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Update "cookbook" to "reference" for links to the GMT 6.5 documentation (#2990)
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examples/gallery/embellishments/colorbar.py

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The :meth:`pygmt.Figure.colorbar` method creates a color scalebar.
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The colormap is set via the ``cmap`` parameter. A full list of available
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color palette tables can be found at :gmt-docs:`cookbook/cpts.html`.
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color palette tables can be found at :gmt-docs:`reference/cpts.html`.
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Use the ``frame`` parameter to add labels to the **x** and **y** axes
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of the colorbar by appending **+l** followed by the desired text. To Add
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and adjust the annotations (**a**) and ticks (**f**) append the letter

examples/gallery/embellishments/colorbars_multiple.py

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This gallery example shows how to create multiple colormaps for different
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subplots. To better understand how GMT modern mode maintains several levels of
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colormaps, please refer to
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:gmt-docs:`cookbook/features.html#gmt-modern-mode-hierarchical-levels` for
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:gmt-docs:`reference/features.html#gmt-modern-mode-hierarchical-levels` for
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details.
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"""
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examples/gallery/lines/linestyles.py

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requested with ``"dashed"`` or ``"-"``. Also combinations of dots and dashes,
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like ``".-"`` for a dot-dashed line, are allowed.
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For more advanced *pen* attributes, see the GMT cookbook
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:gmt-docs:`cookbook/features.html#wpen-attrib`.
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For more advanced *pen* attributes, see the GMT Technical Reference
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:gmt-docs:`reference/features.html#wpen-attrib`.
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"""
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examples/gallery/symbols/custom_symbols.py

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the ``style`` parameter. In total 41 custom symbols are already included of
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which the following plot shows five exemplary ones. The symbols are shown
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underneath their corresponding names. For the remaining symbols see the GMT
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cookbook :gmt-docs:`cookbook/custom-symbols.html`.
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Technical Reference :gmt-docs:`reference/custom-symbols.html`.
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"""
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# %%

examples/gallery/symbols/patterns.py

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*pattern* can either be a number in the range 1-90 or the name of a
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1-, 8-, or 24-bit image raster file. The former will result in one of the 90
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predefined 64 x 64 bit-patterns provided by GMT; an overview can by found at
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:gmt-docs:`cookbook/predefined-patterns.html`.
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:gmt-docs:`reference/predefined-patterns.html`.
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The latter allows the user to create customized, repeating images using image
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raster files.
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By specifying upper case **P** instead of **p** the image will be

examples/gallery/symbols/text_symbols.py

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@@ -15,9 +15,9 @@
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as **+j**\ *justify* to change the justification [Default is CM]. The fill
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color of the text symbols can be set with the ``fill`` parameter, and the
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outline width can be customized with the ``pen`` parameter.
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For all supported octal codes and fonts see the GMT cookbook
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:gmt-docs:`cookbook/octal-codes.html` and
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:gmt-docs:`cookbook/postscript-fonts.html`.
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For all supported octal codes and fonts see the GMT Technical Reference
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:gmt-docs:`reference/octal-codes.html` and
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:gmt-docs:`reference/postscript-fonts.html`.
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"""
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# %%

examples/get_started/02_contour_map.py

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# the Earth relief. The :meth:`pygmt.Figure.grdimage` method uses the input
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# grid to relate the Earth relief values to a specific color within the CPT.
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# In this case, the CPT "oleron" is used; a full list of CPTs can be found
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# at :gmt-docs:`cookbook/cpts.html`.
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# at :gmt-docs:`reference/cpts.html`.
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fig = pygmt.Figure()
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fig.grdimage(grid=grid, frame="a", projection="M10c", cmap="oleron")

examples/projections/nongeo/cartesian_linear.py

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@@ -12,11 +12,11 @@
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floating point data. To plot geographical data in a linear
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projection, see the upstream GMT documentation
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:gmt-docs:`Geographic coordinates
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<cookbook/coordinate-transformations.html#geographic-coordinates>`.
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<reference/coordinate-transformations.html#geographic-coordinates>`.
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To make the linear plot using calendar date/time as input
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coordinates, see the GMT documentation
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:gmt-docs:`Calendar time coordinates
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<cookbook/coordinate-transformations.html#calendar-time-coordinates>`.
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<reference/coordinate-transformations.html#calendar-time-coordinates>`.
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"""
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# %%

