BoghdadyJR/codesearch_python · Datasets at Hugging Face

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def __msgc_step3_discontinuity_localization(self): """ Estimate discontinuity in basis of low resolution image segmentation. :return: discontinuity in low resolution """ import scipy start = self._start_time seg = 1 - self.segmentation.astype(np.int8) sel...
def __multiscale_gc_lo2hi_run(self): # , pyed): """ Run Graph-Cut segmentation with refinement of low resolution multiscale graph. In first step is performed normal GC on low resolution data Second step construct finer grid on edges of segmentation from first step. There...
def __multiscale_gc_hi2lo_run(self): # , pyed): """ Run Graph-Cut segmentation with simplifiyng of high resolution multiscale graph. In first step is performed normal GC on low resolution data Second step construct finer grid on edges of segmentation from first step. The...
def __ordered_values_by_indexes(self, data, inds): """ Return values (intensities) by indexes. Used for multiscale graph cut. data = [[0 1 1], [0 2 2], [0 2 2]] inds = [[0 1 2], [3 4 4], [5 4 4]] return: [...
def __hi2lo_multiscale_indexes(self, mask, orig_shape): # , zoom): """ Function computes multiscale indexes of ndarray. mask: Says where is original resolution (0) and where is small resolution (1). Mask is in small resolution. orig_shape: Original shape of input data. ...
def interactivity(self, min_val=None, max_val=None, qt_app=None): """ Interactive seed setting with 3d seed editor """ from .seed_editor_qt import QTSeedEditor from PyQt4.QtGui import QApplication if min_val is None: min_val = np.min(self.img) if max...
def set_seeds(self, seeds): """ Function for manual seed setting. Sets variable seeds and prepares voxels for density model. :param seeds: ndarray (0 - nothing, 1 - object, 2 - background, 3 - object just hard constraints, no model training, 4 - background just hard cons...
def run(self, run_fit_model=True): """ Run the Graph Cut segmentation according to preset parameters. :param run_fit_model: Allow to skip model fit when the model is prepared before :return: """ if run_fit_model: self.fit_model(self.img, self.voxelsize, self...
def __set_hard_hard_constraints(self, tdata1, tdata2, seeds): """ it works with seed labels: 0: nothing 1: object 1 - full seeds 2: object 2 - full seeds 3: object 1 - not a training seeds 4: object 2 - not a training seeds """ seeds_mask = (seeds ...
def __similarity_for_tlinks_obj_bgr( self, data, voxelsize, # voxels1, voxels2, # seeds, otherfeatures=None ): """ Compute edge values for graph cut tlinks based on image intensity and texture. """ # self.fit_model(data, voxelsize, seed...
def __create_nlinks(self, data, inds=None, boundary_penalties_fcn=None): """ Compute nlinks grid from data shape information. For boundary penalties are data (intensities) values are used. ins: Default is None. Used for multiscale GC. This are indexes of multiscale pixels. Next ...
def debug_get_reconstructed_similarity( self, data3d=None, voxelsize=None, seeds=None, area_weight=1, hard_constraints=True, return_unariesalt=False, ): """ Use actual model to calculate similarity. If no input is given the last image is used. ...
def debug_show_reconstructed_similarity( self, data3d=None, voxelsize=None, seeds=None, area_weight=1, hard_constraints=True, show=True, bins=20, slice_number=None, ): """ Show tlinks. :param data3d: ndarray with input d...
def debug_inspect_node(self, node_msindex): """ Get info about the node. See pycut.inspect_node() for details. Processing is done in temporary shape. :param node_seed: :return: node_unariesalt, node_neighboor_edges_and_weights, node_neighboor_seeds """ return ins...
def debug_interactive_inspect_node(self): """ Call after segmentation to see selected node neighborhood. User have to select one node by click. :return: """ if ( np.sum( np.abs( np.asarray(self.msinds.shape) - np.asarray(sel...
def _ssgc_prepare_data_and_run_computation( self, # voxels1, voxels2, hard_constraints=True, area_weight=1, ): """ Setting of data. You need set seeds if you want use hard_constraints. """ # from PyQt4.QtCore import pyqtRemoveInputHook ...
def resize_to_shape(data, shape, zoom=None, mode="nearest", order=0): """ Function resize input data to specific shape. :param data: input 3d array-like data :param shape: shape of output data :param zoom: zoom is used for back compatibility :mode: default is 'nearest' """ # @TODO remove...
def seed_zoom(seeds, zoom): """ Smart zoom for sparse matrix. If there is resize to bigger resolution thin line of label could be lost. This function prefers labels larger then zero. If there is only one small voxel in larger volume with zeros it is selected. """ # import scipy # loseeds...
def zoom_to_shape(data, shape, dtype=None): """ Zoom data to specific shape. """ import scipy import scipy.ndimage zoomd = np.array(shape) / np.array(data.shape, dtype=np.double) import warnings datares = scipy.ndimage.interpolation.zoom(data, zoomd, order=0, mode="reflect") if da...
def crop(data, crinfo): """ Crop the data. crop(data, crinfo) :param crinfo: min and max for each axis - [[minX, maxX], [minY, maxY], [minZ, maxZ]] """ crinfo = fix_crinfo(crinfo) return data[ __int_or_none(crinfo[0][0]) : __int_or_none(crinfo[0][1]), __int_or_none(crinfo[...
def combinecrinfo(crinfo1, crinfo2): """ Combine two crinfos. First used is crinfo1, second used is crinfo2. """ crinfo1 = fix_crinfo(crinfo1) crinfo2 = fix_crinfo(crinfo2) crinfo = [ [crinfo1[0][0] + crinfo2[0][0], crinfo1[0][0] + crinfo2[0][1]], [crinfo1[1][0] + crinfo2[1][0],...
def crinfo_from_specific_data(data, margin=0): """ Create crinfo of minimum orthogonal nonzero block in input data. :param data: input data :param margin: add margin to minimum block :return: """ # hledáme automatický ořez, nonzero dá indexy logger.debug("crinfo") logger.debug(str(m...
def uncrop(data, crinfo, orig_shape, resize=False, outside_mode="constant", cval=0): """ Put some boundary to input image. :param data: input data :param crinfo: array with minimum and maximum index along each axis [[minX, maxX],[minY, maxY],[minZ, maxZ]]. If crinfo is None, the whole input im...
def fix_crinfo(crinfo, to="axis"): """ Function recognize order of crinfo and convert it to proper format. """ crinfo = np.asarray(crinfo) if crinfo.shape[0] == 2: crinfo = crinfo.T return crinfo
def grid_edges(shape, inds=None, return_directions=True): """ Get list of grid edges :param shape: :param inds: :param return_directions: :return: """ if inds is None: inds = np.arange(np.prod(shape)).reshape(shape) # if not self.segparams['use_boundary_penalties'] and \ ...
