Rearchitect and Reinstate GPU

[onurulgen]

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⚡ Code Analysis Results ⚡

🔴 cppcheck found 122 issues! Click here to see details.

niftyreg/reg-io/png/lpng1510/png.c

Lines 77 to 82 in aac260c

	png_uint_32 save_flags=p->flags;
	png_alloc_size_t num_bytes;
	if (png_ptr == NULL)
	return (NULL);

!Line: 77 - warning: Either the condition 'png_ptr==NULL' is redundant or there is possible null pointer dereference: p. [nullPointerRedundantCheck]

!Line: 80 - note: Assuming that condition 'png_ptr==NULL' is not redundant
!Line: 76 - note: p is assigned '(struct png_struct_def*)png_ptr' here.
!Line: 77 - note: Null pointer dereference

niftyreg/reg-io/niftilib/nifti1_io.c

Lines 6347 to 6352 in aac260c

	buf = (char *)realloc((void *)buf, nbuf+1); /* cut back to proper length */
	if( !buf ) Rc_fprintf_stderr("** NITA: failed to realloc %d bytes\n",nbuf+1);
	return buf ;
	#endif
	}

!Line: 6347 - error: Common realloc mistake: 'buf' nulled but not freed upon failure [memleakOnRealloc]

niftyreg/reg-io/niftilib/nifti1_io.c

Lines 3220 to 3225 in aac260c

	const int cmp = strcmp(test_ext, known_ext);
	if( cmp == 0 ) return cmp;
	/* if anything odd, use default */
	if( !test_ext || !known_ext ) return cmp;

!Line: 3220 - warning: Either the condition '!test_ext' is redundant or there is possible null pointer dereference: test_ext. [nullPointerRedundantCheck]

!Line: 3224 - note: Assuming that condition '!test_ext' is not redundant
!Line: 3220 - note: Null pointer dereference

niftyreg/reg-io/niftilib/nifti1_io.c

Lines 3220 to 3225 in aac260c

	const int cmp = strcmp(test_ext, known_ext);
	if( cmp == 0 ) return cmp;
	/* if anything odd, use default */
	if( !test_ext || !known_ext ) return cmp;

!Line: 3220 - warning: Either the condition '!known_ext' is redundant or there is possible null pointer dereference: known_ext. [nullPointerRedundantCheck]

!Line: 3224 - note: Assuming that condition '!known_ext' is not redundant
!Line: 3220 - note: Null pointer dereference

niftyreg/reg-io/niftilib/nifti1_io.c

Lines 3245 to 3250 in aac260c

	const int cmp = strncmp(test_ext, known_ext, maxlen);
	if( cmp == 0 ) return cmp;
	/* if anything odd, use default */
	if( !test_ext || !known_ext ) return cmp;

!Line: 3245 - warning: Either the condition '!test_ext' is redundant or there is possible null pointer dereference: test_ext. [nullPointerRedundantCheck]

!Line: 3249 - note: Assuming that condition '!test_ext' is not redundant
!Line: 3245 - note: Null pointer dereference

niftyreg/reg-io/niftilib/nifti1_io.c

Lines 3245 to 3250 in aac260c

	const int cmp = strncmp(test_ext, known_ext, maxlen);
	if( cmp == 0 ) return cmp;
	/* if anything odd, use default */
	if( !test_ext || !known_ext ) return cmp;

!Line: 3245 - warning: Either the condition '!known_ext' is redundant or there is possible null pointer dereference: known_ext. [nullPointerRedundantCheck]

!Line: 3249 - note: Assuming that condition '!known_ext' is not redundant
!Line: 3245 - note: Null pointer dereference

niftyreg/reg-io/png/lpng1510/pngread.c

Lines 1104 to 1109 in aac260c

	png_memcpy(png_ptr->longjmp_buffer, tmp_jmp, png_sizeof(jmp_buf));
	#endif
	}
	void PNGAPI

!Line: 1104 - error: Uninitialized variable: tmp_jmp [uninitvar]

niftyreg/reg-io/png/lpng1510/pngwrite.c

Lines 1017 to 1022 in aac260c

	png_memcpy(png_ptr->longjmp_buffer, tmp_jmp, png_sizeof(jmp_buf));
	#endif
	}
	/* Allow the application to select one or more row filters to use. */
	void PNGAPI

!Line: 1017 - error: Uninitialized variable: tmp_jmp [uninitvar]

niftyreg/reg-io/png/reg_png.cpp

Lines 131 to 136 in aac260c

	delete []row_pointers;
	png_destroy_read_struct(&png_ptr, &info_ptr, nullptr);
	fclose (pngFile);
	nifti_set_filenames(niiImage, pngFileName,0,0);
	return niiImage;

!Line: 131 - error: Memory is allocated but not initialized: row_pointers [uninitdata]

https://github.com/onurulgen/niftyreg/blob/aac260c9d15cb37d0a0852c48f45071f56c0cf54/build/third-party/eigen3/Eigen/src/Core/util/Macros.h#L657-L662

!Line: 657 - error: #error Please tell me what is the equivalent of __attribute__((aligned(n))) for your compiler [preprocessorErrorDirective]

niftyreg/reg-lib/cpu/_reg_localTrans.cpp

Lines 1821 to 1826 in aac260c

	memcpy(oldGrid, gridPtrX, splineControlPoint->nvox * splineControlPoint->nbyper);
	if (splineControlPoint->data != nullptr) free(splineControlPoint->data);
	int oldDim[4];
	oldDim[0] = splineControlPoint->dim[0];
	oldDim[1] = splineControlPoint->dim[1];
	oldDim[2] = splineControlPoint->dim[2];

!Line: 1821 - warning: Either the condition 'splineControlPoint->data!=nullptr' is redundant or there is possible null pointer dereference: gridPtrX. [nullPointerRedundantCheck]

!Line: 1822 - note: Assuming that condition 'splineControlPoint->data!=nullptr' is not redundant
!Line: 1820 - note: gridPtrX is assigned 'static_cast<float*>(splineControlPoint->data)' here.
!Line: 1821 - note: Null pointer dereference

niftyreg/reg-lib/cpu/_reg_localTrans.cpp

Lines 1728 to 1733 in aac260c

	memcpy(oldGrid, gridPtrX, splineControlPoint->nvox * splineControlPoint->nbyper);
	if (splineControlPoint->data != nullptr) free(splineControlPoint->data);
	int oldDim[4];
	oldDim[0] = splineControlPoint->dim[0];
	oldDim[1] = splineControlPoint->dim[1];
	oldDim[2] = splineControlPoint->dim[2];

!Line: 1728 - warning: Either the condition 'splineControlPoint->data!=nullptr' is redundant or there is possible null pointer dereference: gridPtrX. [nullPointerRedundantCheck]

!Line: 1729 - note: Assuming that condition 'splineControlPoint->data!=nullptr' is not redundant
!Line: 1727 - note: gridPtrX is assigned 'static_cast<float*>(splineControlPoint->data)' here.
!Line: 1728 - note: Null pointer dereference

niftyreg/reg-lib/cpu/_reg_localTrans.cpp

Lines 1112 to 1117 in aac260c

	if (gridVoxelSpacing[0] == 5. && gridVoxelSpacing[0] == 5. && gridVoxelSpacing[0] == 5. && forceNoLut == false) {
	// Assign a single array that will contain all coefficients
	DataType *coefficients = (DataType*)malloc(125 * 64 * sizeof(DataType));
	// Compute and store all required coefficients
	int coeff_index;
	#ifdef _OPENMP

