Release preparation

BlueBrain · Feb 26, 2019 · 7e36717 · 7e36717
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diff --git a/.github_changelog_generator b/.github_changelog_generator
@@ -1,4 +1,4 @@
-future-release=0.7.1
+future-release=0.8.0
 user=BlueBrain
 project=Brayns
 output=Changelog.md

diff --git a/.gitignore b/.gitignore
@@ -24,3 +24,5 @@ CMakeFiles
 *.includes
 *.creator*
 *.user
+.vscode
+.python-version
diff --git a/Changelog.md b/Changelog.md
@@ -1,5 +1,84 @@
 # Change Log
 
+## [0.8.0](https://github.com/BlueBrain/Brayns/tree/0.8.0) (26-02-2019)
+
+**Implemented enhancements:**
+
+- Remove {detectionDistance} from simulation renderer [\#522](https://github.com/BlueBrain/Brayns/issues/522)
+- Expose camera as translation vector + rotation quaternion [\#517](https://github.com/BlueBrain/Brayns/issues/517)
+- Make the UI component available [\#503](https://github.com/BlueBrain/Brayns/issues/503)
+- feat: improve ui/ux [\#726](https://github.com/BlueBrain/Brayns/pull/726)
+- Replace glut with glfw and imgui [\#718](https://github.com/BlueBrain/Brayns/pull/718)
+- Improve AnimationParameters [\#711](https://github.com/BlueBrain/Brayns/pull/711)
+- feat\(js\): Added UI to update animation speed parameter \(delta\) [\#706](https://github.com/BlueBrain/Brayns/pull/706)
+- Use glm instead of vmmlib [\#705](https://github.com/BlueBrain/Brayns/pull/705)
+- Add shorthand for using OSPRay engine [\#704](https://github.com/BlueBrain/Brayns/pull/704)
+- Draw FPS in screen instead of window title [\#699](https://github.com/BlueBrain/Brayns/pull/699)
+- Fix slow down caused by per-frame update of model size; is only necessary for volumes right now [\#697](https://github.com/BlueBrain/Brayns/pull/697)
+- feat\(js\): do not render model props if it has none [\#690](https://github.com/BlueBrain/Brayns/pull/690)
+- feat\(js\): add tooltips for icon buttons [\#687](https://github.com/BlueBrain/Brayns/pull/687)
+- Make OptiX an engine of Brayns [\#684](https://github.com/BlueBrain/Brayns/pull/684)
+- perf\(js\): use new Image.decode\(\) API to decode images off the main thread [\#682](https://github.com/BlueBrain/Brayns/pull/682)
+- Fix loading of NPOT textures, support loading raw volumes from blob [\#680](https://github.com/BlueBrain/Brayns/pull/680)
+- Refactor subsampling into its own property [\#673](https://github.com/BlueBrain/Brayns/pull/673)
+- feat: expose environment map in the UI [\#671](https://github.com/BlueBrain/Brayns/pull/671)
+- Added properties to materials [\#667](https://github.com/BlueBrain/Brayns/pull/667)
+- Add set-environment-map RPC to replace SceneParameters [\#666](https://github.com/BlueBrain/Brayns/pull/666)
+- Added SDF and Streamlines accessors to Model class [\#651](https://github.com/BlueBrain/Brayns/pull/651)
+- Implemented target string parsing [\#649](https://github.com/BlueBrain/Brayns/pull/649)
+- Add `--play-animation` switch to enable initial simulation playback for demos [\#644](https://github.com/BlueBrain/Brayns/pull/644)
+- Add the ability to scale the Opendeck camera [\#641](https://github.com/BlueBrain/Brayns/pull/641)
+- Add `--version` option [\#634](https://github.com/BlueBrain/Brayns/pull/634)
+- Set default transfer function and renderer for circuit simulations [\#629](https://github.com/BlueBrain/Brayns/pull/629)
+- Fix and move the Perspective Parallax Camera from modules to core [\#628](https://github.com/BlueBrain/Brayns/pull/628)
+- DeflectPlugin improvements [\#626](https://github.com/BlueBrain/Brayns/pull/626)
+- Add description for Property and commandline generation [\#623](https://github.com/BlueBrain/Brayns/pull/623)
+- Add BBIC volume plugin [\#619](https://github.com/BlueBrain/Brayns/pull/619)
+- Removal of metaball and layout options from morphology loading. [\#618](https://github.com/BlueBrain/Brayns/pull/618)
