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Source code for tvb.contrib.scripts.utils.data_structures_utils

# -*- coding: utf-8 -*-
#
#
#  TheVirtualBrain-Contributors Package. This package holds simulator extensions.
#  See also http://www.thevirtualbrain.org
#
# (c) 2012-2022, Baycrest Centre for Geriatric Care ("Baycrest") and others
#
# This program is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software Foundation,
# either version 3 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.  See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with this
# program.  If not, see <http://www.gnu.org/licenses/>.
#
#
#   CITATION:
# When using The Virtual Brain for scientific publications, please cite it as follows:
#
#   Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
#   Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
#       The Virtual Brain: a simulator of primate brain network dynamics.
#   Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
#
#

"""
.. moduleauthor:: Dionysios Perdikis <Denis@tvb.invalid>
"""

import re
from collections import OrderedDict
import itertools
from copy import deepcopy
import numpy as np
from tvb.contrib.scripts.utils.log_error_utils import warning, raise_value_error, raise_import_error
from six import string_types
from tvb.basic.logger.builder import get_logger

logger = get_logger(__name__)


[docs]class CalculusConfig(object): # Normalization configuration WEIGHTS_NORM_PERCENT = 99 # If True a plot will be generated to choose the number of eigenvalues to keep INTERACTIVE_ELBOW_POINT = False MIN_SINGLE_VALUE = np.finfo("single").min MAX_SINGLE_VALUE = np.finfo("single").max MAX_INT_VALUE = np.iinfo(np.int64).max MIN_INT_VALUE = np.iinfo(np.int64).max
[docs]def is_numeric(value): return isinstance(value, (float, np.float, np.float64, np.float32, np.float16, np.float128, int, np.int, np.int0, np.int8, np.int16, np.int32, np.int64, complex, np.complex, np.complex64, np.complex128, np.complex256, np.long, np.number))
[docs]def is_integer(value): return isinstance(value, (int, np.int, np.int0, np.int8, np.int16, np.int32, np.int64))
[docs]def is_float(value): return isinstance(value, (float, np.float, np.float64, np.float32, np.float16, np.float128))
[docs]def vector2scalar(x): if not (isinstance(x, np.ndarray)): return x else: y = np.squeeze(x) if all(y.squeeze() == y[0]): return y[0] else: return reg_dict(x)
[docs]def list_of_strings_to_string(lstr, sep=","): result_str = lstr[0] for s in lstr[1:]: result_str += sep + s return result_str
[docs]def dict_str(d): s = "{" for key, value in d.items(): s += ("\n" + key + ": " + str(value)) s += "}" return s
[docs]def isequal_string(a, b, case_sensitive=False): if case_sensitive: return a == b else: try: return a.lower() == b.lower() except AttributeError: logger.warning("Case sensitive comparison!") return a == b
[docs]def split_string_text_numbers(ls): items = [] for s in ensure_list(ls): match = re.findall('(\d+|\D+)', s) if match: items.append(tuple(match[:2])) return items
[docs]def join_labels_indices_dict(d): out_list = [] for label, ind_list in sort_dict(d).items(): for ind in ind_list: out_list.append(label + "%d" % ind) return out_list
[docs]def construct_import_path(path, package=None): path = path.split(".py")[0] if isinstance(package, string_types): start = path.find(package) else: start = 0 return path[start:].replace("/", ".")
