I'm trying to migrate from Basemap to Cartopy looking demo examples. I have a simple code using both coastlines() and contourf(). I can get both separately but not simultaneously. The data set is a netcdf file containing the sea surface temperature data of the west Med. The code is:
import numpy as np
from netCDF4 import Dataset
import cartopy
import matplotlib.pyplot as plt
# DATA
data = Dataset('20190715.0504.n19.nc','r')
lon = data.variables['lon'][:]
lat = data.variables['lat'][:]
sst = data.variables['mcsst'][0,:,:].squeeze()
xxT,yyT = np.meshgrid(lon,lat)
# PLOT
fig = plt.figure(figsize=(10, 5))
ax1 = fig.add_axes([0.01,0.01,0.98,0.98],projection=cartopy.crs.Mercator())
ax1.coastlines()
#ax1.contourf(xxT,yyT,sst)
ax1.set_extent([16.5, -15.0, 35.0, 46.5])
plt.show()
With this code I get:
If I use:
#ax1.coastlines()
ax1.contourf(xxT,yyT,sst)
ax1.set_extent([16.5, -15.0, 35.0, 46.5])
I get a white rectangle.
If I use:
#ax1.coastlines()
ax1.contourf(xxT,yyT,sst)
ax1.set_extent([16.5,-15.0,35.0,46.5],crs=cartopy.crs.Mercator())
I get the contoured data.
But with both:
ax1.coastlines()
ax1.contourf(xxT,yyT,sst)
ax1.set_extent([16.5,-15.0,35.0,46.5],crs=cartopy.crs.Mercator())
the contour is ok ! but without coastlines. And if finally
ax1.coastlines()
ax1.contourf(xxT,yyT,sst)
ax1.set_extent([16.5,-15.0,35.0,46.5])
only coastlines are shown, not contour !. I try to understand how I have to proceed because problems arose when trying to include this into a GUI with options show/hide for coatlines, features, etc. Just in case I'm using Python 3.7.4, Cartopy 0.17, proj4 5.2, matplotlib 3.1.1. Thanks !
Thanks to swatchai suggestion, although, I still don't understand why I need to use the transform keyword with the specific PlateCarree projection keyword, the code works fine if:
fig = plt.figure(figsize=(10, 5))
ax1 = fig.add_axes([0.01, 0.01, 0.98, 0.98],projection=cartopy.crs.Mercator())
ax1.coastlines('10m')
ax1.set_extent([16.5, -15.0, 35.0, 46.5])
ax1.contourf(xxT,yyT,sst,transform=cartopy.crs.PlateCarree())
Here the result:
Related
I want to plot some coordinates using Plotly express because it allows me a more interactive approach, but I can not find the way to control the scale in the axis in the way I can manage with matplotlib.pyplot in one single line
plt.axis("scaled")
Could you please share some suggestions? Thanks.
Here is the code using Plotly express:
fig = px.scatter(coordinates_utm, x='EASTING', y='NORTHING', title=name,
hover_name=coordinates_utm.index,
hover_data={'NORTHING':':.6f','EASTING': ':.6f'})
fig.add_trace(px.scatter(coordinates_utm_lineal, x='x', y='ylineal',color_discrete_sequence=['red']).data[0])
Here is the code using plt:
fig.show()
plt.figure()
plt.scatter(coordinates_utm_lineal.x,coordinates_utm_lineal.ylineal,s=2)
plt.scatter(coordinates_utm.EASTING,coordinates_utm.NORTHING, s=2)
plt.axis("scaled")
plt.show()
This is my current output
Sadly, you didn't provide a fully reproducible example, so I'm going to create my own.
