/*
* Wrap the getQChi function so that it can be called from python
*/
static PyObject * DiffractionAnalysisWrap_getQChi(
PyObject *self, PyObject *args) {
double centerX, centerY,distance,energy,alpha,beta,rotation;
double xPixel,yPixel;
double pixelLength,pixelHeight;
double cos_beta,sin_beta;
double cos_alpha,sin_alpha;
double cos_rotation,sin_rotation;
double q,chi;
cos_beta = sin_beta=-10;
cos_alpha=sin_alpha = -10;
cos_rotation=sin_rotation= -10;
PyArg_ParseTuple(args,"ddddddddddd|dddddd",¢erX,
¢erY,&distance,&energy,&alpha,&beta,&rotation,&xPixel,
&yPixel,&pixelLength,&pixelHeight,&cos_beta,
&sin_beta,&cos_alpha,&sin_alpha,&cos_rotation,&sin_rotation);
if (cos_beta == -10) cos_beta = cos(beta*PI/180.0);
if (sin_beta == -10) sin_beta = sin(beta*PI/180.0);
if (cos_alpha == -10) cos_alpha = cos(alpha*PI/180.0);
if (sin_alpha == -10) sin_alpha = sin(alpha*PI/180.0);
if (cos_rotation == -10) cos_rotation = cos(rotation*PI/180.0);
if (sin_rotation == -10) sin_rotation = sin(rotation*PI/180.0);
getQChi(centerX,centerY,distance,energy,
xPixel,yPixel,pixelLength,pixelHeight,rotation,
cos_beta,sin_beta,cos_alpha,sin_alpha,
cos_rotation,sin_rotation,&q,&chi);
return Py_BuildValue("dd",q,chi);
}
void residual(double *p, double *qFit, int m, int n, void *data) {
register int i;
struct everything * useful;
double q,chi;
double rotation;
double cos_beta,sin_beta;
double cos_alpha,sin_alpha;
double cos_rotation,sin_rotation;
useful = (struct everything *)(data);
// calculate sin & cos for later use.
cos_alpha = cos(p[4]*PI/180.0);
sin_alpha = sin(p[4]*PI/180.0);
cos_beta = cos(p[5]*PI/180.0);
sin_beta = sin(p[5]*PI/180.0);
rotation = p[6];
cos_rotation = cos(p[6]*PI/180.0);
sin_rotation = sin(p[6]*PI/180.0);
for (i=0;i<n;i++) {
getQChi(p[0],p[1],p[2],p[3],useful->x[i],useful->y[i],
useful->pixelLength,useful->pixelHeight,rotation,cos_beta,
sin_beta,cos_alpha,sin_alpha,cos_rotation,
sin_rotation,&q,&chi);
qFit[i] = q;
}
}
double QxrdCenterFinder::getChi(double x, double y) const
{
double q,chi;
double beta = get_DetectorTilt()*M_PI/180.0;
double rot = get_TiltPlaneRotation()*M_PI/180.0;
if (get_ImplementTilt()) {
getQChi(get_CenterX(), get_CenterY(), get_DetectorDistance(),
get_Energy(),
x, y, get_DetectorXPixelSize(), get_DetectorYPixelSize(),
rot, cos(beta), sin(beta), 1.0, 0.0, cos(rot), sin(rot),
&q, &chi);
} else {
getQChi(get_CenterX(), get_CenterY(), get_DetectorDistance(),
get_Energy(),
x, y, get_DetectorXPixelSize(), get_DetectorYPixelSize(),
0.0, 1.0, 0.0, 1.0, 0.0, 1.0, 0.0,
&q, &chi);
}
return chi;
}
static PyObject * DiffractionAnalysisWrap_integrate(PyObject *self, PyObject *args) {
PyArrayObject *diffractionData;
PyArrayObject *values;
PyArrayObject *integratedIntensity;
int dimensions[1]; // the dimensions of the integrated intensity
double centerX,centerY,distance,energy,alpha,beta,rotation;
double lower,upper;
int num;
double constraintLower,constraintUpper;
double pixelLength,pixelHeight;
double cos_beta,sin_beta,cos_alpha,sin_alpha,cos_rotation,sin_rotation;
unsigned int * total;
int i;
double x,y;
double q,twoTheta,chi;
int qBin,twoThetaBin,chiBin;
double step;