[docs]def format_all_numbers_in_strings(input_strings, num_integers=7, num_decimals=6): numeric_const_pattern = '[-+]? (?: (?: \d* \. \d+ ) | (?: \d+ \.? ) )(?: [Ee] [+-]? \d+ ) ?' rx = re.compile(numeric_const_pattern, re.VERBOSE) integer_format = "%0" + str(num_integers) + "d" num_total = num_integers + num_decimals + 1 float_format = "%0" + str(num_total) + "." + str(num_decimals) + "f" output_strings = [] for inp_str in ensure_list(input_strings): number_strings = rx.findall(inp_str) string_parts = rx.split(inp_str) out_str = "" for string_part, num_str in zip(string_parts, number_strings): try: out_str += string_part + integer_format % int(num_str) except: out_str += string_part + float_format % float(num_str) if len(string_parts) > len(number_strings): out_str += string_parts[-1] output_strings.append(out_str) if len(output_strings) == 1: return output_strings[0] return output_strings
[docs]def formal_repr(instance, attr_dict, sort_dict_flag=False): """ A formal string representation for an object. :param attr_dict: dictionary attribute_name: attribute_value :param instance: Instance to read class name from it """ class_name = instance.__class__.__name__ formal = class_name + "{" if sort_dict_flag: attr_dict = sort_dict(attr_dict) for key, val in attr_dict.items(): if isinstance(val, dict): formal += "\n" + key + "=[" for key2, val2 in val.items(): formal += "\n" + str(key2) + " = " + str(val2) formal += "]" else: formal += "\n" + str(key) + " = " + str(val) return formal + "}"
[docs]def obj_to_dict(obj): """ :param obj: Python object to introspect :return: dictionary after recursively taking obj fields and their values """ if obj is None: return obj if isinstance(obj, (str, int, float)): return obj if isinstance(obj, (np.float32,)): return float(obj) if isinstance(obj, (np.ndarray,)): return obj.tolist() if isinstance(obj, list): ret = [] for val in obj: ret.append(obj_to_dict(val)) return ret ret = {} for key in obj.__dict__: val = getattr(obj, key, None) ret[key] = obj_to_dict(val) return ret
[docs]def reg_dict(x, lbl=None, sort=None): """ :x: a list or np vector :lbl: a list or np vector of labels :return: dictionary """ if not (isinstance(x, (str, int, float, list, np.ndarray))): return x else: if not (isinstance(x, list)): x = np.squeeze(x) x_no = len(x) if not (isinstance(lbl, (list, np.ndarray))): lbl = np.repeat('', x_no) else: lbl = np.squeeze(lbl) labels_no = len(lbl) total_no = min(labels_no, x_no) if x_no <= labels_no: if sort == 'ascend': ind = np.argsort(x).tolist() elif sort == 'descend': ind = np.argsort(x) ind = ind[::-1].tolist() else: ind = range(x_no) else: ind = range(total_no) d = OrderedDict() for i in ind: d[str(i) + '.' + str(lbl[i])] = x[i] if labels_no > total_no: ind_lbl = np.delete(np.array(range(labels_no)), ind).tolist() for i in ind_lbl: d[str(i) + '.' + str(lbl[i])] = None if x_no > total_no: ind_x = np.delete(np.array(range(x_no)), ind).tolist() for i in ind_x: d[str(i) + '.'] = x[i] return d
[docs]def sort_dict(d): return OrderedDict(sorted(d.items(), key=lambda t: t[0]))
[docs]def switch_levels_of_dicts_of_dicts(d): keys = d.values()[0].keys() return {key: {k: d[k][key] for k in d if key in d[k]} for key in keys}
[docs]def dicts_of_lists(dictionary, n=1): for key, value in dictionary.items(): dictionary[key] = ensure_list(dictionary[key]) if len(dictionary[key]) == 1 and n > 1: dictionary[key] = dictionary[key] * n return dictionary
[docs]def iterable_to_dict(obj): d = OrderedDict() for ind, value in enumerate(obj): d["%02d" % ind] = value return d
[docs]def dict_to_list_or_tuple(dictionary, output_obj="list"): dictionary = sort_dict(dictionary) output = dictionary.values() if output_obj == "tuple": output = tuple(output) return output
[docs]def list_of_dicts_to_dict_of_tuples(lst): return dict(zip(lst[0], zip(*list([d.values() for d in lst]))))
[docs]def list_of_dicts_to_dict_of_lists(lst): d = list_of_dicts_to_dict_of_tuples(lst) for key, val in d.items(): d[key] = list(val) return d
[docs]def list_of_dicts_to_dicts_of_ndarrays(lst, shape=None): d = list_of_dicts_to_dict_of_tuples(ensure_list(lst)) if isinstance(shape, tuple): for key, val in d.items(): d[key] = np.reshape(np.stack(d[key]), shape) else: for key, val in d.items(): d[key] = np.stack(d[key]) for sh in d[key].shape[:0:-1]: if sh == 1: d[key] = np.squeeze(d[key], axis=-1) else: break return d
