[23a9beb] | 1 | .. graph_help.rst |
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[0d66541] | 2 | |
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[78f02c3] | 3 | .. This is a port of the original SasView html help file to ReSTructured text |
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| 4 | .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. |
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| 5 | |
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[3fd3d5a4] | 6 | |
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[37bbd5f] | 7 | Plotting Data/Models |
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| 8 | ==================== |
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| 9 | |
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[96423f8] | 10 | SasView generates three different types of graph window: one that displays *1D data* |
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| 11 | (ie, I(Q) vs Q), one that displays *1D residuals* (ie, the difference between the |
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| 12 | experimental data and the theory at the same Q values), and *2D color maps*. |
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| 13 | |
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[0cdf1af] | 14 | Graph window options |
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[3fd3d5a4] | 15 | -------------------- |
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[78f02c3] | 16 | |
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[0cdf1af] | 17 | .. _Invoking_the_graph_menu: |
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[78f02c3] | 18 | |
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[0cdf1af] | 19 | Invoking the graph menu |
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| 20 | ^^^^^^^^^^^^^^^^^^^^^^^ |
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[3fd3d5a4] | 21 | |
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[c89e649] | 22 | To invoke the *Graph Menu* simply right-click on a data/theory plot, or click |
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| 23 | the *Graph Menu* (bullet list) icon in the toolbar at the bottom of the plot. |
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[3fd3d5a4] | 24 | Then select a menu item. |
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[78f02c3] | 25 | |
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[0cdf1af] | 26 | How to Hide-Show-Delete a graph |
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| 27 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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[78f02c3] | 28 | |
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[c89e649] | 29 | To expand a plot window, click the *Maximise* (square) icon in the top-right |
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[3fd3d5a4] | 30 | corner. |
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[78f02c3] | 31 | |
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[c89e649] | 32 | To shrink a plot window, click the *Restore down* (square-on-square) icon in |
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[3fd3d5a4] | 33 | the top-right corner. |
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[78f02c3] | 34 | |
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[c89e649] | 35 | To hide a plot, click the *Minimise* (-) icon in the top-right corner of the |
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[3fd3d5a4] | 36 | plot window. |
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[23a9beb] | 37 | |
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[c89e649] | 38 | To show a hidden plot, select the *Restore up* (square-on-square) icon on the |
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[3fd3d5a4] | 39 | minimised window. |
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| 40 | |
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[c89e649] | 41 | To delete a plot, click the *Close* (x) icon in the top-right corner of the |
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[3fd3d5a4] | 42 | plot window. |
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| 43 | |
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[35f4d43] | 44 | .. note:: |
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| 45 | *If a residuals graph (when fitting data) is hidden, it will not show up |
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| 46 | after computation.* |
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[3fd3d5a4] | 47 | |
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[0cdf1af] | 48 | Dragging a plot |
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| 49 | ^^^^^^^^^^^^^^^ |
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[23a9beb] | 50 | |
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[c89e649] | 51 | Select the *Pan* (crossed arrows) icon in the toolbar at the bottom of the plot |
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| 52 | to activate this option. Move the mouse pointer to the plot. It will change to |
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| 53 | a hand. Then left-click and drag the plot around. The axis values will adjust |
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[3fd3d5a4] | 54 | accordingly. |
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[c89e649] | 55 | |
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[3fd3d5a4] | 56 | To disable dragging mode, unselect the *crossed arrows* icon on the toolbar. |
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[23a9beb] | 57 | |
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[0cdf1af] | 58 | Zooming In-Out on a plot |
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| 59 | ^^^^^^^^^^^^^^^^^^^^^^^^ |
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[78f02c3] | 60 | |
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[c89e649] | 61 | Select the *Zoom* (magnifying glass) button in the toolbar at the bottom of |
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| 62 | the plot to activate this option. Move the mouse pointer to the plot. It will |
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| 63 | change to a cross-hair. Then left-click and drag the pointer around to generate |
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[3fd3d5a4] | 64 | a region of interest. Release the mouse button to generate the new view. |
