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more consistent whitespace/aligment

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augustin_s
2024-03-22 17:29:35 +01:00
parent d2ce6a8e16
commit 80620d1f14
4 changed files with 198 additions and 173 deletions
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34
peakfinder8/cheetahmodules.h
View File

@ -24,23 +24,23 @@ int killNearbyPeaks(tPeakList*, float );
* - All options are dominantly inherited during assembly and pixel integration (see assembleImage.cpp)
* - The default value for all options is "false"
* */
static const uint16_t PIXEL_IS_PERFECT = 0; // Remember to change this value if necessary after adding a new option
static const uint16_t PIXEL_IS_INVALID = 1; // bit 0
static const uint16_t PIXEL_IS_SATURATED = 2; // bit 1
static const uint16_t PIXEL_IS_HOT = 4; // bit 2
static const uint16_t PIXEL_IS_DEAD = 8; // bit 3
static const uint16_t PIXEL_IS_SHADOWED = 16; // bit 4
static const uint16_t PIXEL_IS_IN_PEAKMASK = 32; // bit 5
static const uint16_t PIXEL_IS_TO_BE_IGNORED = 64; // bit 6
static const uint16_t PIXEL_IS_BAD = 128; // bit 7
static const uint16_t PIXEL_IS_OUT_OF_RESOLUTION_LIMITS = 256; // bit 8
static const uint16_t PIXEL_IS_MISSING = 512; // bit 9
static const uint16_t PIXEL_IS_NOISY = 1024; // bit 10
static const uint16_t PIXEL_IS_ARTIFACT_CORRECTED = 2048; // bit 11
static const uint16_t PIXEL_FAILED_ARTIFACT_CORRECTION = 4096; // bit 12
static const uint16_t PIXEL_IS_PEAK_FOR_HITFINDER = 8192; // bit 13
static const uint16_t PIXEL_IS_PHOTON_BACKGROUND_CORRECTED = 16384; // bit 14
static const uint16_t PIXEL_IS_ALL = PIXEL_IS_INVALID | PIXEL_IS_SATURATED | PIXEL_IS_HOT | PIXEL_IS_DEAD | PIXEL_IS_SHADOWED | PIXEL_IS_IN_PEAKMASK | PIXEL_IS_TO_BE_IGNORED | PIXEL_IS_BAD | PIXEL_IS_OUT_OF_RESOLUTION_LIMITS | PIXEL_IS_MISSING | PIXEL_IS_NOISY | PIXEL_IS_ARTIFACT_CORRECTED | PIXEL_FAILED_ARTIFACT_CORRECTION | PIXEL_IS_PEAK_FOR_HITFINDER | PIXEL_IS_PHOTON_BACKGROUND_CORRECTED; // all bits
static const uint16_t PIXEL_IS_PERFECT = 0; // Remember to change this value if necessary after adding a new option
static const uint16_t PIXEL_IS_INVALID = 1; // bit 0
static const uint16_t PIXEL_IS_SATURATED = 2; // bit 1
static const uint16_t PIXEL_IS_HOT = 4; // bit 2
static const uint16_t PIXEL_IS_DEAD = 8; // bit 3
static const uint16_t PIXEL_IS_SHADOWED = 16; // bit 4
static const uint16_t PIXEL_IS_IN_PEAKMASK = 32; // bit 5
static const uint16_t PIXEL_IS_TO_BE_IGNORED = 64; // bit 6
static const uint16_t PIXEL_IS_BAD = 128; // bit 7
static const uint16_t PIXEL_IS_OUT_OF_RESOLUTION_LIMITS = 256; // bit 8
static const uint16_t PIXEL_IS_MISSING = 512; // bit 9
static const uint16_t PIXEL_IS_NOISY = 1024; // bit 10
static const uint16_t PIXEL_IS_ARTIFACT_CORRECTED = 2048; // bit 11
static const uint16_t PIXEL_FAILED_ARTIFACT_CORRECTION = 4096; // bit 12
static const uint16_t PIXEL_IS_PEAK_FOR_HITFINDER = 8192; // bit 13
static const uint16_t PIXEL_IS_PHOTON_BACKGROUND_CORRECTED = 16384; // bit 14
static const uint16_t PIXEL_IS_ALL = PIXEL_IS_INVALID | PIXEL_IS_SATURATED | PIXEL_IS_HOT | PIXEL_IS_DEAD | PIXEL_IS_SHADOWED | PIXEL_IS_IN_PEAKMASK | PIXEL_IS_TO_BE_IGNORED | PIXEL_IS_BAD | PIXEL_IS_OUT_OF_RESOLUTION_LIMITS | PIXEL_IS_MISSING | PIXEL_IS_NOISY | PIXEL_IS_ARTIFACT_CORRECTED | PIXEL_FAILED_ARTIFACT_CORRECTION | PIXEL_IS_PEAK_FOR_HITFINDER | PIXEL_IS_PHOTON_BACKGROUND_CORRECTED; // all bits
