Skip to content

Commit 09cb948

Browse files
AntSimiAntSimi
committed
Add notebooks to git
1 parent fa80acc commit 09cb948

14 files changed

+703
-0
lines changed

‎notebooks/README.md‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
rsync -vrltp doc/python_module notebooks/. --include '*/' --include '*.ipynb' --exclude '*' --prune-empty-dirs

‎notebooks/python_module/02_eddy_identification/pet_display_id.ipynb‎

Lines changed: 54 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,54 @@
1+
{
2+
"cells": [
3+
{
4+
"cell_type": "code",
5+
"execution_count": null,
6+
"metadata": {
7+
"collapsed": false
8+
},
9+
"outputs": [],
10+
"source": [
11+
"%matplotlib inline"
12+
]
13+
},
14+
{
15+
"cell_type": "markdown",
16+
"metadata": {},
17+
"source": [
18+
"\nDisplay identification\n======================\n"
19+
]
20+
},
21+
{
22+
"cell_type": "code",
23+
"execution_count": null,
24+
"metadata": {
25+
"collapsed": false
26+
},
27+
"outputs": [],
28+
"source": [
29+
"from matplotlib import pyplot as plt\nfrom py_eddy_tracker.observations.observation import EddiesObservations\nfrom py_eddy_tracker import data\n\na = EddiesObservations.load_file(data.get_path(\"Anticyclonic_20190223.nc\"))\nc = EddiesObservations.load_file(data.get_path(\"Cyclonic_20190223.nc\"))\n\n# Plot\nfig = plt.figure(figsize=(15, 8))\nax = fig.add_subplot(111)\nax.set_aspect(\"equal\")\nax.set_xlim(0, 360)\nax.set_ylim(-80, 80)\na.display(ax, label=\"Anticyclonic\", color=\"r\", lw=1)\nc.display(ax, label=\"Cyclonic\", color=\"b\", lw=1)\nax.legend(loc=\"upper right\")"
30+
]
31+
}
32+
],
33+
"metadata": {
34+
"kernelspec": {
35+
"display_name": "Python 3",
36+
"language": "python",
37+
"name": "python3"
38+
},
39+
"language_info": {
40+
"codemirror_mode": {
41+
"name": "ipython",
42+
"version": 3
43+
},
44+
"file_extension": ".py",
45+
"mimetype": "text/x-python",
46+
"name": "python",
47+
"nbconvert_exporter": "python",
48+
"pygments_lexer": "ipython3",
49+
"version": "3.7.7"
50+
}
51+
},
52+
"nbformat": 4,
53+
"nbformat_minor": 0
54+
}

