First commit

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.pytest_cache/*
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+docs/index.doctree
+
+# test results
+matplotlibrc
+*psyplot_testresults
+tests/envs/cov_psyplot_py*
+tests/envs/psyplot_py*.html
+
+# PyBuilder
+target/
+
+# Spyder project
+.spyderproject
+
+# Example ipython notebook checkpoints
+*.ipynb_checkpoints/
+
+# test pictures
+tests/test_diagram*.png
+tests/chinese.*
+
+*.pkl

MANIFEST.in

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+include README.rst
+include LICENSE
+include straditize/widgets/icons/*.png
+include straditize/widgets/docs/*.rst
+include straditize/widgets/docs/*.png

README.rst

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+=================================
+Digitizing stratigraphic diagrams
+=================================
+
+STRADITIZE (Stratigraphic Diagram Digitizer) is an open-source program that
+allows stratigraphic figures to be digitized in a single semi-automated
+operation. It is designed to detect multiple plots of variables analyzed along
+the same vertical axis, whether this is a sediment core or any similar
+depth/time series.
+
+Usually, in an age of digital data analysis, gaining access to data from the
+pre-digital era – or any data that is only available as a figure on a page –
+remains a problem and an under-utilized scientific resource.
+
+This program tackles this problem by providing a python package to digitize
+especially pollen diagrams, but also any other type of stratigraphic diagram.
+
+Straditize is written in python and supports mixtures of many different diagram
+types, such as bar plots, line plots, as well as shaded, stacked, and filled
+area plots. The package provides an extensively documented graphical user
+interface for a point-and-click handling of the semi-automatic process, but can
+also be scripted or used from the command line. Other features of STRADITIZE
+include text recognition to interpret the names of the different plotted
+variables, the automatic and semi-automatic recognition of picture artifacts,
+as well an automatic measurement finder to exactly reproduce the data that has
+been used to create the diagram.
+
+**BETA-VERSION**: Straditize is currently in it's beta version. New
+installation methods will be provided and the documentation will be
+significantly improved.
+
+EGU Presentation
+-----------------
+straditize will be presented at the  European Geosciences Union General
+Assembly (EGU) 2018 as a `PICO presentation`_ in the session of
+`Free and Open Source Software (FOSS) for Geoinformatics and Geosciences`_.
+
+The PICO presentation files can be downloaded via http://dx.doi.org/10.13140/RG.2.2.34357.58083
+
+.. _PICO presentation: https://meetingorganizer.copernicus.org/EGU2018/EGU2018-4433.pdf
+.. _Free and Open Source Software (FOSS) for Geoinformatics and Geosciences: https://meetingorganizer.copernicus.org/EGU2018/session/26511
+
+Installation
+------------
+At the moment, straditize has to be installed from the source files, i.e. the
+github repository. We highly recommend to use anaconda_ and install the
+dependencies via::
+
+    conda config --add channels conda-forge
+    conda install -c chilipp/label/dev psyplot-gui scikit-image
+    git clone https://github.com/Chilipp/straditize.git
+    cd straditize
+    python setup.py install
+
+It can then be started from the command line via::
+
+    straditize

icon/CreateICNS.sh

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+mkdir main.iconset
+sips -z 16 16     icon1024.png --out main.iconset/icon_16x16.png
+sips -z 32 32     icon1024.png --out main.iconset/icon_16x16@2x.png
+sips -z 32 32     icon1024.png --out main.iconset/icon_32x32.png
+sips -z 64 64     icon1024.png --out main.iconset/icon_32x32@2x.png
+sips -z 128 128   icon1024.png --out main.iconset/icon_128x128.png
+sips -z 256 256   icon1024.png --out main.iconset/icon_128x128@2x.png
+sips -z 256 256   icon1024.png --out main.iconset/icon_256x256.png
+sips -z 512 512   icon1024.png --out main.iconset/icon_256x256@2x.png
+sips -z 512 512   icon1024.png --out main.iconset/icon_512x512.png
+cp icon1024.png main.iconset/icon_512x512@2x.png
+iconutil -c icns main.iconset
+rm -R main.iconset

icon/CreateICO.sh

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+convert icon1024.png -define icon:auto-resize=64,48,32,16 straditize.ico

