pyGSTi 0.9.12.1__cp38-cp38-win_amd64.whl → 0.9.13__cp38-cp38-win_amd64.whl

pygsti/extras/rb/simulate.py

@@ -1,1020 +0,0 @@
-""" Clifford circuits with Pauli errors simulation functions """
-#***************************************************************************************************
-# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
-# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
-# in this software.
-# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except
-# in compliance with the License.  You may obtain a copy of the License at
-# http://www.apache.org/licenses/LICENSE-2.0 or in the LICENSE file in the root pyGSTi directory.
-#***************************************************************************************************
-
-import os as _os
-import time as _time
-
-import numpy as _np
-
-from pygsti.baseobjs.label import Label as _Lbl
-from pygsti.data.dataset import DataSet as _DataSet
-from pygsti.tools import symplectic as _symp
-
-#from . import sample as _samp
-_samp = None  # MOVED - and this module is deprecated & broken now, so just set to None
-
-
-def random_paulierror_in_chp(q):
-    """
-    todo.
-    """
-    i = _np.random.randint(0, 3)
-
-    if i == 0:
-        return ('p ' + str(q) + '\n') * 2
-
-    elif i == 1:
-        return 'h ' + str(q) + '\n' + ('p ' + str(q) + '\n') * 2 + 'h ' + str(q) + '\n'
-
-    else:
-        return ('p ' + str(q) + '\n') * 2 + 'h ' + str(q) + '\n' + ('p ' + str(q) + '\n') * 2 + 'h ' + str(q) + '\n'
-
-
-def random_pauli_in_chp(q):
-    """
-    todo.
-    """
-    i = _np.random.randint(0, 4)
-
-    if i == 0:
-        return ''
-
-    elif i == 1:
-        return ('p ' + str(q) + '\n') * 2
-
-    elif i == 2:
-        return 'h ' + str(q) + '\n' + ('p ' + str(q) + '\n') * 2 + 'h ' + str(q) + '\n'
-
-    else:
-        return ('p ' + str(q) + '\n') * 2 + 'h ' + str(q) + '\n' + ('p ' + str(q) + '\n') * 2 + 'h ' + str(q) + '\n'
-
-
-def stdgate_to_chp(gate, chpqubits):
-    """
-    todo
-    Converts any of the standard Clifford gates to a chp string.
-    """
-    gatestr = str(gate).split(':')
-    name = gatestr[0]
-    qubits = [chpqubits[q] for q in gatestr[1:]]
-
-    if name == 'Gi':
-        return ''
-
-    elif name == 'Gxpi':
-        s = 'h ' + str(qubits[0]) + '\n'
-        s += ('p ' + str(qubits[0]) + '\n') * 2
-        s += 'h ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gypi':
-        s = ('p ' + str(qubits[0]) + '\n') * 2
-        s += 'h ' + str(qubits[0]) + '\n'
-        s += ('p ' + str(qubits[0]) + '\n') * 2
-        s += 'h ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gzpi':
-        return ('p ' + str(qubits[0]) + '\n') * 2
-
-    elif name == 'Gxpi2':
-        s = 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gxmpi2':
-        s = 'h ' + str(qubits[0]) + '\n'
-        s += ('p ' + str(qubits[0]) + '\n') * 3
-        s += 'h ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gzpi2' or name == 'Gp':
-        return 'p ' + str(qubits[0]) + '\n'
-
-    elif name == 'Gzmpi2' or name == 'Gpdag':
-        return ('p ' + str(qubits[0]) + '\n') * 3
-
-    elif name == 'Gh':
-        return ('h ' + str(qubits[0]) + '\n')
-
-    elif name == 'Gc0':
-        return ''
-
-    elif name == 'Gc1':
-        s = 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc2':
-        s = 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc3':
-        s = 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc4':
-        s = 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc5':
-        s = 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc6':
-        s = 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc7':
-        s = 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc8':
-        s = 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc9':
-        s = 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc10':
-        s = 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc11':
-        s = 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc12':
-        s = 'h ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc13':
-        s = 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc14':
-        s = 'p ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc15':
-        s = 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc16':
-        s = 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc17':
-        s = 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc18':
-        s = 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc19':
-        s = 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc20':
-        s = 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc21':
-        s = 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc22':
-        s = 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'h ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gc23':
-        s = 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        s += 'p ' + str(qubits[0]) + '\n'
-        return s
-
-    elif name == 'Gcnot':
-        return 'c ' + str(qubits[0]) + ' ' + str(qubits[1]) + '\n'
-
-    elif name == 'Gcphase':
-        s = 'h ' + str(qubits[1]) + '\n'
-        s += 'c ' + str(qubits[0]) + ' ' + str(qubits[1]) + '\n'
-        s = 'h ' + str(qubits[1]) + '\n'
-        return s
-
-    else:
-        raise ValueError("{} is an unknown gate! You must make your own `gateinchp` function!".format(gate))
-
-
-class IndDepolErrorModel(object):
-    """
-    todo
-
-    """
-
-    def __init__(self, gate_errors, readout_errors):
-        """
-        todo
-
-        """
-        self.gate_errors = gate_errors
-        self.readout_errors = readout_errors
-
-    def layer_uniform_pauli_probability(self, layer, qubitorder):
-        """
-        todo.
