# Not able to draw closed polygons using pygmt

**URL:** <https://forum.generic-mapping-tools.org/t/not-able-to-draw-closed-polygons-using-pygmt/3663>\
**Category:** PyGMT Q&A\
**Created:** [February 7, 2023, 10:05am UTC](https://forum.generic-mapping-tools.org/t/not-able-to-draw-closed-polygons-using-pygmt/3663 "2023-02-07T10:05:24Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![gilja11](https://avatars.discourse-cdn.com/v4/letter/g/9fc348/32.png) [@gilja11](https://forum.generic-mapping-tools.org/u/gilja11)\
**Post date:** [February 7, 2023, 10:05am UTC](https://forum.generic-mapping-tools.org/t/not-able-to-draw-closed-polygons-using-pygmt/3663/1 "2023-02-07T10:05:24Z")

</div>

Hi all,

I am a complete noob regarding pygmt and just started. I would really really use your help. I am trying to understand how to do some basic operations with pygmt.

I am working on my code and am following tutorial on [1]. The main idea is that I have shapefile that I load in the GeoPandas df. Naturally, I have “geometries” column which stores objects such as Polygon and MultyPolygon. I would like to draw these geometries on my basemap, but it is not working. To be specific, when I do

```python
fig.plot(data=world, pen="1p,black", close=True, color="+z", cmap=True, aspatial="Z=pop_est")

```

I get error `"plot [ERROR]: OGR parsing incomplete (is file missing OGR statements?) - abort"`

Now, in YT video the author of the tutorial [1] didn’t have any problems, but when you look at [1] you can see also there the same error.  
The important snipped of my code is the next one:

```python
fig = pygmt.Figure()
fig.basemap(region=region, projection="M15c", frame=True)
fig.coast(land="black", water="skyblue", borders="1/0.1p,white")

cmap_bounds = pygmt.info(data=shapefile2['Density'], per_column=True)
pygmt.makecpt(cmap="bilbao", series=cmap_bounds)
fig.plot(data = shapefile2, pen="1p,white", close=True, color="+z", aspatial="Z=Density", cmap=True)
fig.show()

```

If you could help I would be really grateful. Thanks in advance 🙂

[1] [https://www.generic-mapping-tools.org/egu22pygmt/ecosystem.html](https://www.generic-mapping-tools.org/egu22pygmt/ecosystem.html)

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<div class="post-metadata">

**Author:** ![weiji14](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/weiji14/32/33_2.png) [@weiji14](https://forum.generic-mapping-tools.org/u/weiji14)\
**Post date:** [March 8, 2023, 3:01am UTC](https://forum.generic-mapping-tools.org/t/not-able-to-draw-closed-polygons-using-pygmt/3663/2 "2023-03-08T03:01:00Z")

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Hmm, I just noticed that the world map isn’t showing up on the Jupyter Book at [Integration with the scientific Python ecosystem 🐍 — Crafting beautiful maps with PyGMT](https://www.generic-mapping-tools.org/egu22pygmt/ecosystem.html#plotting-geospatial-vector-data-with-geopandas-and-pygmt)

 ![image](https://canada1.discourse-cdn.com/flex047/uploads/gmt/original/2X/c/c971b6a253ec39a3744714bdec95ab615ded13ef.png)

But it was showing up ok when the recording was made [https://youtu.be/72war16Mvxs?t=409](https://youtu.be/72war16Mvxs?t=409) around May 2022. It might be that some updated version of `geopandas` or some other library has broken this, let us check first.

Edit: Ah yes, I see that the figure has changed at [deploy: a4e75825c399a35d8327042c3151d7c0f1a54f91 · GenericMappingTools/egu22pygmt@6b59921 · GitHub](https://github.com/GenericMappingTools/egu22pygmt/commit/6b599217fd8fa40eca1346442ddf424fa1e27561#diff-585b8a41ba966334fc39c7d7e6d48e7158bb72e3e0c784feb143e540628afae0). This was how it should have looked like:

 ![](https://canada1.discourse-cdn.com/flex047/uploads/gmt/original/2X/3/3203067211bf65f3708b2588b26d7af3716eb988.png)

Wondering if it’s because geopandas updated their naturalearth\_lowres dataset to v5.0.1 at [Update naturalearth\_lowres dataset to v5.0.1 by rraymondgh · Pull Request #2418 · geopandas/geopandas · GitHub](https://github.com/geopandas/geopandas/pull/2418) causing some changes to the original dataset we used.

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<div class="post-metadata">

**Author:** ![weiji14](https://yyz1.discourse-cdn.com/flex047/user_avatar/forum.generic-mapping-tools.org/weiji14/32/33_2.png) [@weiji14](https://forum.generic-mapping-tools.org/u/weiji14)\
**Post date:** [March 8, 2023, 4:03am UTC](https://forum.generic-mapping-tools.org/t/not-able-to-draw-closed-polygons-using-pygmt/3663/3 "2023-03-08T04:03:01Z")

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Ok, it seems like PyGMT/GMT is unable to handle a mix of Polygon/MultiPolygon vector types in a single OGR file, which is the case for the updated naturalearth\_lowres v5.0.1 dataset. I’ve submitted a bug report at [Unable to handle GeoDataFrame with mixed Polygons/Multipolygons · Issue #2405 · GenericMappingTools/pygmt · GitHub](https://github.com/GenericMappingTools/pygmt/issues/2405) to see if this can be fixed.

As a temporary workaround, you can use [geopandas.GeoDataFrame.explode — GeoPandas 0.12.2+0.gefcb367.dirty documentation](https://geopandas.org/en/v0.12.2/docs/reference/api/geopandas.GeoDataFrame.explode.html) to convert all the MultiPolygons to Polygons (though this would need to be done carefully). Example code:

```python
import pygmt
import geopandas as gpd

world = gpd.read_file(gpd.datasets.get_path('naturalearth_lowres'))
world.head()

# Calculate the populations in millions per capita
world = world[(world.pop_est>0) & (world.name!="Antarctica")]
world['pop_est'] = world.pop_est * 1e-6

# Find the range of data values for creating a colormap
cmap_bounds = pygmt.info(data=world['pop_est'], per_column=True)
cmap_bounds

# Create an instance of the pygmt.Figure class
fig = pygmt.Figure()
# Create a colormap for the figure
pygmt.makecpt(cmap="bilbao", series=cmap_bounds)
# Create a basemap
fig.basemap(region="d", projection="H15c", frame=True)
# Plot the GeoDataFrame
# - Use `close=True` to specify that the polygons should be forced closed
# - Plot the polygon outlines with a 1 point, black pen
# - Set that the color should be based on the `pop_est` using the `color, `cmap`, and `aspatial` parameters
fig.plot(data=world.explode(ignore_index=True), pen="1p,black", close=True, color="+z", cmap=True, aspatial="Z=pop_est")
# Add a colorbar
fig.colorbar(position="JMR", frame='a200+lPopulation (millions)')
# Display the output
fig.show()

```

should produce:

 ![ecosystem_8_1](https://canada1.discourse-cdn.com/flex047/uploads/gmt/original/2X/3/3203067211bf65f3708b2588b26d7af3716eb988.png)