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Documentation updates
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@tribal-tec
tribal-tec committed May 29, 2018
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3 changes: 2 additions & 1 deletion CMakeLists.txt
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Expand Up @@ -216,6 +216,7 @@ endif()

include(CommonCPack)

set(DOXYGEN_EXTRA_INPUT "${PROJECT_SOURCE_DIR}/Changelog.md")
set(DOXYGEN_MAINPAGE_MD README.md)
set(DOXYGEN_EXTRA_INPUT "${PROJECT_SOURCE_DIR}/README.md ${PROJECT_SOURCE_DIR}/Changelog.md")
set(COMMON_PROJECT_DOMAIN ch.epfl.bluebrain)
include(DoxygenRule)
13 changes: 6 additions & 7 deletions README.md
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Expand Up @@ -40,7 +40,7 @@ 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-0.1/index.html)
The [API documentation](http://bluebrain.github.io/Brayns-0.6/index.html)
can be found on [bluebrain.github.io](http://bluebrain.github.io/).

## Using Docker images
Expand Down Expand Up @@ -70,15 +70,14 @@ following tree structure:

```
- src
+- ispc-v1.9.1-linux
+- ispc-v1.9.2-linux
+- OSPRay
+- OptiX
+- BRayns
+- Brayns
```

#### Intel ISPC compiler

Download and extract [ISPC compiler 1.9.1 archive](https://ispc.github.io/downloads.html).
Download and extract [ISPC compiler 1.9.2 archive](https://ispc.github.io/downloads.html).

#### Embree

Expand All @@ -88,7 +87,7 @@ 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 <latest_release>
git checkout v2.17.4
cmake .. -DCMAKE_INSTALL_PREFIX=<Brayns_installation_folder>
make install
```
Expand All @@ -101,7 +100,7 @@ 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 <latest_release>
git checkout v1.5.0
export CMAKE_PREFIX_PATH=<Brayns_installation_folder>
cmake .. -DCMAKE_INSTALL_PREFIX=<Brayns_installation_folder>
make install
Expand Down
78 changes: 38 additions & 40 deletions doc/UserGuide.md
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Expand Up @@ -4,26 +4,31 @@

### Morphologies

#### Loading data

The generic (optional) argument --input-paths can be used command line argument
can be used to specify files and/or folders where to load data from.

#### Loading morphologies

The --morphology-folder command line argument specifies the location of the
SWC or H5 morphology files to be loaded.
SWC or H5 morphology files (supported by the Brion library) can be loaded
easily.

```
braynsViewer --morphology-folder ~/morphologies
braynsViewer ~/morphologies
```

### Loading a circuit

The --circuit-config command line argument define the BlueConfig or
CircuitConfig to be loaded by Brayns. The --circuit-targets command line argument
specified the circuit target (or multiples separated by comma), and the --circuit-report
command line argument specifies the simulation report to be rendered.
BlueConfig or CircuitConfig files (supported by the Brion library) can be
loaded. The --circuit-targets command line argument specified 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 --circuit-config ~/circuits/BlueConfig --circuit-targets Layer1
--circuit-report voltages
braynsViewer ~/circuits/BlueConfig --circuit-targets Layer1 --circuit-report voltages
```

![Layer1](images/Layer1.png)
Expand All @@ -37,7 +42,7 @@ next three values defining the upper bound.

Example of how to define a circuit bounding box:
```
braynsViewer --circuit-config ~/circuits/BlueConfig --circuit-bounding-box -100 -100 -100 100 100 100
braynsViewer ~/circuits/BlueConfig --circuit-bounding-box -100 -100 -100 100 100 100
```

#### Density
Expand All @@ -48,7 +53,7 @@ in 20 will be loaded. Brayns reads the cells in GID order.

Example of how to load 10% of the circuit:
```
braynsViewer --circuit-config ~/circuits/BlueConfig --circuit-density 10
braynsViewer ~/circuits/BlueConfig --circuit-density 10
```

### Loading a NEST circuit
Expand All @@ -71,7 +76,7 @@ of those cells. Units used for the horizontal and vertical spacing are the ones
from the H5 and SWC files.

```
braynsViewer --morphology-folder ~/morphologies --morphology-layout 5 100 100
braynsViewer ~/morphologies --morphology-layout 5 100 100
```

#### Section types
Expand All @@ -84,19 +89,19 @@ wants to visualize the somas and the axons, the --morphology-section-types
command line argument should then be set to 3.

```
braynsViewer --morphology-folder ~/morphologies --morphology-section-types 3
braynsViewer ~/morphologies --morphology-section-types 3
```

![SectionTypes](images/SectionTypesAxonSoma.png)

```
braynsViewer --morphology-folder ~/morphologies --morphology-section-types 5
braynsViewer ~/morphologies --morphology-section-types 5
```

