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Reduce stack pressure (#867)
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@neurolabusc
neurolabusc committed Sep 30, 2024
1 parent b254e16 commit e851138
Showing 1 changed file with 44 additions and 39 deletions.
83 changes: 44 additions & 39 deletions console/nii_dicom_batch.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -8758,7 +8758,8 @@ int saveDcm2Nii(int nConvert, struct TDCMsort dcmSort[], struct TDICOMdata dcmLi
int ret = EXIT_SUCCESS;
// check for repeated echoes - count unique number of echoes
// code below checks for multi-echoes - not required if maxNumberOfEchoes reported in PARREC
int echoNum[kMaxDTI4D];
//reduce stack pressure use malloc, not "int echoNum[kMaxDTI4D];"
int *echoNum = (int *)malloc(kMaxDTI4D * sizeof(int));
int echo = 1;
for (int i = 0; i < dcmList[indx].xyzDim[4]; i++)
echoNum[i] = 0;
Expand All @@ -8772,6 +8773,7 @@ int saveDcm2Nii(int nConvert, struct TDCMsort dcmSort[], struct TDICOMdata dcmLi
echoNum[i] = echo;
}
}
free(echoNum);
if (echo > 1)
dcmList[indx].isMultiEcho = true;
// check for repeated volumes
Expand All @@ -8793,48 +8795,47 @@ int saveDcm2Nii(int nConvert, struct TDCMsort dcmSort[], struct TDICOMdata dcmLi
}
}
// bvec/bval saved for each series (real, phase, magnitude, imaginary) https://github.com/rordenlab/dcm2niix/issues/219
TDTI4D dti4Ds = *dti4D;
// Allocate memory for dti4Ds on the heap
TDTI4D *dti4Ds = (TDTI4D *)malloc(sizeof(TDTI4D));
if (dti4Ds == NULL) {
perror("Failed to allocate memory for dti4Ds");
exit(EXIT_FAILURE);
}
// Copy the content from the original dti4D into dti4Ds
*dti4Ds = *dti4D;
bool isHasDti = (dcmList[indx].CSA.numDti > 0);
if ((isHasDti) && (dcmList[indx].CSA.numDti == dcmList[indx].xyzDim[4])) {
int nDti = 0;
for (int i = 0; i < dcmList[indx].xyzDim[4]; i++) {
if (dti4D->gradDynVol[i] == 1) {
dti4Ds.S[nDti].V[0] = dti4Ds.S[i].V[0];
dti4Ds.S[nDti].V[1] = dti4Ds.S[i].V[1];
dti4Ds.S[nDti].V[2] = dti4Ds.S[i].V[2];
dti4Ds.S[nDti].V[3] = dti4Ds.S[i].V[3];
dti4Ds->S[nDti].V[0] = dti4Ds->S[i].V[0];
dti4Ds->S[nDti].V[1] = dti4Ds->S[i].V[1];
dti4Ds->S[nDti].V[2] = dti4Ds->S[i].V[2];
dti4Ds->S[nDti].V[3] = dti4Ds->S[i].V[3];
nDti++;
}
}
dcmList[indx].CSA.numDti = nDti;
}
// save each series
// Save each series
bool isScaleVariesEnh = dcmList[indx].isScaleVariesEnh; // issue363: any variation in any image
float intenScale = dcmList[indx].intenScale;
float intenIntercept = dcmList[indx].intenIntercept;
float intenScalePhilips = dcmList[indx].intenScalePhilips;
float RWVIntercept = dcmList[indx].RWVIntercept;
float RWVScale = dcmList[indx].RWVScale;
for (int s = 1; s <= series; s++) {
// issue461: assert these values as saveDcm2NiiCore modifies them when it applies Philips scaling
// Reassign these values as saveDcm2NiiCore modifies them
dcmList[indx].intenScale = intenScale;
dcmList[indx].intenIntercept = intenIntercept;
dcmList[indx].intenScalePhilips = intenScalePhilips;
dcmList[indx].RWVIntercept = RWVIntercept;
dcmList[indx].RWVScale = RWVScale;
// for (int i = 0; i < dcmList[indx].xyzDim[4]; i++) //for each volume
// printf("%g<<<!\n", dti4D->triggerDelayTime[i]);
for (int i = 0; i < dcmList[indx].xyzDim[4]; i++) { // for each volume
// Iterate through each volume
for (int i = 0; i < dcmList[indx].xyzDim[4]; i++) {
if (dti4D->gradDynVol[i] == s) {