examples/tutorials/advanced/earth_relief.py

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# :meth:`pygmt.Figure.grdimage` can take the optional parameter ``projection``
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# for the map. In the example below, ``projection`` is set to ``"R12c"`` for
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# a 12-centimeters-wide figure with a Winkel Tripel projection. For a list
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# of available projections, see :gmt-docs:`cookbook/map-projections.html`.
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# of available projections, see :gmt-docs:`reference/map-projections.html`.
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fig = pygmt.Figure()
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fig.grdimage(grid=grid, projection="R12c")
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#
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# :meth:`pygmt.Figure.grdimage` takes the ``cmap`` parameter to set the CPT of
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# the figure. Examples of common CPTs for Earth relief are shown below.
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# A full list of CPTs can be found at :gmt-docs:`cookbook/cpts.html`.
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# A full list of CPTs can be found at :gmt-docs:`reference/cpts.html`.
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# %%
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# Using the *geo* CPT:

examples/tutorials/basics/text.py

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# the ``font`` parameter.
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#
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# A list of all recognized fonts can be found at
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# :gmt-docs:`PostScript Fonts Used by GMT <cookbook/postscript-fonts.html>`,
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# :gmt-docs:`PostScript Fonts Used by GMT <reference/postscript-fonts.html>`,
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# including details of how to use non-default fonts.
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fig = pygmt.Figure()
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#
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# For crafting more advanced styles, including using special symbols and
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# other character sets, be sure to check out the GMT documentation
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# at :gmt-docs:`text.html` and also the cookbook at
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# :gmt-docs:`cookbook/features.html#placement-of-text`. Good luck!
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# at :gmt-docs:`text.html` and also the GMT Technical Reference at
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# :gmt-docs:`reference/features.html#placement-of-text`. Good luck!
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# sphinx_gallery_thumbnail_number = 3

pygmt/helpers/decorators.py

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``registration``, and the domain. The resulting increment value
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depends on whether you have selected a gridline-registered or
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pixel-registered grid; see :gmt-docs:`GMT File Formats
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<cookbook/file-formats.html#gmt-file-formats>` for details.
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<reference/file-formats.html#gmt-file-formats>` for details.
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**Note**: If ``region=grdfile`` is used then the grid spacing and
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the registration have already been initialized; use ``spacing`` and

pygmt/src/grd2cpt.py

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@@ -40,7 +40,7 @@ def grd2cpt(grid, **kwargs):
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figure, subplot, panel, or inset depending on which level
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:func:`pygmt.grd2cpt` is called (for details on how GMT modern mode
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maintains different levels of colormaps please see
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:gmt-docs:`cookbook/features.html#gmt-modern-mode-hierarchical-levels`).
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:gmt-docs:`reference/features.html#gmt-modern-mode-hierarchical-levels`).
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You can use ``output`` to save the CPT to a file. The CPT is based on an
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existing dynamic master CPT of your choice, and the mapping from data value
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to colors is through the data's cumulative distribution function (CDF), so
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cmap : str
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Select the master color palette table (CPT) to use in the
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interpolation. Full list of built-in color palette tables can be found
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at :gmt-docs:`cookbook/cpts.html#built-in-color-palette-tables-cpt`.
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at :gmt-docs:`reference/cpts.html#built-in-color-palette-tables-cpt`.
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background : bool or str
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Select the back- and foreground colors to match the colors for lowest
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and highest *z*-values in the output CPT [Default (``background=True``
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Truncate the incoming CPT so that the lowest and highest z-levels are
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to *zlow* and *zhigh*. If one of these equal NaN then we leave that
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end of the CPT alone. The truncation takes place before any resampling.
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See also :gmt-docs:`cookbook/features.html#manipulating-cpts`.
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See also :gmt-docs:`reference/features.html#manipulating-cpts`.
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output : str
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Optional. The file name with extension .cpt to store the generated CPT
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file. If not given or ``False`` [Default], saves the CPT as the current
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of z-values in the color table. Note that this change of z-direction
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happens before ``truncate`` and ``series`` values are used so the
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latter must be compatible with the changed z-range. See also
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:gmt-docs:`cookbook/features.html#manipulating-cpts`.
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:gmt-docs:`reference/features.html#manipulating-cpts`.
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overrule_bg : str
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Overrule background, foreground, and NaN colors specified in the master
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CPT with the values of the parameters :gmt-term:`COLOR_BACKGROUND`,

