- Add method to know how contour is reject

- Add method a first version to regrid one grid on another (AntSimi#24)

Author: AntSimi

examples/02_eddy_identification/pet_eddy_detection.py

@@ -1,12 +1,13 @@
 """
-Eddy detection
-==============
+Eddy detection : Med
+====================
 
 Script will detect eddies on adt field, and compute u,v with method add_uv(which could use, only if equator is avoid)
 
 Figures will show different step to detect eddies.
 
 """
+from numpy import arange
 from datetime import datetime
 from matplotlib import pyplot as plt
 from py_eddy_tracker.dataset.grid import RegularGridDataset
@@ -26,7 +27,7 @@ def start_axes(title):
 def update_axes(ax, mappable=None):
     ax.grid()
     if mappable:
-        plt.colorbar(mappable, cax=ax.figure.add_axes([0.95, 0.05, 0.01, 0.9]))
+        plt.colorbar(mappable, cax=ax.figure.add_axes([0.94, 0.05, 0.01, 0.9]))
 
 
 # %%
@@ -65,7 +66,7 @@ def update_axes(ax, mappable=None):
 # --------------
 # run identification with slice of 2 mm
 date = datetime(2016, 5, 15)
-a, c = g.eddy_identification("adt", "u", "v", date, 0.002)
+a, c = g.eddy_identification("adt", "u", "v", date, 0.002, shape_error=55)
 
 # %%
 # All closed contour found in this input grid (Display only 1 contour every 4)
@@ -80,11 +81,33 @@ def update_axes(ax, mappable=None):
 update_axes(ax)
 
 # %%
+# Post analyse
+# ------------
 # 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 reject criterion
+#
+# 0. - Accepted (green)
+# 1. - Reject for shape error (red)
+# 2. - Masked value in contour (blue)
+# 3. - Under or over pixel limit bound (black)
+# 4. - Amplitude criterion (yellow)
+ax = start_axes("Contour reject criterion")
+g.contours.display(ax, only_unused=True, lw=0.25, display_criterion=True)
+update_axes(ax)
+
+# %%
+# Display shape error of each tested contour, the limit of shape error is set to 55 %
+ax = start_axes("Contour shape error")
+m = g.contours.display(
+    ax, lw=0.5, field="shape_error", bins=arange(20, 90.1, 5), cmap="seismic"
+)
+update_axes(ax, m)
+
 # %%
 # Contours closed which contains several eddies
 ax = start_axes("ADT contour reject but which contain eddies")
@@ -116,3 +139,14 @@ def update_axes(ax, mappable=None):
 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)
 update_axes(ax, m)
+
+# %%
+# Display speed radius of eddies detected
+ax = start_axes("Eddies speed radius (km)")
+a.filled(
+    ax, "radius_e", vmin=10, vmax=80, cmap="magma_r", factor=0.001, lut=14, ref=-10
+)
+m = c.filled(
+    ax, "radius_e", vmin=10, vmax=80, cmap="magma_r", factor=0.001, lut=14, ref=-10
+)
+update_axes(ax, m)

examples/02_eddy_identification/pet_eddy_detection_gulf_stream.py

@@ -1,12 +1,13 @@
 """
-Eddy detection Gulf stream
-==========================
+Eddy detection : Gulf stream
+============================
 
 Script will detect eddies on adt field, and compute u,v with method add_uv(which could use, only if equator is avoid)
 
 Figures will show different step to detect eddies.
 
