/**
* Returns a V3D object from the Python object given
* to the converter
* @returns A newly constructed V3D object converted
* from the PyObject.
*/
Kernel::Matrix<double> PyObjectToMatrix::operator()() {
if (m_alreadyMatrix) {
return extract<Kernel::Matrix<double>>(m_obj)();
}
PyArrayObject *ndarray = (PyArrayObject *)PyArray_View(
(PyArrayObject *)m_obj.ptr(), PyArray_DescrFromType(NPY_DOUBLE),
&PyArray_Type);
const auto shape = PyArray_DIMS(ndarray);
npy_intp nx(shape[0]), ny(shape[1]);
Kernel::Matrix<double> matrix(nx, ny);
for (npy_intp i = 0; i < nx; i++) {
auto row = matrix[i];
for (npy_intp j = 0; j < ny; j++) {
row[j] = *((double *)PyArray_GETPTR2(ndarray, i, j));
}
}
return matrix;
}
/*
* This function initializes a result array for a reduction operation
* which has no identity. This means it needs to copy the first element
* it sees along the reduction axes to result, then return a view of
* the operand which excludes that element.
*
* If a reduction has an identity, such as 0 or 1, the result should be
* initialized by calling PyArray_AssignZero(result, NULL, NULL) or
* PyArray_AssignOne(result, NULL, NULL), because this function raises an
* exception when there are no elements to reduce (which appropriate iff the
* reduction operation has no identity).
*
* This means it copies the subarray indexed at zero along each reduction axis
* into 'result', then returns a view into 'operand' excluding those copied
* elements.
*
* result : The array into which the result is computed. This must have
* the same number of dimensions as 'operand', but for each
* axis i where 'axis_flags[i]' is True, it has a single element.
* operand : The array being reduced.
* axis_flags : An array of boolean flags, one for each axis of 'operand'.
* When a flag is True, it indicates to reduce along that axis.
* reorderable : If True, the reduction being done is reorderable, which
* means specifying multiple axes of reduction at once is ok,
* and the reduction code may calculate the reduction in an
* arbitrary order. The calculation may be reordered because
* of cache behavior or multithreading requirements.
* out_skip_first_count : This gets populated with the number of first-visit
* elements that should be skipped during the
* iteration loop.
* funcname : The name of the reduction operation, for the purpose of
* better quality error messages. For example, "numpy.max"
* would be a good name for NumPy's max function.
*
* Returns a view which contains the remaining elements on which to do
* the reduction.
*/
NPY_NO_EXPORT PyArrayObject *
PyArray_InitializeReduceResult(
PyArrayObject *result, PyArrayObject *operand,
npy_bool *axis_flags, int reorderable,
npy_intp *out_skip_first_count, const char *funcname)
{
npy_intp *strides, *shape, shape_orig[NPY_MAXDIMS];
PyArrayObject *op_view = NULL;
int idim, ndim, nreduce_axes;
ndim = PyArray_NDIM(operand);
/* Default to no skipping first-visit elements in the iteration */
*out_skip_first_count = 0;
/*
* If this reduction is non-reorderable, make sure there are
* only 0 or 1 axes in axis_flags.
*/
if (!reorderable && check_nonreorderable_axes(ndim,
axis_flags, funcname) < 0) {
return NULL;
}
/* Take a view into 'operand' which we can modify. */
op_view = (PyArrayObject *)PyArray_View(operand, NULL, &PyArray_Type);
if (op_view == NULL) {
return NULL;
}
/*
* Now copy the subarray of the first element along each reduction axis,
* then return a view to the rest.
*
* Adjust the shape to only look at the first element along
* any of the reduction axes. We count the number of reduction axes
* at the same time.
*/
shape = PyArray_SHAPE(op_view);
nreduce_axes = 0;
memcpy(shape_orig, shape, ndim * sizeof(npy_intp));
for (idim = 0; idim < ndim; ++idim) {
if (axis_flags[idim]) {
if (shape[idim] == 0) {
PyErr_Format(PyExc_ValueError,
"zero-size array to reduction operation %s "
"which has no identity",
funcname);
Py_DECREF(op_view);
return NULL;
}
shape[idim] = 1;
++nreduce_axes;
}
}
/*
* Copy the elements into the result to start.