def gen_grid_2d(shape, voxelsize): """ Generate list of edges for a base grid. """ nr, nc = shape nrm1, ncm1 = nr - 1, nc - 1 # sh = nm.asarray(shape) # calculate number of edges, in 2D: (nrows * (ncols - 1)) + ((nrows - 1) * ncols) nedges = 0 for direction in range(len(shape)): ...
def write_grid_to_vtk(fname, nodes, edges, node_flag=None, edge_flag=None): """ Write nodes and edges to VTK file :param fname: VTK filename :param nodes: :param edges: :param node_flag: set if this node is really used in output :param edge_flag: set if this flag is used in output :retur...
def add_nodes(self, coors, node_low_or_high=None): """ Add new nodes at the end of the list. """ last = self.lastnode if type(coors) is nm.ndarray: if len(coors.shape) == 1: coors = coors.reshape((1, coors.size)) nadd = coors.shape[0] ...
def add_edges(self, conn, edge_direction, edge_group=None, edge_low_or_high=None): """ Add new edges at the end of the list. :param edge_direction: direction flag :param edge_group: describes group of edges from same low super node and same direction :param edge_low_or_high: zero...
def _edge_group_substitution( self, ndid, nsplit, idxs, sr_tab, ndoffset, ed_remove, into_or_from ): """ Reconnect edges. :param ndid: id of low resolution edges :param nsplit: number of split :param idxs: indexes of low resolution :param sr_tab: :para...
def generate_base_grid(self, vtk_filename=None): """ Run first step of algorithm. Next step is split_voxels :param vtk_filename: :return: """ nd, ed, ed_dir = self.gen_grid_fcn(self.data.shape, self.voxelsize) self.add_nodes(nd) self.add_edges(ed, ed_dir, ...
def split_voxels(self, vtk_filename=None): """ Second step of algorithm :return:() """ self.cache = {} self.stats["t graph 10"] = time.time() - self.start_time self.msi = MultiscaleArray(self.data.shape, block_size=self.nsplit) # old implementation ...
def mul_block(self, index, val): """Multiply values in block""" self._prepare_cache_slice(index) self.msinds[self.cache_slice] *= val
def select_from_fv_by_seeds(fv, seeds, unique_cls): """ Tool to make simple feature functions take features from feature array by seeds. :param fv: ndarray with lineariezed feature. It's shape is MxN, where M is number of image pixels and N is number of features :param seeds: ndarray with seeds. Doe...
def return_fv_by_seeds(fv, seeds=None, unique_cls=None): """ Return features selected by seeds and unique_cls or selection from features and corresponding seed classes. :param fv: ndarray with lineariezed feature. It's shape is MxN, where M is number of image pixels and N is number of features :par...
def expand(self, expression): """Expands logical constructions.""" self.logger.debug("expand : expression %s", str(expression)) if not is_string(expression): return expression result = self._pattern.sub(lambda var: str(self._variables[var.group(1)]), expression) res...
def get_gutter_client( alias='default', cache=CLIENT_CACHE, **kwargs ): """ Creates gutter clients and memoizes them in a registry for future quick access. Args: alias (str or None): Name of the client. Used for caching. If name is falsy then do not use the cache...
def _modulo(self, decimal_argument): """ The mod operator is prone to floating point errors, so use decimal. 101.1 % 100 >>> 1.0999999999999943 decimal_context.divmod(Decimal('100.1'), 100) >>> (Decimal('1'), Decimal('0.1')) """ _times, remainder = self....
def enabled_for(self, inpt): """ Checks to see if this switch is enabled for the provided input. If ``compounded``, all switch conditions must be ``True`` for the switch to be enabled. Otherwise, any condition needs to be ``True`` for the switch to be enabled. The sw...
def call(self, inpt): """ Returns if the condition applies to the ``inpt``. If the class ``inpt`` is an instance of is not the same class as the condition's own ``argument``, then ``False`` is returned. This also applies to the ``NONE`` input. Otherwise, ``argument`` i...
def switches(self): """ List of all switches currently registered. """ results = [ switch for name, switch in self.storage.iteritems() if name.startswith(self.__joined_namespace) ] return results
def switch(self, name): """ Returns the switch with the provided ``name``. If ``autocreate`` is set to ``True`` and no switch with that name exists, a ``DISABLED`` switch will be with that name. Keyword Arguments: name -- A name of a switch. """ try: ...
def register(self, switch, signal=signals.switch_registered): ''' Register a switch and persist it to the storage. ''' if not switch.name: raise ValueError('Switch name cannot be blank') switch.manager = self self.__persist(switch) signal.call(switch...
def verify(obj, times=1, atleast=None, atmost=None, between=None, inorder=False): """Central interface to verify interactions. `verify` uses a fluent interface:: verify(<obj>, times=2).<method_name>(<args>) `args` can be as concrete as necessary. Often a catch-all is enough, especi...
def when(obj, strict=None): """Central interface to stub functions on a given `obj` `obj` should be a module, a class or an instance of a class; it can be a Dummy you created with :func:`mock`. ``when`` exposes a fluent interface where you configure a stub in three steps:: when(<obj>).<method_...
def when2(fn, args, *kwargs): """Stub a function call with the given arguments Exposes a more pythonic interface than :func:`when`. See :func:`when` for more documentation. Returns `AnswerSelector` interface which exposes `thenReturn`, `thenRaise`, and `thenAnswer` as usual. Always `strict`. ...
def patch(fn, attr_or_replacement, replacement=None): """Patch/Replace a function. This is really like monkeypatching, but note that all interactions will be recorded and can be verified. That is, using `patch` you stay in the domain of mockito. Two ways to call this. Either:: patch(os....
def expect(obj, strict=None, times=None, atleast=None, atmost=None, between=None): """Stub a function call, and set up an expected call count. Usage:: # Given `dog` is an instance of a `Dog` expect(dog, times=1).bark('Wuff').thenReturn('Miau') dog.bark('Wuff') dog.ba...
def unstub(objs): """Unstubs all stubbed methods and functions If you don't pass in any argument, all* registered mocks and patched modules, classes etc. will be unstubbed. Note that additionally, the underlying registry will be cleaned. After an `unstub` you can't :func:`verify` anymore because...
def verifyZeroInteractions(*objs): """Verify that no methods have been called on given objs. Note that strict mocks usually throw early on unexpected, unstubbed invocations. Partial mocks ('monkeypatched' objects or modules) do not support this functionality at all, bc only for the stubbed invocations ...
