Commit fbd8ae16 authored by Michiel Cottaar's avatar Michiel Cottaar Committed by Michiel Cottaar
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Bug fixes/changes suggested by Mo

parent 8ecc39a4
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# Matplotlib tutorial
The main plotting library in python is `matplotlib`.
It provides a simple interface to just explore the data,
......@@ -37,102 +37,102 @@
<a class="anchor" id="basic-plotting-commands"></a>
## Basic plotting commands
Let's start with the basic imports:
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```
import matplotlib.pyplot as plt
import numpy as np
```
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<a class="anchor" id="line"></a>
### Line plots
A basic lineplot can be made just by calling `plt.plot`:
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```
plt.plot([1, 2, 3], [1.3, 4.2, 3.1])
```
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To adjust how the line is plotted, check the documentation:
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```
plt.plot?
```
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As you can see there are a lot of options.
The ones you will probably use most often are:
- `linestyle`: how the line is plotted (set to '' to omit the line)
- `marker`: how the points are plotted (these are not plotted by default)
- `color`: what color to use (defaults to cycling through a set of 7 colors)
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```
theta = np.linspace(0, 2 * np.pi, 101)
plt.plot(np.sin(theta), np.cos(theta))
plt.plot([-0.3, 0.3], [0.3, 0.3], marker='o', linestyle='', markersize=20)
plt.plot(0, -0.1, marker='s', color='black')
x = np.linspace(-0.5, 0.5, 5)
plt.plot(x, x ** 2 - 0.5, linestyle='--', marker='+', color='red')
```
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Because these keywords are so common, you can actually set one or more of them by passing in a string as the third argument.
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```
x = np.linspace(0, 1, 11)
plt.plot(x, x)
plt.plot(x, x ** 2, '--') # sets the linestyle to dashed
plt.plot(x, x ** 3, 's') # sets the marker to square (and turns off the line)
plt.plot(x, x ** 4, '^y:') # sets the marker to triangles (i.e., '^'), linestyle to dotted (i.e., ':'), and the color to yellow (i.e., 'y')
```
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<a class="anchor" id="scatter"></a>
### Scatter plots
The main extra feature of `plt.scatter` over `plt.plot` is that you can vary the color and size of the points based on some other variable array:
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```
x = np.random.rand(30)
y = np.random.rand(30)
plt.scatter(x, y, x * 30, y)
plt.colorbar() # adds a colorbar
```
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The third argument is the variable determining the size, while the fourth argument is the variable setting the color.
<a class="anchor" id="histograms"></a>
### Histograms and bar plots
For a simple histogram you can do this:
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```
r = np.random.rand(1000)
n,bins,_ = plt.hist((r-0.5)**2, bins=30)
```
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where it also returns the number of elements in each bin, as `n`, and
the bin centres, as `bins`.
> The `_` in the third part on the left
......@@ -140,11 +140,11 @@
> of the return structure.
There is also a call for doing bar plots:
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```
samp1 = r[0:10]
samp2 = r[10:20]
bwidth = 0.3
......@@ -152,123 +152,123 @@
plt.bar(xcoord-bwidth, samp1, width=bwidth, color='red', label='Sample 1')
plt.bar(xcoord, samp2, width=bwidth, color='blue', label='Sample 2')
plt.legend(loc='upper left')
```
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> If you want more advanced distribution plots beyond a simple histogram, have a look at the seaborn [gallery](https://seaborn.pydata.org/examples/index.html) for (too?) many options.
