Skip to content

DOC: add tutorial explaining imshow *origin* and *extent* #10947

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 4 commits into from
May 2, 2018
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion doc/_static/mpl.css
Original file line number Diff line number Diff line change
Expand Up @@ -416,7 +416,7 @@ div.deprecated span.versionmodified {
font-weight: bold;
}

div.green {
div.green, div.hint {
color: #468847;
background-color: #dff0d8;
border: 1px solid #d6e9c6;
Expand Down
265 changes: 265 additions & 0 deletions tutorials/intermediate/imshow_extent.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,265 @@
"""
*origin* and *extent* in `~.Axes.imshow`
========================================

:meth:`~.Axes.imshow` allows you to render an image (either a 2D array
which will be color-mapped (based on *norm* and *cmap*) or and 3D RGB(A)
array which will be used as-is) to a rectangular region in dataspace.
The orientation of the image in the final rendering is controlled by
the *origin* and *extent* kwargs (and attributes on the resulting
`~.AxesImage` instance) and the data limits of the axes.

The *extent* kwarg controls the bounding box in data coordinates that
the image will fill specified as ``(left, right, bottom, top)`` in
**data coordinates**, the *origin* kwarg controls how the image fills
that bounding box, and the orientation in the final rendered image is
also affected by the axes limits.

.. hint:: Most of the code below is used for adding labels and informative
text to the plots. The described effects of *origin* and *extent* can be
seen in the plots without the need to follow all code details.

For a quick understanding, you may want to skip the code details below and
directly continue with the discussion of the results.
"""
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec


def index_to_coordinate(index, extent, origin):
"""Return the pixel center of an index."""
left, right, bottom, top = extent

hshift = 0.5 * np.sign(right - left)
left, right = left + hshift, right - hshift
vshift = 0.5 * np.sign(top - bottom)
bottom, top = bottom + vshift, top - vshift

if origin == 'upper':
bottom, top = top, bottom

return {
"[0, 0]": (left, bottom),
"[M', 0]": (left, top),
"[0, N']": (right, bottom),
"[M', N']": (right, top),
}[index]


def get_index_label_pos(index, extent, origin, inverted_xindex):
"""
Return the desired position and horizontal alignment of an index label.
"""
if extent is None:
extent = lookup_extent(origin)
left, right, bottom, top = extent
x, y = index_to_coordinate(index, extent, origin)

is_x0 = index[-2:] == "0]"
halign = 'left' if is_x0 ^ inverted_xindex else 'right'
hshift = 0.5 * np.sign(left - right)
x += hshift * (1 if is_x0 else -1)
return x, y, halign


def get_color(index, data, cmap):
"""Return the data color of an index."""
val = {
"[0, 0]": data[0, 0],
"[0, N']": data[0, -1],
"[M', 0]": data[-1, 0],
"[M', N']": data[-1, -1],
}[index]
return cmap(val / data.max())


def lookup_extent(origin):
"""Return extent for label positioning when not given explicitly."""
if origin == 'lower':
return (-0.5, 6.5, -0.5, 5.5)
else:
return (-0.5, 6.5, 5.5, -0.5)


def set_extent_None_text(ax):
ax.text(3, 2.5, 'equals\nextent=None', size='large',
ha='center', va='center', color='w')


def plot_imshow_with_labels(ax, data, extent, origin, xlim, ylim):
"""Actually run ``imshow()`` and add extent and index labels."""
im = ax.imshow(data, origin=origin, extent=extent)

# extent labels (left, right, bottom, top)
left, right, bottom, top = im.get_extent()
if xlim is None or top > bottom:
upper_string, lower_string = 'top', 'bottom'
else:
upper_string, lower_string = 'bottom', 'top'
if ylim is None or left < right:
port_string, starboard_string = 'left', 'right'
inverted_xindex = False
else:
port_string, starboard_string = 'right', 'left'
inverted_xindex = True
bbox_kwargs = {'fc': 'w', 'alpha': .75, 'boxstyle': "round4"}
ann_kwargs = {'xycoords': 'axes fraction',
'textcoords': 'offset points',
'bbox': bbox_kwargs}
ax.annotate(upper_string, xy=(.5, 1), xytext=(0, -1),
ha='center', va='top', **ann_kwargs)
ax.annotate(lower_string, xy=(.5, 0), xytext=(0, 1),
ha='center', va='bottom', **ann_kwargs)
ax.annotate(port_string, xy=(0, .5), xytext=(1, 0),
ha='left', va='center', rotation=90,
**ann_kwargs)
ax.annotate(starboard_string, xy=(1, .5), xytext=(-1, 0),
ha='right', va='center', rotation=-90,
**ann_kwargs)
ax.set_title('origin: {origin}'.format(origin=origin))