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[78f02c3] | 65 | |
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[3fd3d5a4] | 66 | To disable zoom mode, unselect the *Zoom* button on the toolbar. |
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[78f02c3] | 67 | |
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[c89e649] | 68 | After zooming in on a a region, the *left arrow* or *right arrow* buttons on |
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[3fd3d5a4] | 69 | the toolbar will switch between recent views. |
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[78f02c3] | 70 | |
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[35f4d43] | 71 | The axis range can also be specified manually. To do so go to the *Graph Menu* |
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| 72 | (see Invoking_the_graph_menu_ for further details), choose the *Set Graph Range* |
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| 73 | option and enter the limits in the pop box. |
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| 74 | |
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[c89e649] | 75 | *NOTE! If a wheel mouse is available scrolling the wheel will zoom in/out |
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| 76 | on the current plot (changing both axes). Alternatively, point at the numbers |
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[3fd3d5a4] | 77 | on one axis and scroll the wheel to zoom in/out on just that axis.* |
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[78f02c3] | 78 | |
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[c89e649] | 79 | To return to the original view of the data, click the the *Reset* (home) icon |
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[0cdf1af] | 80 | in the toolbar at the bottom of the plot (see Resetting_the_graph_ for further details). |
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[23a9beb] | 81 | |
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[0cdf1af] | 82 | Saving a plot image |
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| 83 | ^^^^^^^^^^^^^^^^^^^ |
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[78f02c3] | 84 | |
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[c89e649] | 85 | To save the current plot as an image file, right click on the plot to bring up |
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[0cdf1af] | 86 | the *Graph Menu* (see Invoking_the_graph_menu_) and select *Save Image*. |
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[c89e649] | 87 | Alternatively, click on the *Save* (floppy disk) icon in the toolbar at the |
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[3fd3d5a4] | 88 | bottom of the plot. |
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[c89e649] | 89 | |
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| 90 | A dialog window will open. Select a folder, enter a filename, choose an output |
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[3fd3d5a4] | 91 | image type, and click *Save*. |
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| 92 | |
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| 93 | The currently supported image types are: |
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| 94 | |
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| 95 | * EPS (encapsulated postscript) |
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| 96 | * EMF (enhanced metafile) |
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| 97 | * JPG/JPEG (joint photographics experts group) |
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| 98 | * PDF (portable documant format) |
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| 99 | * PNG (portable network graphics) |
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| 100 | * PS (postscript) |
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[78bc3bb2] | 101 | * RAW/RGBA (bitmap, stored as 935x635 pixels of depth 8) |
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[3fd3d5a4] | 102 | * SVG/SVGA (scalable vector graphics) |
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| 103 | * TIF/TIFF (tagged iamge file) |
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| 104 | |
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[0cdf1af] | 105 | Printing a plot |
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| 106 | ^^^^^^^^^^^^^^^ |
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[78f02c3] | 107 | |
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[c89e649] | 108 | To send the current plot to a printer, click on the *Print* (printer) icon in |
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[3fd3d5a4] | 109 | the toolbar at the bottom of the plot. |
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[78f02c3] | 110 | |
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[0cdf1af] | 111 | .. _Resetting_the_graph: |
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[3fd3d5a4] | 112 | |
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[0cdf1af] | 113 | Resetting the graph |
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| 114 | ^^^^^^^^^^^^^^^^^^^ |
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[78f02c3] | 115 | |
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[c89e649] | 116 | To reset the axis range of a graph to its initial values select *Reset Graph |
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[0cdf1af] | 117 | Range* on the *Graph Menu* (see Invoking_the_graph_menu_). Alternatively, use |
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[3fd3d5a4] | 118 | the *Reset* (home) icon in the toolbar at the bottom of the plot. |
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[78f02c3] | 119 | |
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[0cdf1af] | 120 | Modifying the graph |
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| 121 | ^^^^^^^^^^^^^^^^^^^ |
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[23a9beb] | 122 | |
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[35f4d43] | 123 | It is possible to make custom modifications to plots including: |
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[23a9beb] | 124 | |
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[3fd3d5a4] | 125 | * changing the plot window title |