 """
+from numpy import arange
 from datetime import datetime
 from matplotlib import pyplot as plt
 from py_eddy_tracker.dataset.grid import RegularGridDataset
@@ -72,7 +73,7 @@ def update_axes(ax, mappable=None):
 # --------------
 # run identification with slice of 2 mm
 date = datetime(2016, 5, 15)
-a, c = g.eddy_identification("adt", "u", "v", date, 0.002)
+a, c = g.eddy_identification("adt", "u", "v", date, 0.002, shape_error=55)
 
 # %%
 # All closed contour found in this input grid (Display only 1 contour every 5)
@@ -89,12 +90,34 @@ def update_axes(ax, mappable=None):
 update_axes(ax)
 
 # %%
+# Post analyse
+# ------------
 # 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, lw=0.25)
 great_current.display(ax, color="k")
 update_axes(ax)
 
+# %%
+# Contours reject criterion
+#
+# 0. - Accepted (green)
+# 1. - Reject for shape error (red)
+# 2. - Masked value in contour (blue)
+# 3. - Under or over pixel limit bound (black)
+# 4. - Amplitude criterion (yellow)
+ax = start_axes("Contour reject criterion")
+g.contours.display(ax, only_unused=True, lw=0.25, display_criterion=True)
+update_axes(ax)
+
+# %%
+# Display shape error of each tested contour, the limit of shape error is set to 55 %
+ax = start_axes("Contour shape error")
+m = g.contours.display(
+    ax, lw=0.5, field="shape_error", bins=arange(20, 90.1, 5), cmap="seismic"
+)
+update_axes(ax, m)
+
 # %%
 # Contours closed which contains several eddies
 ax = start_axes("ADT contour reject but which contain eddies")

notebooks/python_module/02_eddy_identification/pet_eddy_detection.ipynb

@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\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"
+        "\n# Eddy detection : Med\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"
       ]
     },
     {
@@ -26,7 +26,7 @@
       },
       "outputs": [],
       "source": [
-        "from datetime import datetime\nfrom matplotlib import pyplot as plt\nfrom py_eddy_tracker.dataset.grid import RegularGridDataset\nfrom py_eddy_tracker import data"
+        "from numpy import arange\nfrom datetime import datetime\nfrom matplotlib import pyplot as plt\nfrom py_eddy_tracker.dataset.grid import RegularGridDataset\nfrom py_eddy_tracker import data"
       ]
     },
     {
@@ -37,7 +37,7 @@
       },
       "outputs": [],
       "source": [
-        "def 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]))"
+        "def 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(mappable, cax=ax.figure.add_axes([0.94, 0.05, 0.01, 0.9]))"
       ]
     },
     {
@@ -62,7 +62,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Get u/v\n-------\nU/V are deduced from ADT, this algortihm are not usable around equator (~+- 2\u00b0)\n\n"
+        "## Get u/v\nU/V are deduced from ADT, this algortihm are not usable around equator (~+- 2\u00b0)\n\n"
       ]
     },
     {
@@ -80,7 +80,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Pre-processings\n---------------\nApply high filter to remove long scale to highlight mesoscale\n\n"
+        "## Pre-processings\nApply high filter to remove long scale to highlight mesoscale\n\n"
       ]
     },
     {
@@ -98,7 +98,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Identification\n--------------\nrun identification with slice of 2 mm\n\n"
+        "## Identification\nrun identification with slice of 2 mm\n\n"
       ]
     },
     {
@@ -109,7 +109,7 @@
       },
       "outputs": [],
       "source": [
-        "date = datetime(2016, 5, 15)\na, c = g.eddy_identification(\"adt\", \"u\", \"v\", date, 0.002)"
+        "date = datetime(2016, 5, 15)\na, c = g.eddy_identification(\"adt\", \"u\", \"v\", date, 0.002, shape_error=55)"
       ]
     },
     {
@@ -152,7 +152,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Contours reject from several origin (shape error to high, several extremum in contour, ...)\n\n"
+        "## Post analyse\nContours reject from several origin (shape error to high, several extremum in contour, ...)\n\n"
       ]
     },
     {
@@ -166,6 +166,42 @@
         "ax = start_axes(\"ADT contour reject\")\ng.contours.display(ax, only_unused=True)\nupdate_axes(ax)"
       ]
     },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Contours reject criterion\n\n0. - Accepted (green)\n1. - Reject for shape error (red)\n2. - Masked value in contour (blue)\n3. - Under or over pixel limit bound (black)\n4. - Amplitude criterion (yellow)\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "ax = start_axes(\"Contour reject criterion\")\ng.contours.display(ax, only_unused=True, lw=0.25, display_criterion=True)\nupdate_axes(ax)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Display shape error of each tested contour, the limit of shape error is set to 55 %\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "ax = start_axes(\"Contour shape error\")\nm = g.contours.display(\n    ax, lw=0.5, field=\"shape_error\", bins=arange(20, 90.1, 5), cmap=\"seismic\"\n)\nupdate_axes(ax, m)"
+      ]
+    },
     {
       "cell_type": "markdown",
       "metadata": {},
@@ -188,7 +224,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Output\n------\nDisplay 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"
+        "## Output\nDisplay 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"
       ]
     },
     {
@@ -219,6 +255,24 @@
       "source": [
         "ax = 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)"
       ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Display speed radius of eddies detected\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "ax = start_axes(\"Eddies speed radius (km)\")\na.filled(\n    ax, \"radius_e\", vmin=10, vmax=80, cmap=\"magma_r\", factor=0.001, lut=14, ref=-10\n)\nm = c.filled(\n    ax, \"radius_e\", vmin=10, vmax=80, cmap=\"magma_r\", factor=0.001, lut=14, ref=-10\n)\nupdate_axes(ax, m)"
+      ]
     }
   ],
   "metadata": {

