Updates docs and fixes permissions in linux install (#165)

ISISNeutronMuon · Aug 22, 2024 · 9417714 · 9417714
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diff --git a/docs/add_measurements.rst b/docs/add_measurements.rst
@@ -212,7 +212,7 @@ highlight the corresponding 3D model in the graphics window. It is also possible
 measurement points in the graphics window by selecting **View > Toggle Measurement Labels**.
 
 .. image:: images/measurement_labels.png
-   :scale: 80
+   :scale: 50
    :alt: measurement labels
    :align: center
 

diff --git a/docs/base_computation.rst b/docs/base_computation.rst
@@ -58,20 +58,13 @@ updated to show the selected positioning system.
    :alt: calibration result from positioning table
    :align: center
 
-Select **Calculate Base Matrix** from the |base| button menu next to the goniometer title as shown below this should
-open a file dialog.
-
-.. image:: images/base_computation_example_3.png
-   :scale: 50
-   :alt: calibration result from positioning table
-   :align: center
-
-In the file dialog, Select the calibration file (*goniometer.calib*) from the *examples/base_computation* folder in the
+Select **Calculate Base Matrix** from the |base| button menu next to the goniometer title as shown above this should
+open a file dialog. In the file dialog, Select the calibration file (*goniometer.calib*) from the *examples/base_computation* folder in the
 install directory. This calibration file contains measured fiducial points at 4 different configurations for the 3 DOF
 goniometer on the ENGIN-X instrument. The software will read the file, execute the base matrix computation, and display
 the error for the computation in the dialog shown below.
 
-.. image:: images/base_computation_example_4.png
+.. image:: images/base_computation_example_3.png
    :scale: 50
    :alt: calibration result from positioning table
    :align: center
@@ -85,7 +78,7 @@ Clicking the Accept button in the error report will apply the new base matrix to
 in position and orientation can be seen in the graphic window. Clicking the Cancel button will discard the computed
 matrix.
 
-.. image:: images/base_computation_example_5.png
+.. image:: images/base_computation_example_4.png
    :scale: 50
    :alt: calibration result from positioning table
    :align: center

diff --git a/docs/images/align_sample.png b/docs/images/align_sample.png
diff --git a/docs/images/aligned_sample.png b/docs/images/aligned_sample.png
diff --git a/docs/images/base_computation_example_1.png b/docs/images/base_computation_example_1.png
diff --git a/docs/images/base_computation_example_2.png b/docs/images/base_computation_example_2.png
diff --git a/docs/images/base_computation_example_3.png b/docs/images/base_computation_example_3.png
diff --git a/docs/images/base_computation_example_4.png b/docs/images/base_computation_example_4.png
diff --git a/docs/images/base_computation_example_5.png b/docs/images/base_computation_example_5.png
diff --git a/docs/images/dark-theme.png b/docs/images/dark-theme.png
diff --git a/docs/images/dark_theme.png b/docs/images/dark_theme.png
diff --git a/docs/images/insert_fiducial.png b/docs/images/insert_fiducial.png
diff --git a/docs/images/insert_measurement.png b/docs/images/insert_measurement.png
diff --git a/docs/images/insert_sample.png b/docs/images/insert_sample.png
diff --git a/docs/images/insert_vector.png b/docs/images/insert_vector.png
diff --git a/docs/images/light-theme.png b/docs/images/light-theme.png
diff --git a/docs/images/light_theme.png b/docs/images/light_theme.png
diff --git a/docs/images/measurement_labels.png b/docs/images/measurement_labels.png
diff --git a/docs/images/measurement_point_example_1.png b/docs/images/measurement_point_example_1.png
diff --git a/docs/images/measurement_point_example_2.png b/docs/images/measurement_point_example_2.png
diff --git a/docs/images/measurement_point_example_3.png b/docs/images/measurement_point_example_3.png
diff --git a/docs/images/measurement_point_example_4.png b/docs/images/measurement_point_example_4.png
diff --git a/docs/images/open_existing.png b/docs/images/open_existing.png
diff --git a/docs/images/point_from_graphics.png b/docs/images/point_from_graphics.png
diff --git a/docs/images/positioners.png b/docs/images/positioners.png
diff --git a/docs/images/preferences.png b/docs/images/preferences.png
diff --git a/docs/images/reference_plane.png b/docs/images/reference_plane.png
diff --git a/docs/images/run_sim.png b/docs/images/run_sim.png
diff --git a/docs/images/scene_bounding.png b/docs/images/scene_bounding.png
diff --git a/docs/images/start.png b/docs/images/start.png
diff --git a/docs/interface.rst b/docs/interface.rst
@@ -146,12 +146,12 @@ Toggle Theme
 SScanSS 2 now supports a dark theme. You can toggle between the light and dark theme using the shortcut **Ctrl + Shift + T**. 
 The theme can also be toggled through **View > Toggle Theme**. A button has also been added to the toolbar to easily toggle between the themes. 
 
