--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Docs/stone-object-model-reference.md	Mon Mar 23 13:52:27 2020 +0100
@@ -0,0 +1,439 @@
+## Scene2D and viewport-related object reference
+
+### `Scene2D` 
+
+Represents a collection of layers that display 2D data.
+
+These layers must implement `ISceneLayer`
+
+The layers must be created externally and set to a specific Z-order index 
+with the `SetLayer` method.
+
+The `Scene2D` object merely acts as a layer container. It has no rendering 
+or layer creation facility on its own.
+
+The `Scene2D` contains an `AffineTransform2D` structure that defines how 
+the various layer item coordinates are transformed before being displayed 
+on the viewport (aka canvas)
+
+It is up to each layer type-specific renderer to choose how this transformation
+is used. See the various kinds of layer below for more details.
+
+Examining the `Scene2D` contents can be done either by implementing the 
+`Scene2D::IVisitor` interface and calling `Apply(IVisitor& visitor)` or by 
+iterating between `GetMinDepth()` and `GetMaxDepth()` and calling the 
+`ISceneLayer& GetLayer(int depth)` getter.
+
+### `ISceneLayer` 
+
+Interface that must be implemented by `Scene2D` layers. This is a closed list
+that, as of 2020-03, contains:
+
+```
+  Type_InfoPanel,
+  Type_ColorTexture,
+  Type_Polyline,
+  Type_Text,
+  Type_FloatTexture,
+  Type_LookupTableTexture
+```
+
+Please note that this interface mandates the implementation of a `GetRevision`
+method returning an `uint64_t`. 
+
+The idea is that when a model gets converted to a set of `ISceneLayer` 
+instances, changes in the model that result in changes to the layers must 
+increase the revision number of these layers.
+
+That allows the rendering process to safely assume that a given layers whose
+revision does not change hasn't been modified (this helps with caching).
+
+Every mutable method in `ISceneLayer` instances that possibly change the visual
+representation of an `ISceneLayer` must increase this revision number.
+
+### Implementation: `FloatTextureSceneLayer`
+
+Layer that renders an `Orthanc::ImageAccessor` object that must be convertible
+to `Float32` image.
+
+The constructor only uses the image accessor to perform a copy. It can safely 
+be deleted afterwards.
+
+The input values are mapped to the output values by taking into account various
+properties that can be modified with:
+
+- `SetWindowing`: uses windowing presets like "bone" or "lung"
+- `SetCustomWindowing`: with manual window center and width
+- `SetInverted`: toggles black <-> white inversion after windowing
+- `SetApplyLog`: uses a non-linear response curve described in 
+  https://theailearner.com/2019/01/01/log-transformation/ that expands contrast
+  in dark areas while compressing contrast in bright ones. This is **not** 
+  implemented in the OpenGL renderer!
+
+The corresponding renderers are `OpenGLFloatTextureRenderer` and 
+`CairoFloatTextureRenderer`. The scene transformation is applied during
+rendering.
+
+### Implementation: `ColorTextureSceneLayer`
+
+Layer that renders an `Orthanc::ImageAccessor` object an RGBA image (alpha must
+be premultiplied). 
+
+The constructor only uses the image accessor to perform a copy. It can safely 
+be deleted afterwards.
+
+The corresponding renderers are `OpenGLColorTextureRenderer` and 
+`CairoColorTextureRenderer`. The scene transformation is applied during
+rendering.
+
+### Implementation: `LookupTableTextureSceneLayer`
+
+Layer that renders an `Orthanc::ImageAccessor` object that must be convertible
+to `Float32` image.
+
+The constructor only uses the image accessor to perform a copy. It can safely 
+be deleted afterwards.
+
+The final on-screen color of each pixel is determined by passing the input 
+`Float32` value through a 256-entry look-up table (LUT) that can be passed as 
+an array of either 256 x 3 bytes (for opaque RGB colors) or 256 x 4 bytes (for
+RGBA pixels). The LUT is not specified at construction time, but with 
+calls to `SetLookupTable` or `SetLookupTableGrayscale` (that fills the LUT 
+with a gradient from black to white, fully opaque)
+
+The range of input values that is mapped to the entirety of the LUT is, by
+default, the full image range, but can be customized with `SetRange`.
+
+The corresponding renderers are `OpenGLLookupTableTextureRenderer` and
+`CairoLookupTableTextureRenderer`. The scene transformation is applied during
+rendering.
