Fix equations

docs/source/experiment.rst

@@ -350,13 +350,18 @@ should be created for each configuration that requires a change in the
 instrument calibration (wavelength, detector distance, detector
 translation) or scan angles.
 
+The detector is chosen from a pull-down menu that contains all the
+detectors defined in the *PyFAI* package. This defines the number of
+pixels, their size, and a mask array used to exclude all the pixels
+within gaps between the detector chips.
+
 Calibrate Powder
 ----------------
 This dialog will import a TIFF or CBF file containing measurements of a
 powder calibrant and refine the detector position and coordinates, using
-the PyFAI API. Alternatively, if the calibration parameters are already
-available in a PONI file, they can be directly imported. The resulting
-powder data and calbration parameters are then saved to the
+the *PyFAI* API. Alternatively, if the calibration parameters are
+already available in a PONI file, they can be directly imported. The
+resulting powder data and calbration parameters are then saved to the
 configuration template previously created using the *New Configuration*
 dialog.
 
@@ -441,3 +446,44 @@ powder calibration data and parameters to the configuration file. The
 calibration parameters can also be saved to a PONI file, using the
 "Export Calibration" button. This process should be repeated for each
 entry, after which the dialog can be closed.
+
+Create Mask
+-----------
+This dialog creates a pixel mask that is used to exclude bad pixels from
+further analysis. As described above, when a new configuration file is
+created, a pixel mask that excludes gaps between detector chips is
+automatically added. Additional pixels can be excluded using this
+dialog, either by adding editable shapes that are constructively added
+to the existing mask or by importing the mask from an external file,
+which can store the mask in any image format. The latter is useful if a
+beamline regularly updates a particular detector's mask as bad pixels are identified.
+
+.. warning:: If an external mask is input using "Import Mask", it will
+             overwrite the existing mask. It is important therefore that
+             the external pixel mask also excludes the detector gaps.
+
+After launching the dialog, the current mask can be plotted by clicking
+on "Plot Mask." This overlays the mask on the powder diffraction data to
+enable the center of the beam and other features of the data to be
+identified. 
+
+.. figure:: /images/create-mask.png
+   :align: center
+   :width: 80%
+
+   *Create Mask dialog. The translucent red circle shows the circle
+   created by clicking "Add Shape".*
+
+By clicking on "Add Shape" with either a rectangle or circle selected, a
+translucent shape is added to the plot. By default, it is centered on
+the beam center, but may be moved by dragging the center of the shape
+and/or resized by dragging one of the shape edges. When the shape has
+the correct position and size, click on "Add Shape" again for the shape
+to be added to the current list. A pull-down menu allows existing shapes
+to be selected for removal if necessary.
+
+If a more complicated mask is required, it can be generated by an
+external image editor and imported using "Import Mask".
+
+When the mask is complete, click "Save" to save it to the configuration file.
+

docs/source/introduction.rst

@@ -124,9 +124,12 @@ where
 
 .. math:: 
 
-    \mathbf{d}(x_{p}, y_{p})=\mathcal{D}\mathcal{O}^{-1}_{det}
-    \begin{pmatrix}{x_{p}-x_{c}}\\{y_{p}-y_{c}}\\0\end{pmatrix}-\mathcal{G}
-    \begin{pmatrix}{x_{s}-l_{sd}}\\{y_{s}}\\{z_{s}}\end{pmatrix}
+    \mathbf{d}(x_{p},
+    y_{p})=\mathcal{D}\mathcal{O}^{-1}_{det}
+    \begin{pmatrix}{x_{p}-x_{c}}\\{y_{p}-y_{c}}\\0\end{pmatrix}-
+    \mathcal{G}
+    \begin{pmatrix}{x_{s}}\\{y_{s}}\\{z_{s}}\end{pmatrix}-
+    \begin{pmatrix}{l_{sd}}\\{0}\\{0}\end{pmatrix}
 
 The :math:`\mathcal{B}` matrix is defined by the lattice parameters of
 the sample, as described by Busing and Levy in Acta Cryst. **22**, 457