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‎.hgignore‎

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*.eclipse.*
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*.idea*
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*.project*
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doc/.*
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syntax: regexp
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^build$
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syntax: regexp

‎README.md‎

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### Grid manipulation ###
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Loading grid
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```python
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from py_eddy_tracker.dataset.grid import RegularGridDataset
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grid_name, lon_name, lat_name = 'share/nrt_global_allsat_phy_l4_20190223_20190226.nc', 'longitude', 'latitude'
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h = RegularGridDataset(grid_name, lon_name, lat_name)
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```
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Plotting grid
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```python
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from matplotlib import pyplot as plt
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fig = plt.figure(figsize=(14, 12))
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ax = fig.add_axes([.02, .51, .9, .45])
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ax.set_title('ADT (m)')
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ax.set_ylim(-75, 75)
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ax.set_aspect('equal')
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m = h.display(ax, name='adt', vmin=-1, vmax=1)
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ax.grid(True)
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plt.colorbar(m, cax=fig.add_axes([.94, .51, .01, .45]))
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```
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Filtering
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```python
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h = RegularGridDataset(grid_name, lon_name, lat_name)
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h.bessel_high_filter('adt', 500, order=3)
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```
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Save grid
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```python
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h.write('/tmp/grid.nc')
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```
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Add second plot
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```python
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ax = fig.add_axes([.02, .02, .9, .45])
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ax.set_title('ADT Filtered (m)')
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ax.set_aspect('equal')
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ax.set_ylim(-75, 75)
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m = h.display(ax, name='adt', vmin=-.1, vmax=.1)
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ax.grid(True)
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plt.colorbar(m, cax=fig.add_axes([.94, .02, .01, .45]))
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fig.savefig('share/png/filter.png')
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```
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![signal filtering](share/png/filter.png)
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#### Compute spectrum and spectrum ratio on some area ####
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Load data
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```python
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raw = RegularGridDataset(grid_name, lon_name, lat_name)
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filtered = RegularGridDataset(grid_name, lon_name, lat_name)
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filtered.bessel_low_filter('adt', 150, order=3)
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areas = dict(
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sud_pacific=dict(llcrnrlon=188, urcrnrlon=280, llcrnrlat=-64, urcrnrlat=-7),
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atlantic_nord=dict(llcrnrlon=290, urcrnrlon=340, llcrnrlat=19.5, urcrnrlat=43),
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indien_sud=dict(llcrnrlon=35, urcrnrlon=110, llcrnrlat=-49, urcrnrlat=-26),
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)
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```
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Compute and display spectrum
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```python
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fig = plt.figure(figsize=(10,6))
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ax = fig.add_subplot(111)
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ax.set_title('Spectrum')
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ax.set_xlabel('km')
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for name_area, area in areas.items():
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lon_spec, lat_spec = raw.spectrum_lonlat('adt', area=area)
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mappable = ax.loglog(*lat_spec, label='lat %s raw' % name_area)[0]
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ax.loglog(*lon_spec, label='lon %s raw' % name_area, color=mappable.get_color(), linestyle='--')
