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POL5471 wholeslide gpu update #240

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merged 4 commits into from
Oct 24, 2024
Merged

POL5471 wholeslide gpu update #240

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75b8575
initial test commit
friskluft Oct 17, 2024
4b7daa3
*
friskluft Oct 17, 2024
cc8c277
**
friskluft Oct 18, 2024
3ab4a7e
***
friskluft Oct 21, 2024
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1 change: 1 addition & 0 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -332,6 +332,7 @@ if(USEGPU)
src/nyx/gpu/geomoments_weighting.cu
src/nyx/gpu/glszm.cu
src/nyx/gpu/gpucache.cu
src/nyx/gpu/reducers.cu
)
add_library(nyxus_gpu ${GPU_SOURCE_FILES})

Expand Down
187 changes: 94 additions & 93 deletions src/nyx/env_features.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -85,8 +85,8 @@ bool Environment::spellcheck_raw_featurelist(const std::string& comma_separated_
if (dim() == 2)
{
// Is feature found among 2D features?
Fgroup2D afg;
bool gnameExists = theFeatureSet.find_2D_GroupByString (s_uppr, afg);
int fg; // signed Fgroup2D
bool gnameExists = theFeatureSet.find_2D_GroupByString (s_uppr, fg);

// Intercept an error: 2D feature group exists but requested in the non-2D mode
if (gnameExists && dim() != 2)
Expand All @@ -103,8 +103,8 @@ bool Environment::spellcheck_raw_featurelist(const std::string& comma_separated_
continue;
}

Feature2D af;
bool fnameExists = theFeatureSet.find_2D_FeatureByString (s_uppr, af);
int fcode; // signed Feature2D
bool fnameExists = theFeatureSet.find_2D_FeatureByString (s_uppr, fcode);

// 2D feature group requested on a non-2D mode ?
if (fnameExists && dim() != 2)
Expand All @@ -117,7 +117,7 @@ bool Environment::spellcheck_raw_featurelist(const std::string& comma_separated_
if (!fnameExists)
{
success = false;
std::cerr << "Error: expecting '" << s << "' to be a proper 2D feature name or feature file path\n";
std::cerr << "Error: expecting '" + s + "' to be a proper 2D feature name or feature file path\n";
}
else
fnames.push_back(s_uppr);
Expand Down Expand Up @@ -185,65 +185,67 @@ bool Environment::spellcheck_raw_featurelist(const std::string& comma_separated_
//
bool Environment::expand_2D_featuregroup (const std::string & s)
{
if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_ALL))
int fgcode;
if (! Nyxus::theFeatureSet.find_2D_GroupByString(s, fgcode))
return false; // 's' is a feature name
bool enable = true;
if (fgcode < 0)
{
Nyxus::theFeatureSet.enableAll();

// Handle whole-slide mode differently: disable features irrelevant to this mode (shape, neighbors, etc)
if (singleROI)
{
std::cout << box_text ("Activating whole slide (aka single-ROI) mode\n"
"ATTENTION: disabling inappplicable and time-sonsuming features:\n"
" - morphological features\n"
" - neighbor features\n"
" - GLDM, GLDZM, GLRLM, GLSZM, NGLDM, NGTDM");

theFeatureSet.disableFeatures(BasicMorphologyFeatures::featureset);
theFeatureSet.disableFeatures(EnclosingInscribingCircumscribingCircleFeature::featureset);
theFeatureSet.disableFeatures(ContourFeature::featureset); // and its dependencies below (see file reduce_trivial_rois_manual.cpp)
theFeatureSet.disableFeatures(ConvexHullFeature::featureset); // depends on ContourFeature
theFeatureSet.disableFeatures(FractalDimensionFeature::featureset); // depends on ContourFeature
theFeatureSet.disableFeatures(GeodeticLengthThicknessFeature::featureset); // depends on ContourFeature
theFeatureSet.disableFeatures(NeighborsFeature::featureset); // depends on ContourFeature
theFeatureSet.disableFeatures(RoiRadiusFeature::featureset); // depends on ContourFeature
theFeatureSet.disableFeatures(EllipseFittingFeature::featureset);
theFeatureSet.disableFeatures(EulerNumberFeature::featureset);
theFeatureSet.disableFeatures(ExtremaFeature::featureset);
theFeatureSet.disableFeatures(ErosionPixelsFeature::featureset);
theFeatureSet.disableFeatures(CaliperFeretFeature::featureset);
theFeatureSet.disableFeatures(CaliperMartinFeature::featureset);
theFeatureSet.disableFeatures(CaliperNassensteinFeature::featureset);
theFeatureSet.disableFeatures(ChordsFeature::featureset);

