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Heatmap from 3D-data, with float-numbers

I am trying to generate a heatmap from 3D-data in a csv-file. The csv-file has the format x,y,z for each line. The problem is when I create a array to link the values, I can't use float-numbers as keys. When setting the dtype to int in np.loadtext(), the code works fine; but this makes the resolution only half of what the csv-file can replicate. Is there another way of linking the values?
The code so far is:
import numpy as np
import seaborn as sb
import matplotlib.pyplot as plt
fname = 'test18.csv'
x, y, z = np.loadtxt(fname, delimiter=',', dtype=float).T
pltZ = np.zeros((y.max()+1, x.max()+1), dtype=float)
pltZ[y, x] = z
heat_map = sb.heatmap(pltZ, cmap=plt.cm.rainbow)
plt.show()

matplotlib event.xdata out of timeries range

Having an issue using matplotlib event.xdata when plotting pandas.Timeseries, I tried to reproduce the answer proposed in a very related question, but get a very strange behavior.
Here's the code, adapted to python3 and with a little more stuff in the on_click() function:
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.dates as mdates
def on_click(event):
if event.inaxes is not None:
# provide raw and converted x data
print(f"{event.xdata} --> {mdates.num2date(event.xdata)}")
# add a vertical line at clicked location
line = ax.axvline(x=event.xdata)
plt.draw()
t = pd.date_range('2015-11-01', '2016-01-06', freq='H')
y = np.random.normal(0, 1, t.size).cumsum()
df = pd.DataFrame({'Y':y}, index=t)
fig, ax = plt.subplots()
line = None
df.plot(ax=ax)
fig.canvas.mpl_connect('button_press_event', on_click)
plt.show()
If I launch this, I get the following diagram, with expected date range between Nov. 2015 and Jan. 2016, as is the cursor position information provided in the footer of the window (here 2015-11-01 10:00), and correct location of the vertical lines:
However, the command-line output is as follows:
C:\Users\me\Documents\code\>python matplotlib_even.xdate_num2date.py
402189.6454115977 --> 1102-02-27 15:29:23.562039+00:00
402907.10400704964 --> 1104-02-15 02:29:46.209088+00:00
Those event.xdata values are clearly out of both input data range and x axis data range, and are unusable for later use (like, try to find the closest y value in the serie).
So, does anyone know how I can get a correct xdata?

Something must have changed in the way matplotlib/pandas handles datetime info between the answer to the related question you linked and now. I cannot comment on why, but I found a solution to your problem.
I went digging through the code that shows the coordinates in the bottom left of the status bar, and I found that when you're plotting a timeseries, pandas patches the functions that prints this info and replaces it with this one.
From there, you can see that you need to convert the float value to a Period object.
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
def on_click(event):
print(pd.Period(ordinal=int(event.xdata), freq='H'))
t = pd.date_range('2015-11-01', '2016-01-06', freq='H')
y = np.random.normal(0, 1, t.size).cumsum()
df = pd.DataFrame({'Y': y}, index=t)
fig, ax = plt.subplots()
df.plot(ax=ax)
fig.canvas.mpl_connect('button_press_event', on_click)
plt.show()

HDF5 file to diagram in python

I'm trying to generate some diagrams from an .h5 file but I don't know how to do it.
I'm using pytables, numpy and matplotlib.
The hdf5 files I use contains 2 sets of data, 2 differents curves.
My goal is to get diagrams like this one.
This is what I managed to do for the moment:
import tables as tb
import numpy as np
import matplotlib.pyplot as plt
h5file = tb.openFile(args['FILE'], "a")
for group in h5file.walkGroups("/"):
for array in h5file.walkNodes("/","Array"):
if(isinstance(array.atom.dflt, int)):
tab = np.array(array.read())
x = tab[0]
y = tab[1]
plt.plot(x, y)
plt.show()
x and y values are good but I don't know how to use them, so the result is wrong. I get a triangle instead of what I want ^^
Thank you for your help
EDIT
I solved my problem.
Here is the code :
fig = plt.figure()
tableau = np.array(array.read())
x = tableau[0]
y = tableau[1]
ax1 = fig.add_subplot(211)
ax2 = fig.add_subplot(212)
ax1.plot(x)
ax2.plot(y)
plt.title(array.name)
plt.show()

Interactive pixel information of an image in Python?