+
+### Implementation: `PolylineSceneLayer`
+
+Layer that renders vector-based polygonal lines. 
+
+Polylines can be added with the `AddChain` method, that accepts a `Chain`, that
+is a typedef to `std::vector<ScenePoint2D>`, a flag to specify whether the 
+chain must be automatically close (last point of the vector connected to the
+first one) and the chain color (a `Color` structure).
+
+Please note that the line thickness is, contrary to the color, specified 
+per-chain but rather per-layer. 
+
+If you need multiple line thicknesses, multiple `PolylineSceneLayer` must be
+created.
+
+The corresponding renderers are `OpenGLAdvancedPolylineRenderer` and
+`CairoPolylineRenderer`. The scene transformation is applied during
+rendering.
+
+### Implementation: `TextSceneLayer`
+
+This layers renders a paragraph of text. 
+
+The inputs to the layer can be changed after creation and are:
+- The text iself, supplied as an UTF-8 encoded string in `SetText`
+- The font used for rendering, set by `SetFontIndex`.
+- The text anchoring, through `SetAnchor`: the text can be anchored to 
+  various positions, such as top lef, center, bottom center,... These 
+  various anchors are part of the `BitmapAnchor` enumeration.
+- The text position, relative to its anchor, through `SetPosition`.
+
+The font is supplied as an index. This is an index in the set of fonts 
+that has been registered in the viewport compositor. The following code 
+shows how to set such a font:
+
+```
+std::unique_ptr<OrthancStone::IViewport::ILock> lock(viewport_.Lock());
+lock->GetCompositor().SetFont(0, 
+                              Orthanc::EmbeddedResources::UBUNTU_FONT, 
+                              32, Orthanc::Encoding_Latin1);
+// where 32 is the font size in pixels
+```
+
+This call uses the embedded `UBUNTU_FONT` resource that has been defined in
+the `CMakeLists.txt` file with:
+
+```
+set(ORTHANC_STONE_APPLICATION_RESOURCES 
+  UBUNTU_FONT  ${CMAKE_BINARY_DIR}/ubuntu-font-family-0.83/Ubuntu-R.ttf
+)
+```
+
+Please note that you must supply a font: there is no default font provided by
+the OpenGL or Cairo compositors.
+
+The corresponding renderers are `OpenGLTextRenderer` and
+`CairoTextRenderer`. The scene transformation is not applied during rendering,
+because the text anchoring, position and scaling are computed relative to the
+viewport/canvas.
+
+### Implementation: `InfoPanelSceneLayer`
+
+This layer is designed to display an image, supplied through an 
+`Orthanc::ImageAccessor` reference (only used at construction time).
+
+The image is not transformed according to the normal layer transformation but 
+is rather positioned relative to the canvas, with the same mechanism as the
+`TextSceneLayer` described above.
+
+The image position is specified with the sole means of the `SetAnchor` method.
+
+The corresponding renderers are `OpenGLInfoPanelRenderer` and 
+`CairoInfoPanelRenderer`.
+
+### `IViewport`
+
+https://bitbucket.org/sjodogne/orthanc-stone/src/broker/Framework/Viewport/IViewport.h
+
+(**not** the one in `Deprecated`)
+- Implemented by classes that:
+  - manage the on-screen display of a `Scene2D` trough a compositor.
+  - Own the `ICompositor` object that performs the rendering. 
+  - Own the `Scene2D` (TODO: currently through `ViewportController` --> `Scene2D`)
+  - Provide a `Lock` method that returns a RAII, that must be kept alive when 
+    modifying the underlying objects (controller, compositor, scene), but not 
+    longer.
+
+#### Implementation: `SdlOpenGLViewport`
+- Implementation of a viewport rendered on a SDL window, that uses OpenGL for 
+  rendering.
+- Instantiating this object creates an SDL window. Automatic scaling for hiDPI
+  displays can be toggled on or off. 
+
+#### Implementation: `WebGLViewport`
+- Implementation of a viewport rendered on a DOM canvas, that uses OpenGL for 
+  rendering.
+- Contrary to the SDL OpenGL viewport, the canvas must already be existing 
+  when the ctor is called.
+
+### `ICompositor`
+The interface providing a rendering service for `Scene2D` objects. 
+
+**Subclasses:** `CairoCompositor`, `OpenGLCompositor`
+ 
+You do not need to create compositor instances. They are created for you when
+instantiating a viewport.
