Merge pull request #75 from AllenNeuralDynamics/bugfix/documentation_…

…update Bugfix/documentation update
AllenNeuralDynamics · Jul 4, 2024 · f8e1ce5 · f8e1ce5
2 parents 93d67a7 + f696472
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diff --git a/docs/source/FAQ.rst b/docs/source/FAQ.rst
@@ -12,7 +12,7 @@ Reticle Detection
 
     Make sure your reticle appears similar to these examples:
 
-    .. image:: _static/reticleDetection.jpg
+    .. 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.
@@ -33,17 +33,17 @@ Reticle Detection
 
     1. Brightness is too high or too low:
 
-        .. image:: _static/r_problem1.jpg
+        .. image:: _static/r_problem1.JPG
             :scale: 20%
 
         - Solution: Adjust the brightness to the optimal level.
 
-        .. image:: _static/r_problem2.jpg
+        .. image:: _static/r_problem2.JPG
             :scale: 20%
 
     2. Reticle is out of focus:
 
-        .. image:: _static/r_problem4.jpg
+        .. image:: _static/r_problem4.JPG
             :scale: 20%    
 
         - Solution: Move the camera relative to the reticle so that the center of the reticle is in focus. 
@@ -54,24 +54,24 @@ Reticle Detection
 
     4. Only partial reticle is visible:
 
-        .. image:: _static/r_problem5.jpg
+        .. 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
+        .. image:: _static/r_problem13.JPG
             :scale: 20%   
 
-        .. image:: _static/r_problem11.jpg
+        .. 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
+        .. image:: _static/r_problem9.JPG
             :scale: 20%   
 
         - Solution: Clean the reticle surface to remove any debris or dirt.
@@ -82,7 +82,7 @@ Reticle Detection
 
     8. Reticle background is too dark:
 
-        .. image:: _static/r_problem12.jpg
+        .. 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.  
@@ -118,18 +118,18 @@ General Interface
 
     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
+        .. image:: _static/reset1.JPG
             :scale: 20%
 
     - Solution: Use Spinview to reset the camera resources. Steps to reset the camera resources:
 
         1. Close Parallax.
         2. Open Spinview and start and stop streaming on all cameras to reset the camera resources.
 
-            .. image:: _static/reset2.jpg
+            .. image:: _static/reset2.JPG
                 :scale: 30%
 
-            .. image:: _static/reset3.jpg
+            .. image:: _static/reset3.JPG
                 :scale: 30%
 
         3. Launch Parallax again.
diff --git a/docs/source/ReadMe.rst b/docs/source/ReadMe.rst
@@ -58,7 +58,7 @@ Running Parallax
       - 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
+      .. image:: _static/PathfinderHTTPServer.JPG
          :alt: Enable HTTP server
          :scale: 30%
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -6,7 +6,7 @@
 Welcome to Parallax
 ====================
 
-.. image:: ../../ui/ParallaxReadME.jpg
+.. image:: ../../ui/ParallaxReadME.JPG
    :alt: Parallax
 
 **Parallax** is a graphical user interface designed to streamline the process of setting up and performing acute *in vivo* electrophysiology experiments.

diff --git a/docs/source/userGuide.rst b/docs/source/userGuide.rst
@@ -15,7 +15,7 @@ Reticle Calibration
 
 1. Click on the :blue:`Reticle Detection` button.
 
-    .. image:: _static/reticleDetection.jpg
+    .. image:: _static/reticleDetection.JPG
         :alt: reticle detection
 
     - The reticle will be detected and displayed in the camera view.
@@ -24,12 +24,12 @@ Reticle Calibration
 
 2. Click the positive-x coordinate of the reticle on each camera view.
 
-    .. image:: _static/reticleDetection_posX.jpg
+    .. image:: _static/reticleDetection_posX.JPG
         :alt: positive-x coordinate
 
 3. Reprojection error of reticle points will appear.
 
-    .. image:: _static/reticleDetection_result.jpg
+    .. image:: _static/reticleDetection_result.JPG
         :alt: positive-x coordinate
 
     - Tips: An error under 3.0 µm³ is good. An error under 5.0 µm³ is acceptable.
@@ -48,26 +48,26 @@ Probe Calibration
 
 1. Select the stage you would like to calibrate after finishing reticle calibration.
 
-    .. image:: _static/probeSelect.jpg
+    .. image:: _static/probeSelect.JPG
         :alt: probe selection
 
 
 2. Move the probe tip close to the reticle surface and click on the :blue:`Probe Calibration` button.
 
-    .. image:: _static/probeCalib1.jpg
+    .. image:: _static/probeCalib1.JPG
         :alt: probe selection
 
     Tip: Bring the probe tip close to the reticle surface, as the focus in the camera view is set to the reticle. This helps detect the probe tip location more precisely.
 
 3. Move the probe in the x, y, z directions at least 2 mm.
 
-    .. image:: _static/probeCalib2.jpg
+    .. image:: _static/probeCalib2.JPG
         :alt: probe calibration
 
     - Once the probe has traveled far enough along each axis, the UI for the corresponding axis will turn green.
     - Even if all axes are green, additional movement may be necessary to improve the fit between the local motor coordinates and the global 3D points.
 
-        .. image:: _static/probeCalib3.jpg
+        .. image:: _static/probeCalib3.JPG
             :alt: probe trajectory
             :scale: 20%
 
@@ -76,7 +76,7 @@ Probe Calibration
     - Global coordinates show the probe tip location in the reticle coordinate system.
     - Tip: Try to hit a known point, such as the center of the reticle, to check the accuracy of the probe calibration.
 
-        .. image:: _static/probeCalib4.jpg
+        .. image:: _static/probeCalib4.JPG
             :alt: probe calibration
             :scale: 20%
 

diff --git a/parallax/__init__.py b/parallax/__init__.py
@@ -4,7 +4,7 @@
 
 import os
 
-__version__ = "0.37.17"
+__version__ = "0.37.18"
 
 # allow multiple OpenMP instances
 os.environ["KMP_DUPLICATE_LIB_OK"] = "True"