icon/icon.py

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+"""Create the psyplot icon
+
+This script creates the psyplot icon with a dpi of 128 and a width and height
+of 8 inches. The file is saved it to ``'icon1024.png'``"""
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.patches as mpatches
+import matplotlib.colors as mcol
+
+fig = plt.figure(figsize=(8, 8), dpi=128)
+
+ax = fig.add_axes([0.0, 0.0, 1.0, 1.0], facecolor='none')
+ax.axis('off')
+
+cmap = plt.get_cmap('binary')
+
+xlines = np.arange(0, 41, 5)
+nlines = len(xlines)
+
+colors = np.r_[cmap(np.linspace(0, 0.9, nlines // 2)),
+               cmap(np.linspace(0, 0.9, nlines // 2))[::-1]]
+
+full_cmap = mcol.LinearSegmentedColormap.from_list('Reds_sedR', colors,
+                                                   nlines)
+
+x = np.array([
+    2, 5, 1, 8, 0, 5, 0, 6, 1, 4, 7, 5, 1, 1, 5, 0, 4, 0, 6, 1, 4, 1, 5, 2, 6,
+    8, 5, 0, 3, 0, 6, 2, 1, 3, 2, 5, 7, 5, 4, 3])
+
+for i in xlines:
+    ax.plot(x + i, np.arange(len(x)), color=full_cmap(i/40.), lw=10.0)
+
+patch = mpatches.Circle((0.5, 0.5), radius=0.49, transform=ax.transAxes,
+                        facecolor='k', zorder=0.5)
+# the border of the circle
+border = mpatches.Circle((0.5, 0.5), radius=0.49, transform=ax.transAxes,
+                         facecolor='none', edgecolor='lightgray', linewidth=10,
+                         zorder=10)
+
+for l in ax.lines:
+    l.set_clip_path(patch)
+
+ax.add_patch(patch)
+ax.add_patch(border)
+
+ax.set_xlim(0, 45)
+ax.set_ylim(2.5, 40)
+
+plt.savefig('icon1024.png', transparent=True)

setup.py

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+import os.path as osp
+from setuptools import setup, find_packages
+import sys
+
+needs_pytest = {'pytest', 'test', 'ptr'}.intersection(sys.argv)
+pytest_runner = ['pytest-runner'] if needs_pytest else []
+
+
+def readme():
+    with open('README.rst') as f:
+        return f.read()
+
+
+# read the version from version.py
+with open(osp.join('straditize', 'version.py')) as f:
+    exec(f.read())
+
+
+setup(name='straditize',
+      version=__version__,
+      description='Python package for digitizing pollen diagrams',
+      long_description=readme(),
+      classifiers=[
+        'Development Status :: 1 - Planning',
+        'Intended Audience :: Developers',
+        'Topic :: Scientific/Engineering :: Visualization',
+        'Topic :: Scientific/Engineering :: GIS',
+        'Topic :: Scientific/Engineering',
+        'License :: OSI Approved :: GNU General Public License v2 (GPLv2)',
+        'Programming Language :: Python :: 2',
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.2',
+        'Programming Language :: Python :: 3.3',
+        'Programming Language :: Python :: 3.4',
+        'Programming Language :: Python :: 3.5',
+        'Operating System :: OS Independent',
+      ],
+      keywords=('visualization earth-sciences paleo climate paleoclimate '
+                'pollen diagram digitization database'),
+      url='https://github.com/Chilipp/straditize',
+      author='Philipp Sommer',
+      author_email='philipp.sommer@unil.ch',
+      license="GPLv2",
+      packages=find_packages(exclude=['docs', 'tests*', 'examples']),
+      install_requires=[
+          'psyplot',
+          'psyplot-gui>1.0.1',
+          'scipy',
+          'scikit-image',
+      ],
+      package_data={'straditize': [
+          osp.join('straditize', 'widgets', 'icons', '*.png'),
+          osp.join('straditize', 'widgets', 'docs', '*.rst'),
+          osp.join('straditize', 'widgets', 'docs', '*.png'),
+          ]},
+      include_package_data=True,
+      setup_requires=pytest_runner,
+      tests_require=['pytest'],
+      entry_points={
+          'console_scripts': ['straditize=straditize.__main__:main'],
+          'psyplot_gui': ['straditizer=straditize.widgets:StraditizerWidgets'],
+          },
+      zip_safe=False)

straditize/__init__.py

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+from straditize.version import __version__