Also, I'm not really familiar with plt.axis("scaled"), as I usually use plt.axis("equal"). Reading the documentation associated to plt.axis, they appear to be somewhat similar. See if the following answer can satisfy your needs.
import plotly.express as px
import numpy as np
t = np.linspace(0, 2*np.pi)
x = np.cos(t)
y = np.sin(t)
fig = px.scatter(x=x, y=y)
fig.layout.yaxis.scaleanchor="x"
fig.show()
When using astropy and matplotlib to create a map, the units in the right ascension axis are deg/min/sec, instead of h/m/s. I do not find an easy way in astropy to select the units h/m/s.
For example, if I try to reproduce the map of the Horsehead nebula as in the documentation of astropy.wcs, I get a R.A. axis in deg/min/sec.
The code is simply:
from matplotlib import pyplot as plt
from astropy.io import fits
from astropy.wcs import WCS
from astropy.utils.data import get_pkg_data_filename
filename = get_pkg_data_filename('tutorials/FITS-images/HorseHead.fits')
hdu = fits.open(filename)[0]
wcs = WCS(hdu.header)
fig = plt.figure()
fig.add_subplot(111, projection=wcs)
plt.imshow(hdu.data, origin='lower', cmap=plt.cm.viridis)
plt.xlabel('RA')
plt.ylabel('Dec')
plt.show()
It is supposed to produce this:
correct units
but I get that:
wrong units
You can use:
ax = fig.gca()
ra = ax.coords[0]
ra.set_format_unit('hour')
e.g. as specified here: http://docs.astropy.org/en/stable/visualization/wcsaxes/controlling_axes.html
However, when I ran the same example, it defaulted to hours, so I'm not sure what configuration you have set that defaulted to degrees instead.
I am trying to plot some data on an AzimuthalEquidistant projection using cartopy. However, it gives me a couple of problems. First the coastlines no longer show for this type of projection. Not sure if this is my code or a Cartopy problem. I also notice that if I use a ccrs.PlateCarree() transform in the pcolormesh command the coastlines do show but then, presumably, my data is on the wrong type of prejection?
Second I would prefer if the axis boarder was circular after plotting the data, is it possible to use set_extent or some similar function to do this?
The code below should reproduce the problems, the circle shows how I would like the boarder to look.
import matplotlib.pyplot as plt
import cartopy.crs as ccrs
import matplotlib.patches as mpatches
clat = 55.0
clon = -8.0
lons = np.arange(clon-15,clon+16,0.5)
lats = np.arange(clat-15,clat+16,0.5)
d = np.random.rand(lons.shape[0],lats.shape[0])
trans = ccrs.AzimuthalEquidistant(central_latitude=clat, central_longitude=clon)
ax = plt.axes(projection=trans)
ax.coastlines(resolution='10m')
CB=ax.pcolormesh(lons-0.25, lats-0.25, d.T,
cmap=plt.cm.viridis, alpha=0.5,
transform=trans)#ccrs.PlateCarree())
p1 = mpatches.Circle((clon,clat), radius=15, color='k', lw=5, fill=False,
transform=trans)
ax.add_patch(p1)
If the data you are plotting is in latitude/longitude coordinates then the correct value for the transform keyword is indeed ccrs.PlateCarree(). This is common gotcha for new users. The transform argument tells cartopy what coordinates your data are in, and is completely independent of the projection you want to plot onto.
To make the plot circular you'll need to set the boundary yourself. The Cartopy documentation have a couple of examples of this: http://scitools.org.uk/cartopy/docs/latest/examples/always_circular_stereo.html and http://scitools.org.uk/cartopy/docs/latest/examples/star_shaped_boundary.html.
Is it possible to use Python matplotlib code to draw graph in RStudio?
e.g. below Python matplotlib code:
import numpy as np
import matplotlib.pyplot as plt
n = 256
X = np.linspace(-np.pi,np.pi,n,endpoint=True)
Y = np.sin(2*X)
plt.plot (X, Y+1, color='blue', alpha=1.00)
plt.plot (X, Y-1, color='blue', alpha=1.00)
plt.show()
Output graph will be:
Then I need to write a R Markdown to include these code and generate graph automatically after knitting the markdown.
install.packages('devtools') first, get install_github function
install_github("rstudio/reticulate") install the dev version of reticulate
in r markdown doc, use code below to enable the function.