//
inline bool isAnyOfBitOptionsSet(uint16_t value, uint16_t option) {return ((value & option)!=0);}
//--------------------------------------------------------------------------------------------------------------------

110
peakfinder8/cython/peakfinder8_extension.pyx
View File

@ -9,49 +9,66 @@ from libc.stdlib cimport malloc, free
cdef extern from "peakfinders.h":
ctypedef struct tPeakList:
long nPeaks
long nHot
float peakResolution
float peakResolutionA
float peakDensity
float peakNpix
float peakTotal
int memoryAllocated
long nPeaks_max
long nPeaks
long nHot
float peakResolution
float peakResolutionA
float peakDensity
float peakNpix
float peakTotal
int memoryAllocated
long nPeaks_max
float *peak_maxintensity
float *peak_totalintensity
float *peak_sigma
float *peak_snr
float *peak_npix
float *peak_com_x
float *peak_com_y
long *peak_com_index
float *peak_com_x_assembled
float *peak_com_y_assembled
float *peak_com_r_assembled
float *peak_com_q
float *peak_com_res
float *peak_maxintensity
float *peak_totalintensity
float *peak_sigma
float *peak_snr
float *peak_npix
float *peak_com_x
float *peak_com_y
long *peak_com_index
float *peak_com_x_assembled
float *peak_com_y_assembled
float *peak_com_r_assembled
float *peak_com_q
float *peak_com_res
void allocatePeakList(tPeakList* peak_list, long max_num_peaks)
void freePeakList(tPeakList peak_list)
cdef extern from "peakfinder8.hh":
int peakfinder8(tPeakList *peaklist,
float *data, char *mask, float *pix_r, long asic_nx, long asic_ny,
long nasics_x, long nasics_y, float ADCthresh, float hitfinderMinSNR,
long hitfinderMinPixCount, long hitfinderMaxPixCount,
long hitfinderLocalBGRadius)
int peakfinder8(
tPeakList *peaklist,
float *data,
char *mask,
float *pix_r,
long asic_nx,
long asic_ny,
long nasics_x,
long nasics_y,
float ADCthresh,
float hitfinderMinSNR,
long hitfinderMinPixCount,
long hitfinderMaxPixCount,
long hitfinderLocalBGRadius
)
def peakfinder_8(int max_num_peaks,
numpy.ndarray[numpy.float32_t, ndim=2, mode="c"] data,
numpy.ndarray[numpy.int8_t, ndim=2, mode="c"] mask,
numpy.ndarray[numpy.float32_t, ndim=2, mode="c"] pix_r,
long asic_nx, long asic_ny,
long nasics_x, long nasics_y, float adc_thresh, float hitfinder_min_snr,
long hitfinder_min_pix_count, long hitfinder_max_pix_count,
long hitfinder_local_bg_radius):
def peakfinder_8(
int max_num_peaks,
numpy.ndarray[numpy.float32_t, ndim=2, mode="c"] data,
numpy.ndarray[numpy.int8_t, ndim=2, mode="c"] mask,
numpy.ndarray[numpy.float32_t, ndim=2, mode="c"] pix_r,
long asic_nx,
long asic_ny,
long nasics_x,
long nasics_y,
float adc_thresh,
float hitfinder_min_snr,
long hitfinder_min_pix_count,
long hitfinder_max_pix_count,
long hitfinder_local_bg_radius
):
cdef numpy.int8_t *mask_pointer = &mask[0,0]
cdef char *mask_char_pointer = <char*> mask_pointer
@ -59,10 +76,21 @@ def peakfinder_8(int max_num_peaks,
cdef tPeakList peak_list
allocatePeakList(&peak_list, max_num_peaks)
peakfinder8(&peak_list, &data[0,0], mask_char_pointer, &pix_r[0,0],
asic_nx, asic_ny, nasics_x, nasics_y,
adc_thresh, hitfinder_min_snr, hitfinder_min_pix_count,
hitfinder_max_pix_count, hitfinder_local_bg_radius)
peakfinder8(
&peak_list,
&data[0,0],
mask_char_pointer,
&pix_r[0,0],
asic_nx,
asic_ny,