[docs]def arrays_of_dicts_to_dicts_of_ndarrays(arr): lst = arr.flatten().tolist() d = list_of_dicts_to_dicts_of_ndarrays(lst) for key, val in d.items(): d[key] = np.reshape(d[key], arr.shape) return d
[docs]def dicts_of_lists_to_lists_of_dicts(dictionary): return [dict(zip(dictionary, t)) for t in zip(*dictionary.values())]
[docs]def ensure_list(arg): if not (isinstance(arg, list)): try: # if iterable if isinstance(arg, (string_types, dict)): arg = [arg] elif hasattr(arg, "__iter__"): arg = list(arg) else: # if not iterable arg = [arg] except: # if not iterable arg = [arg] return arg
[docs]def ensure_string(arg): if not (isinstance(arg, string_types)): if arg is None: return "" else: return ensure_list(arg)[0] else: return arg
[docs]def flatten_list(lin, sort=False, recursive=False): lout = [] for sublist in lin: if recursive and isinstance(sublist, (list, tuple)): temp = flatten_list(list(sublist)) else: temp = [sublist] for item in temp: lout.append(item) if sort: lout.sort() return lout
[docs]def flatten_tuple(t, sort=False, recursive=True): return tuple(flatten_list(list(t), sort, recursive))
[docs]def extract_integer_intervals(iterable, print=False): def generator(iterable): iterable = sorted(set(iterable)) for key, group in itertools.groupby(enumerate(iterable), lambda t: t[1] - t[0]): group = list(group) yield [group[0][1], group[-1][1]] if print: output = "" for element in generator(iterable): if element[0] == element[1]: output += "%d, " % element[0] else: output += "%d...%d, " % tuple(element) output = output[:-2] else: output = [] for element in generator(iterable): if element[0] == element[1]: output.append([element[0]]) else: output.append(element) return output
[docs]def set_list_item_by_reference_safely(ind, item, lst): while ind >= len(lst): lst.append(None) lst.__setitem__(ind, item)
[docs]def get_list_or_tuple_item_safely(obj, key): try: return obj[int(key)] except: return None
[docs]def delete_list_items_by_indices(lin, inds, start_ind=0): lout = [] for ind, l in enumerate(lin): if ind + start_ind not in inds: lout.append(l) return lout
[docs]def delete_list_items_by_values(lin, values): lout = [] for l in lin: if l not in values: lout.append(l) return lout
[docs]def rotate_n_list_elements(lst, n): lst = ensure_list(lst) n_lst = len(lst) if n_lst != n and n_lst != 0: if n_lst == 1: lst *= n elif n_lst > n: lst = lst[:n] else: old_lst = list(lst) while n_lst < n: lst += old_lst[0] old_lst = old_lst[1:] + old_lst[:1] return lst
[docs]def linear_index_to_coordinate_tuples(linear_index, shape): if len(linear_index) > 0: coordinates_tuple = np.unravel_index(linear_index, shape) return zip(*[ca.flatten().tolist() for ca in coordinates_tuple]) else: return []
[docs]def find_labels_inds(labels, keys, modefun="find", two_way_search=False, break_after=np.iinfo(np.int64).max): if isequal_string(modefun, "equal"): modefun = lambda x, y: isequal_string(x, y) else: if two_way_search: modefun = lambda x, y: (x.find(y) >= 0) or (y.find(x) >= 0) else: modefun = lambda x, y: x.find(y) >= 0 inds = [] keys = ensure_list(keys) labels = ensure_list(labels) counts = 0 for key in keys: for label in labels: if modefun(label, key): inds.append(labels.index(label)) counts += 1 if counts >= break_after: return inds return inds
[docs]def extract_dict_stringkeys(d, keys, modefun="find", two_way_search=False, break_after=CalculusConfig.MAX_INT_VALUE, remove=False): # TODO: test that it works after modifying with find_labels_inds if remove: out_dict = deepcopy(d) else: out_dict = {} inds_found = find_labels_inds(d.keys(), keys, modefun, two_way_search, break_after) for ikey, (key, value) in enumerate(d.items()): if ikey in inds_found: if remove: del out_dict[key] else: out_dict.update({key: value}) return out_dict
[docs]def get_val_key_for_first_keymatch_in_dict(name, pkeys, **kwargs): pkeys += ["_".join([name, pkey]) for pkey in pkeys] temp = extract_dict_stringkeys(kwargs, pkeys, modefun="equal", break_after=1) if len(temp) > 0: return temp.values()[0], temp.keys()[0].split("_")[-1] else: return None, None