```{r setup, include=FALSE}
library(knitr)
library(reticulate)
knitr::knit_engines$set(python = reticulate::eng_python)
```
Try it , you will get what you want and don't need to save any image.
One possible solution is save the plot as a image, then load the file to markdown.
### Call python code sample
```{r,engine='python'}
import numpy as np
import matplotlib.pyplot as plt
n = 256
X = np.linspace(-np.pi,np.pi,n,endpoint=True)
Y = np.sin(2*X)
fig, ax = plt.subplots( nrows=1, ncols=1 )
ax.plot (X, Y+1, color='blue', alpha=1.00)
ax.plot (X, Y-1, color='blue', alpha=1.00)
#plt.show()
fig.savefig('foo.png', bbox_inches='tight')
print "finished"
```
Output image:
#### The End
Output:
You can do that with reticulate, but most time in trying to follow a tutorial in doing that you may encounter some technicalities that weren't sufficiently explained.
My answer is a little late but I hope it's a thorough walkthrough of doing it the right way - not rendering it and then loading it as a png but have the python code executed more "natively".
Step 1: Configure Python from RStudio
You want to insert an R chunk, and run the following code to configure the path to the version of Python you want to use. The default python that comes shipped with most OS is usually the outdated python 2 and is not where you install your packages. That is the reason why it's important to do this, to make sure Rstudio will use the specified python instance where your matplotlib library (and the other libraries you will be using for that project) can be found:
library(reticulate)
# change the following to point to the desired path on your system
use_python('/Users/Samuel/anaconda3/bin/python')
# prints the python configuration
py_config()
You should expect to see that your session is configured with the settings you specified:
python: /Users/Samuel/anaconda3/bin/python
libpython: /Users/Samuel/anaconda3/lib/libpython3.6m.dylib
pythonhome: /Users/Samuel/anaconda3:/Users/Samuel/anaconda3
version: 3.6.3 |Anaconda custom (64-bit)| (default, Oct 6 2017, 12:04:38) [GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)]
numpy: /Users/Samuel/anaconda3/lib/python3.6/site-packages/numpy
numpy_version: 1.15.2
python versions found:
/Users/Samuel/anaconda3/bin/python
/usr/bin/python
/usr/local/bin/python
/usr/local/bin/python3
/Users/Samuel/.virtualenvs/r-tensorflow/bin/python
Step 2: The familiar plt.show
Add a Python chunk (not R!) in your R Markdown document (see attached screenshot) and you can now write native Python code. This means that the familiar plt.show() and plt.imshow() will work without any extra work. It will be rendered and can be compiled into HTML / PDF using knitr.
This will work:
plt.imshow(my_image, cmap='gray')
Or a more elaborated example:
import numpy as np
import matplotlib.pyplot as plt
import os
import cv2
DATADIR = '/Users/Samuel/Datasets/PetImages'
CATEGORIES = ['Dog', 'Cat']
for category in CATEGORIES:
path = os.path.join(DATADIR, category) # path to cat or dog dir
for img in os.listdir(path):
img_array = cv2.imread(os.path.join(path,img), cv2.IMREAD_GRAYSCALE)
plt.imshow(img_array, cmap='gray')
plt.show()
break
break
Output:
Step 3: Knit to HTML / PDF / Word etc
Proceed to knit as usual. The end product is a beautifully formatted document done in Python code using R Markdown. RStudio has come a long way and I'm surprised the level of support it has for Python code isn't more known so hoping anyone that stumbled upon this answer will find it informative and learned something new.
I have been working with reticulate and R Markdown and you should specify your virtual environment. For example my R Markdown starts as follows:
{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, warning = FALSE, cache.lazy = FALSE)
library(reticulate)
use_condaenv('pytorch') ## yes, you can run pytorch and tensor flow too
Then you can work in either language. So, for plotting with matplotlib, I have found that you need the PyQt5 module to make it all run smoothly. The following makes a nice plot inside R Markdown - it's a separate chunk.