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[35f4d43] | 126 | * changing the default legend location and toggling it on/off |
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| 127 | * changing the axis label text |
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| 128 | * changing the axis label units |
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| 129 | * changing the axis label font & font colour |
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[3fd3d5a4] | 130 | * adding/removing a text string |
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| 131 | * adding a grid overlay |
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[23a9beb] | 132 | |
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[35f4d43] | 133 | The legend and text strings can be drag and dropped around the plot |
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| 134 | |
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| 135 | These options are accessed through the *Graph Menu* (see Invoking_the_graph_menu_) |
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| 136 | and selecting *Modify Graph Appearance* (for axis labels, grid overlay and |
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| 137 | legend position) or *Add Text* to add textual annotations, selecting font, color, |
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| 138 | style and size. *Remove Text* will remove the last annotation added. To change |
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| 139 | the legend. *Window Title* allows a custom title to be entered instead of Graph |
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| 140 | x. |
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| 141 | |
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[0cdf1af] | 142 | Changing scales |
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| 143 | ^^^^^^^^^^^^^^^ |
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[78f02c3] | 144 | |
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[3fd3d5a4] | 145 | This menu option is only available with 1D data. |
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| 146 | |
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[0cdf1af] | 147 | From the *Graph Menu* (see Invoking_the_graph_menu_) select *Change Scale*. A |
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[c89e649] | 148 | dialog window will appear in which it is possible to choose different |
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[3fd3d5a4] | 149 | transformations of the x (usually Q) or y (usually I(Q)) axes, including: |
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| 150 | |
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| 151 | * x, x^2, x^4, ln(x), log10(x), log10(x^4) |
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| 152 | * y, 1/y, ln(y), y^2, y.(x^4), 1/sqrt(y), |
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| 153 | * log10(y), ln(y.x), ln(y.x^2), ln(y.x^4), log10(y.x^4) |
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[c89e649] | 154 | |
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[3fd3d5a4] | 155 | A *View* option includes short-cuts to common SAS transformations, such as: |
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| 156 | |
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| 157 | * linear |
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| 158 | * Guinier |
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| 159 | * X-sectional Guinier |
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| 160 | * Porod |
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| 161 | * Kratky |
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| 162 | |
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[c89e649] | 163 | For properly corrected and scaled data, these SAS transformations can be used |
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| 164 | to estimate, for example, Rg, rod diameter, or SANS incoherent background |
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[0cdf1af] | 165 | levels, via a linear fit (see Making_a_linear_fit_). |
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[3fd3d5a4] | 166 | |
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[0cdf1af] | 167 | Toggling scales |
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| 168 | ^^^^^^^^^^^^^^^ |
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[3fd3d5a4] | 169 | |
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| 170 | This menu option is only available with 2D data. |
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| 171 | |
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[0cdf1af] | 172 | From the *Graph Menu* (see Invoking_the_graph_menu_) select *Toggle Linear/Log |
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[c89e649] | 173 | Scale* to switch between a linear to log intensity scale. The type of scale |
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[3fd3d5a4] | 174 | selected is written alongside the colour scale. |
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| 175 | |
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[0cdf1af] | 176 | 2D color maps |
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| 177 | ^^^^^^^^^^^^^ |
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[3fd3d5a4] | 178 | |
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| 179 | This menu option is only available with 2D data. |
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| 180 | |
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[a9dc4eb] | 181 | From the *Graph Menu* (see Invoking_the_graph_menu_) select *2D Color Map* to |
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[c89e649] | 182 | choose a different color scale for the image and/or change the maximum or |
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[3fd3d5a4] | 183 | minimum limits of the scale. |
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| 184 | |
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[0cdf1af] | 185 | Getting data coordinates |
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| 186 | ^^^^^^^^^^^^^^^^^^^^^^^^ |
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[3fd3d5a4] | 187 | |
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[c89e649] | 188 | Clicking anywhere in the plot window will cause the current coordinates to be |
