I am trying to plot heatmap with average values with x and y axes denote physical parameters.
import csv
import matplotlib.pyplot as plt
from scipy import stats
import numpy as np
#.......................................................................
# URL for temp.csv https://github.com/paragkan/dyanmic-recrystallization/blob/main/temp.csv
#.......................................................................
def read_csv(xfile):
infile = open(xfile, 'r')
table = []
for row in csv.reader(infile):
table.append(row)
infile.close() # better leave that file alone.
for c in range (0, len(table[0])):
for r in range(0, len(table)):
try:
table[r][c] = float(table[r][c])
except:
pass
return table
#.......................................................................
xfile = 'temp.csv'
table = read_csv(xfile)
x = []
y = []
z = []
for i in range(0, len(table)):
x.append(int(1/table[i][0]))
y.append(table[i][1])
z.append(table[i][2])
extent = [min(x), max(x), min(y), max(y)]
d = stats.binned_statistic_2d(x, y, z, statistic='mean', bins = [5, 5])
fig, ax = plt.subplots()
extent = [min(x), max(x), min(y), max(y)]
# im = ax.imshow(d[0].T, cmap='RdBu_r', interpolation='nearest', origin='lower', extent=extent)
im = ax.imshow(d[0].T, cmap='RdBu_r', interpolation='nearest', origin='lower')
print(d[0])
print(d[1])
print(d[2])
# ax.set_xticks(d[1])
# ax.set_yticks(d[2])
cbar = ax.figure.colorbar(im, ax = ax, shrink = 1)
# average = d[0].T
# xdist = d[1]
# ydist = d[2]
# for i in range(0, len(d[1])-1):
# for j in range(len(d[2])-1):
# xcord = (xdist[j] + xdist[j+1])/2
# ycord = (ydist[i] + ydist[i+1])/2
# txtext = plt.text(xcord, ycord, round(average[i][j], 2), fontsize = 12, ha="center", va="center", color="w")
plt.show()
plt.close()
Printed Output
[[0.00658065 0.01352 0.03897 0.09360667 0.15375806]
[ nan nan nan nan nan]
[0.00704516 0.02388 0.11518667 0.37206333 0.69959677]
[ nan nan nan nan nan]
[0.00575484 0.01212 0.05937667 0.22448333 0.46173226]]
[ 923. 962.8 1002.6 1042.4 1082.2 1122. ]
[ 2.83236704 4.58410957 6.33585211 8.08759464 9.83933718 11.59107971]
Without extent
With extent=extent
When I use 'extent' parameter or custom axes ticks using set_xticks, the map is not showing correctly. Without 'extent', everything is fine but then the axes ticks are indexed as 0, 1, 2, 3. Kindly help me resolve this issue. It is also OK if someone suggests another python package to plot heatmap with binned stats, I require saved graphs to be used in a manuscript.
Expected Plot
What I need is, the edges of the bins in the graph should show the actual bin's dimension. If xedges are = [900, 925, 975, ..], the ticks on the x-axis should start with 900, and the next tick should be on the next bin edge showing 925. The same for y-axis.
temp.csv
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