# index labels
for index in ["[0, 0]", "[0, N']", "[M', 0]", "[M', N']"]:
tx, ty, halign = get_index_label_pos(index, extent, origin,
inverted_xindex)
facecolor = get_color(index, data, im.get_cmap())
ax.text(tx, ty, index, color='white', ha=halign, va='center',
bbox={'boxstyle': 'square', 'facecolor': facecolor})
if xlim:
ax.set_xlim(*xlim)
if ylim:
ax.set_ylim(*ylim)


def generate_imshow_demo_grid(extents, xlim=None, ylim=None):
N = len(extents)
fig = plt.figure(tight_layout=True)
fig.set_size_inches(6, N * (11.25) / 5)
gs = GridSpec(N, 5, figure=fig)

columns = {'label': [fig.add_subplot(gs[j, 0]) for j in range(N)],
'upper': [fig.add_subplot(gs[j, 1:3]) for j in range(N)],
'lower': [fig.add_subplot(gs[j, 3:5]) for j in range(N)]}
x, y = np.ogrid[0:6, 0:7]
data = x + y

for origin in ['upper', 'lower']:
for ax, extent in zip(columns[origin], extents):
plot_imshow_with_labels(ax, data, extent, origin, xlim, ylim)

for ax, extent in zip(columns['label'], extents):
text_kwargs = {'ha': 'right',
'va': 'center',
'xycoords': 'axes fraction',
'xy': (1, .5)}
if extent is None:
ax.annotate('None', **text_kwargs)
ax.set_title('extent=')
else:
left, right, bottom, top = extent
text = ('left: {left:0.1f}\nright: {right:0.1f}\n' +
'bottom: {bottom:0.1f}\ntop: {top:0.1f}\n').format(
left=left, right=right, bottom=bottom, top=top)

ax.annotate(text, **text_kwargs)
ax.axis('off')
return columns


###############################################################################
#
# Default extent
# --------------
#
# First, let's have a look at the default `extent=None`

generate_imshow_demo_grid(extents=[None])

###############################################################################
#
# Generally, for an array of shape (M, N), the first index runs along the
# vertical, the second index runs along the horizontal.
# The pixel centers are at integer positions ranging from 0 to ``N' = N - 1``
# horizontally and from 0 to ``M' = M - 1`` vertically.
# *origin* determines how to the data is filled in the bounding box.
#
# For ``origin='lower'``:
#
# - [0, 0] is at (left, bottom)
# - [M', 0] is at (left, top)
# - [0, N'] is at (right, bottom)
# - [M', N'] is at (right, top)
#
# ``origin='upper'`` reverses the vertical axes direction and filling:
#
# - [0, 0] is at (left, top)
# - [M', 0] is at (left, bottom)
# - [0, N'] is at (right, top)
# - [M', N'] is at (right, bottom)
#
# In summary, the position of the [0, 0] index as well as the extent are
# influenced by *origin*:
#
# ====== =============== ==========================================
# origin [0, 0] position extent
# ====== =============== ==========================================
# upper top left ``(-0.5, numcols-0.5, numrows-0.5, -0.5)``
# lower bottom left ``(-0.5, numcols-0.5, -0.5, numrows-0.5)``
# ====== =============== ==========================================
#
# The default value of *origin* is set by :rc:`image.origin` which defaults
# to ``'upper'`` to match the matrix indexing conventions in math and
# computer graphics image indexing conventions.
#
#
# Explicit extent
# ---------------
#
# By setting *extent* we define the coordinates of the image area. The
# underlying image data is interpolated/resampled to fill that area.
#
# If the axes is set to autoscale, then the view limits of the axes are set
# to match the *extent* which ensures that the coordinate set by
# ``(left, bottom)`` is at the bottom left of the axes! However, this
# may invert the axis so they do not increase in the 'natural' direction.
#

extents = [(-0.5, 6.5, -0.5, 5.5),
(-0.5, 6.5, 5.5, -0.5),
(6.5, -0.5, -0.5, 5.5),
(6.5, -0.5, 5.5, -0.5)]

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This set of examples doesn't really help me because the "extents" is still the same as the extents I'd expect from the underlying data array size. Wouldn't it be more illustrative to go from 0-15 or something? The phrase "...a bounding box in data space" is also mysterious. I think of the matrix as being the data and a bounding box on the data means a clip to me. But what you mean is that the extents are the x and y co-ordinates over which the matrix is placed.

The docs say "The location, in data-coordinates, of the lower-left and upper-right corners" ; I prefer "data-coordinates"

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The point is to show how inverting the left vs right or top vs bottom changes the image around. Using different limits would make that a harder apples-to-apples comparison.

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

yes But it didn’t help me understand what extents actually is on the first place

I’ll admit this flipping the axes seems like the wrong behaviour. I’d have expected the matrix to flip. But I doubt I’ll get that changed here. ;-)

columns = generate_imshow_demo_grid(extents)
set_extent_None_text(columns['upper'][1])
set_extent_None_text(columns['lower'][0])


###############################################################################
#
# Explicit extent and axes limits
# -------------------------------
#
# If we fix the axes limits by explicity setting `set_xlim` / `set_ylim`, we
# force a certain size and orientation of the axes.
# This can decouple the 'left-right' and 'top-bottom' sense of the image from
# the orientation on the screen.
#
# In the example below we have chosen the limits slightly larger than the
# extent (note the white areas within the Axes).
#
# While we keep the extents as in the examples before, the coordinate (0, 0)
# is now explicitly put at the bottom left and values increase to up and to
# the right (from the viewer point of view).
# We can see that:
#
# - The coordinate ``(left, bottom)`` anchors the image which then fills the
# box going towards the ``(right, top)`` point in data space.
# - The first column is always closest to the 'left'.
# - *origin* controls if the first row is closest to 'top' or 'bottom'.
# - The image may be inverted along either direction.
# - The 'left-right' and 'top-bottom' sense of the image may be uncoupled from
# the orientation on the screen.

generate_imshow_demo_grid(extents=[None] + extents,
xlim=(-2, 8), ylim=(-1, 6))