+- Fix VRPN plugin, add floor projection and OpenDeck plugin [\#616](https://github.com/BlueBrain/Brayns/pull/616)
+- Add support for multiple frameBuffers [\#612](https://github.com/BlueBrain/Brayns/pull/612)
+- Use property map for all loader properties [\#611](https://github.com/BlueBrain/Brayns/pull/611)
+- Moved circuit and morphology loaders to the new CircuitViewer plugin [\#606](https://github.com/BlueBrain/Brayns/pull/606)
+- Support CUDA 10 in OptiX [\#605](https://github.com/BlueBrain/Brayns/pull/605)
+- Add 'default-bvh-flag' command line option [\#599](https://github.com/BlueBrain/Brayns/pull/599)
+- Support subsampling again after OSPRay 1.7 upgrade [\#598](https://github.com/BlueBrain/Brayns/pull/598)
+- Add a target state to the camera. Bug fixes. [\#597](https://github.com/BlueBrain/Brayns/pull/597)
+- Transfer function per model [\#594](https://github.com/BlueBrain/Brayns/pull/594)
+- Replaced lookat, target, position by quaternion, position in the camera [\#591](https://github.com/BlueBrain/Brayns/pull/591)
+- Moving to OSPRay 1.7.x [\#589](https://github.com/BlueBrain/Brayns/pull/589)
+- Use rockets python client [\#587](https://github.com/BlueBrain/Brayns/pull/587)
+- Clip planes in ortho camera and new API [\#576](https://github.com/BlueBrain/Brayns/pull/576)
+
+**Fixed bugs:**
+
+- If all spheres centers are coplanar in an XYZ file, nothing gets rendererd. [\#588](https://github.com/BlueBrain/Brayns/issues/588)
+- Fix rounding issue when converting to RGB during streaming [\#730](https://github.com/BlueBrain/Brayns/pull/730)
+- Increase timer resolution to fix FPS numbers [\#721](https://github.com/BlueBrain/Brayns/pull/721)
+- Provide customized obj importer to overcome 256MB limit [\#719](https://github.com/BlueBrain/Brayns/pull/719)
+- Workaround for https://github.com/assimp/assimp/issues/2337 [\#717](https://github.com/BlueBrain/Brayns/pull/717)
+- Fix tracking glasses x-axis inversion [\#716](https://github.com/BlueBrain/Brayns/pull/716)
+- fix\(js\): prevent file select dialog open on space/enter [\#715](https://github.com/BlueBrain/Brayns/pull/715)
+- fix\(js\): do not throw when image decoding fails [\#713](https://github.com/BlueBrain/Brayns/pull/713)
+- fix\(js\): fix clip plane update [\#708](https://github.com/BlueBrain/Brayns/pull/708)
+- Fix Rockets deadlock in plugins [\#696](https://github.com/BlueBrain/Brayns/pull/696)
+- fix\(js\): ignore app bar height when calculating default snapshot height [\#689](https://github.com/BlueBrain/Brayns/pull/689)
+- fix\(js\): add temp fix for horizontal scroll due to sliders [\#683](https://github.com/BlueBrain/Brayns/pull/683)
+- Fix wrong mesh progress reporting and subsequent crash [\#668](https://github.com/BlueBrain/Brayns/pull/668)
+- Fix crash when updating property map from UI [\#631](https://github.com/BlueBrain/Brayns/pull/631)
+- Fix crash with RocketsPlugin and VRPNPlugin loaded [\#630](https://github.com/BlueBrain/Brayns/pull/630)
+- Enforce consistent stream ID when using DeflectPixelOp [\#615](https://github.com/BlueBrain/Brayns/pull/615)
+
+**Closed issues:**
+
+- Remove geometry params in favor of generic loader properties [\#500](https://github.com/BlueBrain/Brayns/issues/500)
+- Port "Circuit Viewer" use case from RTNeuron to Brayns [\#372](https://github.com/BlueBrain/Brayns/issues/372)
+
+**Merged pull requests:**
+
+- refactor\(js\): move request notifications to the bottom of the window [\#676](https://github.com/BlueBrain/Brayns/pull/676)
+- Removed Model::createMissingMaterials [\#672](https://github.com/BlueBrain/Brayns/pull/672)
+- Remove legacy scene cache file support [\#660](https://github.com/BlueBrain/Brayns/pull/660)
+
 ## [0.7.1](https://github.com/BlueBrain/Brayns/tree/0.7.1) (26-09-2018)
 
 **Implemented enhancements:**

diff --git a/README.md b/README.md
@@ -45,10 +45,7 @@ Command line arguments are documented in the [User Guide](doc/UserGuide.md).
 