!Line: 1112 - style: Same expression 'gridVoxelSpacing[0]==5.' found multiple times in chain of '&&' operators. [duplicateExpression]

niftyreg/reg-lib/cpu/_reg_localTrans.cpp

Lines 3756 to 3761 in aac260c

	(jacImg1[i].m[0][0] * img2DispPtrX[i] +
	jacImg1[i].m[0][1] * img2DispPtrY[i] +
	jacImg1[i].m[0][2] * img2DispPtrZ[i]);
	resPtrY[i] =
	(jacImg2[i].m[1][0] * img1DispPtrX[i] +
	jacImg2[i].m[1][1] * img1DispPtrY[i] +

!Line: 3756 - error: Memory is allocated but not initialized: jacImg1[i].m[0][0] [uninitdata]

niftyreg/reg-lib/cpu/_reg_localTrans.cpp

Lines 3782 to 3787 in aac260c

	(jacImg1[i].m[0][0] * img2DispPtrX[i] +
	jacImg1[i].m[0][1] * img2DispPtrY[i]);
	resPtrY[i] =
	(jacImg2[i].m[1][0] * img1DispPtrX[i] +
	jacImg2[i].m[1][1] * img1DispPtrY[i])
	-

!Line: 3782 - error: Memory is allocated but not initialized: jacImg1[i].m[0][0] [uninitdata]

niftyreg/reg-lib/cpu/_reg_localTrans.cpp

Lines 3752 to 3757 in aac260c

	(jacImg2[i].m[0][0] * img1DispPtrX[i] +
	jacImg2[i].m[0][1] * img1DispPtrY[i] +
	jacImg2[i].m[0][2] * img1DispPtrZ[i])
	-
	(jacImg1[i].m[0][0] * img2DispPtrX[i] +
	jacImg1[i].m[0][1] * img2DispPtrY[i] +

!Line: 3752 - error: Memory is allocated but not initialized: jacImg2[i].m[0][0] [uninitdata]

niftyreg/reg-lib/cpu/_reg_localTrans.cpp

Lines 3779 to 3784 in aac260c

	(jacImg2[i].m[0][0] * img1DispPtrX[i] +
	jacImg2[i].m[0][1] * img1DispPtrY[i])
	-
	(jacImg1[i].m[0][0] * img2DispPtrX[i] +
	jacImg1[i].m[0][1] * img2DispPtrY[i]);
	resPtrY[i] =

!Line: 3779 - error: Memory is allocated but not initialized: jacImg2[i].m[0][0] [uninitdata]

niftyreg/reg-lib/cpu/_reg_measure.h

Lines 16 to 21 in aac260c

	reg_measure() {
	NR_FUNC_CALLED();
	}
	/// @brief Measure class destructor
	virtual ~reg_measure() {}

!Line: 16 - warning: Member variable 'reg_measure::referenceImage' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_measure.h

Lines 16 to 21 in aac260c

	reg_measure() {
	NR_FUNC_CALLED();
	}
	/// @brief Measure class destructor
	virtual ~reg_measure() {}

!Line: 16 - warning: Member variable 'reg_measure::referenceMask' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_measure.h

Lines 16 to 21 in aac260c

	reg_measure() {
	NR_FUNC_CALLED();
	}
	/// @brief Measure class destructor
	virtual ~reg_measure() {}

!Line: 16 - warning: Member variable 'reg_measure::warpedImage' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_measure.h

Lines 16 to 21 in aac260c

	reg_measure() {
	NR_FUNC_CALLED();
	}
	/// @brief Measure class destructor
	virtual ~reg_measure() {}

!Line: 16 - warning: Member variable 'reg_measure::warpedGradient' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_measure.h

Lines 16 to 21 in aac260c

	reg_measure() {
	NR_FUNC_CALLED();
	}
	/// @brief Measure class destructor
	virtual ~reg_measure() {}

!Line: 16 - warning: Member variable 'reg_measure::voxelBasedGradient' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_measure.h

Lines 16 to 21 in aac260c

	reg_measure() {
	NR_FUNC_CALLED();
	}
	/// @brief Measure class destructor
	virtual ~reg_measure() {}

!Line: 16 - warning: Member variable 'reg_measure::localWeightSim' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_measure.h

Lines 16 to 21 in aac260c

	reg_measure() {
	NR_FUNC_CALLED();
	}
	/// @brief Measure class destructor
	virtual ~reg_measure() {}

!Line: 16 - warning: Member variable 'reg_measure::isSymmetric' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_measure.h

Lines 16 to 21 in aac260c

	reg_measure() {
	NR_FUNC_CALLED();
	}
	/// @brief Measure class destructor
	virtual ~reg_measure() {}

!Line: 16 - warning: Member variable 'reg_measure::floatingImage' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_measure.h

Lines 16 to 21 in aac260c

	reg_measure() {
	NR_FUNC_CALLED();
	}
	/// @brief Measure class destructor
	virtual ~reg_measure() {}

!Line: 16 - warning: Member variable 'reg_measure::floatingMask' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_measure.h

Lines 16 to 21 in aac260c

	reg_measure() {
	NR_FUNC_CALLED();
	}
	/// @brief Measure class destructor
	virtual ~reg_measure() {}

!Line: 16 - warning: Member variable 'reg_measure::warpedImageBw' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_measure.h

Lines 16 to 21 in aac260c

	reg_measure() {
	NR_FUNC_CALLED();
	}
	/// @brief Measure class destructor
	virtual ~reg_measure() {}

!Line: 16 - warning: Member variable 'reg_measure::warpedGradientBw' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_measure.h

Lines 16 to 21 in aac260c

	reg_measure() {
	NR_FUNC_CALLED();
	}
	/// @brief Measure class destructor
	virtual ~reg_measure() {}

!Line: 16 - warning: Member variable 'reg_measure::voxelBasedGradientBw' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_measure.h

Lines 16 to 21 in aac260c

	reg_measure() {
	NR_FUNC_CALLED();
	}
	/// @brief Measure class destructor
	virtual ~reg_measure() {}

!Line: 16 - warning: Member variable 'reg_measure::referenceTimePoints' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_nmi.cpp

Lines 16 to 21 in aac260c

	reg_nmi::reg_nmi(): reg_measure() {
	this->jointHistogramPro = nullptr;
	this->jointHistogramLog = nullptr;
	this->entropyValues = nullptr;
	this->jointHistogramProBw = nullptr;
	this->jointHistogramLogBw = nullptr;

!Line: 16 - warning: Member variable 'reg_nmi::totalBinNumber' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_nmi.h

Lines 111 to 116 in aac260c

	void operator=(const SafeArray&) {};
	SafeArray(const SafeArray&) {};
	DataTYPE *data;
	};

!Line: 111 - warning: Member variable 'SafeArray::data' is not assigned a value in 'SafeArray::operator='. [operatorEqVarError]

niftyreg/reg-lib/cpu/_reg_nmi.h

Lines 112 to 117 in aac260c

	SafeArray(const SafeArray&) {};
	DataTYPE *data;
	};
	//-----------------------------------------------------------------------------

!Line: 112 - warning: Member variable 'SafeArray::data' is not initialized in the copy constructor. [uninitMemberVarPrivate]

niftyreg/reg-lib/cpu/_reg_nmi.h

Lines 211 to 216 in aac260c

	reg_multichannel_nmi() {}
	/// @brief reg_multichannel_nmi class destructor
	virtual ~reg_multichannel_nmi() {}
	/// @brief Returns the nmi value forwards
	virtual double GetSimilarityMeasureValueFw() override { return 0; }

!Line: 211 - warning: Member variable 'reg_multichannel_nmi::referenceBinNumber' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_nmi.h

