Add example about tracking

Author: AntSimi

examples/08_tracking_manipulation/pet_run_a_tracking.py

@@ -0,0 +1,76 @@
+"""
+Track in python
+===============
+
+This example didn't replace EddyTracking, we remove check that application do and also postprocessing step.
+"""
+
+# %%
+
+from py_eddy_tracker.data import get_remote_sample
+from py_eddy_tracker.tracking import Correspondances
+from py_eddy_tracker.featured_tracking.area_tracker import AreaTracker
+from numpy import where, empty
+from py_eddy_tracker.gui import GUI
+
+
+# %%
+# Function to have track with contiguous longitude
+def wrap_longitude(eddies):
+    lon = eddies.longitude
+    first = where(eddies.obs["n"] == 0)[0]
+    nb_obs = empty(first.shape, dtype="u4")
+    nb_obs[:-1] = first[1:] - first[:-1]
+    nb_obs[-1] = lon.shape[0] - first[-1]
+    lon0 = (lon[first] - 180).repeat(nb_obs)
+    lon[:] = (lon - lon0) % 360 + lon0
+
+
+# %%
+# Get remote data, we will keep only 180 first days
+file_objects = get_remote_sample(
+    "eddies_med_adt_allsat_dt2018/Anticyclonic_2010_2011_2012"
+)[:180]
+
+# %%
+# We run a traking with a tracker which use contour overlap
+c = Correspondances(datasets=file_objects, class_method=AreaTracker)
+c.track()
+c.prepare_merging()
+# We have now an eddy object
+eddies_area_tracker = c.merge(raw_data=False)
+wrap_longitude(eddies_area_tracker)
+
+# %%
+# We run a traking with default tracker
+c = Correspondances(datasets=file_objects)
+c.track()
+c.prepare_merging()
+eddies_default_tracker = c.merge(raw_data=False)
+wrap_longitude(eddies_default_tracker)
+
+# %%
+# Start GUI to compare tracking
+g = GUI(
+    Acyc_area_tracker=eddies_area_tracker, Acyc_default_tracker=eddies_default_tracker
+)
+g.now = 22000
+g.bbox = 0, 9, 36, 40
+g.adjust()
+g.show()
+
+# %%
+# Start GUI with area tracker
+g = GUI(Acyc_area_tracker=eddies_area_tracker)
+g.now = 22000
+g.bbox = 0, 9, 36, 40
+g.adjust()
+g.show()
+
+# %%
+# Start GUI with default one
+g = GUI(Acyc_default_tracker=eddies_default_tracker)
+g.now = 22000
+g.bbox = 0, 9, 36, 40
+g.adjust()
+g.show()

notebooks/python_module/02_eddy_identification/pet_eddy_detection.ipynb

@@ -188,7 +188,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Display detected eddies, dashed lines represent effective contour \nand solid lines represent contour of maximum of speed. See figure 1 of https://doi.org/10.1175/JTECH-D-14-00019.1\n\n"
+        "Display detected eddies, dashed lines represent effective contour\nand solid lines represent contour of maximum of speed. See figure 1 of https://doi.org/10.1175/JTECH-D-14-00019.1\n\n"
       ]
     },
     {

