Replace plt.show() with fig.show() in the docs

docs/source/algorithms/ConvertToReflectometryQ-v1.rst

@@ -205,7 +205,7 @@ achieved by running the algorithm below.
         axes.set_xlim([-0.0004,0.0004])
         axes.set_ylim([0,0.2])
 
-        plt.show()
+        fig.show()
 
     threadsafe_call(patch_plot, dump_vertexes)
 

docs/source/algorithms/ConvertToReflectometryQ-v2.rst

@@ -203,7 +203,7 @@ achieved by running the algorithm below.
         axes.set_xlim([-0.0004,0.0004])
         axes.set_ylim([0,0.2])
 
-        plt.show()
+        fig.show()
 
     threadsafe_call(patch_plot, dump_vertexes)
 

docs/source/algorithms/CopySample-v1.rst

@@ -130,7 +130,7 @@ After running this example code, the sample shapes can be plotted (see :ref:`Mes
         axes.set_mesh_axes_equal(mesh)
         axes.view_init(elev=20, azim=80)
 
-        plt.show()
+        fig.show()
 
 
 

docs/source/algorithms/HB2AReduce-v1.rst

@@ -100,7 +100,7 @@ Usage
        ax.plot(ws, specNum=num)
    plt.legend()
    #fig.savefig('HB2AReduce_1.png')
-   plt.show()
+   fig.show()
 
 .. figure:: /images/HB2AReduce_1.png
 
@@ -117,7 +117,7 @@ Usage
    fig, ax = plt.subplots(subplot_kw={'projection':'mantid'})
    ax.plot(ws)
    #fig.savefig('HB2AReduce_2.png')
-   plt.show()
+   fig.show()
 
 .. figure:: /images/HB2AReduce_2.png
 
@@ -134,7 +134,7 @@ Usage
    fig, ax = plt.subplots(subplot_kw={'projection':'mantid'})
    ax.plot(ws)
    #fig.savefig('HB2AReduce_3.png')
-   plt.show()
+   fig.show()
 
 .. figure:: /images/HB2AReduce_3.png
 
@@ -151,7 +151,7 @@ Usage
    fig, ax = plt.subplots(subplot_kw={'projection':'mantid'})
    ax.plot(ws)
    #fig.savefig('HB2AReduce_4.png')
-   plt.show()
+   fig.show()
 
 .. figure:: /images/HB2AReduce_4.png
 
@@ -168,7 +168,7 @@ Usage
    fig, ax = plt.subplots(subplot_kw={'projection':'mantid'})
    ax.plot(ws)
    #fig.savefig('HB2AReduce_5.png')
-   plt.show()
+   fig.show()
 
 .. figure:: /images/HB2AReduce_5.png
 
@@ -191,7 +191,7 @@ single anode *vs* temperature.
    fig, ax = plt.subplots(subplot_kw={'projection':'mantid'})
    ax.plot(ws, specNum=8) # anode8
    #fig.savefig('HB2AReduce_6.png')
-   plt.show()
+   fig.show()
 
 .. figure:: /images/HB2AReduce_6.png
 

docs/source/algorithms/LagrangeILLReduction-v1.rst

@@ -51,10 +51,12 @@ Usage
     eis = result.readX(0)
     temperatures = run.getLogData('temperature').value
 
-    plt.plot(eis, temperatures)
-    plt.xlabel("Ei (meV)")
-    plt.ylabel("temperature (K)")
-    plt.show()
+    fig, ax = plt.subplots(subplot_kw={'projection': 'mantid'})
+
+    ax.plot(eis, temperatures)
+    ax.set_xlabel("Ei (meV)")
+    ax.set_ylabel("temperature (K)")
+    fig.show()
 
 
 **Multiple monochromators example**

docs/source/algorithms/SetSample-v1.rst

@@ -334,7 +334,7 @@ After running this example code to rotate a cuboid by 30° anti-clockwise around
    axes.set_mesh_axes_equal(mesh)
    axes.view_init(elev=20, azim=80)
 
-   plt.show()
+   fig.show()
 
 .. categories::
 

docs/source/algorithms/SingleCrystalDiffuseReduction-v1.rst

@@ -240,7 +240,7 @@ Usage
    fig, ax = plt.subplots(subplot_kw={'projection':'mantid'})
    c = ax.pcolormesh(mtd['output'],vmin=0, vmax=1e-5)
    fig.colorbar(c)
-   plt.show()
+   fig.show()
 
 .. figure:: /images/SingleCrystalDiffuseReduction_corelli_multiple_sym_bkg_HH0.png
 

docs/source/concepts/HowToDefineGeometricShape.rst

@@ -332,7 +332,7 @@ Here the dimensions are used to define a 2m x 4m x 0.2m cuboid with its centre a
     axes.text(10.5,11.5,11, "WIDTH", color='b', fontsize=12)
     axes.text(11,9.5,9, "HEIGHT", color='purple', fontsize=12)
 
-    plt.show()
+    fig.show()
 
 In the next example, four points are used to describe a 2m x 0.8m x 0.4m cuboid with the its centre at the origin.
 