double intensity;
char *type;
char *constraintType;
int doPolarizationCorrection;
int doConstraint;
double P;
int verbose;
int doGreaterThanMask;
double greaterThanMask;
int doLessThanMask;
double lessThanMask;
int doPolygonMask;
PyArrayObject * polygonsX;
PyArrayObject * polygonsY;
PyArrayObject * polygonBeginningsIndex;
PyArrayObject * polygonNumberOfItems;
verbose = 0;
// get the parameters out of the python call
PyArg_ParseTuple(args,"O!dddddddddiddiidididiO!O!O!O!ddss",
&PyArray_Type,&diffractionData,
¢erX,¢erY,
&distance,
&energy,
&alpha,&beta,&rotation,
&lower,&upper,
&num,
&constraintLower,&constraintUpper,
&doConstraint,
&doPolarizationCorrection,&P,
&doGreaterThanMask,&greaterThanMask,
&doLessThanMask,&lessThanMask,
&doPolygonMask,
&PyArray_Type,&polygonsX,
&PyArray_Type,&polygonsY,
&PyArray_Type,&polygonBeginningsIndex,
&PyArray_Type,&polygonNumberOfItems,
&pixelLength,
&pixelHeight,
&type,
&constraintType);
// the types of integration
// Remeber, strcmp returns 0 when they equal
if (strcmp(type,"Q") != 0 && strcmp(type,"2theta") != 0 && strcmp(type,"chi") != 0) {
PyErr_SetString( PyExc_Exception, "The type of integration must be Q, 2theta, or chi");
return 0;
}
if (verbose) {
printf("Doing Intensity Integration");
printf(" The integration is over '%s'\n",type);
printf(" Constrain the integration? %i\n",doConstraint);
if (doConstraint) {
printf(" The Type of constraint is '%s'\n",constraintType);
}
}
if (doConstraint) {
if (doConstraint && strcmp(type,"Q")==0 && strcmp(constraintType,"chi")!=0) {
PyErr_SetString( PyExc_Exception,
"Cannot perform the desired integration. If the integration type is Q, the constrain integration type must be chi");
return 0;
}
if (doConstraint && strcmp(type,"2theta")==0 && strcmp(constraintType,"chi")!=0) {
PyErr_SetString( PyExc_Exception,
"Cannot perform the desired integration. If the integration type is 2theta, the constrain integration type must be chi");
return 0;
}
if (doConstraint && strcmp(type,"chi")==0 && strcmp(constraintType,"Q")!=0 && strcmp(constraintType,"2theta")!=0) {
PyErr_SetString( PyExc_Exception,
"Cannot perform the desired integration. If the integration type is chi, the constrain integration type must be either Q or 2theta");
return 0;
}
}
// passed array has to be 2 dimensional ints
if (diffractionData->nd != 2 || diffractionData->descr->type_num != PyArray_INT) {
PyErr_SetString(PyExc_Exception,"diffractionData must be two-dimensional and of type integer");
return 0;
}
// create a new Numeric data structure to hold the integrated intensity
dimensions[0]=num;
integratedIntensity=(PyArrayObject *)PyArray_FromDims(1,dimensions,PyArray_DOUBLE);
values = (PyArrayObject *)PyArray_FromDims(1,dimensions,PyArray_DOUBLE);
// store totals also in a regular c data structure.
total = malloc(num*sizeof(unsigned int) );
if (total == NULL) {
PyErr_SetString(PyExc_MemoryError,"No Memeory to create temporary data structure");
return 0;
}
// initialize the data to 0
for (i=0;i<num;i++) {
total[i]=0;
*(double *)(integratedIntensity->data + i*integratedIntensity->strides[0])=0;
}
// calculate sin & cos for later use.