Lines 211 to 216 in aac260c

	reg_multichannel_nmi() {}
	/// @brief reg_multichannel_nmi class destructor
	virtual ~reg_multichannel_nmi() {}
	/// @brief Returns the nmi value forwards
	virtual double GetSimilarityMeasureValueFw() override { return 0; }

!Line: 211 - warning: Member variable 'reg_multichannel_nmi::floatingBinNumber' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_nmi.h

Lines 211 to 216 in aac260c

	reg_multichannel_nmi() {}
	/// @brief reg_multichannel_nmi class destructor
	virtual ~reg_multichannel_nmi() {}
	/// @brief Returns the nmi value forwards
	virtual double GetSimilarityMeasureValueFw() override { return 0; }

!Line: 211 - warning: Member variable 'reg_multichannel_nmi::totalBinNumber' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_nmi.h

Lines 211 to 216 in aac260c

	reg_multichannel_nmi() {}
	/// @brief reg_multichannel_nmi class destructor
	virtual ~reg_multichannel_nmi() {}
	/// @brief Returns the nmi value forwards
	virtual double GetSimilarityMeasureValueFw() override { return 0; }

!Line: 211 - warning: Member variable 'reg_multichannel_nmi::jointHistogramProp' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_nmi.h

Lines 211 to 216 in aac260c

	reg_multichannel_nmi() {}
	/// @brief reg_multichannel_nmi class destructor
	virtual ~reg_multichannel_nmi() {}
	/// @brief Returns the nmi value forwards
	virtual double GetSimilarityMeasureValueFw() override { return 0; }

!Line: 211 - warning: Member variable 'reg_multichannel_nmi::jointHistogramLog' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_nmi.h

Lines 211 to 216 in aac260c

	reg_multichannel_nmi() {}
	/// @brief reg_multichannel_nmi class destructor
	virtual ~reg_multichannel_nmi() {}
	/// @brief Returns the nmi value forwards
	virtual double GetSimilarityMeasureValueFw() override { return 0; }

!Line: 211 - warning: Member variable 'reg_multichannel_nmi::entropyValues' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_nmi.h

Lines 211 to 216 in aac260c

	reg_multichannel_nmi() {}
	/// @brief reg_multichannel_nmi class destructor
	virtual ~reg_multichannel_nmi() {}
	/// @brief Returns the nmi value forwards
	virtual double GetSimilarityMeasureValueFw() override { return 0; }

!Line: 211 - warning: Member variable 'reg_multichannel_nmi::jointHistogramPropBw' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_nmi.h

Lines 211 to 216 in aac260c

	reg_multichannel_nmi() {}
	/// @brief reg_multichannel_nmi class destructor
	virtual ~reg_multichannel_nmi() {}
	/// @brief Returns the nmi value forwards
	virtual double GetSimilarityMeasureValueFw() override { return 0; }

!Line: 211 - warning: Member variable 'reg_multichannel_nmi::jointHistogramLogBw' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_nmi.h

Lines 211 to 216 in aac260c

	reg_multichannel_nmi() {}
	/// @brief reg_multichannel_nmi class destructor
	virtual ~reg_multichannel_nmi() {}
	/// @brief Returns the nmi value forwards
	virtual double GetSimilarityMeasureValueFw() override { return 0; }

!Line: 211 - warning: Member variable 'reg_multichannel_nmi::entropyValuesBw' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_dti.cpp

Lines 16 to 21 in aac260c

	reg_dti::reg_dti(): reg_measure() {
	NR_FUNC_CALLED();
	}
	/* *************************************************************** */
	// This function is directly the same as that used for reg_ssd
	void reg_dti::InitialiseMeasure(nifti_image *refImg,

!Line: 16 - warning: Member variable 'reg_dti::dtIndicies' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_dti.cpp

Lines 16 to 21 in aac260c

	reg_dti::reg_dti(): reg_measure() {
	NR_FUNC_CALLED();
	}
	/* *************************************************************** */
	// This function is directly the same as that used for reg_ssd
	void reg_dti::InitialiseMeasure(nifti_image *refImg,

!Line: 16 - warning: Member variable 'reg_dti::currentValue' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_mind.cpp

Lines 285 to 290 in aac260c

	reg_mind::reg_mind(): reg_ssd() {
	this->referenceImageDescriptor = nullptr;
	this->floatingImageDescriptor = nullptr;
	this->warpedFloatingImageDescriptor = nullptr;
	this->warpedReferenceImageDescriptor = nullptr;
	this->mindType = MIND_TYPE;

!Line: 285 - warning: Member variable 'reg_mind::descriptorNumber' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_blockMatching.h

Lines 60 to 65 in aac260c

	_reg_blockMatchingParam()
	: totalBlockNumber(0),
	totalBlock(0),
	percent_to_keep(0),
	dim(0),
	referencePosition(0),

!Line: 60 - warning: Member variable '_reg_blockMatchingParam::blockNumber' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cpu/_reg_blockMatching.h

Lines 60 to 65 in aac260c

	_reg_blockMatchingParam()
	: totalBlockNumber(0),
	totalBlock(0),
	percent_to_keep(0),
	dim(0),
	referencePosition(0),

!Line: 60 - warning: Member variable '_reg_blockMatchingParam::definedActiveBlockNumber' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/AladinContent.cpp

Lines 19 to 24 in aac260c

	blockMatchingParams = new _reg_blockMatchingParam();
	initialise_block_matching_method(reference,
	blockMatchingParams,
	currentPercentageOfBlockToUse,
	inlierLts,
	stepSizeBlock,

!Line: 19 - warning: Class 'AladinContent' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]

niftyreg/reg-lib/AladinContent.cpp

Lines 19 to 24 in aac260c

	blockMatchingParams = new _reg_blockMatchingParam();
	initialise_block_matching_method(reference,
	blockMatchingParams,
	currentPercentageOfBlockToUse,
	inlierLts,
	stepSizeBlock,

!Line: 19 - warning: Class 'AladinContent' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]

niftyreg/reg-lib/Optimiser.cpp

Lines 179 to 184 in aac260c

	ConjugateGradient<T>::ConjugateGradient(): Optimiser<T>::Optimiser() {
	this->array1 = nullptr;
	this->array1Bw = nullptr;
	this->array2 = nullptr;
	this->array2Bw = nullptr;
	NR_FUNC_CALLED();

!Line: 179 - warning: Member variable 'ConjugateGradient < float >::firstCall' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/Optimiser.cpp

Lines 179 to 184 in aac260c

	ConjugateGradient<T>::ConjugateGradient(): Optimiser<T>::Optimiser() {
	this->array1 = nullptr;
	this->array1Bw = nullptr;
	this->array2 = nullptr;
	this->array2Bw = nullptr;
	NR_FUNC_CALLED();

!Line: 179 - warning: Member variable 'ConjugateGradient < double >::firstCall' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/AffineDeformationFieldKernel.h

Lines 7 to 12 in aac260c

	static std::string GetName() {
	return "AffineDeformationFieldKernel";
	}
	AffineDeformationFieldKernel() : Kernel() {}
	virtual ~AffineDeformationFieldKernel() {}
	virtual void Calculate(bool compose = false) = 0;

!Line: 7 - warning: The class 'AffineDeformationFieldKernel' defines member function with name 'GetName' also defined in its parent class 'Kernel'. [duplInheritedMember]