def verifyNoUnwantedInteractions(objs): """Verifies that expectations set via `expect` are met E.g.:: expect(os.path, times=1).exists(...).thenReturn(True) os.path('/foo') verifyNoUnwantedInteractions(os.path) # ok, called once If you leave out the argument all* registered obje...
def verifyStubbedInvocationsAreUsed(*objs): """Ensure stubs are actually used. This functions just ensures that stubbed methods are actually used. Its purpose is to detect interface changes after refactorings. It is meant to be invoked usually without arguments just before :func:`unstub`. """ ...
def get_function_host(fn): """Destructure a given function into its host and its name. The 'host' of a function is a module, for methods it is usually its instance or its class. This is safe only for methods, for module wide, globally declared names it must be considered experimental. For all reas...
def get_obj(path): """Return obj for given dotted path. Typical inputs for `path` are 'os' or 'os.path' in which case you get a module; or 'os.path.exists' in which case you get a function from that module. Just returns the given input in case it is not a str. Note: Relative imports not suppo...
def get_obj_attr_tuple(path): """Split path into (obj, attribute) tuple. Given `path` is 'os.path.exists' will thus return `(os.path, 'exists')` If path is not a str, delegates to `get_function_host(path)` """ if not isinstance(path, str): return get_function_host(path) if path.start...
def spy(object): """Spy an object. Spying means that all functions will behave as before, so they will be side effects, but the interactions can be verified afterwards. Returns Dummy-like, almost empty object as proxy to `object`. The returned object must be injected and used by the code under ...
def spy2(fn): # type: (...) -> None """Spy usage of given `fn`. Patches the module, class or object `fn` lives in, so that all interactions can be recorded; otherwise executes `fn` as before, so that all side effects happen as before. E.g.:: import time spy(time.time) do_...
def mock(config_or_spec=None, spec=None, strict=OMITTED): """Create 'empty' objects ('Mocks'). Will create an empty unconfigured object, that you can pass around. All interactions (method calls) will be recorded and can be verified using :func:`verify` et.al. A plain `mock()` will be not `strict`,...
def importPuppetClasses(self, smartProxyId): """ Function importPuppetClasses Force the reload of puppet classes @param smartProxyId: smartProxy Id @return RETURN: the API result """ return self.api.create('{}/{}/import_puppetclasses' .form...
def get_templates(model): """ Return a list of templates usable by a model. """ for template_name, template in templates.items(): if issubclass(template.model, model): yield (template_name, template.layout._meta.verbose_name)
def attach(layouts, *kwargs): """ Registers the given layout(s) classes admin site: @pages.register(Page) class Default(PageLayout): pass """ def _model_admin_wrapper(layout_class): register(layout_class, layouts[0]) return layout_class return _model_admin_wra...
def enhance(self): """ Function enhance Enhance the object with new item or enhanced items """ self.update({'os_default_templates': SubDict(self.api, self.objName, self.payloadObj, self.key, SubItemOsDefaultTe...
def get_api_envs(): """Get required API keys from environment variables.""" client_id = os.environ.get('CLIENT_ID') user_id = os.environ.get('USER_ID') if not client_id or not user_id: raise ValueError('API keys are not found in the environment') return client_id, user_id
def api_call(method, end_point, params=None, client_id=None, access_token=None): """Call given API end_point with API keys. :param method: HTTP method (e.g. 'get', 'delete'). :param end_point: API endpoint (e.g. 'users/john/sets'). :param params: Dictionary to be sent in the query string (e.g. {'myparam...
def request_upload_secret(self, secret_id): """ :return: json with "keyId" as secret and "url" for posting key """ return self._router.post_request_upload_secret(org_id=self.organizationId, instance_id=self.instanceId, ...
def checkAndCreate(self, key, payload, domainId): """ Function checkAndCreate Check if a subnet exists and create it if not @param key: The targeted subnet @param payload: The targeted subnet description @param domainId: The domainId to be attached wiuth the subnet @retu...
def removeDomain(self, subnetId, domainId): """ Function removeDomain Delete a domain from a subnet @param subnetId: The subnet Id @param domainId: The domainId to be attached wiuth the subnet @return RETURN: boolean """ subnetDomainIds = [] for domain in...
def exclusive(via=threading.Lock): """ Mark a callable as exclusive :param via: factory for a Lock to guard the callable Guards the callable against being entered again before completion. Explicitly raises a :py:exc:`RuntimeError` on violation. :note: If applied to a method, it is exclusive a...
def service(flavour): r""" Mark a class as implementing a Service Each Service class must have a ``run`` method, which does not take any arguments. This method is :py:meth:`~.ServiceRunner.adopt`\ ed after the daemon starts, unless * the Service has been garbage collected, or * the ServiceUnit...
def execute(self, payload, args, flavour: ModuleType, kwargs): """ Synchronously run ``payload`` and provide its output If ``args`` and/or ``*kwargs`` are provided, pass them to ``payload`` upon execution. """ if args or kwargs: payload = functools.partial(payl...
def adopt(self, payload, args, flavour: ModuleType, kwargs): """ Concurrently run ``payload`` in the background If ``args`` and/or ``kwargs`` are provided, pass them to ``payload`` upon execution. """ if args or kwargs: payload = functools.partial(payload, ar...
def accept(self): """ Start accepting synchronous, asynchronous and service payloads Since services are globally defined, only one :py:class:`ServiceRunner` may :py:meth:`accept` payloads at any time. """ if self._meta_runner: raise RuntimeError('payloads sch...
def shutdown(self): """Shutdown the accept loop and stop running payloads""" self._must_shutdown = True self._is_shutdown.wait() self._meta_runner.stop()
def milestones(ctx, list, close): """View/edit/close milestones on github """ repos = get_repos(ctx.parent.agile.get('labels')) if list: _list_milestones(repos) elif close: click.echo('Closing milestones "%s"' % close) _close_milestone(repos, close) else: click.ec...
