Merge branch 'master' into actions

.ci/docker/ubuntu/Dockerfile

@@ -1,6 +1,6 @@
 # MegaMol Ubuntu CI Environment
 
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
   build-essential \
@@ -12,16 +12,16 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
   libomp-dev \
 # vcpkg:
   curl zip unzip tar \
+# vcpkg zeromq:
+  pkg-config \
 # vcpkg meson (for libsystemd):
-  python3-distutils python3-jinja2 \
+  python3-jinja2 \
 # ci checks:
   clang-format clang-tidy \
 # glfw:
   xorg-dev \
-# gmp:
+# libsodium / gmp:
   autoconf libtool \
-# mpfr:
-  autoconf-archive \
 # thrift:
   flex bison \
 # GL/glu.h:

plugins/datatools/src/datatools.cpp

@@ -88,6 +88,7 @@
 #include "table/TableSelectionTx.h"
 #include "table/TableSort.h"
 #include "table/TableSplit.h"
+#include "table/TableStandardize.h"
 #include "table/TableToLines.h"
 #include "table/TableToParticles.h"
 #include "table/TableWhere.h"
@@ -179,6 +180,7 @@ class DatatoolsPluginInstance : public megamol::core::factories::AbstractPluginI
         this->module_descriptions.RegisterAutoDescription<megamol::datatools::ParticleInstantiator>();
         this->module_descriptions.RegisterAutoDescription<megamol::datatools::MPDCGrid>();
         this->module_descriptions.RegisterAutoDescription<megamol::datatools::table::TableSplit>();
+        this->module_descriptions.RegisterAutoDescription<megamol::datatools::table::TableStandardize>();
         this->module_descriptions.RegisterAutoDescription<megamol::datatools::CSVWriter>();
         this->module_descriptions.RegisterAutoDescription<megamol::datatools::clustering::ParticleIColClustering>();
         this->module_descriptions.RegisterAutoDescription<megamol::datatools::AddParticleColors>();