-
-        """
-        if len(layer) > 0:
-            return 1 - _np.prod([1 - _np.array([4 * self.gate_errors[gate].get(q, 0) / 3
-                                                for q in qubitorder]) for gate in layer], axis=0)
-        else:
-            return _np.zeros(len(qubitorder), float)
-
-    def readout_uniform_pauli_probability(self, qubitorder):
-        """
-        todo
-
-        """
-        return 1 - _np.prod([1 - _np.array([4 * self.readout_errors[q1].get(q2, 0) / 3
-                                            for q2 in qubitorder]) for q1 in qubitorder], axis=0)
-
-
-def depolarizing_errors_circuit_simulator(circuitlist, shots, errormodel, gate_to_chp=None,
-                                          aux_info_list=None, collision_action='keepseparate',
-                                          outdir='', perge_chp_files=True, returnds=True,
-                                          verbosity=1):
-    """
-    todo.
-
-    """
-    if returnds:
-        ds = _DataSet(collision_action=collision_action)
-    else:
-        ds = []
-    assert(_os.path.isfile("chp")), "This simulator uses the chp.c code.\n" + \
-        "It must be compiled to an executable called `chp` and situated in this folder!"
-
-    try:
-        _os.mkdir(outdir)
-        if perge_chp_files:
-            perge_dir = True
-        else:
-            perge_dir = False
-    except:
-        perge_dir = False
-        pass
-
-    time0 = _time.time()
-
-    if gate_to_chp is None: gate_to_chp = stdgate_to_chp
-
-    percentdone = 0
-    for cind, circuit in enumerate(circuitlist):
-        print(cind)
-        time1 = _time.time()
-
-        if verbosity > 0:
-            if verbosity > 1:
-                print("{0:.2f}".format(cind / len(circuitlist)), end=' ')
-            else:
-                if int(_np.floor(cind / len(circuitlist))) > percentdone:
-                    percentdone += 1
-                    print("  - Simulation {} percent complete.".format(percentdone))
-
-        n = circuit.num_lines
-        depth = circuit.depth
-
-        # Set up the CHP qubit labels: could be different CHP labels for each circuit.
-        aschpq = {label: str(i) for i, label in enumerate(circuit.line_labels)}
-
-        # A list containing the CHP string for each error-free circuit layer.
-        perfect_chpstrings = [''.join([gate_to_chp(gate, aschpq) for gate in circuit.layer(i)])
-                              for i in range(depth)]
-
-        # Find the probability of error in each circuit layer.
-        errorprobs = [errormodel.layer_uniform_pauli_probability(circuit.layer(lind), circuit.line_labels)
-                      for lind in range(circuit.depth)]
-        # Add measurement error at the end
-        errorprobs.append(errormodel.readout_uniform_pauli_probability(circuit.line_labels))
-
-        time2 = _time.time()
-
-        for sample in range(shots):
-
-            # Sample errors for the circuit. Note that if 1 then a uniformly random Pauli is sampled, so
-            # there is a 1/4 chance of no error even if this is 1. This is correct.
-            #print(errorprobs)
-            haserror = [_np.random.binomial(1, ep) for ep in errorprobs]
-            #for lind in range(depth):
-            #    print('-', lind)
-            #    print(haserror[lind])
-            #    print([random_pauli_in_chp(q) for q in range(n) if haserror[lind][q] == 1])
-            # Construct the CHP string for each error layer.
-            error_chpstrings = [''.join([''] + [random_pauli_in_chp(q) for q in range(n) if haserror[lind][q] == 1])
-                                for lind in range(depth)]
-
-            # Interleave the perfect and error CHP strings and then join.
-            chpstring = '#\n' + ''.join([val for pair in zip(perfect_chpstrings, error_chpstrings) for val in pair])
-
-            # Add the readout error
-            chpstring += ''.join([''] + [random_pauli_in_chp(q) for q in range(n) if haserror[depth][q] == 1])
-
-            # Add a measurement on all the qubits.
-            chpstring += '\n'.join(['m ' + aschpq[q] for q in circuit.line_labels]) + '\n'
-            #print(chpstring)
-            with open(outdir + "/circuit-{}-instance-{}.chp".format(cind, sample), 'w') as f:
-                f.write(chpstring)
-
-            # Run CHP on this file.
