Skip to content

add example of exploration of a covariance matrix #652

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.

Sign up for GitHub

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 3 commits into from
Oct 17, 2024
Merged

add example of exploration of a covariance matrix #652

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
cdddf87
add cov matrix example
kushalkolar Oct 14, 2024
8ddfca8
new file: examples/machine_learning/README.rst
kushalkolar Oct 14, 2024
d3ad576
update conf.py with machine_learning examples section
kushalkolar Oct 17, 2024
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
5 changes: 3 additions & 2 deletions docs/source/conf.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -56,15 +56,16 @@
"subsection_order": ExplicitOrder(
[
"../../examples/image",
"../../examples/heatmap",
"../../examples/image_widget",
"../../examples/gridplot",
"../../examples/line",
"../../examples/line_collection",
"../../examples/scatter",
"../../examples/heatmap",
"../../examples/misc",
"../../examples/selection_tools",
"../../examples/machine_learning",
"../../examples/guis",
"../../examples/misc",
"../../examples/qt",
]
),
Expand Down
2 changes: 2 additions & 0 deletions examples/machine_learning/README.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
Machine Learning Examples
=========================
94 changes: 94 additions & 0 deletions examples/machine_learning/covariance.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,94 @@
"""
Explore Covariance Matrix
=========================

Example showing how you can explore a covariance matrix with a selector tool.
"""

# test_example = false
# sphinx_gallery_pygfx_docs = 'animate 10s'


import fastplotlib as fpl
from sklearn import datasets
from sklearn.preprocessing import StandardScaler

# load faces dataset
faces = datasets.fetch_olivetti_faces()
data = faces["data"]

# sort the data so it's easier to understand the covariance matrix
targets = faces["target"]
sort_indices = targets.argsort()
targets_sorted = targets[sort_indices]

X = data[sort_indices]

# scale the data w.r.t. mean and standard deviation
X = StandardScaler().fit_transform(X)

# compute covariance matrix
X = X.T
cov = X @ X.T / X.shape[1]

# reshaped image for each sample wil be 64 x 64 pixels
img = cov[0].reshape(64, 64)

# figure kwargs for image widget
# controller_ids = [[0, 1]] so we get independent controllers for each supblot
# the covariance matrix is 4096 x 4096 and the reshaped image ix 64 x 64
figure_kwargs = {"size": (700, 400), "controller_ids": [[0, 1]]}

# create image widget
iw = fpl.ImageWidget(
data=[cov, img], # display the covariance matrix and reshaped image of a row
cmap="bwr", # diverging colormap
names=["covariance", "row image"],
figure_kwargs=figure_kwargs,
)

# graphic that corresponds to image widget data array 0
# 0 is the covariance matrix, 1 is the reshaped image of a row from the covariance matrix

# add a linear selector to select y axis values so we can select rows of the cov matrix
selector_cov = iw.managed_graphics[0].add_linear_selector(axis="y")

# if you are exploring other types of matrices which are not-symmetric
# you can also add a column selector by setting axis="x"

# set vmin vmax
for g in iw.managed_graphics:
g.vmin, g.vmax = -1, 1


# event handler when the covariance matrix row changes
@selector_cov.add_event_handler("selection")
def update_img(ev):
# get the row index
ix = ev.get_selected_index()

# get the image the corresponds to this row
img = cov[ix].reshape(64, 64)

# change the reshaped image graphic data
iw.managed_graphics[1].data = img


figure = iw.figure # not required, just for the docs gallery to pick it up


# move the selector programmatically, this is mainly for the docs gallery
# for real use you can interact with the selector with your mouse
def animate():
selector_cov.selection += 1


iw.figure.add_animations(animate)

iw.show()

# NOTE: `if __name__ == "__main__"` is NOT how to use fastplotlib interactively
# please see our docs for using fastplotlib interactively in ipython and jupyter
if __name__ == "__main__":
print(__doc__)
fpl.run()
Loading