nasics_x,
nasics_y,
adc_thresh,
hitfinder_min_snr,
hitfinder_min_pix_count,
hitfinder_max_pix_count,
hitfinder_local_bg_radius
)
cdef int i
cdef float peak_x, peak_y, peak_value
@ -71,10 +99,10 @@ def peakfinder_8(int max_num_peaks,
cdef vector[double] peak_list_value
num_peaks = peak_list.nPeaks
if num_peaks > max_num_peaks:
num_peaks = max_num_peaks
for i in range(0, num_peaks):
peak_x = peak_list.peak_com_x[i]

223
peakfinder8/peakfinders.cpp
View File

@ -20,54 +20,53 @@
* Create arrays for remembering Bragg peak data
*/
void allocatePeakList(tPeakList *peak, long NpeaksMax) {
peak->nPeaks = 0;
peak->nPeaks_max = NpeaksMax;
peak->nHot = 0;
peak->peakResolution = 0;
peak->peakResolutionA = 0;
peak->peakDensity = 0;
peak->peakNpix = 0;
peak->peakTotal = 0;
peak->nPeaks = 0;
peak->nPeaks_max = NpeaksMax;
peak->nHot = 0;
peak->peakResolution = 0;
peak->peakResolutionA = 0;
peak->peakDensity = 0;
peak->peakNpix = 0;
peak->peakTotal = 0;
peak->peak_maxintensity = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_totalintensity = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_sigma = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_snr = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_npix = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_com_x = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_com_y = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_com_index = (long *) calloc(NpeaksMax, sizeof(long));
peak->peak_com_x_assembled = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_com_y_assembled = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_com_r_assembled = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_com_q = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_com_res = (float *) calloc(NpeaksMax, sizeof(float));
peak->memoryAllocated = 1;
peak->peak_maxintensity = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_totalintensity = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_sigma = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_snr = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_npix = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_com_x = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_com_y = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_com_index = (long *) calloc(NpeaksMax, sizeof(long));
peak->peak_com_x_assembled = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_com_y_assembled = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_com_r_assembled = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_com_q = (float *) calloc(NpeaksMax, sizeof(float));
peak->peak_com_res = (float *) calloc(NpeaksMax, sizeof(float));
peak->memoryAllocated = 1;
}
/*
* Clean up Bragg peak arrays
*/
void freePeakList(tPeakList peak) {
free(peak.peak_maxintensity);
free(peak.peak_totalintensity);
free(peak.peak_sigma);
free(peak.peak_snr);
free(peak.peak_npix);
free(peak.peak_com_x);
free(peak.peak_com_y);
free(peak.peak_com_index);
free(peak.peak_com_x_assembled);
free(peak.peak_com_y_assembled);
free(peak.peak_com_r_assembled);
free(peak.peak_com_q);
free(peak.peak_com_res);
peak.memoryAllocated = 0;
free(peak.peak_maxintensity);
free(peak.peak_totalintensity);
free(peak.peak_sigma);
free(peak.peak_snr);
free(peak.peak_npix);
free(peak.peak_com_x);
free(peak.peak_com_y);
free(peak.peak_com_index);