*/
if (PyArray_CopyInto(result, op_view) < 0) {
Py_DECREF(op_view);
return NULL;
}
/*
* If there is one reduction axis, adjust the view's
* shape to only look at the remaining elements
*/
if (nreduce_axes == 1) {
strides = PyArray_STRIDES(op_view);
for (idim = 0; idim < ndim; ++idim) {
if (axis_flags[idim]) {
shape[idim] = shape_orig[idim] - 1;
((PyArrayObject_fields *)op_view)->data += strides[idim];
}
}
}
/* If there are zero reduction axes, make the view empty */
else if (nreduce_axes == 0) {
for (idim = 0; idim < ndim; ++idim) {
shape[idim] = 0;
}
}
/*
* Otherwise iterate over the whole operand, but tell the inner loop
* to skip the elements we already copied by setting the skip_first_count.
*/
else {
*out_skip_first_count = PyArray_SIZE(result);
Py_DECREF(op_view);
Py_INCREF(operand);
op_view = operand;
}
return op_view;
}
NPY_NO_EXPORT PyObject *
__New_PyArray_Std(PyArrayObject *self, int axis, int rtype, PyArrayObject *out,
int variance, int num)
{
PyObject *obj1 = NULL, *obj2 = NULL, *obj3 = NULL;
PyArrayObject *arr1 = NULL, *arr2 = NULL, *arrnew = NULL;
PyObject *ret = NULL, *newshape = NULL;
int i, n;
npy_intp val;
arrnew = (PyArrayObject *)PyArray_CheckAxis(self, &axis, 0);
if (arrnew == NULL) {
return NULL;
}
/* Compute and reshape mean */
arr1 = (PyArrayObject *)PyArray_EnsureAnyArray(
PyArray_Mean(arrnew, axis, rtype, NULL));
if (arr1 == NULL) {
Py_DECREF(arrnew);
return NULL;
}
n = PyArray_NDIM(arrnew);
newshape = PyTuple_New(n);
if (newshape == NULL) {
Py_DECREF(arr1);
Py_DECREF(arrnew);
return NULL;
}
for (i = 0; i < n; i++) {
if (i == axis) {
val = 1;
}
else {
val = PyArray_DIM(arrnew,i);
}
PyTuple_SET_ITEM(newshape, i, PyInt_FromLong((long)val));
}
arr2 = (PyArrayObject *)PyArray_Reshape(arr1, newshape);
Py_DECREF(arr1);
Py_DECREF(newshape);
if (arr2 == NULL) {
Py_DECREF(arrnew);
return NULL;
}
/* Compute x = x - mx */
arr1 = (PyArrayObject *)PyArray_EnsureAnyArray(
PyNumber_Subtract((PyObject *)arrnew, (PyObject *)arr2));
Py_DECREF(arr2);
if (arr1 == NULL) {
Py_DECREF(arrnew);
return NULL;
}
/* Compute x * x */
if (PyArray_ISCOMPLEX(arr1)) {
obj3 = PyArray_Conjugate(arr1, NULL);
}
else {
obj3 = (PyObject *)arr1;
Py_INCREF(arr1);
}
if (obj3 == NULL) {
Py_DECREF(arrnew);
return NULL;
}
arr2 = (PyArrayObject *)PyArray_EnsureAnyArray(
PyArray_GenericBinaryFunction(arr1, obj3, n_ops.multiply));
Py_DECREF(arr1);
Py_DECREF(obj3);
if (arr2 == NULL) {
Py_DECREF(arrnew);
return NULL;
}
if (PyArray_ISCOMPLEX(arr2)) {
obj3 = PyObject_GetAttrString((PyObject *)arr2, "real");
switch(rtype) {
case NPY_CDOUBLE:
rtype = NPY_DOUBLE;
break;
case NPY_CFLOAT:
rtype = NPY_FLOAT;
break;
case NPY_CLONGDOUBLE:
rtype = NPY_LONGDOUBLE;
break;
}
}
else {
obj3 = (PyObject *)arr2;
Py_INCREF(arr2);
}
if (obj3 == NULL) {
Py_DECREF(arrnew);
return NULL;
}
/* Compute add.reduce(x*x,axis) */
obj1 = PyArray_GenericReduceFunction((PyArrayObject *)obj3, n_ops.add,
axis, rtype, NULL);
Py_DECREF(obj3);
Py_DECREF(arr2);
if (obj1 == NULL) {
Py_DECREF(arrnew);
return NULL;
}
n = PyArray_DIM(arrnew,axis);
Py_DECREF(arrnew);
n = (n-num);
if (n == 0) {
n = 1;
}
obj2 = PyFloat_FromDouble(1.0/((double )n));
if (obj2 == NULL) {
Py_DECREF(obj1);
return NULL;
}
ret = PyNumber_Multiply(obj1, obj2);
Py_DECREF(obj1);
Py_DECREF(obj2);
if (!variance) {
arr1 = (PyArrayObject *)PyArray_EnsureAnyArray(ret);