+
+### `ViewportController`
+This concrete class is instantiated by its `IViewport` owner. 
+
+**TODO:** its functionality is not well defined and should be moved into the 
+viewport base class. Support for measuring tools should be moved to a special
+interactor.
+
+- contains:
+  - array of `MeasureTool`
+  - ref to `IViewport`
+  - `activeTracker_`
+  - owns a `Scene2D`
+  - weak ref to `UndoStack`
+  - cached `canvasToSceneFactor_`
+
+- contains logic to:
+  - pass commands to undostack (trivial)
+  - logic to locate `MeasureTool` in the HitTest
+  - OTOH, the meat of the measuring tool logic (highlighting etc..) is 
+    done in app-specific code (`VolumeSlicerWidget` for IBA)
+  - accept new Scene transform and notify listeners
+  - **the code that uses the interactor** (`HandleMousePress`) is only 
+    called by the new `WebAssemblyViewport` !!! **TODO** clean this mess
+
+### `IViewportInteractor`
+- must provide logic to respond to `CreateTracker`
+
+### `DefaultViewportInteractor`
+- provides Pan+Rotate+Zoom trackers
+
+### `WebGLViewportsRegistry`
+
+This class is a singleton (accessible through `GetWebGLViewportsRegistry()` 
+that deals with context losses in the WebGL contexts.
+
+You use it by creating a WebGLViewport in the following fashion:
+
+```
+boost::shared_ptr<OrthancStone::WebGLViewport> viewport(
+  OrthancStone::GetWebGLViewportsRegistry().Add(canvasId));
+```
+
+## Source data related
+
+### `IVolumeSlicer`
+
+A very simple interface with a single method:
+`IVolumeSlicer::IExtractedSlice* ExtractSlice(const CoordinateSystem3D& cuttingPlane)`
+
+### `IVolumeSlicer::IExtractedSlice`
+
+On a slice has been extracted from a volume by an `IVolumeSlicer`, it can
+report its *revision number*. 
+
+If another call to `ExtractSlice` with the same cutting plane is made, but 
+the returned slice revision is different, it means that the volume has 
+changed and the scene layer must be refreshed.
+
+Please see `VolumeSceneLayerSource::Update` to check how this logic is 
+implemented.
+
+
+### `OrthancSeriesVolumeProgressiveLoader`
+
+This class implements `IVolumeSlicer` (and `IObservable`) and can be used to 
+load a volume stored in a Dicom series on an Orthanc server.
+
+Over the course of the series loading, various notifications are sent:
+
+The first one is `OrthancStone::DicomVolumeImage::GeometryReadyMessage` that
+is sent when the volume extent and geometric properties are known.
+
+Then, as slices get loaded and the volume is filled,  
+`OrthancStone::DicomVolumeImage::ContentUpdatedMessage` are sent.
+
+Once all the highest-quality slices have been loaded, the 
+`OrthancSeriesVolumeProgressiveLoader::VolumeImageReadyInHighQuality` 
+notification is sent.
+
+Please note that calling `ExtractSlice` *before* the geometry is loaded will
+yield an instance of `InvalidSlice` that cannot be used to create a layer.
+
+On the other hand, 
+
+### `VolumeSceneLayerSource`
+
+This class makes the bridge between a volume (supplied by an `IVolumeSlicer`
+interface) and a `Scene2D`. 
+
+Please note that the bulk of the work is done the objects implementing 
+`IVolumeSlicer` and this object merely connects things together.
+
+For instance, deciding whether an image (texture) or vector (polyline) layer
+is done by the `IVolumeSlicer` implementation.
+
+- contains:
+  - reference to Scene2D
+  - `layerIndex_` (fixed at ctor) that is the index, in the Scene2D layer 
+    stack, of the layer that will be created/updated
+  - `IVolumeSlicer`
+
+- contains logic to:
+  - extract a slice from the slicer and set/refresh the Scene2D layer at 
+    the supplied `layerIndex_`
+  - refresh this based on the slice revision or configuration revision
+  - accept a configuration that will be applied to the layer
+  - the `Update()` method will 
+
+## Updates and the configurators
+
+`ISceneLayer` does not expose mutable methods. 
+
+The way to change a layer once it has been created is through configurator 
+objets.
+
+If you plan to set (even only once) or modify some layer properties after 
+layer creation, you need to create a matching configurator objet.
