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<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def cmd(command, ignore_stderr=False, raise_on_return=False, timeout=None, encoding="utf-8"): """ Run a shell command and have it automatically decoded and print...
result = run(command, timeout=timeout, shell=True) if raise_on_return: result.check_returncode() print(result.stdout.decode(encoding)) if not ignore_stderr and result.stderr: print(result.stderr.decode(encoding))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def pushd(directory): """Change working directories in style and stay organized! :param directory: Where do you want to go and remember? :return: saved directory...
directory = os.path.expanduser(directory) _saved_paths.insert(0, os.path.abspath(os.getcwd())) os.chdir(directory) return [directory] + _saved_paths
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def popd(): """Go back to where you once were. :return: saved directory stack """
try: directory = _saved_paths.pop(0) except IndexError: return [os.getcwd()] os.chdir(directory) return [directory] + _saved_paths
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def find(name=None, ext=None, directory=".", match_case=False, disable_glob=False, depth=None): """ Designed for the interactive interpreter by making default or...
return find_files_list(directory=directory, ext=ext, name=name, match_case=match_case, disable_glob=disable_glob, depth=depth)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def head(file_path, lines=10, encoding="utf-8", printed=True, errors='strict'): """ Read the first N lines of a file, defaults to 10 :param file_path: Path to fi...
data = [] with open(file_path, "rb") as f: for _ in range(lines): try: if python_version >= (2, 7): data.append(next(f).decode(encoding, errors=errors)) else: data.append(next(f).decode(encoding)) except Sto...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def tail(file_path, lines=10, encoding="utf-8", printed=True, errors='strict'): """ A really silly way to get the last N lines, defaults to 10. :param file_path:...
data = deque() with open(file_path, "rb") as f: for line in f: if python_version >= (2, 7): data.append(line.decode(encoding, errors=errors)) else: data.append(line.decode(encoding)) if len(data) > lines: data.popleft(...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def cp(src, dst, overwrite=False): """ Copy files to a new location. :param src: list (or string) of paths of files to copy :param dst: file or folder to copy it...
if not isinstance(src, list): src = [src] dst = os.path.expanduser(dst) dst_folder = os.path.isdir(dst) if len(src) > 1 and not dst_folder: raise OSError("Cannot copy multiple item to same file") for item in src: source = os.path.expanduser(item) destination = (d...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def cut(string, characters=2, trailing="normal"): """ Split a string into a list of N characters each. .. code:: python reusables.cut("abcdefghi") # ['ab', 'cd',...
split_str = [string[i:i + characters] for i in range(0, len(string), characters)] if trailing != "normal" and len(split_str[-1]) != characters: if trailing.lower() == "remove": return split_str[:-1] if trailing.lower() == "combine" and len(split_str) >= 2: ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def int_to_roman(integer): """ Convert an integer into a string of roman numbers. .. code: python reusables.int_to_roman(445) # 'CDXLV' :param integer: :return: ...
if not isinstance(integer, int): raise ValueError("Input integer must be of type int") output = [] while integer > 0: for r, i in sorted(_roman_dict.items(), key=lambda x: x[1], reverse=True): while integer >= i: output.append(r) ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def roman_to_int(roman_string): """ Converts a string of roman numbers into an integer. .. code: python reusables.roman_to_int("XXXVI") # 36 :param roman_string:...
roman_string = roman_string.upper().strip() if "IIII" in roman_string: raise ValueError("Malformed roman string") value = 0 skip_one = False last_number = None for i, letter in enumerate(roman_string): if letter not in _roman_dict: raise ValueError("Malformed roman s...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def task_list(): """ Scans the modules set in RQ_JOBS_MODULES for RQ jobs decorated with @task Compiles a readable list for Job model task choices """
try: jobs_module = settings.RQ_JOBS_MODULE except AttributeError: raise ImproperlyConfigured(_("You have to define RQ_JOBS_MODULE in settings.py")) if isinstance(jobs_module, string_types): jobs_modules = (jobs_module,) elif isinstance(jobs_module, (tuple, list)): jobs_...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def rq_job(self): """The last RQ Job this ran on"""
if not self.rq_id or not self.rq_origin: return try: return RQJob.fetch(self.rq_id, connection=get_connection(self.rq_origin)) except NoSuchJobError: return
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def rq_link(self): """Link to Django-RQ status page for this job"""
if self.rq_job: url = reverse('rq_job_detail', kwargs={'job_id': self.rq_id, 'queue_index': queue_index_by_name(self.rq_origin)}) return '<a href="{}">{}</a>'.format(url, self.rq_id)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def fix_module(job): """ Fix for tasks without a module. Provides backwards compatibility with < 0.1.5 """
modules = settings.RQ_JOBS_MODULE if not type(modules) == tuple: modules = [modules] for module in modules: try: module_match = importlib.import_module(module) if hasattr(module_match, job.task): job.task = '{}.{}'.format(module, job.task) ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_checks(self): """Return a list of functions to use when testing values."""
