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kerautret merged 5 commits into from
Apr 4, 2026
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Merged

Fixing subsampling tool #481

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e62abce
changerlog
dcoeurjo Mar 3, 2026
e1777d4
changerlog
dcoeurjo Mar 3, 2026
1a44b91
bugfix
dcoeurjo Mar 3, 2026
c9d4b04
simpler subsampling
dcoeurjo Mar 3, 2026
85e01ba
Merge branch 'main' into volsubmressage
kerautret Apr 4, 2026
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2 changes: 2 additions & 0 deletions ChangeLog.md
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@
- Default branch set to main instead old master.
(Bertrand Kerautret [477](https://github.com/DGtal-team/DGtalTools/pull/477))

- *volumetric*
- volSubSample: domains are shown before performing the subsampling and bugfix for the lowerbound (David Coeurjolly [481](https://github.com/DGtal-team/DGtalTools/pull/481)

# DGtalTools 2.1

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165 changes: 83 additions & 82 deletions volumetric/volSubSample.cpp
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Expand Up @@ -43,65 +43,65 @@ using namespace Z3i;


/**

@page volSubSample volSubSample

@brief Brutally sub samples a vol file (division by 2 in each direction).
@ingroup volumetrictools

@b Usage: ./volumetric/volSubSample [OPTIONS] 1 [2]


@b Allowed @b options @b are :
@b Allowed @b options @b are :
@code
Positionals:
1 TEXT:FILE REQUIRED Input vol file.
2 TEXT=result.vol Output filename.

1 TEXT:FILE REQUIRED Input vol file.
2 TEXT=result.vol Output filename.
Options:
-h,--help Print this help message and exit
-i,--input TEXT:FILE REQUIRED Input vol file.
-o,--output TEXT=result.vol Output filename.
-f,--function TEXT:{mean,none,max,min,mean}=mean
Function used to the down-sampling: {none,max, min, mean}

-h,--help Print this help message and exit
-i,--input TEXT:FILE REQUIRED Input vol file.
-o,--output TEXT=result.vol Output filename.
-f,--function TEXT:{mean,none,max,min,mean}=mean
Function used to the down-sampling: {none,max, min, mean}
Positionals:
1 TEXT:FILE REQUIRED Input vol file.
2 TEXT=result.vol Output filename.

1 TEXT:FILE REQUIRED Input vol file.
2 TEXT=result.vol Output filename.
Options:
-h,--help Print this help message and exit
-i,--input TEXT:FILE REQUIRED Input vol file.
-o,--output TEXT=result.vol Output filename.
-f,--function TEXT:{mean,none,max,min,mean}=mean
Function used to the down-sampling: {none,max, min, mean}

-h,--help Print this help message and exit
-i,--input TEXT:FILE REQUIRED Input vol file.
-o,--output TEXT=result.vol Output filename.
-f,--function TEXT:{mean,none,max,min,mean}=mean
Function used to the down-sampling: {none,max, min, mean}
@endcode

@b Example:
You can apply several sub sampling:
@b Example:
You can apply several sub sampling:
@code
$ volSubSample $DGtal/examples/samples/lobster.vol lobster2.vol -f mean
$ volSubSample lobster2.vol lobster4.vol -f mean
$ volSubSample lobster4.vol lobster8.vol -f mean
@endcode

You can display the result by extracting the surface using \ref 3dVolMarchingCubes:

@code
$ 3dVolMarchingCubes $DGtal/examples/samples/lobster.vol lobster.off -t 30
$ 3dVolMarchingCubes lobster2.vol -t 30 lobster2.off
$ 3dVolMarchingCubes lobster4.vol -t 30 lobster4.off
$ 3dVolMarchingCubes lobster8.vol -t 30 lobster8.off
$ meshViewer lobster.off lobster2.off lobster4.off lobster8.off -n
@endcode

You can display the result by extracting the surface using \ref 3dVolMarchingCubes:
@code
$ 3dVolMarchingCubes $DGtal/examples/samples/lobster.vol lobster.off -t 30
$ 3dVolMarchingCubes lobster2.vol -t 30 lobster2.off
$ 3dVolMarchingCubes lobster4.vol -t 30 lobster4.off
$ 3dVolMarchingCubes lobster8.vol -t 30 lobster8.off
$ meshViewer lobster.off lobster2.off lobster4.off lobster8.off -n
@endcode
You should obtain such a result:
@image html resVolSubSample.png "Resulting visualization."