free(peak.peak_com_x_assembled);
free(peak.peak_com_y_assembled);
free(peak.peak_com_r_assembled);
free(peak.peak_com_q);
free(peak.peak_com_res);
peak.memoryAllocated = 0;
}
/*
* Peakfinder 8
* Version before modifications during Cherezov December 2014 LE80
@ -100,7 +99,7 @@ int peakfinder8(tPeakList *peaklist, float *data, char *mask, float *pix_r, long
long e;
long *inx = (long *) calloc(pix_nn, sizeof(long));
long *iny = (long *) calloc(pix_nn, sizeof(long));
float thisI, thisIraw;
float thisI, thisIraw;
float totI,totIraw;
float maxI, maxIraw;
float snr;
@ -160,100 +159,100 @@ int peakfinder8(tPeakList *peaklist, float *data, char *mask, float *pix_r, long
long *peakpixels = (long *) calloc(hitfinderMaxPixCount, sizeof(long));
char *peakpixel = (char *) calloc(pix_nn, sizeof(char));
char *rthreshold_changed = (char *) malloc(lmaxr*sizeof(char));
char *rthreshold_changed = (char *) malloc(lmaxr*sizeof(char));
int *pix_rint = (int *) malloc(pix_nn*sizeof(int));
long *pixels_check = (long *) malloc(pix_nn*sizeof(long));
int *pix_rint = (int *) malloc(pix_nn*sizeof(int));
long *pixels_check = (long *) malloc(pix_nn*sizeof(long));
long peakCounter = 0;
long peakCounter = 0;
for(long i=0; i<lmaxr; i++) {
rthreshold[i] = 1e9;
rthreshold_changed[i] = 1;
rthreshold_changed[i] = 1;
}
for(long i=0;i<pix_nn;i++){
pix_rint[i] = lrint(pix_r[i]);
pixels_check[i] = i;
}
long n_pixels_check = pix_nn;
for(long i=0;i<pix_nn;i++){
pix_rint[i] = lrint(pix_r[i]);
pixels_check[i] = i;
}
long n_pixels_check = pix_nn;
// Compute sigma and average of data values at each radius
// From this, compute the ADC threshold to be applied at each radius
// Iterate a few times to reduce the effect of positive outliers (ie: peaks)
long thisr;
float thisoffset, thissigma;
float thisthreshold;
int counter = 0;
bool rthreshold_converged = false;
float thisthreshold;
int counter = 0;
bool rthreshold_converged = false;
//goto END;
//goto END;
// for(long counter=0; counter<5; counter++) {
while ( !rthreshold_converged & counter < 10 ) {
//printf("counter %i %i\n", counter, n_pixels_check);
counter++;
while ( !rthreshold_converged & counter < 10 ) {
//printf("counter %i %i\n", counter, n_pixels_check);
counter++;
//for(long i=0; i<lmaxr; i++) {
// roffset[i] = 0;
// rsigma[i] = 0;
// rcount[i] = 0;
//}
memset(roffset,0,lmaxr*sizeof(float));
memset(rsigma, 0,lmaxr*sizeof(float));
memset(rcount, 0,lmaxr*sizeof(long));
memset(rsigma, 0,lmaxr*sizeof(float));
memset(rcount, 0,lmaxr*sizeof(long));
long new_pixels_check=0;
long new_pixels_check=0;
//for(long i=0;i<pix_nn;i++){
for(long i_pixel=0; i_pixel<n_pixels_check; i_pixel++) {
long i = pixels_check[i_pixel];
thisr = pix_rint[i];
if ( rthreshold_changed[thisr] == 1 ) {
if(mask[i] != 0) {
if(temp[i] < rthreshold[thisr]) {
roffset[thisr] += temp[i];
rsigma[thisr] += (temp[i]*temp[i]);
rcount[thisr] += 1;
}
pixels_check[new_pixels_check] = i;
new_pixels_check++;
}
long i = pixels_check[i_pixel];
thisr = pix_rint[i];
if ( rthreshold_changed[thisr] == 1 ) {
if(mask[i] != 0) {
if(temp[i] < rthreshold[thisr]) {
roffset[thisr] += temp[i];
rsigma[thisr] += (temp[i]*temp[i]);
rcount[thisr] += 1;
}
pixels_check[new_pixels_check] = i;
new_pixels_check++;
}
}
}
n_pixels_check = new_pixels_check;
n_pixels_check = new_pixels_check;
rthreshold_converged = true;
