Add pargraph in example and use jupyterlab instead jupyter

Author: AntSimi

README.md

@@ -1,4 +1,4 @@
-[![Documentation Status](https://readthedocs.org/projects/py-eddy-tracker/badge/?version=latest)](https://py-eddy-tracker.readthedocs.io/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/py-eddy-tracker/badge/?version=latest)](https://py-eddy-tracker.readthedocs.io/en/latest/?badge=latest) [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/AntSimi/py-eddy-tracker/master?urlpath=lab/tree/notebooks/python_module/)
 
 # README #
 

doc/conf.py

@@ -50,9 +50,7 @@
         'binderhub_url': 'https://mybinder.org',
         'dependencies': ['../requirements.txt'],
         # Optional keys
-        # 'filepath_prefix': '<prefix>' # A prefix to prepend to any filepaths in Binder links.
-        # 'notebooks_dir': '<notebooks-directory-name>' # Jupyter notebooks for Binder will be copied to this directory (relative to built documentation root).
-        # 'use_jupyter_lab': <bool> # Whether Binder links should start Jupyter Lab instead of the Jupyter Notebook interface.
+        'use_jupyter_lab': True
     }
 }
 

doc/index.rst

@@ -27,20 +27,13 @@ Welcome to py-eddy-tracker's documentation!
    grid_load_display
    spectrum
 
-
 .. toctree::
    :maxdepth: 2
    :caption: Tracking
 
    run_tracking
    custom_tracking
 
-.. toctree::
-   :maxdepth: 2
-   :caption: Work with eddies
-
-   observation_manipulation
-
 .. toctree::
    :maxdepth: 2
    :caption: code

doc/observation_manipulation.rst

@@ -8,9 +8,12 @@
 from py_eddy_tracker.observations.observation import EddiesObservations
 from py_eddy_tracker import data
 
+# %%
+# Load detection files
 a = EddiesObservations.load_file(data.get_path("Anticyclonic_20190223.nc"))
 c = EddiesObservations.load_file(data.get_path("Cyclonic_20190223.nc"))
 
+# %%
 # Plot
 fig = plt.figure(figsize=(15, 8))
 ax = fig.add_subplot(111)

examples/02_eddy_identification/pet_display_id.py

@@ -12,7 +12,7 @@
 from py_eddy_tracker.dataset.grid import RegularGridDataset
 from py_eddy_tracker import data
 
-
+# %%
 def start_axes(title):
     fig = plt.figure(figsize=(13, 5))
     ax = fig.add_axes([0.03, 0.03, 0.90, 0.94])
@@ -28,6 +28,8 @@ def update_axes(ax, mappable=None):
         plt.colorbar(m, cax=ax.figure.add_axes([0.95, 0.05, 0.01, 0.9]))
 
 
+# %%
+# Load Input grid, ADT will be used to detect eddies
 g = RegularGridDataset(
     data.get_path("dt_med_allsat_phy_l4_20160515_20190101.nc"), "longitude", "latitude"
 )
@@ -36,6 +38,8 @@ def update_axes(ax, mappable=None):
 m = g.display(ax, "adt", vmin=-0.15, vmax=0.15)
 update_axes(ax, m)
 
+# %%
+# U/V are deduced from ADT, this algortihm are not usable around equator (~+- 2°)
 g.add_uv("adt")
 ax = start_axes("U/V deduce from ADT (m)")
 ax.set_xlim(2.5, 9), ax.set_ylim(37.5, 40)
@@ -44,27 +48,38 @@ def update_axes(ax, mappable=None):
 ax.quiver(g.x_c, g.y_c, u, v, scale=10)
 update_axes(ax, m)
 
+# %%
+# Apply high filter to remove long scale to highlight mesoscale
 g.bessel_high_filter("adt", 500, order=2)
-
 ax = start_axes("ADT (m) filtered (500km, order 2)")
 m = g.display(ax, "adt", vmin=-0.15, vmax=0.15)
 update_axes(ax, m)
 
+# %%
+#  Run identification with slice of 2 mm
 date = datetime(2016, 5, 15)
 a, c = g.eddy_identification("adt", "u", "v", date, 0.002)
 
+# %%
+# All closed contour found in this input grid (Display only 1 contour every 4)
 ax = start_axes("ADT closed contour (only 1 / 4 levels)")
 g.contours.display(ax, step=4)
 update_axes(ax)
 
+# %%
+# Contours include in eddies
 ax = start_axes("ADT contour used as eddies")
 g.contours.display(ax, only_used=True)
 update_axes(ax)
 
+# %%
+# Contours reject from several origin (shape error to high, several extremum in contour, ...)
 ax = start_axes("ADT contour reject")
 g.contours.display(ax, only_unused=True)
 update_axes(ax)
 
+# %%
+# Contours closed which contains several eddies
 ax = start_axes("ADT contour reject but which contain eddies")
 g.contours.label_contour_unused_which_contain_eddies(a)
 g.contours.label_contour_unused_which_contain_eddies(c)
@@ -76,12 +91,16 @@ def update_axes(ax, mappable=None):
 ax.legend()
 update_axes(ax)
 
+# %%
+# Display detected eddies
 ax = start_axes("Eddies detected")
 a.display(ax, color="r", linewidth=0.5, label="Anticyclonic", ref=-10)
 c.display(ax, color="b", linewidth=0.5, label="Cyclonic", ref=-10)
 ax.legend()
 update_axes(ax)
 