‎notebooks/python_module/02_eddy_identification/pet_eddy_detection.ipynb‎

Lines changed: 54 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,54 @@
1+
{
2+
"cells": [
3+
{
4+
"cell_type": "code",
5+
"execution_count": null,
6+
"metadata": {
7+
"collapsed": false
8+
},
9+
"outputs": [],
10+
"source": [
11+
"%matplotlib inline"
12+
]
13+
},
14+
{
15+
"cell_type": "markdown",
16+
"metadata": {},
17+
"source": [
18+
"\nEddy detection\n==============\n\nScript will detect eddies on adt field, and compute u,v with method add_uv(which could use, only if equator is avoid)\n\nFigures will show different step to detect eddies.\n"
19+
]
20+
},
21+
{
22+
"cell_type": "code",
23+
"execution_count": null,
24+
"metadata": {
25+
"collapsed": false
26+
},
27+
"outputs": [],
28+
"source": [
29+
"from datetime import datetime\nfrom matplotlib import pyplot as plt\nfrom py_eddy_tracker.dataset.grid import RegularGridDataset\nfrom py_eddy_tracker import data\n\n\ndef start_axes(title):\n fig = plt.figure(figsize=(13, 5))\n ax = fig.add_axes([0.03, 0.03, 0.90, 0.94])\n ax.set_xlim(-6, 36.5), ax.set_ylim(30, 46)\n ax.set_aspect(\"equal\")\n ax.set_title(title)\n return ax\n\n\ndef update_axes(ax, mappable=None):\n ax.grid()\n if mappable:\n plt.colorbar(m, cax=ax.figure.add_axes([0.95, 0.05, 0.01, 0.9]))\n\n\ng = RegularGridDataset(\n data.get_path(\"dt_med_allsat_phy_l4_20160515_20190101.nc\"), \"longitude\", \"latitude\"\n)\n\nax = start_axes(\"ADT (m)\")\nm = g.display(ax, \"adt\", vmin=-0.15, vmax=0.15)\nupdate_axes(ax, m)\n\ng.add_uv(\"adt\")\nax = start_axes(\"U/V deduce from ADT (m)\")\nax.set_xlim(2.5, 9), ax.set_ylim(37.5, 40)\nm = g.display(ax, \"adt\", vmin=-0.15, vmax=0.15)\nu, v = g.grid(\"u\").T, g.grid(\"v\").T\nax.quiver(g.x_c, g.y_c, u, v, scale=10)\nupdate_axes(ax, m)\n\ng.bessel_high_filter(\"adt\", 500, order=2)\n\nax = start_axes(\"ADT (m) filtered (500km, order 2)\")\nm = g.display(ax, \"adt\", vmin=-0.15, vmax=0.15)\nupdate_axes(ax, m)\n\ndate = datetime(2016, 5, 15)\na, c = g.eddy_identification(\"adt\", \"u\", \"v\", date, 0.002)\n\nax = start_axes(\"ADT closed contour (only 1 / 4 levels)\")\ng.contours.display(ax, step=4)\nupdate_axes(ax)\n\nax = start_axes(\"ADT contour used as eddies\")\ng.contours.display(ax, only_used=True)\nupdate_axes(ax)\n\nax = start_axes(\"ADT contour reject\")\ng.contours.display(ax, only_unused=True)\nupdate_axes(ax)\n\nax = start_axes(\"ADT contour reject but which contain eddies\")\ng.contours.label_contour_unused_which_contain_eddies(a)\ng.contours.label_contour_unused_which_contain_eddies(c)\ng.contours.display(\n ax, only_contain_eddies=True, color=\"k\", lw=1, label=\"Could be interaction contour\"\n)\na.display(ax, color=\"r\", linewidth=0.5, label=\"Anticyclonic\", ref=-10)\nc.display(ax, color=\"b\", linewidth=0.5, label=\"Cyclonic\", ref=-10)\nax.legend()\nupdate_axes(ax)\n\nax = start_axes(\"Eddies detected\")\na.display(ax, color=\"r\", linewidth=0.5, label=\"Anticyclonic\", ref=-10)\nc.display(ax, color=\"b\", linewidth=0.5, label=\"Cyclonic\", ref=-10)\nax.legend()\nupdate_axes(ax)\n\nax = start_axes(\"Eddies speed radius (km)\")\na.scatter(ax, \"radius_s\", vmin=10, vmax=50, s=80, ref=-10, cmap=\"jet\", factor=0.001)\nm = c.scatter(ax, \"radius_s\", vmin=10, vmax=50, s=80, ref=-10, cmap=\"jet\", factor=0.001)\nupdate_axes(ax, m)"
30+
]
31+
}
32+
],
33+
"metadata": {
34+
"kernelspec": {
35+
"display_name": "Python 3",
36+
"language": "python",
37+
"name": "python3"
38+
},
39+
"language_info": {
40+
"codemirror_mode": {
41+
"name": "ipython",
42+
"version": 3
43+
},
44+
"file_extension": ".py",
45+
"mimetype": "text/x-python",
46+
"name": "python",
47+
"nbconvert_exporter": "python",
48+
"pygments_lexer": "ipython3",
49+
"version": "3.7.7"
50+
}
51+
},
52+
"nbformat": 4,
53+
"nbformat_minor": 0
54+
}