// enabling GaborFeature
// enabling ImageMomentsFeature
// enabling GLCMFeature

theFeatureSet.disableFeatures(GLDMFeature::featureset); // costs about 4.72 %
theFeatureSet.disableFeatures(GLDZMFeature::featureset); // costs about 38.14 %
theFeatureSet.disableFeatures(GLRLMFeature::featureset); // costs about 17.29 %
theFeatureSet.disableFeatures(GLSZMFeature::featureset); // costs about 15.94 %
theFeatureSet.disableFeatures(NGLDMfeature::featureset); // costs about 3.57 %
theFeatureSet.disableFeatures(NGTDMFeature::featureset); // costs about 5.13 %
}

return true;
fgcode = -fgcode;
enable = false;
}
if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_BUT_GABOR))

if ((Fgroup2D)fgcode == Fgroup2D::FG2_ALL)
{
Nyxus::theFeatureSet.enableAll();
auto F = { Feature2D::GABOR };
Nyxus::theFeatureSet.disableFeatures(F);
Nyxus::theFeatureSet.enableAll (enable);
return true;
}
if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_ALL_BUT_GLCM))

if ((Fgroup2D)fgcode == Fgroup2D::FG2_WHOLESLIDE)
{
Nyxus::theFeatureSet.enableAll();
theFeatureSet.disableFeatures(GLCMFeature::featureset);
Nyxus::theFeatureSet.enableAll(enable);

// Handle whole-slide mode differently: disable features irrelevant to this mode (shape, neighbors, etc)
std::cout << box_text(
"Activating whole slide (aka single-ROI) mode\n"
"Using GPU is advised!\n"
"ATTENTION: disabling inappplicable and time-sonsuming features:\n"
" - morphological features\n"
" - neighbor features\n"
" - GLDZM");

theFeatureSet.disableFeatures (BasicMorphologyFeatures::featureset);
theFeatureSet.disableFeatures (EnclosingInscribingCircumscribingCircleFeature::featureset);
// enabling ContourFeature (builds a special trivial wholeslide contour)
theFeatureSet.disableFeatures (ConvexHullFeature::featureset); // depends on ContourFeature
theFeatureSet.disableFeatures (FractalDimensionFeature::featureset); // depends on ContourFeature
theFeatureSet.disableFeatures (GeodeticLengthThicknessFeature::featureset); // depends on ContourFeature
theFeatureSet.disableFeatures (NeighborsFeature::featureset); // no neighbors for whole slide; depends on ContourFeature
theFeatureSet.disableFeatures (RoiRadiusFeature::featureset); // depends on ContourFeature
theFeatureSet.disableFeatures (EllipseFittingFeature::featureset);
theFeatureSet.disableFeatures (EulerNumberFeature::featureset);
theFeatureSet.disableFeatures (ExtremaFeature::featureset);
theFeatureSet.disableFeatures (ErosionPixelsFeature::featureset);
theFeatureSet.disableFeatures (CaliperFeretFeature::featureset);
theFeatureSet.disableFeatures (CaliperMartinFeature::featureset);
theFeatureSet.disableFeatures (CaliperNassensteinFeature::featureset);
theFeatureSet.disableFeatures (ChordsFeature::featureset);