-            _os.system("./chp " + outdir + "/circuit-{}-instance-{}.chp > ".format(cind, sample)
-                       + outdir + "/circuit-{}-instance-{}-out.txt".format(cind, sample))
-
-        countdict = {}
-        for sample in range(shots):
-
-            with open(outdir + "/circuit-{}-instance-{}-out.txt".format(cind, sample), 'r') as f:
-                #print(cind,sample)
-                outasdict = {}
-                for i, line in enumerate(f):
-                    if i > 3:
-                        line = line.strip(' \n')
-                        line = line.split(' ')
-                        # todo : this assumes definite outcome circuits, so fix that
-                        # by instead counting forward from the start of the line.
-                        outasdict[circuit.line_labels[int(line[-2][:-1])]] = line[-1]
-
-                #print(outasdict)
-                bitstring = ''.join([outasdict[q] for q in circuit.line_labels])
-
-            if perge_chp_files:
-                _os.system("rm " + outdir + "/circuit-{}-instance-{}.chp".format(cind, sample))
-                _os.system("rm " + outdir + "/circuit-{}-instance-{}-out.txt".format(cind, sample))
-
-            try:
-                countdict[bitstring] += 1
-            except:
-                countdict[bitstring] = 1
-
-            if aux_info_list is not None:
-                aux = aux_info_list[cind]
-            else:
-                aux = None
-
-        if returnds:
-            ds.add_count_dict(circuit, countdict, record_zero_counts=False, aux=aux)
-        else:
-            ds.append(countdict)
-
-        time3 = _time.time()
-
-        if verbosity > 1:
-            print("({0:.2f}, {1:.2f})".format(time2 - time1, time3 - time2), end=', ')
-    print("Total time: {0:.2f})".format(time3 - time0))
-
-    if perge_dir:
-        _os.system("rmdir " + outdir)
-
-    return ds
-
-
-def circuit_simulator_for_tensored_independent_pauli_errors(circuit, pspec, errormodel, counts,
-                                                            alloutcomes=False, idle1q_placeholder='I'):
-    """
-    A Clifford circuit simulator for an error model whereby each gate in the circuit induces independent Pauli
-    errors on some or all of the qubits, with user-specified error probabilities that can vary between gate
-    and between Pauli. State preparation and measurements errors are restricted to bit-flip errors on the output.
-
-    This simulator is a stochastic-unravelling simulator that uses an efficient-in-qubit-number representation
-    of the action of Clifford gates on Paulis. Specifically, it samples Pauli errors according to the error
-    statistics provided, and propogates them through the layers of Clifford gates in the circuit using the
-    conjugation action of the Cliffords on Paulis (as represented by 2n X 2n symplectic matrices for n qubits).
-    This is repeated for the number of counts (`counts`) requested. So, this function takes a time to run that
-    scales as (counts * n^2 * circuit depth). Therefore, this method will be slower than the pyGSTi density-matrix
-    simulators at low qubit number and high `counts`.
-
-    Parameters
-    ----------
-    circuit : Circuit
-        The circuit to simulate. It should only contain gates that are also contained  within the provided
-        QubitProcessorSpec `pspec` and are Clifford gates.
-
-    pspec : QubitProcessorSpec
-        The QubitProcessorSpec that defines the device. The Clifford model in QubitProcessorSpec should contain all of
-        the gates that are in the circuit.
-
-    errormodel : dict
-        A dictionary defining the error model. This errormodel should have keys that are Label objects (the
-        elements of the circuit). The values for a particular Label is an (n,4) numpy array of floats, that
-        encodes the errors caused by the gate specified by that Label. The (i,j) value in the array is the
-        probability that this gate is followed by Pauli i where Pauli 0 = identity, Pauli 1 = X, Pauli 2 = Y
-        and Pauli 3 = Z. So, if the arrray is [1.,0.,0.,0.] in every row then there is no errors, if it is
-        [1-p,p/3,p/3,p/3] in row j then there is equal probability of each Pauli error on qubit j with an
-        error probability of p.
-
-        Some simple error models can be auto-constructed using `create_locally_gate_independent_pauli_error_model()`
-        or create_iid_pauli_error_model()`.
-
-    counts : The number of counts, i.e., the number of repeats of the circuit that data should be generated for.
-
-    alloutcomes : bool, optional
-        If True then a dictionary is returned where the keys are all possible outcomes (i.e., all length n
-        bit strings) and the values are the counts for all of the outcomes. If False, then the returned
-        dictionary only contains keys for those outcomes that happen at least once.
-
-    TODO: docstring: idle1q_placeholder
-
-    Returns
-    -------
-    dict
-        A dictionary of simulated measurement outcome counts.