def start_console(local_vars={}): '''Starts a console; modified from code.interact''' transforms.CONSOLE_ACTIVE = True transforms.remove_not_allowed_in_console() sys.ps1 = prompt console = ExperimentalInteractiveConsole(locals=local_vars) console.interact(banner=banner)
def push(self, line): """Transform and push a line to the interpreter. The line should not have a trailing newline; it may have internal newlines. The line is appended to a buffer and the interpreter's runsource() method is called with the concatenated contents of the buffer as...
def dump(obj, f, preserve=False): """Write dict object into file :param obj: the object to be dumped into toml :param f: the file object :param preserve: optional flag to preserve the inline table in result """ if not f.write: raise TypeError('You can only dump an object into a file obj...
def dumps(obj, preserve=False): """Stringifies a dict as toml :param obj: the object to be dumped into toml :param preserve: optional flag to preserve the inline table in result """ f = StringIO() dump(obj, f, preserve) return f.getvalue()
def license_loader(lic_dir=LIC_DIR): """Loads licenses from the given directory.""" lics = [] for ln in os.listdir(lic_dir): lp = os.path.join(lic_dir, ln) with open(lp) as lf: txt = lf.read() lic = License(txt) lics.append(lic) return lics
def get_vector(self, max_choice=3): """Return pseudo-choice vectors.""" vec = {} for dim in ['forbidden', 'required', 'permitted']: if self.meta[dim] is None: continue dim_vec = map(lambda x: (x, max_choice), self.meta[dim]) vec[dim] = dict(dim...
def entity(ctx, debug, uncolorize, **kwargs): """ CLI for tonomi.com using contrib-python-qubell-client To enable completion: eval "$(_NOMI_COMPLETE=source nomi)" """ global PROVIDER_CONFIG if debug: log.basicConfig(level=log.DEBUG) log.getLogger("requests.packages.urlli...
def import_app(files, category, overwrite, id, name): """ Upload application from file. By default, file name will be used as application name, with "-vXX.YYY" suffix stripped. Application is looked up by one of these classifiers, in order of priority: app-id, app-name, filename. If app-id is prov...
def show_account(): """ Exports current account configuration in shell-friendly form. Takes into account explicit top-level flags like --organization. """ click.echo("# tonomi api") for (key, env) in REVERSE_MAPPING.items(): value = QUBELL.get(key, None) if value: ...
def generate_session_token(refresh_token, verbose): """ Generates new session token from the given refresh token. :param refresh_token: refresh token to generate from :param verbose: whether expiration time should be added to output """ platform = _get_platform(authenticated=False) session_...
def runcommand(cosmology='WMAP5'): """ Example interface commands """ # Return the WMAP5 cosmology concentration predicted for # z=0 range of masses Mi = [1e8, 1e9, 1e10] zi = 0 print("Concentrations for haloes of mass %s at z=%s" % (Mi, zi)) output = commah.run(cosmology=cosmology, zi=zi, ...
def plotcommand(cosmology='WMAP5', plotname=None): """ Example ways to interrogate the dataset and plot the commah output """ # Plot the c-M relation as a functon of redshift xarray = 10**(np.arange(1, 15, 0.2)) yval = 'c' # Specify the redshift range zarray = np.arange(0, 5, 0.5) xtitle ...
def enhance(self): """ Function enhance Enhance the object with new item or enhanced items """ self.update({'puppetclasses': SubDict(self.api, self.objName, self.payloadObj, self.key, SubItemPuppetClasses)}) ...
def add_transformers(line): '''Extract the transformers names from a line of code of the form from __experimental__ import transformer1 [,...] and adds them to the globally known dict ''' assert FROM_EXPERIMENTAL.match(line) line = FROM_EXPERIMENTAL.sub(' ', line) # we now have: " tra...
def import_transformer(name): '''If needed, import a transformer, and adds it to the globally known dict The code inside a module where a transformer is defined should be standard Python code, which does not need any transformation. So, we disable the import hook, and let the normal module impo...
def extract_transformers_from_source(source): '''Scan a source for lines of the form from __experimental__ import transformer1 [,...] identifying transformers to be used. Such line is passed to the add_transformer function, after which it is removed from the code to be executed. ''' ...
def remove_not_allowed_in_console(): '''This function should be called from the console, when it starts. Some transformers are not allowed in the console and they could have been loaded prior to the console being activated. We effectively remove them and print an information message specific to that tr...
def transform(source): '''Used to convert the source code, making use of known transformers. "transformers" are modules which must contain a function transform_source(source) which returns a tranformed source. Some transformers (for example, those found in the standard library ...
def _match(self, request, response): """Match all requests/responses that satisfy the following conditions: * An Admin App; i.e. the path is something like /admin/some_app/ * The ``include_flag`` is not in the response's content """ is_html = 'text/html' in response.get('Conten...
def _chosen_css(self): """Read the minified CSS file including STATIC_URL in the references to the sprite images.""" css = render_to_string(self.css_template, {}) for sprite in self.chosen_sprites: # rewrite path to sprites in the css css = css.replace(sprite, settings.STATI...
def _embed(self, request, response): """Embed Chosen.js directly in html of the response.""" if self._match(request, response): # Render the <link> and the <script> tags to include Chosen. head = render_to_string( "chosenadmin/_head_css.html", {"ch...
def clean_up(self): """ Close the I2C bus """ self.log.debug("Closing I2C bus for address: 0x%02X" % self.address) self.bus.close()
def write_quick(self): """ Send only the read / write bit """ self.bus.write_quick(self.address) self.log.debug("write_quick: Sent the read / write bit")
def write_byte(self, cmd, value): """ Writes an 8-bit byte to the specified command register """ self.bus.write_byte_data(self.address, cmd, value) self.log.debug( "write_byte: Wrote 0x%02X to command register 0x%02X" % ( value, cmd ) ...
def write_word(self, cmd, value): """ Writes a 16-bit word to the specified command register """ self.bus.write_word_data(self.address, cmd, value) self.log.debug( "write_word: Wrote 0x%04X to command register 0x%02X" % ( value, cmd ) ...
def write_raw_byte(self, value): """ Writes an 8-bit byte directly to the bus """ self.bus.write_byte(self.address, value) self.log.debug("write_raw_byte: Wrote 0x%02X" % value)

