docs: update image captions

Author: ycexiao

doc/source/examples.rst

@@ -7,9 +7,9 @@ Examples
 Sequential fitting
 ===================
 
--------------------------
+---------
 r series
--------------------------
+---------
 
 In certain modeling situations the user could benefit from fitting a data set through a series of refinements that differ one from another by the corresponding fitting ranges. An example of this when one wants to study the details of the local- to average-structure crossover in a complex material. PDFgui has a pre-written macro that automates the setup of this type of refinement.
 
@@ -26,7 +26,7 @@ In certain modeling situations the user could benefit from fitting a data set th
        :align: center
        :figwidth: 100%
 
-       Figure 3.5: Appearance of the setup panel for specifying an incremental r-series fit conditions.
+       Figure 2.1: Appearance of the setup panel for specifying an incremental r-series fit conditions.
 
 
    The first row deals with the increment setup of the upper r of the refinements. User should specify the first and the last fit maximum r-value, and corresponding step (increment), all in units of Angstroms.
@@ -38,9 +38,9 @@ In certain modeling situations the user could benefit from fitting a data set th
 
 
 .. _temperature-series:
-----------------------------------------
+------------------
 temperature series
-----------------------------------------
+------------------
 
 Frequently, one must handle a large number of data sets originating from a single sample collected at various temperatures. One of the common modeling schemes in such cases is to perform sequential fitting of such data series, which is known to yield well behaved modeling parameters.
 
@@ -66,7 +66,7 @@ The data collected at NPDF instrument at LANSCE at Los Alamos National Laborator
      :align: center
      :figwidth: 100%
 
-     Figure 3.6: Setting up a T-series sequential refinement for LaMnO3. Ordering by temperature will ensure that the fits are linked correctly.
+     Figure 2.2: Setting up a T-series sequential refinement for LaMnO3. Ordering by temperature will ensure that the fits are linked correctly.
 
 4. Order the data by temperature. The data can be ordered by temperature by clicking the “Temperature” header.
 
@@ -86,7 +86,7 @@ The data collected at NPDF instrument at LANSCE at Los Alamos National Laborator
      :figwidth: 100%
 
 
-     Figure 3.7: Displaying the refinement results as a function of external parameter: T-series refinement of LaMnO3, example of isotropic ADP of oxygen atom on general position in *Pbnm* setting. Notable are the offsets just above 700 K (Jahn-Teller transition), and at around 1000 K when sample converts from orthorhombic to rhombohedral symmetry.
+     Figure 2.3: Displaying the refinement results as a function of external parameter: T-series refinement of LaMnO3, example of isotropic ADP of oxygen atom on general position in *Pbnm* setting. Notable are the offsets just above 700 K (Jahn-Teller transition), and at around 1000 K when sample converts from orthorhombic to rhombohedral symmetry.
 
 
 Despite quite high temperatures, an onset of the static offset above the transition temperature is clearly marked by this parameter, as apparent in Figure 3.7. Curious user could repeat the same T-series refinement restricting the refinement range upper limit to say 5-6 Angstroms and observe the outcome. The refinement sequence execution should be very quick in this case
@@ -122,7 +122,7 @@ in contrast to 32 inverse Angstroms in previous example.
      :align: center
      :figwidth: 100%
 
-     Figure 3.8: After loading of the Ca-doping data series of LaMnO3 system, proper doping assignment needs to be carried out, as the doping levels introspected from the file names in this example incorrectly reflect the scientific situation. Note that dopant atom has to be present in the template seed used to generate the linked sequence of fits.
+     Figure 2.4: After loading of the Ca-doping data series of LaMnO3 system, proper doping assignment needs to be carried out, as the doping levels introspected from the file names in this example incorrectly reflect the scientific situation. Note that dopant atom has to be present in the template seed used to generate the linked sequence of fits.
 
 
 3. Click on “Add” button. Using “Shift” and mouse-select operation you should select all the data sets mentioned in the above list, and then press “Open” button.
@@ -147,7 +147,7 @@ graphically such that various converged fit parameters are plotted versus Ca con
      :align: center
      :figwidth: 100%
 
-     Figure 3.9: Sequence of refined parameters, such as lattice constants, can be plotted vs doping using PDFgui plotting facilities. Figure features lattice parameter *b* in *Pbnm* space group setting for series of Ca-doped LaMnO3 samples for doping concentrations between 0 and 0.28 at 10 K temperature.
+     Figure 2.5: Sequence of refined parameters, such as lattice constants, can be plotted vs doping using PDFgui plotting facilities. Figure features lattice parameter *b* in *Pbnm* space group setting for series of Ca-doped LaMnO3 samples for doping concentrations between 0 and 0.28 at 10 K temperature.
 
