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Generate python notebook and html report for segmentation models #200

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a870269
Fix export to html
javier-alvarez Sep 5, 2020
68c87ce
Refactor reports
javier-alvarez Sep 6, 2020
0700ae8
Test file for report generation
javier-alvarez Sep 7, 2020
e3992c8
Merge remote-tracking branch 'origin/master' into jaalvare/segmentati…
javier-alvarez Sep 7, 2020
fcdfb2b
Fix segmentation report
javier-alvarez Sep 7, 2020
62aa055
Fix segmentation report
javier-alvarez Sep 7, 2020
09688cc
Fix display
javier-alvarez Sep 7, 2020
8a9589f
Fix display
javier-alvarez Sep 7, 2020
48a6dc0
Fix generate report path to metrics
javier-alvarez Sep 8, 2020
859c502
Add logging
javier-alvarez Sep 8, 2020
fe56fdc
Move generate report
javier-alvarez Sep 8, 2020
f37d136
Move generate report
javier-alvarez Sep 9, 2020
d6abc75
Merge remote-tracking branch 'origin/master' into jaalvare/segmentati…
javier-alvarez Sep 14, 2020
026870f
Undo changes
javier-alvarez Sep 14, 2020
cc64742
Fix boxplot
javier-alvarez Sep 14, 2020
c4e69ad
Fix mypy
javier-alvarez Sep 15, 2020
21e4888
Merge remote-tracking branch 'origin/master' into jaalvare/segmentati…
javier-alvarez Sep 14, 2020
04bf3db
Merge remote-tracking branch 'origin/master' into jaalvare/segmentati…
javier-alvarez Sep 15, 2020
9ebc378
Fix mypy
javier-alvarez Sep 15, 2020
3bb8ea7
Fix report
javier-alvarez Sep 15, 2020
26d2ced
Fix html
javier-alvarez Sep 15, 2020
8a5c08b
Add check to test
javier-alvarez Sep 15, 2020
9106067
Merge branch 'master' into jaalvare/segmentation_reports
javier-alvarez Sep 15, 2020
03ad107
Add nbconvert
javier-alvarez Sep 16, 2020
78cdf25
Merge branch 'jaalvare/segmentation_reports' of https://github.com/mi…
javier-alvarez Sep 15, 2020
6700797
Fix typo
javier-alvarez Sep 16, 2020
484c9f2
Add dependency
javier-alvarez Sep 16, 2020
bdcfd21
Change dependecy
javier-alvarez Sep 16, 2020
c6a3f7a
Move to reduce dependencies
javier-alvarez Sep 16, 2020
62be306
Merge remote-tracking branch 'origin/master' into jaalvare/segmentati…
javier-alvarez Sep 15, 2020
4884999
Merge remote-tracking branch 'origin/master' into jaalvare/segmentati…
javier-alvarez Sep 17, 2020
c1b0116
Update aml-sdk
javier-alvarez Sep 18, 2020
088a61e
Update aml-sdk
javier-alvarez Sep 18, 2020
d02bca4
Fix type
javier-alvarez Sep 18, 2020
f6eaed4
Fix type
javier-alvarez Sep 18, 2020
4af90c6
Revert README.md
javier-alvarez Sep 18, 2020
594e925
Revert env
javier-alvarez Sep 18, 2020
1f0dc8e
Add to package
javier-alvarez Sep 18, 2020
a58c42e
Fix file reader
javier-alvarez Sep 18, 2020
d64581a
Change path
javier-alvarez Sep 19, 2020
1c2b189
Fix path
javier-alvarez Sep 19, 2020
ed0fa05
Fix path
javier-alvarez Sep 20, 2020
b4a5ab3
Merge branch 'master' into jaalvare/segmentation_reports
javier-alvarez Sep 21, 2020
77f81cf
Merge remote-tracking branch 'origin/master' into jaalvare/segmentati…
ant0nsc Sep 21, 2020
de3ee33
PR comments
ant0nsc Sep 21, 2020
4242d56
tests and cleanup
ant0nsc Sep 21, 2020
3b0695f
cleanup
ant0nsc Sep 21, 2020
5b4aaed
Merge remote-tracking branch 'origin/master' into jaalvare/segmentati…
ant0nsc Sep 21, 2020
f7d4c38
message
ant0nsc Sep 21, 2020
3fb9d48
test fixes
ant0nsc Sep 21, 2020
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ant0nsc committed Sep 21, 2020
commit f7d4c38154e8786f361b7501142c3896d0c167df
1 change: 1 addition & 0 deletions InnerEye/ML/reports/segmentation_report.py
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ def plot_scores_for_csv(path_csv: str) -> None:
Displays all the tables and figures given a csv file with segmentation metrics
Columns expected: Patient,Structure,Dice,HausdorffDistance_mm,MeanDistance_mm
"""
print(f"Reading raw metrics data from: {path_csv}")
df = pd.read_csv(path_csv)
with pd.option_context('display.max_rows', None, 'display.max_columns', None, 'display.width', 150):
display_metric(df, MetricsFileColumns.Dice.value, high_values_are_good=True)
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