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POL5645 Combinable 3D features
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Co-authored-by: Sameeul Samee <sameeul@gmail.com>
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@friskluft @sameeul
friskluft and sameeul authored Jan 23, 2025
1 parent a8de931 commit 7701dc5
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Showing 4 changed files with 80 additions and 162 deletions.
191 changes: 46 additions & 145 deletions src/nyx/env_features.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@
#include "features/3d_ngldm.h"
#include "features/3d_ngtdm.h"
#include "features/3d_gldzm.h"
#include "features/3d_glrlm.h"
#include "features/3d_glszm.h"
#include "features/roi_radius.h"
#include "helpers/helpers.h"
Expand Down Expand Up @@ -131,8 +132,8 @@ bool Environment::spellcheck_raw_featurelist(const std::string& comma_separated_

if (dim() == 3)
{
// Is feature found among 2D features?
Fgroup3D afg;
// Is feature found among 3D features?
int afg; // signed Fgroup3D
bool gnameExists = theFeatureSet.find_3D_GroupByString (s_uppr, afg);

// Intercept an error: 3D feature group exists but requested in the non-3D mode
Expand All @@ -150,7 +151,7 @@ bool Environment::spellcheck_raw_featurelist(const std::string& comma_separated_
continue;
}

Feature3D af;
int af; // signed Feature3D
bool fnameExists = theFeatureSet.find_3D_FeatureByString (s_uppr, af);

// 3D feature group requested on a non-3D mode ?
Expand Down Expand Up @@ -353,11 +354,19 @@ bool Environment::expand_2D_featuregroup (const std::string & s)
//
bool Environment::expand_3D_featuregroup (const std::string& s)
{
// mutually exclusive groups:
if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup3D::FG3_ALL))
int fgcode;
if (!Nyxus::theFeatureSet.find_3D_GroupByString(s, fgcode))
return false; // 's' is a feature name
bool enable = true;
if (fgcode < 0)
{
theFeatureSet.enableAll(false);
fgcode = -fgcode;
enable = false;
}

// mutually exclusive groups:
if ((Fgroup3D)fgcode == Fgroup3D::FG3_ALL)
{
auto F =
{
Feature3D::COV,
Expand Down Expand Up @@ -439,172 +448,61 @@ bool Environment::expand_3D_featuregroup (const std::string& s)
#endif
};

theFeatureSet.enableFeatures (F);
theFeatureSet.enableFeatures (D3_GLCM_feature::featureset);
theFeatureSet.enableFeatures (D3_GLDZM_feature::featureset);
theFeatureSet.enableFeatures (D3_GLSZM_feature::featureset);
theFeatureSet.enableFeatures (F, enable);
theFeatureSet.enableFeatures (D3_GLCM_feature::featureset, enable);
theFeatureSet.enableFeatures (D3_GLDM_feature::featureset, enable);
theFeatureSet.enableFeatures (D3_GLDZM_feature::featureset, enable);
theFeatureSet.enableFeatures (D3_GLRLM_feature::featureset, enable);
theFeatureSet.enableFeatures (D3_GLSZM_feature::featureset, enable);
theFeatureSet.enableFeatures (D3_NGLDM_feature::featureset, enable);
theFeatureSet.enableFeatures (D3_NGTDM_feature::featureset, enable);

return true;
}

if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup3D::FG3_GLCM))
if ((Fgroup3D)fgcode == Fgroup3D::FG3_GLCM)
{
theFeatureSet.enableAll (false);
theFeatureSet.enableFeatures (D3_GLCM_feature::featureset);
theFeatureSet.enableFeatures (D3_GLCM_feature::featureset, enable);
return true;
}

if (s == Nyxus::theFeatureSet.findGroupNameByCode (Fgroup3D::FG3_GLDM))
if ((Fgroup3D)fgcode == Fgroup3D::FG3_GLDM)
{
theFeatureSet.enableAll (false);
theFeatureSet.enableFeatures (D3_GLDM_feature::featureset);
theFeatureSet.enableFeatures (D3_GLDM_feature::featureset, enable);
return true;
}

if (s == Nyxus::theFeatureSet.findGroupNameByCode (Fgroup3D::FG3_NGLDM))
if ((Fgroup3D)fgcode == Fgroup3D::FG3_NGLDM)
{
theFeatureSet.enableAll (false);
theFeatureSet.enableFeatures (D3_NGLDM_feature::featureset);
theFeatureSet.enableFeatures (D3_NGLDM_feature::featureset, enable);
return true;
}