!Line: 11 - note: Parent function 'Kernel::GetName'
!Line: 7 - note: Derived function 'AffineDeformationFieldKernel::GetName'

niftyreg/reg-lib/ConvolutionKernel.h

Lines 8 to 13 in aac260c

	static std::string GetName() {
	return "ConvolutionKernel";
	}
	ConvolutionKernel() : Kernel() {}
	virtual ~ConvolutionKernel() {}
	virtual void Calculate(nifti_image *image, float *sigma, ConvKernelType kernelType, int *mask = nullptr, bool *timePoints = nullptr, bool *axis = nullptr) = 0;

!Line: 8 - warning: The class 'ConvolutionKernel' defines member function with name 'GetName' also defined in its parent class 'Kernel'. [duplInheritedMember]

!Line: 11 - note: Parent function 'Kernel::GetName'
!Line: 8 - note: Derived function 'ConvolutionKernel::GetName'

niftyreg/reg-lib/BlockMatchingKernel.h

Lines 7 to 12 in aac260c

	static std::string GetName() {
	return "BlockMatchingKernel";
	}
	BlockMatchingKernel() : Kernel() {}
	virtual ~BlockMatchingKernel() {}
	virtual void Calculate() = 0;

!Line: 7 - warning: The class 'BlockMatchingKernel' defines member function with name 'GetName' also defined in its parent class 'Kernel'. [duplInheritedMember]

!Line: 11 - note: Parent function 'Kernel::GetName'
!Line: 7 - note: Derived function 'BlockMatchingKernel::GetName'

niftyreg/reg-lib/ResampleImageKernel.h

Lines 8 to 13 in aac260c

	static std::string GetName() {
	return "ResampleImageKernel";
	}
	ResampleImageKernel() : Kernel() {}
	virtual ~ResampleImageKernel() {}
	virtual void Calculate(int interp, float paddingValue, bool *dtiTimePoint = nullptr, mat33 *jacMat = nullptr) = 0;

!Line: 8 - warning: The class 'ResampleImageKernel' defines member function with name 'GetName' also defined in its parent class 'Kernel'. [duplInheritedMember]

!Line: 11 - note: Parent function 'Kernel::GetName'
!Line: 8 - note: Derived function 'ResampleImageKernel::GetName'

niftyreg/reg-lib/LtsKernel.h

Lines 7 to 12 in aac260c

	static std::string GetName() {
	return "LtsKernel";
	}
	LtsKernel() : Kernel() {}
	virtual ~LtsKernel() {}
	virtual void Calculate(bool affine) = 0;

!Line: 7 - warning: The class 'LtsKernel' defines member function with name 'GetName' also defined in its parent class 'Kernel'. [duplInheritedMember]

!Line: 11 - note: Parent function 'Kernel::GetName'
!Line: 7 - note: Derived function 'LtsKernel::GetName'

niftyreg/reg-lib/_reg_aladin.cpp

Lines 5 to 10 in aac260c

	reg_aladin<T>::reg_aladin() {
	this->executableName = (char*)"Aladin";
	this->affineTransformation.reset(new mat44);
	this->inputTransformName = nullptr;

!Line: 5 - warning: Member variable 'reg_aladin < float >::captureRangeVox' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/_reg_aladin.cpp

Lines 282 to 287 in aac260c

	this->affineTransformation->m[0][3] = floCOM[0] - refCOM[0];
	this->affineTransformation->m[1][3] = floCOM[1] - refCOM[1];
	this->affineTransformation->m[2][3] = floCOM[2] - refCOM[2];
	}
	}
	}

!Line: 282 - error: Uninitialized variable: floCOM [legacyUninitvar]

niftyreg/reg-lib/_reg_aladin_sym.cpp

Lines 111 to 116 in aac260c

	this->affineTransformation->m[0][3] = floCOG[0] - refCOG[0];
	this->affineTransformation->m[1][3] = floCOG[1] - refCOG[1];
	this->affineTransformation->m[2][3] = floCOG[2] - refCOG[2];
	}
	*this->affineTransformationBw = nifti_mat44_inverse(*this->affineTransformation);
	}

!Line: 111 - error: Uninitialized variable: floCOG [legacyUninitvar]

niftyreg/reg-lib/_reg_base.cpp

Lines 17 to 22 in aac260c

	reg_base<T>::reg_base(int refTimePoints, int floTimePoints) {
	SetPlatformType(PlatformType::Cpu);
	maxIterationNumber = 150;
	optimiseX = true;
	optimiseY = true;

!Line: 17 - warning: Member variable 'reg_base < float >::bestWMeasure' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/_reg_base.cpp

Lines 17 to 22 in aac260c

	reg_base<T>::reg_base(int refTimePoints, int floTimePoints) {
	SetPlatformType(PlatformType::Cpu);
	maxIterationNumber = 150;
	optimiseX = true;
	optimiseY = true;

!Line: 17 - warning: Member variable 'reg_base < float >::currentWMeasure' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/_reg_base.cpp

Lines 17 to 22 in aac260c

	reg_base<T>::reg_base(int refTimePoints, int floTimePoints) {
	SetPlatformType(PlatformType::Cpu);
	maxIterationNumber = 150;
	optimiseX = true;
	optimiseY = true;

!Line: 17 - warning: Member variable 'reg_base < float >::currentWLand' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/_reg_base.cpp

Lines 17 to 22 in aac260c

	reg_base<T>::reg_base(int refTimePoints, int floTimePoints) {
	SetPlatformType(PlatformType::Cpu);
	maxIterationNumber = 150;
	optimiseX = true;
	optimiseY = true;

!Line: 17 - warning: Member variable 'reg_base < float >::bestWLand' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/_reg_base.cpp

Lines 17 to 22 in aac260c

	reg_base<T>::reg_base(int refTimePoints, int floTimePoints) {
	SetPlatformType(PlatformType::Cpu);
	maxIterationNumber = 150;
	optimiseX = true;
	optimiseY = true;

!Line: 17 - warning: Member variable 'reg_base < float >::funcProgressCallback' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/_reg_base.cpp

Lines 17 to 22 in aac260c

	reg_base<T>::reg_base(int refTimePoints, int floTimePoints) {
	SetPlatformType(PlatformType::Cpu);
	maxIterationNumber = 150;
	optimiseX = true;
	optimiseY = true;

!Line: 17 - warning: Member variable 'reg_base < float >::paramsProgressCallback' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/_reg_base.h

Lines 144 to 149 in aac260c

	virtual void SetPlatformType(const PlatformType platformType) {
	platform.reset(new Platform(platformType));
	measure.reset(platform->CreateMeasure());
	}
	virtual void SetGpuIdx(const unsigned gpuIdx) { platform->SetGpuIdx(gpuIdx); }

!Line: 144 - style: Virtual function 'SetPlatformType' is called from constructor 'reg_base < float >(int refTimePoints,int floTimePoints)' at line 18. Dynamic binding is not used. [virtualCallInConstructor]

!Line: 18 - note: Calling SetPlatformType
!Line: 144 - note: SetPlatformType is a virtual function

niftyreg/reg-lib/_reg_f3d.cpp

Lines 18 to 23 in aac260c

	reg_f3d<T>::reg_f3d(int refTimePoints, int floTimePoints):
	reg_base<T>::reg_base(refTimePoints, floTimePoints) {
	this->executableName = (char*)"NiftyReg F3D";
	bendingEnergyWeight = 0.001;
	linearEnergyWeight = 0.01;

!Line: 18 - warning: Member variable 'reg_f3d < float >::currentWJac' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/_reg_f3d.cpp

Lines 18 to 23 in aac260c

	reg_f3d<T>::reg_f3d(int refTimePoints, int floTimePoints):
	reg_base<T>::reg_base(refTimePoints, floTimePoints) {
	this->executableName = (char*)"NiftyReg F3D";
	bendingEnergyWeight = 0.001;
	linearEnergyWeight = 0.01;