-.. image:: images/light-theme.png
+.. image:: images/light_theme.png
+   :scale: 50
    :alt: Light Theme
    :align: center
 
-.. image:: images/dark-theme.png
+.. image:: images/dark_theme.png
+   :scale: 50
    :alt: Dark Theme
    :align: center
-
-
diff --git a/docs/scene.rst b/docs/scene.rst
@@ -59,7 +59,7 @@ can be used to visualize how the sample relates to the coordinate system when th
 action is global so showing the sample bounding box in the sample scene will render it in the instrument scene.
 
 .. image:: images/scene_bounding.png
-   :scale: 80
+   :scale: 50
    :alt: Scene with bounding box
    :align: center
 

diff --git a/docs/selecting_points.rst b/docs/selecting_points.rst
@@ -17,28 +17,26 @@ Add a tube sample to the project. Click **Insert > Primitives > Tube** then clic
    :alt: Insert Sample
    :align: center
 
-
 **************************
 Select a Measurement Point
 **************************
 Click the **Insert > Measurement Points > Graphical Selection**. Select the point tool in the **Selection Tools** tab,
-and try to add a point at the position (-60, 20, 10) by clicking with the mouse cursor.
+and try to add a point roughly at the position (-60, 20, 10) by clicking with the mouse cursor.
 
 .. image:: images/measurement_point_example_2.png
    :scale: 50
    :alt: Select a Point
    :align: center
 
 * Move the XY plane to 10 from the origin in the **Define Plane** tab.
-* Move the mouse cursor to -60 in the X (horizontal) direction and 20 in the Y (vertical) direction. Use cursor
+* Move the mouse cursor close to -60 in the X (horizontal) direction and 20 in the Y (vertical) direction. Use cursor
   location in the status bar.
 * Click the left mouse button to add a measurement point to that location.
 * Click the **Add Points** to save points before moving the plane otherwise unsaved points will be lost
 
-While this is not the optimal use of the graphical selection tools (i.e the key-in method should be used if the coordinates
-of measurement are already known), this should typically be used if you need to add a group of points (i.e using the line or
-area tool) with known start and/or end positions.
-
+.. note:: This is not the optimal use of the graphical selection tools (i.e the key-in method should be used if the coordinates
+       of measurement are already known), this should typically be used if you need to add a group of points (i.e using the line or
+       area tool) with known start and/or end positions.
 
 *************************
 Add Equally Spaced Points

diff --git a/examples/base_computation/base_computation.h5 b/examples/base_computation/base_computation.h5
diff --git a/installer/linux/install.sh b/installer/linux/install.sh
@@ -119,6 +119,7 @@ python_exec="./envs/sscanss/bin/python"
 CFLAGS=$(./envs/sscanss/bin/python3-config --includes)
 export CFLAGS=$CFLAGS
 $python_exec -m pip install --no-cache-dir --no-index --no-build-isolation --find-links packages -r "./sscanss/requirements.txt" >/dev/null
+chmod 777 -R "./envs/sscanss/lib/python3.10/site-packages/PyQt6/"
 if [ "$INSTALL_EDITOR" = y ]; then
     $python_exec "./sscanss/make.py" --build-sscanss --build-editor >/dev/null
 else

diff --git a/sscanss/app/dialogs/insert.py b/sscanss/app/dialogs/insert.py
@@ -23,7 +23,6 @@ class InsertPrimitiveDialog(QtWidgets.QWidget):
     def __init__(self, primitive, parent):
         super().__init__(parent)
         self.parent = parent
-        self.parent_model = self.parent.presenter.model
         self.parent.scenes.switchToSampleScene()
         self.primitive = primitive
 
@@ -118,7 +117,6 @@ class InsertPointDialog(QtWidgets.QWidget):
     def __init__(self, point_type, parent):
         super().__init__(parent)
         self.parent = parent
-        self.parent_model = parent.presenter.model
         self.parent.scenes.switchToSampleScene()
         self.point_type = point_type
         self.title = f'Add {point_type.value} Point'
@@ -261,9 +259,11 @@ def updateAlignment(self):
         """Updates the list of alignments after selection change or vector update"""
         align_count = self.parent_model.measurement_vectors.shape[2]
         if align_count != self.alignment_combobox.count() - 1:
-            self.alignment_combobox.clear()
             alignment_list = [f'{i + 1}' for i in range(align_count)]
             alignment_list.append(self.add_new_text)
+            self.alignment_combobox.blockSignals(True)
+            self.alignment_combobox.clear()
+            self.alignment_combobox.blockSignals(False)
             self.alignment_combobox.addItems(alignment_list)
 
         self.alignment_combobox.setCurrentIndex(self.parent.scenes.rendered_alignment)
@@ -471,6 +471,7 @@ def prepareMesh(self):
         else:
             self.old_distance = None
             self.parent.scenes.removePlane()
+            self.reference_planes.clear()
         self.view.reset()
 
     def updateCursorStatus(self, point):