<a class="anchor" id="error"></a>
### Adding error bars
If your data is not completely perfect and has for some obscure reason some uncertainty associated with it,
you can plot these using `plt.error`:
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```
x = np.arange(5)
y1 = [0.3, 0.5, 0.7, 0.1, 0.3]
yerr = [0.12, 0.28, 0.1, 0.25, 0.6]
xerr = 0.3
plt.errorbar(x, y1, yerr, xerr, marker='s', linestyle='')
```
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<a class="anchor" id="shade"></a>
### Shading regions
An area below a plot can be shaded using `plt.fill`
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```
x = np.linspace(0, 2, 100)
plt.fill(x, np.sin(x * np.pi))
```
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This can be nicely combined with a polar projection, to create 2D orientation distribution functions:
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```
plt.subplot(projection='polar')
theta = np.linspace(0, 2 * np.pi, 100)
plt.fill(theta, np.exp(-2 * np.cos(theta) ** 2))
```
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The area between two lines can be shaded using `fill_between`:
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```
x = np.linspace(0, 10, 1000)
y = 5 * np.sin(5 * x) + x - 0.1 * x ** 2
yl = x - 0.1 * x ** 2 - 5
yu = yl + 10
plt.plot(x, y, 'r')
plt.fill_between(x, yl, yu)
```
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<a class="anchor" id="image"></a>
### Displaying images
The main command for displaying images is `plt.imshow` (use `plt.pcolor` for cases where you do not have a regular grid)
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```
import nibabel as nib
import os.path as op
nim = nib.load(op.expandvars('${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz'), mmap=False)
imdat = nim.get_data().astype(float)
imslc = imdat[:,:,70]
plt.imshow(imslc, cmap=plt.cm.gray)
plt.colorbar()
plt.grid('off')
plt.axis('off')
```
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Note that matplotlib will use the **voxel data orientation**, and that
configuring the plot orientation is **your responsibility**. To rotate a
slice, simply transpose the data (`.T`). To invert the data along along an
axis, you don't need to modify the data - simply swap the axis limits around:
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```
plt.imshow(imslc.T, cmap=plt.cm.gray)
plt.xlim(reversed(plt.xlim()))
plt.ylim(reversed(plt.ylim()))
plt.colorbar()
plt.grid('off')
plt.axis('off')
```
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> It is easier to produce informative brain images using nilearn or fsleyes
<a class="anchor" id="annotations"></a>
### Adding lines, arrows, and text
Adding horizontal/vertical lines, arrows, and text:
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```
plt.axhline(-1) # horizontal line
plt.axvline(1) # vertical line
plt.arrow(0.2, -0.2, 0.2, -0.8, length_includes_head=True, width=0.01)
plt.text(0.5, 0.5, 'middle of the plot', transform=plt.gca().transAxes, ha='center', va='center')
plt.annotate("line crossing", (1, -1), (0.8, -0.8), arrowprops={}) # adds both text and arrow; need to set the arrowprops keyword for the arrow to be plotted
```
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By default the locations of the arrows and text will be in data coordinates (i.e., whatever is on the axes),
however you can change that. For example to find the middle of the plot in the last example we use
axes coordinates, which are always (0, 0) in the lower left and (1, 1) in the upper right.
See the matplotlib [transformations tutorial](https://matplotlib.org/stable/tutorials/advanced/transforms_tutorial.html)
......@@ -294,45 +294,45 @@
In that case we want to be more explicit about what sub-plot we want to add the artist to.
We can do this by switching from the "procedural" interface used above to the "object-oriented" interface.
The commands are very similar, we just have to do a little more setup.
For example, the equivalent of `plt.plot([1, 2, 3], [1.3, 4.2, 3.1])` is:
%% Cell type:code id:660d1559 tags:
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```
fig = plt.figure()
ax = fig.add_subplot()
ax.plot([1, 2, 3], [1.3, 4.2, 3.1])
```
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Note that here we explicitly create the figure and add a single sub-plot to the figure.
We then call the `plot` function explicitly on this figure.
The "Axes" object has all of the same plotting command as we used above,
although the commands to adjust the properties of things like the title, x-axis, and y-axis are slighly different.
`plt.getp` gives a helpful summary of the properties of a matplotlib object (and what you might change):
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```
plt.getp(ax)
```
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When going through this list carefully you might have spotted that the plotted line is stored in the `lines` property.
Let's have a look at this line in more detail
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```
plt.getp(ax.lines[0])
```
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This shows us all the properties stored about this line,
including its coordinates in many different formats
(`data`, `path`, `xdata`, `ydata`, or `xydata`),
the line style and width (`linestyle`, `linewidth`), `color`, etc.
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<a class="anchor" id="subplots"></a>
## Multiple plots (i.e., subplots)
As stated one of the strengths of the object-oriented interface is that it is easier to work with multiple plots.
While we could do this in the procedural interface:
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```
plt.subplot(221)
plt.title("Upper left")
plt.subplot(222)
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plt.title("Lower left")
plt.subplot(224)
plt.title("Lower right")
```
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For such a simple example, this works fine. But for longer examples you would find yourself constantly looking back through the
code to figure out which of the subplots this specific `plt.title` command is affecting.