return [ self.is_date, self.is_datetime, self.is_integer, self.is_float, self.default]
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def clean_text(self, text): '''Clean text using bleach.''' if text is None: return '' text = re.sub(ILLEGAL_CHARACTERS_RE, '', text) if '<' in text or '&lt' in text: text = clean(text, tags=self.tags, strip=self.strip) return unescape(text)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def path(self, category = None, image = None, feature = None): """ Constructs the path to categories, images and features. This path function assumes that the ...
filename = None if not category is None: filename = join(self.impath, str(category)) if not image is None: assert not category is None, "The category has to be given if the image is given" filename = join(filename, '%s_%s.png' % (str(category)...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_image(self, cat, img): """ Loads an image from disk. """
filename = self.path(cat, img) data = [] if filename.endswith('mat'): data = loadmat(filename)['output'] else: data = imread(filename) if self.size is not None: return imresize(data, self.size) else: return data
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_feature(self, cat, img, feature): """ Load a feature from disk. """
filename = self.path(cat, img, feature) data = loadmat(filename) name = [k for k in list(data.keys()) if not k.startswith('__')] if self.size is not None: return imresize(data[name.pop()], self.size) return data[name.pop()]
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def save_image(self, cat, img, data): """Saves a new image."""
filename = self.path(cat, img) mkdir(filename) if type(data) == np.ndarray: data = Image.fromarray(data).convert('RGB') data.save(filename)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def save_feature(self, cat, img, feature, data): """Saves a new feature."""
filename = self.path(cat, img, feature) mkdir(filename) savemat(filename, {'output':data})
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def randsample(vec, nr_samples, with_replacement = False): """ Draws nr_samples random samples from vec. """
if not with_replacement: return np.random.permutation(vec)[0:nr_samples] else: return np.asarray(vec)[np.random.randint(0, len(vec), nr_samples)]
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def dict_fun(data, function): """ Apply a function to all values in a dictionary, return a dictionary with results. Parameters data : dict a dictionary whose val...
return dict((k, function(v)) for k, v in list(data.items()))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def load(path, variable='Datamat'): """ Load datamat at path. Parameters: path : string Absolute path of the file to load from. """
f = h5py.File(path,'r') try: dm = fromhdf5(f[variable]) finally: f.close() return dm
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def filter(self, index): #@ReservedAssignment """ Filters a datamat by different aspects. This function is a device to filter the datamat by certain logical cond...
return Datamat(categories=self._categories, datamat=self, index=index)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def copy(self): """ Returns a copy of the datamat. """
return self.filter(np.ones(self._num_fix).astype(bool))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def save(self, path): """ Saves Datamat to path. Parameters: path : string Absolute path of the file to save to. """
f = h5py.File(path, 'w') try: fm_group = f.create_group('Datamat') for field in self.fieldnames(): try: fm_group.create_dataset(field, data = self.__dict__[field]) except (TypeError,) as e: # Assuming field ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def set_param(self, key, value): """ Set the value of a parameter. """
self.__dict__[key] = value self._parameters[key] = value
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def by_field(self, field): """ Returns an iterator that iterates over unique values of field Parameters: field : string Filters the datamat for every unique valu...
for value in np.unique(self.__dict__[field]): yield self.filter(self.__dict__[field] == value)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def add_field(self, name, data): """ Add a new field to the datamat. Parameters: name : string Name of the new field data : list Data for the new field, must be ...