// enabling GaborFeature
// enabling ImageMomentsFeature
//
// enabling GLCMFeature
// enabling GLDMFeature
theFeatureSet.disableFeatures(GLDZMFeature::featureset); // costs about 82 %
// enabling GLRLMFeature
// enabling GLSZMFeature
// enabling NGLDMfeature
// enabling NGTDMFeature

return true;
}

if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_EASY))
if ((Fgroup2D) fgcode == Fgroup2D::FG2_EASY)
{
theFeatureSet.enableAll();
theFeatureSet.disableFeatures(GaborFeature::featureset);
Expand All @@ -253,19 +255,18 @@ bool Environment::expand_2D_featuregroup (const std::string & s)
return true;
}

if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_NEIG))
if ((Fgroup2D) fgcode == Fgroup2D::FG2_NEIG)
{
theFeatureSet.enableAll();
theFeatureSet.enableFeatures(NeighborsFeature::featureset);
Nyxus::theFeatureSet.enableFeatures (NeighborsFeature::featureset, enable);
return true;
}

if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_INTENSITY))
if ((Fgroup2D) fgcode == Fgroup2D::FG2_INTENSITY)
{
theFeatureSet.enableFeatures(PixelIntensityFeatures::featureset);
Nyxus::theFeatureSet.enableFeatures (PixelIntensityFeatures::featureset, enable);
return true;
}
if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_MORPHOLOGY))
if ((Fgroup2D) fgcode == Fgroup2D::FG2_MORPHOLOGY)
{
auto F = {
Feature2D::AREA_PIXELS_COUNT,
Expand Down Expand Up @@ -297,10 +298,10 @@ bool Environment::expand_2D_featuregroup (const std::string & s)
Feature2D::EDGE_MIN_INTENSITY,
Feature2D::CIRCULARITY,
Feature2D::MASS_DISPLACEMENT };
theFeatureSet.enableFeatures(F);
Nyxus::theFeatureSet.enableFeatures (F, enable);
return true;
}
if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_BASIC_MORPHOLOGY))
if ((Fgroup2D)fgcode == Fgroup2D::FG2_BASIC_MORPHOLOGY)
{
auto F = {
Feature2D::AREA_PIXELS_COUNT,
Expand All @@ -311,61 +312,61 @@ bool Environment::expand_2D_featuregroup (const std::string & s)
Feature2D::BBOX_XMIN,
Feature2D::BBOX_HEIGHT,
Feature2D::BBOX_WIDTH };
theFeatureSet.enableFeatures(F);
Nyxus::theFeatureSet.enableFeatures (F, enable);
return true;
}
if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_GLCM))
if ((Fgroup2D)fgcode == Fgroup2D::FG2_GLCM)
{
theFeatureSet.enableFeatures(GLCMFeature::featureset);
Nyxus::theFeatureSet.enableFeatures (GLCMFeature::featureset, enable);
return true;
}
if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_GLRLM))
if ((Fgroup2D)fgcode == Fgroup2D::FG2_GLRLM)
{
theFeatureSet.enableFeatures(GLRLMFeature::featureset);
Nyxus::theFeatureSet.enableFeatures (GLRLMFeature::featureset, enable);
return true;
}
if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_GLDZM))
if ((Fgroup2D)fgcode == Fgroup2D::FG2_GLDZM)
{
theFeatureSet.enableFeatures(GLDZMFeature::featureset);
Nyxus::theFeatureSet.enableFeatures (GLDZMFeature::featureset, enable);
return true;
}
if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_GLSZM))
if ((Fgroup2D)fgcode == Fgroup2D::FG2_GLSZM)
{
theFeatureSet.enableFeatures(GLSZMFeature::featureset);
Nyxus::theFeatureSet.enableFeatures (GLSZMFeature::featureset, enable);
return true;
}
if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_GLDM))
if ((Fgroup2D)fgcode == Fgroup2D::FG2_GLDM)
{
theFeatureSet.enableFeatures(GLDMFeature::featureset);
Nyxus::theFeatureSet.enableFeatures(GLDMFeature::featureset, enable);
return true;
}
if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_NGLDM))
if ((Fgroup2D)fgcode == Fgroup2D::FG2_NGLDM)
{
theFeatureSet.enableFeatures(NGLDMfeature::featureset);
Nyxus::theFeatureSet.enableFeatures (NGLDMfeature::featureset, enable);
return true;
}
if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_NGTDM))
if ((Fgroup2D)fgcode == Fgroup2D::FG2_NGTDM)
{
theFeatureSet.enableFeatures(NGTDMFeature::featureset);
Nyxus::theFeatureSet.enableFeatures (NGTDMFeature::featureset, enable);
return true;
}