!Line: 18 - warning: Member variable 'reg_f3d < float >::currentWBE' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/_reg_f3d.cpp

Lines 18 to 23 in aac260c

	reg_f3d<T>::reg_f3d(int refTimePoints, int floTimePoints):
	reg_base<T>::reg_base(refTimePoints, floTimePoints) {
	this->executableName = (char*)"NiftyReg F3D";
	bendingEnergyWeight = 0.001;
	linearEnergyWeight = 0.01;

!Line: 18 - warning: Member variable 'reg_f3d < float >::currentWLE' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/_reg_f3d.cpp

Lines 18 to 23 in aac260c

	reg_f3d<T>::reg_f3d(int refTimePoints, int floTimePoints):
	reg_base<T>::reg_base(refTimePoints, floTimePoints) {
	this->executableName = (char*)"NiftyReg F3D";
	bendingEnergyWeight = 0.001;
	linearEnergyWeight = 0.01;

!Line: 18 - warning: Member variable 'reg_f3d < float >::bestWJac' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/_reg_f3d.cpp

Lines 18 to 23 in aac260c

	reg_f3d<T>::reg_f3d(int refTimePoints, int floTimePoints):
	reg_base<T>::reg_base(refTimePoints, floTimePoints) {
	this->executableName = (char*)"NiftyReg F3D";
	bendingEnergyWeight = 0.001;
	linearEnergyWeight = 0.01;

!Line: 18 - warning: Member variable 'reg_f3d < float >::bestWBE' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/_reg_f3d.cpp

Lines 18 to 23 in aac260c

	reg_f3d<T>::reg_f3d(int refTimePoints, int floTimePoints):
	reg_base<T>::reg_base(refTimePoints, floTimePoints) {
	this->executableName = (char*)"NiftyReg F3D";
	bendingEnergyWeight = 0.001;
	linearEnergyWeight = 0.01;

!Line: 18 - warning: Member variable 'reg_f3d < float >::bestWLE' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cl/ClContextSingleton.cpp

Lines 16 to 21 in aac260c

	this->platformIds = (cl_platform_id *)alloca(sizeof(cl_platform_id) * this->numPlatforms);
	errNum = clGetPlatformIDs(this->numPlatforms, this->platformIds, nullptr);
	CheckErrNum(errNum, "Failed to find any OpenCL platforms.");
	errNum = clGetDeviceIDs(this->platformIds[0], CL_DEVICE_TYPE_ALL, 0, nullptr, &this->numDevices);
	CheckErrNum(errNum, "Failed to find OpenCL devices.");

!Line: 16 - warning: Obsolete function 'alloca' called. [allocaCalled]

niftyreg/reg-lib/cl/ClContextSingleton.cpp

Lines 57 to 62 in aac260c

	size_t *info = (size_t*)alloca(sizeof(size_t) * paramValueSize);
	errNum = clGetDeviceInfo(this->devices[this->clIdx], CL_DEVICE_MAX_WORK_GROUP_SIZE, paramValueSize, info, nullptr);
	CheckErrNum(errNum, "Failed to find OpenCL device info CL_DEVICE_MAX_WORK_GROUP_SIZE2");
	this->maxThreads = *info;
	this->maxBlocks = 65535;
	}

!Line: 57 - warning: Obsolete function 'alloca' called. [allocaCalled]

niftyreg/reg-lib/cl/ClContextSingleton.cpp

Lines 78 to 83 in aac260c

	cl_uint *info = (cl_uint*)alloca(sizeof(cl_uint) * paramValueSize);
	errNum = clGetDeviceInfo(this->devices[this->clIdx], CL_DEVICE_MAX_COMPUTE_UNITS, paramValueSize, info, nullptr);
	CheckErrNum(errNum, "Failed to find OpenCL device info ");
	cl_uint numProcs = *info;
	maxProcs = numProcs;

!Line: 78 - warning: Obsolete function 'alloca' called. [allocaCalled]

niftyreg/reg-lib/cl/ClContextSingleton.cpp

Lines 86 to 91 in aac260c

	cl_uint *infoD1 = (cl_uint*)alloca(sizeof(cl_uint) * paramValueSizeDOUBE1);
	errNum = clGetDeviceInfo(this->devices[this->clIdx], CL_DEVICE_PREFERRED_VECTOR_WIDTH_DOUBLE, paramValueSizeDOUBE1, infoD1, nullptr);
	CheckErrNum(errNum, "Failed to find OpenCL device info ");
	cl_uint numD1 = *infoD1;
	errNum = clGetDeviceInfo(this->devices[this->clIdx], CL_DEVICE_NATIVE_VECTOR_WIDTH_DOUBLE, 0, nullptr, &paramValueSizeDOUBE2);

!Line: 86 - warning: Obsolete function 'alloca' called. [allocaCalled]

niftyreg/reg-lib/cl/ClContextSingleton.cpp

Lines 93 to 98 in aac260c

	cl_uint *infoD2 = (cl_uint*)alloca(sizeof(cl_uint) * paramValueSizeDOUBE2);
	errNum = clGetDeviceInfo(this->devices[this->clIdx], CL_DEVICE_NATIVE_VECTOR_WIDTH_DOUBLE, paramValueSizeDOUBE2, infoD2, nullptr);
	CheckErrNum(errNum, "Failed to find OpenCL device info ");
	cl_uint numD2 = *infoD2;
	if (numD1 > 0 || numD2 > 0) {

!Line: 93 - warning: Obsolete function 'alloca' called. [allocaCalled]

niftyreg/reg-lib/cl/ClContextSingleton.cpp

Lines 113 to 118 in aac260c

	cl_uint *info = (cl_uint*)alloca(sizeof(cl_uint) * paramValueSize);
	errNum = clGetDeviceInfo(this->devices[i], CL_DEVICE_MAX_COMPUTE_UNITS, paramValueSize, info, nullptr);
	CheckErrNum(errNum, "Failed to find OpenCL device info ");
	cl_uint numProcs = *info;
	const bool found = numProcs > maxProcs;
	this->clIdx = found ? i : this->clIdx;

!Line: 113 - warning: Obsolete function 'alloca' called. [allocaCalled]

niftyreg/reg-lib/cl/ClContextSingleton.cpp

Lines 124 to 129 in aac260c

	cl_uint *infoD1 = (cl_uint*)alloca(sizeof(cl_uint) * paramValueSizeDOUBE1);
	errNum = clGetDeviceInfo(this->devices[i], CL_DEVICE_PREFERRED_VECTOR_WIDTH_DOUBLE, paramValueSizeDOUBE1, infoD1, nullptr);
	CheckErrNum(errNum, "Failed to find OpenCL device info ");
	cl_uint numD1 = *infoD1;
	errNum = clGetDeviceInfo(this->devices[i], CL_DEVICE_NATIVE_VECTOR_WIDTH_DOUBLE, 0, nullptr, &paramValueSizeDOUBE2);

!Line: 124 - warning: Obsolete function 'alloca' called. [allocaCalled]

niftyreg/reg-lib/cl/ClContextSingleton.cpp

Lines 131 to 136 in aac260c

	cl_uint *infoD2 = (cl_uint*)alloca(sizeof(cl_uint) * paramValueSizeDOUBE2);
	errNum = clGetDeviceInfo(this->devices[i], CL_DEVICE_NATIVE_VECTOR_WIDTH_DOUBLE, paramValueSizeDOUBE2, infoD2, nullptr);
	CheckErrNum(errNum, "Failed to find OpenCL device info ");
	cl_uint numD2 = *infoD2;
	if (numD1 > 0 || numD2 > 0) {