if name in self._fields: raise ValueError if not len(data) == self._num_fix: raise ValueError self._fields.append(name) self.__dict__[name] = data
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def add_field_like(self, name, like_array): """ Add a new field to the Datamat with the dtype of the like_array and the shape of the like_array except for the fi...
new_shape = list(like_array.shape) new_shape[0] = len(self) new_data = ma.empty(new_shape, like_array.dtype) new_data.mask = True self.add_field(name, new_data)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def rm_field(self, name): """ Remove a field from the datamat. Parameters: name : string Name of the field to be removed """
if not name in self._fields: raise ValueError self._fields.remove(name) del self.__dict__[name]
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def add_parameter(self, name, value): """ Adds a parameter to the existing Datamat. Fails if parameter with same name already exists or if name is otherwise in t...
if name in self._parameters: raise ValueError("'%s' is already a parameter" % (name)) elif name in self.__dict__: raise ValueError("'%s' conflicts with the Datamat name-space" % (name)) self.__dict__[name] = value self._parameters[name] = self.__dict__[name]
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def rm_parameter(self, name): """ Removes a parameter to the existing Datamat. Fails if parameter doesn't exist. """
if name not in self._parameters: raise ValueError("no '%s' parameter found" % (name)) del self._parameters[name] del self.__dict__[name]
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def parameter_to_field(self, name): """ Promotes a parameter to a field by creating a new array of same size as the other existing fields, filling it with the cu...
if name not in self._parameters: raise ValueError("no '%s' parameter found" % (name)) if self._fields.count(name) > 0: raise ValueError("field with name '%s' already exists" % (name)) data = np.array([self._parameters[name]]*self._num_fix) self.rm_parameter(nam...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def join(self, fm_new, minimal_subset=True): """ Adds content of a new Datamat to this Datamat. If a parameter of the Datamats is not equal or does not exist in ...
# Check if parameters are equal. If not, promote them to fields. ''' for (nm, val) in fm_new._parameters.items(): if self._parameters.has_key(nm): if (val != self._parameters[nm]): self.parameter_to_field(nm) fm_new.parameter_t...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _draw(self, prev_angle = None, prev_length = None): """ Draws a new length- and angle-difference pair and calculates length and angle absolutes matching the ...
if (prev_angle is None) or (prev_length is None): (length, angle)= np.unravel_index(self.drawFrom('self.firstLenAng_cumsum', self.getrand('self.firstLenAng_cumsum')), self.firstLenAng_shape) angle = angle-((self.firstLenAng_shape[...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def sample(self): """ Draws a trajectory length, first coordinates, lengths, angles and length-angle-difference pairs according to the empirical distribution. Ea...
lenghts = [] angles = [] coordinates = [] fix = [] sample_size = int(round(self.trajLen_borders[self.drawFrom('self.trajLen_cumsum', self.getrand('self.trajLen_cumsum'))])) coordinates.append([0, 0]) fix.append(1) while len(coordinates) < sample...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def relative_bias(fm, scale_factor = 1, estimator = None): """ Computes the relative bias, i.e. the distribution of saccade angles and amplitudes. Parameters: fm...
assert 'fix' in fm.fieldnames(), "Can not work without fixation numbers" excl = fm.fix - np.roll(fm.fix, 1) != 1 # Now calculate the direction where the NEXT fixation goes to diff_x = (np.roll(fm.x, 1) - fm.x)[~excl] diff_y = (np.roll(fm.y, 1) - fm.y)[~excl] # Make a histogram of dif...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def get_velocity(samplemat, Hz, blinks=None): ''' Compute velocity of eye-movements. Samplemat must contain fields 'x' and 'y', specifying the x,y coordinates of gaze location. The function assumes that the values in x,y are sampled continously at a rate specified by 'Hz'. ''' Hz = float(Hz...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def fixation_detection(samplemat, saccades, Hz=200, samples2fix=None, respect_trial_borders=False, sample_times=None): ''' Detect Fixation from saccades. Fixations are defined as intervals between saccades. This function also calcuates start and end times (in ms) for each fixatio...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def parse(parse_obj, agent=None, etag=None, modified=None, inject=False): """Parse a subscription list and return a dict containing the results. :param parse_obj...