@@ -406,7 +406,7 @@ In the next example, four points are used to describe a 2m x 0.8m x 0.4m cuboid
     axes.scatter(0,0,0, color='b')
     axes.text(0,0.1,-0.15, "ORIGIN", color='b', fontsize=12)
 
-    plt.show()
+    fig.show()
 
 
 Hexahedron

docs/source/fitting/fitfunctions/BivariateGaussian.rst

@@ -53,7 +53,7 @@ Here is an example of fitting a 2D histogram:
     x, y = np.mgrid[-0.5:0.5:.01, -0.5:0.5:.01]
     pos = np.dstack((x, y))
     Z = rv.pdf(pos)
-    Z += 0.1*(np.random.random(x.shape) - 0.5) # Noise
+    Z += 1.5*(np.random.random(x.shape) - 0.5) # Noise
 
     # Here we'll format it so we can fit this as a 1D function:
     ZForFitting = np.empty(Z.shape + (2,))
@@ -86,16 +86,12 @@ Here is an example of fitting a 2D histogram:
     ZFit = bvg.function2D(pos)
 
     #Plot the results
-    plt.figure(1)
-    plt.clf()
-    plt.subplot(1,2,1)
-    plt.imshow(Z, origin='lower')
-    plt.title('Data')
-    plt.subplot(1,2,2)
-    plt.imshow(ZFit, origin='lower')
-    plt.title('Fit')
-    plt.show()
-
+    fig, axes = plt.subplots(nrows=1, ncols=2, subplot_kw={'projection': 'mantid'})
+    axes[0].imshow(Z, origin='lower')
+    axes[0].set_title('Data')
+    axes[1].imshow(ZFit, origin='lower')
+    axes[1].set_title('Fit')
+    fig.show()
 
 
 .. categories::

docs/source/interfaces/direct/Crystal Field Python Interface.rst

@@ -142,8 +142,9 @@ After the peak shape is defined a spectrum can be calculated::
 The output is a tuple of two 1d numpy arrays (x, y) that can be used with `matplotlib` to plot::
 
   import matplotlib.pyplot as plt
-  plt.plot(*sp)
-  plt.show()
+  fig, ax = plt.subplots(subplot_kw={'projection': 'mantid'})
+  ax.plot(*sp)
+  fig.show()
 
 .. image:: /images/CrystalFieldSpectrum1.png
    :height: 300

docs/source/plotting/1DPlotsHelp.rst

@@ -85,14 +85,15 @@ Scripting
 
 Click the generate a script button |GenerateAScript.png| on a 1D Plot:
 
-.. code-block:: python
+.. plot::
+   :include-source:
 
    # import mantid algorithms, numpy and matplotlib
+   from mantid.simpleapi import *
    import matplotlib.pyplot as plt
    from mantid.plots.utility import MantidAxType
-   from mantid.api import AnalysisDataService as ADS
 
-   MAR11060 = ADS.retrieve('MAR11060')
+   MAR11060 = Load('MAR11060')
 
    fig, axes = plt.subplots(edgecolor='#ffffff', num='MAR11060-1', subplot_kw={'projection': 'mantid'})
    axes.plot(MAR11060, color='#1f77b4', label='MAR11060: spec 1', wkspIndex=0)
@@ -105,29 +106,7 @@ Click the generate a script button |GenerateAScript.png| on a 1D Plot:
    axes.set_ylabel('Counts ($\\mu s$)$^{-1}$')
    legend = axes.legend(fontsize=8.0).set_draggable(True).legend
 