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lon_spec, lat_spec = filtered.spectrum_lonlat('adt', area=area)
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mappable = ax.loglog(*lat_spec, label='lat %s high' % name_area)[0]
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ax.loglog(*lon_spec, label='lon %s high' % name_area, color=mappable.get_color(), linestyle='--')
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ax.set_xscale('log')
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ax.legend()
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ax.grid()
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fig.savefig('share/png/spectrum.png')
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```
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![spectrum](share/png/spectrum.png)
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Compute and display spectrum ratio
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```python
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fig = plt.figure(figsize=(10,6))
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ax = fig.add_subplot(111)
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ax.set_title('Spectrum ratio')
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ax.set_xlabel('km')
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for name_area, area in areas.items():
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lon_spec, lat_spec = filtered.spectrum_lonlat('adt', area=area, ref=raw)
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mappable = ax.plot(*lat_spec, label='lat %s high' % name_area)[0]
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ax.plot(*lon_spec, label='lon %s high' % name_area, color=mappable.get_color(), linestyle='--')
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ax.set_xscale('log')
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ax.legend()
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ax.grid()
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fig.savefig('share/png/spectrum_ratio.png')
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```
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![spectrum ratio](share/png/spectrum_ratio.png)
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#### Run an identification on a grid ####
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Activate verbose
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```python
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import logging
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logging.getLogger().setLevel('DEBUG') # Values: ERROR, WARNING, INFO, DEBUG
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```
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Run identification
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```python
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from datetime import datetime
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h = RegularGridDataset(grid_name, lon_name, lat_name)
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h.bessel_high_filter('adt', 500, order=3)
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date = datetime(2019, 2, 23)
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a, c = h.eddy_identification(
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'adt', 'ugos', 'vgos', # Variable to use for identification
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date, # Date of identification
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0.002, # step between two isolines of detection (m)
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pixel_limit=(5, 2000), # Min and max of pixel can be include in contour
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shape_error=55, # Error maximal of circle fitting over contour to be accepted
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bbox_surface_min_degree=.125 ** 2, # degrees surface minimal to take in account contour
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)
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```
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Plot identification
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```python
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fig = plt.figure(figsize=(15,7))
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ax = fig.add_axes([.03,.03,.94,.94])
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ax.set_title('Eddies detected -- Cyclonic(red) and Anticyclonic(blue)')
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ax.set_ylim(-75,75)
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ax.set_xlim(0,360)
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ax.set_aspect('equal')
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a.display(ax, color='b', linewidth=.5)
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c.display(ax, color='r', linewidth=.5)
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ax.grid()
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fig.savefig('share/png/eddies.png')
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```
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![eddies detected](share/png/eddies.png)
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Save identification datas
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```python
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with Dataset(date.strftime('share/Anticyclonic_%Y%m%d.nc'), 'w') as h:
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a.to_netcdf(h)
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with Dataset(date.strftime('share/Cyclonic_%Y%m%d.nc'), 'w') as h:
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c.to_netcdf(h)
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```