Short version: is there a Python method for displaying an image which shows, in real time, the pixel indices and intensities? So that as I move the cursor over the image, I have a continually updated display such as pixel[103,214] = 198 (for grayscale) or pixel[103,214] = (138,24,211) for rgb?
Long version:
Suppose I open a grayscale image saved as an ndarray im and display it with imshow from matplotlib:
im = plt.imread('image.png')
plt.imshow(im,cm.gray)
What I get is the image, and in the bottom right of the window frame, an interactive display of the pixel indices. Except that they're not quite, as the values are not integers: x=134.64 y=129.169 for example.
If I set the display with correct resolution:
plt.axis('equal')
the x and y values are still not integers.
The imshow method from the spectral package does a better job:
import spectral as spc
spc.imshow(im)
Then in the bottom right I now have pixel=[103,152] for example.
However, none of these methods also shows the pixel values. So I have two questions:
Can the imshow from matplotlib (and the imshow from scikit-image) be coerced into showing the correct (integer) pixel indices?
Can any of these methods be extended to show the pixel values as well?

There a couple of different ways to go about this.
You can monkey-patch ax.format_coord, similar to this official example. I'm going to use a slightly more "pythonic" approach here that doesn't rely on global variables. (Note that I'm assuming no extent kwarg was specified, similar to the matplotlib example. To be fully general, you need to do a touch more work.)
import numpy as np
import matplotlib.pyplot as plt
class Formatter(object):
def __init__(self, im):
self.im = im
def __call__(self, x, y):
z = self.im.get_array()[int(y), int(x)]
return 'x={:.01f}, y={:.01f}, z={:.01f}'.format(x, y, z)
data = np.random.random((10,10))
fig, ax = plt.subplots()
im = ax.imshow(data, interpolation='none')
ax.format_coord = Formatter(im)
plt.show()
Alternatively, just to plug one of my own projects, you can use mpldatacursor for this. If you specify hover=True, the box will pop up whenever you hover over an enabled artist. (By default it only pops up when clicked.) Note that mpldatacursor does handle the extent and origin kwargs to imshow correctly.
import numpy as np
import matplotlib.pyplot as plt
import mpldatacursor
data = np.random.random((10,10))
fig, ax = plt.subplots()
ax.imshow(data, interpolation='none')
mpldatacursor.datacursor(hover=True, bbox=dict(alpha=1, fc='w'))
plt.show()
Also, I forgot to mention how to show the pixel indices. In the first example, it's just assuming that i, j = int(y), int(x). You can add those in place of x and y, if you'd prefer.
With mpldatacursor, you can specify them with a custom formatter. The i and j arguments are the correct pixel indices, regardless of the extent and origin of the image plotted.
For example (note the extent of the image vs. the i,j coordinates displayed):
import numpy as np
import matplotlib.pyplot as plt
import mpldatacursor
data = np.random.random((10,10))
fig, ax = plt.subplots()
ax.imshow(data, interpolation='none', extent=[0, 1.5*np.pi, 0, np.pi])
mpldatacursor.datacursor(hover=True, bbox=dict(alpha=1, fc='w'),
formatter='i, j = {i}, {j}\nz = {z:.02g}'.format)
plt.show()

An absolute bare-bones "one-liner" to do this: (without relying on datacursor)
def val_shower(im):
return lambda x,y: '%dx%d = %d' % (x,y,im[int(y+.5),int(x+.5)])
plt.imshow(image)
plt.gca().format_coord = val_shower(ims)
It puts the image in closure so makes sure if you have multiple images each will display its own values.

