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Added SAXS capabilities to integrator.
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@marinerhemant
marinerhemant committed Sep 3, 2024
1 parent 719baa5 commit e4cc80f
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Showing 2 changed files with 67 additions and 38 deletions.
77 changes: 50 additions & 27 deletions FF_HEDM/src/IntegratorZarr.c
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Original file line number Diff line number Diff line change
Expand Up @@ -351,9 +351,9 @@ int main(int argc, char **argv)
char* arr;
int32_t dsize;
char *resultFolder;
int locImTransOpt, nFrames, nDarks, nFloods, bytesPerPx=2;
int locImTransOpt, locTemp=-1, locPres=-1, locI=-1, locI0=-1, nFrames, nDarks, nFloods, bytesPerPx=2;
int darkLoc=-1,dataLoc=-1,floodLoc=-1;
double Temperature = 0, Pressure = 0;
double *Temperature, *Pressure, *I, *I0;
while ((zip_stat_index(arch, count, 0, finfo)) == 0) {
if (strstr(finfo->name,"analysis/process/analysis_parameters/ResultFolder/0")!=NULL){
arr = calloc(finfo->size + 1, sizeof(char));
Expand Down Expand Up @@ -399,28 +399,6 @@ int main(int argc, char **argv)
free(arr);
free(data);
}
if (strstr(finfo->name,"analysis/process/analysis_parameters/Temperature/0")!=NULL){
arr = calloc(finfo->size + 1, sizeof(char));
fd = zip_fopen_index(arch, count, 0);
zip_fread(fd, arr, finfo->size);
dsize = sizeof(double);
data = (char*)malloc((size_t)dsize);
dsize = blosc1_decompress(arr,data,dsize);
Temperature = *(double *)&data[0];
free(arr);
free(data);
}
if (strstr(finfo->name,"analysis/process/analysis_parameters/Pressure/0")!=NULL){
arr = calloc(finfo->size + 1, sizeof(char));
fd = zip_fopen_index(arch, count, 0);
zip_fread(fd, arr, finfo->size);
dsize = sizeof(double);
data = (char*)malloc((size_t)dsize);
dsize = blosc1_decompress(arr,data,dsize);
Pressure = *(double *)&data[0];
free(arr);
free(data);
}
if (strstr(finfo->name,"analysis/process/analysis_parameters/X/0")!=NULL){
arr = calloc(finfo->size + 1, sizeof(char));
fd = zip_fopen_index(arch, count, 0);
Expand Down Expand Up @@ -797,6 +775,18 @@ int main(int argc, char **argv)
if (strstr(finfo->name,"analysis/process/analysis_parameters/ImTransOpt/0")!=NULL){
locImTransOpt = count;
}
if (strstr(finfo->name,"measurement/process/scan_parameters/Temperature/0")!=NULL){
locTemp = count;
}
if (strstr(finfo->name,"measurement/process/scan_parameters/Pressure/0")!=NULL){
locPres = count;
}
if (strstr(finfo->name,"measurement/process/scan_parameters/I/0")!=NULL){
locI = count;
}
if (strstr(finfo->name,"measurement/process/scan_parameters/I0/0")!=NULL){
locI0 = count;
}
count++;
}
int rc = ReadBins(resultFolder);
Expand All @@ -823,6 +813,34 @@ int main(int argc, char **argv)
nFrames = nFrames - skipFrame; // This ensures we don't over-read.