pygmt/src/makecpt.py

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@@ -34,7 +34,7 @@ def makecpt(**kwargs):
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figure, subplot, panel, or inset depending on which level
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:func:`pygmt.makecpt` is called (for details on how GMT modern mode
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maintains different levels of colormaps please see
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:gmt-docs:`cookbook/features.html#gmt-modern-mode-hierarchical-levels`).
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:gmt-docs:`reference/features.html#gmt-modern-mode-hierarchical-levels`).
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You can use ``output`` to save the CPT to a file.
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You define an equidistant
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set of contour intervals or pass your own z-table or list, and create a new
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cmap : str
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Select the master color palette table (CPT) to use in the
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interpolation. Full list of built-in color palette tables can be found
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at :gmt-docs:`cookbook/cpts.html#built-in-color-palette-tables-cpt`.
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at :gmt-docs:`reference/cpts.html#built-in-color-palette-tables-cpt`.
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background : bool or str
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Select the back- and foreground colors to match the colors for lowest
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and highest *z*-values in the output CPT [Default (``background=True``
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Truncate the incoming CPT so that the lowest and highest z-levels are
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to *zlow* and *zhigh*. If one of these equal NaN then we leave that
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end of the CPT alone. The truncation takes place before any resampling.
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See also :gmt-docs:`cookbook/features.html#manipulating-cpts`.
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See also :gmt-docs:`reference/features.html#manipulating-cpts`.
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output : str
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Optional. The file name with extension .cpt to store the generated CPT
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file. If not given or ``False`` [Default], saves the CPT as the current
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of z-values in the color table. Note that this change of z-direction
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happens before ``truncate`` and ``series`` values are used so the
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latter must be compatible with the changed z-range. See also
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:gmt-docs:`cookbook/features.html#manipulating-cpts`.
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:gmt-docs:`reference/features.html#manipulating-cpts`.
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overrule_bg : str
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Overrule background, foreground, and NaN colors specified in the master
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CPT with the values of the parameters :gmt-term:`COLOR_BACKGROUND`,

pygmt/src/select.py

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*linefile*\ **+d**\ *dist*\ [**+p**].
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Pass all records whose locations are within *dist* of any of the line
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segments in the ASCII :gmt-docs:`multiple-segment file
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<cookbook/file-formats.html#optional-segment-header-records>`
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<reference/file-formats.html#optional-segment-header-records>`
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*linefile*. If *dist* is zero, we will scan each sub-header in
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*linefile* for an embedded **-D**\ *dist* setting that sets each
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line's individual distance value. Distances are Cartesian and in
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*polygonfile*.
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Pass all records whose locations are within one of the closed
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polygons in the ASCII :gmt-docs:`multiple-segment file
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<cookbook/file-formats.html#optional-segment-header-records>`
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<reference/file-formats.html#optional-segment-header-records>`
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*polygonfile*. For spherical polygons (lon, lat), make sure no
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consecutive points are separated by 180 degrees or more in longitude.
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resolution : str

pygmt/src/shift_origin.py

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move the origin relative to its current location.
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Detailed usage at
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:gmt-docs:`cookbook/options.html#plot-positioning-and-layout-the-x-y-options`
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:gmt-docs:`reference/options.html#plot-positioning-and-layout-the-x-y-options`
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Parameters
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----------

pygmt/src/text.py

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The text strings passed via the ``text`` parameter can contain ASCII
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characters and non-ASCII characters defined in the ISOLatin1+ encoding
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(i.e., IEC_8859-1), and the Symbol and ZapfDingbats character sets.
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See :gmt-docs:`cookbook/octal-codes.html` for the full list of supported
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See :gmt-docs:`reference/octal-codes.html` for the full list of supported
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non-ASCII characters.
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Full option list at :gmt-docs:`text.html`

pygmt/src/velo.py

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will be transparent. **Note**: Using ``cmap`` and ``zvalue="+e"``
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will update the uncertainty fill color based on the selected measure
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in ``zvalue`` [Default is magnitude error]. More details at
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:gmt-docs:`cookbook/features.html#gfill-attrib`.
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:gmt-docs:`reference/features.html#gfill-attrib`.
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fill : str
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Set color or pattern for filling symbols [Default is no fill].
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**Note**: Using ``cmap`` (and optionally ``zvalue``) will update the
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symbol fill color based on the selected measure in ``zvalue``
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[Default is magnitude]. More details at
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:gmt-docs:`cookbook/features.html#gfill-attrib`.
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:gmt-docs:`reference/features.html#gfill-attrib`.
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scale : float or bool
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[*scale*].
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Scale symbol sizes and pen widths on a per-record basis using the

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