‎notebooks/python_module/06_grid_manipulation/pet_hide_pixel_out_eddies.ipynb‎

Lines changed: 54 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,54 @@
1+
{
2+
"cells": [
3+
{
4+
"cell_type": "code",
5+
"execution_count": null,
6+
"metadata": {
7+
"collapsed": false
8+
},
9+
"outputs": [],
10+
"source": [
11+
"%matplotlib inline"
12+
]
13+
},
14+
{
15+
"cell_type": "markdown",
16+
"metadata": {},
17+
"source": [
18+
"\nSelect pixel in eddies\n======================\n"
19+
]
20+
},
21+
{
22+
"cell_type": "code",
23+
"execution_count": null,
24+
"metadata": {
25+
"collapsed": false
26+
},
27+
"outputs": [],
28+
"source": [
29+
"from matplotlib import pyplot as plt\nfrom matplotlib.path import Path\nfrom numpy import ones\nfrom py_eddy_tracker.observations.observation import EddiesObservations, custom_concat\nfrom py_eddy_tracker.dataset.grid import RegularGridDataset\nfrom py_eddy_tracker import data\n\na = EddiesObservations.load_file(data.get_path(\"Anticyclonic_20190223.nc\"))\ng = RegularGridDataset(\n data.get_path(\"nrt_global_allsat_phy_l4_20190223_20190226.nc\"),\n \"longitude\",\n \"latitude\",\n)\n\n# Plot\nfig = plt.figure(figsize=(12, 6))\nax = fig.add_axes((0.05, 0.05, 0.9, 0.9))\nax.set_aspect(\"equal\")\nax.set_xlim(10, 70)\nax.set_ylim(-50, -25)\nx_name, y_name = a.intern(False)\nadt = g.grid(\"adt\")\nmask = ones(adt.shape, dtype='bool')\nfor eddy in a:\n i, j = Path(custom_concat(eddy[x_name], eddy[y_name])).pixels_in(g)\n mask[i, j] = False\nadt.mask[:] += ~mask\ng.display(ax, \"adt\")\na.display(ax, label=\"Anticyclonic\", color=\"g\", lw=1, extern_only=True)\n\nfig = plt.figure(figsize=(12, 6))\nax = fig.add_axes((0.05, 0.05, 0.9, 0.9))\nax.set_aspect(\"equal\")\nax.set_xlim(10, 70)\nax.set_ylim(-50, -25)\nadt.mask[:] = mask\ng.display(ax, \"adt\")\na.display(ax, label=\"Anticyclonic\", color=\"g\", lw=1, extern_only=True)"
30+
]
31+
}
32+
],
33+
"metadata": {
34+
"kernelspec": {
35+
"display_name": "Python 3",
36+
"language": "python",
37+
"name": "python3"
38+
},
39+
"language_info": {
40+
"codemirror_mode": {
41+
"name": "ipython",
42+
"version": 3
43+
},
44+
"file_extension": ".py",
45+
"mimetype": "text/x-python",
46+
"name": "python",
47+
"nbconvert_exporter": "python",
48+
"pygments_lexer": "ipython3",
49+
"version": "3.7.7"
50+
}
51+
},
52+
"nbformat": 4,
53+
"nbformat_minor": 0
54+
}

‎notebooks/python_module/08_tracking_manipulation/pet_display_field.ipynb‎

Lines changed: 54 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,54 @@
1+
{
2+
"cells": [
3+
{
4+
"cell_type": "code",
5+
"execution_count": null,
6+
"metadata": {
7+
"collapsed": false
8+
},
9+
"outputs": [],
10+
"source": [
11+
"%matplotlib inline"
12+
]
13+
},
14+
{
15+
"cell_type": "markdown",
16+
"metadata": {},
17+
"source": [
18+
"\nDisplay fields\n==============\n"
19+
]
20+
},
21+
{
22+
"cell_type": "code",
23+
"execution_count": null,
24+
"metadata": {
25+
"collapsed": false
26+
},
27+
"outputs": [],
28+
"source": [
29+
"from matplotlib import pyplot as plt\nfrom py_eddy_tracker.observations.tracking import TrackEddiesObservations\nimport py_eddy_tracker_sample\n\nc = TrackEddiesObservations.load_file(\n py_eddy_tracker_sample.get_path(\"eddies_med_adt_allsat_dt2018/Cyclonic.zarr\")\n)\n\nc = c.extract_with_length((180, -1))\n\n# Plot\nfig = plt.figure(figsize=(12, 6))\nax = fig.add_axes((0.05, 0.1, 0.9, 0.9))\nax.set_aspect(\"equal\")\nax.set_xlim(-6, 36.5), ax.set_ylim(30, 46)\nm = c.scatter(ax, \"amplitude\", ref=-10, vmin=0, vmax=0.1)\nax.grid()\n\ncb = plt.colorbar(\n m, cax=fig.add_axes([0.05, 0.07, 0.9, 0.01]), orientation=\"horizontal\"\n)\ncb.set_label(\"Amplitude (m)\")"
30+
]
31+
}
32+
],
33+
"metadata": {
34+
"kernelspec": {
35+
"display_name": "Python 3",
36+
"language": "python",
37+
"name": "python3"
38+
},
39+
"language_info": {
40+
"codemirror_mode": {
41+
"name": "ipython",
42+
"version": 3
43+
},
44+
"file_extension": ".py",
45+
"mimetype": "text/x-python",
46+
"name": "python",
47+
"nbconvert_exporter": "python",
48+
"pygments_lexer": "ipython3",
49+
"version": "3.7.7"
50+
}
51+
},
52+
"nbformat": 4,
53+
"nbformat_minor": 0
54+
}

