another image to transform
Example
-------
>>> import an... | python | def transform(self, X, y=None):
"""
Generate a set of multi-resolution ANTsImage types
Arguments
---------
X : ANTsImage
image to transform
y : ANTsImage (optional)
another image to transform
Example
-------
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237,184 | ANTsX/ANTsPy | ants/contrib/sampling/transforms.py | LocallyBlurIntensity.transform | def transform(self, X, y=None):
"""
Locally blur an image by applying a gradient anisotropic diffusion filter.
Arguments
---------
X : ANTsImage
image to transform
y : ANTsImage (optional)
another image to transform.
Example
----... | python | def transform(self, X, y=None):
"""
Locally blur an image by applying a gradient anisotropic diffusion filter.
Arguments
---------
X : ANTsImage
image to transform
y : ANTsImage (optional)
another image to transform.
Example
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237,185 | ANTsX/ANTsPy | ants/utils/get_ants_data.py | get_data | def get_data(name=None):
"""
Get ANTsPy test data filename
ANTsR function: `getANTsRData`
Arguments
---------
name : string
name of test image tag to retrieve
Options:
- 'r16'
- 'r27'
- 'r64'
- 'r85'
- 'ch2'
... | python | def get_data(name=None):
"""
Get ANTsPy test data filename
ANTsR function: `getANTsRData`
Arguments
---------
name : string
name of test image tag to retrieve
Options:
- 'r16'
- 'r27'
- 'r64'
- 'r85'
- 'ch2'
... | [
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237,186 | ANTsX/ANTsPy | ants/utils/invariant_image_similarity.py | convolve_image | def convolve_image(image, kernel_image, crop=True):
"""
Convolve one image with another
ANTsR function: `convolveImage`
Arguments
---------
image : ANTsImage
image to convolve
kernel_image : ANTsImage
image acting as kernel
crop : boolean
whether to automatica... | python | def convolve_image(image, kernel_image, crop=True):
"""
Convolve one image with another
ANTsR function: `convolveImage`
Arguments
---------
image : ANTsImage
image to convolve
kernel_image : ANTsImage
image acting as kernel
crop : boolean
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237,187 | ANTsX/ANTsPy | ants/utils/ndimage_to_list.py | ndimage_to_list | def ndimage_to_list(image):
"""
Split a n dimensional ANTsImage into a list
of n-1 dimensional ANTsImages
Arguments
---------
image : ANTsImage
n-dimensional image to split
Returns
-------
list of ANTsImage types
Example
-------
>>> import ants
>>> image = ... | python | def ndimage_to_list(image):
"""
Split a n dimensional ANTsImage into a list
of n-1 dimensional ANTsImages
Arguments
---------
image : ANTsImage
n-dimensional image to split
Returns
-------
list of ANTsImage types
Example
-------
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>>> image = ... | [
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... | Split a n dimensional ANTsImage into a list
of n-1 dimensional ANTsImages
Arguments
---------
image : ANTsImage
n-dimensional image to split
Returns
-------
list of ANTsImage types
Example
-------
>>> import ants
>>> image = ants.image_read(ants.get_ants_data('r16'... | [
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237,188 | ANTsX/ANTsPy | ants/utils/process_args.py | _int_antsProcessArguments | def _int_antsProcessArguments(args):
"""
Needs to be better validated.
"""
p_args = []
if isinstance(args, dict):
for argname, argval in args.items():
if '-MULTINAME-' in argname:
# have this little hack because python doesnt support
# multiple dic... | python | def _int_antsProcessArguments(args):
"""
Needs to be better validated.
"""
p_args = []
if isinstance(args, dict):
for argname, argval in args.items():
if '-MULTINAME-' in argname:
# have this little hack because python doesnt support
# multiple dic... | [
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237,189 | ANTsX/ANTsPy | ants/learn/decomposition.py | initialize_eigenanatomy | def initialize_eigenanatomy(initmat, mask=None, initlabels=None, nreps=1, smoothing=0):
"""
InitializeEigenanatomy is a helper function to initialize sparseDecom
and sparseDecom2. Can be used to estimate sparseness parameters per
eigenvector. The user then only chooses nvecs and optional
regularizat... | python | def initialize_eigenanatomy(initmat, mask=None, initlabels=None, nreps=1, smoothing=0):
"""
InitializeEigenanatomy is a helper function to initialize sparseDecom
and sparseDecom2. Can be used to estimate sparseness parameters per
eigenvector. The user then only chooses nvecs and optional
regularizat... | [
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Arguments
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initmat : np.ndarray or ANTsImage
input mat... | [
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237,190 | ANTsX/ANTsPy | ants/learn/decomposition.py | eig_seg | def eig_seg(mask, img_list, apply_segmentation_to_images=False, cthresh=0, smooth=1):
"""
Segment a mask into regions based on the max value in an image list.
