import Utils, numpy as np, scipy.sparse as sp class BaseRx(object): """SimPEG Receiver Object""" locs = None #: Locations (nRx x nDim) knownRxTypes = None #: Set this to a list of strings to ensure that txType is known projGLoc = 'CC' #: Projection grid location, default is CC storeProjections = True #: Store calls to getP (organized by mesh) def __init__(self, locs, rxType, **kwargs): self.locs = locs self.rxType = rxType self._Ps = {} Utils.setKwargs(self, **kwargs) @property def rxType(self): """Receiver Type""" return getattr(self, '_rxType', None) @rxType.setter def rxType(self, value): known = self.knownRxTypes if known is not None: assert value in known, "rxType must be in ['%s']" % ("', '".join(known)) self._rxType = value @property def nD(self): """Number of data in the receiver.""" return self.locs.shape[0] def getP(self, mesh): """ Returns the projection matrices as a list for all components collected by the receivers. .. note:: Projection matrices are stored as a dictionary listed by meshes. """ if mesh in self._Ps: return self._Ps[mesh] P = mesh.getInterpolationMat(self.locs, self.projGLoc) if self.storeProjections: self._Ps[mesh] = P return P class BaseTimeRx(BaseRx): """SimPEG Receiver Object""" times = None #: Times when the receivers were active. projTLoc = 'N' def __init__(self, locs, times, rxType, **kwargs): self.times = times BaseRx.__init__(self, locs, rxType, **kwargs) @property def nD(self): """Number of data in the receiver.""" return self.locs.shape[0] * len(self.times) def getSpatialP(self, mesh): """ Returns the spatial projection matrix. .. note:: This is not stored in memory, but is created on demand. """ return mesh.getInterpolationMat(self.locs, self.projGLoc) def getTimeP(self, timeMesh): """ Returns the time projection matrix. .. note:: This is not stored in memory, but is created on demand. """ return timeMesh.getInterpolationMat(self.times, self.projTLoc) def getP(self, mesh, timeMesh): """ Returns the projection matrices as a list for all components collected by the receivers. .. note:: Projection matrices are stored as a dictionary (mesh, timeMesh) if storeProjections is True """ if (mesh, timeMesh) in self._Ps: return self._Ps[(mesh, timeMesh)] Ps = self.getSpatialP(mesh) Pt = self.getTimeP(timeMesh) P = sp.kron(Pt, Ps) if self.storeProjections: self._Ps[(mesh, timeMesh)] = P return P class BaseTx(object): """SimPEG Transmitter Object""" loc = None #: Location [x,y,z] rxList = None #: SimPEG Receiver List rxPair = BaseRx knownTxTypes = None #: Set this to a list of strings to ensure that txType is known def __init__(self, loc, txType, rxList, **kwargs): assert type(rxList) is list, 'rxList must be a list' for rx in rxList: assert isinstance(rx, self.rxPair), 'rxList must be a %s'%self.rxPair.__name__ assert len(set(rxList)) == len(rxList), 'The rxList must be unique' self.loc = loc self.txType = txType self.rxList = rxList Utils.setKwargs(self, **kwargs) @property def txType(self): """Transmitter Type""" return getattr(self, '_txType', None) @txType.setter def txType(self, value): known = self.knownTxTypes if known is not None: assert value in known, "txType must be in ['%s']" % ("', '".join(known)) self._txType = value @property def nD(self): """Number of data""" return self.vnD.sum() @property def vnD(self): """Vector number of data""" return np.array([rx.nD for rx in self.rxList]) class Data(object): """Fancy data storage by Tx and Rx""" def __init__(self, survey, v=None): self.survey = survey self._dataDict = {} for tx in self.survey.txList: self._dataDict[tx] = {} if v is not None: self.fromvec(v) def _ensureCorrectKey(self, key): if type(key) is tuple: if len(key) is not 2: raise KeyError('Key must be [Tx, Rx]') if key[0] not in self.survey.txList: raise KeyError('Tx Key must be a transmitter in the survey.') if key[1] not in key[0].rxList: raise KeyError('Rx Key must be a receiver for the transmitter.') return key elif isinstance(key, self.survey.txPair): if key not in self.survey.txList: raise KeyError('Key must be a transmitter in the survey.') return key, None else: raise KeyError('Key must be [Tx] or [Tx,Rx]') def __setitem__(self, key, value): tx, rx = self._ensureCorrectKey(key) assert rx is not None, 'set data using [Tx, Rx]' assert isinstance(value, np.ndarray), 'value must by ndarray' assert value.size == rx.nD, "value must have the same number of data as the transmitter." self._dataDict[tx][rx] = Utils.mkvc(value) def __getitem__(self, key): tx, rx = self._ensureCorrectKey(key) if rx is not None: if rx not in self._dataDict[tx]: raise Exception('Data for receiver has not yet been set.') return self._dataDict[tx][rx] return np.concatenate([self[tx,rx] for rx in tx.rxList]) def tovec(self): return np.concatenate([self[tx] for tx in self.survey.txList]) def fromvec(self, v): v = Utils.mkvc(v) assert v.size == self.survey.nD, 'v must have the correct number of data.' indBot, indTop = 0, 0 for tx in self.survey.txList: for rx in tx.rxList: indTop += rx.nD self[tx, rx] = v[indBot:indTop] indBot += rx.nD class Fields(object): """Fancy Field Storage u[:,'phi'] = phi print u[tx0,'phi'] """ knownFields = None #: Known fields, a dict with locations, e.g. {"e": "E", "phi": "CC"} aliasFields = None #: Aliased fields, a dict with [alias, location, function], e.g. {"b":["e","F",lambda(F,e,ind)]} dtype = float #: dtype is the type of the storage matrix. This can be a dictionary. def __init__(self, mesh, survey, **kwargs): self.survey = survey self.mesh = mesh Utils.setKwargs(self, **kwargs) self._fields = {} if self.knownFields is None: raise Exception('knownFields cannot be set to None') if self.aliasFields is None: self.aliasFields = {} allFields = [k for k in self.knownFields] + [a for a in self.aliasFields] assert len(allFields) == len(set(allFields)), 'Aliased fields and Known Fields have overlapping definitions.' self.startup() def startup(self): pass @property def approxSize(self): """The approximate cost to storing all of the known fields.""" sz = 0.0 for f in self.knownFields: loc =self.knownFields[f] sz += np.array(self._storageShape(loc)).prod()*8.0/(1024**2) return "%e MB"%sz def _storageShape(self, loc): nTx = self.survey.nTx nP = {'CC': self.mesh.nC, 'N': self.mesh.nN, 'F': self.mesh.nF, 'E': self.mesh.nE}[loc] return (nP, nTx) def _initStore(self, name): if name in self._fields: return self._fields[name] assert name in self.knownFields, 'field name is not known.' loc = self.knownFields[name] if type(self.dtype) is dict: dtype = self.dtype[name] else: dtype = self.dtype field = np.zeros(self._storageShape(loc), dtype=dtype) self._fields[name] = field return field def _txIndex(self, txTestList): if type(txTestList) is slice: ind = txTestList else: if type(txTestList) is not list: txTestList = [txTestList] for txTest in txTestList: if txTest not in self.survey.txList: raise KeyError('Invalid Transmitter, not in survey list.') ind = np.in1d(self.survey.txList, txTestList) return ind def _nameIndex(self, name, accessType): if type(name) is slice: assert name == slice(None,None,None), 'Fancy field name slicing is not supported... yet.' name = None if name is None: return if accessType=='set' and name not in self.knownFields: if name in self.aliasFields: raise KeyError("Invalid field name (%s) for setter, you can't set an aliased property"%name) else: raise KeyError('Invalid field name (%s) for setter'%name) elif accessType=='get' and (name not in self.knownFields and name not in self.aliasFields): raise KeyError('Invalid field name (%s) for getter'%name) return name def _indexAndNameFromKey(self, key, accessType): if type(key) is not tuple: key = (key,) if len(key) == 1: key += (None,) assert len(key) == 2, 