cos_beta = cos(beta*PI/180.0);
sin_beta = sin(beta*PI/180.0);
cos_alpha = cos(alpha*PI/180.0);
sin_alpha = sin(alpha*PI/180.0);
cos_rotation = cos(rotation*PI/180.0);
sin_rotation = sin(rotation*PI/180.0);
// calulate the step size between different bins
step = (upper-lower)*1.0/(num-1.0);
if (verbose) {
printf(" lower = %f, upper = %f\n",lower,upper);
printf(" num = %d, step = %f\n",num,step);
}
for (x=0.0;x<diffractionData->dimensions[0];x++) {
for (y=0.0;y<diffractionData->dimensions[1];y++) {
// treat each type of integration differently
if (strcmp(type,"Q")==0) {
// calculate the q chi cordiante for each pixel
getQChi(centerX,centerY,distance,energy,x,y,pixelLength,
pixelHeight,rotation,cos_beta,sin_beta,cos_alpha,
sin_alpha,cos_rotation,sin_rotation,&q,&chi);
// find the right bin to put it in
qBin = (int)((q-lower)*1.0/step);
// if the bin exists, put it into the bin
if (qBin >=0 && qBin < num) {
// constraint must be of the chi value
// if chi is out of the constraint range, then ignore this value
if (doConstraint && (chi < constraintLower || chi > constraintUpper))
continue;
intensity = (double)*(int *)(diffractionData->data +
((int)x)*diffractionData->strides[0] +
((int)y)*diffractionData->strides[1]);
if (doPolarizationCorrection)
intensity = polarizationCorrection(intensity,P,twoTheta,chi);
// if we are doing maskinging, make sure the intensity has the
// right bounds and is not in a polygon mask. Otherwise, ignore
// the current pixel
if ( (doGreaterThanMask && intensity > greaterThanMask) ||
(doLessThanMask && intensity < lessThanMask) ||
(doPolygonMask && isInPolygons(polygonsX,polygonsY,
polygonBeginningsIndex,polygonNumberOfItems,x,y)))
continue;
total[qBin]+=1;
*(double *)(integratedIntensity->data +
qBin*integratedIntensity->strides[0]) += intensity;
}
} else if (strcmp(type,"2theta")==0) {
getTwoThetaChi(centerX,centerY,distance,x,y,pixelLength,
pixelHeight,rotation,cos_beta,sin_beta,cos_alpha,
sin_alpha,cos_rotation,sin_rotation,&twoTheta,&chi);
// find the right bin to put it in
twoThetaBin = (int)((twoTheta-lower)*1.0/step);
// if the bin exists, put it into the bin
if (twoThetaBin >=0 && twoThetaBin < num) {
// constraint must be of the chi value
// if chi is out of the constraint range, then ignore this value
if (doConstraint && (chi < constraintLower || chi > constraintUpper))
continue;
intensity = (double)*(int *)(diffractionData->data +
((int)x)*diffractionData->strides[0] +
((int)y)*diffractionData->strides[1]);
if (doPolarizationCorrection)
intensity = polarizationCorrection(intensity,P,twoTheta,chi);
// if we are doing maskinging, make sure the intensity has the
// right bounds and is not in a polygon mask. Otherwise, ignore
// the current pixel
if ( (doGreaterThanMask && intensity > greaterThanMask) ||
(doLessThanMask && intensity < lessThanMask) ||
(doPolygonMask && isInPolygons(polygonsX,polygonsY,
polygonBeginningsIndex,polygonNumberOfItems,x,y)))
continue;
total[twoThetaBin]+=1;
*(double *)(integratedIntensity->data +
twoThetaBin*integratedIntensity->strides[0]) += (double)intensity;
}
} else if (strcmp(type,"chi")==0) {
getTwoThetaChi(centerX,centerY,distance,x,y,pixelLength,
pixelHeight,rotation,cos_beta,sin_beta,cos_alpha,
sin_alpha,cos_rotation,sin_rotation,&twoTheta,&chi);
q = convertTwoThetaToQ(twoTheta,convertEnergyToWavelength(energy));
// find the right bin to put it in
chiBin = (int)((chi-lower)*1.0/step);
// chi values can vary from -360 to 360. If our value is not in a bin, check
// if 360-chi fall in a bin. Since the chi range is at most 360 degrees,
// we will never have to bin something in two places.