guarantees = common.SuperDict({ 'bozo': 0, 'feeds': [], 'lists': [], 'opportunities': [], 'meta': common.SuperDict(), 'version': '', }) fileobj, info = _mkfile(parse_obj, (agent or USER_AGENT), etag, modified) guarantees.update(info) if not fileobj: ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def fixations(self): ''' Filter the fixmat such that it only contains fixations on images in categories that are also in the categories object''' if not self._fixations: raise RuntimeError('This Images object does not have' +' an associated fixmat') if len(lis...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def data(self, value): """ Saves a new image to disk """
self.loader.save_image(self.category, self.image, value)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def fixations(self): """ Returns all fixations that are on this image. A precondition for this to work is that a fixmat is associated with this Image object. """
if not self._fixations: raise RuntimeError('This Images object does not have' +' an associated fixmat') return self._fixations[(self._fixations.category == self.category) & (self._fixations.filenumber == self.image)]
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def generate(self): """ Generator for creating the cross-validation slices. Returns A tuple of that contains two fixmats (training and test) and two Category obj...
for _ in range(0, self.num_slices): #1. separate fixmat into test and training fixmat subjects = np.unique(self.fm.SUBJECTINDEX) test_subs = randsample(subjects, self.subject_hold_out*len(subjects)) train_subs = [x for x in subject...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def prepare_data(fm, max_back, dur_cap=700): ''' Computes angle and length differences up to given order and deletes suspiciously long fixations. Input fm: Fixmat Fixmat for which to comput angle and length differences max_back: Int Computes delta angle and ampli...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def saccadic_momentum_effect(durations, forward_angle, summary_stat=nanmean): """ Computes the mean fixation duration at forward angles. """
durations_per_da = np.nan * np.ones((len(e_angle) - 1,)) for i, (bo, b1) in enumerate(zip(e_angle[:-1], e_angle[1:])): idx = ( bo <= forward_angle) & ( forward_angle < b1) & ( ~np.isnan(durations)) durations_per_da[i] = summary_stat(durations[idx]) return...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def ior_effect(durations, angle_diffs, length_diffs, summary_stat=np.mean, parallel=True, min_samples=20): """ Computes a measure of fixation durations at delta ...
raster = np.empty((len(e_dist) - 1, len(e_angle) - 1), dtype=object) for a, (a_low, a_upp) in enumerate(zip(e_angle[:-1], e_angle[1:])): for d, (d_low, d_upp) in enumerate(zip(e_dist[:-1], e_dist[1:])): idx = ((d_low <= length_diffs) & (length_diffs < d_upp) & (a_low <= a...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def predict_fixation_duration( durations, angles, length_diffs, dataset=None, params=None): """ Fits a non-linear piecewise regression to fixtaion durations for ...
if dataset is None: dataset = np.ones(durations.shape) corrected_durations = np.nan * np.ones(durations.shape) for i, ds in enumerate(np.unique(dataset)): e = lambda v, x, y, z: (leastsq_dual_model(x, z, *v) - y) v0 = [120, 220.0, -.1, 0.5, .1, .1] id_ds = dataset == ds ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def subject_predictions(fm, field='SUBJECTINDEX', method=predict_fixation_duration, data=None): ''' Calculates the saccadic momentum effect for individual subjects. Removes any effect of amplitude differences. The parameters are fitted on unbinned data. The effects are comp...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def intersubject_scores(fm, category, predicting_filenumbers, predicting_subjects, predicted_filenumbers, predicted_subjects, controls = True, scale_factor = 1): ...
predicting_fm = fm[ (ismember(fm.SUBJECTINDEX, predicting_subjects)) & (ismember(fm.filenumber, predicting_filenumbers)) & (fm.category == category)] predicted_fm = fm[ (ismember(fm.SUBJECTINDEX,predicted_subjects)) & (ismember(fm.filenumber,predicted_filenumbers))& ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def intersubject_scores_random_subjects(fm, category, filenumber, n_train, n_predict, controls=True, scale_factor = 1): """ Calculates how well the fixations of ...
subjects = np.unique(fm.SUBJECTINDEX) if len(subjects) < n_train + n_predict: raise ValueError("""Not enough subjects in fixmat""") # draw a random sample of subjects for testing and evaluation, according # to the specified set sizes (n_train, n_predict) np.random.shuffle(subjects) pred...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def upper_bound(fm, nr_subs = None, scale_factor = 1): """ compute the inter-subject consistency upper bound for a fixmat. Input: fm : a fixmat instance nr_subs ...