The recommended way to this instead is:
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```
fig, axes = plt.subplots(nrows=2, ncols=2)
axes[0, 0].set_title("Upper left")
axes[0, 1].set_title("Upper right")
axes[1, 0].set_title("Lower left")
axes[1, 1].set_title("Lower right")
```
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Here we use `plt.subplots`, which creates both a new figure for us and a grid of sub-plots.
The returned `axes` object is in this case a 2x2 array of `Axes` objects, to which we set the title using the normal numpy indexing.
> Seaborn is great for creating grids of closely related plots. Before you spent a lot of time implementing your own have a look if seaborn already has what you want on their [gallery](https://seaborn.pydata.org/examples/index.html)
<a class="anchor" id="layout"></a>
### Adjusting plot layout
The default layout of sub-plots often leads to overlap between the labels/titles of the various subplots (as above) or to excessive amounts of whitespace in between. We can often fix this by just adding `fig.tight_layout` (or `plt.tight_layout`) after making the plot:
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```
fig, axes = plt.subplots(nrows=2, ncols=2)
axes[0, 0].set_title("Upper left")
axes[0, 1].set_title("Upper right")
axes[1, 0].set_title("Lower left")
axes[1, 1].set_title("Lower right")
fig.tight_layout()
```
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Uncomment `fig.tight_layout` and see how it adjusts the spacings between the plots automatically to reduce the whitespace.
If you want more explicit control, you can use `fig.subplots_adjust` (or `plt.subplots_adjust` to do this for the active figure).
For example, we can remove any whitespace between the plots using:
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```
np.random.seed(1)
fig, axes = plt.subplots(nrows=2, ncols=2, sharex=True, sharey=True)
for ax in axes.flat:
......@@ -409,18 +409,18 @@
ax.scatter(np.random.randn(10) + offset[0], np.random.randn(10) + offset[1])
fig.suptitle("group of plots, sharing x- and y-axes")
fig.subplots_adjust(wspace=0, hspace=0, top=0.9)
```
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<a class="anchor" id="grid-spec"></a>
### Advanced grid configurations (GridSpec)
You can create more advanced grid layouts using [GridSpec](https://matplotlib.org/stable/tutorials/intermediate/gridspec.html).
An example taken from that website is:
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```
fig = plt.figure(constrained_layout=True)
gs = fig.add_gridspec(3, 3)
f3_ax1 = fig.add_subplot(gs[0, :])
......@@ -433,34 +433,34 @@
f3_ax4.set_title('gs[-1, 0]')
f3_ax5 = fig.add_subplot(gs[-1, -2])
f3_ax5.set_title('gs[-1, -2]')
```
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<a class="anchor" id="styling"></a>
## Styling your plot
<a class="anchor" id="labels"></a>
### Setting title and labels
You can edit a large number of plot properties by using the `Axes.set_*` interface.
We have already seen several examples of this above, but here is one more:
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```
fig, axes = plt.subplots()
axes.plot([1, 2, 3], [2.3, 4.1, 0.8])
axes.set_xlabel('xlabel')
axes.set_ylabel('ylabel')
axes.set_title('title')
```
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You can also set any of these properties by calling `Axes.set` directly:
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```
fig, axes = plt.subplots()
axes.plot([1, 2, 3], [2.3, 4.1, 0.8])
axes.set(
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ylabel='ylabel',
title='title',
)
```
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> To match the matlab API and save some typing the equivalent commands in the procedural interface do not have the `set_` preset. So, they are `plt.xlabel`, `plt.ylabel`, `plt.title`. This is also true for many of the `set_` commands we will see below.
You can edit the font of the text when setting the label or after the fact using the object-oriented interface:
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```
fig, axes = plt.subplots()
axes.plot([1, 2, 3], [2.3, 4.1, 0.8])
axes.set_xlabel("xlabel", color='red')
axes.set_ylabel("ylabel")
axes.get_yaxis().get_label().set_fontsize('larger')
```
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<a class="anchor" id="axis"></a>
### Editing the x- and y-axis
We can change many of the properties of the x- and y-axis by using `set_` commands.
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- The text shown for the ticks can be set using `ax.set_xticklabels` (or as a second argument to `plt.xticks`)
- The style of the ticks can be adjusted by looping through the ticks (obtained through `ax.get_xticks` or calling `plt.xticks` without arguments).