{python plot}
import PyQt5
import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
from matplotlib.pyplot import figure
data = pd.read_csv('Subscriptions.csv',index_col='Date', parse_dates=True)
# make the nice plot
# set the figure size
fig = plt.figure(figsize = (15,10))
# the series
ax1 = fig.add_subplot(211)
ax1.plot(data.index.values, data.Opens, color = 'green', label = 'Opens')
# plot the legend for the first plot
ax1.legend(loc = 'upper right', fontsize = 14)
plt.ylabel('Opens', fontsize=16)
# Hide the top x axis
ax1.axes.get_xaxis().set_visible(False)
####### NOW PLOT THE OTHER SERIES ON A SINGLE PLOT
# plot 212 is the MI series
# plot series
ax2 = fig.add_subplot(212)
ax2.plot(data.index.values, data.Joiners, color = 'orange', label = 'Joiners')
# plot the legend for the second plot
ax2.legend(loc = 'upper right', fontsize = 14)
# set the fontsize for the bottom plot
plt.ylabel('Joiners', fontsize=16)
plt.tight_layout()
plt.show()
You get the following from this:
I don't have the reputation points to add a comment, but Bryan's answer above was the only one to work for me. Adding plt.tight_layout() made the difference. I added that line to the following simple code and the plot displayed.
{python evaluate}
plt.scatter(X_train, y_train, color = 'gray')
plt.plot(X_train, regresssion_model_sklearn.predict(X_train), color = 'red')
plt.ylabel('Salary')
plt.xlabel('Number of Years of Experience')
plt.title('Salary vs. Years of Experience')
plt.tight_layout()
plt.show()
I have two shapefiles. One is a point feature shapefile, named "point.shp", the other is a polygon shapefile named "polygon.shp". Both I want to add to a map using cartopy.
I managed to add the "polygon.shp", but failed with the "point.shp".
Here's my code:
import matplotlib.pyplot as plt
from cartopy import crs
from cartopy.io.shapereader import Reader
from cartopy.feature import ShapelyFeature
ax = plt.axes(projection=crs.PlateCarree())
# add the polygon file, worked
ax.add_geometries(Reader("polygon.shp").geometries(), crs.PlateCarree(), facecolor='w')
# or(also worked):
ax.add_feature(ShapelyFeature(Reader("polygon.shp").geometries(), crs.PlateCarree(), facecolor='r'))
# but these two ways both failed with the "point.shp"
ax.add_geometries(Reader("point.shp").geometries(), crs.PlateCarree())
# or, this doesn't work neither:
ax.add_feature(ShapelyFeature(Reader("polygon.shp").geometries(), crs.PlateCarree(), facecolor='r'))
Does any one know how to do this, or why, without retrieving all the points' x, y coords and then plotting them?
And with coordinates(x, y values), ax.plot() works, but ax.scatter() fails, why?
Thanks
add_geometries currently turns a geometry into a polygon and then colours it appropriately, which of course means that when you pass points the add_geometries, the polygons are not visible. Potentially cartopy could do a better job of this in the future, but in the meantime, it sounds like you just want to use something like scatter to visualize your data.
You can achieve this by getting the x and y coordinate values out of the geometry and passing these straight on to scatter with the appropriate transform:
import cartopy.crs as ccrs
import cartopy.io
import matplotlib.pyplot as plt
fname = cartopy.io.shapereader.natural_earth(resolution='10m',
category='cultural',
name='populated_places_simple')
plt.figure(figsize=(12, 6))
ax = plt.axes(projection=ccrs.Robinson())
ax.set_title('Populated places of the world.')
ax.coastlines()
points = list(cartopy.io.shapereader.Reader(fname).geometries())
ax.scatter([point.x for point in points],
[point.y for point in points],
transform=ccrs.Geodetic())
plt.show()
HTH