Source code for tvb.core.adapters.arguments_serialisation

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This is a framework helper module.
Some framework datatypes have functions that will be called via http by the TVB GUI.
These functions will receive some arguments as strings and return json serializable structures usually dicts.
This module contains functions to parse those strings and construct those responses.

.. moduleauthor:: Mihai Andrei <>
import numpy
from tvb.basic import exceptions

[docs]def parse_slice(slice_string): """ Parse a slicing expression >>> parse_slice("::1, :") (slice(None, None, 1), slice(None, None, None)) >>> parse_slice("2") 2 >>> parse_slice("[2]") 2 """ ret = [] slice_string = slice_string.replace(' ', '') # remove surrounding brackets if any if slice_string[0] == '[' and slice_string[-1] == ']': slice_string = slice_string[1:-1] for d in slice_string.split(','): frags = d.split(':') if len(frags) == 1: if frags[0] == '': ret.append(slice(None)) else: ret.append(int(frags[0])) elif len(frags) <= 3: frags = [int(d) if d else None for d in frags] ret.append(slice(*frags)) else: raise ValueError('invalid slice') if len(ret) > 1: return tuple(ret) else: return ret[0]
[docs]def slice_str(slice_or_tuple): """ >>> slice_str(slice(1, None, 2)) '1::2' >>> slice_str((slice(None, None, 2), slice(None), 4)) '::2, :, 4' Does not handle ... yet """ def sl_str(s): if isinstance(s, slice): if s.start is s.step is None: return '%s' % (s.stop if s.stop is not None else ':') r = '%s:%s' % (s.start or '', s.stop or '') if s.step is not None: r += ':%d' % s.step return r else: return str(int(s)) if isinstance(slice_or_tuple, tuple): return '[' + ', '.join(sl_str(s) for s in slice_or_tuple) + ']' else: return '[' + sl_str(slice_or_tuple) + ']'
[docs]def preprocess_space_parameters(x, y, z, max_x, max_y, max_z): """ Covert ajax call parameters into numbers and validate them. :param x: coordinate :param y: coordinate :param z: coordinate that will be reversed :param max_x: maximum x accepted value :param max_y: maximum y accepted value :param max_z: maximum z accepted value :return: (x, y, z) as integers, Z reversed """ x, y, z = int(x), int(y), int(z) if not 0 <= x <= max_x or not 0 <= y <= max_y or not 0 <= z <= max_z: msg = "Coordinates out of boundaries: [x,y,z] = [{0}, {1}, {2}]".format(x, y, z) raise exceptions.ValidationException(msg) # Reverse Z z = max_z - z - 1 return x, y, z
[docs]def preprocess_time_parameters(t1, t2, time_length): """ Covert ajax call parameters into numbers and validate them. :param t1: start time :param t2: end time :param time_length: maximum time length in current TS :return: (t1, t2, t2-t1) as numbers """ from_idx = int(t1) to_idx = int(t2) if not 0 <= from_idx < to_idx <= time_length: msg = "Time indexes out of boundaries: from {0} to {1}".format(from_idx, to_idx) raise exceptions.ValidationException(msg) current_time_line = max(to_idx - from_idx, 1) return from_idx, to_idx, current_time_line
[docs]def postprocess_voxel_ts(ts, slices, background_value=None, background_min=None, background_max=None, label=None): """ Read TimeLine from TS and prepare the result for TSVolumeViewer. :param ts: TS instance, with read_data_slice method :param slices: slices for reading from H5 :return: A complex dictionary with information about current voxel. """ if background_value is not None: time_line = background_value else: time_line = ts.read_data_slice(slices).flatten() result = dict(data=time_line.tolist(), min=background_min or float(min(time_line)), max=background_max or float(max(time_line)), mean=float(numpy.mean(time_line)), median=float(numpy.median(time_line)), variance=float(numpy.var(time_line)), deviation=float(numpy.std(time_line)), label=label) return result