dataLoc += skipFrame;
darkLoc += skipFrame;
Pressure = (double *) calloc(nFrames,sizeof(*Pressure));
Temperature = (double *) calloc(nFrames,sizeof(*Temperature));
I = (double *) calloc(nFrames,sizeof(*I));
I0 = (double *) calloc(nFrames,sizeof(*I0));
if (locPres >0){
zip_stat_index(arch, locPres, 0, finfo); s = calloc(finfo->size + 1, sizeof(char)); fd = zip_fopen_index(arch, locPres, 0); zip_fread(fd, s, finfo->size);
dsize = (nFrames+skipFrame)*sizeof(double); data = (char*)malloc((size_t)dsize); dsize = blosc1_decompress(s,data,dsize);
for (iter=skipFrame;iter<nFrames+skipFrame;iter++) Pressure[iter-skipFrame] = *(double *)&data[iter+sizeof(double)];
free(s); free(data);
}
if (locTemp > 0){
zip_stat_index(arch, locTemp, 0, finfo); s = calloc(finfo->size + 1, sizeof(char)); fd = zip_fopen_index(arch, locTemp, 0); zip_fread(fd, s, finfo->size);
dsize = (nFrames+skipFrame)*sizeof(double); data = (char*)malloc((size_t)dsize); dsize = blosc1_decompress(s,data,dsize);
for (iter=skipFrame;iter<nFrames+skipFrame;iter++) Temperature[iter-skipFrame] = *(double *)&data[iter+sizeof(double)];
free(s); free(data);
}
if (locI > 0){
zip_stat_index(arch, locI, 0, finfo); s = calloc(finfo->size + 1, sizeof(char)); fd = zip_fopen_index(arch, locI, 0); zip_fread(fd, s, finfo->size);
dsize = (nFrames+skipFrame)*sizeof(double); data = (char*)malloc((size_t)dsize); dsize = blosc1_decompress(s,data,dsize);
for (iter=skipFrame;iter<nFrames+skipFrame;iter++) I[iter-skipFrame] = *(double *)&data[iter+sizeof(double)];
free(s); free(data);
}
if (locI0 > 0){
zip_stat_index(arch, locI0, 0, finfo); s = calloc(finfo->size + 1, sizeof(char)); fd = zip_fopen_index(arch, locI0, 0); zip_fread(fd, s, finfo->size);
dsize = (nFrames+skipFrame)*sizeof(double); data = (char*)malloc((size_t)dsize); dsize = blosc1_decompress(s,data,dsize);
for (iter=skipFrame;iter<nFrames+skipFrame;iter++) I0[iter-skipFrame] = *(double *)&data[iter+sizeof(double)];
free(s); free(data);
}
double *Image;
int a,b;
pixelvalue *ImageIn;
Expand Down Expand Up @@ -982,15 +1000,17 @@ int main(int argc, char **argv)
char *locData;
locData = calloc(NrPixelsY*NrPixelsZ*bytesPerPx,sizeof(*locData));
int32_t dsz = NrPixelsY*NrPixelsZ*bytesPerPx;
double presThis, tempThis, iThis, i0This;
for (i=0;i<nFrames;i++){
if (chunkFiles>0){
if ((i%chunkFiles) == 0){
memset(chunkArr,0,bigArrSize*sizeof(*chunkArr));
firstOme = omeArr[i];
presThis = 0; tempThis = 0; iThis = 0; i0This = 0;
}
}
printf("Processing frame number: %d of %d of file %s.\n",i+1,nFrames,DataFN);

presThis += Pressure[i]; tempThis += Temperature[i]; iThis += I[i]; i0This = I0[i];
dsz = blosc1_decompress(&allData[sizeArr[i*2+1]],locData,dsz);
memcpy(ImageInTU,locData,dsz);
for (j=0;j<NrPixelsY*NrPixelsZ;j++) ImageInT[j] = (double)ImageInTU[j];
Expand Down Expand Up @@ -1091,11 +1111,14 @@ int main(int argc, char **argv)
H5LTmake_dataset_double(file_id, chunkSetName, 2, dim_chunk, chunkArr);
H5LTset_attribute_int(file_id, chunkSetName, "LastFrameNumber", &i, 1);
int nSum = (int)((omeArr[i] - firstOme)/omeStep) + 1;
presThis /= nSum; tempThis /= nSum; iThis /= nSum; i0This /= nSum;
H5LTset_attribute_int(file_id, chunkSetName, "Number Of Frames Summed", &nSum, 1);