 The following platforms and build environments are tested:
 
-* Linux: Ubuntu 16.04, Debian 9, RHEL 6.8 (Makefile, x64)
-
-The [API documentation](http://bluebrain.github.io/Brayns-0.6/index.html)
-can be found on [bluebrain.github.io](http://bluebrain.github.io/).
+* Linux: Ubuntu 16.04, Debian 9, RHEL 7 (Makefile, x64)
 
 ## Using Docker images
 
@@ -94,7 +91,7 @@ Clone embree in the same folder level as ISPC compiler
   git clone https://github.com/embree/embree.git
   mkdir embree/Build
   cd embree/Build
-  git checkout v2.17.4
+  git checkout v3.2.3
   cmake .. -DCMAKE_INSTALL_PREFIX=<Brayns_installation_folder>
   make install
 ```
@@ -107,7 +104,7 @@ Clone OSPRay in the same folder level as ISPC compiler
   git clone https://github.com/ospray/OSPRay.git
   mkdir OSPRay/Build
   cd OSPRay/Build
-  git checkout v1.5.0
+  git checkout v1.7.3
   export CMAKE_PREFIX_PATH=<Brayns_installation_folder>
   cmake .. -DCMAKE_INSTALL_PREFIX=<Brayns_installation_folder>
   make install
@@ -158,7 +155,6 @@ cmake .. -DBRAYNS_VRPN_ENABLED=ON:OFF
 ```
 cmake .. -DBRAYNS_OPTIX_ENABLED=ON:OFF
 cmake .. -DBRAYNS_OPENDECK_ENABLED=ON:OFF
-cmake .. -DBRAYNS_STEREOSCOPY_ENABLED=ON:OFF
 ```
 
 ## Running Brayns viewer

diff --git a/doc/Architecture.odp b/doc/Architecture.odp
diff --git a/doc/UserGuide.md b/doc/UserGuide.md
@@ -7,197 +7,8 @@ Brayns takes any number of files or folders as argument. To open a single file:
 braynsViewer model.obj
 ```
 