+
+For instance, in the `VolumeSceneLayerSource`, the `SetConfigurator` method
+will store a `ILayerStyleConfigurator* configurator_`.
+
+In the `OrthancView` ctor, you can see how it is used:
+
+```
+std::unique_ptr<GrayscaleStyleConfigurator> style(
+  new GrayscaleStyleConfigurator);
+
+style->SetLinearInterpolation(true);
+
+...<some more code>...
+
+std::unique_ptr<LookupTableStyleConfigurator> config(
+  new LookupTableStyleConfigurator);
+
+config->SetLookupTable(Orthanc::EmbeddedResources::COLORMAP_HOT);
+
+```
+
+The configurator type are created according to the type of layer.¸
+
+Later, in `VolumeSceneLayerSource::Update(const CoordinateSystem3D& plane)`, 
+if the cutting plane has **not** changed and if the layer revision has **not**
+changed, we test `configurator_->GetRevision() != lastConfiguratorRevision_` 
+and, if different, we call `configurator_->ApplyStyle(scene_.GetLayer(layerDepth_));`
+
+This allows to change layer properties that do not depend on the layer model
+contents.
+
+On the other hand, if the layer revision has changed, when compared to the 
+last time it has been rendered (stored in `lastRevision_`), then we need to 
+ask the slice to create a brand new layer.
+
+Another way to see it is that layer rendering depend on model data and view 
+data. The model data is not mutable in the layer and, if the model changes, the 
+layer must be recreated.
+
+If only the view properties change (the configurator), we call ApplyStyle 
+(that **will** mutate some of the layer internals)
+
+Please note that the renderer does **not** know about the configurator : the 
+renderer uses properies in the layer and does not care whether those have 
+been set once at construction time or at every frame (configuration time).
+
+
+## Cookbook
+
+### Simple application
+
+#### Building
+
+In order to create a Stone application, you need to:
+
+- CMake-based application:
+    ```
+    include(${STONE_SOURCES_DIR}/Resources/CMake/OrthancStoneConfiguration.cmake)
+    ```
+  with this library target that you have to define:
+    ```
+    add_library(OrthancStone STATIC ${ORTHANC_STONE_SOURCES})
+    ```
+  then link with this library:
+    ```
+    target_link_libraries(MyStoneApplication OrthancStone)
+    ```
+
+Building is supported with emscripten, Visual C++ (>= 9.0), gcc...
+
+emscripten recommended version >= 1.38.41
+
+These are very rough guidelines. See the `Samples` folder for actual examples.
+
+#### Structure
+
+The code requires a loader (object that )
+
+Initialize:
+
+```
+Orthanc::Logging::Initialize();
+Orthanc::Logging::EnableInfoLevel(true);
+```
+Call, in WASM:
+```
+DISPATCH_JAVASCRIPT_EVENT("StoneInitialized");
+```
+
+
+
+# TODO order
+- **IBA** remove SDL Console failed attempt
+- **IBA** understand refresh issue --> push fix
+- **IBA** move main.cpp to tests/
+- **IBA** Remove deprecated tag from loaders and rename loaders (ensure "Progressive" only means spatially progressive, not in terms of quality.. make sure Yoann doesn't need Jpeg)
+- **IBA** 
+
+
+# Notes
+
+- It is NOT possible to abandon the existing loaders : they contain too much loader-specific getters
+
+
+

--- a/Framework/Volumes/VolumeSceneLayerSource.cpp	Tue Mar 17 19:21:01 2020 +0100
+++ b/Framework/Volumes/VolumeSceneLayerSource.cpp	Mon Mar 23 13:52:27 2020 +0100
@@ -42,12 +42,13 @@
   }
 
 
-  VolumeSceneLayerSource::VolumeSceneLayerSource(Scene2D& scene,
-                                                 int layerDepth,
-                                                 const boost::shared_ptr<IVolumeSlicer>& slicer) :
-    scene_(scene),
-    layerDepth_(layerDepth),
-    slicer_(slicer)
+  VolumeSceneLayerSource::VolumeSceneLayerSource(
+    Scene2D& scene,
+    int layerDepth,
+    const boost::shared_ptr<IVolumeSlicer>& slicer)
+    : scene_(scene)
+    , layerDepth_(layerDepth)
+    , slicer_(slicer)
   {
     if (slicer == NULL)
     {