Figure.plot: Add the "symbol" parameter to support plotting data points with varying symbols #1117

core-man · 2021-03-24T10:05:56Z

Description of proposed changes

We can only plot different symbols via the data parameter in the plot method. This PR allows passing an array as symbols via the new symbol parameter. Meanwhile, we have to set style="0.2c", or set 1d-array sizes using style=True and sizes=sizes. Therefore, we now have four ways to set symbols and sizes, e.g.,

constant symbol and size: style="c0.5c"
constant symbol and different sizes: style="cc" + sizes=sizes
different symbols and constant size: style="0.5c" + symbol=symbol
different symbols and sizes: style=True + sizes=sizes + symbol=symbol

Two tests are added:

test_plot_fail_1d_array_using_data: Raise GMTInvalidInput if symbol is used with data parameter. Actually, I rename test_plot_fail_color_size_intensity to be this test function since we should raise such an error for 1d-array color, size, intensity and symbol parameters if they are used with the data parameter. (originally posted in The transparency parameter of plot/plot3d methods can be 1d array #1098 (comment))
test_plot_symbols: test 1d-array symbol (all are "c") with style="0.5c".

Related #1076

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Run make format and make check to make sure the code follows the style guide.
Add tests for new features or tests that would have caught the bug that you're fixing.
Add new public functions/methods/classes to doc/api/index.rst.
Write detailed docstrings for all functions/methods.
If adding new functionality, add an example to docstrings or tutorials.

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core-man · 2021-04-13T07:41:41Z

1c48b39: If the symbol parameter is used, we will automatically set style to be True if it is not set by the user.

Therefore, now we can plot different symbols and sizes like this: symbol=symbol, sizes=sizes. Note that the sizes parameter only accepts int and float (e.g., 1, 0.5) and does not accept string (e.g., 0.5c), so the unit can have to be set by the PROJ_LENGTH_UNIT using the config method if we don't want to use the default cm. (Also posted in #1076 (comment))

core-man · 2021-04-13T07:58:12Z

pygmt/src/plot.py

@@ -206,15 +210,18 @@ def plot(self, x=None, y=None, data=None, sizes=None, direction=None, **kwargs):
    kind = data_kind(data, x, y)

    extra_arrays = []
-    if "S" in kwargs and kwargs["S"][0] in "vV" and direction is not None:
-        extra_arrays.extend(direction)
+    if "S" in kwargs and isinstance(kwargs["S"], str):


I added isinstance(kwargs["S"], str) in case that the style parameter is True, False, None, int, or float.

seisman · 2021-04-14T06:16:04Z

@core-man I think the co-existence of style and symbol parameters will lead to more confusion. We should discuss what we would like to use about the plot() and plot3d() functions.

core-man · 2021-04-14T06:34:23Z

@core-man I think the co-existence of style and symbol parameters will lead to more confusion. We should discuss what we would like to use about the plot() and plot3d() functions.

Actually, I'd like to fully avoid using the style parameter, and use a more Pythonic way, e.g., sizes, symbol, direction. But now I don't know if how much work will have to be done before the style parameter is avoided since plot/plot3d still have many unimplemented and complicated features/options.

We could remove the style parameter now and directly use symbol instead (see your suggestion in #1072 (comment)? What do you think? This is also related to Backwards compatibility and deprecation policy (#1120).

seisman · 2021-05-07T04:51:59Z

I believe we need more discussions about what we would like to see about the plot() function.
I'll convert this PR to draft.

weiji14 · 2021-05-18T21:45:36Z

pygmt/tests/test_plot.py

+        projection="X4c",
+        color="blue",
+        sizes=np.full(len(data[:, 0]), 0.5),
+        symbol=np.full(len(data[:, 0]), "c"),


At the moment, this test is checking that plotting all symbols as circles (c) work. A better test would be to test a mix of symbols such as circles (c), triangles (t), squares (s), etc (like your example in #1076 (comment)).

seisman · 2024-10-24T02:34:14Z

The CI failures are caused by the codecov step. It's likely that codecov can't get the OIDC token for forks.

Edit: Likely related to upstream issue at codecov/codecov-action#1594.

weiji14 · 2024-10-28T23:44:44Z

pygmt/src/plot.py

@@ -87,6 +89,8 @@ def plot(self, data=None, x=None, y=None, size=None, direction=None, **kwargs):
    size : 1-D array
        The size of the data points in units specified using ``style``.
        Only valid if using ``x``/``y``.
+    symbol : 1-D array


Symbol can also be a single string right? E.g. symbol="t" for triangle. I think we need to add another unit test for the "constant-symbol and different sizes" case as mentioned at #1117 (comment)

Suggested change

symbol : 1-D array

symbol : str or 1-D array

No, similar to the size parameter, symbol must be a 1-D array.

Hmm ok, I just tried with symbol="t" and it plotted a straight line:

import pygmt fig = pygmt.Figure() fig.plot( x=[1, 2, 3, 4], y=[1, 1, 1, 1], region=[0, 5, 0, 2], projection="X2c", fill="blue", size=[0.1, 0.2, 0.3, 0.4], symbol="t", frame="af", ) fig.show()

So yes, it does have to be a 1-D array.

Hm. Maybe writing "list of str" is clearer here?

1-D array is used here to match the types of other parameters. We probably can change it to Sequence[str] when we add typing hints.

weiji14

Cheers @seisman for getting this over the line, I've tested this locally and it looks good. The changes look simple but there were a lot of refactorings in the PyGMT codebase to get this to work! Also thanks again @core-man for starting this effort 3 years ago, we'll finally be able to release this in PyGMT v0.14.0 🎉

P.S. We should also port these changes to plot3d later.

yvonnefroehlich · 2024-10-29T09:05:42Z

pygmt/src/plot.py

@@ -87,6 +89,8 @@ def plot(self, data=None, x=None, y=None, size=None, direction=None, **kwargs):
    size : 1-D array
        The size of the data points in units specified using ``style``.