if (s == Nyxus::theFeatureSet.findGroupNameByCode (Fgroup3D::FG3_NGTDM))
if ((Fgroup3D)fgcode == Fgroup3D::FG3_NGTDM)
{
theFeatureSet.enableAll (false);
theFeatureSet.enableFeatures (D3_NGTDM_feature::featureset);
theFeatureSet.enableFeatures (D3_NGTDM_feature::featureset, enable);
return true;
}

if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup3D::FG3_GLCM))
if ((Fgroup3D)fgcode == Fgroup3D::FG3_GLDZM)
{
theFeatureSet.enableAll (false);

auto F =
{
Nyxus::Feature3D::GLCM_ACOR,
Nyxus::Feature3D::GLCM_ASM,
Nyxus::Feature3D::GLCM_CLUPROM,
Nyxus::Feature3D::GLCM_CLUSHADE,
Nyxus::Feature3D::GLCM_CLUTEND,
Nyxus::Feature3D::GLCM_CONTRAST,
Nyxus::Feature3D::GLCM_CORRELATION,
Nyxus::Feature3D::GLCM_DIFAVE,
Nyxus::Feature3D::GLCM_DIFENTRO,
Nyxus::Feature3D::GLCM_DIFVAR,
Nyxus::Feature3D::GLCM_DIS,
Nyxus::Feature3D::GLCM_ENERGY,
Nyxus::Feature3D::GLCM_ENTROPY,
Nyxus::Feature3D::GLCM_HOM1,
Nyxus::Feature3D::GLCM_HOM2,
Nyxus::Feature3D::GLCM_ID,
Nyxus::Feature3D::GLCM_IDN,
Nyxus::Feature3D::GLCM_IDM,
Nyxus::Feature3D::GLCM_IDMN,
Nyxus::Feature3D::GLCM_INFOMEAS1,
Nyxus::Feature3D::GLCM_INFOMEAS2,
Nyxus::Feature3D::GLCM_IV,
Nyxus::Feature3D::GLCM_JAVE,
Nyxus::Feature3D::GLCM_JE,
Nyxus::Feature3D::GLCM_JMAX,
Nyxus::Feature3D::GLCM_JVAR,
Nyxus::Feature3D::GLCM_SUMAVERAGE,
Nyxus::Feature3D::GLCM_SUMENTROPY,
Nyxus::Feature3D::GLCM_SUMVARIANCE,
Nyxus::Feature3D::GLCM_VARIANCE,
Nyxus::Feature3D::GLCM_ASM_AVE,
Nyxus::Feature3D::GLCM_ACOR_AVE,
Nyxus::Feature3D::GLCM_CLUPROM_AVE,
Nyxus::Feature3D::GLCM_CLUSHADE_AVE,
Nyxus::Feature3D::GLCM_CLUTEND_AVE,
Nyxus::Feature3D::GLCM_CONTRAST_AVE,
Nyxus::Feature3D::GLCM_CORRELATION_AVE,
Nyxus::Feature3D::GLCM_DIFAVE_AVE,
Nyxus::Feature3D::GLCM_DIFENTRO_AVE,
Nyxus::Feature3D::GLCM_DIFVAR_AVE,
Nyxus::Feature3D::GLCM_DIS_AVE,
Nyxus::Feature3D::GLCM_ENERGY_AVE,
Nyxus::Feature3D::GLCM_ENTROPY_AVE,
Nyxus::Feature3D::GLCM_HOM1_AVE,
Nyxus::Feature3D::GLCM_ID_AVE,
Nyxus::Feature3D::GLCM_IDN_AVE,
Nyxus::Feature3D::GLCM_IDM_AVE,
Nyxus::Feature3D::GLCM_IDMN_AVE,
Nyxus::Feature3D::GLCM_IV_AVE,
Nyxus::Feature3D::GLCM_JAVE_AVE,
Nyxus::Feature3D::GLCM_JE_AVE,
Nyxus::Feature3D::GLCM_INFOMEAS1_AVE,
Nyxus::Feature3D::GLCM_INFOMEAS2_AVE,
Nyxus::Feature3D::GLCM_VARIANCE_AVE,
Nyxus::Feature3D::GLCM_JMAX_AVE,
Nyxus::Feature3D::GLCM_JVAR_AVE,
Nyxus::Feature3D::GLCM_SUMAVERAGE_AVE,
Nyxus::Feature3D::GLCM_SUMENTROPY_AVE,
Nyxus::Feature3D::GLCM_SUMVARIANCE_AVE
};