-    """
-    n = circuit.number_of_lines
-
-    if set(circuit.line_labels) != set(pspec.qubit_labels):
-        assert(set(circuit.line_labels).issubset(set(pspec.qubit_labels)))
-        reduced_errormodel = errormodel.copy()
-        mask = _np.zeros(pspec.num_qubits, bool)
-        for i in range(pspec.num_qubits):
-            if pspec.qubit_labels[i] in circuit.line_labels:
-                mask[i] = True
-        for key in list(reduced_errormodel.keys()):
-            errormatrix = reduced_errormodel[key]
-            assert(_np.shape(errormatrix)[0] == pspec.num_qubits), "Format of `errormodel` incorrect!"
-            if len(_np.shape(errormatrix)) == 2:
-                reduced_errormodel[key] = errormatrix[mask, :]
-            elif len(_np.shape(errormatrix)) == 1:
-                reduced_errormodel[key] = errormatrix[mask]
-            else: raise ValueError("Format of `errormodel` incorrect!")
-    else:
-        reduced_errormodel = errormodel
-
-    results = {}
-
-    if alloutcomes:
-        for i in range(2**n):
-            result = tuple(_symp.int_to_bitstring(i, n))
-            results[result] = 0
-
-    for i in range(0, counts):
-        result = oneshot_circuit_simulator_for_tensored_independent_pauli_errors(
-            circuit, pspec, reduced_errormodel, idle1q_placeholder)
-        try: results[result] += 1
-        except: results[result] = 1
-
-    return results
-
-
-def oneshot_circuit_simulator_for_tensored_independent_pauli_errors(circuit, pspec, errormodel, idle1q_placeholder='I'):
-    """
-    Generates a single measurement result for the `circuit_simulator_for_tensored_independent_pauli_errors()`
-    simulator
-
-    Parameters
-    ----------
-    circuit : Circuit
-        The circuit to simulate. It should only contain gates that are also contained  within the provided
-        QubitProcessorSpec `pspec` and are Clifford gates.
-
-    pspec : QubitProcessorSpec
-        The QubitProcessorSpec that defines the device. The Clifford model in QubitProcessorSpec should contain all of
-        the gates that are in the circuit.
-
-    errormodel : dict
-        A dictionary defining the error model. This errormodel should have keys that are Label objects (the
-        elements of the circuit). The values for a particular Label is an (n,4) numpy array of floats, that
-        encodes the errors caused by the gate specified by that Label. The (i,j) value in the array is the
-        probability that this gate is followed by Pauli i where Pauli 0 = identity, Pauli 1 = X, Pauli 2 = Y
-        and Pauli 3 = Z. So, if the arrray is [1.,0.,0.,0.] in every row then there is no errors, if it is
-        [1-p,p/3,p/3,p/3] in row j then there is equal probability of each Pauli error on qubit j with an
-        error probability of p.
-
-    TODO: docstring: idle1q_placeholder
-
-    Returns
-    -------
-    tuple
-        A tuple of values that are 0 or 1, corresponding to the results of a z-measurement on all the qubits.
-        The ordering of this tuple corresponds to the ordering of the wires in the circuit.
-    """
-    n = circuit.number_of_lines
-    depth = circuit.depth
-    sout, pout = _symp.prep_stabilizer_state(n, zvals=None)
-    srep = pspec.models['clifford'].compute_clifford_symplectic_reps()
-    I = _np.identity(2 * n, int)
-
-    for l in range(depth):
-
-        layer = circuit.layer_with_idles(l, idle_gate_name=idle1q_placeholder)
-        s, p = _symp.symplectic_rep_of_clifford_layer(layer, n, q_labels=circuit.line_labels, srep_dict=srep)
-        # Apply the perfect layer to the current state.
-        sout, pout = _symp.apply_clifford_to_stabilizer_state(s, p, sout, pout)
-
-        # Consider each gate in the layer, and apply Pauli errors with the relevant probs.
-        for gate in layer:
-            # Sample a pauli vector for the gate
-            gerror_p = _np.zeros(2 * n, int)
-            sampledvec = _np.array([list(_np.random.multinomial(1, pp)) for pp in errormodel[gate]])
-            # Z and Y both map X - > -X under conjugation, which is encoded with the upper half of
-            # the p vector being set to 2.
-            gerror_p[:n] = 2 * (sampledvec[:, 3] ^ sampledvec[:, 2])
-            # X and Y both map Z - > -Z under conjugation, which is encoded with the lower half of
-            # the p vector being set to 2.
-            gerror_p[n:] = 2 * (sampledvec[:, 1] ^ sampledvec[:, 2])
-
-            sout, pout = _symp.apply_clifford_to_stabilizer_state(I, gerror_p, sout, pout)
-
-    output = []
-    for q in range(n):
-        measurement_out = _symp.pauli_z_measurement(sout, pout, q)
-        # The probability of the '1' outcome
-        oneprob = measurement_out[1]
-        # Sample a bit with that probability to be 1.
