Documentation update

.gitignore

@@ -1,6 +1,5 @@
 *.swp
 __pycache__/
-*.jpg
 parallax/*.png
 *.log
 *.npy

docs/requirements.txt

@@ -1,3 +1,4 @@
 Sphinx
 sphinx-jinja
-furo
+furo
+docutils

docs/source/FAQ.rst

@@ -0,0 +1,135 @@
+FAQs
+================
+
+.. _reticle_detection_faqs:
+
+Reticle Detection
+------------------------
+
+.. _faq_r_0:
+
+- **Q. How should the reticle look in the view?**
+
+    Here are some examples of how the reticle should look in the view:
+
+    .. image:: _static/reticleDetection.jpg
+        :scale: 20%
+
+    - **Centered and in focus:** The reticle should be well-centered in the view, with its center in clear focus.
+
+    - **Properly illuminated:** The reticle should be evenly lit without any harsh reflections or shadow regions.
+
+    - **Appropriate size:** The reticle should occupy a significant portion of the view, avoiding being too small or too large.
+
+    - **Clear and unobstructed:** The reticle surface should be clean, free of debris, dirt, or any obstructions, including probes, that could interfere with detection. 
+
+    - **Consistent background:** The background should be plain and consistent, without any patterns or irregularities that might affect detection.
+
+.. _faq_r_1:
+
+- **Q. Reticle is not detected. What should I do?**
+
+    Possible Reasons and Solutions:
+
+    1. Brightness is too high or too low:
+
+        .. image:: _static/r_problem1.jpg
+            :scale: 20%
+
+        - Solution: Adjust the brightness to the optimal level.
+
+        .. image:: _static/r_problem2.jpg
+            :scale: 20%
+
+    2. Reticle is out of focus:
+
+        .. image:: _static/r_problem4.jpg
+            :scale: 20%    
+
+        - Solution: Close up the camera view to the center of the reticle so that the center of the reticle is in focus. 
+
+    3. Reticle view is too small:
+
+        - Solution: Zoom in the camera view so that the reticle view is larger.
+
+    4. Only partial reticle is visible:
+
+        .. image:: _static/r_problem5.jpg
+            :scale: 20%   
+
+        - Solution: Ensure the reticle is well-centered in the view.
+
+    5. Inconsistent lighting such as light reflection or shadow regions:
+
+        .. image:: _static/r_problem13.jpg
+            :scale: 20%   
+
+        .. image:: _static/r_problem11.jpg
+            :scale: 20%   
+
+        - Solution: Make sure the reticle background has consistent lighting.
+
+    6. Occlusion of reticle due to dirt or debris:
+
+        .. image:: _static/r_problem9.jpg
+            :scale: 20%   
+
+        - Solution: Clean the reticle surface to remove any debris or dirt.
+
+    7. Inconsistent background images:
+
+        - Solution: Avoid attaching paper tapes or creating patterns on the background. Attaching regular paper to the back of the reticle is recommended.
+
+    8. Too dark reticle background:
+
+        .. image:: _static/r_problem12.jpg
+            :scale: 20%  
+
+        - Solution: Use a white paper as a background to increase the contrast between the reticle and the background.  
+
+
+.. _faq_r_2:
+
+- **Q. Reprojection error is too high. How to fix it?**
+
+    Possible Reasons and Solutions:
+
+    1. Debris or dirt on the reticle surface causing misalignment:
+
+        - Solution: Clean the reticle surface to remove any debris or dirt, which the algorithm may mistakenly identify as part of the reticle.
+
+    2. View is too far from the reticle, making it appear too small:
+
+        - Solution: Move the camera closer to the reticle to ensure it occupies a larger portion of the view.
+
+    3. Reticle view is too skewed, causing a small in-focus region:
+
+        - Solution: Adjust the camera position so that the view is less skewed, and the face of the reticle appears as flat as possible.
+
+
+.. _general_faqs:
+
+General Interface
+------------------------
+
+.. _faq_g_1:
+
+- **Q. If I turn on Parallax, it shows noisy data on the view and does not display the camera view. What should I do?**
+
+    Parallax is currently under development, and some functions are not stable. If camera resources are not cleared up in the previous session, such as when the app exits forcefully or the camera interface is unplugged, it can cause this issue.
+
+        .. image:: _static/reset1.jpg
+            :scale: 20%
+
+    - Solution: Use Spinview to reset the camera resources. Steps to reset the camera resources:
+
+        1. Turn off Parallax.
+        2. Open Spinview and start and stop streaming on all cameras to reset the camera resources.
+
+            .. image:: _static/reset2.jpg
+                :scale: 30%
+
+            .. image:: _static/reset3.jpg
+                :scale: 30%
+
+        3. Turn on Parallax again.

