Bug fix for segmentation fault and remove flat images (#26)

* AreTomo2 1.1.0: Reduced dependency of library files. Provided the source of remaining library files in LibSrc. Improved CTF estimation * AreTomo2 1.1.1 revised the generation of Imod files. * AreTomo2 1.1.2: add user manual and bug fix. * AreTomo2 1.1.3, bug fix and removing flat tilt images in tilt series. --------- Co-authored-by: Shawn Zheng <[email protected]>
czimaginginstitute · Aug 19, 2024 · 01e7219 · 01e7219
1 parent e9f8941
commit 01e7219
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Showing 5 changed files with 35 additions and 4 deletions.
diff --git a/CAreTomoMain.cpp b/CAreTomoMain.cpp
@@ -20,8 +20,8 @@ int main(int argc, char* argv[])
 	if(argc == 2)
 	{	if(strcasecmp(argv[1], "--version") == 0 ||
 		   strcasecmp(argv[1], "-v") == 0)
-		{	printf("AreTomo2 version 1.1.2\n"
-			       "Built on Feb 20 2024\n");
+		{	printf("AreTomo2 version 1.1.3\n"
+			       "Built on Aug 19 2024\n");
 		}
 		else if(strcasecmp(argv[1], "--help") == 0)
 		{	printf("\nUsage: AreTomo2 Tags\n");

diff --git a/CProcessThread.cpp b/CProcessThread.cpp
@@ -256,6 +256,7 @@ void CProcessThread::mRotAlign(void)
 
 void CProcessThread::mFindTiltOffset(void)
 {
+	m_fTiltOffset = 0.0f;
 	CInput* pInput = CInput::GetInstance();
 	if(pInput->m_afTiltCor[0] < 0) return;
 	//-----------------

diff --git a/MrcUtil/CRemoveDarkFrames.cpp b/MrcUtil/CRemoveDarkFrames.cpp
@@ -69,8 +69,12 @@ void CRemoveDarkFrames::DoIt
 	pDarkFrames->Setup(s_pTomoStack);
 	//-----------------
 	for(int i=0; i<iAllFrms; i++)
-	{	float fRatio = (float)fabs(pfMeans[i]) / 
-		   (pfStds[i] + 0.000001f);
+	{	if(pfStds[i] <= 1e-10)
+		{	pDarkFrames->AddDark(i);
+			continue;
+		}
+		//----------------
+		float fRatio = (float)fabs(pfMeans[i]) / pfStds[i];
 		if(fRatio > fTol) continue;
 		//----------------
 		pDarkFrames->AddDark(i);

diff --git a/ProjAlign/CCalcReproj.cpp b/ProjAlign/CCalcReproj.cpp
@@ -108,6 +108,17 @@ void CCalcReproj::mFindProjRange(float* pfTiltAngles, bool* pbSkipProjs)
 		iEnd = i;
 	}
 	//---------------------------------------------
+	// 1) Prevent an unusual situation where the
+	// angular step is so large causing stretching
+	// factor larger that allowed. 2) In that case
+	// we just use the nearest lower tilt image.
+	//---------------------------------------------
+	if(iStart < 0 || iEnd < 0)
+	{	int iSign = (fProjA > 0) ? 1 : -1;
+		iStart = m_iProjIdx - iSign;
+		iEnd = iStart;
+	}
+	//-----------------
 	if((iEnd - iStart) > 9) iEnd = iStart + 9;
 	m_aiProjRange[0] = iStart;
 	m_aiProjRange[1] = iEnd;

diff --git a/Readme.txt b/Readme.txt
@@ -375,3 +375,18 @@ AreTomo2 1.1.2 [02-20-2024]
    and then subtract the min and add 1. The line number is then iAcqIdx - 1.
 2. DoseWeight/CWeightTomoStack: Check if iAcqIdx is 0-based. If so, add
    1 to it.
+
+AreTomo2 1.1.3 [06-17-2024]
+---------------------------
+1. Bug fix: random tilt angle values saved in .aln file.
+   1) m_fTiltOffset in CProcessThread.cpp was not inititialized. Some
+      system initializes it with a random large numbers. When -TiltCor -1
+      is used, tilt offset is not estimated and m_fTiltOffset stores the 
+      random value, rather than zero that is added to the tilt angles.
+      Fix: added m_fTiltOffset = 0 in mFindTiltOffset. [06-17-2024]
+2. Bug fix: AreTomo2 crashed when tilt angle file only has one column.
+   1) To be done.
+3. Bug fix: ProjAlign/CCalcReproj::mFindProjRange: needs to check whether
+   m_aiProjRange constains -1. Fixed on 08-19-2024.
+4. Added in MrcUtil/CRemoveDarkFrames.cpp a check for flat images that have
+   very small sigma. They are rejected.