theFeatureSet.enableFeatures(F);
theFeatureSet.enableFeatures (D3_GLDZM_feature::featureset, enable);
return true;
}

if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup3D::FG3_GLDZM))
if ((Fgroup3D)fgcode == Fgroup3D::FG3_GLSZM)
{
theFeatureSet.enableAll (false);
theFeatureSet.enableFeatures (D3_GLDZM_feature::featureset);
return true;
}

if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup3D::FG3_GLSZM))
{
theFeatureSet.enableAll (false);
theFeatureSet.enableFeatures (D3_GLSZM_feature::featureset);
theFeatureSet.enableFeatures (D3_GLSZM_feature::featureset, enable);
return true;
}

if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup3D::FG3_GLRLM))
if ((Fgroup3D)fgcode == Fgroup3D::FG3_GLRLM)
{
theFeatureSet.enableAll(false);

auto F =
{
Nyxus::Feature3D::GLRLM_SRE,
Nyxus::Feature3D::GLRLM_LRE,
Nyxus::Feature3D::GLRLM_GLN,
Nyxus::Feature3D::GLRLM_GLNN,
Nyxus::Feature3D::GLRLM_RLN,
Nyxus::Feature3D::GLRLM_RLNN,
Nyxus::Feature3D::GLRLM_RP,
Nyxus::Feature3D::GLRLM_GLV,
Nyxus::Feature3D::GLRLM_RV,
Nyxus::Feature3D::GLRLM_RE,
Nyxus::Feature3D::GLRLM_LGLRE,
Nyxus::Feature3D::GLRLM_HGLRE,
Nyxus::Feature3D::GLRLM_SRLGLE,
Nyxus::Feature3D::GLRLM_SRHGLE,
Nyxus::Feature3D::GLRLM_LRLGLE,
Nyxus::Feature3D::GLRLM_LRHGLE,

Nyxus::Feature3D::GLRLM_SRE_AVE,
Nyxus::Feature3D::GLRLM_LRE_AVE,
Nyxus::Feature3D::GLRLM_GLN_AVE,
Nyxus::Feature3D::GLRLM_GLNN_AVE,
Nyxus::Feature3D::GLRLM_RLN_AVE,
Nyxus::Feature3D::GLRLM_RLNN_AVE,
Nyxus::Feature3D::GLRLM_RP_AVE,
Nyxus::Feature3D::GLRLM_GLV_AVE,
Nyxus::Feature3D::GLRLM_RV_AVE,
Nyxus::Feature3D::GLRLM_RE_AVE,
Nyxus::Feature3D::GLRLM_LGLRE_AVE,
Nyxus::Feature3D::GLRLM_HGLRE_AVE,
Nyxus::Feature3D::GLRLM_SRLGLE_AVE,
Nyxus::Feature3D::GLRLM_SRHGLE_AVE,
Nyxus::Feature3D::GLRLM_LRLGLE_AVE,
Nyxus::Feature3D::GLRLM_LRHGLE_AVE
};

theFeatureSet.enableFeatures(F);
theFeatureSet.enableFeatures (D3_GLRLM_feature::featureset, enable);
return true;
}

// unrecognized feature group
return false;
}

Expand Down Expand Up @@ -643,6 +541,8 @@ void Environment::expand_featuregroups()
continue;
}

// try to interpret 's' as a group name

if (dim() == 2)
{
if (expand_2D_featuregroup (s))
Expand All @@ -656,24 +556,25 @@ void Environment::expand_featuregroups()
}

// 's' is an individual feature name, not feature group name. Process it now

if (dim() == 2)
{
int fcode; // signed Feature2D
if (!theFeatureSet.find_2D_FeatureByString (s, fcode))
if (!Nyxus::theFeatureSet.find_2D_FeatureByString (s, fcode))
throw std::invalid_argument("Error: '" + s + "' is not a valid 2D feature name \n");

theFeatureSet.enableFeature (fcode);
Nyxus::theFeatureSet.enableFeature (fcode);

continue;
}

if (dim() == 3)
{
Feature3D a;
if (!theFeatureSet.find_3D_FeatureByString(s, a))
int a; // signed Feature3D
if (!Nyxus::theFeatureSet.find_3D_FeatureByString(s, a))
throw std::invalid_argument("Error: '" + s + "' is not a valid 3D feature name \n");

theFeatureSet.enableFeature (int(a));
Nyxus::theFeatureSet.enableFeature (int(a));
continue;
}
}
Expand Down
32 changes: 24 additions & 8 deletions src/nyx/featureset.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -945,7 +945,6 @@ bool FeatureSet::find_2D_GroupByString (
enable = name[0] == '+' ? 1 : -1;
}