notebooks/python_module/08_tracking_manipulation/pet_run_a_tracking.ipynb

@@ -0,0 +1,180 @@
+{
+  "cells": [
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "%matplotlib inline"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "\nTrack in python\n===============\n\nThis example didn't replace EddyTracking, we remove check that application do and also postprocessing step.\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "from py_eddy_tracker.data import get_remote_sample\nfrom py_eddy_tracker.tracking import Correspondances\nfrom py_eddy_tracker.featured_tracking.area_tracker import AreaTracker\nfrom numpy import where, empty\nfrom py_eddy_tracker.gui import GUI"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Function to have track with contiguous longitude\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "def wrap_longitude(eddies):\n    lon = eddies.longitude\n    first = where(eddies.obs[\"n\"] == 0)[0]\n    nb_obs = empty(first.shape, dtype=\"u4\")\n    nb_obs[:-1] = first[1:] - first[:-1]\n    nb_obs[-1] = lon.shape[0] - first[-1]\n    lon0 = (lon[first] - 180).repeat(nb_obs)\n    lon[:] = (lon - lon0) % 360 + lon0"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Get remote data, we will keep only 180 first days\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "file_objects = get_remote_sample(\n    \"eddies_med_adt_allsat_dt2018/Anticyclonic_2010_2011_2012\"\n)[:180]"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "We run a traking with a tracker which use contour overlap\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "c = Correspondances(datasets=file_objects, class_method=AreaTracker)\nc.track()\nc.prepare_merging()\n# We have now an eddy object\neddies_area_tracker = c.merge(raw_data=False)\nwrap_longitude(eddies_area_tracker)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "We run a traking with default tracker\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "c = Correspondances(datasets=file_objects)\nc.track()\nc.prepare_merging()\neddies_default_tracker = c.merge(raw_data=False)\nwrap_longitude(eddies_default_tracker)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Start GUI to compare tracking\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "g = GUI(\n    Acyc_area_tracker=eddies_area_tracker, Acyc_default_tracker=eddies_default_tracker\n)\ng.now = 22000\ng.bbox = 0, 9, 36, 40\ng.adjust()\ng.show()"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Start GUI with area tracker\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "g = GUI(Acyc_area_tracker=eddies_area_tracker)\ng.now = 22000\ng.bbox = 0, 9, 36, 40\ng.adjust()\ng.show()"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Start GUI with default one\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "g = GUI(Acyc_default_tracker=eddies_default_tracker)\ng.now = 22000\ng.bbox = 0, 9, 36, 40\ng.adjust()\ng.show()"
+      ]
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3",
+      "language": "python",
+      "name": "python3"
+    },
+    "language_info": {
+      "codemirror_mode": {
+        "name": "ipython",
+        "version": 3
+      },
+      "file_extension": ".py",
+      "mimetype": "text/x-python",
+      "name": "python",
+      "nbconvert_exporter": "python",
+      "pygments_lexer": "ipython3",
+      "version": "3.7.7"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 0
+}

share/fig.py

@@ -1,5 +1,7 @@
 from matplotlib import pyplot as plt
 from py_eddy_tracker.dataset.grid import RegularGridDataset
+from datetime import datetime
+import logging
 
 grid_name, lon_name, lat_name = (
     "nrt_global_allsat_phy_l4_20190223_20190226.nc",
@@ -29,10 +31,7 @@
 fig.savefig("png/filter.png")
 
 
-import logging
-
 logging.getLogger().setLevel("DEBUG")  # Values: ERROR, WARNING, INFO, DEBUG
-from datetime import datetime
 
 h = RegularGridDataset(grid_name, lon_name, lat_name)
 h.bessel_high_filter("adt", 500, order=3)

src/py_eddy_tracker/generic.py

@@ -185,7 +185,7 @@ def fit_circle(x_vec, y_vec):
     datas[:, 0] = 2.0 * (x_vec[1:] - x_mean) / scale
     datas[:, 1] = 2.0 * (y_vec[1:] - y_mean) / scale
 
-    (center_x, center_y, radius), residuals, rank, s = lstsq(datas, norme / norme_max)
+    (center_x, center_y, radius), _, _, _ = lstsq(datas, norme / norme_max)
 
     # Unscale data and get circle variables
     radius += center_x ** 2 + center_y ** 2

src/py_eddy_tracker/gui.py

@@ -108,6 +108,10 @@ def set_initial_values(self):
     def now(self):
         return self.settings["now"]
 
+    @now.setter
+    def now(self, value):
+        self.settings["now"] = value
+
     @property
     def period(self):
         return self.settings["period"]
@@ -116,6 +120,11 @@ def period(self):
     def bbox(self):
         return self.map.get_xlim(), self.map.get_ylim()
 
+    @bbox.setter
+    def bbox(self, values):
+        self.map.set_xlim(values[0], values[1])
+        self.map.set_ylim(values[2], values[3])
+
     def indexs(self, dataset):
         (x0, x1), (y0, y1) = self.bbox
         x, y = dataset.longitude, dataset.latitude

tests/test_obs.py

@@ -1,6 +1,5 @@
 from py_eddy_tracker.observations.observation import EddiesObservations
 from py_eddy_tracker.data import get_path
-from netCDF4 import Dataset
 
 a = EddiesObservations.load_file(get_path("Anticyclonic_20190223.nc"))
 c = EddiesObservations.load_file(get_path("Cyclonic_20190223.nc"))