rthreshold_converged = true;
for(long i=0; i<lmaxr; i++) {
if ( rthreshold_changed[i] == 1 ) {
if(rcount[i] == 0) {
roffset[i] = 0;
rsigma[i] = 0;
thisthreshold = 1e9;
//rthreshold[i] = ADCthresh; // For testing
}
else {
thisoffset = roffset[i]/rcount[i];
thissigma = sqrt(rsigma[i]/rcount[i] - (thisoffset)*(thisoffset));
roffset[i] = thisoffset;
rsigma[i] = thissigma;
thisthreshold = roffset[i] + hitfinderMinSNR*rsigma[i];
if(thisthreshold < ADCthresh)
thisthreshold = ADCthresh;
//rthreshold[i] = ADCthresh; // For testing
}
rthreshold_changed[i] = 0;
if ( fabs(thisthreshold-rthreshold[i]) > 0.1*rsigma[i] ) {
rthreshold_changed[i] = 1;
rthreshold_converged = false;
}
rthreshold[i] = thisthreshold;
}
if ( rthreshold_changed[i] == 1 ) {
if(rcount[i] == 0) {
roffset[i] = 0;
rsigma[i] = 0;
thisthreshold = 1e9;
//rthreshold[i] = ADCthresh; // For testing
}
else {
thisoffset = roffset[i]/rcount[i];
thissigma = sqrt(rsigma[i]/rcount[i] - (thisoffset)*(thisoffset));
roffset[i] = thisoffset;
rsigma[i] = thissigma;
thisthreshold = roffset[i] + hitfinderMinSNR*rsigma[i];
if(thisthreshold < ADCthresh)
thisthreshold = ADCthresh;
//rthreshold[i] = ADCthresh; // For testing
}
rthreshold_changed[i] = 0;
if ( fabs(thisthreshold-rthreshold[i]) > 0.1*rsigma[i] ) {
rthreshold_changed[i] = 1;
rthreshold_converged = false;
}
rthreshold[i] = thisthreshold;
}
}
}
com_x=0;
com_y=0;
//goto END;
//goto END;
for(long mj=0; mj<nasics_y; mj++){
for(long mi=0; mi<nasics_x; mi++){
@ -361,21 +360,21 @@ int peakfinder8(tPeakList *peaklist, float *data, char *mask, float *pix_r, long
com_y = peak_com_y/fabs(totI);
com_e = lrint(com_x) + lrint(com_y)*pix_nx;
long com_xi = lrint(com_x) - mi*asic_nx;
long com_yi = lrint(com_y) - mj*asic_ny;
long com_xi = lrint(com_x) - mi*asic_nx;
long com_yi = lrint(com_y) - mj*asic_ny;
/*
* Calculate the local signal-to-noise ratio and local background in an annulus around this peak
* (excluding pixels which look like they might be part of another peak)
*/
float localSigma=0;
float localOffset=0;
long ringWidth = 2*hitfinderLocalBGRadius;
float localSigma=0;
float localOffset=0;
long ringWidth = 2*hitfinderLocalBGRadius;
float sumI = 0;
float sumIsquared = 0;
long np_sigma = 0;
float sumI = 0;
float sumIsquared = 0;
long np_sigma = 0;
long np_counted = 0;
float fbgr;
float backgroundMaxI=0;
@ -474,7 +473,6 @@ int peakfinder8(tPeakList *peaklist, float *data, char *mask, float *pix_r, long
com_e = lrint(com_x) + lrint(com_y)*pix_nx;
/*
* Calculate signal-to-noise and apply SNR criteria
*/
@ -538,7 +536,7 @@ int peakfinder8(tPeakList *peaklist, float *data, char *mask, float *pix_r, long
}
}
//END: ;
//END: ;
free(temp);
free(inx);
@ -552,15 +550,14 @@ int peakfinder8(tPeakList *peaklist, float *data, char *mask, float *pix_r, long
free(rcount);
free(rthreshold);
free(pix_rint);
free(pixels_check);
free(rthreshold_changed);
free(pix_rint);
free(pixels_check);
free(rthreshold_changed);
peaklist->nPeaks = peakCounter;
return(peaklist->nPeaks);
/*************************************************/
}

4
peakfinder8/peakfinders.h
View File

@ -13,8 +13,8 @@
typedef struct {
public:
long nPeaks;
long nHot;
long nPeaks;
long nHot;
float peakResolution; // Radius of 80% of peaks
float peakResolutionA; // Radius of 80% of peaks
float peakDensity; // Density of peaks within this 80% figure