def __msgc_step3_discontinuity_localization(self): """ Estimate discontinuity in basis of low resolution image segmentation. :return: discontinuity in low resolution """ import scipy start = self._start_time seg = 1 - self.segmentation.astype(np.int8) sel...

def __multiscale_gc_lo2hi_run(self): # , pyed): """ Run Graph-Cut segmentation with refinement of low resolution multiscale graph. In first step is performed normal GC on low resolution data Second step construct finer grid on edges of segmentation from first step. There...

def __multiscale_gc_hi2lo_run(self): # , pyed): """ Run Graph-Cut segmentation with simplifiyng of high resolution multiscale graph. In first step is performed normal GC on low resolution data Second step construct finer grid on edges of segmentation from first step. The...

def __ordered_values_by_indexes(self, data, inds): """ Return values (intensities) by indexes. Used for multiscale graph cut. data = [[0 1 1], [0 2 2], [0 2 2]] inds = [[0 1 2], [3 4 4], [5 4 4]] return: [...

def __hi2lo_multiscale_indexes(self, mask, orig_shape): # , zoom): """ Function computes multiscale indexes of ndarray. mask: Says where is original resolution (0) and where is small resolution (1). Mask is in small resolution. orig_shape: Original shape of input data. ...

def interactivity(self, min_val=None, max_val=None, qt_app=None): """ Interactive seed setting with 3d seed editor """ from .seed_editor_qt import QTSeedEditor from PyQt4.QtGui import QApplication if min_val is None: min_val = np.min(self.img) if max...

def set_seeds(self, seeds): """ Function for manual seed setting. Sets variable seeds and prepares voxels for density model. :param seeds: ndarray (0 - nothing, 1 - object, 2 - background, 3 - object just hard constraints, no model training, 4 - background just hard cons...

def run(self, run_fit_model=True): """ Run the Graph Cut segmentation according to preset parameters. :param run_fit_model: Allow to skip model fit when the model is prepared before :return: """ if run_fit_model: self.fit_model(self.img, self.voxelsize, self...

def __set_hard_hard_constraints(self, tdata1, tdata2, seeds): """ it works with seed labels: 0: nothing 1: object 1 - full seeds 2: object 2 - full seeds 3: object 1 - not a training seeds 4: object 2 - not a training seeds """ seeds_mask = (seeds ...

def __similarity_for_tlinks_obj_bgr( self, data, voxelsize, # voxels1, voxels2, # seeds, otherfeatures=None ): """ Compute edge values for graph cut tlinks based on image intensity and texture. """ # self.fit_model(data, voxelsize, seed...

def __create_nlinks(self, data, inds=None, boundary_penalties_fcn=None): """ Compute nlinks grid from data shape information. For boundary penalties are data (intensities) values are used. ins: Default is None. Used for multiscale GC. This are indexes of multiscale pixels. Next ...

def debug_get_reconstructed_similarity( self, data3d=None, voxelsize=None, seeds=None, area_weight=1, hard_constraints=True, return_unariesalt=False, ): """ Use actual model to calculate similarity. If no input is given the last image is used. ...

def debug_show_reconstructed_similarity( self, data3d=None, voxelsize=None, seeds=None, area_weight=1, hard_constraints=True, show=True, bins=20, slice_number=None, ): """ Show tlinks. :param data3d: ndarray with input d...

def debug_inspect_node(self, node_msindex): """ Get info about the node. See pycut.inspect_node() for details. Processing is done in temporary shape. :param node_seed: :return: node_unariesalt, node_neighboor_edges_and_weights, node_neighboor_seeds """ return ins...

def debug_interactive_inspect_node(self): """ Call after segmentation to see selected node neighborhood. User have to select one node by click. :return: """ if ( np.sum( np.abs( np.asarray(self.msinds.shape) - np.asarray(sel...

def _ssgc_prepare_data_and_run_computation( self, # voxels1, voxels2, hard_constraints=True, area_weight=1, ): """ Setting of data. You need set seeds if you want use hard_constraints. """ # from PyQt4.QtCore import pyqtRemoveInputHook ...

def resize_to_shape(data, shape, zoom=None, mode="nearest", order=0): """ Function resize input data to specific shape. :param data: input 3d array-like data :param shape: shape of output data :param zoom: zoom is used for back compatibility :mode: default is 'nearest' """ # @TODO remove...

def seed_zoom(seeds, zoom): """ Smart zoom for sparse matrix. If there is resize to bigger resolution thin line of label could be lost. This function prefers labels larger then zero. If there is only one small voxel in larger volume with zeros it is selected. """ # import scipy # loseeds...

def zoom_to_shape(data, shape, dtype=None): """ Zoom data to specific shape. """ import scipy import scipy.ndimage zoomd = np.array(shape) / np.array(data.shape, dtype=np.double) import warnings datares = scipy.ndimage.interpolation.zoom(data, zoomd, order=0, mode="reflect") if da...

def crop(data, crinfo): """ Crop the data. crop(data, crinfo) :param crinfo: min and max for each axis - [[minX, maxX], [minY, maxY], [minZ, maxZ]] """ crinfo = fix_crinfo(crinfo) return data[ __int_or_none(crinfo[0][0]) : __int_or_none(crinfo[0][1]), __int_or_none(crinfo[...

def combinecrinfo(crinfo1, crinfo2): """ Combine two crinfos. First used is crinfo1, second used is crinfo2. """ crinfo1 = fix_crinfo(crinfo1) crinfo2 = fix_crinfo(crinfo2) crinfo = [ [crinfo1[0][0] + crinfo2[0][0], crinfo1[0][0] + crinfo2[0][1]], [crinfo1[1][0] + crinfo2[1][0],...

def crinfo_from_specific_data(data, margin=0): """ Create crinfo of minimum orthogonal nonzero block in input data. :param data: input data :param margin: add margin to minimum block :return: """ # hledáme automatický ořez, nonzero dá indexy logger.debug("crinfo") logger.debug(str(m...

def uncrop(data, crinfo, orig_shape, resize=False, outside_mode="constant", cval=0): """ Put some boundary to input image. :param data: input data :param crinfo: array with minimum and maximum index along each axis [[minX, maxX],[minY, maxY],[minZ, maxZ]]. If crinfo is None, the whole input im...