[docs]def labels_to_inds(labels, target_labels): if isinstance(target_labels, string_types): return_single_element = True target_labels = ensure_list(target_labels) else: target_labels = list(target_labels) return_single_element = False inds = [] for lbl in target_labels: inds.append(labels.index(lbl)) if return_single_element: # if there was only one label string input return inds[0] else: return inds
[docs]def generate_region_labels(n_regions, labels=[], str=". ", numbering=True, numbers=[]): if len(numbers) != n_regions: numbers = list(range(n_regions)) if len(labels) == n_regions: if numbering: return np.array([str.join(["%d", "%s"]) % tuple(l) for l in zip(numbers, labels)]) else: return np.array(labels) else: return np.array(["%d" % l for l in numbers])
[docs]def monopolar_to_bipolar(labels, indices=None, data=None): if indices is None: indices = range(len(labels)) bipolar_lbls = [] bipolar_inds = [[], []] for ind in range(len(indices) - 1): iS1 = indices[ind] iS2 = indices[ind + 1] if (labels[iS1][0] == labels[iS2][0]) and \ int(re.findall(r'\d+', labels[iS1])[0]) == \ int(re.findall(r'\d+', labels[iS2])[0]) - 1: bipolar_lbls.append(labels[iS1] + "-" + labels[iS2]) bipolar_inds[0].append(iS1) bipolar_inds[1].append(iS2) if isinstance(data, np.ndarray): data = data[bipolar_inds[0]] - data[bipolar_inds[1]] return bipolar_lbls, bipolar_inds, data else: return bipolar_lbls, bipolar_inds
[docs]def where(condition, one, two): if np.any(condition): return one else: return two # This function is meant to confirm that two objects assumingly of the same type are equal, i.e., identical
[docs]def assert_equal_objects(obj1, obj2, attributes_dict=None, logger=None): def print_not_equal_message(attr, field1, field2, logger): # logger.error("\n\nValueError: Original and read object field "+ attr + " not equal!") # raise_value_error("\n\nOriginal and read object field " + attr + " not equal!") warning("Original and read object field " + attr + " not equal!" + "\nOriginal field:\n" + str(field1) + "\nRead object field:\n" + str(field2), logger) if isinstance(obj1, dict): get_field1 = lambda obj, key: obj[key] if not (isinstance(attributes_dict, dict)): attributes_dict = dict() for key in obj1.keys(): attributes_dict.update({key: key}) elif isinstance(obj1, (list, tuple)): get_field1 = lambda obj, key: get_list_or_tuple_item_safely(obj, key) indices = range(len(obj1)) attributes_dict = dict(zip([str(ind) for ind in indices], indices)) else: get_field1 = lambda obj, attribute: getattr(obj, attribute) if not (isinstance(attributes_dict, dict)): attributes_dict = dict() for key in obj1.__dict__.keys(): attributes_dict.update({key: key}) if isinstance(obj2, dict): get_field2 = lambda obj, key: obj.get(key, None) elif isinstance(obj2, (list, tuple)): get_field2 = lambda obj, key: get_list_or_tuple_item_safely(obj, key) else: get_field2 = lambda obj, attribute: getattr(obj, attribute, None) equal = True for attribute in attributes_dict: # print attributes_dict[attribute] field1 = get_field1(obj1, attributes_dict[attribute]) field2 = get_field2(obj2, attributes_dict[attribute]) try: # TODO: a better hack for the stupid case of an ndarray of a string, such as model.zmode or pmode # For non numeric types if isinstance(field1, string_types) or isinstance(field1, list) or isinstance(field1, dict) \ or (isinstance(field1, np.ndarray) and field1.dtype.kind in 'OSU'): if np.any(field1 != field2): print_not_equal_message(attributes_dict[attribute], field1, field2, logger) equal = False # For numeric numpy arrays: elif isinstance(field1, np.ndarray) and not field1.dtype.kind in 'OSU': # TODO: handle better accuracy differences, empty matrices and complex numbers... if field1.shape != field2.shape: print_not_equal_message(attributes_dict[attribute], field1, field2, logger) equal = False elif np.any(np.float32(field1) - np.float32(field2) > 0): print_not_equal_message(attributes_dict[attribute], field1, field2, logger) equal = False # For numeric scalar types elif is_numeric(field1): if np.float32(field1) - np.float32(field2) > 0: print_not_equal_message(attributes_dict[attribute], field1, field2, logger) equal = False else: equal = assert_equal_objects(field1, field2, logger=logger) except: try: warning("Comparing str(objects) for field " + str(attributes_dict[attribute]) + " because there was an error!", logger) if np.any(str(field1) != str(field2)): print_not_equal_message(attributes_dict[attribute], field1, field2, logger) equal = False except: raise_value_error("ValueError: Something went wrong when trying to compare " + str(attributes_dict[attribute]) + " !", logger) if equal: return True else: return False
