build system and module refactoring + simple histogram scratch (#20)

* scratch adding histogram to image views

Histograms should come from some sort of histogram service. This is
currently just a POC.

* custom logger implementation w/o spdlog

* missing cmake file

* fix tests

* use operator<< over direct stream exposure

* rm print header

* add threading test + refactor towards interface libraries

omits the need for =target_include_directories= calls /everywhere/

* rm print header

* rm constexpr

* templated thread_pool

* fix doxyfile

* default enable doc building

* czi reader refactor

* rm erroneous include expression

* clang-format

* single lib include with PUBLIC visibility

* compile imgui stdlib

* clang format

* documentation update

centralize `LogLevelToString` to `ILog.hpp`

update docs and examples

lib/imaging/impl/include/PixelariumCzi.hpp

@@ -0,0 +1,100 @@
+#pragma once
+
+#include <memory>
+#include <string>
+
+#include "ILog.hpp"
+#include "IPixelariumImage.hpp"
+#include "libCZI.h"
+#include "libCZI_Pixels.h"
+
+namespace
+{
+struct CvPixelTypeAndSize
+{
+    int size{-1};
+    int type{-1};
+};
+
+template <typename P>
+[[nodiscard]] constexpr auto GetCVPixelTypeAndSize(P p) noexcept -> CvPixelTypeAndSize
+{
+    switch (p)
+    {
+        case libCZI::PixelType::Gray8:
+            return {1, CV_8U};
+        case libCZI::PixelType::Gray16:
+            return {2, CV_16U};
+        case libCZI::PixelType::Bgr24:
+            return {3, CV_8UC3};
+        case libCZI::PixelType::Bgra32:
+            return {4, CV_8UC4};
+        case libCZI::PixelType::Gray32:
+            return {4, CV_32S};
+        case libCZI::PixelType::Gray32Float:
+            return {4, CV_32F};
+        default:
+            return {};
+    }
+}
+}  // namespace
+
+namespace pixelarium::imaging
+{
+/// @brief An implementation of IImageQuery to work on CZI images.
+/// @note  Check the documentation here https://zeiss.github.io/libczi/pages/mainpage.html#czi-in-a-nutshell
+struct CziParams : public IImageQuery
+{
+    /// @brief A map providing the start coordinate for each dimension in the CZI
+    std::unordered_map<libCZI::DimensionIndex, int> dimension_map;
+};
+
+/// @brief Implements support for .czi-images in the realm of IPixelariumImage
+class PixelariumCzi : public IPixelariumImageCvMat
+{
+    using Log = pixelarium::utils::log::ILog;
+
+   public:
+    explicit PixelariumCzi(const std::string& uri, const Log& log);
+    ~PixelariumCzi()
+    {
+        if (this->czi_reader_) this->czi_reader_->Close();
+    }
+
+    // IPixelariumImage member implementations
+   public:
+    std::optional<cv::Mat> TryGetImage() override;
+
+    std::optional<cv::Mat> TryGetImage(const IImageQuery&) override;
+
+    std::vector<std::optional<cv::Mat>> TryGetImages(const IImageQuery&) override
+    {
+        // ToDo: proper error
+        throw std::runtime_error("Not implemented.");
+    }
+
+   public:
+    bool Empty() const noexcept override { return this->is_empty_; }
+
+    const libCZI::SubBlockStatistics& GetStatistics() const { return this->image_statistics_; }
+
+   public:
+    const static ImageFileType type_{ImageFileType::kCzi};
+
+   private:
+    std::optional<cv::Mat> SubblockToCvMat(int index);
+
+   private:
+    // this should be set by each image getter
+    // after a new cv::Mat could be instantiated
+    bool is_empty_{true};
+
+    libCZI::SubBlockStatistics image_statistics_;
+
+    std::shared_ptr<libCZI::ICZIReader> czi_reader_;
+
+    std::unordered_map<libCZI::DimensionIndex, int> dimension_map_;
+
+    const Log& log_;
+};
+}  // namespace pixelarium::imaging

lib/imaging/impl/include/PixelariumJpg.hpp

@@ -0,0 +1,43 @@
+#pragma once
+
+#include <stdexcept>
+#include <string>
+
+#include "IPixelariumImage.hpp"
+
+namespace pixelarium::imaging
+{
+/// @brief Implements support for .jpg-images in the realm of IPixelariumImage
+class PixelariumJpg : public IPixelariumImageCvMat
+{
+   public:
+    explicit PixelariumJpg(const std::string& url);
+
+    // IPixelariumImage member implementations
+   public:
+    std::optional<cv::Mat> TryGetImage() override;
+
+    std::optional<cv::Mat> TryGetImage(const IImageQuery&) override
+    {
+        // ToDo: proper error
+        throw std::runtime_error("Not possible with jpg.");
+    }
+
+    std::vector<std::optional<cv::Mat>> TryGetImages(const IImageQuery&) override
+    {
+        // ToDo: proper error
+        throw std::runtime_error("Not possible with jpg.");
+    }
+
+   public:
+    bool Empty() const noexcept override { return this->is_empty_; }
+
+   public:
+    const static ImageFileType type_{ImageFileType::kJpg};
+
+   private:
+    // this should be set by each image getter
+    // after a new cv::Mat could be instantiated
+    bool is_empty_{true};
+};
+}  // namespace pixelarium::imaging