!Line: 131 - warning: Obsolete function 'alloca' called. [allocaCalled]

niftyreg/reg-lib/cl/ClAladinContent.cpp

Lines 5 to 10 in aac260c

	ClAladinContent::ClAladinContent(nifti_image *referenceIn,
	nifti_image *floatingIn,
	int *referenceMaskIn,
	mat44 *transformationMatrixIn,
	size_t bytesIn,
	const unsigned percentageOfBlocks,

!Line: 5 - warning: Member variable 'ClAladinContent::referenceDims' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cl/ClAladinContent.cpp

Lines 5 to 10 in aac260c

	ClAladinContent::ClAladinContent(nifti_image *referenceIn,
	nifti_image *floatingIn,
	int *referenceMaskIn,
	mat44 *transformationMatrixIn,
	size_t bytesIn,
	const unsigned percentageOfBlocks,

!Line: 5 - warning: Member variable 'ClAladinContent::floatingDims' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cl/ClAladinContent.cpp

Lines 5 to 10 in aac260c

	ClAladinContent::ClAladinContent(nifti_image *referenceIn,
	nifti_image *floatingIn,
	int *referenceMaskIn,
	mat44 *transformationMatrixIn,
	size_t bytesIn,
	const unsigned percentageOfBlocks,

!Line: 5 - warning: Member variable 'ClAladinContent::nVoxels' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cl/ClAladinContent.cpp

Lines 157 to 162 in aac260c

	if (warped->nbyper != NIFTI_TYPE_FLOAT32) {
	reg_tools_changeDatatype<float>(warped);
	}
	AladinContent::SetWarped(warped);
	warpedImageClmem = clCreateBuffer(clContext, CL_MEM_READ_WRITE | CL_MEM_USE_HOST_PTR, warped->nvox * sizeof(float), warped->data, &errNum);
	sContext->CheckErrNum(errNum, "ClAladinContent::SetWarped failed to allocate memory (warpedImageClmem): ");

!Line: 157 - warning: Either the condition 'warped!=nullptr' is redundant or there is possible null pointer dereference: warped. [nullPointerRedundantCheck]

!Line: 154 - note: Assuming that condition 'warped!=nullptr' is not redundant
!Line: 157 - note: Null pointer dereference

niftyreg/reg-lib/cl/ClAffineDeformationFieldKernel.cpp

Lines 70 to 75 in aac260c

	cl_uint * info = (cl_uint *)alloca(sizeof(cl_uint) * paramValueSize);
	errNum = clGetDeviceInfo(sContext->GetDeviceId(), CL_DEVICE_MAX_WORK_GROUP_SIZE, paramValueSize, info, nullptr);
	sContext->CheckErrNum(errNum, "Failed to GetDeviceId() OpenCL device info ");
	maxWG = *info;
	//8=default value

!Line: 70 - warning: Obsolete function 'alloca' called. [allocaCalled]

niftyreg/reg-lib/cl/InfoDevice.h

Lines 29 to 34 in aac260c

	T * field = (T *) alloca(sizeof(T) * paramValueSize);
	sContext->CheckErrNum(clGetDeviceInfo(id, name, paramValueSize, field, nullptr), "Failed to find OpenCL device info ");
	switch (name) {
	case CL_DEVICE_TYPE: {
	const cl_device_type deviceType = *(reinterpret_cast<cl_device_type*>(field));

!Line: 29 - warning: Obsolete function 'alloca' called. [allocaCalled]

niftyreg/reg-apps/reg_average.cpp

Lines 231 to 236 in aac260c

	return average_matrix;
	}
	mat44 compute_affine_demean(size_t matrixNumber,
	char **inputAffName)
	{

!Line: 231 - warning: Uninitialized variable: average_matrix [uninitvar]

!Line: 135 - note: Assuming condition is false
!Line: 231 - note: Uninitialized variable: average_matrix

niftyreg/reg-apps/reg_transform.cpp

Lines 374 to 379 in aac260c

	inputTransformationImage->intent_p1==LIN_SPLINE_GRID ||
	inputTransformationImage->intent_p1==CUB_SPLINE_GRID ||
	inputTransformationImage->intent_p1==SPLINE_VEL_GRID)
	{
	// Create a field image from the reference image
	outputTransformationImage=nifti_copy_nim_info(referenceImage);

!Line: 374 - warning: Possible null pointer dereference: inputTransformationImage [nullPointer]

!Line: 324 - note: Assignment 'inputTransformationImage=nullptr', assigned value is 0
!Line: 327 - note: Assuming condition is false
!Line: 374 - note: Null pointer dereference

niftyreg/reg-apps/reg_transform.cpp

Lines 541 to 546 in aac260c

	switch(Round(outputTransformationImage->intent_p1))
	{
	case DEF_FIELD:
	NR_INFO("The deformation field has been saved as:");
	NR_INFO(param->outputTransName);
	break;

!Line: 541 - warning: Either the condition 'outputTransformationImage!=nullptr' is redundant or there is possible null pointer dereference: outputTransformationImage. [nullPointerRedundantCheck]

!Line: 560 - note: Assuming that condition 'outputTransformationImage!=nullptr' is not redundant
!Line: 541 - note: Null pointer dereference

niftyreg/reg-apps/reg_transform.cpp

Lines 924 to 929 in aac260c

	inputTransformationImage->intent_p1==LIN_SPLINE_GRID ||
	inputTransformationImage->intent_p1==CUB_SPLINE_GRID ||
	inputTransformationImage->intent_p1==SPLINE_VEL_GRID)
	{
	// Create a field image from the reference image
	deformationFieldImage=nifti_copy_nim_info(referenceImage);

!Line: 924 - warning: Possible null pointer dereference: inputTransformationImage [nullPointer]

!Line: 874 - note: Assignment 'inputTransformationImage=nullptr', assigned value is 0
!Line: 877 - note: Assuming condition is false
!Line: 924 - note: Null pointer dereference

niftyreg/reg-lib/cl/blockMatchingKernel.cl

Lines 139 to 144 in aac260c

	const int yImageIn = yImage + y * 4;
	for (int x=-1; x<2; ++x) {
	const int xImageIn = xImage + x * 4;
	// Compute the index in the local shared memory
	const int sharedIndex = ((y+1)*4+idy)*12+(x+1)*4+idx;

!Line: 139 - error: Signed integer overflow for expression 'y*4'. [integerOverflow]

!Line: 138 - note: Assignment 'y=-1', assigned value is -1
!Line: 139 - note: Integer overflow

niftyreg/reg-lib/cl/blockMatchingKernel.cl

Lines 141 to 146 in aac260c

	const int xImageIn = xImage + x * 4;
	// Compute the index in the local shared memory
	const int sharedIndex = ((y+1)*4+idy)*12+(x+1)*4+idx;
	// Compute the index of the voxel under consideration

!Line: 141 - error: Signed integer overflow for expression 'x*4'. [integerOverflow]

!Line: 140 - note: Assignment 'x=-1', assigned value is -1
!Line: 141 - note: Integer overflow

niftyreg/reg-lib/cl/blockMatchingKernel.cl

Lines 295 to 300 in aac260c

	const int zImageIn = zImage + n * 4;
	for (int m=-1; m<2; ++m) {
	const int yImageIn = yImage + m * 4;
	for (int l=-1; l<2; ++l) {
	const int xImageIn = xImage + l * 4;

!Line: 295 - error: Signed integer overflow for expression 'n*4'. [integerOverflow]