-        bit = _np.random.binomial(1, oneprob)
-        output.append(bit)
-
-    # Add measurement errors, by bit-flipping with some probability
-    try:
-        measurement_errors = errormodel['measure']
-    except:
-        measurement_errors = [0 for i in range(n)]
-
-    add_to_outcome = _np.array([_np.random.binomial(1, p) for p in measurement_errors])
-    output = tuple(_np.array(output) ^ add_to_outcome)
-    outputasstring = ''
-    for s in output: outputasstring += str(s)
-    return outputasstring
-
-
-def rb_with_pauli_errors(pspec, errormodel, lengths, k, counts, qubit_subset=None, filename=None, rbtype='DRB',
-                         rbspec=None, returndata=True, appenddata=False, verbosity=0, idle1q_placeholder='I'):
-    """
-    Simulates RB with Pauli errors. Can be used to simulated Clifford RB, direct RB and mirror RB. This
-    function:
-
-        1) Samples RB circuits
-        2) Simulates the RB circuit with the specified Pauli-errors error model
-        3) Records the summary RB data to file and/or returns this RB data.
-
-    Step 1 is implemented using the in-built RB samplers. For more information see rb.sample. Step 2
-    is implemented using the `circuit_simulator_for_tensored_independent_pauli_errors()` stochastic
-    errors circuit simulator. See that function for more details.
-
-    Parameters
-    ----------
-    pspec : QubitProcessorSpec
-        The QubitProcessorSpec that defines the device.
-
-    errormodel : dict
-        A dictionary defining the error model. This errormodel should have keys that are Label objects
-        corresponding to the gates in `pspec`. The values for a particular Label is an (n,4) numpy array of
-        floats, that encodes the errors caused by the gate specified by that Label. The (i,j) value in the
-        array is the probability that this gate is followed by Pauli i where Pauli 0 = identity, Pauli 1 = X,
-        Pauli 2 = Y and Pauli 3 = Z. So, if the arrray is [1.,0.,0.,0.] in every row then there is no errors,
-        if it is [1-p,p/3,p/3,p/3] in row j then there is equal probability of each Pauli error on qubit j with an
-        error probability of p.
-
-        Some simple error models can be auto-constructed using `create_locally_gate_independent_pauli_error_model()`
-        or create_iid_pauli_error_model()`.
-
-    lengths : list
-        A list of the RB lengths to sample and simulate circuits at. E.g., for Clifford RB this is the number
-        of Cliffords in the uncompiled circuit - 2 (see `rb.sample.clifford_rb_circuit()`).
-
-    k : int
-        The number of circuits to sample and simulate at each RB length.
-
-    counts : int
-        The number of counts for each circuit.
-
-    qubit_subset : list
-        If not None, a list of qubit labels that the RB experiment should be over, that is a subset of the
-        qubits in `pspec`.
-
-    filename : str, optional
-        A filename for where to save the data (if None, the data is not saved to file).
-
-    rbtype : {'DRB', 'CRB', 'MRB'}
-        The RB type to simulate. 'DRB' corresponds to direct RB, 'CRB' corresponds to Clifford RB,
-        and 'MRB' corresponds to mirror RB.
-
-    rbspec : list, optional
-        Handed to the RB sampling function for all arguments after `pspec` and the RB lengths, which are the first
-        two arguments handed to the relevant function. See the relevant RB circuit sampling functions for details.
-
-    returndata : bool, optional
-        Whether to return the data
-
-    appenddata : bool, optional
-        If writing to file (i.e., `filename` is not None), whether to append the data to an already existing file
-        or to write over any existing file.
-
-    verbosity : int, optional
-        The amount of print-to-screen.
-
-    Returns
-    -------
-    None or RBSummaryDataset
-        If `returndata` an RBSummaryDataset containing the results. Else, None
-
-    """
-    if rbspec is None:
-        rbspec = []
-    assert(rbtype == 'CRB' or rbtype == 'DRB' or rbtype == 'MRB'), "RB type not valid!"
