Adds ? button next to auto cor finding buttons

Adds help pages for COR

Fixes #703

docs/user_guide/reconstructions/center_of_rotation.rst

@@ -0,0 +1,81 @@
+.. _Center of Rotation:
+
+Center of Rotation and Tilt
+===========================
+
+Center of Rotation (COR) and Tilt usage
+---------------------------------------
+
+The correct center of rotation is required for a good reconstruction.
+We provide two automatic ways of getting a center of rotation.
+However, sometimes the values they find are not accurate, so there is also a manual way
+to adjust the center of rotation.
+
+The algorithms used for reconstruction require a COR for each sinogram,
+i.e. a list of CORs equal to the number of sinograms (also equal to the number of rows in a projection).
+This is abstracted away and the two final values that are used are: center of rotation and tilt.
+
+In that case the COR refers to the value at sinogram 0 (also referred to as slice 0).
+Using the tilt we then use a linear regression to calculate the COR for each sinogram in the data.
+
+
+Entering known COR and tilt
+---------------------------
+
+If the COR and tilt are already known you can enter them in the "Enter known COR/Tilt manually here" section
+and press "Fit from COR/Tilt above". In this case you can go immediately to reconstruction.
+
+Correlate 0 and 180
+-------------------
+
+This automatic COR algorithm finds the shift between the projections at 0 and 180 degrees.
+The projection exactly at 180 degrees is necessary for the best result.
+We provide the option of loading a 180 degree projection in the load dialog.
+
+If not provided with a 180 degree projection, the algorithm will use the projection
+at the middle of the stack. This is usually not exactly 180 degrees, and
+so the resulting COR  will be a few pixels off.
+
+This is not a problem and could be rectified either by adding a manual COR or using
+the minimisation algorithm.
+
+Minimise error
+--------------
+
+This automatic COR algorithm uses the square sum of the projection as a noise heuristic.
+It minimises the noise in order to find the best COR for that sinogram.
+
+It does so for a number of sinograms (slices) and adds the result in the COR table.
+
+This algorithm may not work well on noisy data or with very bright outliers, as the
+minimisation can get lost in a local minima and not find the best reconstructed slice.
+As the same heuristic is also used in the manual "Refine" window, to highlight
+one of the choices as the best, the behaviour can also be seen there.
+
+In this case the best action is to use the correlate as a starting point,
+and go immediately to manual COR correction.
+
+Manual COR correction
+---------------------
+
+Due to the limitations of the algorithms above there is also a manual way of calculating the COR -
+using the "COR Table - refine manually" part of the GUI.
+
+In that table you can click Add to add a new COR for the currently selected slice. Once added
+you can click the row and then "Refine" which will take you
+to a window that reconstructs the sinogram with multiple CORs simultaneously, and allows you
+to visually pick the best one.
+
+After you have two or more CORs in the table, a fit will be performed in order to find the COR and tilt
+using the data from the table rows.
+
+It is sometimes good enough to add a COR at the top of your data and the bottom.
+Once the best CORs for those are found, the resulting tilt should be accurate.
+To increase the accuracy further add more COR rows.
+
+To reconstruction
+-----------------
+
+Once you have a satisfactory value of COR or tilt, you are ready to proceed to the "Reconstruct" tab.
+
+Information about the filters and algorithms can be found in the other pages of the :ref:`Reconstruction Help page`.

docs/user_guide/reconstructions/index.rst

@@ -1,3 +1,5 @@
+.. _Reconstruction Help page:
+
 Reconstruction Help page
 ========================
 
@@ -6,5 +8,6 @@ Reconstruction Help page
    :maxdepth: 1
    :caption: Contents:
 
+   center_of_rotation
    algorithms
    filters

mantidimaging/gui/ui/recon_window.ui

@@ -25,16 +25,7 @@
         <property name="sizeConstraint">
          <enum>QLayout::SetMaximumSize</enum>
         </property>
-        <property name="leftMargin">
-         <number>9</number>
-        </property>
-        <property name="topMargin">
-         <number>9</number>
-        </property>
-        <property name="rightMargin">
-         <number>9</number>
-        </property>
-        <property name="bottomMargin">
+        <property name="margin">
          <number>9</number>
         </property>
         <item>
@@ -198,12 +189,12 @@
                    <property name="toolTip">
                     <string>Use the CoR and Tilt above to generate a CoR for each of the slice indices in the table below</string>
                    </property>
-                   <property name="toolTipDuration">
-                    <number>2</number>
-                   </property>
                    <property name="text">
                     <string>Fit from COR/Tilt above</string>
                    </property>
+                   <property name="toolTipDuration" stdset="0">
+                    <number>2</number>
+                   </property>
                   </widget>
                  </item>
                 </layout>
@@ -240,6 +231,19 @@
                  </property>
                 </widget>
                </item>
+               <item>
+                <widget class="QPushButton" name="corHelpButton">
+                 <property name="maximumSize">
+                  <size>
+                   <width>25</width>
+                   <height>16777215</height>
+                  </size>
+                 </property>
+                 <property name="text">
+                  <string>?</string>
+                 </property>
+                </widget>
+               </item>
               </layout>
              </widget>
             </item>

mantidimaging/gui/windows/recon/view.py

@@ -39,6 +39,7 @@ class ReconstructWindowView(BaseMainWindowView):
 
     correlateBtn: QPushButton
     minimiseBtn: QPushButton
+    corHelpButton: QPushButton
 
     reconTab: QWidget
 
@@ -144,7 +145,8 @@ def on_row_change(item, _):
             lambda: self.presenter.notify(PresN.RECONSTRUCT_PREVIEW_SLICE))  # type: ignore
 
         self.pixelSize.valueChanged.connect(lambda: self.presenter.notify(PresN.RECONSTRUCT_PREVIEW_SLICE))
-        self.reconHelpButton.clicked.connect(self.open_help_webpage)
+        self.reconHelpButton.clicked.connect(lambda: self.open_help_webpage("reconstructions/index"))
+        self.corHelpButton.clicked.connect(lambda: self.open_help_webpage("reconstructions/center_of_rotation"))
 
     def remove_selected_cor(self):
         return self.tableView.removeSelectedRows()
@@ -344,8 +346,8 @@ def set_correlate_buttons_enabled(self, enabled: bool):
         self.correlateBtn.setEnabled(enabled)
         self.minimiseBtn.setEnabled(enabled)
 
-    def open_help_webpage(self):
+    def open_help_webpage(self, page: str):
         try:
-            open_help_webpage(SECTION_USER_GUIDE, "reconstructions/index")
+            open_help_webpage(SECTION_USER_GUIDE, page)
         except RuntimeError as err:
             self.show_error_dialog(str(err))