Matplotlib: Move ticklabels between ticks

Question

I want to create a visualization of a confusion matrix using matplotlib. Parameters to the methods shown below are the class labels (alphabet), the classification results as a list of lists (conf_arr) and an output filename. I am pretty happy with the result so far, with one last problem:

I am not able to center the axis tick labels between the gridlines. If I pass the extent parameter to the imshow method as below, the grid is aligned as I would like it to be. If I comment it out, the grid is missaligned but the labels are were I would like them to be. I think I need a way to move the ticklabel between the associated tick and the next tick but I do not know if and how this is possible.

To summarize, I want the grid/ticks like in the left image, but the ticklabels positioned like in the right image:

def create_confusion_matrix(alphabet, conf_arr, outputname):
    norm_conf = []
    width = len(conf_arr)
    height = len(conf_arr[0])
    for i in conf_arr:
        a = 0
        tmp_arr = []
        a = sum(i, 0)
        for j in i:
            tmp_arr.append(float(j)/float(a))
        norm_conf.append(tmp_arr)

    fig = plt.figure(figsize=(14,14))
    #fig = plt.figure()
    plt.clf()
    ax = fig.add_subplot(111)
    ax.set_aspect(1)
    ax.grid(which='major')
    res = ax.imshow(np.array(norm_conf), cmap=plt.cm.binary, 
                    interpolation='none', aspect='1', vmax=1,
                    ##Commenting out this line sets labels correctly,
                    ##but the grid is off
                    extent=[0, width, height, 0]
                    )
    divider = make_axes_locatable(ax)
    cax = divider.append_axes("right", size="5%", pad=0.2)
    cb = fig.colorbar(res, cax=cax)

    #Axes
    ax.set_xticks(range(width))
    ax.set_xticklabels(alphabet, rotation='vertical')
    ax.xaxis.labelpad = 0.5
    ax.set_yticks(range(height))
    ax.set_yticklabels(alphabet, rotation='horizontal')
    #plt.tight_layout()
    plt.savefig(outputname, format='png')

The produced image looks like this:

Answer 1

As you've noticed, they're centered by default and you're overriding the default behavior by specifying extent=[0, width, height, 0].

There are a number of ways to handle this. One is to use pcolor and set the edgecolors and linestyles to look like the gridlines (you actually need pcolor and not pcolormesh for this to work). However, you'll have to change the extents to get the ticks in the center as imshow does by default.

import matplotlib.pyplot as plt
import numpy as np

data = np.random.random((10,10))
labels = 'abcdefghij'

fig, ax = plt.subplots()
im = ax.pcolor(data, cmap='gray', edgecolor='black', linestyle=':', lw=1)
fig.colorbar(im)

# Shift ticks to be at 0.5, 1.5, etc
for axis in [ax.xaxis, ax.yaxis]:
    axis.set(ticks=np.arange(0.5, len(labels)), ticklabels=labels)

plt.show()

Alternatively, you could turn on the minor grid and place it at the pixel boundaries. Because you want fixed labels, we'll just set everything manually. Otherwise, a MultipleLocator would make more sense:

import matplotlib.pyplot as plt
import numpy as np

data = np.random.random((10,10))
labels = 'abcdefghij'

fig, ax = plt.subplots()
im = ax.imshow(data, cmap='gray', interpolation='none')
fig.colorbar(im)

# Set the major ticks at the centers and minor tick at the edges
locs = np.arange(len(labels))
for axis in [ax.xaxis, ax.yaxis]:
    axis.set_ticks(locs + 0.5, minor=True)
    axis.set(ticks=locs, ticklabels=labels)

# Turn on the grid for the minor ticks
ax.grid(True, which='minor')

plt.show()

Answer 2

Alternatively: have you tried im = ax.matshow(data, cmap='gray') instead of imshow()? This should also place the ticklabels on the correct position.