Skip to content

Update distogram definition #5

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

Open
sohmandal wants to merge 3 commits into
base: master
Choose a base branch
from
Open

Update distogram definition #5

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
8030c07
Fix params
sohmandal Mar 8, 2023
bf0ba9c
Fix parentheses
sohmandal Mar 8, 2023
d94d452
Prevent distance matrix values to be normalised
sohmandal Mar 8, 2023
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
8 changes: 4 additions & 4 deletions bioimage_phenotyping/shapes.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -164,15 +164,15 @@ def df_to_distance_matrix(df):


#%TODO Number of bins matters
def df_to_distogram(df, hist_range=(0, 1)):
def df_to_distogram(df):
return df_to_distance_matrix(df).apply(
lambda x: np.histogram(x, bins=2 * len(x), range=hist_range)[0],
lambda x: np.histogram(x, bins=64, range=(0,1.414))[0],
axis=1,
result_type="expand",
)


def distance_matrix_to_cyclic_distograms(distmat, hist_range=(0, 1)):
def distance_matrix_to_cyclic_distograms(distmat):
cyclic_distograms = []

distmat = np.array(distmat)
Expand All @@ -187,7 +187,7 @@ def distance_matrix_to_cyclic_distograms(distmat, hist_range=(0, 1)):
a = [item for sublist in a for item in sublist]
a = np.array(a)

distogram = np.histogram(a, bins=2 * len(a), range=hist_range)[0]
distogram = np.histogram(a, bins=64, range=(0,1.414))[0]
cyclic_distograms.append(distogram)

cyclic_distograms = [item for sublist in cyclic_distograms for item in sublist]
Expand Down
115 changes: 59 additions & 56 deletions splines.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion splines.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -142,7 +142,7 @@ def normalise_nd(arr):
df_distance_matrix = (
(df_splinedist.pipe(shapes.df_to_distance_matrix))
.rename(index={"Control Points": "Control Points Dist"}, level="Features")
.bip.preprocess()
# .bip.preprocess()
)

df_distogram = (
Expand Down