/* sqrt() */
ret = PyArray_GenericUnaryFunction(arr1, n_ops.sqrt);
Py_DECREF(arr1);
}
if (ret == NULL) {
return NULL;
}
if (PyArray_CheckExact(self)) {
goto finish;
}
if (PyArray_Check(self) && Py_TYPE(self) == Py_TYPE(ret)) {
goto finish;
}
arr1 = (PyArrayObject *)PyArray_EnsureArray(ret);
if (arr1 == NULL) {
return NULL;
}
ret = PyArray_View(arr1, NULL, Py_TYPE(self));
Py_DECREF(arr1);
finish:
if (out) {
if (PyArray_AssignArray(out, (PyArrayObject *)ret,
NULL, NPY_DEFAULT_ASSIGN_CASTING) < 0) {
Py_DECREF(ret);
return NULL;
}
Py_DECREF(ret);
Py_INCREF(out);
return (PyObject *)out;
}
return ret;
}
static PyObject *frputvect(PyObject *self, PyObject *args, PyObject *keywds) {
FrFile *oFile;
FrameH *frame;
FrProcData *proc;
FrAdcData *adc;
FrSimData *sim;
FrVect *vect;
int verbose=0, nData, nBits, type, subType, arrayType;
double dx, sampleRate, start;
char blank[] = "";
char *filename=NULL, *history=NULL;
char channel[MAX_STR_LEN], x_unit[MAX_STR_LEN], y_unit[MAX_STR_LEN], kind[MAX_STR_LEN];
PyObject *temp;
char msg[MAX_STR_LEN];
PyObject *channellist, *channellist_iter, *framedict, *array;
PyArrayIterObject *arrayIter;
PyArray_Descr *temp_descr;
static char *kwlist[] = {"filename", "channellist", "history", "verbose",
NULL};
/*--------------- unpack arguments --------------------*/
verbose = 0;
/* The | in the format string indicates the next arguments are
optional. They are simply not assigned anything. */
if (!PyArg_ParseTupleAndKeywords(args, keywds, "sO|si", kwlist,
&filename, &channellist, &history, &verbose)) {
Py_RETURN_NONE;
}
FrLibSetLvl(verbose);
if (history == NULL) {
history = blank;
}
/*-------- create frames, create vectors, and fill them. ------*/
// Channel-list must be any type of sequence
if (!PySequence_Check(channellist)) {
PyErr_SetNone(PyExc_TypeError);
return NULL;
}
// Get channel name from first dictionary
framedict = PySequence_GetItem(channellist, (Py_ssize_t)0);
if (framedict == NULL) {
PyErr_SetString(PyExc_ValueError, "channellist is empty!");
return NULL;
}
PyDict_ExtractString(channel, framedict, "name");
Py_XDECREF(framedict);
if (PyErr_Occurred()) {return NULL;}
if (verbose > 0) {
printf("Creating frame %s...\n", channel);
}
frame = FrameNew(channel);
if (frame == NULL) {
snprintf(msg, MAX_STR_LEN, "FrameNew failed (%s)", FrErrorGetHistory());
PyErr_SetString(PyExc_FrError, msg);
return NULL;
}
if (verbose > 0) {
printf("Now iterating...\n");
}
// Iterators allow one to deal with non-contiguous arrays
channellist_iter = PyObject_GetIter(channellist);
arrayIter = NULL;
while ((framedict = PyIter_Next(channellist_iter))) {
if (verbose > 0) {
printf("In loop...\n");
}
// Extract quantities from dict -- all borrowed references
PyDict_ExtractString(channel, framedict, "name");
CHECK_ERROR;
start = PyDict_ExtractDouble(framedict, "start");
CHECK_ERROR;
dx = PyDict_ExtractDouble(framedict, "dx");
CHECK_ERROR;
array = PyDict_GetItemString(framedict, "data");
if (!PyArray_Check(array)) {
snprintf(msg, MAX_STR_LEN, "data is not an array");
PyErr_SetString(PyExc_TypeError, msg);
}
CHECK_ERROR;
nData = PyArray_SIZE(array);
nBits = PyArray_ITEMSIZE(array)*8;
arrayType = PyArray_TYPE(array);
// kind, x_unit, y_unit, type, and subType have default values
temp = PyDict_GetItemString(framedict, "kind");
if (temp != NULL) {strncpy(kind, PyString_AsString(temp), MAX_STR_LEN);}