plugins/datatools/src/table/TableStandardize.cpp

@@ -0,0 +1,238 @@
+/**
+ * MegaMol
+ * Copyright (c) 2024, MegaMol Dev Team
+ * All rights reserved.
+ */
+
+#include "TableStandardize.h"
+
+#include <algorithm>
+#include <limits>
+
+#include <Eigen/Dense>
+
+#include "mmcore/param/EnumParam.h"
+#include "mmcore/utility/log/Log.h"
+
+using namespace megamol::datatools;
+using namespace megamol::datatools::table;
+using namespace megamol;
+
+std::string TableStandardize::ModuleName = std::string("TableStandardize");
+
+template<typename T>
+static inline double Lerp(T v0, T v1, T t) {
+    return (1 - t) * v0 + t * v1;
+}
+
+// https://stackoverflow.com/a/37708864/705750
+template<typename T>
+static inline std::vector<T> Quantile(const std::vector<T>& inData, const std::vector<T>& probs) {
+    if (inData.empty()) {
+        return std::vector<T>();
+    }
+
+    if (1 == inData.size()) {
+        return std::vector<T>(1, inData[0]);
+    }
+
+    std::vector<T> data = inData;
+    std::sort(data.begin(), data.end());
+    std::vector<T> quantiles;
+
+    for (size_t i = 0; i < probs.size(); ++i) {
+        T poi = Lerp<T>(-0.5, data.size() - 0.5, probs[i]);
+
+        size_t left = std::max(int64_t(std::floor(poi)), int64_t(0));
+        size_t right = std::min(int64_t(std::ceil(poi)), int64_t(data.size() - 1));
+
+        T datLeft = data.at(left);
+        T datRight = data.at(right);
+
+        T quantile = Lerp<T>(datLeft, datRight, poi - left);
+
+        quantiles.push_back(quantile);
+    }
+
+    return quantiles;
+}
+
+TableStandardize::TableStandardize()
+        : core::Module()
+        , dataOutSlot("dataOut", "Output")
+        , dataInSlot("dataIn", "Input")
+        , stratSlot("strategy", "which standardization approach to use")
+        , frameID(-1)
+        , in_datahash(std::numeric_limits<unsigned long>::max())
+        , out_datahash(0) {
+
+    this->dataInSlot.SetCompatibleCall<TableDataCallDescription>();
+    this->MakeSlotAvailable(&this->dataInSlot);
+
+    this->dataOutSlot.SetCallback(
+        TableDataCall::ClassName(), TableDataCall::FunctionName(0), &TableStandardize::processData);
+    this->dataOutSlot.SetCallback(
+        TableDataCall::ClassName(), TableDataCall::FunctionName(1), &TableStandardize::getExtent);
+    this->MakeSlotAvailable(&this->dataOutSlot);
+
+    auto enump = new core::param::EnumParam(Strategies::STANDARD);
+    enump->SetTypePair(Strategies::OFF, "Off (nop)");
+    enump->SetTypePair(Strategies::STANDARD, "Standard");
+    enump->SetTypePair(Strategies::MINMAX, "MinMax");
+    enump->SetTypePair(Strategies::MAXABS, "MaxAbs");
+    enump->SetTypePair(Strategies::ROBUST, "Robust");
+    this->stratSlot << enump;
+    this->MakeSlotAvailable(&this->stratSlot);
+}
+
+TableStandardize::~TableStandardize() {
+    this->Release();
+}
+
+bool TableStandardize::create() {
+    return true;
+}
+
+void TableStandardize::release() {}
+
+bool TableStandardize::processData(core::Call& c) {
+    try {
+        TableDataCall* outCall = dynamic_cast<TableDataCall*>(&c);
+        if (outCall == NULL)
+            return false;
+
+        TableDataCall* inCall = this->dataInSlot.CallAs<TableDataCall>();
+        if (inCall == NULL)
+            return false;
+
+        inCall->SetFrameID(outCall->GetFrameID());
+        if (!(*inCall)())
+            return false;
+
+        if (this->in_datahash != inCall->DataHash() || this->frameID != inCall->GetFrameID() ||
+            this->AnyParameterDirty()) {
+            this->in_datahash = inCall->DataHash();
+            this->frameID = inCall->GetFrameID();
+            this->ResetAllDirtyFlags();
+            this->out_datahash++;
+
+            column_count = inCall->GetColumnsCount();
+            column_infos = inCall->GetColumnsInfos();
+            row_count = inCall->GetRowsCount();
+            in_data = inCall->GetData();
+
+            const auto strat = this->stratSlot.Param<core::param::EnumParam>()->Value();
+
+            this->info.clear();
+            this->info.resize(column_count);
+            this->data.clear();
+            this->data.reserve(column_count * row_count);
+            this->data.insert(this->data.end(), &in_data[0], &in_data[column_count * row_count]);
+
+            // eigen would have liked column-major, but...
+            Eigen::Map<Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>> out_mat(
+                this->data.data(), row_count, column_count);
+
+            switch (strat) {
+            case Strategies::OFF:
+                // bypass
+                for (int x = 0; x < column_count; ++x) {
+                    this->info[x].SetName(column_infos[x].Name());
+                }
+                break;
+            case Strategies::STANDARD: {
+                for (int x = 0; x < column_count; ++x) {
+                    auto mean = out_mat.col(x).mean();
+                    out_mat.col(x) -= Eigen::VectorXf::Constant(row_count, mean);
+                    auto std_dev = sqrt(out_mat.col(x).cwiseProduct(out_mat.col(x)).sum() / (row_count - 1));
+                    out_mat.col(x) /= std_dev;
+                    this->info[x].SetName(column_infos[x].Name() + "_std");
+                }
+                break;
+            }
+            case Strategies::MINMAX: {
+                for (int x = 0; x < column_count; ++x) {
+                    auto min = out_mat.col(x).minCoeff();
+                    out_mat.col(x) -= Eigen::VectorXf::Constant(row_count, min);
+                    auto max = out_mat.col(x).maxCoeff();
+                    out_mat.col(x) / max;
+                    this->info[x].SetName(column_infos[x].Name() + "_minmax");
+                }
+                break;
+            }
+            case Strategies::MAXABS: {
+                for (int x = 0; x < column_count; ++x) {
+                    auto maxabs = out_mat.col(x).cwiseAbs().maxCoeff();
+                    out_mat.col(x) / maxabs;
+                    this->info[x].SetName(column_infos[x].Name() + "_maxabs");
+                }
+                break;
+            }
+            case Strategies::ROBUST: {
+                for (int x = 0; x < column_count; ++x) {
+                    // https://stackoverflow.com/a/62698308/705750
+                    // auto copy = out_mat.col(x).replicate(1, 1).reshaped();
+                    //std::sort(copy.begin(), copy.end());
+                    //auto median =
+                    //    copy.size() % 2 == 0 ? copy.segment((copy.size() - 2) / 2, 2).mean() : copy(copy.size() / 2);
+                    auto copy = std::vector<float>(out_mat.col(x).data(), out_mat.col(x).data() + row_count);
+                    auto quartiles = Quantile<float>(copy, {0.25, 0.5, 0.75});
+
+                    out_mat.col(x) -= Eigen::VectorXf::Constant(row_count, quartiles[1]);
+                    out_mat.col(x) /= (quartiles[2] - quartiles[0]);
+                    this->info[x].SetName(column_infos[x].Name() + "_robust");
+                }
+                break;
+            }
+            }
+
+            for (int x = 0; x < column_count; ++x) {
+                this->info[x].SetType(column_infos[x].Type());
+                this->info[x].SetMinimumValue(out_mat.col(x).minCoeff());
+                this->info[x].SetMaximumValue(out_mat.col(x).maxCoeff());
+            }
+        }
+
+        outCall->SetFrameCount(inCall->GetFrameCount());
+        outCall->SetFrameID(this->frameID);
+        outCall->SetDataHash(this->out_datahash);
+
+        if (!this->info.empty()) {
+            outCall->Set(
+                this->info.size(), this->data.size() / this->info.size(), this->info.data(), this->data.data());
+        } else {
+            outCall->Set(0, 0, NULL, NULL);
+        }
+    } catch (...) {
+        megamol::core::utility::log::Log::DefaultLog.WriteError(
+            _T("%hs: Failed to execute processData\n"), ModuleName.c_str());
+        return false;
+    }
+
+    return true;
+}
+
+bool TableStandardize::getExtent(core::Call& c) {
+    try {
+        TableDataCall* outCall = dynamic_cast<TableDataCall*>(&c);
+        if (outCall == NULL)
+            return false;
+
+        TableDataCall* inCall = this->dataInSlot.CallAs<TableDataCall>();
+        if (inCall == NULL)
+            return false;
+
+        inCall->SetFrameID(outCall->GetFrameID());
+        if (!(*inCall)(1))
+            return false;
+
+        outCall->SetFrameCount(inCall->GetFrameCount());
+        outCall->SetDataHash(this->out_datahash); // TODO: this is actually crap if somebody properly checks it
+    } catch (...) {
+        megamol::core::utility::log::Log::DefaultLog.WriteError(
+            _T("Failed to execute %hs::getExtent\n"), ModuleName.c_str());
+        return false;
+    }
+
+    return true;
+}