if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_GEOMOMENTS))
if ((Fgroup2D)fgcode == Fgroup2D::FG2_GEOMOMENTS)
{
theFeatureSet.enableFeatures (Smoms2D_feature::featureset);
theFeatureSet.enableFeatures (Imoms2D_feature::featureset);
Nyxus::theFeatureSet.enableFeatures (Smoms2D_feature::featureset, enable);
Nyxus::theFeatureSet.enableFeatures (Imoms2D_feature::featureset, enable);
return true;
}

if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_GEOMOMENTS_I))
if ((Fgroup2D)fgcode == Fgroup2D::FG2_GEOMOMENTS_I)
{
theFeatureSet.enableFeatures(Imoms2D_feature::featureset);
Nyxus::theFeatureSet.enableFeatures (Imoms2D_feature::featureset, enable);
return true;
}

if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_GEOMOMENTS_S))
if ((Fgroup2D)fgcode == Fgroup2D::FG2_GEOMOMENTS_S)
{
theFeatureSet.enableFeatures(Smoms2D_feature::featureset);
Nyxus::theFeatureSet.enableFeatures (Smoms2D_feature::featureset, enable);
return true;
}

Expand Down Expand Up @@ -487,15 +488,14 @@ bool Environment::expand_IMQ_featuregroup (const std::string & s)
return false;
}


void Environment::expand_featuregroups()
{
// initially, no features are enabled
theFeatureSet.enableAll(false);
for (auto& s : recognizedFeatureNames) // Second, iterate uppercased feature names
{
// Enforce the feature names to be in uppercase
s = Nyxus::toupper(s);

// enable/disable feature groups and individual features according to user's choice
for (auto& s : recognizedFeatureNames)
{
if (is_imq()) {
if (expand_IMQ_featuregroup (s))
return;
Expand Down Expand Up @@ -523,11 +523,12 @@ void Environment::expand_featuregroups()
// 's' is an individual feature name, not feature group name. Process it now
if (dim() == 2)
{
Feature2D a;
if (!theFeatureSet.find_2D_FeatureByString(s, a))
int fcode; // signed Feature2D
if (!theFeatureSet.find_2D_FeatureByString (s, fcode))
throw std::invalid_argument("Error: '" + s + "' is not a valid 2D feature name \n");

theFeatureSet.enableFeature (int(a));
theFeatureSet.enableFeature (fcode);

continue;
}

Expand Down
12 changes: 11 additions & 1 deletion src/nyx/environment.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -779,7 +779,10 @@ bool Environment::parse_cmdline(int argc, char** argv)
rawFeatures = featureList;
}

// --Make sure all the feature names are legal and cast to uppercase (class FeatureSet understands uppercase names)
// -- uppercase it (class FeatureSet understands uppercase names)
rawFeatures = Nyxus::toupper (rawFeatures);

// --Make sure all the feature names are correct
if (!spellcheck_raw_featurelist(rawFeatures, recognizedFeatureNames))
{
std::cerr << "Stopping due to errors while parsing user requested features\n";
Expand All @@ -797,6 +800,13 @@ bool Environment::parse_cmdline(int argc, char** argv)
return false;
}

// -- check if any feature is enablesd as a result of expanding user's choice
if (theFeatureSet.numOfEnabled() == 0)
{
std::cerr << "Error: no features are selected. Stopping \n";
return false;
}

//==== Parse resolution
if (rawXYRes.length() > 0)
{
Expand Down
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