def fix_crinfo(crinfo, to="axis"): """ Function recognize order of crinfo and convert it to proper format. """ crinfo = np.asarray(crinfo) if crinfo.shape[0] == 2: crinfo = crinfo.T return crinfo

def grid_edges(shape, inds=None, return_directions=True): """ Get list of grid edges :param shape: :param inds: :param return_directions: :return: """ if inds is None: inds = np.arange(np.prod(shape)).reshape(shape) # if not self.segparams['use_boundary_penalties'] and \ ...

def gen_grid_2d(shape, voxelsize): """ Generate list of edges for a base grid. """ nr, nc = shape nrm1, ncm1 = nr - 1, nc - 1 # sh = nm.asarray(shape) # calculate number of edges, in 2D: (nrows * (ncols - 1)) + ((nrows - 1) * ncols) nedges = 0 for direction in range(len(shape)): ...

def write_grid_to_vtk(fname, nodes, edges, node_flag=None, edge_flag=None): """ Write nodes and edges to VTK file :param fname: VTK filename :param nodes: :param edges: :param node_flag: set if this node is really used in output :param edge_flag: set if this flag is used in output :retur...

def add_nodes(self, coors, node_low_or_high=None): """ Add new nodes at the end of the list. """ last = self.lastnode if type(coors) is nm.ndarray: if len(coors.shape) == 1: coors = coors.reshape((1, coors.size)) nadd = coors.shape[0] ...

def add_edges(self, conn, edge_direction, edge_group=None, edge_low_or_high=None): """ Add new edges at the end of the list. :param edge_direction: direction flag :param edge_group: describes group of edges from same low super node and same direction :param edge_low_or_high: zero...

def _edge_group_substitution( self, ndid, nsplit, idxs, sr_tab, ndoffset, ed_remove, into_or_from ): """ Reconnect edges. :param ndid: id of low resolution edges :param nsplit: number of split :param idxs: indexes of low resolution :param sr_tab: :para...

def generate_base_grid(self, vtk_filename=None): """ Run first step of algorithm. Next step is split_voxels :param vtk_filename: :return: """ nd, ed, ed_dir = self.gen_grid_fcn(self.data.shape, self.voxelsize) self.add_nodes(nd) self.add_edges(ed, ed_dir, ...

def split_voxels(self, vtk_filename=None): """ Second step of algorithm :return:() """ self.cache = {} self.stats["t graph 10"] = time.time() - self.start_time self.msi = MultiscaleArray(self.data.shape, block_size=self.nsplit) # old implementation ...

def mul_block(self, index, val): """Multiply values in block""" self._prepare_cache_slice(index) self.msinds[self.cache_slice] *= val

def select_from_fv_by_seeds(fv, seeds, unique_cls): """ Tool to make simple feature functions take features from feature array by seeds. :param fv: ndarray with lineariezed feature. It's shape is MxN, where M is number of image pixels and N is number of features :param seeds: ndarray with seeds. Doe...

def return_fv_by_seeds(fv, seeds=None, unique_cls=None): """ Return features selected by seeds and unique_cls or selection from features and corresponding seed classes. :param fv: ndarray with lineariezed feature. It's shape is MxN, where M is number of image pixels and N is number of features :par...

def expand(self, expression): """Expands logical constructions.""" self.logger.debug("expand : expression %s", str(expression)) if not is_string(expression): return expression result = self._pattern.sub(lambda var: str(self._variables[var.group(1)]), expression) res...

def get_gutter_client( alias='default', cache=CLIENT_CACHE, **kwargs ): """ Creates gutter clients and memoizes them in a registry for future quick access. Args: alias (str or None): Name of the client. Used for caching. If name is falsy then do not use the cache...

def _modulo(self, decimal_argument): """ The mod operator is prone to floating point errors, so use decimal. 101.1 % 100 >>> 1.0999999999999943 decimal_context.divmod(Decimal('100.1'), 100) >>> (Decimal('1'), Decimal('0.1')) """ _times, remainder = self....

def enabled_for(self, inpt): """ Checks to see if this switch is enabled for the provided input. If ``compounded``, all switch conditions must be ``True`` for the switch to be enabled. Otherwise, *any* condition needs to be ``True`` for the switch to be enabled. The sw...

def call(self, inpt): """ Returns if the condition applies to the ``inpt``. If the class ``inpt`` is an instance of is not the same class as the condition's own ``argument``, then ``False`` is returned. This also applies to the ``NONE`` input. Otherwise, ``argument`` i...

def switches(self): """ List of all switches currently registered. """ results = [ switch for name, switch in self.storage.iteritems() if name.startswith(self.__joined_namespace) ] return results

def switch(self, name): """ Returns the switch with the provided ``name``. If ``autocreate`` is set to ``True`` and no switch with that name exists, a ``DISABLED`` switch will be with that name. Keyword Arguments: name -- A name of a switch. """ try: ...

def register(self, switch, signal=signals.switch_registered): ''' Register a switch and persist it to the storage. ''' if not switch.name: raise ValueError('Switch name cannot be blank') switch.manager = self self.__persist(switch) signal.call(switch...

def verify(obj, times=1, atleast=None, atmost=None, between=None, inorder=False): """Central interface to verify interactions. `verify` uses a fluent interface:: verify(<obj>, times=2).<method_name>(<args>) `args` can be as concrete as necessary. Often a catch-all is enough, especi...

def when(obj, strict=None): """Central interface to stub functions on a given `obj` `obj` should be a module, a class or an instance of a class; it can be a Dummy you created with :func:`mock`. ``when`` exposes a fluent interface where you configure a stub in three steps:: when(<obj>).<method_...

def when2(fn, *args, **kwargs): """Stub a function call with the given arguments Exposes a more pythonic interface than :func:`when`. See :func:`when` for more documentation. Returns `AnswerSelector` interface which exposes `thenReturn`, `thenRaise`, and `thenAnswer` as usual. Always `strict`. ...

def patch(fn, attr_or_replacement, replacement=None): """Patch/Replace a function. This is really like monkeypatching, but *note* that all interactions will be recorded and can be verified. That is, using `patch` you stay in the domain of mockito. Two ways to call this. Either:: patch(os....

def expect(obj, strict=None, times=None, atleast=None, atmost=None, between=None): """Stub a function call, and set up an expected call count. Usage:: # Given `dog` is an instance of a `Dog` expect(dog, times=1).bark('Wuff').thenReturn('Miau') dog.bark('Wuff') dog.ba...