-Alternatively, to open all supported files in a folder:
-```
-braynsViewer ~/datasets/
-```
-
-## Neurons
-
-### Loading individual morphologies
-
-SWC or H5 morphology files (supported by the
-[Brion](https://github.com/BlueBrain/Brion) library) can be loaded easily.
-
-```
-braynsViewer ~/morphologies
-```
-
-### Loading a NEURON simulation
-
-BlueConfig or CircuitConfig files (supported by the Brion library) can be
-loaded. The ```--circuit-targets``` command line argument specifies the circuit target
-(or multiples separated by comma), and the ```--circuit-report``` command line
-argument specifies the simulation report to be rendered.
-
-Example of how to load a circuit with voltages simulation for layer 1 cells:
-
-```
-braynsViewer ~/circuits/BlueConfig --circuit-targets Layer1 --circuit-report voltages
-```
-
-![Layer1](images/Layer1.png)
-
-#### Bounding box
-
-Defining a bounding box will prevent any geometry located outside of the box
-from being loaded. The ```--circuit-bounding-box``` command line argument takes six
-float values. The first three values being the lower bound of the box, and the
-next three values defining the upper bound.
-
-Example of how to define a circuit bounding box:
-```
-braynsViewer ~/circuits/BlueConfig --circuit-bounding-box -100 -100 -100 100 100 100
-```
-
-#### Density
-
-The ```--circuit-density``` command line argument defines how many of the circuit
-cells should be loaded. For example, if a density of 5 is specified, one cell
-in 20 will be loaded. Brayns reads the cells in GID order.
-
-Example of how to load 10% of the circuit:
-```
-braynsViewer ~/circuits/BlueConfig --circuit-density 10
-```
-
-### Options
-
-#### Layout
-When loading several morphologies, Brayns allows the user to position them with
-a specific layout. Typically, the user might want to visualize cells next to
-each other. The ```--morphology-layout``` command line argument specifies the number
-of cells per line, as well as the horizontal and vertical spacing between each
-of those cells. Units used for the horizontal and vertical spacing are the ones
-from the H5 and SWC files.
-
-```
-braynsViewer ~/morphologies --morphology-layout 5 100 100
-```
-
-#### Section types
-
-Brayns allows the user to specify which section type of the morpholoy should be
-loaded. Sections type are soma, axon, dendrite and apical dendrite. Those types
-can be combined together by adding their corresponding values (1 for the soma,
-2 for the Axon, 4 for dendrites and 8 for apical dendrites). For example, if one
-wants to visualize the somas and the axons, the ```--morphology-section-types```
-command line argument should then be set to 3.
-
-```
-braynsViewer ~/morphologies --morphology-section-types 3
-```
-
-![SectionTypes](images/SectionTypesAxonSoma.png)
-
-```
-braynsViewer ~/morphologies --morphology-section-types 5
-```
-
-![SectionTypesSomaDendrites](images/SectionTypesAxonDendrites.png)
-
-```
-braynsViewer ~/morphologies --morphology-section-types 9
-```
-
-![SectionTypesSomaApicalDendrites](images/SectionTypesAxonApicalDendrites.png)
-
-#### Geometry quality
-
-Brayns supports three quality levels for morphologies. The low quality draws
-one line per section, the medium quality divides the number of segment by 4, and
-the high quality renders the full morphology.
-
-```
-braynsViewer ~/morphologies --geometry-quality low
-```
-
-![GeometryQualityLow](images/GeometryQualityLow.png)
-
-
-```
-braynsViewer ~/morphologies --geometry-quality medium
-```
-
-![GeometryQualityMedium](images/GeometryQualityMedium.png)
-
-
-```
-braynsViewer ~/morphologies --geometry-quality high
-```
-
-![GeometryQualityHigh](images/GeometryQualityHigh.png)
-
-#### Radius multiplier
-
-The ```--radius-multiplier``` command line parameters specifies the multiplier applied
-to morphology radii. Typically, a value of 3 multiplies all radii by 3.
-
-```
-braynsViewer ~/morphologies --radius-multiplier 3
-```
-
-![RadiusMultiplier](images/RadiusMultiplier3.png)
-
-#### Radius correction
-
-The ```--radius-correction``` command line parameters specifies a unique radius
-applied to all segments of the morphology. The unit is the one of the loaded
-H5/SWC files.
-
-```
-braynsViewer ~/morphologies --radius-correction 1
-```
-
-![RadiusCorrection](images/RadiusCorrection1.png)
-
-#### Color scheme
-
-The ```--color-scheme``` command line argument specifies how materials are applied to
-the morphology. Available values are:
-
-| Argument             | Description
-| ---------------------| -------------
-| neuron-by-id         | Each neuron has a different color
-| neuron-by-segment-id | Somas are white, axons are blue, dendrites are red, and apical dendrites are purple
-| neuron-by-layer      | A different color is assigned for every layer. All neurons belonging to a specific layer as the same color
-| neuron-by-mtype      | Each morphological type has a different color
-| neuron-by-etype      | Each electro-physiologic type has a different color
-| protein-by-id        | Each protein has a different color
-| protein-atoms        | Atoms have standard colors
-| protein-chains       | Each chain has a different color
-
-```
-braynsViewer ~/morphologies --color-scheme neuron-by-id
-```
-
-![ColorSchemeNeuronById](images/ColorSchemeID.png)
-
-```
-braynsViewer ~/morphologies --color-scheme neuron-by-segment-type
-```
-
-![ColorSchemeNeuronBySegmentType](images/ColorSchemeSegmentType.png)
-
-#### Realistic somas
-
-Command line arguments starting with metaballs tell Brayns to reconstruct somas using the metaballs algorithm. The ```--metaballs-grid-size``` command line
-argument defines the precision of the generated mesh. The ```--metaballs-threshold```
-command line argument specifies the threshold for the isosurface defined by
-function [f(x,y,z) = x^2 + y^2 + z^2]. The ```--metaballs-samples-from-soma```
-command line argument defines how many samples from around the soma should be
-considered when generating the mesh.
-
-```
-braynsViewer ~/morphologies --metaballs-grid-size 60 --metaballs-threshold 1 --metaballs-samples-from-soma 5
-```
-
-![EnhancedSomas](images/EnhancedSoma.png)
-
 ## Molecules
 
-### Loading a single molecule
-
 PDB files can be easily loaded:
 
 ```
@@ -206,28 +17,18 @@ braynsViewer 4IMY.pdb
 
 ![PDBFile](images/PDBFile.png)
 
-### Loading molecules from folder
-
-Loads all PDB file located in the specified folder:
-
-```
-braynsViewer ~/hiv --color-scheme protein-chains
-```
-
-![PDBFolder](images/PDBFolder.png)
 
 ## Meshes
 
-### Loading meshes
-
 Brayns can load file formats supported by the [assimp](https://github.com/assimp/assimp) library.
 