-
-    if filename is not None:
-        if not appenddata:
-            with open(filename, 'w') as f:
-                f.write('# Results from a {} simulation\n'.format(rbtype))
-                f.write('# Number of qubits\n')
-                if qubit_subset is None: f.write(str(pspec.num_qubits))
-                else: f.write(str(len(qubit_subset)))
-                f.write('\n# RB length // Success counts // Total counts '
-                        '// Circuit depth // Circuit two-qubit gate count\n')
-
-    n = pspec.num_qubits
-    lengthslist = []
-    scounts = []
-    cdepths = []
-    c2Qgcounts = []
-
-    for i in range(k):
-
-        if verbosity > 0:
-            print("- Sampling and simulating circuit {} of {} at each of {} lengths".format(i + 1, k, len(lengths)))
-            print("  - Number of circuits complete = ", end='')
-
-        for lind, l in enumerate(lengths):
-
-            lengthslist.append(l)
-
-            if rbtype == 'DRB':
-                c, idealout = _samp.direct_rb_circuit(pspec, l, qubit_subset, *rbspec)
-            elif rbtype == 'CRB':
-                c, idealout = _samp.clifford_rb_circuit(pspec, l, qubit_subset, *rbspec)
-            elif rbtype == 'MRB':
-                c, idealout = _samp.mirror_rb_circuit(pspec, l, qubit_subset, *rbspec)
-
-            #if verbosity > 0:
-            #    print(" complete")
-            #    print(" - Simulating circuit...",end='')
-
-            outcome = circuit_simulator_for_tensored_independent_pauli_errors(
-                c, pspec, errormodel, counts, alloutcomes=False, idle1q_placeholder=idle1q_placeholder)
-            #EGN: Hardcoded 'I' here. Could make this into an arg, but there's really
-            #  no need for the user to modify this unless they use 'I' as a gate label.
-            if verbosity > 0: print(lind + 1, end=',')
-
-            # Add the number of success counts to the list
-#            scounts.append(outcome.get(idealout,0))
-            scounts.append(outcome.get(''.join(str(idealbit) for idealbit in idealout), 0))
-            cdepths.append(c.depth)
-            c2Qgcounts.append(c.two_q_gate_count())
-
-            # Write the data to file in each round.
-            if filename is not None:
-                with open(filename, 'a') as f:
-                    f.write('{} {} {} {} {}\n'.format(l, scounts[-1], counts, cdepths[-1], c2Qgcounts[-1]))
-
-        if verbosity > 0: print('')
-    if returndata:
-
-        from . import results as _res
-        data = _res.RBSummaryDataset(n, lengthslist, success_counts=scounts, total_counts=counts,
-                                     circuit_depths=cdepths, circuit_twoQgate_counts=c2Qgcounts)
-        return data
-
-
-def create_iid_pauli_error_model(pspec, one_qubit_gate_errorrate, two_qubit_gate_errorrate, idle_errorrate,
-                                 measurement_errorrate=0., ptype='uniform', idle1q_placeholder='I'):
-    """
-    Returns a dictionary encoding a Pauli-stochastic error model whereby the errors are the same on all the
-    1-qubit gates, and the same on all 2-qubit gates. The probability of the 3 different Pauli errors on each
-    qubit is specified by `ptype` and can either be uniform, or always X, Y, or Z errors.
-
-    The dictionary returned is in the appropriate format for the
-    `circuit_simulator_for_tensored_independent_pauli_errors()` circuit simulator function.
-
-    Parameters
-    ----------
-    pspec : QubitProcessorSpec
-        The QubitProcessorSpec that defines the device.
-
-    one_qubit_gate_errorrate : float
-        The 1-qubit gates error rate (the probability of a Pauli error on the target qubit) not including
-        idle gates.
-
-    two_qubit_gate_errorrate : float
-        The 2-qubit gates error rate (the total probability of a Pauli error on either qubit the gate acts
-        on -- each qubit has independent errors with equal probabilities).
-
-    idle_errorrate : float
-        The idle gates error rate.
-
-    measurement_errorrate : flip
-        The measurement error rate for all of the qubits. This is the probability that a qubits measurement
-        result is bit-flipped.
-
-    ptype : str, optional
-        Can be 'uniform', 'X', 'Y' or 'Z'. If 'uniform' then 3 Pauli errors are equally likely, if 'X', 'Y' or
-        'Z' then the errors are always Pauli X, Y or Z errors, respectively.
-
-    TODO: docstring idle1q_placeholder
-
-    Returns
-    -------
-    dict
-        An dict that encodes the error model described above in the format required for the simulator
-        `circuit_simulator_for_tensored_independent_pauli_errors()`.
-
-    """
-    if ptype == 'uniform':
-        def error_row(er): return _np.array([1 - er, er / 3, er / 3, er / 3])
-
-    elif ptype == 'X':
-        def error_row(er): return _np.array([1 - er, er, 0., 0.])
-
-    elif ptype == 'Y':
-        def error_row(er): return _np.array([1 - er, 0., er, 0.])
-
-    elif ptype == 'Z':
-        def error_row(er): return _np.array([1 - er, 0., 0., er])
-    else:
-        raise ValueError("Error model type not understood! Set `ptype` to a valid option.")