 
 
@@ -258,7 +258,7 @@ and is used here.
      :align: center
      :figwidth: 100%
 
-     Figure 3.10: Fitting the structure of a nanoparticle: 3nm CdSe nanoparticle example.
+     Figure 2.6: Fitting the structure of a nanoparticle: 3nm CdSe nanoparticle example.
 
 
 Further improvements can be obtained by introducing anisotropic ADPs, where again values related to the z-direction will remain abnormally large most probably due to the stacking related disorder.A detailed description of this system and successful PDF modeling can be found in this publication: `Quantitative size-dependent structure and strain determination of CdSe nanoparticles using atomic pair distribution function analysis <https://link.aps.org/doi/10.1103/PhysRevB.76.115413>`_.

doc/source/extras.rst

@@ -35,15 +35,15 @@ Since several formal
 plotting examples were given through the tutorial exercise, and having simplicity of usage in
 mind, no other plotting examples are provided, hoping that the usage is sufficiently simple
 for users to master individually with ease. An example plot of Rw vs refinement step is
-shown in Figure 4.1 for Ni example.
+shown in Figure 3.1 for Ni example.
 
 
 
   .. figure:: images/fig4-01.png
      :align: center
      :figwidth: 100%
 
-     Figure 4.1: Plotting window featuring Rw vs refinement step for Ni example. The basic functionality for manipulating the plot is provided through icons on the tool bar of the plotting window.
+     Figure 3.1: Plotting window featuring Rw vs refinement step for Ni example. The basic functionality for manipulating the plot is provided through icons on the tool bar of the plotting window.
 
 
 
@@ -102,7 +102,7 @@ An example Ni structure visualization with AtomEye is shown in Figure 4.2.
      :align: center
      :figwidth: 100%
 
-     Figure 4.2: Using AtomEye functionality (if installed on your system) for 3D visualization of the initial and refined PDF structures: example of Ni structure.
+     Figure 3.2: Using AtomEye functionality (if installed on your system) for 3D visualization of the initial and refined PDF structures: example of Ni structure.
 
 ================================
 Advanced usage and special needs

doc/source/tutorial.rst

@@ -39,7 +39,7 @@ pane, and the ``PDFfit2 Output`` panel.
    :align: center
    :figwidth: 100%
 
-   Figure 2.1: Appearance of a PDFgui window after a structure model  is loaded.
+   Figure 1.1:  Appearance of a PDFgui window after a structure model  is loaded.
 
 The ``Fit Tree`` is used in setting up a fit protocol. The ``Plot Control`` serves the user’s needs
 for graphically displaying the fits, as well as various fit-related parameters. The content of
@@ -82,7 +82,7 @@ Procedure:
        valid structure model file, a ``.stru`` or a ``.cif`` file.
     3. Note, an alternative workflow for adding structural models is to select ``New Phase`` from the ``Phases`` dropdown menu.
 
-   If you select the Phase in the ``Fit Tree`` by left clicking on it, you will see in the right panel 3 tabs, ``Configure``, ``Constraints``, ``Results``. As shown in the Figure 2.1. Feel free to click one these tabs and look inside.
+   If you select the Phase in the ``Fit Tree`` by left clicking on it, you will see in the right panel 3 tabs, ``Configure``, ``Constraints``, ``Results``. As shown in the Figure 1.1. Feel free to click one these tabs and look inside.
 
    The ``Configure`` panel displays configuration information from the structure file. The top portion contains lattice parameters, phase scale factor, and a set of parameters intended to be used to account for correlated atomic motion effects that typically sharpen the nearest neighbor PDF peak. These are ``delta1``, ``delta2``, ``sratio``, and ``rcut``. The ``spdiameter`` and ``stepcut`` parameters include scatterer size effects in the PDF. These parameters will be described later. The bottom part of the panel contains standard unit cell content related information such as atomic species, their fractional coordinates, anisotropic ADPs, and site occupancies. The ``Constraints`` panel will hold the constraints we will set up for our fits, it should be empty now, and the results tab will contain the results of any fit.
 
@@ -102,7 +102,7 @@ Procedure:
       :align: center
       :figwidth: 100%
 
-      Figure 2.2: Appearance of a PDFgui window after a PDF dataset is loaded.
+      Figure 1.2:  Appearance of a PDFgui window after a PDF dataset is loaded.
 