nr_subs_total = len(np.unique(fm.SUBJECTINDEX)) if not nr_subs: nr_subs = nr_subs_total - 1 assert (nr_subs < nr_subs_total) # initialize output structure; every measure gets one dict with # category numbers as keys and numpy-arrays as values intersub_scores = [] for measure in rang...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def lower_bound(fm, nr_subs = None, nr_imgs = None, scale_factor = 1): """ Compute the spatial bias lower bound for a fixmat. Input: fm : a fixmat instance nr_su...
nr_subs_total = len(np.unique(fm.SUBJECTINDEX)) if nr_subs is None: nr_subs = nr_subs_total - 1 assert (nr_subs < nr_subs_total) # initialize output structure; every measure gets one dict with # category numbers as keys and numpy-arrays as values sb_scores = [] for measure in range(...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def ind2sub(ind, dimensions): """ Calculates subscripts for indices into regularly spaced matrixes. """
# check that the index is within range if ind >= np.prod(dimensions): raise RuntimeError("ind2sub: index exceeds array size") cum_dims = list(dimensions) cum_dims.reverse() m = 1 mult = [] for d in cum_dims: m = m*d mult.append(m) mult.pop() mult.reverse() ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def sub2ind(indices, dimensions): """ An exemplary sub2ind implementation to create randomization scripts. This function calculates indices from subscripts into ...
# check that none of the indices exceeds the size of the array if any([i > j for i, j in zip(indices, dimensions)]): raise RuntimeError("sub2ind:an index exceeds its dimension's size") dims = list(dimensions) dims.append(1) dims.remove(dims[0]) dims.reverse() ind = list(indices) ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def RestoreTaskStoreFactory(store_class, chunk_size, restore_file, save_file): """ Restores a task store from file. """
intm_results = np.load(restore_file) intm = intm_results[intm_results.files[0]] idx = np.isnan(intm).flatten().nonzero()[0] partitions = math.ceil(len(idx) / float(chunk_size)) task_store = store_class(partitions, idx.tolist(), save_file) task_store.num_tasks = len(idx) # Also set up matric...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def xmlrpc_reschedule(self): """ Reschedule all running tasks. """
if not len(self.scheduled_tasks) == 0: self.reschedule = list(self.scheduled_tasks.items()) self.scheduled_tasks = {} return True
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def xmlrpc_task_done(self, result): """ Take the results of a computation and put it into the results list. """
(task_id, task_results) = result del self.scheduled_tasks[task_id] self.task_store.update_results(task_id, task_results) self.results += 1 return True
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def xmlrpc_save2file(self, filename): """ Save results and own state into file. """
savefile = open(filename,'wb') try: pickle.dump({'scheduled':self.scheduled_tasks, 'reschedule':self.reschedule},savefile) except pickle.PicklingError: return -1 savefile.close() return 1
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def run(self): """This function needs to be called to start the computation."""
(task_id, tasks) = self.server.get_task() self.task_store.from_dict(tasks) for (index, task) in self.task_store: result = self.compute(index, task) self.results.append(result) self.server.task_done((task_id, self.results))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def from_dict(self, description): """Configures the task store to be the task_store described in description"""
assert(self.ident == description['ident']) self.partitions = description['partitions'] self.indices = description['indices']
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def partition(self): """Partitions all tasks into groups of tasks. A group is represented by a task_store object that indexes a sub- set of tasks."""
step = int(math.ceil(self.num_tasks / float(self.partitions))) if self.indices == None: slice_ind = list(range(0, self.num_tasks, step)) for start in slice_ind: yield self.__class__(self.partitions, list(range(start, start + ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def fit3d(samples, e_x, e_y, e_z, remove_zeros = False, **kw): """Fits a 3D distribution with splines. Input: samples: Array Array of samples from a probability ...
height, width, depth = len(e_y)-1, len(e_x)-1, len(e_z)-1 (p_est, _) = np.histogramdd(samples, (e_x, e_y, e_z)) p_est = p_est/sum(p_est.flat) p_est = p_est.flatten() if remove_zeros: non_zero = ~(p_est == 0) else: non_zero = (p_est >= 0) basis = spline_base3d(width,hei...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def fit2d(samples,e_x, e_y, remove_zeros = False, p_est = None, **kw): """Fits a 2D distribution with splines. Input: samples: Matrix or list of arrays If matrix...