def unstub(*objs): """Unstubs all stubbed methods and functions If you don't pass in any argument, *all* registered mocks and patched modules, classes etc. will be unstubbed. Note that additionally, the underlying registry will be cleaned. After an `unstub` you can't :func:`verify` anymore because...

def verifyZeroInteractions(*objs): """Verify that no methods have been called on given objs. Note that strict mocks usually throw early on unexpected, unstubbed invocations. Partial mocks ('monkeypatched' objects or modules) do not support this functionality at all, bc only for the stubbed invocations ...

def verifyNoUnwantedInteractions(*objs): """Verifies that expectations set via `expect` are met E.g.:: expect(os.path, times=1).exists(...).thenReturn(True) os.path('/foo') verifyNoUnwantedInteractions(os.path) # ok, called once If you leave out the argument *all* registered obje...

def verifyStubbedInvocationsAreUsed(*objs): """Ensure stubs are actually used. This functions just ensures that stubbed methods are actually used. Its purpose is to detect interface changes after refactorings. It is meant to be invoked usually without arguments just before :func:`unstub`. """ ...

def get_function_host(fn): """Destructure a given function into its host and its name. The 'host' of a function is a module, for methods it is usually its instance or its class. This is safe only for methods, for module wide, globally declared names it must be considered experimental. For all reas...

def get_obj(path): """Return obj for given dotted path. Typical inputs for `path` are 'os' or 'os.path' in which case you get a module; or 'os.path.exists' in which case you get a function from that module. Just returns the given input in case it is not a str. Note: Relative imports not suppo...

def get_obj_attr_tuple(path): """Split path into (obj, attribute) tuple. Given `path` is 'os.path.exists' will thus return `(os.path, 'exists')` If path is not a str, delegates to `get_function_host(path)` """ if not isinstance(path, str): return get_function_host(path) if path.start...

def spy(object): """Spy an object. Spying means that all functions will behave as before, so they will be side effects, but the interactions can be verified afterwards. Returns Dummy-like, almost empty object as proxy to `object`. The *returned* object must be injected and used by the code under ...

def spy2(fn): # type: (...) -> None """Spy usage of given `fn`. Patches the module, class or object `fn` lives in, so that all interactions can be recorded; otherwise executes `fn` as before, so that all side effects happen as before. E.g.:: import time spy(time.time) do_...

def mock(config_or_spec=None, spec=None, strict=OMITTED): """Create 'empty' objects ('Mocks'). Will create an empty unconfigured object, that you can pass around. All interactions (method calls) will be recorded and can be verified using :func:`verify` et.al. A plain `mock()` will be not `strict`,...

def importPuppetClasses(self, smartProxyId): """ Function importPuppetClasses Force the reload of puppet classes @param smartProxyId: smartProxy Id @return RETURN: the API result """ return self.api.create('{}/{}/import_puppetclasses' .form...

def get_templates(model): """ Return a list of templates usable by a model. """ for template_name, template in templates.items(): if issubclass(template.model, model): yield (template_name, template.layout._meta.verbose_name)

def attach(*layouts, **kwargs): """ Registers the given layout(s) classes admin site: @pages.register(Page) class Default(PageLayout): pass """ def _model_admin_wrapper(layout_class): register(layout_class, layouts[0]) return layout_class return _model_admin_wra...

def enhance(self): """ Function enhance Enhance the object with new item or enhanced items """ self.update({'os_default_templates': SubDict(self.api, self.objName, self.payloadObj, self.key, SubItemOsDefaultTe...

def get_api_envs(): """Get required API keys from environment variables.""" client_id = os.environ.get('CLIENT_ID') user_id = os.environ.get('USER_ID') if not client_id or not user_id: raise ValueError('API keys are not found in the environment') return client_id, user_id

def api_call(method, end_point, params=None, client_id=None, access_token=None): """Call given API end_point with API keys. :param method: HTTP method (e.g. 'get', 'delete'). :param end_point: API endpoint (e.g. 'users/john/sets'). :param params: Dictionary to be sent in the query string (e.g. {'myparam...

def request_upload_secret(self, secret_id): """ :return: json with "keyId" as secret and "url" for posting key """ return self._router.post_request_upload_secret(org_id=self.organizationId, instance_id=self.instanceId, ...

def checkAndCreate(self, key, payload, domainId): """ Function checkAndCreate Check if a subnet exists and create it if not @param key: The targeted subnet @param payload: The targeted subnet description @param domainId: The domainId to be attached wiuth the subnet @retu...

def removeDomain(self, subnetId, domainId): """ Function removeDomain Delete a domain from a subnet @param subnetId: The subnet Id @param domainId: The domainId to be attached wiuth the subnet @return RETURN: boolean """ subnetDomainIds = [] for domain in...

def exclusive(via=threading.Lock): """ Mark a callable as exclusive :param via: factory for a Lock to guard the callable Guards the callable against being entered again before completion. Explicitly raises a :py:exc:`RuntimeError` on violation. :note: If applied to a method, it is exclusive a...

def service(flavour): r""" Mark a class as implementing a Service Each Service class must have a ``run`` method, which does not take any arguments. This method is :py:meth:`~.ServiceRunner.adopt`\ ed after the daemon starts, unless * the Service has been garbage collected, or * the ServiceUnit...

def execute(self, payload, *args, flavour: ModuleType, **kwargs): """ Synchronously run ``payload`` and provide its output If ``*args*`` and/or ``**kwargs`` are provided, pass them to ``payload`` upon execution. """ if args or kwargs: payload = functools.partial(payl...

def adopt(self, payload, *args, flavour: ModuleType, **kwargs): """ Concurrently run ``payload`` in the background If ``*args*`` and/or ``**kwargs`` are provided, pass them to ``payload`` upon execution. """ if args or kwargs: payload = functools.partial(payload, *ar...

def accept(self): """ Start accepting synchronous, asynchronous and service payloads Since services are globally defined, only one :py:class:`ServiceRunner` may :py:meth:`accept` payloads at any time. """ if self._meta_runner: raise RuntimeError('payloads sch...

def shutdown(self): """Shutdown the accept loop and stop running payloads""" self._must_shutdown = True self._is_shutdown.wait() self._meta_runner.stop()

def milestones(ctx, list, close): """View/edit/close milestones on github """ repos = get_repos(ctx.parent.agile.get('labels')) if list: _list_milestones(repos) elif close: click.echo('Closing milestones "%s"' % close) _close_milestone(repos, close) else: click.ec...