notebooks/python_module/02_eddy_identification/pet_eddy_detection_gulf_stream.ipynb

@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\n# Eddy detection Gulf stream\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"
+        "\n# Eddy detection : Gulf stream\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"
       ]
     },
     {
@@ -26,7 +26,7 @@
       },
       "outputs": [],
       "source": [
-        "from datetime import datetime\nfrom matplotlib import pyplot as plt\nfrom py_eddy_tracker.dataset.grid import RegularGridDataset\nfrom py_eddy_tracker import data\nfrom py_eddy_tracker.eddy_feature import Contours"
+        "from numpy import arange\nfrom datetime import datetime\nfrom matplotlib import pyplot as plt\nfrom py_eddy_tracker.dataset.grid import RegularGridDataset\nfrom py_eddy_tracker import data\nfrom py_eddy_tracker.eddy_feature import Contours"
       ]
     },
     {
@@ -109,7 +109,7 @@
       },
       "outputs": [],
       "source": [
-        "date = datetime(2016, 5, 15)\na, c = g.eddy_identification(\"adt\", \"u\", \"v\", date, 0.002)"
+        "date = datetime(2016, 5, 15)\na, c = g.eddy_identification(\"adt\", \"u\", \"v\", date, 0.002, shape_error=55)"
       ]
     },
     {
@@ -152,7 +152,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Contours reject from several origin (shape error to high, several extremum in contour, ...)\n\n"
+        "## Post analyse\nContours reject from several origin (shape error to high, several extremum in contour, ...)\n\n"
       ]
     },
     {
@@ -166,6 +166,42 @@
         "ax = start_axes(\"ADT contour reject\")\ng.contours.display(ax, only_unused=True, lw=0.25)\ngreat_current.display(ax, color=\"k\")\nupdate_axes(ax)"
       ]
     },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Contours reject criterion\n\n0. - Accepted (green)\n1. - Reject for shape error (red)\n2. - Masked value in contour (blue)\n3. - Under or over pixel limit bound (black)\n4. - Amplitude criterion (yellow)\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "ax = start_axes(\"Contour reject criterion\")\ng.contours.display(ax, only_unused=True, lw=0.25, display_criterion=True)\nupdate_axes(ax)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Display shape error of each tested contour, the limit of shape error is set to 55 %\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "ax = start_axes(\"Contour shape error\")\nm = g.contours.display(\n    ax, lw=0.5, field=\"shape_error\", bins=arange(20, 90.1, 5), cmap=\"seismic\"\n)\nupdate_axes(ax, m)"
+      ]
+    },
     {
       "cell_type": "markdown",
       "metadata": {},