if (chiBin <0 || chiBin >= num) {
chi-=360;
chiBin = (int)((chi-lower)*1.0/step);
}
// if the bin exists, put it into the bin
if (chiBin >=0 && chiBin < num) {
// if chi is out of the constraint range, then ignore this value
if (doConstraint && strcmp(constraintType,"Q")==0 &&
(q < constraintLower || q > constraintUpper))
continue;
if (doConstraint && strcmp(constraintType,"2theta")==0 &&
(twoTheta < constraintLower || twoTheta > constraintUpper))
continue;
intensity = (double)*(int *)(diffractionData->data +
(int)x*diffractionData->strides[0] +
((int)y)*diffractionData->strides[1]);
if (doPolarizationCorrection)
intensity = polarizationCorrection(intensity,P,twoTheta,chi);
// if we are doing masking, make sure the intensity has the
// right bounds and is not in a polygon mask. Otherwise, ignore
// the current pixel
if ( (doGreaterThanMask && intensity > greaterThanMask) ||
(doLessThanMask && intensity < lessThanMask) ||
(doPolygonMask && isInPolygons(polygonsX,polygonsY,
polygonBeginningsIndex,polygonNumberOfItems,x,y)))
continue;
total[chiBin]+=1;
*(double *)(integratedIntensity->data +
chiBin*integratedIntensity->strides[0]) += intensity;
}
}
}
}
for (i=0;i<num;i++) {
// set the values values
*(double *)(values->data + i*values->strides[0]) = (lower + (i+0.5)*step);
if (total[i]>=1) {
*(double *)(integratedIntensity->data + i*integratedIntensity->strides[0]) /= total[i];
// clip all intensity values to be at least 0.
if (*(double *)(integratedIntensity->data + i*integratedIntensity->strides[0]) < 0)
*(double *)(integratedIntensity->data + i*integratedIntensity->strides[0]) = 0;
} else {
// -1 means nothing was put into the bin
*(double *)(integratedIntensity->data + i*integratedIntensity->strides[0]) = -1;
}
}
// free the array we created so that we do not cause a memory leak
free(total);
// Why I have to do this is described http://mail.python.org/pipermail/python-list/2002-October/167549.html
return Py_BuildValue("NN",values,integratedIntensity);
}
/*
* Finds one particular peak and returns the x,y cordinates of it
* by modifying peakX and peakY
*/
struct both * constantChiSlice(PyArrayObject * diffractionData,double xCenter,
double yCenter,double distance,double energy,double pixelLength,
double pixelHeight,double alpha,double beta,double rotation,double qLower,
double qUpper, double chi,int * numValues) {
double x1,y1;
double x2,y2;
double cos_beta,sin_beta,cos_alpha,sin_alpha,cos_rotation,sin_rotation;
double m;
int xSize,ySize;
double xUpperFirst,yUpperFirst,xLowerFirst,yLowerFirst;
double xUpperSecond,yUpperSecond,xLowerSecond,yLowerSecond;
double xCurrent,yCurrent;
int dataLow,dataHigh;
int xLow,xHigh,yLow,yHigh;
int counter;
double qCurrent,chiCurrent;
double dataInterpolate;
struct both * vals;
cos_beta = cos(beta*PI/180.0);
sin_beta = sin(beta*PI/180.0);
cos_alpha = cos(alpha*PI/180.0);
sin_alpha = sin(alpha*PI/180.0);
cos_rotation = cos(rotation*PI/180.0);
sin_rotation = sin(rotation*PI/180.0);
// find the beginning & ending pixel values for our Q,chi range.
getXY(xCenter,yCenter,distance,energy,qLower,chi,
pixelLength,pixelHeight,rotation,cos_beta,sin_beta,
cos_alpha,sin_alpha,cos_rotation,sin_rotation,&x1,&y1);
getXY(xCenter,yCenter,distance,energy,qUpper,chi,
pixelLength,pixelHeight,rotation,cos_beta,sin_beta,
cos_alpha,sin_alpha,cos_rotation,sin_rotation,&x2,&y2);
xSize = diffractionData->dimensions[0];
ySize = diffractionData->dimensions[0];
// If the two points to find values between are off the image,
// Point the answer to nothing.