else {snprintf(kind, MAX_STR_LEN, "PROC");}
temp = PyDict_GetItemString(framedict, "x_unit");
if (temp != NULL) {strncpy(x_unit, PyString_AsString(temp), MAX_STR_LEN);}
else {strncpy(x_unit, blank, MAX_STR_LEN);}
temp = PyDict_GetItemString(framedict, "y_unit");
if (temp != NULL) {strncpy(y_unit, PyString_AsString(temp), MAX_STR_LEN);}
else {strncpy(y_unit, blank, MAX_STR_LEN);}
temp = PyDict_GetItemString(framedict, "type");
if (temp != NULL) {type = (int)PyInt_AsLong(temp);}
else {type = 1;}
temp = PyDict_GetItemString(framedict, "subType");
if (temp != NULL) {subType = (int)PyInt_AsLong(temp);}
else {subType = 0;}
// check for errors
CHECK_ERROR;
if (dx <= 0 || array == NULL || nData==0) {
temp = PyObject_Str(framedict);
snprintf(msg, MAX_STR_LEN, "Input dictionary contents: %s", PyString_AsString(temp));
Py_XDECREF(temp);
FrameFree(frame);
Py_XDECREF(framedict);
Py_XDECREF(channellist_iter);
PyErr_SetString(PyExc_ValueError, msg);
return NULL;
}
if (verbose > 0) {
printf("type = %d, subType = %d, start = %f, dx = %f\n",
type, subType, start, dx);
}
sampleRate = 1./dx;
if (verbose > 0) {
printf("Now copying data to vector...\n");
}
// Create empty vector (-typecode ==> empty) with metadata,
// then copy data to vector
vect = NULL;
arrayIter = (PyArrayIterObject *)PyArray_IterNew(array);
if(arrayType == NPY_INT16) {
vect = FrVectNew1D(channel,-FR_VECT_2S,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataS[arrayIter->index] = *((npy_int16 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
else if(arrayType == NPY_INT32) {
vect = FrVectNew1D(channel,-FR_VECT_4S,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataI[arrayIter->index] = *((npy_int32 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
else if(arrayType == NPY_INT64) {
vect = FrVectNew1D(channel,-FR_VECT_8S,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataL[arrayIter->index] = *((npy_int64 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
else if(arrayType == NPY_UINT8) {
vect = FrVectNew1D(channel,-FR_VECT_1U,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataU[arrayIter->index] = *((npy_uint8 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
else if(arrayType == NPY_UINT16) {
vect = FrVectNew1D(channel,-FR_VECT_2U,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataUS[arrayIter->index] = *((npy_uint16 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
else if(arrayType == NPY_UINT32) {
vect = FrVectNew1D(channel,-FR_VECT_4U,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataUI[arrayIter->index] = *((npy_uint32 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
else if(arrayType == NPY_UINT64) {
vect = FrVectNew1D(channel,-FR_VECT_8U,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataUL[arrayIter->index] = *((npy_uint64 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
else if(arrayType == NPY_FLOAT32) {
vect = FrVectNew1D(channel,-FR_VECT_4R,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataF[arrayIter->index] = *((npy_float32 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
else if(arrayType == NPY_FLOAT64) {
vect = FrVectNew1D(channel,-FR_VECT_8R,nData,dx,x_unit,y_unit);
while (arrayIter->index < arrayIter->size) {
vect->dataD[arrayIter->index] = *((npy_float64 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}}