[docs]def shape_to_size(shape): shape = np.array(shape) shape = shape[shape > 0] return np.int(np.max([shape.prod(), 1]))
[docs]def shape_to_ndim(shape, squeeze=False): if squeeze: shape = filter(lambda x: not (np.any(np.in1d(x, [0, 1]))), list(shape)) return len(shape)
[docs]def linspace_broadcast(start, stop, num_steps, maxdims=3): x_star = np.linspace(0, 1, num_steps) dims = 0 x = None while x is None and dims < maxdims: try: x = (x_star[:, None] * (stop - start) + start) except: x_star = x_star[:, np.newaxis] dims = dims + 1 return x
[docs]def squeeze_array_to_scalar(arr): arr = np.array(arr) if arr.size == 1: return arr elif np.all(arr == arr[0]): return arr[0] else: return arr
[docs]def assert_arrays(params, shape=None, transpose=False): # type: (object, object) -> object if shape is None or \ not (isinstance(shape, tuple) and len(shape) in range(3) and np.all([isinstance(s, (int, np.int)) for s in shape])): shape = None shapes = [] # list of all unique shapes n_shapes = [] # list of all unique shapes' frequencies size = 0 # initial shape else: size = shape_to_size(shape) for ip in range(len(params)): # Convert all accepted types to np arrays: if isinstance(params[ip], np.ndarray): pass elif isinstance(params[ip], (list, tuple)): # assuming a list or tuple of symbols... params[ip] = np.array(params[ip]).astype(type(params[ip][0])) elif is_numeric(params[ip]): params[ip] = np.array(params[ip]) else: try: import sympy except: raise_import_error("sympy import failed") if isinstance(params[ip], tuple(sympy.core.all_classes)): params[ip] = np.array(params[ip]) else: raise_value_error("Input " + str(params[ip]) + " of type " + str(type(params[ip])) + " is not numeric, " "of type np.ndarray, nor Symbol") if shape is None: # Only one size > 1 is acceptable if params[ip].size != size: if size > 1 and params[ip].size > 1: raise_value_error("Inputs are of at least two distinct sizes > 1") elif params[ip].size > size: size = params[ip].size # Construct a kind of histogram of all different shapes of the inputs: ind = np.array([(x == params[ip].shape) for x in shapes]) if np.any(ind): ind = np.where(ind)[0] # TODO: handle this properly n_shapes[int(ind)] += 1 else: shapes.append(params[ip].shape) n_shapes.append(1) else: if params[ip].size > size: raise_value_error("At least one input is of a greater size than the one given!") if shape is None: # Keep only shapes of the correct size ind = np.array([shape_to_size(s) == size for s in shapes]) shapes = np.array(shapes)[ind] n_shapes = np.array(n_shapes)[ind] # Find the most frequent shape ind = np.argmax(n_shapes) shape = tuple(shapes[ind]) if transpose and len(shape) > 1: if (transpose is "horizontal" or "row" and shape[0] > shape[1]) or \ (transpose is "vertical" or "column" and shape[0] < shape[1]): shape = list(shape) temp = shape[1] shape[1] = shape[0] shape[0] = temp shape = tuple(shape) # Now reshape or tile when necessary for ip in range(len(params)): try: if params[ip].shape != shape: if params[ip].size in [0, 1]: params[ip] = np.tile(params[ip], shape) else: params[ip] = np.reshape(params[ip], shape) except: # TODO: maybe make this an explicit message logger.info("\n\nWTF?") if len(params) == 1: return params[0] else: return tuple(params)
[docs]def make_float(x, precision="64"): if isinstance(x, np.ndarray): if isequal_string(precision, "64"): return x.astype(np.float64) elif isequal_string(precision, "32"): return x.astype(np.float32) else: return x.astype(np.float) else: if isequal_string(precision, "64"): return np.float64(x) elif isequal_string(precision, "32"): np.float32(x) else: return np.float(x)