if p_est is None: height = len(e_y)-1 width = len(e_x)-1 (p_est, _) = np.histogramdd(samples, (e_x, e_y)) else: p_est = p_est.T width, height = p_est.shape # p_est contains x in dim 1 and y in dim 0 shape = p_est.shape p_est = (p_est/sum(p_est.flat)).resha...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def fit1d(samples, e, remove_zeros = False, **kw): """Fits a 1D distribution with splines. Input: samples: Array Array of samples from a probability distribution...
samples = samples[~np.isnan(samples)] length = len(e)-1 hist,_ = np.histogramdd(samples, (e,)) hist = hist/sum(hist) basis, knots = spline_base1d(length, marginal = hist, **kw) non_zero = hist>0 model = linear_model.BayesianRidge() if remove_zeros: model.fit(basis[non_zero, :], ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def knots_from_marginal(marginal, nr_knots, spline_order): """ Determines knot placement based on a marginal distribution. It places knots such that each knot co...
cumsum = np.cumsum(marginal) cumsum = cumsum/cumsum.max() borders = np.linspace(0,1,nr_knots) knot_placement = [0] + np.unique([np.where(cumsum>=b)[0][0] for b in borders[1:-1]]).tolist() +[len(marginal)-1] knots = augknt(knot_placement, spline_order) return knots
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def spline_base3d( width, height, depth, nr_knots_x = 10.0, nr_knots_y = 10.0, nr_knots_z=10, spline_order = 3, marginal_x = None, marginal_y = None, marginal_z =...
if not nr_knots_z < depth: raise RuntimeError("Too many knots for size of the base") basis2d, (knots_x, knots_y) = spline_base2d(height, width, nr_knots_x, nr_knots_y, spline_order, marginal_x, marginal_y) if marginal_z is not None: knots_z = knots_from_marginal(marginal_z, n...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def spline(x,knots,p,i=0.0): """Evaluates the ith spline basis given by knots on points in x"""
assert(p+1<len(knots)) return np.array([N(float(u),float(i),float(p),knots) for u in x])
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def augknt(knots,order): """Augment knot sequence such that some boundary conditions are met."""
a = [] [a.append(knots[0]) for t in range(0,order)] [a.append(k) for k in knots] [a.append(knots[-1]) for t in range(0,order)] return np.array(a)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def N(u,i,p,knots): """Compute Spline Basis Evaluates the spline basis of order p defined by knots at knot i and point u. """
if p == 0: if knots[i] < u and u <=knots[i+1]: return 1.0 else: return 0.0 else: try: k = (( float((u-knots[i]))/float((knots[i+p] - knots[i]) )) * N(u,i,p-1,knots)) except ZeroDivisionError: k = 0.0 tr...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def prediction_scores(prediction, fm, **kw): """ Evaluates a prediction against fixations in a fixmat with different measures. The default measures which are use...
if prediction == None: return [np.NaN for measure in scores] results = [] for measure in scores: (args, _, _, _) = inspect.getargspec(measure) if len(args)>2: # Filter dictionary, such that only the keys that are # expected by the measure are in it ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def kldiv_model(prediction, fm): """ wraps kldiv functionality for model evaluation input: prediction: 2D matrix the model salience map fm : fixmat Should be fil...
(_, r_x) = calc_resize_factor(prediction, fm.image_size) q = np.array(prediction, copy=True) q -= np.min(q.flatten()) q /= np.sum(q.flatten()) return kldiv(None, q, distp = fm, scale_factor = r_x)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def kldiv(p, q, distp = None, distq = None, scale_factor = 1): """ Computes the Kullback-Leibler divergence between two distributions. Parameters p : Matrix The ...
assert q != None or distq != None, "Either q or distq have to be given" assert p != None or distp != None, "Either p or distp have to be given" try: if p == None: p = compute_fdm(distp, scale_factor = scale_factor) if q == None: q = compute_fdm(distq, scale_factor =...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def kldiv_cs_model(prediction, fm): """ Computes Chao-Shen corrected KL-divergence between prediction and fdm made from fixations in fm. Parameters : prediction ...