if (ceil(x1)<0 || floor(x1)>xSize || ceil(y1)<0 ||
floor(y1)>=ySize || ceil(x2)<0 ||
floor(x2) >= xSize || ceil(y2)<0 || floor(y2)>=ySize) {
return NULL;
}
// Make sure that xLower < xUpper for our first sweep
if (x1>x2) {
xUpperFirst=x1;yUpperFirst=y1;
xLowerFirst=x2;yLowerFirst=y2;
} else {
xLowerFirst=x1;yLowerFirst=y1;
xUpperFirst=x2;yUpperFirst=y2;
}
// Make sure that yLower < yUpperfor our second sweep
if (y1 > y2) {
xUpperSecond=x1;yUpperSecond=y1;
xLowerSecond=x2;yLowerSecond=y2;
} else {
xLowerSecond=x1;yLowerSecond=y1;
xUpperSecond=x2;yUpperSecond=y2;
}
// figure out all the data points to sample
*numValues = ( (int)floor(xUpperFirst)-(int)ceil(xLowerFirst) +1 );
if (yUpperSecond != yLowerSecond)
*numValues += ( (int)floor(yUpperSecond)-(int)ceil(yLowerSecond) +1 );
vals=malloc( sizeof(struct both) );
vals->first = malloc( (*numValues)*sizeof(double) );
vals->second = malloc( (*numValues)*sizeof(double) );
m=(yUpperFirst-yLowerFirst)*1.0/(xUpperFirst-xLowerFirst);
counter=0;
for(xCurrent=ceil(xLowerFirst);xCurrent<=floor(xUpperFirst);xCurrent++) {
// get all points that lie on constant integer y values in the image
yCurrent=yLowerFirst +m*(xCurrent-xLowerFirst);
yHigh = (int)ceil(yCurrent);
yLow = (int)floor(yCurrent);
dataLow=*(int *)(diffractionData->data + ((int)xCurrent)*diffractionData->strides[0] +
yLow*diffractionData->strides[1]);
dataHigh=*(int *)(diffractionData->data + ((int)xCurrent)*diffractionData->strides[0] +
yHigh*diffractionData->strides[1]);
dataInterpolate = dataLow + (yCurrent-yLow)*(dataHigh-dataLow);
getQChi(xCenter,yCenter,distance,energy,xCurrent,yCurrent,
pixelLength,pixelHeight,rotation,cos_beta,sin_beta,cos_alpha,
sin_alpha,cos_rotation,sin_rotation,&qCurrent,&chiCurrent);
vals->first[counter] = qCurrent;
vals->second[counter] = dataInterpolate;
counter++;
}
if (yUpperSecond - yLowerSecond > .00001 ) {
m=(xUpperSecond-xLowerSecond)*1.0/(yUpperSecond-yLowerSecond);
for (yCurrent=(int)ceil(yLowerSecond);yCurrent<=(int)floor(yUpperSecond);yCurrent++) {
// get all points that lie on constant integer x values in the image
xCurrent = xLowerSecond + m*(yCurrent-yLowerSecond);
xHigh=(int)ceil(xCurrent);
xLow=(int)floor(xCurrent);
dataLow=*(int *)(diffractionData->data + xLow*diffractionData->strides[0] +
((int)yCurrent)*diffractionData->strides[1]);
dataHigh=*(int *)(diffractionData->data + xHigh*diffractionData->strides[0] +
((int)yCurrent)*diffractionData->strides[1]);
dataInterpolate = dataLow + (xCurrent-xLow)*(dataHigh-dataLow);
getQChi(xCenter,yCenter,distance,energy,xCurrent,yCurrent,
pixelLength,pixelHeight,rotation,cos_beta,sin_beta,cos_alpha,
sin_alpha,cos_rotation,sin_rotation,&qCurrent,&chiCurrent);
vals->first[counter] = qCurrent;
vals->second[counter] = dataInterpolate;
counter++;
}
}
// now, counter must equal *numValues. Return success
return vals;
}