[docs]def make_int(x, precision="64"): if isinstance(x, np.ndarray): if isequal_string(precision, "64"): return x.astype(np.int64) elif isequal_string(precision, "32"): return x.astype(np.int32) else: return x.astype(np.int) else: if isequal_string(precision, "64"): return np.int64(x) elif isequal_string(precision, "32"): np.int32(x) else: return np.int(x)
[docs]def copy_object_attributes(obj1, obj2, attr1, attr2=None, deep_copy=False, check_none=False): attr1 = ensure_list(attr1) if attr2 is None: attr2 = attr1 else: attr2 = ensure_list(attr2) if deep_copy: fcopy = lambda a1, a2: setattr(obj2, a2, deepcopy(getattr(obj1, a1))) else: fcopy = lambda a1, a2: setattr(obj2, a2, getattr(obj1, a1)) if check_none: for a1, a2 in zip(attr1, attr2): if getattr(obj2, a2) is None: fcopy(a1, a2) else: for a1, a2 in zip(attr1, attr2): fcopy(a1, a2) return obj2
[docs]def sort_events_by_x_and_y(events, x="senders", y="times", filter_x=None, filter_y=None, exclude_x=[], exclude_y=[]): xs = np.array(flatten_list(events[x])) if filter_x is None: xlabels = np.unique(xs).tolist() else: xlabels = np.unique(flatten_list(filter_x)).tolist() for xlbl in exclude_x: try: xlabels.remove(xlbl) except: pass ys = flatten_list(events[y]) if filter_y is not None: ys = [yy for yy in ys if yy in flatten_list(filter_y)] for yy in exclude_y: try: ys.remove(yy) except: pass ys = np.array(ys) sorted_events = OrderedDict() for xlbl in xlabels: sorted_events[xlbl] = np.sort(ys[xs == xlbl]) return sorted_events
[docs]def data_xarray_from_continuous_events(events, times, senders, variables=[], filter_senders=None, exclude_senders=[], name=None, dims_names=["Variable", "Neuron", "Time"]): unique_times = np.unique(times).tolist() if filter_senders is None: filter_senders = np.unique(senders).tolist() else: filter_senders = np.unique(flatten_list(filter_senders)).tolist() exclude_senders = ensure_list(exclude_senders) for sender in exclude_senders: filter_senders.remove(sender) variables = ensure_list(variables) if len(variables) is None: variables = list(events.keys()) dims_names = ensure_list(dims_names) coords = OrderedDict() coords[dims_names[0]] = variables coords[dims_names[1]] = filter_senders coords[dims_names[2]] = unique_times n_senders = len(filter_senders) n_times = len(unique_times) data = np.empty((len(variables), n_senders, n_times)) last_time = times[0] i_time = unique_times.index(last_time) i_sender = -1 for id, (time, sender) in enumerate(zip(times, senders)): # Try best guess of next sender: i_sender += 1 if i_sender >= n_senders: i_sender = 0 if filter_senders[i_sender] != sender: try: i_sender = filter_senders.index(sender) except: break # This sender is not one of the chosen filter_senders if time != last_time: last_time = time # Try best guess of next time index: i_time += 1 if i_time >= n_times: i_time = n_times - 1 if time != unique_times[i_time]: i_time = unique_times.index(time) for i_var, var in enumerate(variables): data[i_var, i_sender, i_time] = events[var][id] try: from xarray import DataArray return DataArray(data, dims=list(coords.keys()), coords=coords, name=name) except: # Return a dictionary as a plan B' return {"data": data, "dims": list(coords.keys()), "coords": coords, "name": name}
[docs]def concatenate_heterogeneous_DataArrays(data, concat_dim_name, data_keys=None, name=None, fill_value=np.nan, transpose_dims=None): from pandas import Series from xarray import concat from pandas import Index if isinstance(data, (dict, Series)): if data_keys is None: data_keys = ensure_list(data.keys()) if isinstance(data, dict): # dict data = ensure_list(data.values()) else: # pd.Series if name is None: name = data.name data = ensure_list(data.values) data = concat(data, Index(data_keys, name=concat_dim_name), fill_value=fill_value) data.name = name if transpose_dims: data = data.transpose(*transpose_dims) return data
[docs]def property_to_fun(property): if hasattr(property, "__call__"): return property else: return lambda *args, **kwargs: property
[docs]def series_loop_generator(ser, inds_or_keys=None): index = list(ser.index) if inds_or_keys is None: inds_or_keys = index else: inds_or_keys = ensure_list(inds_or_keys) for index_or_key in inds_or_keys: if isinstance(index_or_key, string_types): lbl = index_or_key id = index.index(index_or_key) else: lbl = index[index_or_key] id = index_or_key pop = ser[index_or_key] yield id, lbl, pop