// search
auto itr = Nyxus::UserFacing2dFeaturegroupNames.find (s);

Expand All @@ -957,39 +956,56 @@ bool FeatureSet::find_2D_GroupByString (
return true;
}

bool FeatureSet::find_3D_FeatureByString (const std::string & name, Feature3D & f)
bool FeatureSet::find_3D_FeatureByString (const std::string & name, int & f)
{
int enable = 1;

// strip possible set operation '+' or '-'
std::string s = name;

if (name[0] == '-' || name[0] == '+')
s = name.substr(1);
// digest optional unary operator (sign)
if (std::ispunct(name[0]))
if (name[0] == '-' || name[0] == '+')
{
s = name.substr(1);
enable = name[0] == '+' ? 1 : -1;
}
else
return false; // invalid unary operator

// search
auto it_f = Nyxus::UserFacing_3D_featureNames.find (s);
auto it_f = Nyxus::UserFacing_3D_featureNames.find(s);

if (it_f == Nyxus::UserFacing_3D_featureNames.end())
return false;

f = it_f->second;
f = enable * (int)it_f->second;

return true;
}

bool FeatureSet::find_3D_GroupByString (const std::string & name, Fgroup3D & grpCode)
bool FeatureSet::find_3D_GroupByString (const std::string & name, int & grpCode)
{
int enable = 1;

// strip possible set operation '+' or '-'
std::string s = name;

// digest optional unary operator (sign)
if (name[0] == '-' || name[0] == '+')
{
s = name.substr(1);
enable = name[0] == '+' ? 1 : -1;
}

// search
auto itr = Nyxus::UserFacing3dFeaturegroupNames.find (s);

if (itr == Nyxus::UserFacing3dFeaturegroupNames.end())
return false;

grpCode = itr->second;
grpCode = enable * (int)itr->second;

return true;
}

Expand Down
14 changes: 7 additions & 7 deletions src/nyx/featureset.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -854,7 +854,7 @@ namespace Nyxus
enum class Fgroup2D
{
FG2_ALL = 0,
FG2_WHOLESLIDE,
FG2_WHOLESLIDE, // FG2_WHOLESLIDE is FG2_ALL for whole slides
FG2_INTENSITY,
FG2_MORPHOLOGY,
FG2_BASIC_MORPHOLOGY,
Expand Down Expand Up @@ -925,10 +925,10 @@ class FeatureSet
for (auto f : F)
m_enabledFeatures[(int)f] = enable;
}
void enableFeatures(const std::initializer_list<Nyxus::Feature3D>& desiredFeatures)
void enableFeatures(const std::initializer_list<Nyxus::Feature3D>& F, bool enable = true)
{
for (auto f : desiredFeatures)
m_enabledFeatures[(int)f] = true;
for (auto f : F)
m_enabledFeatures[(int)f] = enable;
}
void enableFeatures(const std::initializer_list<Nyxus::FeatureIMQ>& desiredFeatures) {
for (auto f : desiredFeatures)
Expand Down Expand Up @@ -1039,10 +1039,10 @@ class FeatureSet
cnt++;
return cnt;
}
bool find_2D_FeatureByString (const std::string& name, int& f); // 'f' is signed Feature2D
bool find_2D_FeatureByString (const std::string & name, int & f); // 'f' is signed Feature2D
bool find_2D_GroupByString (const std::string& group_name, int & group_code); // 'group_code' is signed Nyxus::Fgroup2D
bool find_3D_FeatureByString (const std::string & feature_name, Nyxus::Feature3D & feature_code);
bool find_3D_GroupByString (const std::string & group_name, Nyxus::Fgroup3D & group_code);
bool find_3D_FeatureByString (const std::string & feature_name, int & feature_code);
bool find_3D_GroupByString (const std::string & group_name, int & group_code);
bool find_IMQ_FeatureByString (const std::string & feature_name, Nyxus::FeatureIMQ & feature_code);
bool find_IMQ_GroupByString (const std::string & group_name, Nyxus::FgroupIMQ & group_code);

Expand Down
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