# compute histogram of fixations needed for ChaoShen corrected kl-div # image category must exist (>-1) and image_size must be non-empty assert(len(fm.image_size) == 2 and (fm.image_size[0] > 0) and (fm.image_size[1] > 0)) assert(-1 not in fm.category) # check whether fixmat contains fixati...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def chao_shen(q): """ Computes some terms needed for the Chao-Shen KL correction. """
yx = q[q > 0] # remove bins with zero counts n = np.sum(yx) p = yx.astype(float)/n f1 = np.sum(yx == 1) # number of singletons in the sample if f1 == n: # avoid C == 0 f1 -= 1 C = 1 - (f1/n) # estimated coverage of the sample pa = C * p # coverage adjusted empirical frequencies ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def correlation_model(prediction, fm): """ wraps numpy.corrcoef functionality for model evaluation input: prediction: 2D Matrix the model salience map fm: fixmat...
(_, r_x) = calc_resize_factor(prediction, fm.image_size) fdm = compute_fdm(fm, scale_factor = r_x) return np.corrcoef(fdm.flatten(), prediction.flatten())[0,1]
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def nss_model(prediction, fm): """ wraps nss functionality for model evaluation input: prediction: 2D matrix the model salience map fm : fixmat Fixations that de...
(r_y, r_x) = calc_resize_factor(prediction, fm.image_size) fix = ((np.array(fm.y-1)*r_y).astype(int), (np.array(fm.x-1)*r_x).astype(int)) return nss(prediction, fix)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def nss(prediction, fix): """ Compute the normalized scanpath salience input: fix : list, l[0] contains y, l[1] contains x """
prediction = prediction - np.mean(prediction) prediction = prediction / np.std(prediction) return np.mean(prediction[fix[0], fix[1]])
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def roc_model(prediction, fm, ctr_loc = None, ctr_size = None): """ wraps roc functionality for model evaluation Parameters: prediction: 2D array the model salie...
# check if prediction is a valid numpy array assert type(prediction) == np.ndarray # check whether scaling preserved aspect ratio (r_y, r_x) = calc_resize_factor(prediction, fm.image_size) # read out values in the fdm at actual fixation locations # .astype(int) floors numbers in np.array y...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def fast_roc(actuals, controls): """ approximates the area under the roc curve for sets of actuals and controls. Uses all values appearing in actuals as threshol...
assert(type(actuals) is np.ndarray) assert(type(controls) is np.ndarray) actuals = np.ravel(actuals) controls = np.ravel(controls) if np.isnan(actuals).any(): raise RuntimeError('NaN found in actuals') if np.isnan(controls).any(): raise RuntimeError('NaN found in controls') ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def emd_model(prediction, fm): """ wraps emd functionality for model evaluation requires: OpenCV python bindings input: prediction: the model salience map fm : f...
(_, r_x) = calc_resize_factor(prediction, fm.image_size) gt = fixmat.compute_fdm(fm, scale_factor = r_x) return emd(prediction, gt)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def emd(prediction, ground_truth): """ Compute the Eart Movers Distance between prediction and model. This implementation uses opencv for doing the actual work. ...
import opencv if not (prediction.shape == ground_truth.shape): raise RuntimeError('Shapes of prediction and ground truth have' + ' to be equal. They are: %s, %s' %(str(prediction.shape), str(ground_truth.shape))) (x, y) = np.meshgrid(list(rang...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _get_parser(f): """ Gets the parser for the command f, if it not exists it creates a new one """
_COMMAND_GROUPS[f.__module__].load() if f.__name__ not in _COMMAND_GROUPS[f.__module__].parsers: parser = _COMMAND_GROUPS[f.__module__].parser_generator.add_parser(f.__name__, help=f.__doc__, description=f.__doc__) pars...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def discoverEndpoint(url, test_urls=True, headers={}, timeout=None, request=None, debug=False): """Discover any WebMention endpoint for a given URL. :param link:...