-   plt.show()
-
-.. plot::
-
-   # import mantid algorithms, numpy and matplotlib
-   from mantid.simpleapi import *
-   import matplotlib.pyplot as plt
-   from mantid.plots.utility import MantidAxType
-
-   MAR11060 = Load('MAR11060')
-
-   fig, axes = plt.subplots(edgecolor='#ffffff', num='MAR11060-1', subplot_kw={'projection': 'mantid'})
-   axes.plot(MAR11060, color='#1f77b4', label='MAR11060: spec 1', specNum=1)
-   axes.plot(MAR11060, color='#ff7f0e', label='MAR11060: spec 2', specNum=2)
-   axes.plot(MAR11060, color='#2ca02c', label='MAR11060: spec 3', specNum=3)
-   axes.tick_params(axis='x', which='major', **{'gridOn': False, 'tick1On': True, 'tick2On': False, 'label1On': True, 'label2On': False, 'size': 6, 'tickdir': 'out', 'width': 1})
-   axes.tick_params(axis='y', which='major', **{'gridOn': False, 'tick1On': True, 'tick2On': False, 'label1On': True, 'label2On': False, 'size': 6, 'tickdir': 'out', 'width': 1})
-   axes.set_title('MAR11060')
-   axes.set_xlabel('Time-of-flight ($\\mu s$)')
-   axes.set_ylabel('Counts ($\\mu s$)$^{-1}$')
-   legend = axes.legend(fontsize=8.0) # .set_draggable(True).legend # uncomment to set the legend draggable
-
-   plt.show()
+   fig.show()
 
 For more advice: :ref:`02_scripting_plots`
 
@@ -199,40 +178,8 @@ Scripting
 
 An example script for a Tiled Plot:
 
-.. code-block:: python
-
-   # import mantid algorithms, numpy and matplotlib
-   from mantid.simpleapi import *
-   import matplotlib.pyplot as plt
-   from mantid.plots.utility import MantidAxType
-   from mantid.api import AnalysisDataService as ADS
-
-   MAR11060 = ADS.retrieve('MAR11060') #May replace with Load('MAR11060')
-
-   fig, axes = plt.subplots(edgecolor='#ffffff', ncols=2, nrows=2, num='MAR11060-1', subplot_kw={'projection': 'mantid'})
-   axes[0][0].plot(MAR11060, color='#1f77b4', label='MAR11060: spec 1', wkspIndex=0)
-   axes[0][0].set_xlabel('Time-of-flight ($\\mu s$)')
-   axes[0][0].set_ylabel('Counts ($\\mu s$)$^{-1}$')
-   legend = axes[0][0].legend(fontsize=8.0).set_draggable(True).legend
-
-   axes[0][1].plot(MAR11060, color='#1f77b4', label='MAR11060: spec 2', wkspIndex=1)
-   axes[0][1].set_xlabel('Time-of-flight ($\\mu s$)')
-   axes[0][1].set_ylabel('Counts ($\\mu s$)$^{-1}$')
-   legend = axes[0][1].legend(fontsize=8.0).set_draggable(True).legend
-
-   axes[1][0].plot(MAR11060, color='#1f77b4', label='MAR11060: spec 3', wkspIndex=2)
-   axes[1][0].set_xlabel('Time-of-flight ($\\mu s$)')
-   axes[1][0].set_ylabel('Counts ($\\mu s$)$^{-1}$')
-   legend = axes[1][0].legend(fontsize=8.0).set_draggable(True).legend
-
-   axes[1][1].plot(MAR11060, color='#1f77b4', label='MAR11060: spec 4', wkspIndex=3)
-   axes[1][1].set_xlabel('Time-of-flight ($\\mu s$)')
-   axes[1][1].set_ylabel('Counts ($\\mu s$)$^{-1}$')
-   legend = axes[1][1].legend(fontsize=8.0).set_draggable(True).legend
-
-   plt.show()
-
 .. plot::
+   :include-source:
 
    # import mantid algorithms, numpy and matplotlib
    from mantid.simpleapi import *
@@ -262,7 +209,7 @@ An example script for a Tiled Plot:
    axes[1][1].set_ylabel('Counts ($\\mu s$)$^{-1}$')
    legend = axes[1][1].legend(fontsize=8.0) #.set_draggable(True).legend # uncomment to set the legend draggable
 
-   plt.show()
+   fig.show()
 
 For more advice: :ref:`02_scripting_plots`
 

docs/source/plotting/3DPlotsHelp.rst

@@ -83,7 +83,8 @@ Basic example of plotting a `Surface <https://matplotlib.org/mpl_toolkits/mplot3
 
     fig, ax = plt.subplots(subplot_kw={'projection':'mantid3d'})
     ax.plot_surface(data, cmap='viridis')
-    plt.show()
+
+    fig.show()
 