For example:
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```
fig, axes = plt.subplots()
axes.errorbar([0, 1, 2], [0.8, 0.4, -0.2], 0.1, linestyle='-', marker='s')
axes.set_xticks((0, 1, 2))
......@@ -516,21 +516,21 @@
axes.set_yticks((0, 0.5, 1))
axes.set_yticklabels(('0', '50%', '100%'))
fig.tight_layout()
```
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As illustrated earlier, we can get a more complete list of the things we could change about the x-axis by looking at its properties:
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```
plt.getp(axes.get_xlabel())
plt.getp(axes.get_xaxis())
```
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<a class="anchor" id="faq"></a>
## FAQ
<a class="anchor" id="double-image"></a>
### Why am I getting two images?
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In this notebook we were using the `inline` backend, which is the default when running in a notebook.
While very robust, this backend has the disadvantage that it only produces static plots.
We could have had interactive plots if only we had changed backends to `nbagg`.
You can change backends in the IPython terminal/notebook using:
%% Cell type:code id:93dbeb6e tags:
%% Cell type:code id:1620a4da tags:
```
%matplotlib nbagg
```
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> If you are using Jupyterlab (new version of the jupyter notebook) the `nbagg` backend will not work. Instead you will have to install `ipympl` and then use the `widgets` backend to get an interactive backend (this also works in the old notebooks).
In python scripts, this will give you a syntax error and you should instead use:
%% Cell type:code id:c16b4394 tags:
%% Cell type:code id:b67ee344 tags:
```
import matplotlib
matplotlib.use("osx")
matplotlib.use("MacOSX")
```
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Usually, the default backend will be fine, so you will not have to set it.
Note that setting it explicitly will make your script less portable.
......
......@@ -159,7 +159,7 @@ imdat = nim.get_data().astype(float)
imslc = imdat[:,:,70]
plt.imshow(imslc, cmap=plt.cm.gray)
plt.colorbar()
plt.grid('off')
plt.axis('off')
```
Note that matplotlib will use the **voxel data orientation**, and that
......@@ -173,7 +173,7 @@ plt.imshow(imslc.T, cmap=plt.cm.gray)
plt.xlim(reversed(plt.xlim()))
plt.ylim(reversed(plt.ylim()))
plt.colorbar()
plt.grid('off')
plt.axis('off')
```
> It is easier to produce informative brain images using nilearn or fsleyes
......@@ -375,7 +375,7 @@ fig.tight_layout()
As illustrated earlier, we can get a more complete list of the things we could change about the x-axis by looking at its properties:
```
plt.getp(axes.get_xlabel())
plt.getp(axes.get_xaxis())
```
<a class="anchor" id="faq"></a>
......@@ -410,7 +410,7 @@ You can change backends in the IPython terminal/notebook using:
In python scripts, this will give you a syntax error and you should instead use:
```
import matplotlib
matplotlib.use("osx")
matplotlib.use("MacOSX")
```
Usually, the default backend will be fine, so you will not have to set it.
Note that setting it explicitly will make your script less portable.
\ No newline at end of file
%% Cell type:markdown id: tags:
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# Plotting with python
The main plotting module in python is `matplotlib`. There is a lot
that can be done with it - see the [webpage](https://matplotlib.org/gallery/index.html)
......@@ -25,17 +25,17 @@
## Inside a notebook
Inside a jupyter notebook you get access to this in a slightly
different way, compared to other modules:
%% Cell type:code id: tags:
%% Cell type:code id:35ff2bd1 tags:
```
%matplotlib inline
```
%% Cell type:markdown id: tags:
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This only needs to be done once in a notebook, like for standard imports.
> There are also other alternatives, including interactive versions - see the practical on Jupyter notebooks for more information about this.
......@@ -44,11 +44,11 @@
with some simple examples.
<a class="anchor" id="2D-plots"></a>
### 2D plots
%% Cell type:code id: tags:
%% Cell type:code id:0963c7e2 tags:
```
import matplotlib.pyplot as plt
import numpy as np
......@@ -62,48 +62,48 @@
plt.plot(x, sinx**2)
plt.xlim(-np.pi, np.pi)
plt.title('Our first plots')
```
%% Cell type:markdown id: tags:
%% Cell type:markdown id:801fad5d tags:
> Note that the `plt.style.use('bmh')` command is not necessary, but it
> does make nicer looking plots in general. You can use `ggplot`
> instead of `bmh` if you want something resembling plots made by R.
> For a list of options run: `print(plt.style.available)`