docs/source/ReadMe.rst

@@ -0,0 +1,100 @@
+Getting Started
+====================
+
+Prerequisites
+--------------
+   - **Python~=3.8** 
+      - Recommended to install via `Anaconda`_ or `Miniconda`_
+      - Python 3.8 is required for the Spinnaker library.
+   - `Pathfinder MPM Software`_ version 2.8.0 or later
+   - `Spinnaker SDK`_ (Recommended)
+   - PySpin (for Linux or Mac OS users)
+
+   .. _Anaconda: https://www.anaconda.com/products/individual
+   .. _Miniconda: https://docs.conda.io/en/latest/miniconda.html
+   .. _Pathfinder MPM Software: https://www.newscaletech.com/multi-probe-micromanipulator/mpm-system-pathfinder-software/
+   .. _Spinnaker SDK: https://www.flir.com/products/spinnaker-sdk/?vertical=machine+vision&segment=iis
+
+Installing and Upgrading
+-------------------------
+   **1. Create a virtual environment using Python 3.8 and activate it:**
+      - On Windows:
+
+      .. code-block:: bash
+
+         python -m venv venv
+         ./venv/Scripts/activate
+
+      - On Linux/Mac:
+
+      .. code-block:: bash
+
+         python -m venv venv
+         source venv/bin/activate
+
+   **2. Install the latest version:**
+      .. code-block:: bash
+
+         pip install parallax-app
+
+      To upgrade to the latest version:
+
+      .. code-block:: bash
+
+         pip install parallax-app --upgrade
+
+   **3. To install the camera interface:**
+      .. code-block:: bash
+
+         pip install parallax-app[camera]
+
+Running Parallax
+----------------
+1. **Run the Pathfinder MPM Software application** to connect to the manipulator:
+
+   - Run Pathfinder MPM Software (v2.8.0 or later) in administrator mode.
+   - Enable the HTTP server.
+      - Version 2.8.0 of the Pathfinder MPM software includes an HTTP listener that can send probe information to a client program.
+      - Enable the HTTP server in the "MPM System Setup" dialog.
+      - Click the "Enable HTTP Server" checkbox to turn on the service.
+
+      .. image:: _static/PathfinderHTTPServer.jpg
+         :alt: Enable HTTP server
+         :scale: 30%
+
+2. **Run the Parallax application:**
+
+   .. code-block:: bash
+
+      python -m parallax
+
+
+Other Things to Note
+---------------------
+**Development Mode**
+
+   1. Clone the repository:
+
+      .. code-block:: bash
+
+         git clone https://github.com/AllenNeuralDynamics/parallax.git
+
+   2. Install dependencies:
+
+      .. code-block:: bash
+
+         pip install -e .[dev]
+
+**Documentation**
+
+   1. Install dependencies:
+
+      .. code-block:: bash
+
+         pip install -e .[docs]
+
+   2. Create the documentation HTML files:
+
+      .. code-block:: bash
+
+         sphinx-build -b html docs/source docs/_build

docs/source/_static/custom.css

@@ -0,0 +1,9 @@
+.red {
+    color: red;
+}
+.yellow {
+    color: yellow;
+}
+.blue {
+    color: blue;
+}