'must be [Tx, fieldName]' txTestList, name = key name = self._nameIndex(name, accessType) ind = self._txIndex(txTestList) return ind, name def __setitem__(self, key, value): ind, name = self._indexAndNameFromKey(key, 'set') if name is None: freq = key assert type(value) is dict, 'New fields must be a dictionary, if field is not specified.' newFields = value elif name in self.knownFields: newFields = {name: value} else: raise Exception('Unknown setter') for name in newFields: field = self._initStore(name) self._setField(field, newFields[name], name, ind) def __getitem__(self, key): ind, name = self._indexAndNameFromKey(key, 'get') if name is None: out = {} for name in self._fields: out[name] = self._getField(name, ind) return out return self._getField(name, ind) def _setField(self, field, val, name, ind): if isinstance(val, np.ndarray) and (field.shape[1] == 1 or val.ndim == 1): val = Utils.mkvc(val,2) field[:,ind] = val def _getField(self, name, ind): if name in self._fields: out = self._fields[name][:,ind] else: # Aliased fields alias, loc, func = self.aliasFields[name] if type(func) is str: assert hasattr(self, func), 'The alias field function is a string, but it does not exist in the Fields class.' func = getattr(self, func) out = func(self._fields[alias][:,ind], ind) if out.shape[1] == 1: out = Utils.mkvc(out) return out def __contains__(self, other): if other in self.aliasFields: other = self.aliasFields[other][0] return self._fields.__contains__(other) class TimeFields(Fields): """Fancy Field Storage for time domain problems u[:,'phi', timeInd] = phi print u[tx0,'phi'] """ def _storageShape(self, loc): nP = {'CC': self.mesh.nC, 'N': self.mesh.nN, 'F': self.mesh.nF, 'E': self.mesh.nE}[loc] nTx = self.survey.nTx nT = self.survey.prob.nT return (nP, nTx, nT + 1) def _indexAndNameFromKey(self, key, accessType): if type(key) is not tuple: key = (key,) if len(key) == 1: key += (None,) if len(key) == 2: key += (slice(None,None,None),) assert len(key) == 3, 'must be [Tx, fieldName, times]' txTestList, name, timeInd = key name = self._nameIndex(name, accessType) txInd = self._txIndex(txTestList) return (txInd, timeInd), name def _correctShape(self, name, ind, deflate=False): txInd, timeInd = ind if name in self.knownFields: loc = self.knownFields[name] else: loc = self.aliasFields[name][1] nP, total_nTx, total_nT = self._storageShape(loc) nTx = np.ones(total_nTx, dtype=bool)[txInd].sum() nT = np.ones(total_nT, dtype=bool)[timeInd].sum() shape = nP, nTx, nT if deflate: shape = tuple([s for s in shape if s > 1]) return shape def _setField(self, field, val, name, ind): txInd, timeInd = ind shape = self._correctShape(name, ind) if Utils.isScalar(val): field[:,txInd,timeInd] = val return if val.size != np.array(shape).prod(): raise ValueError('Incorrect size for data.') correctShape = field[:,txInd,timeInd].shape field[:,txInd,timeInd] = val.reshape(correctShape, order='F') def _getField(self, name, ind): txInd, timeInd = ind if name in self._fields: out = self._fields[name][:,txInd,timeInd] else: # Aliased fields alias, loc, func = self.aliasFields[name] if type(func) is str: assert hasattr(self, func), 'The alias field function is a string, but it does not exist in the Fields class.' func = getattr(self, func) pointerFields = self._fields[alias][:,txInd,timeInd] pointerShape = self._correctShape(alias, ind, deflate=True) pointerFields = pointerFields.reshape(pointerShape, order='F') if len(pointerShape) < 3: out = func(pointerFields, txInd) else: #loop over the time steps nT = pointerShape[2] out = range(nT) for i in range(nT): out[i] = func(pointerFields[:,:,i], txInd) out[i] = out[i][:,:,np.newaxis] out = np.concatenate(out, axis=2) shape = self._correctShape(name, ind, deflate=True) return out.reshape(shape, order='F') class BaseSurvey(object): """Survey holds the observed data, and