H5LTset_attribute_double(file_id, chunkSetName, "FirstOme", &firstOme, 1);
H5LTset_attribute_double(file_id, chunkSetName, "LastOme", &omeArr[i], 1);
H5LTset_attribute_double(file_id, chunkSetName, "Temperature", &Temperature, 1);
H5LTset_attribute_double(file_id, chunkSetName, "Pressure", &Pressure, 1);
H5LTset_attribute_double(file_id, chunkSetName, "Temperature", &tempThis, 1);
H5LTset_attribute_double(file_id, chunkSetName, "Pressure", &presThis, 1);
H5LTset_attribute_double(file_id, chunkSetName, "I", &iThis, 1);
H5LTset_attribute_double(file_id, chunkSetName, "I0", &i0This, 1);
}
}
}
Expand Down
28 changes: 17 additions & 11 deletions utils/ffGenerateZip.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -228,8 +228,24 @@ def applyCorrectionNumba(img,dark,darkpreproc,doStd):
data[stFrame:enFrame,:,:] = dataT
searchStr = 'startOmeOverride'
if searchStr in hf2:
stOmeOver = sp_pro_meas.create_dataset(searchStr,dtype=np.int32,shape=(1,),chunks=(1,),compressor=compressor)
stOmeOver = sp_pro_meas.create_dataset(searchStr,dtype=np.double,shape=(1,),chunks=(1,),compressor=compressor)
stOmeOver[:] = hf2[searchStr][()][0]
searchStr = '/measurement/instrument/GSAS2_PVS/Pressure'
if searchStr in hf2:
pressureDSet = sp_pro_meas.create_dataset(searchStr.split('/')[-1],dtype=np.double,shape=(nFrames,),chunks=(nFrames,),compressor=compressor)
pressureDSet[:] = hf2[searchStr][()]
searchStr = '/measurement/instrument/GSAS2_PVS/Temperature'
if searchStr in hf2:
pressureDSet = sp_pro_meas.create_dataset(searchStr.split('/')[-1],dtype=np.double,shape=(nFrames,),chunks=(nFrames,),compressor=compressor)
pressureDSet[:] = hf2[searchStr][()]
searchStr = '/measurement/instrument/GSAS2_PVS/I'
if searchStr in hf2:
pressureDSet = sp_pro_meas.create_dataset(searchStr.split('/')[-1],dtype=np.double,shape=(nFrames,),chunks=(nFrames,),compressor=compressor)
pressureDSet[:] = hf2[searchStr][()]
searchStr = '/measurement/instrument/GSAS2_PVS/I0'
if searchStr in hf2:
pressureDSet = sp_pro_meas.create_dataset(searchStr.split('/')[-1],dtype=np.double,shape=(nFrames,),chunks=(nFrames,),compressor=compressor)
pressureDSet[:] = hf2[searchStr][()]
hf2.close()
elif 'zip' in InputFN[-5:]:
# This is a zarray dataset. Just copy over the data.
Expand Down Expand Up @@ -779,16 +795,6 @@ def applyCorrectionNumba(img,dark,darkpreproc,doStd):
outArr = np.array([float(line.split()[1])]).astype(np.double)
spWL = sp_pro_analysis.create_dataset(searchStr,dtype=np.double,shape=(1,),chunks=(1,),compressor=compressor)
spWL[:] = outArr
searchStr = 'Temperature'
if line.startswith(f'{searchStr} '):
outArr = np.array([float(line.split()[1])]).astype(np.double)
spTemp = sp_pro_analysis.create_dataset(searchStr,dtype=np.double,shape=(1,),chunks=(1,),compressor=compressor)
spTemp[:] = outArr
searchStr = 'Pressure'
if line.startswith(f'{searchStr} '):
outArr = np.array([float(line.split()[1])]).astype(np.double)
spPr = sp_pro_analysis.create_dataset(searchStr,dtype=np.double,shape=(1,),chunks=(1,),compressor=compressor)
spPr[:] = outArr
searchStr = 'Width'
if line.startswith(f'{searchStr} '):
outArr = np.array([float(line.split()[1])]).astype(np.double)
Expand Down

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