All of the examples that I have seen only work if your x and y extents start from 0. Here is code that uses your image extents to find the z value.
import numpy as np
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
d = np.array([[i+j for i in range(-5, 6)] for j in range(-5, 6)])
im = ax.imshow(d)
im.set_extent((-5, 5, -5, 5))
def format_coord(x, y):
"""Format the x and y string display."""
imgs = ax.get_images()
if len(imgs) > 0:
for img in imgs:
try:
array = img.get_array()
extent = img.get_extent()
# Get the x and y index spacing
x_space = np.linspace(extent[0], extent[1], array.shape[1])
y_space = np.linspace(extent[3], extent[2], array.shape[0])
# Find the closest index
x_idx= (np.abs(x_space - x)).argmin()
y_idx= (np.abs(y_space - y)).argmin()
# Grab z
z = array[y_idx, x_idx]
return 'x={:1.4f}, y={:1.4f}, z={:1.4f}'.format(x, y, z)
except (TypeError, ValueError):
pass
return 'x={:1.4f}, y={:1.4f}, z={:1.4f}'.format(x, y, 0)
return 'x={:1.4f}, y={:1.4f}'.format(x, y)
# end format_coord
ax.format_coord = format_coord
If you are using PySide/PyQT here is an example to have a mouse hover tooltip for the data
import matplotlib
matplotlib.use("Qt4Agg")
matplotlib.rcParams["backend.qt4"] = "PySide"
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
# Mouse tooltip
from PySide import QtGui, QtCore
mouse_tooltip = QtGui.QLabel()
mouse_tooltip.setFrameShape(QtGui.QFrame.StyledPanel)
mouse_tooltip.setWindowFlags(QtCore.Qt.ToolTip)
mouse_tooltip.setAttribute(QtCore.Qt.WA_TransparentForMouseEvents)
mouse_tooltip.show()
def show_tooltip(msg):
msg = msg.replace(', ', '\n')
mouse_tooltip.setText(msg)
pos = QtGui.QCursor.pos()
mouse_tooltip.move(pos.x()+20, pos.y()+15)
mouse_tooltip.adjustSize()
fig.canvas.toolbar.message.connect(show_tooltip)
# Show the plot
plt.show()

with Jupyter you can do so either with datacursor(myax)or by ax.format_coord.
Sample code:
%matplotlib nbagg
import numpy as np
import matplotlib.pyplot as plt
X = 10*np.random.rand(5,3)
fig,ax = plt.subplots()
myax = ax.imshow(X, cmap=cm.jet,interpolation='nearest')
ax.set_title('hover over the image')
datacursor(myax)
plt.show()
the datacursor(myax) can also be replaced with ax.format_coord = lambda x,y : "x=%g y=%g" % (x, y)

In case you, like me, work on Google Colab, this solutions do not work as Colab disabled interactive feature of images for matplotlib.
Then you might simply use Plotly:
https://plotly.com/python/imshow/
import plotly.express as px
import numpy as np
img_rgb = np.array([[[255, 0, 0], [0, 255, 0], [0, 0, 255]],
[[0, 255, 0], [0, 0, 255], [255, 0, 0]]
], dtype=np.uint8)
fig = px.imshow(img_rgb)
fig.show()

Matplotlib has built-in interactive plot which logs pixel values at the corner of the screen.
To setup first install pip install ipympl
Then use either %matplotlib notebook or %matplotlib widget instead of %matplotlib inline
The drawback with plotly or Bokeh is that they don't work on Pycharm.
For more information take a look at the doc

To get interactive pixel information of an image use the module imagetoolbox
To download the module open the command prompt and write
pip install imagetoolbox
Write the given code to get interactive pixel information of an image
enter image description here
Output:enter image description here