// dti4D->gradDynVol[i] = s;
// nVol ++;
dcmList[indx].TE = dti4D->TE[i];
dcmList[indx].TR = dti4D->TR[i];
// dcmList[indx].intenScale = dti4D->intenScale[i];
// dcmList[indx].intenIntercept = dti4D->intenIntercept[i];
// dcmList[indx].intenScalePhilips = dti4D->intenScalePhilips[i];
// dcmList[indx].RWVScale = dti4D->RWVScale[i];
// dcmList[indx].RWVIntercept = dti4D->RWVIntercept[i];
dcmList[indx].isHasPhase = dti4D->isPhase[i];
dcmList[indx].isHasReal = dti4D->isReal[i];
dcmList[indx].isHasImaginary = dti4D->isImaginary[i];
Expand All @@ -8845,41 +8846,45 @@ int saveDcm2Nii(int nConvert, struct TDCMsort dcmSort[], struct TDICOMdata dcmLi
}
}
dcmList[indx].isScaleVariesEnh = false;
if (isScaleVariesEnh) { // check if intensity scale varies for this particular output image, this will force 32-bit output
if (isScaleVariesEnh) {
int nz = 0;
for (int i = 0; i < dcmList[indx].xyzDim[4]; i++) { // for each volume
for (int i = 0; i < dcmList[indx].xyzDim[4]; i++) {
if (dti4D->gradDynVol[i] == s) {
for (int z = 0; z < dcmList[indx].xyzDim[3]; z++) { // for each slice
for (int z = 0; z < dcmList[indx].xyzDim[3]; z++) {
int ix = (i * dcmList[indx].xyzDim[3]) + z;
dti4Ds.intenScale[nz] = dti4D->intenScale[ix];
dti4Ds.intenIntercept[nz] = dti4D->intenIntercept[ix];
dti4Ds.intenScalePhilips[nz] = dti4D->intenScalePhilips[ix];
dti4Ds.RWVIntercept[nz] = dti4D->RWVIntercept[ix];
dti4Ds.RWVScale[nz] = dti4D->RWVScale[ix];
dti4Ds->intenScale[nz] = dti4D->intenScale[ix];
dti4Ds->intenIntercept[nz] = dti4D->intenIntercept[ix];
dti4Ds->intenScalePhilips[nz] = dti4D->intenScalePhilips[ix];
dti4Ds->RWVIntercept[nz] = dti4D->RWVIntercept[ix];
dti4Ds->RWVScale[nz] = dti4D->RWVScale[ix];
nz++;
} // for z: each slice
} // if series matches
} // for each volume
}
}
}
for (int i = 0; i < nz; i++) {
if (dti4Ds.intenIntercept[i] != dti4Ds.intenIntercept[0])
if (dti4Ds->intenIntercept[i] != dti4Ds->intenIntercept[0])
dcmList[indx].isScaleVariesEnh = true;
if (dti4Ds.intenScale[i] != dti4Ds.intenScale[0])
if (dti4Ds->intenScale[i] != dti4Ds->intenScale[0])
dcmList[indx].isScaleVariesEnh = true;
if (dti4Ds.intenScalePhilips[i] != dti4Ds.intenScalePhilips[0])
if (dti4Ds->intenScalePhilips[i] != dti4Ds->intenScalePhilips[0])
dcmList[indx].isScaleVariesEnh = true;
}
dcmList[indx].intenScale = dti4Ds.intenScale[0];
dcmList[indx].intenIntercept = dti4Ds.intenIntercept[0];
dcmList[indx].intenScalePhilips = dti4Ds.intenScalePhilips[0];
dcmList[indx].RWVIntercept = dti4Ds.RWVIntercept[0];
dcmList[indx].RWVScale = dti4Ds.RWVScale[0];

dcmList[indx].intenScale = dti4Ds->intenScale[0];
dcmList[indx].intenIntercept = dti4Ds->intenIntercept[0];
dcmList[indx].intenScalePhilips = dti4Ds->intenScalePhilips[0];
dcmList[indx].RWVIntercept = dti4Ds->RWVIntercept[0];
dcmList[indx].RWVScale = dti4Ds->RWVScale[0];
}
if (s > 1)
dcmList[indx].CSA.numDti = 0; // only save bvec for first type (magnitude)
int ret2 = saveDcm2NiiCore(nConvert, dcmSort, dcmList, nameList, opts, &dti4Ds, s);
// Call the save function, passing the pointer to dti4Ds
int ret2 = saveDcm2NiiCore(nConvert, dcmSort, dcmList, nameList, opts, dti4Ds, s);
if (ret2 != EXIT_SUCCESS)
ret = ret2; // return EXIT_SUCCESS only if ALL are successful
ret = ret2;
}
// Free the heap-allocated memory
free(dti4Ds);
return ret;
} // saveDcm2Nii()

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