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[3fd3d5a4] | 189 | displayed in the status bar at the very bottom-left of the SasView window. |
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[c89e649] | 190 | |
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[3fd3d5a4] | 191 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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[23a9beb] | 192 | |
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[0cdf1af] | 193 | Dataset menu options |
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| 194 | -------------------- |
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| 195 | |
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| 196 | .. _Invoking_the_dataset_menu: |
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| 197 | |
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| 198 | Invoking the dataset menu |
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| 199 | ^^^^^^^^^^^^^^^^^^^^^^^^^ |
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| 200 | |
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| 201 | From the *Graph Menu* (see Invoking_the_graph_menu_) highlight a plotted |
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[3fd3d5a4] | 202 | dataset. |
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| 203 | |
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[0cdf1af] | 204 | Getting data info |
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| 205 | ^^^^^^^^^^^^^^^^^ |
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[3fd3d5a4] | 206 | |
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[0cdf1af] | 207 | In the *Dataset Menu* (see Invoking_the_dataset_menu_), highlight a data set |
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[c89e649] | 208 | and select *DataInfo* to bring up a data information dialog panel for that |
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[3fd3d5a4] | 209 | data set. |
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| 210 | |
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[0cdf1af] | 211 | Saving data |
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| 212 | ^^^^^^^^^^^ |
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[3fd3d5a4] | 213 | |
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[0cdf1af] | 214 | In the *Dataset Menu* (see Invoking_the_dataset_menu_), select *Save Points as |
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[c89e649] | 215 | a File* (if 1D data) or *Save as a file(DAT)* (if 2D data). A save dialog will |
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[3fd3d5a4] | 216 | appear. |
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| 217 | |
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[c89e649] | 218 | 1D data can be saved in either ASCII text (.TXT) or CanSAS/SASXML (.XML) |
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[a9dc4eb] | 219 | formats (see :ref:`Formats`). |
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[1394952] | 220 | |
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[a9dc4eb] | 221 | 2D data can only be saved in the NIST 2D format (.DAT) (see :ref:`Formats`). |
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[78f02c3] | 222 | |
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[0cdf1af] | 223 | .. _Making_a_linear_fit: |
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[78f02c3] | 224 | |
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[0cdf1af] | 225 | Making a linear fit |
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| 226 | ^^^^^^^^^^^^^^^^^^^ |
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[78f02c3] | 227 | |
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[3fd3d5a4] | 228 | Linear fit performs a simple ( y(x)=ax+b ) linear fit within the plot window. |
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| 229 | |
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[0cdf1af] | 230 | In the *Dataset Menu* (see Invoking_the_dataset_menu_), select *Linear Fit*. A |
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[c89e649] | 231 | fitting dialog will appear. Set some initial parameters and data limits and |
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| 232 | click *Fit*. The fitted parameter values are displayed and the resulting line |
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| 233 | calculated from them is added to the plot. |
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[3fd3d5a4] | 234 | |
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| 235 | This option is most useful for performing simple Guinier, XS Guinier, and |
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[c89e649] | 236 | Porod type analyses, for example, to estimate Rg, a rod diameter, or incoherent |
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[3fd3d5a4] | 237 | background level, respectively. |
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| 238 | |
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| 239 | The following figure shows an example of a Guinier analysis using this option |
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[78f02c3] | 240 | |
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| 241 | .. image:: guinier_fit.png |
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| 242 | |
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[0cdf1af] | 243 | Removing data from the plot |
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| 244 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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[3fd3d5a4] | 245 | |
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[0cdf1af] | 246 | In the *Dataset Menu* (see Invoking_the_dataset_menu_), select *Remove*. The |
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[3fd3d5a4] | 247 | selected data will be removed from the plot. |
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| 248 | |
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[35f4d43] | 249 | .. note:: |
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| 250 | The Remove data set action cannot be undone. |
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[78f02c3] | 251 | |
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[0cdf1af] | 252 | Show-Hide error bars |
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| 253 | ^^^^^^^^^^^^^^^^^^^^ |