!Line: 294 - note: Assignment 'n=-1', assigned value is -1
!Line: 295 - note: Integer overflow

niftyreg/reg-lib/cl/blockMatchingKernel.cl

Lines 297 to 302 in aac260c

	const int yImageIn = yImage + m * 4;
	for (int l=-1; l<2; ++l) {
	const int xImageIn = xImage + l * 4;
	// Compute the index in the local shared memory
	const int sharedIndex = (((n+1)*4+idz)*12+(m+1)*4+idy)*12+(l+1)*4+idx;

!Line: 297 - error: Signed integer overflow for expression 'm*4'. [integerOverflow]

!Line: 296 - note: Assignment 'm=-1', assigned value is -1
!Line: 297 - note: Integer overflow

niftyreg/reg-lib/cl/blockMatchingKernel.cl

Lines 299 to 304 in aac260c

	const int xImageIn = xImage + l * 4;
	// Compute the index in the local shared memory
	const int sharedIndex = (((n+1)*4+idz)*12+(m+1)*4+idy)*12+(l+1)*4+idx;
	// Compute the index of the voxel under consideration

!Line: 299 - error: Signed integer overflow for expression 'l*4'. [integerOverflow]

!Line: 298 - note: Assignment 'l=-1', assigned value is -1
!Line: 299 - note: Integer overflow

niftyreg/reg-lib/cl/resampleKernel.cl

Lines 86 to 91 in aac260c

	basis[1] = relative;
	basis[0] = (real_t) 1.0 - relative;
	}
	/* *************************************************************** */
	/* *************************************************************** */
	__inline void interpNearestNeighKernel(real_t relative, real_t *basis)

!Line: 86 - error: Array index out of bounds; 'basis' buffer size is 8 and it is accessed at offset 8. [ctuArrayIndex]

!Line: 255 - note: Calling function interpLinearKernel, 2nd argument is uninitialized
!Line: 86 - note: Using argument basis

niftyreg/reg-lib/cuda/optimizeKernel.cu

Lines 50 to 55 in aac260c

	NR_ERROR("Parameter " << hostDevInfo << " is wrong");
	if (hostDevInfo > 0)
	NR_ERROR(hostDevInfo << " superdiagonals of an intermediate bidiagonal form B did not converge to zero");
	else
	NR_INFO(hostDevInfo << ": operation successful");
	free(hostDevInfo);

!Line: 50 - error: Shifting by a negative value is undefined behaviour [shiftNegative]

niftyreg/reg-lib/cuda/optimizeKernel.cu

Lines 294 to 299 in aac260c

	populateLengthsKernel <<< numBlocks, 512 >>>(lengths_d, warped_d, newWarped_d, m / 3);
	// The initial vector with all the input points
	thrust::device_ptr<float> reference_d_ptr(reference_d);
	thrust::device_vector<float> vecReference_d(reference_d_ptr, reference_d_ptr + m);

!Line: 294 - error: Shifting 32-bit value by 512 bits is undefined behaviour [shiftTooManyBits]

niftyreg/reg-lib/cuda/optimizeKernel.cu

Lines 326 to 331 in aac260c

	populateMatrixA <<< numBlocks, 512 >>>(AR_d, reference_d, m / 3); //test 2
	//calculate SVD on the GPU
	cusolverSVD(AR_d, m, n, Sigma_d, VT_d, U_d);
	//calculate the pseudoinverse
	cublasPseudoInverse(transformation, AR_d, warped_d, VT_d, Sigma_d, U_d, m, n);

!Line: 326 - error: Shifting 32-bit value by 512 bits is undefined behaviour [shiftTooManyBits]

niftyreg/reg-lib/cuda/optimizeKernel.cu

Lines 348 to 353 in aac260c

	transformWarpedPointsKernel <<< numBlocks, 512 >>>(final_d, referencePos_d, newWarpedPos_d, m / 3); //test 1
	double distance = sortAndReduce(lengths_d, referencePos_d, warpedPos_d, newWarpedPos_d, numBlocks, num_to_keep, m);
	// If the change is not substantial or we are getting worst, we return
	if ((distance > lastDistance) || (lastDistance - distance) < TOLERANCE) break;

!Line: 348 - error: Shifting 32-bit value by 512 bits is undefined behaviour [shiftTooManyBits]

niftyreg/reg-lib/cuda/optimizeKernel.cu

Lines 387 to 392 in aac260c

	transformWarpedPointsKernel <<< numBlocks, 512 >>>(final_d, warped_d, newWarped_d, m / 3); //test 1
	cudaMemcpy(warped_d, newWarped_d, m * sizeof(float), cudaMemcpyDeviceToDevice);
	// run the local search optimization routine
	affineLocalSearch3DCuda(cpuMat, final_d, A_d, Sigma_d, U_d, VT_d, newWarped_d, reference_d, warped_d, lengths_d, numBlocks, numToKeep, m, n);

!Line: 387 - error: Shifting 32-bit value by 512 bits is undefined behaviour [shiftTooManyBits]

niftyreg/reg-lib/cuda/CudaToolsKernels.cu

Lines 79 to 84 in aac260c

	gradient[tid] = realGradient;
	}
	}
	/* *************************************************************** */
	__global__ void ApplyConvolutionWindowAlongXKernel(float4 *smoothedImage,
	cudaTextureObject_t imageTexture,

!Line: 79 - error: Uninitialized variable: realGradient.w [uninitvar]

niftyreg/reg-lib/cuda/CudaToolsKernels.cu

Lines 79 to 84 in aac260c

	gradient[tid] = realGradient;
	}
	}
	/* *************************************************************** */
	__global__ void ApplyConvolutionWindowAlongXKernel(float4 *smoothedImage,
	cudaTextureObject_t imageTexture,

!Line: 79 - error: Uninitialized struct member: realGradient.w [uninitStructMember]

niftyreg/reg-lib/cuda/CudaTools.cu

Lines 406 to 410 in aac260c

	setGradientToZero(gradCuda, voxelNumber);
	}
	/* *************************************************************** */
	} // namespace NiftyReg::Cuda
	/* *************************************************************** */

!Line: 406 - error: Uninitialized variable: setGradientToZero [legacyUninitvar]

niftyreg/reg-lib/cuda/CudaCompute.cu

Lines 126 to 131 in aac260c

	float4 dofValue = currentDofCuda[index]; scale; // To capture scale
	const float4 bestValue = tex1Dfetch<float4>(bestDofTexture, index);
	const float4 gradValue = tex1Dfetch<float4>(gradientTexture, index);
	if constexpr (optimiseX)
	dofValue.x = bestValue.x + scale * gradValue.x;
	if constexpr (optimiseY)

!Line: 126 - warning: Unused variable value 'scale' [constStatement]

niftyreg/reg-lib/cuda/blockMatchingKernel.cu

Lines 126 to 131 in aac260c

	const int yImageIn = yImage + y * 4;
	for (int x = -1; x < 2; ++x) {
	const int xImageIn = xImage + x * 4;
	const int sharedIndex = ((y + 1) * 4 + idy) * 12 + (x + 1) * 4 + idx;
	const int indexXYIn = yImageIn * imageSize.x + xImageIn;
	const bool valid =

!Line: 126 - error: Signed integer overflow for expression 'y*4'. [integerOverflow]

!Line: 125 - note: Assignment 'y=-1', assigned value is -1
!Line: 126 - note: Integer overflow

niftyreg/reg-lib/cuda/blockMatchingKernel.cu

Lines 128 to 133 in aac260c

	const int xImageIn = xImage + x * 4;
	const int sharedIndex = ((y + 1) * 4 + idy) * 12 + (x + 1) * 4 + idx;
	const int indexXYIn = yImageIn * imageSize.x + xImageIn;
	const bool valid =
	(xImageIn > -1 && xImageIn < (int)imageSize.x) &&
	(yImageIn > -1 && yImageIn < (int)imageSize.y);