‎doc/Makefile‎

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# Makefile for Sphinx documentation
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#
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# You can set these variables from the command line.
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SPHINXOPTS =
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SPHINXBUILD = sphinx-build
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PAPER =
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BUILDDIR = .build
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# User-friendly check for sphinx-build
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ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
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$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
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endif
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# Internal variables.
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PAPEROPT_a4 = -D latex_paper_size=a4
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PAPEROPT_letter = -D latex_paper_size=letter
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ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
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# the i18n builder cannot share the environment and doctrees with the others
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I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
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.PHONY: help
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help:
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@echo "Please use \`make <target>' where <target> is one of"
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@echo " html to make standalone HTML files"
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@echo " dirhtml to make HTML files named index.html in directories"
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@echo " singlehtml to make a single large HTML file"
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@echo " pickle to make pickle files"
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@echo " json to make JSON files"
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@echo " htmlhelp to make HTML files and a HTML help project"
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@echo " qthelp to make HTML files and a qthelp project"
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@echo " applehelp to make an Apple Help Book"
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@echo " devhelp to make HTML files and a Devhelp project"
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@echo " epub to make an epub"
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@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
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@echo " latexpdf to make LaTeX files and run them through pdflatex"
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@echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
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@echo " text to make text files"
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@echo " man to make manual pages"
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@echo " texinfo to make Texinfo files"
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@echo " info to make Texinfo files and run them through makeinfo"
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@echo " gettext to make PO message catalogs"
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@echo " changes to make an overview of all changed/added/deprecated items"
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@echo " xml to make Docutils-native XML files"
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@echo " pseudoxml to make pseudoxml-XML files for display purposes"
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@echo " linkcheck to check all external links for integrity"
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@echo " doctest to run all doctests embedded in the documentation (if enabled)"
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@echo " coverage to run coverage check of the documentation (if enabled)"
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.PHONY: clean
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clean:
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rm -rf $(BUILDDIR)/*
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.PHONY: html
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html:
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$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
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@echo
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@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
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.PHONY: dirhtml
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dirhtml:
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$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
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@echo
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@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
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.PHONY: singlehtml
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singlehtml:
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$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
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@echo
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@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
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.PHONY: pickle
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pickle:
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$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
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@echo
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@echo "Build finished; now you can process the pickle files."
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.PHONY: json
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json:
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$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
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@echo
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@echo "Build finished; now you can process the JSON files."
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.PHONY: htmlhelp
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htmlhelp:
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$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
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@echo
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@echo "Build finished; now you can run HTML Help Workshop with the" \
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".hhp project file in $(BUILDDIR)/htmlhelp."
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.PHONY: qthelp
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qthelp:
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$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
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@echo
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@echo "Build finished; now you can run "qcollectiongenerator" with the" \
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".qhcp project file in $(BUILDDIR)/qthelp, like this:"
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@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/py-eddy-tracker.qhcp"
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@echo "To view the help file:"
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@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/py-eddy-tracker.qhc"
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.PHONY: applehelp
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applehelp:
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$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
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@echo
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@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
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@echo "N.B. You won't be able to view it unless you put it in" \
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"~/Library/Documentation/Help or install it in your application" \
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"bundle."
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.PHONY: devhelp
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devhelp:
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$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
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@echo
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@echo "Build finished."
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@echo "To view the help file:"
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@echo "# mkdir -p $$HOME/.local/share/devhelp/py-eddy-tracker"
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@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/py-eddy-tracker"
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@echo "# devhelp"
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.PHONY: epub
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epub:
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$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
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@echo
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@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
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.PHONY: latex
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latex:
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$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
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@echo
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@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
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@echo "Run \`make' in that directory to run these through (pdf)latex" \
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"(use \`make latexpdf' here to do that automatically)."
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.PHONY: latexpdf
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latexpdf:
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$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
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@echo "Running LaTeX files through pdflatex..."
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$(MAKE) -C $(BUILDDIR)/latex all-pdf
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@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
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.PHONY: latexpdfja
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latexpdfja:
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$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
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@echo "Running LaTeX files through platex and dvipdfmx..."
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$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
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@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
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.PHONY: text
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text:
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$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
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@echo
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@echo "Build finished. The text files are in $(BUILDDIR)/text."
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.PHONY: man
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man:
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$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
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@echo
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@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
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.PHONY: texinfo
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texinfo:
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$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
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@echo
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@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
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@echo "Run \`make' in that directory to run these through makeinfo" \
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"(use \`make info' here to do that automatically)."
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.PHONY: info
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info:
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$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
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@echo "Running Texinfo files through makeinfo..."
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make -C $(BUILDDIR)/texinfo info
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@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
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.PHONY: gettext
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gettext:
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$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
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@echo
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@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
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.PHONY: changes
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changes:
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$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
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@echo
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@echo "The overview file is in $(BUILDDIR)/changes."
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.PHONY: linkcheck
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linkcheck:
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$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
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@echo
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@echo "Link check complete; look for any errors in the above output " \
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"or in $(BUILDDIR)/linkcheck/output.txt."
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.PHONY: doctest
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doctest:
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$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
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@echo "Testing of doctests in the sources finished, look at the " \
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"results in $(BUILDDIR)/doctest/output.txt."
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.PHONY: coverage
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coverage:
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$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
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@echo "Testing of coverage in the sources finished, look at the " \
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"results in $(BUILDDIR)/coverage/python.txt."
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.PHONY: xml
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xml:
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$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
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@echo
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@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
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.PHONY: pseudoxml
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pseudoxml:
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$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
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@echo
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@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

‎doc/autodoc/eddy_feature.rst‎

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Eddy Features
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=============
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.. automodule:: py_eddy_tracker.eddy_feature
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:members:
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:undoc-members:
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:show-inheritance:
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‎doc/autodoc/featured_tracking.rst‎

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Featured tracking
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=================
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.. automodule:: py_eddy_tracker.featured_tracking.old_tracker_reference
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:members:
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:undoc-members:
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:show-inheritance:

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