@see
@ref volSubSample.cpp

*/


Expand All @@ -128,8 +128,8 @@ Val maxVal(Image const& image, Point const& p, Domain const& domain)
++it)
if ( domain.isInside(*it) && image( *it) > v) v=image(*it);

return v;
}
return v;
}
template<typename Val, typename Image, typename Point, typename Domain>
Val minVal(Image const& image, Point const& p, Domain const& domain)
{
Expand All @@ -140,8 +140,8 @@ Val minVal(Image const& image, Point const& p, Domain const& domain)
++it)
if ( domain.isInside(*it)&& image( *it) < v) v=image(*it);

return v;
}
return v;
}
template<typename Val, typename Image, typename Point, typename Domain>
Val meanVal(Image const& image, Point const& p, Domain const& domain)
{
Expand All @@ -152,12 +152,12 @@ Val meanVal(Image const& image, Point const& p, Domain const& domain)
it != itend;
++it)
if ( domain.isInside(*it) )
{
nb++;
v+=image(*it);
}
{
nb++;
v+=image(*it);
}
return static_cast<unsigned char>( v/nb );
}
}


int main(int argc, char**argv)
Expand All @@ -171,28 +171,29 @@ int main(int argc, char**argv)
std::string function {"mean"};

app.description("Brutally sub sample a vol file (division by 2 in each direction).\n Basic usage: \n \tvolSubSample <volFileName> <volOutputFileName> ");


app.add_option("-i,--input,1", inputFileName, "Input vol file." )
->required()
->check(CLI::ExistingFile);
app.add_option("-o,--output,2", outputFileName, "Output filename.");
app.add_option("-f,--function", function, "Function used to the down-sampling: {none,max, min, mean}")
-> check(CLI::IsMember({"mean", "none", "max", "min", "mean"}));
-> check(CLI::IsMember({"mean", "none", "max", "min", "mean"}));

app.get_formatter()->column_width(40);
CLI11_PARSE(app, argc, argv);
// END parse command line using CLI ----------------------------------------------


trace.beginBlock("Loading file");
typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char> MyImageC;

MyImageC imageC = VolReader< MyImageC >::importVol ( inputFileName );
MyImageC outputImage( Z3i::Domain( imageC.domain().lowerBound(),
(imageC.domain().upperBound()-imageC.domain().lowerBound())/Vector().diagonal(2)));

MyImageC outputImage( Z3i::Domain( imageC.domain().lowerBound() / 2, imageC.domain().upperBound() / 2));
trace.info()<<"Input vol: "<<imageC<<std::endl;
trace.info()<<"Output vol: "<<outputImage<<std::endl;
trace.endBlock();

Point subvector = Vector().diagonal(2);
Point p;
unsigned char val;
Expand All @@ -202,40 +203,40 @@ int main(int argc, char**argv)
//Fast Copy
if (function == "none")
for(MyImageC::Domain::ConstIterator it = outputImage.domain().begin(),
itend = outputImage.domain().end(); it != itend; ++it)
{
p = (*it) * 2;
outputImage.setValue( *it , imageC( p ));
}
itend = outputImage.domain().end(); it != itend; ++it)
{
p = (*it) * 2;
outputImage.setValue( *it , imageC( p ));
}
else
if (function == "max")
for(MyImageC::Domain::ConstIterator it = outputImage.domain().begin(),
itend = outputImage.domain().end(); it != itend; ++it)
{
val = maxVal<unsigned char, MyImageC, Point>(imageC, *it, imageC.domain());
outputImage.setValue( *it , val );
}
itend = outputImage.domain().end(); it != itend; ++it)
{
val = maxVal<unsigned char, MyImageC, Point>(imageC, *it, imageC.domain());
outputImage.setValue( *it , val );
}
else
if (function == "min")
for(MyImageC::Domain::ConstIterator it = outputImage.domain().begin(),
itend = outputImage.domain().end(); it != itend; ++it)
{
val = minVal<unsigned char, MyImageC, Point>(imageC, *it, imageC.domain());
outputImage.setValue( *it , val);
}
else

if (function == "mean")
for(MyImageC::Domain::ConstIterator it = outputImage.domain().begin(),
itend = outputImage.domain().end(); it != itend; ++it)
{
val = meanVal<unsigned char, MyImageC, Point>(imageC, *it, imageC.domain());
outputImage.setValue( *it , val );
}
for(MyImageC::Domain::ConstIterator it = outputImage.domain().begin(),
itend = outputImage.domain().end(); it != itend; ++it)
{
val = minVal<unsigned char, MyImageC, Point>(imageC, *it, imageC.domain());
outputImage.setValue( *it , val);
}
else
trace.error() << "Bad function !"<<std::endl;



if (function == "mean")
for(MyImageC::Domain::ConstIterator it = outputImage.domain().begin(),
itend = outputImage.domain().end(); it != itend; ++it)
{
val = meanVal<unsigned char, MyImageC, Point>(imageC, *it, imageC.domain());
outputImage.setValue( *it , val );
}
else
trace.error() << "Bad function !"<<std::endl;


trace.endBlock();

trace.beginBlock("Exporting...");
Expand Down
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