Python Matplotlib add Colorbar

i've got a problem using MatlobLib with "Custom" Shapes from a shapereader. Importing and viewing inserted faces works fine, but i'm not able to place a colorbar on my figure.
I already tried several ways from the tutorial, but im quite sure there is a smart solution for this problem.
maybe somebody can help me, my current code is attached below:
from formencode.national import pycountry
import itertools
from matplotlib import cm, pyplot
from matplotlib import
from mpl_toolkits.basemap import Basemap
from numpy.dual import norm
import cartopy.crs as ccrs
import cartopy.io.shapereader as shpreader
import matplotlib as mpl
import matplotlib.colors as colors
import matplotlib.mlab as mlab
import matplotlib.pyplot as plt
import numpy as np
def draw_map_for_non_normalized_data_with_alpha2_counrty_description(data, title=None):
m = Basemap()
ax = plt.axes(projection=ccrs.PlateCarree())
list = []
sum = 0
for key in data:
sum += data[key]
for key in data.keys():
new_val = (data[key]+0.00)/sum
list.append(new_val)
data[key] = new_val
#===========================================================================
# print str(min(list))
# print str(max(list))
#===========================================================================
cmap = mpl.cm.cool
colors = matplotlib.colors.Normalize(min(list)+0.0, max(list)+0.0)
labels = []
features = []
for country in shpreader.Reader(shapename).records():
a3_code = country.attributes["gu_a3"]
try :
a2_code = pycountry.countries.get(alpha3=a3_code).alpha2
except:
a2_code = ""
if a2_code in data:
val = data[a2_code]
color = cm.jet(norm(val))
print str(val) + " value for color: " + str(color)
labels.append(country.attributes['name_long'])
feat = ax.add_geometries(country.geometry, ccrs.PlateCarree(), facecolor=color, label=country.attributes['name_long'])
features.append(feat)
#ax.legend(features, labels, loc='upper right')
#===========================================================================
# fig = pyplot.figure(figsize=(8,3))
# ax1 = fig.add_axes([0.05, 0.80, 0.9, 0.15])
#===========================================================================
#cbar = m.colorbar(location='bottom')
cb1 = mpl.colorbar.ColorbarBase(ax, cmap=cmap,norm=colors,orientation='horizontal')
cb1.set_label('foo')
m.drawcoastlines()
m.drawcountries()
if title:
plt.title(title)
plt.show()
as you can see inside the code, i already tried several ways, but none of them worked for me.
maybe somebody has "the" hint for me.
thanks for help,
kind regards

As mentioned in the comments above, i would think twice about mixing Basemap and Cartopy, is there a specific reason to do so? Both are basically doing the same thing, extending Matplotlib with geographical plotting capabilities. Both are valid to use, they both have their pro's and con's.
In your example you have a Basemap axes m, a Cartopy axes ax and you are using the Pylab interface by using plt. which operates on the currently active axes. Perhaps it theoretically possible, but it seems prone to errors to me.
I cant modify your example to make it work, since the data is missing and your code is not valid Python, the indentation for the function is incorrect for example. But here is a Cartopy-only example showing how you can plot a Shapefile and use the same cmap/norm combination to add a colorbar to the axes.
One difference with your code is that you provide the axes containing the map to the ColorbarBase function, this should be a seperate axes specifically for the colorbar.
import cartopy.crs as ccrs
import matplotlib.pyplot as plt
import matplotlib as mpl
import cartopy.io.shapereader as shpreader
fig, ax = plt.subplots(figsize=(12,6),
subplot_kw={'projection': ccrs.PlateCarree()})
norm = mpl.colors.Normalize(vmin=0, vmax=1000000)
cmap = plt.cm.RdYlBu_r
for n, country in enumerate(shpreader.Reader(r'D:\ne_50m_admin_0_countries_lakes.shp').records()):
ax.add_geometries(country.geometry, ccrs.PlateCarree(),
facecolor=cmap(norm(country.attributes['gdp_md_est'])),
label=country.attributes['name'])
ax.set_title('gdp_md_est')
cax = fig.add_axes([0.95, 0.2, 0.02, 0.6])
cb = mpl.colorbar.ColorbarBase(cax, cmap=cmap, norm=norm, spacing='proportional')
cb.set_label('gdp_md_est')