-
-    perQ_twoQ_errorrate = 1 - (1 - two_qubit_gate_errorrate)**(1 / 2)
-    n = pspec.num_qubits
-
-    errormodel = {}
-
-    if idle1q_placeholder is not None:
-        #Added by EGN: special behavior needed when Model has
-        # an gate name used to designate a perfect 1-qubit idle op (used as placeholder).
-        # This translates to a set of "<gatename>:X" operation labels all w/idle_errorrate
-        idleLbl = idle1q_placeholder
-        for q in pspec.qubit_labels:
-            gl = _Lbl(idleLbl, q)
-            errormodel[gl] = _np.zeros((n, 4), float)
-            errormodel[gl][:, 0] = _np.ones(n, float)
-            errormodel[gl][pspec.qubit_labels.index(q), :] = error_row(idle_errorrate)
-
-    for gate in pspec.models['clifford'].primitive_op_labels:
-        errormodel[gate] = _np.zeros((n, 4), float)
-        errormodel[gate][:, 0] = _np.ones(n, float)
-
-        # If not a CNOT, it is a 1-qubit gate / idle.
-        if gate.num_qubits == 2:
-            q1 = gate.qubits[0]
-            q2 = gate.qubits[1]
-            er = perQ_twoQ_errorrate
-            errormodel[gate][pspec.qubit_labels.index(q1), :] = error_row(er)
-            errormodel[gate][pspec.qubit_labels.index(q2), :] = error_row(er)
-
-        elif gate.num_qubits == 1:
-            q = gate.qubits[0]
-            er = one_qubit_gate_errorrate
-
-            errormodel[gate][pspec.qubit_labels.index(q), :] = error_row(er)
-
-        else:
-            raise ValueError("The QubitProcessorSpec must only contain 1- and 2- qubit gates!")
-
-    errormodel['measure'] = _np.array([measurement_errorrate for q in range(n)])
-
-    return errormodel
-
-
-def create_locally_gate_independent_pauli_error_model(pspec, gate_errorrate_dict, measurement_errorrate_dict=None,
-                                                      ptype='uniform', idle1q_placeholder='I'):
-    """
-    Returns a dictionary encoding a Pauli-stochastic error model whereby the errors are independent of the gates,
-    with a qubit subject to an error after a circuit layer with the probabilities specified by the dict
-    `gate_errorrate_dict`. The probability of the 3 different Pauli errors on each qubit is specified by
-    `ptype` and can either be uniform, or always X, Y, or Z errors.
-
-    The dictionary returned is in the appropriate format for the
-    `circuit_simulator_for_tensored_independent_pauli_errors()` circuit simulator function.
-
-    Parameters
-    ----------
-    pspec : QubitProcessorSpec
-        The QubitProcessorSpec that defines the device.
-
-    gate_errorrate_dict : dict
-        A dict where the keys are elements of pspec.qubit_labels and the values are floats in [0,1].
-        The element for qubit with label `q` is the error probability for that qubit.
-
-    measurement_errorrate_dict : dict
-        A dict where the keys are elements of pspec.qubit_labels and the values are floats in [0,1].
-        The element for qubit with label `q` is the measurement bit-flip error probability for that qubit.
-        All qubits that do not have a measurement error rate specified are assumed to have perfect measurements.
-
-    ptype : str, optional
-        Can be 'uniform', 'X', 'Y' or 'Z'. If 'uniform' then 3 Pauli errors are equally likely, if 'X', 'Y' or
-        'Z' then the errors are always Pauli X, Y or Z errors, respectively.
-
-    TODO: docstring: idle1q_placeholder
-
-    Returns
-    -------
-    dict
-        An dict that encodes the error model described above in the format required for the simulator
-        `circuit_simulator_for_tensored_independent_pauli_errors()`.
-
-    """
-    if measurement_errorrate_dict is None:
-        measurement_errorrate_dict = {}
-    if ptype == 'uniform':
-        def error_row(er): return _np.array([1 - er, er / 3, er / 3, er / 3])
-
-    elif ptype == 'X':
-        def error_row(er): return _np.array([1 - er, er, 0., 0.])
-
-    elif ptype == 'Y':
-        def error_row(er): return _np.array([1 - er, 0., er, 0.])
-
-    elif ptype == 'Z':
-        def error_row(er): return _np.array([1 - er, 0., 0., er])
-    else:
-        raise ValueError("Error model type not understood! Set `ptype` to a valid option.")
-
-    n = pspec.num_qubits
-
-    errormodel = {}
-
-    if idle1q_placeholder is not None:
-        #Added by EGN: special behavior needed when Model has
-        # an gate name used to designate a perfect 1-qubit idle op (used as placeholder).