At a given voxel the segmentation label will contain the index to the image
that has the largest value. If the 3rd image has the greatest value,
... | python | def eig_seg(mask, img_list, apply_segmentation_to_images=False, cthresh=0, smooth=1):
"""
Segment a mask into regions based on the max value in an image list.
At a given voxel the segmentation label will contain the index to the image
that has the largest value. If the 3rd image has the greatest value,
... | [
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At a given voxel the segmentation label will contain the index to the image
that has the largest value. If the 3rd image has the greatest value,
the segmentation label will be 3 at that voxel.
Arguments
---------
mask : ANTsIm... | [
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237,191 | ANTsX/ANTsPy | ants/utils/label_stats.py | label_stats | def label_stats(image, label_image):
"""
Get label statistics from image
ANTsR function: `labelStats`
Arguments
---------
image : ANTsImage
Image from which statistics will be calculated
label_image : ANTsImage
Label image
Returns
-------
ndarray ?
... | python | def label_stats(image, label_image):
"""
Get label statistics from image
ANTsR function: `labelStats`
Arguments
---------
image : ANTsImage
Image from which statistics will be calculated
label_image : ANTsImage
Label image
Returns
-------
ndarray ?
... | [
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ANTsR function: `labelStats`
Arguments
---------
image : ANTsImage
Image from which statistics will be calculated
label_image : ANTsImage
Label image
Returns
-------
ndarray ?
Example
-------
>>> import ants
... | [
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] | 638020af2cdfc5ff4bdb9809ffe67aa505727a3b | https://github.com/ANTsX/ANTsPy/blob/638020af2cdfc5ff4bdb9809ffe67aa505727a3b/ants/utils/label_stats.py#L8-L41 |
237,192 | ANTsX/ANTsPy | ants/core/ants_image.py | ANTsImage.spacing | def spacing(self):
"""
Get image spacing
Returns
-------
tuple
"""
libfn = utils.get_lib_fn('getSpacing%s'%self._libsuffix)
return libfn(self.pointer) | python | def spacing(self):
"""
Get image spacing
Returns
-------
tuple
"""
libfn = utils.get_lib_fn('getSpacing%s'%self._libsuffix)
return libfn(self.pointer) | [
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Returns
-------
tuple | [
"Get",
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"spacing"
] | 638020af2cdfc5ff4bdb9809ffe67aa505727a3b | https://github.com/ANTsX/ANTsPy/blob/638020af2cdfc5ff4bdb9809ffe67aa505727a3b/ants/core/ants_image.py#L95-L104 |
237,193 | ANTsX/ANTsPy | ants/core/ants_image.py | ANTsImage.set_spacing | def set_spacing(self, new_spacing):
"""
Set image spacing
Arguments
---------
new_spacing : tuple or list
updated spacing for the image.
should have one value for each dimension
Returns
-------
None
"""
if not isin... | python | def set_spacing(self, new_spacing):
"""
Set image spacing
Arguments
---------
new_spacing : tuple or list
updated spacing for the image.
should have one value for each dimension
Returns
-------
None
"""
if not isin... | [
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Arguments
---------
new_spacing : tuple or list
updated spacing for the image.
should have one value for each dimension
Returns
-------
None | [
"Set",
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"spacing"
] | 638020af2cdfc5ff4bdb9809ffe67aa505727a3b | https://github.com/ANTsX/ANTsPy/blob/638020af2cdfc5ff4bdb9809ffe67aa505727a3b/ants/core/ants_image.py#L106-L126 |
237,194 | ANTsX/ANTsPy | ants/core/ants_image.py | ANTsImage.origin | def origin(self):
"""
Get image origin
Returns
-------
tuple
"""
libfn = utils.get_lib_fn('getOrigin%s'%self._libsuffix)
return libfn(self.pointer) | python | def origin(self):
"""
Get image origin
Returns
-------
tuple
"""
libfn = utils.get_lib_fn('getOrigin%s'%self._libsuffix)
return libfn(self.pointer) | [
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] | Get image origin
Returns
-------
tuple | [
"Get",
"image",
"origin"
] | 638020af2cdfc5ff4bdb9809ffe67aa505727a3b | https://github.com/ANTsX/ANTsPy/blob/638020af2cdfc5ff4bdb9809ffe67aa505727a3b/ants/core/ants_image.py#L129-L138 |
237,195 | ANTsX/ANTsPy | ants/core/ants_image.py | ANTsImage.set_origin | def set_origin(self, new_origin):
"""
Set image origin
Arguments
---------
new_origin : tuple or list
updated origin for the image.
