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NIH Deeplesion#1769

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zl190 wants to merge 59 commits intotensorflow:masterfrom
zl190:master
Open

NIH Deeplesion#1769
zl190 wants to merge 59 commits intotensorflow:masterfrom
zl190:master

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@zl190 zl190 commented Mar 30, 2020

Add Dataset

Description

The DeepLesion dataset contains 32,120 axial computed tomography (CT) slices
from 10,594 CT scans (studies) of 4,427 unique patients. There are 1–3 lesions
in each image with accompanying bounding boxes and size measurements,
adding up to 32,735 lesions altogether. The lesion annotations were
mined from NIH’s picture archiving and communication system (PACS).

Checklist

  • Address all TODO's
  • Add alphabetized import to subdirectory's __init__.py
  • Run download_and_prepare successfully
  • Add checksums file
  • Properly cite in BibTeX format
  • Add passing test(s)
  • Add test data
  • Add data generation script (if applicable)
  • Lint code

zl190 and others added 30 commits November 21, 2019 18:09
add url, citation and description
a0c9117
data can be downloaded from remote
3414ae9
update .gitignore to ignore jupyter notebook
f0420e8
add pandas as DATASET_EXTRAS for deeplesion in setup.py
c3b4d24
finished split and generate example part; test on local
0438e3f
add instruction of manually place the data; this version relies on ma…
cef0c06 
…nually download data
add data for test; test passed; refine the document;
576f3a2
resolve suggested changes from us
1d94cfd
replace pandas with csv; fix a variale name inconsisent error; format…
a9fe3a1 
…ed manual_down_instruction
@zl190
merged
e5a6aed
@zl190
fix the bug that fake_examples/zipfile03 not exist
bf4f0eb
@zl190
add comments and minor change the code for readability
fd0bf36
@zl190
Merge pull request #8 from jason-zl190/add_config
affb29c 
add comments and minor change the code for readability
@zl190
delete empty line; remove unused line
e4ed2b6
@zl190
Merge pull request #9 from jason-zl190/fix_nit
385c030 
delete empty line; remove unused line
@zl190
replace a class with a simpler function; update comments
4ff137d
@zl190
shorter the code according to cyfra's suggestion
e0e6848
@zl190
allow multiple bboxs associateiated with an image
5cd77c6
@zl190
Merge pull request #10 from jason-zl190/fix_nit
f20db6b 
Fix nit
@zl190
Merge branch 'master' into jasonfix
67f62e3
@zl190
refine the code and comment based on the suggestions from cyfra
5f1839a
@zl190
Merge pull request #11 from jason-zl190/fix_nit
c09e675 
refine the code and comment based on the suggestions from cyfra
@zl190
add url, citation and description
30e4a94
@zl190
data can be downloaded from remote
eaa7fa2
@zl190
update .gitignore to ignore jupyter notebook
d04ac1c
@zl190
add pandas as DATASET_EXTRAS for deeplesion in setup.py
4a7d5c8
@zl190
add data for test; test passed; refine the document;
737d58a
@zl190
resolve suggested changes from us
bd59fcf
@zl190
finished split and generate example part; test on local
62aacb4
@zl190
replace pandas with csv; fix a variale name inconsisent error; format…
924cadd 
…ed manual_down_instruction
zl190 and others added 9 commits January 7, 2020 00:14
@zl190
Merge pull request #13 from jason-zl190/jasonfix
7d5ea3a 
merge jasonfix into master
@zl190
refactor the code to read data directly from archives
e4f08d5
@zl190
chagne version to 1.0.0
008fd1c
@zl190
add three configs for 2d object detection, 2d classification, and 3d …
34e8187 
…object detection
@zl190
Merge pull request #16 from jason-zl190/two_configs
b400799 
add two more configs
@zl190
improve filter methond used to generate normal scans
697b9cf
@zl190
replace two configs: 2d and 2d_clf with two new configs:
f1e6fa8 
the two new configs named `abnormal` and `normal`. `abnormal` contains the same
data and features as the previous `2d` except the feature `label`. On the other
hand, `normal` contains only normal data(the same number as `abnormal`). The
`label` features has been removed from two new configs because data contained
in the two new configs is pure. This change aims to support more flexible data
usage.
@zl190
confiict solved
f54c8e1
@zl190
add test to the changed configs
d7fe91d
@googlebot googlebot added the cla: yes Author has signed CLA label Mar 30, 2020
@zl190 zl190 mentioned this pull request Mar 30, 2020
Open
@tfds-bot tfds-bot added the community:please_review Community - We need your help to review this PR. label Mar 31, 2020
@zl190 zl190 mentioned this pull request Mar 31, 2020
Closed
@Conchylicultor Conchylicultor added the dataset request Request for a new dataset to be added label Apr 2, 2020
cyfra
cyfra suggested changes Apr 8, 2020
View reviewed changes
Comment thread tensorflow_datasets/object_detection/deeplesion.py Outdated
Comment thread tensorflow_datasets/object_detection/deeplesion.py Outdated
Comment thread tensorflow_datasets/object_detection/deeplesion.py Outdated
Comment thread tensorflow_datasets/object_detection/deeplesion.py Outdated
Comment thread tensorflow_datasets/object_detection/deeplesion.py Outdated
Comment thread tensorflow_datasets/object_detection/deeplesion.py Outdated
Comment thread tensorflow_datasets/object_detection/deeplesion.py Outdated
Comment thread tensorflow_datasets/object_detection/deeplesion.py
@tfds-bot tfds-bot added author:please_respond Author - please respond to the recent comments. and removed community:please_review Community - We need your help to review this PR. labels Apr 8, 2020
@Ouwen
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Ouwen commented Apr 8, 2020

@jason-zl190

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zl190 commented Apr 9, 2020

@cyfra Thanks for your review and advice. I changed the code as your suggestion. Please let me know if there is anything I missed.

@tfds-bot tfds-bot added tfds:is_reviewing TFDS team: PTAL and removed author:please_respond Author - please respond to the recent comments. labels Apr 9, 2020
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