lib/imaging/impl/include/PixelariumMem.hpp

@@ -0,0 +1,47 @@
+#pragma once
+
+#include <stdexcept>
+#include <string>
+
+#include "ILog.hpp"
+#include "IPixelariumImage.hpp"
+
+namespace pixelarium::imaging
+{
+/// @brief Implements support for in-memory images in the realm of IPixelariumImage
+class PixelariumMem : public IPixelariumImageCvMat
+{
+    using Log = pixelarium::utils::log::ILog;
+
+   public:
+    explicit PixelariumMem(const cv::Mat& img, const std::string& name, const Log& log);
+
+    // IPixelariumImage member implementations
+   public:
+    std::optional<cv::Mat> TryGetImage() override;
+
+    std::optional<cv::Mat> TryGetImage(const IImageQuery&) override { throw std::runtime_error("Not implemented."); }
+
+    std::vector<std::optional<cv::Mat>> TryGetImages(const IImageQuery&) override
+    {
+        throw std::runtime_error("Not implemented.");
+    }
+
+    void SetImage(const cv::Mat& img) { this->img_ = img; }
+
+    std::string Name() const noexcept override { return this->name_; }
+
+    bool Empty() const noexcept override { return this->is_empty_; }
+
+   public:
+    const static ImageFileType type_{ImageFileType::kMemory};
+
+   private:
+    // this should be set by each image getter
+    // after a new cv::Mat could be instantiated
+    bool is_empty_{true};
+    cv::Mat img_;
+    const Log& log_;
+    std::string name_;
+};
+}  // namespace pixelarium::imaging

lib/imaging/impl/include/PixelariumPng.hpp

@@ -0,0 +1,42 @@
+#pragma once
+
+#include <stdexcept>
+#include <string>
+
+#include "IPixelariumImage.hpp"
+
+namespace pixelarium::imaging
+{
+/// @brief Implements support for .png-images in the realm of IPixelariumImage
+class PixelariumPng : public IPixelariumImageCvMat
+{
+   public:
+    explicit PixelariumPng(const std::string& url);
+
+    // IPixelariumImage member implementations
+   public:
+    std::optional<cv::Mat> TryGetImage() override;
+
+    std::optional<cv::Mat> TryGetImage(const IImageQuery&) override
+    {
+        // ToDo: proper error
+        throw std::runtime_error("Not possible with png.");
+    }
+
+    std::vector<std::optional<cv::Mat>> TryGetImages(const IImageQuery&) override
+    {
+        // ToDo: proper error
+        throw std::runtime_error("Not possible with png.");
+    }
+
+    bool Empty() const noexcept override { return this->is_empty_; }
+
+   public:
+    const static ImageFileType type_{ImageFileType::kPng};
+
+   private:
+    // this should be set by each image getter
+    // after a new cv::Mat could be instantiated
+    bool is_empty_{true};
+};
+}  // namespace pixelarium::imaging

lib/imaging/impl/include/PixelariumTiff.hpp

@@ -0,0 +1,46 @@
+#pragma once
+
+#include <stdexcept>
+#include <string>
+
+#include "ILog.hpp"
+#include "IPixelariumImage.hpp"
+
+namespace pixelarium::imaging
+{
+/// @brief Implements support for .tiff-images in the realm of IPixelariumImage
+class PixelariumTiff : public IPixelariumImageCvMat
+{
+    using Log = pixelarium::utils::log::ILog;
+
+   public:
+    explicit PixelariumTiff(const std::string& uri, const Log& log);
+
+    // IPixelariumImage member implementations
+   public:
+    std::optional<cv::Mat> TryGetImage() override;
+
+    std::optional<cv::Mat> TryGetImage(const IImageQuery&) override
+    {
+        // ToDo: proper error
+        throw std::runtime_error("Not possible with tiff.");
+    }
+
+    std::vector<std::optional<cv::Mat>> TryGetImages(const IImageQuery&) override
+    {
+        // ToDo: proper error
+        throw std::runtime_error("Not possible with tiff.");
+    }
+
+    bool Empty() const noexcept override { return this->is_empty_; }
+
+   public:
+    const static ImageFileType type_{ImageFileType::kTiff};
+
+   private:
+    // this should be set by each image getter
+    // after a new cv::Mat could be instantiated
+    bool is_empty_{true};
+    const Log& log_;
+};
+}  // namespace pixelarium::imaging