 ```
-braynsViewer ~/meshes
+braynsViewer mesh.obj|ply
 ```
 
 ![Mesh](images/Mesh.png)
 
+
 ## Point cloud
 
 A XYZ file is a binary encoded list of x,y and z double positions.
@@ -236,21 +37,6 @@ A XYZ file is a binary encoded list of x,y and z double positions.
 braynsViewer sample.xyz
 ```
 
-## Cache file
-
-In order to accelerate the loading of large scenes, models can be dumped into
-binary files that can then be reloaded by Brayns. The ```--save-cache-file``` command
-line argument specifies the filename of the file into which the 3D scene should
-be saved. The ```--load-cache-file``` command line argument specifies the file to be
-loaded by Brayns. Note that cache files are only supported by the OSPRay engine.
-Any other command line parameter defining a data source will be ignored by
-Brayns.
-
-```
-braynsViewer --save-cache-file cache
-braynsViewer --load-cache-file cache
-```
-
 ## Volumes
 
 Brayns currently only supports 8-bit raw volume. The ```--volume-dimensions```
@@ -295,7 +81,6 @@ by the renderer. Five cameras are currently supported:
 | perspective          | Perspective camera
 | orthographic         | Orthographic camera
 | panoramic            | 360 degrees camera
-| clipped              | Perspective camera allowing clipping planes
 
 ```
 braynsViewer --camera orthographic

diff --git a/doc/images/AmbientOcclusion.png b/doc/images/AmbientOcclusion.png
diff --git a/doc/images/Architecture.png b/doc/images/Architecture.png
diff --git a/doc/images/Brayns1.jpg b/doc/images/Brayns1.jpg
diff --git a/doc/images/Brayns2.jpg b/doc/images/Brayns2.jpg
diff --git a/doc/images/Brayns3.jpg b/doc/images/Brayns3.jpg
diff --git a/doc/images/Brayns4.jpg b/doc/images/Brayns4.jpg
diff --git a/doc/images/Brayns5.jpg b/doc/images/Brayns5.jpg
diff --git a/doc/images/Brayns6.jpg b/doc/images/Brayns6.jpg
diff --git a/doc/images/Brayns7.jpg b/doc/images/Brayns7.jpg
diff --git a/doc/images/ColorSchemeID.png b/doc/images/ColorSchemeID.png
diff --git a/doc/images/ColorSchemeSegmentType.png b/doc/images/ColorSchemeSegmentType.png
diff --git a/doc/images/EnhancedSoma.png b/doc/images/EnhancedSoma.png
diff --git a/doc/images/GeometryQualityHigh.png b/doc/images/GeometryQualityHigh.png
diff --git a/doc/images/GeometryQualityLow.png b/doc/images/GeometryQualityLow.png
diff --git a/doc/images/GeometryQualityMedium.png b/doc/images/GeometryQualityMedium.png
diff --git a/doc/images/Layer1.png b/doc/images/Layer1.png
diff --git a/doc/images/PDBFolder.png b/doc/images/PDBFolder.png
diff --git a/doc/images/RadiusCorrection1.png b/doc/images/RadiusCorrection1.png
diff --git a/doc/images/RadiusMultiplier1.png b/doc/images/RadiusMultiplier1.png
diff --git a/doc/images/RadiusMultiplier3.png b/doc/images/RadiusMultiplier3.png
diff --git a/doc/images/SectionTypesAxonApicalDendrites.png b/doc/images/SectionTypesAxonApicalDendrites.png
diff --git a/doc/images/SectionTypesAxonDendrites.png b/doc/images/SectionTypesAxonDendrites.png
diff --git a/doc/images/SectionTypesAxonSoma.png b/doc/images/SectionTypesAxonSoma.png
diff --git a/doc/images/Shadows.png b/doc/images/Shadows.png
diff --git a/doc/images/SoftShadows.png b/doc/images/SoftShadows.png
diff --git a/doc/images/VolumeGI.png b/doc/images/VolumeGI.png