-        # This translates to a set of "<gatename>:X" operation labels all w/appropriate errorrate
-        idleLbl = idle1q_placeholder
-        for q in pspec.qubit_labels:
-            gl = _Lbl(idleLbl, q)
-            er = gate_errorrate_dict[q]
-            errormodel[gl] = _np.zeros((n, 4), float)
-            errormodel[gl][:, 0] = _np.ones(n, float)
-            errormodel[gl][pspec.qubit_labels.index(q), :] = error_row(er)
-
-    for gate in pspec.models['clifford'].primitive_op_labels:
-        errormodel[gate] = _np.zeros((n, 4), float)
-        errormodel[gate][:, 0] = _np.ones(n, float)
-
-        for q in gate.qubits:
-            er = gate_errorrate_dict[q]
-            errormodel[gate][pspec.qubit_labels.index(q)] = error_row(er)
-
-    errormodel['measure'] = _np.array([measurement_errorrate_dict.get(q, 0.) for q in pspec.qubit_labels])
-
-    return errormodel
-
-#
-# TODO : DOES THIS NEED AND IDLE PLACEHOLDER?
-#
-
-
-def create_local_pauli_error_model(pspec, one_qubit_gate_errorrate_dict, two_qubit_gate_errorrate_dict,
-                                   measurement_errorrate_dict=None, ptype='uniform'):
-    """
-    Returns a dictionary encoding a Pauli-stochastic error model whereby the errors caused by a gate act
-    only on the "target" qubits of the gate, all the 1-qubit gates on a qubit have the same error rate,
-    and all the 2-qubit gates on a qubit have the same error rate. The probability of the 3 different Pauli
-    errors on each qubit is specified by `ptype` and can either be uniform, or always X, Y, or Z errors.
-
-    The dictionary returned is in the appropriate format for the
-    `circuit_simulator_for_tensored_independent_pauli_errors()` circuit simulator function.
-
-    Parameters
-    ----------
-    pspec : QubitProcessorSpec
-        The QubitProcessorSpec that defines the device.
-
-    one_qubit_gate_errorrate_dict : dict
-        A dict where the keys are elements of pspec.qubit_labels and the values are floats in [0,1].
-        The element for qubit with label `q` is the error probability for all 1-qubit gates on that qubit
-
-    two_qubit_gate_errorrate_dict : dict
-        A dict where the keys are 2-qubit gates in pspec and the values are floats in [0,1]. This is the
-        error probability for the 2-qubit gate, split evenly into independent Pauli errors on each of the
-        qubits the gate is intended to act on.
-
-    measurement_errorrate_dict : dict
-        A dict where the keys are elements of pspec.qubit_labels and the values are floats in [0,1].
-        The element for qubit with label `q` is the measurement bit-flip error probability for that qubit.
-        All qubits that do not have a measurement error rate specified are assumed to have perfect measurements.
-
-
-    ptype : str, optional
-        Can be 'uniform', 'X', 'Y' or 'Z'. If 'uniform' then 3 Pauli errors are equally likely, if 'X', 'Y' or
-        'Z' then the errors are always Pauli X, Y or Z errors, respectively.
-
-    Returns
-    -------
-    dict
-        An dict that encodes the error model described above in the format required for the simulator
-        `circuit_simulator_for_tensored_independent_pauli_errors()`.
-
-    """
-    if measurement_errorrate_dict is None:
-        measurement_errorrate_dict = {}
-    if ptype == 'uniform':
-        def error_row(er): return _np.array([1 - er, er / 3, er / 3, er / 3])
-
-    elif ptype == 'X':
-        def error_row(er): return _np.array([1 - er, er, 0., 0.])
-
-    elif ptype == 'Y':
-        def error_row(er): return _np.array([1 - er, 0., er, 0.])
-
-    elif ptype == 'Z':
-        def error_row(er): return _np.array([1 - er, 0., 0., er])
-    else:
-        raise ValueError("Error model type not understood! Set `ptype` to a valid option.")
-
-    n = pspec.num_qubits
-
-    errormodel = {}
-    for gate in list(pspec.models['clifford'].primitive_op_labels):
-        errormodel[gate] = _np.zeros((n, 4), float)
-        errormodel[gate][:, 0] = _np.ones(n, float)
-
-        if gate.num_qubits == 1:
-            er = one_qubit_gate_errorrate_dict[gate.qubits[0]]
-        elif gate.num_qubits == 2:
-            er = 1 - (1 - two_qubit_gate_errorrate_dict[gate])**(0.5)
-        else: raise ValueError("Only 1- and 2-qubit gates supported!")
-
-        for q in gate.qubits:
-            errormodel[gate][pspec.qubit_labels.index(q)] = error_row(er)
-
-    errormodel['measure'] = _np.array([measurement_errorrate_dict.get(q, 0.) for q in pspec.qubit_labels])
-
-    return errormodel