the standard deviations.""" __metaclass__ = Utils.SimPEGMetaClass std = None #: Estimated Standard Deviations dobs = None #: Observed data dtrue = None #: True data, if data is synthetic mtrue = None #: True model, if data is synthetic counter = None #: A SimPEG.Utils.Counter object def __init__(self, **kwargs): Utils.setKwargs(self, **kwargs) txPair = BaseTx #: Transmitter Pair @property def txList(self): """Transmitter List""" return getattr(self, '_txList', None) @txList.setter def txList(self, value): assert type(value) is list, 'txList must be a list' assert np.all([isinstance(tx, self.txPair) for tx in value]), 'All transmitters must be instances of %s' % self.txPair.__name__ assert len(set(value)) == len(value), 'The txList must be unique' self._txList = value @property def prob(self): """ The geophysical problem that explains this survey, use:: survey.pair(prob) """ return getattr(self, '_prob', None) @property def mesh(self): """Mesh of the paired problem.""" if self.ispaired: return self.prob.mesh raise Exception('Pair survey to a problem to access the problems mesh.') def pair(self, p): """Bind a problem to this survey instance using pointers""" assert hasattr(p, 'surveyPair'), "Problem must have an attribute 'surveyPair'." assert isinstance(self, p.surveyPair), "Problem requires survey object must be an instance of a %s class."%(p.surveyPair.__name__) if p.ispaired: raise Exception("The problem object is already paired to a survey. Use prob.unpair()") self._prob = p p._survey = self def unpair(self): """Unbind a problem from this survey instance""" if not self.ispaired: return self.prob._survey = None self._prob = None @property def ispaired(self): return self.prob is not None @property def nD(self): """Number of data""" return self.vnD.sum() @property def vnD(self): """Vector number of data""" return np.array([tx.nD for tx in self.txList]) @property def nTx(self): """Number of Transmitters""" return len(self.txList) @Utils.count @Utils.requires('prob') def dpred(self, m, u=None): """dpred(m, u=None) Create the projected data from a model. The field, u, (if provided) will be used for the predicted data instead of recalculating the fields (which may be expensive!). .. math:: d_\\text{pred} = P(u(m)) Where P is a projection of the fields onto the data space. """ if u is None: u = self.prob.fields(m) return Utils.mkvc(self.projectFields(u)) @Utils.count def projectFields(self, u): """projectFields(u) This function projects the fields onto the data space. .. math:: d_\\text{pred} = \mathbf{P} u(m) """ raise NotImplemented('projectFields is not yet implemented.') @Utils.count def projectFieldsDeriv(self, u): """projectFieldsDeriv(u) This function s the derivative of projects the fields onto the data space. .. math:: \\frac{\partial d_\\text{pred}}{\partial u} = \mathbf{P} """ raise NotImplemented('projectFields is not yet implemented.') @Utils.count def residual(self, m, u=None): """residual(m, u=None) :param numpy.array m: geophysical model :param numpy.array u: fields :rtype: numpy.array :return: data residual The data residual: .. math:: \mu_\\text{data} = \mathbf{d}_\\text{pred} - \mathbf{d}_\\text{obs} """ return Utils.mkvc(self.dpred(m, u=u) - self.dobs) @property def isSynthetic(self): "Check if the data is synthetic." return self.mtrue is not None def makeSyntheticData(self, m, std=0.05, u=None): """ Make synthetic data given a model, and a standard deviation. :param numpy.array m: geophysical model :param numpy.array std: standard deviation :param numpy.array u: fields for the given model (if pre-calculated) """ if getattr(self, 'dobs', None) is not None: raise Exception('Survey already has dobs.') self.mtrue = m self.dtrue = self.dpred(m, u=u) noise = std*abs(self.dtrue)*np.random.randn(*self.dtrue.shape) self.dobs = self.dtrue+noise self.std = self.dobs*0 + std