‎notebooks/python_module/08_tracking_manipulation/pet_display_track.ipynb‎

Lines changed: 54 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,54 @@
1+
{
2+
"cells": [
3+
{
4+
"cell_type": "code",
5+
"execution_count": null,
6+
"metadata": {
7+
"collapsed": false
8+
},
9+
"outputs": [],
10+
"source": [
11+
"%matplotlib inline"
12+
]
13+
},
14+
{
15+
"cell_type": "markdown",
16+
"metadata": {},
17+
"source": [
18+
"\nDisplay Tracks\n======================\n"
19+
]
20+
},
21+
{
22+
"cell_type": "code",
23+
"execution_count": null,
24+
"metadata": {
25+
"collapsed": false
26+
},
27+
"outputs": [],
28+
"source": [
29+
"from matplotlib import pyplot as plt\nfrom py_eddy_tracker.observations.tracking import TrackEddiesObservations\nimport py_eddy_tracker_sample\n\na = TrackEddiesObservations.load_file(\n py_eddy_tracker_sample.get_path(\"eddies_med_adt_allsat_dt2018/Anticyclonic.zarr\")\n)\nc = TrackEddiesObservations.load_file(\n py_eddy_tracker_sample.get_path(\"eddies_med_adt_allsat_dt2018/Cyclonic.zarr\")\n)\n\na = a.extract_with_length((7 * 20, -1))\nc = c.extract_with_length((7 * 20, -1))\na.position_filter(median_half_window=1, loess_half_window=5)\nc.position_filter(median_half_window=1, loess_half_window=5)\n\n# Plot\nfig = plt.figure(figsize=(12, 5))\nax = fig.add_axes((0.05, 0.1, 0.9, 0.9))\nax.set_aspect(\"equal\")\nax.set_xlim(-6, 36.5), ax.set_ylim(30, 46)\na.plot(ax, ref=-10, label=\"Anticyclonic\", color=\"r\", lw=0.1)\nc.plot(ax, ref=-10, label=\"Cyclonic\", color=\"b\", lw=0.1)\nax.legend()\nax.grid()"
30+
]
31+
}
32+
],
33+
"metadata": {
34+
"kernelspec": {
35+
"display_name": "Python 3",
36+
"language": "python",
37+
"name": "python3"
38+
},
39+
"language_info": {
40+
"codemirror_mode": {
41+
"name": "ipython",
42+
"version": 3
43+
},
44+
"file_extension": ".py",
45+
"mimetype": "text/x-python",
46+
"name": "python",
47+
"nbconvert_exporter": "python",
48+
"pygments_lexer": "ipython3",
49+
"version": "3.7.7"
50+
}
51+
},
52+
"nbformat": 4,
53+
"nbformat_minor": 0
54+
}