/* FrVects don't have complex pointers. Numpy stores complex
numbers in the same way, but we have to trick it into giving
us a (real) float pointer. */
else if(arrayType == NPY_COMPLEX64) {
vect = FrVectNew1D(channel,-FR_VECT_8C,nData,dx,x_unit,y_unit);
temp_descr = PyArray_DescrFromType(NPY_FLOAT32);
temp = PyArray_View((PyArrayObject *)array, temp_descr, NULL);
Py_XDECREF(temp_descr);
Py_XDECREF(arrayIter);
arrayIter = (PyArrayIterObject *)PyArray_IterNew(temp);
while (arrayIter->index < arrayIter->size) {
vect->dataF[arrayIter->index] = *((npy_float32 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}
Py_XDECREF(temp);}
else if(arrayType == NPY_COMPLEX128) {
vect = FrVectNew1D(channel,-FR_VECT_16C,nData,dx,x_unit,y_unit);
temp_descr = PyArray_DescrFromType(NPY_FLOAT64);
temp = PyArray_View((PyArrayObject *)array, temp_descr, NULL);
Py_XDECREF(temp_descr);
Py_XDECREF(arrayIter);
arrayIter = (PyArrayIterObject *)PyArray_IterNew(temp);
while (arrayIter->index < arrayIter->size) {
vect->dataD[arrayIter->index] = *((npy_float64 *)arrayIter->dataptr);
PyArray_ITER_NEXT(arrayIter);}
Py_XDECREF(temp);}
else PyErr_SetString(PyExc_TypeError, msg);
if (PyErr_Occurred()) {
if (vect != NULL) FrVectFree(vect);
FrameFree(frame);
Py_XDECREF(framedict);
Py_XDECREF(channellist_iter);
Py_XDECREF(arrayIter);
return NULL;
}
if (verbose > 0) {
printf("Done copying...\n");
FrameDump(frame, stdout, 6);
}
// Add Fr*Data to frame and attach vector to Fr*Data
if (strncmp(kind, "PROC", MAX_STR_LEN)==0) {
proc = FrProcDataNew(frame, channel, sampleRate, 1, nBits);
FrVectFree(proc->data);
proc->data = vect;
proc->type = type;
proc->subType = subType;
frame->GTimeS = (npy_uint32)start;
frame->GTimeN = (npy_uint32)((start-(frame->GTimeS))*1e9);
if (type==1) { // time series
proc->tRange = nData*dx;
frame->dt = nData*dx;
} else if (type==2) { // frequency series
proc->fRange = nData*dx;
}
} else if (strncmp(kind, "ADC", MAX_STR_LEN)==0) {
adc = FrAdcDataNew(frame, channel, sampleRate, 1, nBits);
FrVectFree(adc->data);
adc->data = vect;
frame->dt = nData*dx;
frame->GTimeS = (npy_uint32)start;
frame->GTimeN = (npy_uint32)((start-(frame->GTimeS))*1e9);
} else {// Already tested that kind is one of these strings above
sim = FrSimDataNew(frame, channel, sampleRate, 1, nBits);
FrVectFree(sim->data);
sim->data = vect;
frame->dt = nData*dx;
frame->GTimeS = (npy_uint32)start;
frame->GTimeN = (npy_uint32)((start-(frame->GTimeS))*1e9);
}
if (verbose > 0) {
printf("Attached vect to frame.\n");
}
// Clean up (all python objects in loop should be borrowed references)
Py_XDECREF(framedict);
Py_XDECREF(arrayIter);
} // end iteration over channellist
Py_XDECREF(channellist_iter);
// At this point, there should be no Python references left!
/*------------- Write file -----------------------------*/
oFile = FrFileONewH(filename, 1, history); // 1 ==> gzip contents
if (oFile == NULL) {
snprintf(msg, MAX_STR_LEN, "%s\n", FrErrorGetHistory());
PyErr_SetString(PyExc_FrError, msg);
FrFileOEnd(oFile);
return NULL;
}
if (FrameWrite(frame, oFile) != FR_OK) {
snprintf(msg, MAX_STR_LEN, "%s\n", FrErrorGetHistory());
PyErr_SetString(PyExc_FrError, msg);
FrFileOEnd(oFile);
return NULL;
}
/* The FrFile owns data and vector memory. Do not free them separately. */
FrFileOEnd(oFile);
FrameFree(frame);
Py_RETURN_NONE;
};