 For more advice: :ref:`02_scripting_plots`
 
@@ -150,7 +151,8 @@ Basic example of plotting a `Wireframe <https://matplotlib.org/mpl_toolkits/mplo
 
     fig, ax = plt.subplots(subplot_kw={'projection':'mantid3d'})
     ax.plot_wireframe(data, color='#1f77b4')
-    plt.show()
+
+    fig.show()
 
 For more advice: :ref:`02_scripting_plots`
 

docs/source/plotting/ColorfillPlotsHelp.rst

@@ -68,31 +68,8 @@ Scripting
 
 Click the generate a script button |GenerateAScript.png| on a `Colorfill Plot <https://matplotlib.org/3.2.1/api/_as_gen/matplotlib.pyplot.imshow.html>`_:
 
-.. code-block:: python
-
-   import matplotlib.pyplot as plt
-   import numpy as np
-   from matplotlib.colors import LogNorm
-   from matplotlib.ticker import LogLocator
-   from mantid.api import AnalysisDataService as ADS
-
-   MAR11060 = ADS.retrieve('MAR11060')
-
-   fig, axes = plt.subplots(figsize=[8.0, 7.0], num='MAR11060-1', subplot_kw={'projection': 'mantid'})
-   cfill = axes.imshow(MAR11060, aspect='auto', cmap='viridis', distribution=False, origin='lower')
-   cfill.set_norm(LogNorm(vmin=0.0001, vmax=3792.3352))
-   # If no ticks appear on the color bar remove the subs argument inside the LogLocator below
-   cbar = fig.colorbar(cfill, ax=[axes], ticks=LogLocator(subs=np.arange(1, 10)), pad=0.06)
-   cbar.set_label('Counts ($\\mu s$)$^{-1}$')
-   axes.set_title('MAR11060')
-   axes.set_xlabel('Time-of-flight ($\\mu s$)')
-   axes.set_ylabel('Spectrum')
-   axes.set_xlim([5.0, 19992.0])
-   axes.set_ylim([0.5, 922.5])
-
-   plt.show()
-
 .. plot::
+   :include-source:
 
    # import mantid algorithms, numpy and matplotlib
    from mantid.simpleapi import *
@@ -116,7 +93,7 @@ Click the generate a script button |GenerateAScript.png| on a `Colorfill Plot <h
    axes.set_xlim([5.0, 19992.0])
    axes.set_ylim([0.5, 922.5])
 
-   plt.show()
+   fig.show()
 
 For more advice:
 
@@ -200,7 +177,8 @@ Basic example of plotting a `Contour Plot <https://matplotlib.org/api/_as_gen/ma
    cbar=fig.colorbar(c)
    cbar.set_label('Counts ($\mu s$)$^{-1}$') #add text to colorbar
    fig.tight_layout()
-   plt.show()
+
+   fig.show()
 
 For more advice:
 

docs/source/plotting/MeshPlotHelp.rst

@@ -114,7 +114,7 @@ Note Component index 0 is usually the Container.
    sample = ws.getInstrument().getSample().getPos() - source
    arrow(axes, sample, origin=(0,0,-0.04))
    axes.view_init(vertical_axis='y', elev=30, azim=-135)
-   plt.show()
+   fig.show()
 
 
 Plot a cuboid sample shape, rotate it by the goniometer and add lattice vector arrows.
@@ -192,7 +192,7 @@ Plot a cuboid sample shape, rotate it by the goniometer and add lattice vector a
       arrow(axes, reciprocal_lattice[:,i], color = colors[i], linestyle = '--')
 
    axes.view_init(vertical_axis='y', elev=27, azim=50)
-   plt.show()
+   fig.show()
 
 
 **Other Plotting Documentation**

docs/source/plotting/WaterfallPlotsHelp.rst

@@ -132,7 +132,7 @@ An example script for a Waterfall Plot:
    # Update the offsets
    ax.update_waterfall(x_offset=10, y_offset=30)
 
-   plt.show()
+   fig.show()
 
 For more advice: :ref:`02_scripting_plots`
 

docs/source/release/v5.1.0/mantidworkbench.rst

@@ -92,7 +92,8 @@ Plotting
     ax3d[0].set_title("Surface")
     ax3d[1].set_title("Wireframe")
 
-    #plt.show()# uncomment to show the plots
+    #figC.show()# uncomment to show the plots
+    #fig3d.show()
 
 - The Advanced Plotting menu is now in Workbench. This enables creating surface and contour plots of three or more workspaces, and choosing which log value to plot against.