if test_urls: URLValidator(message='invalid URL')(url) # status, webmention endpointURL = None debugOutput = [] try: if request is not None: targetRequest = request else: targetRequest = requests.get(url, verify=False, headers=headers, timeout=timeou...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def indent_text(string, indent_level=2): """Indent every line of text in a newline-delimited string"""
indented_lines = [] indent_spaces = ' ' * indent_level for line in string.split('\n'): indented_lines.append(indent_spaces + line) return '\n'.join(indented_lines)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def download(url, target, headers=None, trackers=()): """Download a file using requests. This is like urllib.request.urlretrieve, but: - requests validates SSL c...
if headers is None: headers = {} headers.setdefault('user-agent', 'requests_download/'+__version__) r = requests.get(url, headers=headers, stream=True) r.raise_for_status() for t in trackers: t.on_start(r) with open(target, 'wb') as f: for chunk in r.iter_content(chunk...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def write(parsed_obj, spec=None, filename=None): """Writes an object created by `parse` to either a file or a bytearray. If the object doesn't end on a byte boun...
if not isinstance(parsed_obj, BreadStruct): raise ValueError( 'Object to write must be a structure created ' 'by bread.parse') if filename is not None: with open(filename, 'wb') as fp: parsed_obj._data_bits[:parsed_obj._length].tofile(fp) else: r...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def deploy_file(file_path, bucket): """ Uploads a file to an S3 bucket, as a public file. """
# Paths look like: # index.html # css/bootstrap.min.css logger.info("Deploying {0}".format(file_path)) # Upload the actual file to file_path k = Key(bucket) k.key = file_path try: k.set_contents_from_filename(file_path) k.set_acl('public-read') except socket.err...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def deploy(www_dir, bucket_name): """ Deploy to the configured S3 bucket. """
# Set up the connection to an S3 bucket. conn = boto.connect_s3() bucket = conn.get_bucket(bucket_name) # Deploy each changed file in www_dir os.chdir(www_dir) for root, dirs, files in os.walk('.'): for f in files: # Use full relative path. Normalize to remove dot. ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def has_changed_since_last_deploy(file_path, bucket): """ Checks if a file has changed since the last time it was deployed. :param file_path: Path to file which ...
msg = "Checking if {0} has changed since last deploy.".format(file_path) logger.debug(msg) with open(file_path) as f: data = f.read() file_md5 = hashlib.md5(data.encode('utf-8')).hexdigest() logger.debug("file_md5 is {0}".format(file_md5)) key = bucket.get_key(file_path) ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def main(): """ Entry point for the package, as defined in setup.py. """
# Log info and above to console logging.basicConfig( format='%(levelname)s: %(message)s', level=logging.INFO) # Get command line input/output arguments msg = 'Instantly deploy static HTML sites to S3 at the command line.' parser = argparse.ArgumentParser(description=msg) parser.add_ar...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def start_sikuli_process(self, port=None): """ This keyword is used to start sikuli java process. If library is inited with mode "OLD", sikuli java process is st...
if port is None or int(port) == 0: port = self._get_free_tcp_port() self.port = port start_retries = 0 started = False while start_retries < 5: try: self._start_sikuli_java_process() except RuntimeError as err: ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def EXPIRING_TOKEN_LIFESPAN(self): """ Return the allowed lifespan of a token as a TimeDelta object. Defaults to 30 days. """
try: val = settings.EXPIRING_TOKEN_LIFESPAN except AttributeError: val = timedelta(days=30) return val
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def expired(self): """Return boolean indicating token expiration."""
now = timezone.now() if self.created < now - token_settings.EXPIRING_TOKEN_LIFESPAN: return True return False
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def process(self): """ Store the actual process in _process. If it doesn't exist yet, create it. """
if hasattr(self, '_process'): return self._process else: self._process = self._get_process() return self._process
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _get_process(self): """ Create the process by running the specified command. """
command = self._get_command() return subprocess.Popen(command, bufsize=-1, close_fds=True, stdout=subprocess.PIPE, stdin=subprocess.PIPE)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def tokenize_list(self, text): """ Split a text into separate words. """
return [self.get_record_token(record) for record in self.analyze(text)]
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def is_stopword(self, text): """ Determine whether a single word is a stopword, or whether a short phrase is made entirely of stopwords, disregarding context. Us...
found_content_word = False for record in self.analyze(text): if not self.is_stopword_record(record): found_content_word = True break return not found_content_word