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MRC file format bug and compatibility fixes. #4019

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merged 3 commits into from
Apr 24, 2023
Merged

MRC file format bug and compatibility fixes. #4019

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3b643f5
BUG: Remove dead code in MRC Header
blowekamp Apr 19, 2023
e7ffba6
BUG: Fix MRC zero spacing for tilt series
blowekamp Apr 19, 2023
8ca5d1f
BUG: MRC write full machine stamp
blowekamp Apr 19, 2023
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4 changes: 2 additions & 2 deletions Modules/IO/MRC/include/itkMRCHeaderObject.h
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Original file line number Diff line number Diff line change
Expand Up @@ -164,8 +164,8 @@ class ITKIOMRC_EXPORT MRCHeaderObject : public LightObject
float zorg;

char cmap[4]; /**< Contains "MAP " */
char stamp[4]; /**< First byte has 17 for big- or 68 for
little-endian */
char stamp[4]; /**< First two bytes have 17 and 17 for big-endian or
68 and 68 for little-endian */
float rms;

// ALL HEADERS:
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49 changes: 0 additions & 49 deletions Modules/IO/MRC/src/itkMRCHeaderObject.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -110,55 +110,6 @@ MRCHeaderObject::SetHeader(const Header * buffer)
this->m_ExtendedHeader = nullptr;
this->m_ExtendedFeiHeader = nullptr;

SizeValueType extendedHeaderBytes = 0;
if (this->m_Header.nreal & 1)
{
extendedHeaderBytes += 2;
}
if (this->m_Header.nreal & 2)
{
extendedHeaderBytes += 6;
}
if (this->m_Header.nreal & 4)
{
extendedHeaderBytes += 3;
}
if (this->m_Header.nreal & 8)
{
extendedHeaderBytes += 2;
}
if (this->m_Header.nreal & 16)
{
extendedHeaderBytes += 2;
}
if (this->m_Header.nreal & 32)
{
extendedHeaderBytes += 4;
}
if (this->m_Header.nreal & 64)
{
extendedHeaderBytes += 2;
}
if (this->m_Header.nreal & 128)
{
extendedHeaderBytes += 4;
}
if (this->m_Header.nreal & 256)
{
extendedHeaderBytes += 2;
}
if (this->m_Header.nreal & 512)
{
extendedHeaderBytes += 4;
}
if (this->m_Header.nreal & 1024)
{
extendedHeaderBytes += 2;
}
// TODO: all the above to set extendedHeaderBytes, yet extendedHeaderBytes is unused!
itkWarningMacro(<< "extendedHeaderBytes is: " << extendedHeaderBytes
<< "If you see this log please contact https://github.com/InsightSoftwareConsortium/ITK/pull/2778");
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this->m_ExtendedHeaderSize = this->m_Header.next;

// check to make sure the data makes sense
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20 changes: 6 additions & 14 deletions Modules/IO/MRC/src/itkMRCImageIO.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -200,20 +200,10 @@ MRCImageIO::ReadImageInformation()
}
}

if (header.xlen == 0.0f && header.ylen == 0.0f && header.zlen == 0.0f)
{
// if the spacing was not set in the header then this is the
// default
m_Spacing[0] = 1.0;
m_Spacing[1] = 1.0;
m_Spacing[2] = 1.0;
}
else
{
m_Spacing[0] = header.xlen / static_cast<float>(header.mx);
m_Spacing[1] = header.ylen / static_cast<float>(header.my);
m_Spacing[2] = header.zlen / static_cast<float>(header.mz);
}
// if the spacing was not set in the header then 1.0 is the default
m_Spacing[0] = header.xlen != 0.0f ? header.xlen / static_cast<float>(header.mx) : 1.0;
m_Spacing[1] = header.ylen != 0.0f ? header.ylen / static_cast<float>(header.my) : 1.0;
m_Spacing[2] = header.zlen != 0.0f ? header.zlen / static_cast<float>(header.mz) : 1.0;

// copy the origin
m_Origin[0] = header.xorg;
Expand Down Expand Up @@ -368,10 +358,12 @@ MRCImageIO::UpdateHeaderFromImageIO()
if (ByteSwapper<void *>::SystemIsBigEndian())
{
header.stamp[0] = 17;
header.stamp[1] = 17;
}
else
{
header.stamp[0] = 68;
header.stamp[1] = 68;
}

header.alpha = 90;
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8 changes: 8 additions & 0 deletions Modules/IO/MRC/test/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -34,3 +34,11 @@ itk_add_test(NAME itkMRCImageIOTest2c
DATA{${ITK_DATA_ROOT}/Input/RGBTestImageLZW.tif}
${ITK_TEST_OUTPUT_DIR}/itkMRCImageIOTest2c.mrc
38a2dcfc08812e04b1528f15ca3d2ab7)
itk_add_test(NAME itkMRCImageIOTest2d
COMMAND ITKIOMRCTestDriver
--compare-MD5 ${ITK_TEST_OUTPUT_DIR}/itkMRCImageIOTest2d.mrc
96093c8573ce2b4f197f0b0bfcc574bf
itkMRCImageIOTest2
DATA{Input/tilt_uint8.mrc}
${ITK_TEST_OUTPUT_DIR}/itkMRCImageIOTest2d.mrc
96093c8573ce2b4f197f0b0bfcc574bf)
1 change: 1 addition & 0 deletions Modules/IO/MRC/test/Input/tilt_uint8.mrc.sha512
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
332985f125b8584b9ba158faef6294cd2f2a9e8d9fb5b7f05a74b08089b2d4e13465c1c483e42b6c4263dac9af19542a8bd5ff33dc627507ba60c976a3cb5b0a
3 changes: 3 additions & 0 deletions Modules/IO/MRC/test/itkMRCImageIOTest2.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,9 @@
#include "itkMetaDataObject.h"
#include "itkTestingHashImageFilter.h"


static_assert(sizeof(itk::MRCHeaderObject::Header) == 1024, " Ill defined MRC Header struct");

namespace
{

Expand Down