![SectionTypesSomaDendrites](images/SectionTypesAxonDendrites.png)

```
braynsViewer --morphology-folder ~/morphologies --morphology-section-types 9
braynsViewer ~/morphologies --morphology-section-types 9
```

![SectionTypesSomaApicalDendrites](images/SectionTypesAxonApicalDendrites.png)
Expand All @@ -108,21 +113,21 @@ one line per section, the medium quality divides the number of segment by 4, and
the high quality renders the full morphology.

```
braynsViewer --morphology-folder ~/morphologies --geometry-quality low
braynsViewer ~/morphologies --geometry-quality low
```

![GeometryQualityLow](images/GeometryQualityLow.png)


```
braynsViewer --morphology-folder ~/morphologies --geometry-quality medium
braynsViewer ~/morphologies --geometry-quality medium
```

![GeometryQualityMedium](images/GeometryQualityMedium.png)


```
braynsViewer --morphology-folder ~/morphologies --geometry-quality high
braynsViewer ~/morphologies --geometry-quality high
```

![GeometryQualityHigh](images/GeometryQualityHigh.png)
Expand All @@ -133,7 +138,7 @@ The --radius-multiplier command line parameters specifies the multiplier applied
to morphology radii. Typically, a value of 3 multipliers all radii by 3.

```
braynsViewer --morphology-folder ~/morphologies --radius-multiplier 3
braynsViewer ~/morphologies --radius-multiplier 3
```

![RadiusMultiplier](images/RadiusMultiplier3.png)
Expand All @@ -145,7 +150,7 @@ applied to all segments of the morphology. The unit is the one of the loaded
H5/SWC files.

```
braynsViewer --morphology-folder ~/morphologies --radius-correction 1
braynsViewer ~/morphologies --radius-correction 1
```

![RadiusCorrection](images/RadiusCorrection1.png)
Expand All @@ -166,14 +171,13 @@ belonging to a specific layer as the same color
- protein-chains: Each chain has a different color

```
braynsViewer --morphology-folder ~/morphologies --color-scheme neuron-by-id
braynsViewer ~/morphologies --color-scheme neuron-by-id
```

![ColorSchemeNeuronById](images/ColorSchemeID.png)

```
braynsViewer --morphology-folder ~/morphologies
--color-scheme neuron-by-segment-type
braynsViewer ~/morphologies --color-scheme neuron-by-segment-type
```

![ColorSchemeNeuronBySegmentType](images/ColorSchemeSegmentType.png)
Expand All @@ -185,8 +189,7 @@ to the 3D scene. Available values are:
- bounding-box: Adds a bounding box to the loaded dataset

```
braynsViewer --morphology-folder ~/morphologies
--scene-environment bounding-box
braynsViewer ~/morphologies --scene-environment bounding-box
```

![SceneEnvironmentBoundingBox](images/SceneEnvironmentBoundingBox.png)
Expand All @@ -202,8 +205,7 @@ command line argument defines how many samples from around the should be
considered to generate the mesh.

```
braynsViewer --morphology-folder ~/morphologies --metaballs-grid-size 60
--metaballs-threshold 1 --metaballs-samples-from-soma 5
braynsViewer ~/morphologies --metaballs-grid-size 60 --metaballs-threshold 1 --metaballs-samples-from-soma 5
```

![EnhancedSomas](images/EnhancedSoma.png)
Expand All @@ -212,22 +214,20 @@ braynsViewer --morphology-folder ~/morphologies --metaballs-grid-size 60

### Loading a single molecule

The --pdb-file command line argument specifies the PDB file to be loaded by
Brayns.
PDB files can be easily loaded:

```
braynsViewer --pdb-file 4IMY.pdb
braynsViewer 4IMY.pdb
```

![PDBFile](images/PDBFile.png)

### Loading molecules from folder

The --pdb-folder command line argument loads all PDB file located in the
specified folder.
Loads all PDB file located in the specified folder.

```
braynsViewer --pdb-folder ~/hiv --color-scheme protein-chains
braynsViewer ~/hiv --color-scheme protein-chains
```

![PDBFolder](images/PDBFolder.png)
Expand All @@ -236,22 +236,20 @@ braynsViewer --pdb-folder ~/hiv --color-scheme protein-chains

### Loading meshes

The --mesh-folder command line argument specifies the folder from which meshes
are loaded. Brayns can load file formats supported by the [assimp|https://github.com/assimp/assimp] library.
Brayns can load file formats supported by the [assimp|https://github.com/assimp/assimp] library.

```
braynsViewer --mesh-folder ~/meshes
braynsViewer ~/meshes
```

![Meshes](images/Meshes.png)
![Mesh](images/Mesh.png)

## Point cloud

The --xyzb-file command line argument specifies the XYZB file to be loaded. A
XYZB file is a binary encoded list of x,y and z double positions.
A XYZ file is a binary encoded list of x,y and z double positions.

```
braynsViewer --xyzb-file sample.xyzb
braynsViewer sample.xyz
```

## Cache file
Expand Down

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