plugins/datatools/src/table/TableStandardize.h

@@ -0,0 +1,99 @@
+/**
+ * MegaMol
+ * Copyright (c) 2024, MegaMol Dev Team
+ * All rights reserved.
+ */
+
+#pragma once
+
+#include "datatools/table/TableDataCall.h"
+#include "mmcore/Call.h"
+#include "mmcore/CalleeSlot.h"
+#include "mmcore/CallerSlot.h"
+#include "mmcore/Module.h"
+#include "mmcore/param/ParamSlot.h"
+
+namespace megamol::datatools::table {
+
+/*
+ * Module to manipulate table (copy) via a LUA script.
+ */
+class TableStandardize : public core::Module {
+public:
+    static std::string ModuleName;
+    static std::string defaultScript;
+
+    /** Return module class name */
+    static const char* ClassName() {
+        return ModuleName.c_str();
+    }
+
+    /** Return module class description */
+    static const char* Description() {
+        return "Standardize table data (copy). Helps dimensionality reduction and clustering by reducing bias towards "
+               "large values.";
+    }
+
+    /** Module is always available */
+    static bool IsAvailable() {
+        return true;
+    }
+
+    /** Ctor */
+    TableStandardize();
+
+    /** Dtor */
+    ~TableStandardize() override;
+
+protected:
+    /** Lazy initialization of the module */
+    bool create() override;
+
+    /** Resource release */
+    void release() override;
+
+private:
+    /** Data callback */
+    bool processData(core::Call& c);
+
+    bool getExtent(core::Call& c);
+
+    /** Data output slot */
+    core::CalleeSlot dataOutSlot;
+
+    /** Data output slot */
+    core::CallerSlot dataInSlot;
+
+    /** Parameter slot for strategy selection */
+    core::param::ParamSlot stratSlot;
+
+    // inspired by SciKit learn
+    enum Strategies { OFF, STANDARD, MINMAX, MAXABS, ROBUST };
+
+    /** ID of the current frame */
+    int frameID;
+
+    /** Hash of the current data */
+    size_t in_datahash, out_datahash;
+
+    /** Vector storing the actual float data */
+    std::vector<float> data;
+
+    /** Vector storing information about columns */
+    std::vector<TableDataCall::ColumnInfo> info;
+
+    /** number of columns coming in */
+    int column_count = 0;
+
+    /** info of about columns coming in */
+    const TableDataCall::ColumnInfo* column_infos = nullptr;
+
+    /** number of rows coming in */
+    int row_count = 0;
+
+    /** the data coming in */
+    const float* in_data = nullptr;
+
+}; /* end class TableStandardize */
+
+} // namespace megamol::datatools::table