def start_console(local_vars={}): '''Starts a console; modified from code.interact''' transforms.CONSOLE_ACTIVE = True transforms.remove_not_allowed_in_console() sys.ps1 = prompt console = ExperimentalInteractiveConsole(locals=local_vars) console.interact(banner=banner)

def push(self, line): """Transform and push a line to the interpreter. The line should not have a trailing newline; it may have internal newlines. The line is appended to a buffer and the interpreter's runsource() method is called with the concatenated contents of the buffer as...

def dump(obj, f, preserve=False): """Write dict object into file :param obj: the object to be dumped into toml :param f: the file object :param preserve: optional flag to preserve the inline table in result """ if not f.write: raise TypeError('You can only dump an object into a file obj...

def dumps(obj, preserve=False): """Stringifies a dict as toml :param obj: the object to be dumped into toml :param preserve: optional flag to preserve the inline table in result """ f = StringIO() dump(obj, f, preserve) return f.getvalue()

def license_loader(lic_dir=LIC_DIR): """Loads licenses from the given directory.""" lics = [] for ln in os.listdir(lic_dir): lp = os.path.join(lic_dir, ln) with open(lp) as lf: txt = lf.read() lic = License(txt) lics.append(lic) return lics

def get_vector(self, max_choice=3): """Return pseudo-choice vectors.""" vec = {} for dim in ['forbidden', 'required', 'permitted']: if self.meta[dim] is None: continue dim_vec = map(lambda x: (x, max_choice), self.meta[dim]) vec[dim] = dict(dim...

def entity(ctx, debug, uncolorize, **kwargs): """ CLI for tonomi.com using contrib-python-qubell-client To enable completion: eval "$(_NOMI_COMPLETE=source nomi)" """ global PROVIDER_CONFIG if debug: log.basicConfig(level=log.DEBUG) log.getLogger("requests.packages.urlli...

def import_app(files, category, overwrite, id, name): """ Upload application from file. By default, file name will be used as application name, with "-vXX.YYY" suffix stripped. Application is looked up by one of these classifiers, in order of priority: app-id, app-name, filename. If app-id is prov...

def show_account(): """ Exports current account configuration in shell-friendly form. Takes into account explicit top-level flags like --organization. """ click.echo("# tonomi api") for (key, env) in REVERSE_MAPPING.items(): value = QUBELL.get(key, None) if value: ...

def generate_session_token(refresh_token, verbose): """ Generates new session token from the given refresh token. :param refresh_token: refresh token to generate from :param verbose: whether expiration time should be added to output """ platform = _get_platform(authenticated=False) session_...

def runcommand(cosmology='WMAP5'): """ Example interface commands """ # Return the WMAP5 cosmology concentration predicted for # z=0 range of masses Mi = [1e8, 1e9, 1e10] zi = 0 print("Concentrations for haloes of mass %s at z=%s" % (Mi, zi)) output = commah.run(cosmology=cosmology, zi=zi, ...

def plotcommand(cosmology='WMAP5', plotname=None): """ Example ways to interrogate the dataset and plot the commah output """ # Plot the c-M relation as a functon of redshift xarray = 10**(np.arange(1, 15, 0.2)) yval = 'c' # Specify the redshift range zarray = np.arange(0, 5, 0.5) xtitle ...

def enhance(self): """ Function enhance Enhance the object with new item or enhanced items """ self.update({'puppetclasses': SubDict(self.api, self.objName, self.payloadObj, self.key, SubItemPuppetClasses)}) ...

def add_transformers(line): '''Extract the transformers names from a line of code of the form from __experimental__ import transformer1 [,...] and adds them to the globally known dict ''' assert FROM_EXPERIMENTAL.match(line) line = FROM_EXPERIMENTAL.sub(' ', line) # we now have: " tra...

def import_transformer(name): '''If needed, import a transformer, and adds it to the globally known dict The code inside a module where a transformer is defined should be standard Python code, which does not need any transformation. So, we disable the import hook, and let the normal module impo...

def extract_transformers_from_source(source): '''Scan a source for lines of the form from __experimental__ import transformer1 [,...] identifying transformers to be used. Such line is passed to the add_transformer function, after which it is removed from the code to be executed. ''' ...

def remove_not_allowed_in_console(): '''This function should be called from the console, when it starts. Some transformers are not allowed in the console and they could have been loaded prior to the console being activated. We effectively remove them and print an information message specific to that tr...

def transform(source): '''Used to convert the source code, making use of known transformers. "transformers" are modules which must contain a function transform_source(source) which returns a tranformed source. Some transformers (for example, those found in the standard library ...

def _match(self, request, response): """Match all requests/responses that satisfy the following conditions: * An Admin App; i.e. the path is something like /admin/some_app/ * The ``include_flag`` is not in the response's content """ is_html = 'text/html' in response.get('Conten...

def _chosen_css(self): """Read the minified CSS file including STATIC_URL in the references to the sprite images.""" css = render_to_string(self.css_template, {}) for sprite in self.chosen_sprites: # rewrite path to sprites in the css css = css.replace(sprite, settings.STATI...

def _embed(self, request, response): """Embed Chosen.js directly in html of the response.""" if self._match(request, response): # Render the <link> and the <script> tags to include Chosen. head = render_to_string( "chosenadmin/_head_css.html", {"ch...

def clean_up(self): """ Close the I2C bus """ self.log.debug("Closing I2C bus for address: 0x%02X" % self.address) self.bus.close()

def write_quick(self): """ Send only the read / write bit """ self.bus.write_quick(self.address) self.log.debug("write_quick: Sent the read / write bit")

def write_byte(self, cmd, value): """ Writes an 8-bit byte to the specified command register """ self.bus.write_byte_data(self.address, cmd, value) self.log.debug( "write_byte: Wrote 0x%02X to command register 0x%02X" % ( value, cmd ) ...

def write_word(self, cmd, value): """ Writes a 16-bit word to the specified command register """ self.bus.write_word_data(self.address, cmd, value) self.log.debug( "write_word: Wrote 0x%04X to command register 0x%02X" % ( value, cmd ) ...

def write_raw_byte(self, value): """ Writes an 8-bit byte directly to the bus """ self.bus.write_byte(self.address, value) self.log.debug("write_raw_byte: Wrote 0x%02X" % value)