Add links to tutorials

Author: Sparks29032

docs/source/funcxy.rst

@@ -2,6 +2,7 @@
 
 Using funcxy with Commonly-Used Diffraction Software
 ####################################################
+
 The general xy morph ``funcxy`` can be used to tune parameters
 of many popular diffraction software functions.
 
@@ -11,6 +12,7 @@ and `PyFai <https://pyfai.readthedocs.io/en/stable/>`_.
 
 Getting a Better PDF with PDFgetx3
 ==================================
+
 In PDFgetx3, the ``PDFGetter`` takes in a 1D diffraction
 pattern I(Q) and returns a PDF G(r).
 
@@ -33,6 +35,7 @@ glass background. We want to match a target calculated PDF G(r)
 stored in a file named ``target.cgr``.
 Let's also say we have a measured I(Q) of the
 glass background ``background.chi``.
+
 .. code-block:: python
 
      from diffpy.pdfgetx.pdfgetter import PDFGetter
@@ -65,13 +68,12 @@ glass background ``background.chi``.
          "qmaxinst": 25.0, "rpoly": 0.9
      }
 
-     morph_info, morph_table = morph_arrays(
+     morph_info, morphed_gr = morph_arrays(
                                      sample_iq, target_gr,
                                      funcxy=(wrap, params_to_morph)
                                  )
 
-
-You can now plot ``morph_table`` against your ``target_gr`` to see
+You can now plot ``morphed_gr`` against your ``target_gr`` to see
 how well your morphing refinement of the PDF-getting parameters
 as done!
 To see what the refined values of the parameters are,
@@ -88,6 +90,7 @@ call to ``morph_arrays``.
 
 Performing Detector Calibration with PyFai
 ==========================================
+
 When performing azimuthal integration, it is important to
 ensure your beam center and detector distances are calibrated.
 However, it is possible that they have shifted
@@ -96,10 +99,24 @@ across measurements. Here, we will use morphing to the rescue!
 Let's say we just measured a diffraction pattern stored
 as a NumPy object in ``diffraction_image.npy``, but some
 of the detector geometries are off.
+Our azimuthally integrated ``sample.chi`` looks a bit off.
 Before this measurement, you measured an amazing
 I(Q) pattern ``target.chi`` with a perfectly calibrated
 sample-to-detector distance and beam center.
-We will use morphing to try to recalibrate.
+We will use morphing to try to match the integration of
+the 2D pattern to the target 1D function.
+
+For the integration, we will need some information, such as
+the wavelength of the beam,
+the size of each pixel in the 2D image
+(``pixel1`` is the horizontal length in meters and
+``pixel2`` is the vertical length in meters),
+and a guess of the beam center.
+This information can be found on the
+`PyFai documentation <https://pyfai.readthedocs.io/en/stable/usage/cookbook/integration_with_python.html>`_.
+For our example, let's say we have a ``1024``x``1024`` pixel image
+where each pixel is a ``100`` micron by ``100`` micron region, and
+our wavelength was ``1.11`` angstroms.
 
 .. code-block:: python
 
@@ -110,18 +127,55 @@ We will use morphing to try to recalibrate.
      from diffpy.utils.parsers.loaddata import loadData
 
      pattern_2d = np.load("diffraction_image.npy")
-     wavelength = #
-     pixel1 = #
-     pixel2 = #
+     wavelength = 0.1110e-9  # in m
+     pixel1 = 1e-4  # in m
+     pixel2 = 1e-4  # in m
+     cent_x = 511   # in number of pixels
+     cent_y = 511   # in number of pixels
 
      ai = pyfai.AzimuthalIntegrator()
      ai.wavelength = wavelength
      detector = pfd.Detector()
      detector.max_shape = pattern_2d.shape
 
+
      def wrap(x, y, sample_to_detector_dist, cent_offset_x, cent_offset_y):
          detector.pixel1 = pixel1
          detector.pixel2 = pixel2
+         ai.detector = detector
 
+         ai.setFit2D(
+             directDist=sample_to_detector_dist,
+             centerX=cent_x+cent_offset_x,
+             centerY=cent_y+cent_offset_y
+         )
 
-         ai.detector = detector
+         return ai.integrate1D_ng(
+                 pattern_2d,
+                 npt=1000, unit="q_A^-1",
+                 method="mean"
+             )
+
+
+     params_to_morph = {
+         "sample_to_detector_dist": 60,  # in mm
+         "cent_offset_x": 0,  # in number of pixels
+         "cent_offset_y": 0  # in number of pixels
+     }
+
+     sample_chi = loadData("sample.chi")
+     target_chi = loadData("target.chi")
+
+     morph_info, morphed_chi = morph_arrays(
+                                     sample_chi, target_chi,
+                                     funcxy=(wrap, params_to_morph)
+                                 )
+
+You can now plot ``morphed_chi`` against your ``target_chi``
+to see if the refinement has helped in the calibration!
+To see the calibrated values, you can print out ``morph_info``.
+
+If you would like to morph over other PyFai parameters
+(e.g. ``rot1``, ``tilt``, ``wavelength``),
+you can adjust the wrapper function ``wrap`` to take in
+these parameters.

docs/source/morphpy.rst

@@ -10,6 +10,11 @@ This page is intended for those acquainted with the basic morphs
 described in the aforementioned quickstart tutorial who want to use ``diffpy.morph`` in their
 Python scripts.
 
+For those looking to use the Python-specific morph ``MorphFuncxy`` (described below)
+with commonly used diffraction software like `PDFgetx3 <https://www.diffpy.org/products/pdfgetx.html>`_
+and `PyFai <https://pyfai.readthedocs.io/en/stable/>`_ are directed to the
+`funcxy tutorials <funcxy.html>`__.
+
 Python Morphing Functions
 =========================
 
@@ -408,8 +413,10 @@ This is equivalent to applying a ``MorphFuncx`` and ``MorphFuncy``
 simultaneously.
 
 This morph is useful when you want to apply operations that modify both
-the grid and function value. A PDF-specific example includes computing
-PDFs from 1D diffraction data (see paragraph at the end of this section).
+the grid and function value.
+Examples of using ``MorphFuncxy`` with ``PyFai`` azimuthal integration
+and ``PDFgetx3`` PDF calculation are included `here <funcxy.html>`__.
+
 
 For this tutorial, we will go through two examples. One simple one
 involving shifting a function in the ``x`` and ``y`` directions, and

docs/source/tutorials.rst

@@ -8,6 +8,14 @@ Tutorials for these are included below. The files required for these tutorials c
 
 For a full list of options offered by ``diffpy.morph``, please run ``diffpy.morph --help`` on the command line.
 
+Using MorphFuncxy
+=================
+
+Examples of how to use the general morph ``MorphFuncxy`` with commonly used
+diffraction software like `PDFgetx3 <https://www.diffpy.org/products/pdfgetx.html>`_
+and `PyFai <https://pyfai.readthedocs.io/en/stable/>`_ are directed to the
+`funcxy tutorials <funcxy.html>`__.
+
 Performing Multiple Morphs
 ==========================