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Drag Window/Contrast / Better Zoom (#55)
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* Update simple-dash.ipynb

adding link to download html file

* Update environment.yml

reverting back to standard appmode and using jupyter_notebook_url

* Update README.md

updating links to use new style for passing variables

* Delete dashboard.ipynb

updating dashboard

* Add files via upload

adding updated dashboard

* Create __init__.py

first limited version of notebook functions as giant mega-file #41

* Update postBuild

removing appmode activate since conda takes care of it

* Update __init__.py

making pep8speaks happy or at least trying

* Update __init__.py

trying again to make @pep8speaks happy

* Update __init__.py

one last try

* Update environment.yml

adding jupyter dashboards

* Delete dashboard.ipynb

updating dashboard

* Add files via upload

adding new version of dashboard

* Update anno_app.ipynb

show the toolbar, add a windowing tool by dragging and fix the zoom to work more reliably
still need to work on making the figure big enough

* Update postBuild

switch to high resolution images

* Update anno_app.ipynb

tweaking zoom to only set one axis, updating to higher resolution images

* Update .travis.yml

enabling globstar for notebook analysis

* Update .travis.yml

changing to **

* Update .travis.yml

Fixes #60

* Update README.md

adding fancy badges

* Create pytest.ini

adding doctests

* Update .travis.yml

add code to fix backed to agg

* Update .travis.yml

added type checking with mypy

* Update __init__.py

adding test to binary_correct

* Update __init__.py

making pep8 happy

* Update .travis.yml

removing agg mode line (probably only an issue in binder)

* Create setup.cfg

adding setup files to make a more serious package

* Create setup.py

first very simple setup.y

* Update postBuild

adding package to environment

* Create sheets.py

moving sheets functions to sheets

* Create widgets.py

moving widgets into their own file

* Update __init__.py

cleaned up __init__

* Update anno_app.ipynb

moving annotation and widget code to library

* Delete dashboard.ipynb

moving dashboard to notebooks

* Add files via upload

adding lightweight dashboard to notebooks

* Delete simple-dash.ipynb

updating simpledash

* Add files via upload

adding new version of simple dash

* Update dashboard.ipynb

fixing task path

* Update __init__.py

adding relative path support

* moving notebooks to notebook directory

* fixing bug in dashboard, trying soo hard to make @pep8speaks happy

* removing unneeded imports, fixing get user code to inspect the local variables as well, fixing bug in dashboard

* adding test for safe_json, changing order of tests

* fixing long lines and adding more tests

* fixing get_user_id function, adding tests for plotly

* fixing buggy version of pytest on mac/darwin, refactoring code out of init adding task, adding tests

* removing pytest line in travis (it seemed to uninstall matplotlib???)

* splitting up tests, fixing flake8 issues

* fixing notebook execution code

* moving notebooks to its own build

* adding fancy format function

* fixing style issues, adding encode b64 for numpy arrays

* changing to master
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kmader authored Aug 30, 2018
1 parent 7bb36c4 commit 6631c28
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22 changes: 2 additions & 20 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,8 @@ sample_data/*
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
Expand All @@ -25,17 +23,14 @@ wheels/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
Expand All @@ -47,41 +42,30 @@ coverage.xml
*.cover
.hypothesis/
.pytest_cache/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# Jupyter Notebook
.ipynb_checkpoints

# pyenv
.python-version

# celery beat schedule file
celerybeat-schedule

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
Expand All @@ -90,16 +74,14 @@ venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.Rproj.user
.idea/
21 changes: 12 additions & 9 deletions .travis.yml
Original file line number Diff line number Diff line change
Expand Up @@ -9,15 +9,18 @@ cache:

env:
matrix:
- DISTRIB="conda" PYTHON_VERSION="3.6" COVERAGE="false"
- DISTRIB="conda" PYTHON_VERSION="3.6" TO_TEST=CODE
- DISTRIB="conda" PYTHON_VERSION="3.6" TO_TEST=NOTEBOOKS
- DISTRIB="conda" PYTHON_VERSION="3.6" TO_TEST=STYLE

install: source build_tools/travis_install.sh

install:
- source build_tools/travis_install.sh
- pip install pytest-cov codecov mypy flake8

script:
- for nb in *ipynb; do
jupyter nbconvert --ExecutePreprocessor.timeout=3600 --execute "$nb" --to markdown |& tee nb_to_md.txt;
traceback=$(grep "Traceback (most recent call last):" nb_to_md.txt);
if [[ $traceback ]]; then
exit 1;
fi;
done
- if [ "$TO_TEST" = "CODE" ]; then mypy -p jupyanno --ignore-missing-imports; fi
- if [ "$TO_TEST" = "CODE" ]; then pytest --cov=jupyanno; fi
- if [ "$TO_TEST" = "CODE" ]; then codecov; fi
- if [ "$TO_TEST" = "STYLE" ]; then flake8 --ignore E501,F401; fi
- if [ "$TO_TEST" = "NOTEBOOKS" ]; then source build_tools/travis_notebooks.sh; fi
6 changes: 3 additions & 3 deletions README.md
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@@ -1,11 +1,11 @@
# jupyanno
# jupyanno [![Build Status](https://travis-ci.org/chestrays/jupyanno.svg?branch=master)](https://travis-ci.org/chestrays/jupyanno) [![codecov](https://codecov.io/gh/chestrays/jupyanno/branch/master/graph/badge.svg)](https://codecov.io/gh/chestrays/jupyanno)

A simple set of jupyter-based tools for quickly annotating images using IPython widgets. The toolkit is made to be easily extensible and suggestions / improvements are welcome.

# Chest X-Ray Task

Here we have a demo chest X-Ray task where the annotation and viewing of a sample dataset can be done entirely with these tools.

[![Binder Annotation Tool](https://img.shields.io/badge/launch-annotation_tool-red.svg)](https://mybinder.org/v2/gh/chestrays/jupyanno/master?urlpath=%2Fmuapps%2Frandom_githubber%2Fanno_app.ipynb)
[![Binder Dashboard Tool](https://img.shields.io/badge/launch-dashboard-blue.svg)](https://mybinder.org/v2/gh/chestrays/jupyanno/master?urlpath=%2Fmuapps%2Fadmin%2Fdashboard.ipynb)
[![Binder Annotation Tool](https://img.shields.io/badge/launch-annotation_tool-red.svg)](https://mybinder.org/v2/gh/chestrays/jupyanno/master?urlpath=%2Fapps%2Fanno_app.ipynb%3Fuser%3Drandom_githubber)
[![Binder Dashboard Tool](https://img.shields.io/badge/launch-dashboard-blue.svg)](https://mybinder.org/v2/gh/chestrays/jupyanno/master?urlpath=%2Fapps%2Fdashboard.ipynb%3Fuser%3Drandom_githubber)
[![Google Sheets Results](https://img.shields.io/badge/show-sheets-green.svg)](https://docs.google.com/spreadsheets/d/1T02tRhe3IUUHYsMchc7hmH8nVI3uR0GffdX1PNxKIZA/edit#gid=1178875150)
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