should have one value for each dimension
Returns
-------
None
"""
if not isinstanc... | python | def set_origin(self, new_origin):
"""
Set image origin
Arguments
---------
new_origin : tuple or list
updated origin for the image.
should have one value for each dimension
Returns
-------
None
"""
if not isinstanc... | [
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Arguments
---------
new_origin : tuple or list
updated origin for the image.
should have one value for each dimension
Returns
-------
None | [
"Set",
"image",
"origin"
] | 638020af2cdfc5ff4bdb9809ffe67aa505727a3b | https://github.com/ANTsX/ANTsPy/blob/638020af2cdfc5ff4bdb9809ffe67aa505727a3b/ants/core/ants_image.py#L140-L160 |
237,196 | ANTsX/ANTsPy | ants/core/ants_image.py | ANTsImage.direction | def direction(self):
"""
Get image direction
Returns
-------
tuple
"""
libfn = utils.get_lib_fn('getDirection%s'%self._libsuffix)
return libfn(self.pointer) | python | def direction(self):
"""
Get image direction
Returns
-------
tuple
"""
libfn = utils.get_lib_fn('getDirection%s'%self._libsuffix)
return libfn(self.pointer) | [
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Returns
-------
tuple | [
"Get",
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] | 638020af2cdfc5ff4bdb9809ffe67aa505727a3b | https://github.com/ANTsX/ANTsPy/blob/638020af2cdfc5ff4bdb9809ffe67aa505727a3b/ants/core/ants_image.py#L163-L172 |
237,197 | ANTsX/ANTsPy | ants/core/ants_image.py | ANTsImage.set_direction | def set_direction(self, new_direction):
"""
Set image direction
Arguments
---------
new_direction : numpy.ndarray or tuple or list
updated direction for the image.
should have one value for each dimension
Returns
-------
None
... | python | def set_direction(self, new_direction):
"""
Set image direction
Arguments
---------
new_direction : numpy.ndarray or tuple or list
updated direction for the image.
should have one value for each dimension
Returns
-------
None
... | [
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Arguments
---------
new_direction : numpy.ndarray or tuple or list
updated direction for the image.
should have one value for each dimension
Returns
-------
None | [
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] | 638020af2cdfc5ff4bdb9809ffe67aa505727a3b | https://github.com/ANTsX/ANTsPy/blob/638020af2cdfc5ff4bdb9809ffe67aa505727a3b/ants/core/ants_image.py#L174-L197 |
237,198 | ANTsX/ANTsPy | ants/core/ants_image.py | ANTsImage.astype | def astype(self, dtype):
"""
Cast & clone an ANTsImage to a given numpy datatype.
Map:
uint8 : unsigned char
uint32 : unsigned int
float32 : float
float64 : double
"""
if dtype not in _supported_dtypes:
raise ValueEr... | python | def astype(self, dtype):
"""
Cast & clone an ANTsImage to a given numpy datatype.
Map:
uint8 : unsigned char
uint32 : unsigned int
float32 : float
float64 : double
"""
if dtype not in _supported_dtypes:
raise ValueEr... | [
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Map:
uint8 : unsigned char
uint32 : unsigned int
float32 : float
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237,199 | ANTsX/ANTsPy | ants/core/ants_image.py | ANTsImage.new_image_like | def new_image_like(self, data):
"""
Create a new ANTsImage with the same header information, but with
a new image array.
Arguments
---------
data : ndarray or py::capsule
New array or pointer for the image.
It must have the same shape as the cur... | python | def new_image_like(self, data):
"""
Create a new ANTsImage with the same header information, but with
a new image array.
Arguments
---------
data : ndarray or py::capsule
New array or pointer for the image.
It must have the same shape as the cur... | [
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a new image array.
Arguments
---------
data : ndarray or py::capsule
New array or pointer for the image.
It must have the same shape as the current
image data.
Returns
... | [
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