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[3fd3d5a4] | 254 | |
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[0cdf1af] | 255 | In the *Dataset Menu* (see Invoking_the_dataset_menu_), select *Show Error Bar* |
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[c89e649] | 256 | or *Hide Error Bar* to switch between showing/hiding the errors associated |
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| 257 | with the chosen dataset. |
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[3fd3d5a4] | 258 | |
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[0cdf1af] | 259 | Modify plot properties |
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| 260 | ^^^^^^^^^^^^^^^^^^^^^^ |
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[3fd3d5a4] | 261 | |
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[0cdf1af] | 262 | In the *Dataset Menu* (see Invoking_the_dataset_menu_), select *Modify Plot |
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[c89e649] | 263 | Property* to change the size, color, or shape of the displayed marker for the |
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[35f4d43] | 264 | chosen dataset, or to change the dataset label that appears in the plot legend |
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| 265 | box. |
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[78f02c3] | 266 | |
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| 267 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 268 | |
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[0cdf1af] | 269 | 2D data averaging |
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[78f02c3] | 270 | ----------------- |
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| 271 | |
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[3fd3d5a4] | 272 | Purpose |
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[0cdf1af] | 273 | ^^^^^^^ |
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[3fd3d5a4] | 274 | |
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| 275 | This feature is only available with 2D data. |
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[23a9beb] | 276 | |
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[c89e649] | 277 | 2D data averaging allows you to perform different types of averages on your |
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| 278 | data. The region to be averaged is displayed in the plot window and its limits |
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[3fd3d5a4] | 279 | can be modified by dragging the boundaries around. |
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[78f02c3] | 280 | |
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[0cdf1af] | 281 | How to average |
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| 282 | ^^^^^^^^^^^^^^ |
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[78f02c3] | 283 | |
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[0cdf1af] | 284 | In the *Dataset Menu* (see Invoking_the_dataset_menu_), select one of the |
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[3fd3d5a4] | 285 | following averages |
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[78f02c3] | 286 | |
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[3fd3d5a4] | 287 | * Perform Circular Average |
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| 288 | * Sector [Q view] |
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| 289 | * Annulus [Phi view] |
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| 290 | * Box sum |
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| 291 | * Box averaging in Qx |
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| 292 | * Box averaging on Qy |
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[78f02c3] | 293 | |
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[c89e649] | 294 | A 'slicer' will appear (except for *Perform Circular Average*) in the plot that |
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| 295 | you can drag by clicking on a slicer's handle. When the handle is highlighted |
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[3fd3d5a4] | 296 | in red, it means that the slicer can move/change size. |
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[78f02c3] | 297 | |
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[c89e649] | 298 | *NOTE! The slicer size will reset if you try to select a region greater than |
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[3fd3d5a4] | 299 | the size of the data.* |
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| 300 | |
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[c89e649] | 301 | Alternatively, once a 'slicer' is active you can also select the region to |
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| 302 | average by bringing back the *Dataset Menu* and selecting *Edit Slicer |
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| 303 | Parameters*. A dialog window will appear in which you can enter values to |
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[3fd3d5a4] | 304 | define a region or select the number of points to plot (*nbins*). |
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| 305 | |
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[c89e649] | 306 | A separate plot window will also have appeared, displaying the requested |
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[3fd3d5a4] | 307 | average. |
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| 308 | |
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[35f4d43] | 309 | .. note:: |
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| 310 | The displayed average only updates when input focus is moved back to |
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| 311 | that window; ie, when the mouse pointer is moved onto that plot. |
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[3fd3d5a4] | 312 | |
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[c89e649] | 313 | Selecting *Box Sum* automatically brings up the 'Slicer Parameters' dialog in |
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[3fd3d5a4] | 314 | order to display the average numerically, rather than graphically. |
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| 315 | |
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| 316 | To remove a 'slicer', bring back the *Dataset menu* and select *Clear Slicer*. |