+# %%
+# Display speed radius of eddies detected
 ax = start_axes("Eddies speed radius (km)")
 a.scatter(ax, "radius_s", vmin=10, vmax=50, s=80, ref=-10, cmap="jet", factor=0.001)
 m = c.scatter(ax, "radius_s", vmin=10, vmax=50, s=80, ref=-10, cmap="jet", factor=0.001)

examples/02_eddy_identification/pet_eddy_detection.py

@@ -11,19 +11,26 @@
 from py_eddy_tracker.dataset.grid import RegularGridDataset
 from py_eddy_tracker import data
 
+# %%
+# Load an eddy file which contains contours
 a = EddiesObservations.load_file(data.get_path("Anticyclonic_20190223.nc"))
+
+# %%
+# Load a grid where we want found pixels in eddies or out
 g = RegularGridDataset(
     data.get_path("nrt_global_allsat_phy_l4_20190223_20190226.nc"),
     "longitude",
     "latitude",
 )
 
-# Plot
+# %%
+# For each contours, we will get pixels indice in contour.
 fig = plt.figure(figsize=(12, 6))
 ax = fig.add_axes((0.05, 0.05, 0.9, 0.9))
 ax.set_aspect("equal")
 ax.set_xlim(10, 70)
 ax.set_ylim(-50, -25)
+# We will used the outter contour
 x_name, y_name = a.intern(False)
 adt = g.grid("adt")
 mask = ones(adt.shape, dtype='bool')
@@ -33,7 +40,7 @@
 adt.mask[:] += ~mask
 g.display(ax, "adt")
 a.display(ax, label="Anticyclonic", color="g", lw=1, extern_only=True)
-
+# %%
 fig = plt.figure(figsize=(12, 6))
 ax = fig.add_axes((0.05, 0.05, 0.9, 0.9))
 ax.set_aspect("equal")

examples/06_grid_manipulation/pet_hide_pixel_out_eddies.py

@@ -8,13 +8,15 @@
 from py_eddy_tracker.observations.tracking import TrackEddiesObservations
 import py_eddy_tracker_sample
 
+# %%
+# Load an experimental cyclonic atlas, we keep only eddies which are follow more than 180 days
 c = TrackEddiesObservations.load_file(
     py_eddy_tracker_sample.get_path("eddies_med_adt_allsat_dt2018/Cyclonic.zarr")
 )
-
 c = c.extract_with_length((180, -1))
 
-# Plot
+# %%
+# Plot amplitude field
 fig = plt.figure(figsize=(12, 6))
 ax = fig.add_axes((0.05, 0.1, 0.9, 0.9))
 ax.set_aspect("equal")

examples/08_tracking_manipulation/pet_display_field.py

@@ -8,18 +8,23 @@
 from py_eddy_tracker.observations.tracking import TrackEddiesObservations
 import py_eddy_tracker_sample
 
+# %%
+# Load experimental atlas, and keep only eddies longer than 20 weeks
 a = TrackEddiesObservations.load_file(
     py_eddy_tracker_sample.get_path("eddies_med_adt_allsat_dt2018/Anticyclonic.zarr")
 )
 c = TrackEddiesObservations.load_file(
     py_eddy_tracker_sample.get_path("eddies_med_adt_allsat_dt2018/Cyclonic.zarr")
 )
-
 a = a.extract_with_length((7 * 20, -1))
 c = c.extract_with_length((7 * 20, -1))
+
+# %%
+# Position filtering for nice display
 a.position_filter(median_half_window=1, loess_half_window=5)
 c.position_filter(median_half_window=1, loess_half_window=5)
 
+# %%
 # Plot
 fig = plt.figure(figsize=(12, 5))
 ax = fig.add_axes((0.05, 0.1, 0.9, 0.9))

examples/08_tracking_manipulation/pet_display_track.py

@@ -1,20 +1,22 @@
 """
 One Track
 ===================
-
 """
 from matplotlib import pyplot as plt
 from py_eddy_tracker.observations.tracking import TrackEddiesObservations
 import py_eddy_tracker_sample
 
+# %%
+# Load experimental atlas, and we select one eddy
 a = TrackEddiesObservations.load_file(
     py_eddy_tracker_sample.get_path("eddies_med_adt_allsat_dt2018/Anticyclonic.zarr")
 )
-
 eddy = a.extract_ids([9672])
 eddy_f = a.extract_ids([9672])
 eddy_f.position_filter(median_half_window=1, loess_half_window=5)
 
+# %%
+# plot
 fig = plt.figure(figsize=(12, 5))
 ax = fig.add_axes((0.05, 0.05, 0.9, 0.9))
 ax.set_xlim(17.5, 22)
@@ -24,12 +26,15 @@
 eddy.plot(ax, color="r", lw=0.5)
 eddy_f.scatter(ax, "n", cmap="jet", s=80)
 
+# %%
 fig = plt.figure(figsize=(12, 5))
 ax = fig.add_axes((0.05, 0.05, 0.9, 0.9))
 ax.set_xlim(17, 23)
 ax.set_ylim(34.5, 37)
 ax.set_aspect("equal")
 ax.grid()
-eddy.plot(ax, color="r", lw=0.5, label='track')
-eddy.index(range(0, len(eddy), 40)).display(ax, intern_only=True, label='observations every 40')
+eddy.plot(ax, color="r", lw=0.5, label="track")
+eddy.index(range(0, len(eddy), 40)).display(
+    ax, intern_only=True, label="observations every 40"
+)
 ax.legend()