From f4c5e6463040bc010b7fc8f3ac01d5b1c7b5347d Mon Sep 17 00:00:00 2001
From: albertmena <12760268+albertmena@users.noreply.github.com>
Date: Thu, 28 May 2026 10:58:34 +0200
Subject: [PATCH] Fix SonarCloud BLOCKER reliability issues

- metadata_static.cpp: validate label before indexing data[] in labelType()
- rwJPEG.cpp: free buffer allocation to prevent memory leak
- matrix2d.cpp: fix sizeof(T) in memcpy; add NOSONAR on NR pointer arithmetic
- matrix2d.h: add NOSONAR on out-of-bounds NR pointer arithmetic
- matrix1d.h: call coreDeallocate() in coreAllocate() to prevent leak
- xmipp_strings.cpp: fix negative-index bug when _width=0 and I<0

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 core/matrix1d.h          | 1 +
 core/matrix2d.cpp        | 4 ++--
 core/matrix2d.h          | 2 +-
 core/metadata_static.cpp | 7 ++++++-
 core/rwJPEG.cpp          | 1 +
 core/xmipp_strings.cpp   | 5 ++++-
 6 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/core/matrix1d.h b/core/matrix1d.h
index dc73e4a2..64e0deb5 100644
--- a/core/matrix1d.h
+++ b/core/matrix1d.h
@@ -375,6 +375,7 @@ class Matrix1D
             return;
         }
 
+        coreDeallocate();
         vdim = _vdim;
         vdata = new T[vdim];
         memset(vdata, 0, vdim * sizeof(T));
diff --git a/core/matrix2d.cpp b/core/matrix2d.cpp
index 35614494..e209505b 100644
--- a/core/matrix2d.cpp
+++ b/core/matrix2d.cpp
@@ -850,7 +850,7 @@ void Matrix2D<T>::toVector(Matrix1D<T>& op1) const
         if (VEC_XSIZE(op1)!=mdimx)
             op1.resizeNoCopy(mdimx);
 
-        memcpy(&VEC_ELEM(op1,0),&MAT_ELEM(*this,0,0),mdimx*sizeof(double));
+        memcpy(&VEC_ELEM(op1,0),&MAT_ELEM(*this,0,0),mdimx*sizeof(T));
 
         op1.setRow();
     }
@@ -1286,7 +1286,7 @@ T** Matrix2D<T>::adaptForNumericalRecipes() const
        for (int j = 0; j < mdimx; j++)
            m[i+1][j+1] = mdata[i*mdimx + j];
 
-   return m;
+   return m; // NOSONAR - intentional 1-based NR pointer arithmetic
 }
 
 template<typename T>
diff --git a/core/matrix2d.h b/core/matrix2d.h
index 5ecd06da..942c19a9 100644
--- a/core/matrix2d.h
+++ b/core/matrix2d.h
@@ -874,7 +874,7 @@ class Matrix2D
      */
     inline T* adaptForNumericalRecipes2() const
     {
-        return mdata - 1 - mdimx;
+        return mdata - 1 - mdimx; // NOSONAR - intentional 1-based NR pointer arithmetic
     }
 
     /** Load 2D array from numerical recipes result.
diff --git a/core/metadata_static.cpp b/core/metadata_static.cpp
index 2b3ec2f9..82133a8a 100644
--- a/core/metadata_static.cpp
+++ b/core/metadata_static.cpp
@@ -249,12 +249,17 @@ bool MDL::isValidLabel(const String &labelName)
 
 MDLabelType MDL::labelType(const MDLabel label)
 {
+    if (!isValidLabel(label))
+        REPORT_ERROR(ERR_MD_BADLABEL, "Invalid label");
     return data[label]->type;
 }
 
 MDLabelType MDL::labelType(const String &labelName)
 {
-    return data[str2Label(labelName)]->type;
+    MDLabel label = str2Label(labelName);
+    if (!isValidLabel(label))
+        REPORT_ERROR(ERR_MD_BADLABEL, "Invalid label");
+    return data[label]->type;
 }
 
 std::map<String, MDLabel>& MDL::getLabelDict()
diff --git a/core/rwJPEG.cpp b/core/rwJPEG.cpp
index 0e268ace..b2c3694d 100644
--- a/core/rwJPEG.cpp
+++ b/core/rwJPEG.cpp
@@ -107,6 +107,7 @@ int ImageBase::readJPEG(size_t select_img)
     jpeg_finish_decompress( &cinfo );
     jpeg_destroy_decompress( &cinfo );
     delete[] row_pointer[0];
+    delete[] buffer;
 
     return 0;
 }
diff --git a/core/xmipp_strings.cpp b/core/xmipp_strings.cpp
index 001527a6..c75da512 100644
--- a/core/xmipp_strings.cpp
+++ b/core/xmipp_strings.cpp
@@ -261,13 +261,16 @@ String integerToString(int I, int _width, char fill_with)
     if (SGN(I) < 0)
         width--;
 
-    if (width == 0)
+    if (width <= 0)
+    {
+        width = 0;
         do
         {
             Iaux /= 10;
             width++;
         }
         while (Iaux != 0);
+    }
 
     // Fill the number with the fill character
     for (int i = 0; i < width; i++)