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[78f02c3] | 317 | |
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[0cdf1af] | 318 | Unmasked circular average |
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| 319 | ^^^^^^^^^^^^^^^^^^^^^^^^^ |
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[23a9beb] | 320 | |
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[c89e649] | 321 | This operation will perform an average in constant Q-rings around the (x,y) |
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[3fd3d5a4] | 322 | pixel location of the beam center. |
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[78f02c3] | 323 | |
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[0cdf1af] | 324 | Masked circular average |
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| 325 | ^^^^^^^^^^^^^^^^^^^^^^^ |
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[78f02c3] | 326 | |
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[c89e649] | 327 | This operation is the same as 'Unmasked Circular Average' except that any |
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[3fd3d5a4] | 328 | masked region is excluded. |
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[78f02c3] | 329 | |
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[0cdf1af] | 330 | Sector average [Q View] |
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| 331 | ^^^^^^^^^^^^^^^^^^^^^^^ |
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[23a9beb] | 332 | |
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[3fd3d5a4] | 333 | This operation averages in constant Q-arcs. |
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| 334 | |
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[c89e649] | 335 | The width of the sector is specified in degrees (+/- |delta|\|phi|\) each side |
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[3fd3d5a4] | 336 | of the central angle (|phi|\). |
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[78f02c3] | 337 | |
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[0cdf1af] | 338 | Annular average [|phi| View] |
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| 339 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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[3fd3d5a4] | 340 | |
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[c89e649] | 341 | This operation performs an average between two Q-values centered on (0,0), |
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[3fd3d5a4] | 342 | and averaged over a specified number of pixels. |
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[78f02c3] | 343 | |
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[c89e649] | 344 | The data is returned as a function of angle (|phi|\) in degrees with zero |
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[3fd3d5a4] | 345 | degrees at the 3 O'clock position. |
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[78f02c3] | 346 | |
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[0cdf1af] | 347 | Box sum |
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| 348 | ^^^^^^^ |
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[78f02c3] | 349 | |
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[3fd3d5a4] | 350 | This operation performs a sum of counts in a 2D region of interest. |
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| 351 | |
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[c89e649] | 352 | When editing the slicer parameters, the user can enter the length and the width |
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[3fd3d5a4] | 353 | the rectangular slicer and the coordinates of the center of the rectangle. |
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[78f02c3] | 354 | |
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[23a9beb] | 355 | Box Averaging in Qx |
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[0cdf1af] | 356 | ^^^^^^^^^^^^^^^^^^^ |
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[78f02c3] | 357 | |
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[3fd3d5a4] | 358 | This operation computes an average I(Qx) for the region of interest. |
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| 359 | |
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[c89e649] | 360 | When editing the slicer parameters, the user can control the length and the |
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| 361 | width the rectangular slicer. The averaged output is calculated from constant |
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| 362 | bins with rectangular shape. The resultant Q values are nominal values, that |
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[3fd3d5a4] | 363 | is, the central value of each bin on the x-axis. |
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[78f02c3] | 364 | |
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[23a9beb] | 365 | Box Averaging in Qy |
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[0cdf1af] | 366 | ^^^^^^^^^^^^^^^^^^^ |
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[78f02c3] | 367 | |
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[3fd3d5a4] | 368 | This operation computes an average I(Qy) for the region of interest. |
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[23a9beb] | 369 | |
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[c89e649] | 370 | When editing the slicer parameters, the user can control the length and the |
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| 371 | width the rectangular slicer. The averaged output is calculated from constant |
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| 372 | bins with rectangular shape. The resultant Q values are nominal values, that |
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[3fd3d5a4] | 373 | is, the central value of each bin on the x-axis. |
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[78f02c3] | 374 | |
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[3fd3d5a4] | 375 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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[78f02c3] | 376 | |
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[35f4d43] | 377 | .. note:: This help document was last modified by Paul Butler, 05 September, 2016 |
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