‎notebooks/python_module/08_tracking_manipulation/pet_one_track.ipynb‎

Lines changed: 54 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,54 @@
1+
{
2+
"cells": [
3+
{
4+
"cell_type": "code",
5+
"execution_count": null,
6+
"metadata": {
7+
"collapsed": false
8+
},
9+
"outputs": [],
10+
"source": [
11+
"%matplotlib inline"
12+
]
13+
},
14+
{
15+
"cell_type": "markdown",
16+
"metadata": {},
17+
"source": [
18+
"\nOne Track\n===================\n"
19+
]
20+
},
21+
{
22+
"cell_type": "code",
23+
"execution_count": null,
24+
"metadata": {
25+
"collapsed": false
26+
},
27+
"outputs": [],
28+
"source": [
29+
"from matplotlib import pyplot as plt\nfrom py_eddy_tracker.observations.tracking import TrackEddiesObservations\nimport py_eddy_tracker_sample\n\na = TrackEddiesObservations.load_file(\n py_eddy_tracker_sample.get_path(\"eddies_med_adt_allsat_dt2018/Anticyclonic.zarr\")\n)\n\neddy = a.extract_ids([9672])\neddy_f = a.extract_ids([9672])\neddy_f.position_filter(median_half_window=1, loess_half_window=5)\n\nfig = plt.figure(figsize=(12, 5))\nax = fig.add_axes((0.05, 0.05, 0.9, 0.9))\nax.set_xlim(17.5, 22)\nax.set_ylim(35, 36.5)\nax.set_aspect(\"equal\")\nax.grid()\neddy.plot(ax, color=\"r\", lw=0.5)\neddy_f.scatter(ax, \"n\", cmap=\"jet\", s=80)\n\nfig = plt.figure(figsize=(12, 5))\nax = fig.add_axes((0.05, 0.05, 0.9, 0.9))\nax.set_xlim(17, 23)\nax.set_ylim(34.5, 37)\nax.set_aspect(\"equal\")\nax.grid()\neddy.plot(ax, color=\"r\", lw=0.5, label='track')\neddy.index(range(0, len(eddy), 40)).display(ax, intern_only=True, label='observations every 40')\nax.legend()"
30+
]
31+
}
32+
],
33+
"metadata": {
34+
"kernelspec": {
35+
"display_name": "Python 3",
36+
"language": "python",
37+
"name": "python3"
38+
},
39+
"language_info": {
40+
"codemirror_mode": {
41+
"name": "ipython",
42+
"version": 3
43+
},
44+
"file_extension": ".py",
45+
"mimetype": "text/x-python",
46+
"name": "python",
47+
"nbconvert_exporter": "python",
48+
"pygments_lexer": "ipython3",
49+
"version": "3.7.7"
50+
}
51+
},
52+
"nbformat": 4,
53+
"nbformat_minor": 0
54+
}

‎notebooks/python_module/08_tracking_manipulation/pet_select_track_across_area.ipynb‎

Lines changed: 54 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,54 @@
1+
{
2+
"cells": [
3+
{
4+
"cell_type": "code",
5+
"execution_count": null,
6+
"metadata": {
7+
"collapsed": false
8+
},
9+
"outputs": [],
10+
"source": [
11+
"%matplotlib inline"
12+
]
13+
},
14+
{
15+
"cell_type": "markdown",
16+
"metadata": {},
17+
"source": [
18+
"\nTracks which go through area\n============================\n"
19+
]
20+
},
21+
{
22+
"cell_type": "code",
23+
"execution_count": null,
24+
"metadata": {
25+
"collapsed": false
26+
},
27+
"outputs": [],
28+
"source": [
29+
"from matplotlib import pyplot as plt\nfrom py_eddy_tracker.observations.tracking import TrackEddiesObservations\nimport py_eddy_tracker_sample\n\nc = TrackEddiesObservations.load_file(\n py_eddy_tracker_sample.get_path(\"eddies_med_adt_allsat_dt2018/Cyclonic.zarr\")\n)\nc.position_filter(median_half_window=1, loess_half_window=5)\nx0, x1, y0, y1 = 3, 4, 37, 38\narea = dict(llcrnrlon=x0, llcrnrlat=y0, urcrnrlon=x1, urcrnrlat=y1)\nc_subset = c.extract_with_area(area, full_path=True)\nfig = plt.figure(figsize=(12, 5))\nax = fig.add_axes((0.05, 0.05, 0.9, 0.9))\nax.set_xlim(-1, 9)\nax.set_ylim(36, 40)\nax.set_aspect(\"equal\")\nax.grid()\nc.plot(ax, color=\"gray\", lw=0.1, ref=-10, label=\"all tracks\")\nc_subset.plot(ax, color=\"red\", lw=0.2, ref=-10, label=\"selected tracks\")\nax.plot(\n (x0, x0, x1, x1, x0,),\n (y0, y1, y1, y0, y0,),\n color=\"green\",\n lw=1.5,\n label=\"Box of selection\",\n)\nax.legend()"
30+
]
31+
}
32+
],
33+
"metadata": {
34+
"kernelspec": {
35+
"display_name": "Python 3",
36+
"language": "python",
37+
"name": "python3"
38+
},
39+
"language_info": {
40+
"codemirror_mode": {
41+
"name": "ipython",
42+
"version": 3
43+
},
44+
"file_extension": ".py",
45+
"mimetype": "text/x-python",
46+
"name": "python",
47+
"nbconvert_exporter": "python",
48+
"pygments_lexer": "ipython3",
49+
"version": "3.7.7"
50+
}
51+
},
52+
"nbformat": 4,
53+
"nbformat_minor": 0
54+
}

0 commit comments

Comments
 (0)