    The ``Configure``
    panel displays configuration information from the data file. It should be noted that depend-ing on the software used to prepare the experimental PDF from the raw data, the file may
@@ -140,7 +140,7 @@ Procedure:
 	:align: center
 	:figwidth: 100%
 
-	Figure 2.3: Adjusting data set related configuration.
+	Figure 1.3:  Adjusting data set related configuration.
 
    Since there is no physical information in the region of of r below the nearest neighbor PDF peak position (as seen in the plot), and since this region is often affected by noise and experimental artifacts, it is wise to exclude it from fitting.
    We therefore set the value of the lower boundary of the ``Fit range`` to 1.7. (Note that the
@@ -156,7 +156,7 @@ Procedure:
 	:align: center
 	:figwidth: 100%
 
-	Figure 2.4: Setting up the refinement parameters and constraints of the structure model.
+	Figure 1.4:  Setting up the refinement parameters and constraints of the structure model.
 
    Here we are defining "variables" that will be refined and giving them names
    variable "@1", "@2", etc. and linking them to model parameters by typing them
@@ -173,7 +173,7 @@ Procedure:
 	:align: center
 	:figwidth: 100%
 
-	Figure 2.5: Setting up the refinement parameters and constraints of the PDF data.
+	Figure 1.5:  Setting up the refinement parameters and constraints of the PDF data.
 
    When we assign the three parameters ``a``, ``b`` and ``c`` to the same variable,
    ``@2``, we are implicitly ensuring that the refinement will respect
@@ -215,7 +215,7 @@ Procedure:
 	:align: center
 	:figwidth: 100%
 
-	Figure 2.6: Reviewing the fit parameters and conditions.
+	Figure 1.6:  Reviewing the fit parameters and conditions.
 
 
     2. When you are satisfied with the configuration, click the "gear" icon |gear| on the toolbar and watch the fit progress in the terminal window. The refinement can be stopped prematurely by clicking on the “stop” icon |stop| on the tool bar. During the refinement the refinement progress will be directly reported in the PDFfit2 Output panel.
@@ -228,7 +228,7 @@ Procedure:
 	:align: center
 	:figwidth: 100%
 
-	Figure 2.7: Refinement progress is displayed in the PDFfit2 Output panel.
+	Figure 1.7:  Refinement progress is displayed in the PDFfit2 Output panel.
 
 
 
@@ -239,7 +239,7 @@ Procedure:
 	:align: center
 	:figwidth: 100%
 
-	Figure 2.8: Updating the set of initial values of refined parameters.
+	Figure 1.8:  Updating the set of initial values of refined parameters.
 
 7. Plot the results:
     1. Select the data in the fit (in this case the `Ni-xray.gr` dataset) by left clicking it.
@@ -270,13 +270,13 @@ Procedure:
 	:align: center
 	:figwidth: 100%
 
-	Figure 2.9:An example of PDFgui plotting capabilities: displaying a fit.
+	Figure 1.9: An example of PDFgui plotting capabilities:  displaying a fit.
 
     .. figure:: images/fig2-10.png
 	:align: center
 	:figwidth: 100%
 
-	Figure 2.10:An example of PDFgui plotting capabilities: displaying a parameter.
+	Figure 1.10: An example of PDFgui plotting capabilities:  displaying a parameter.
 
 
 8. Save your project for later use.
@@ -309,7 +309,7 @@ In the previous example the initial structure was defined by an existing file. H
 	:align: center
 	:figwidth: 100%
 
-	Figure 3.1: Expanding the unit cell using space group information.
+	Figure 1.11:  Expanding the unit cell using space group information.
 
 4. Generate symmetry constraints:
     1. Select the "Constraints" tab.
@@ -346,7 +346,7 @@ calculate Ni PDF using neutron radiation.
 	:align: center
 	:figwidth: 100%
 
-	Figure 3.2: An example of the calculation configuration panel.
+	Figure 1.12:  An example of the calculation configuration panel.
 
 Conditions to be specified include radiation type, calculation
 range and corresponding r-grid size, as well as instrument resolution and maximum momentum transfer parameters. For the later two, the default values of parameters could be
@@ -390,7 +390,7 @@ Learn how to string together fits.
 	:align: center
 	:figwidth: 100%
 
-	Figure 3.3: An example of linked fits.
+	Figure 1.13:  An example of linked fits.
 
 5. Add more fit parameters:
     1. Select the "Constraints" tab of the `Ni.stru` phase below "Fit 1_copy".