Merge pull request #203 from zhujun98/gui

Update documentation

docs/docs/installation.md

@@ -1,40 +1,52 @@
 A modern C++ compiler supporting C++17 is required.
 
-```sh
-module load gcc/11.3.0
-```
+## From source
 
-## Installing the reconstruction server
+We recommend using the [Anaconda](https://www.anaconda.com/download) environment.
 
+### Installing the reconstruction server
 
-On the GPU node `x02da-gpu-1`
+On a GPU node (Linux only),
 
 ```sh
-cd /afs/psi.ch/project/TOMCAT_dev/recastx
-git clone --recursive <repo>
+git clone --recursive https://github.com/<repo>/recastx.git
+cd recastx
 
 conda env create -f environment-recon.yml
 conda activate recastx-recon
 
-mkdir build && cd build
-cmake .. -DCMAKE_PREFIX_PATH=${CONDA_PREFIX:-"$(dirname $(which conda))/../"} \
-         -DBUILD_TEST=ON 
+module load gcc/11.3.0  # optional
+mkdir build-recon && cd build-recon
+cmake .. -DCMAKE_PREFIX_PATH=${CONDA_PREFIX:-"$(dirname $(which conda))/../"}
 make -j12 && make install
 ```
 
-## Installing the GUI
+### Installing the GUI
 
-On the graphics workstation `x02da-gws-3`
+On a graphics node or a laptop (Linux / MacOS),
 
 ```sh
-cd /afs/psi.ch/project/TOMCAT_dev/recastx
-git clone --recursive <repo>
+git clone --recursive https://github.com/<repo>/recastx.git
+cd recastx
 
 conda env create -f environment-gui.yml
 conda activate recastx-gui
 
+module load gcc/11.3.0  # optional
 mkdir build-gui && cd build-gui
 cmake .. -DCMAKE_PREFIX_PATH=${CONDA_PREFIX:-"$(dirname $(which conda))/../"} \
-         -DBUILD_GUI=ON -DBUILD_TEST=ON 
+         -DBUILD_GUI=ON
 make -j12 && make install
-```
+```
+
+## Package managers
+
+TBD
+
+## Deployment
+
+### At TOMCAT
+
+- GPU node: `x02da-gpu-1`
+- Graphics workstation: `x02da-gws-3`
+- DAQ node: `xbl-daq-36`

docs/docs/user_guide/usage.md

@@ -1,66 +1,62 @@
 ![architecture](../media/recastx-architecture.png)
 
-### At TOMCAT
+## Step 1: Starting the reconstruction server
 
-#### Step 1: Start the GUI
+```sh
+conda activate recastx-recon
+```
 
-Log in (no ssh) onto the graphics workstation `x02da-gws-3` and open a terminal
+For a local data source:
 ```sh
-conda activate recastx-gui
-recastx-gui --recon-host x02da-gpu-1
+recastx-recon  --rows 800 --cols 384 --angles 400
 ```
 
-Or on the Ra cluster, you can only run the OpenGL GUI inside a [NoMachine](https://www.psi.ch/en/photon-science-data-services/remote-interactive-access
-) client by
+For a remote data source (e.g. DAQ node):
 ```sh
-vglrun recastx-gui --recon-host x02da-gpu-1
+recastx-recon --rows 800 --cols 384 --angles 400 --daq-host <hostname> 
 ```
-**Note**: there is still a problem of linking the OpenGL GUI on Ra.
 
-Or on a local PC
+For more information, type
 ```sh
-ssh -L 9971:localhost:9971 x02da-gpu-1
+recastx-recon -h
 ```
 
-#### Step 2: Start the reconstruction server
+## Step 2: Starting the GUI
 
 ```sh
-conda activate recastx-recon
+conda activate recastx-gui
+```
 
-# Receiving the data stream and running the GUI both locally
-recastx-recon  --rows 800 --cols 384 --angles 400
+You can specify the reconstruction server
+```sh
+recastx-gui --recon-host <hostname>
+```
 
-# Receiving the data stream from a DAQ node
-recastx-recon --daq-host xbl-daq-36 --rows 800 --cols 384 --angles 400
+or make use of local port forwarding
+```sh
+ssh -L 9971:localhost:9971 <hostname>
+recastx-gui
 ```
 
-For more information, type
+You can also start the GUI on a node with [NoMachine](https://www.psi.ch/en/photon-science-data-services/remote-interactive-access
+) installed
 ```sh
-recastx-recon -h
+vglrun recastx-gui --recon-host <hostname>
 ```
 
-#### Step 3: Stream the data
+## Step 3: Streaming the data
 
-**Option1**: Streaming data from files on the GPU node
+### Option 1: streaming data from an area detector
 
-Install [foamstream](https://github.com/zhujun98/foamstream.git), and stream real
-experimental data, for example, by
-```sh
-foamstream-tomcat --datafile pet1 --ordered
+Contact the corresponding specialists at the facility.
 
-# pet1: recastx-recon --rows 800 --cols 384 --angles 400 --threads 32
-# h1: recastx-recon --rows 2016 --cols 288 --angles 500 --threads 32
+### Option 2: streaming data from files
 
-```
-or stream fake data, for example, by
+We recommend using [foamstream](https://github.com/zhujun98/foamstream.git).
 ```sh
-foamstream-tomcat --rows 800 --cols 384 --projections 10000
-```
-
-**Option2**: On the DAQ node
+pip install foamstream
 
-Start data acquisition with GigaFRoST camera.
-
-### At other facilities
+foamstream-tomcat --datafile pet1
+```
 
-TBD: a data adaptor should be needed
+Please feel free to use your own file streamer as long as the [data protocol](./data_protocol.md) is compatible.

docs/mkdocs.yml

@@ -5,6 +5,7 @@ nav:
   - User Guide:
       - Getting started: user_guide/usage.md
       - GUI: user_guide/gui.md
+      - Data protocol: user_guide/data_protocol.md
   - FAQ: faq.md
 theme:
   name: material

gui/include/application.hpp

@@ -31,7 +31,7 @@ class Application {
 
     int width_ = 1440;
     int height_ = 1080;
-    const std::string title_ = "RECASTX - Quasi-3D Real-time Tomographic Reconstruction";
+    const std::string title_ = "RECASTX - REConstruction of Arbitrary Slabs in Tomography X";
 
     ImVec4 bg_color_ = ImVec4(0.5f, 0.5f, 0.5f, 1.0f);