Hm. But if size is used with symbol the unit for size is given by the GMT / PyGMT defaults, correct?
Using style for specifing the unit in this case would be super confusing, e.g.:

... size=[0.5, 0.8, 0.9], symbol=["s", "c", "d"], style="c", # now centimeters, not circle ...

Actually, it produces three circles with different sizes.

I want to emphasize that the "style" parameter was introduced in very early PyGMT versions. The docstrings are mostly copied from the upstream GMT documentation without further polishes, so they may make no sense for PyGMT.

yvonnefroehlich · 2024-10-29T09:15:18Z

pygmt/tests/test_plot.py

+        projection="X4c",
+        fill="blue",
+        size=[0.1, 0.2, 0.3, 0.4],
+        symbol=["c", "t", "i", "s"],


Do size and symbol need to have to same length? Or is something like:

size=[0.1, 0.2, 0.3, 0.4], # different sizes but same symbol symbol=["c"],

or

size=[0.4], # same size but different symbols symbol=["c", "t", "i", "s"],

allowed?

Currently, they must be the same size.

Now I figured it out: One has to use the size or symbol parameter together with the style parameter 🙂.

yvonnefroehlich

I feel this introduction part in the docs for Figure.plot needs some adjustment to account for this newly added symbol parameter and to avoid confusions:

pygmt/pygmt/src/plot.py

Lines 65 to 70 in ce89ccb

    
               If a symbol is selected and no symbol size given, then plot will 
        
               interpret the third column of the input data as symbol size. Symbols 
        
               whose size is <= 0 are skipped. If no symbols are specified then the 
        
               symbol code (see ``style`` below) must be present as last column in the 
        
               input. If ``style`` is not used, a line connecting the data points will 
        
               be drawn instead. To explicitly close polygons, use ``close``. Select a

yvonnefroehlich

This is definitely a nice enhancement!

So far, I only made some comments (will be back to work at the end of this week).

I feel there can be some confusions regarding the style, symbol, and size parameters. Maybe we should also extend or add a gallery example for this new parameter?

seisman · 2024-10-29T15:27:41Z

I feel this introduction part in the docs for Figure.plot needs some adjustment to account for this newly added symbol parameter and to avoid confusions:

pygmt/pygmt/src/plot.py

Lines 65 to 70 in ce89ccb

If a symbol is selected and no symbol size given, then plot will

interpret the third column of the input data as symbol size. Symbols

whose size is <= 0 are skipped. If no symbols are specified then the

symbol code (see ``style`` below) must be present as last column in the

input. If ``style`` is not used, a line connecting the data points will

be drawn instead. To explicitly close polygons, use ``close``. Select a

Currently, docstrings of most PyGMT methods/functions are copied literally from the upstream GMT documentation and may make no sense to PyGMT. I think we need to polish most docstrings carefully.

I feel there can be some confusions regarding the style, symbol, and size parameters. Maybe we should also extend or add a gallery example for this new parameter?

Yes, definitely.

core-man added 3 commits March 24, 2021 17:51

Add test_plot_symbols.png into DVC

41a9e6a

Allow passing an array as symbols for plot

ebeabea

Add tests for 1d-array symbols for plot

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core-man marked this pull request as draft March 24, 2021 10:06

Merge branch 'master' into plot-1d-array-symbol

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core-man self-assigned this Mar 24, 2021

seisman mentioned this pull request Mar 25, 2021

plot and plot3d: Allow passing an array as symbol #1076

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Merge branch 'master' into plot-1d-array-symbol

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core-man added 2 commits April 13, 2021 15:24

Automactically set style to True if symbol is used

1c48b39

Update test_plot_symbols.png

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Update test_plot_symbols

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core-man commented Apr 13, 2021

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core-man mentioned this pull request Apr 13, 2021

Wrap histogram #1072

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Wrap wiggle #1145

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seisman marked this pull request as draft May 7, 2021 04:52

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weiji14 added the enhancement Improving an existing feature label May 18, 2021

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seisman added 9 commits September 26, 2024 21:45

Merge branch 'main' into plot-1d-array-symbol

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Fix comment in tests

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Add a new baseline image

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seisman marked this pull request as ready for review October 23, 2024 16:40

seisman changed the title ~~Allow passing an array as symbols for plot~~ Figure.plot: Add the "symbol" parameter to support plotting data points with varying symbols Oct 23, 2024

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Figure.plot3d: Add the "symbol" parameter to support plotting data points with varying symbols #3559

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Extend / Add gallery example to explain "symbol" parameter of "Figure.plot" #3595

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Figure.plot: Add the "symbol" parameter to support plotting data points with varying symbols #1117

Figure.plot: Add the "symbol" parameter to support plotting data points with varying symbols #1117

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seisman commented Oct 29, 2024

		@@ -87,6 +89,8 @@ def plot(self, data=None, x=None, y=None, size=None, direction=None, **kwargs):
		size : 1-D array
		The size of the data points in units specified using ``style``.

	If a symbol is selected and no symbol size given, then plot will
	interpret the third column of the input data as symbol size. Symbols
	whose size is <= 0 are skipped. If no symbols are specified then the
	symbol code (see ``style`` below) must be present as last column in the
	input. If ``style`` is not used, a line connecting the data points will
	be drawn instead. To explicitly close polygons, use ``close``. Select a

Figure.plot: Add the "symbol" parameter to support plotting data points with varying symbols #1117

Figure.plot: Add the "symbol" parameter to support plotting data points with varying symbols #1117

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