!Line: 128 - error: Signed integer overflow for expression 'x*4'. [integerOverflow]

!Line: 127 - note: Assignment 'x=-1', assigned value is -1
!Line: 128 - note: Integer overflow

niftyreg/reg-lib/cuda/blockMatchingKernel.cu

Lines 236 to 241 in aac260c

	const int zImageIn = zImage + z * 4;
	for (int y = -1; y < 2; ++y) {
	const int yImageIn = yImage + y * 4;
	for (int x = -1; x < 2; ++x) {
	const int xImageIn = xImage + x * 4;
	const int sharedIndex = (((z + 1) * 4 + idz) * 12 + (y + 1) * 4 + idy) * 12 + (x + 1) * 4 + idx;

!Line: 236 - error: Signed integer overflow for expression 'z*4'. [integerOverflow]

!Line: 235 - note: Assignment 'z=-1', assigned value is -1
!Line: 236 - note: Integer overflow

niftyreg/reg-lib/cuda/blockMatchingKernel.cu

Lines 238 to 243 in aac260c

	const int yImageIn = yImage + y * 4;
	for (int x = -1; x < 2; ++x) {
	const int xImageIn = xImage + x * 4;
	const int sharedIndex = (((z + 1) * 4 + idz) * 12 + (y + 1) * 4 + idy) * 12 + (x + 1) * 4 + idx;
	const unsigned indexXYZIn = xImageIn + imageSize.x * (yImageIn + zImageIn * imageSize.y);
	const bool valid =

!Line: 238 - error: Signed integer overflow for expression 'y*4'. [integerOverflow]

!Line: 237 - note: Assignment 'y=-1', assigned value is -1
!Line: 238 - note: Integer overflow

niftyreg/reg-lib/cuda/blockMatchingKernel.cu

Lines 240 to 245 in aac260c

	const int xImageIn = xImage + x * 4;
	const int sharedIndex = (((z + 1) * 4 + idz) * 12 + (y + 1) * 4 + idy) * 12 + (x + 1) * 4 + idx;
	const unsigned indexXYZIn = xImageIn + imageSize.x * (yImageIn + zImageIn * imageSize.y);
	const bool valid =
	(xImageIn > -1 && xImageIn < (int)imageSize.x) &&
	(yImageIn > -1 && yImageIn < (int)imageSize.y) &&

!Line: 240 - error: Signed integer overflow for expression 'x*4'. [integerOverflow]

!Line: 239 - note: Assignment 'x=-1', assigned value is -1
!Line: 240 - note: Integer overflow

niftyreg/reg-lib/cuda/_reg_measure_gpu.h

Lines 20 to 25 in aac260c

	reg_measure_gpu() {}
	/// @brief Measure class destructor
	virtual ~reg_measure_gpu() {}
	virtual void InitialiseMeasure(nifti_image *refImg,
	float *refImgCuda,

!Line: 20 - warning: Member variable 'reg_measure_gpu::referenceImageCuda' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cuda/_reg_measure_gpu.h

Lines 20 to 25 in aac260c

	reg_measure_gpu() {}
	/// @brief Measure class destructor
	virtual ~reg_measure_gpu() {}
	virtual void InitialiseMeasure(nifti_image *refImg,
	float *refImgCuda,

!Line: 20 - warning: Member variable 'reg_measure_gpu::floatingImageCuda' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cuda/_reg_measure_gpu.h

Lines 20 to 25 in aac260c

	reg_measure_gpu() {}
	/// @brief Measure class destructor
	virtual ~reg_measure_gpu() {}
	virtual void InitialiseMeasure(nifti_image *refImg,
	float *refImgCuda,

!Line: 20 - warning: Member variable 'reg_measure_gpu::referenceMaskCuda' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cuda/_reg_measure_gpu.h

Lines 20 to 25 in aac260c

	reg_measure_gpu() {}
	/// @brief Measure class destructor
	virtual ~reg_measure_gpu() {}
	virtual void InitialiseMeasure(nifti_image *refImg,
	float *refImgCuda,

!Line: 20 - warning: Member variable 'reg_measure_gpu::activeVoxelNumber' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cuda/_reg_measure_gpu.h

Lines 20 to 25 in aac260c

	reg_measure_gpu() {}
	/// @brief Measure class destructor
	virtual ~reg_measure_gpu() {}
	virtual void InitialiseMeasure(nifti_image *refImg,
	float *refImgCuda,

!Line: 20 - warning: Member variable 'reg_measure_gpu::warpedImageCuda' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cuda/_reg_measure_gpu.h

Lines 20 to 25 in aac260c

	reg_measure_gpu() {}
	/// @brief Measure class destructor
	virtual ~reg_measure_gpu() {}
	virtual void InitialiseMeasure(nifti_image *refImg,
	float *refImgCuda,

!Line: 20 - warning: Member variable 'reg_measure_gpu::warpedGradientCuda' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cuda/_reg_measure_gpu.h

Lines 20 to 25 in aac260c

	reg_measure_gpu() {}
	/// @brief Measure class destructor
	virtual ~reg_measure_gpu() {}
	virtual void InitialiseMeasure(nifti_image *refImg,
	float *refImgCuda,

!Line: 20 - warning: Member variable 'reg_measure_gpu::voxelBasedGradientCuda' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cuda/_reg_measure_gpu.h

Lines 20 to 25 in aac260c

	reg_measure_gpu() {}
	/// @brief Measure class destructor
	virtual ~reg_measure_gpu() {}
	virtual void InitialiseMeasure(nifti_image *refImg,
	float *refImgCuda,

!Line: 20 - warning: Member variable 'reg_measure_gpu::localWeightSimCuda' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cuda/_reg_measure_gpu.h

Lines 20 to 25 in aac260c

	reg_measure_gpu() {}
	/// @brief Measure class destructor
	virtual ~reg_measure_gpu() {}
	virtual void InitialiseMeasure(nifti_image *refImg,
	float *refImgCuda,

!Line: 20 - warning: Member variable 'reg_measure_gpu::floatingMaskCuda' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cuda/_reg_measure_gpu.h

Lines 20 to 25 in aac260c

	reg_measure_gpu() {}
	/// @brief Measure class destructor
	virtual ~reg_measure_gpu() {}
	virtual void InitialiseMeasure(nifti_image *refImg,
	float *refImgCuda,

!Line: 20 - warning: Member variable 'reg_measure_gpu::warpedImageBwCuda' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cuda/_reg_measure_gpu.h

Lines 20 to 25 in aac260c

	reg_measure_gpu() {}
	/// @brief Measure class destructor
	virtual ~reg_measure_gpu() {}
	virtual void InitialiseMeasure(nifti_image *refImg,
	float *refImgCuda,

!Line: 20 - warning: Member variable 'reg_measure_gpu::warpedGradientBwCuda' is not initialized in the constructor. [uninitMemberVar]

niftyreg/reg-lib/cuda/_reg_measure_gpu.h

Lines 20 to 25 in aac260c

	reg_measure_gpu() {}
	/// @brief Measure class destructor
	virtual ~reg_measure_gpu() {}
	virtual void InitialiseMeasure(nifti_image *refImg,
	float *refImgCuda,

!Line: 20 - warning: Member variable 'reg_measure_gpu::voxelBasedGradientBwCuda' is not initialized in the constructor. [uninitMemberVar]