refactor: update notebook

to use long tracker
WilhelmusLab · Dec 7, 2024 · 50ecf06 · 50ecf06
1 parent 13dc002
commit 50ecf06
Showing 1 changed file with 136 additions and 15 deletions.
diff --git a/notebooks/track-floes/track-floes.ipynb b/notebooks/track-floes/track-floes.ipynb
@@ -27,9 +27,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "using IceFloeTracker: pairfloes, deserialize, PaddedView, float64, mosaicview, Gray\n",
-    "using DataFrames\n",
-    "imshow(x) = Gray.(x);\n"
+    "using IceFloeTracker: deserialize, addfloemasks!, adduuid!, add_passtimes!, addψs!, long_tracker, imshow"
    ]
   },
   {
@@ -80,26 +78,133 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Load data\n",
-    "pth = joinpath(HOME, \"test\", \"test_inputs\", \"tracker\")\n",
-    "floedata = deserialize(joinpath(pth,\"tracker_test_data.dat\"))\n",
-    "passtimes = deserialize(joinpath(pth,\"passtimes.dat\"))\n",
+    "begin # Load data\n",
+    "    pth = joinpath(HOME, \"test\", \"test_inputs\", \"tracker\")\n",
+    "    floedata = deserialize(joinpath(pth, \"tracker_test_data.dat\"))\n",
+    "    # test/test_inputs/tracker/tracker_test_data.dat\n",
+    "    passtimes = deserialize(joinpath(pth, \"passtimes.dat\"))\n",
+    "    props, imgs = deepcopy.([floedata.props, floedata.imgs])\n",
     "\n",
-    "latlonimgpth = joinpath(HOME, \"test\", \"test_inputs\", \"NE_Greenland_truecolor.2020162.aqua.250m.tiff\")\n",
+    "    # This order is important: masks, uuids, passtimes, ψs\n",
+    "    addfloemasks!(props, imgs)\n",
+    "    adduuid!(props)\n",
+    "    add_passtimes!(props, passtimes)\n",
+    "    addψs!(props)\n",
+    "end\n",
     "\n",
-    "props, imgs = deepcopy(floedata.props), deepcopy(floedata.imgs);\n",
+    "begin # Filter out floes with area less than `floe_area_threshold` pixels\n",
+    "    floe_area_threshold = 400\n",
+    "    for (i, prop) in enumerate(props)\n",
+    "        props[i] = prop[prop[:, :area].>=floe_area_threshold, :];\n",
+    "        sort!(props[i], :area, rev=true);\n",
+    "    end\n",
+    "end\n",
     "\n",
-    "# Filter out floes with area less than 350 pixels\n",
-    "for (i, prop) in enumerate(props)\n",
-    "    props[i] = prop[prop[:, :area].>=350, :]\n",
-    "end"
+    "# Delete some floes\n",
+    "deleteat!(props[1], 1); # delete the first floe in day 1 so it doesn't have a match in day 2\n",
+    "deleteat!(props[2], 5); # delete the fifth floe in day 2 so it doesn't have a match in day 1\n",
+    "\n",
+    "# All floes in days 1 and 2 have a match in day 3\n",
+    "# Expected: 5 trajectories, 3 of length 3 and 2 of length 2\n",
+    "nothing # suppress output -- not particularly informative. See the next block."
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### 4. Pair and label floes"
+    "### 4. View floe data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Day 1\n",
+    "props[1][!, [:uuid, :passtime, :area]]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "imshow(imgs[1])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "imshow(props[1][1, :mask])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Day 2\n",
+    "props[2][!, [:uuid, :passtime, :area]]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "imshow(imgs[2]) # slightly rotated version of the image in day 1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "imshow(props[2][1, :mask])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Day 3\n",
+    "props[3][!, [:uuid, :passtime, :area]]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "imshow(props[3][1, :mask]) # missing in day 1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "imshow(props[3][5, :mask]) # missing in day 2"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 5. Pair and label floes"
    ]
   },
   {
@@ -109,7 +214,23 @@
    "outputs": [],
    "source": [
     "# Get paired floes with labels\n",
-    "pairs = pairfloes(imgs, props, passtimes, latlonimgpth, condition_thresholds, mc_thresholds)"
+    "trajectories = long_tracker(props, condition_thresholds, mc_thresholds);"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 6. View trajectories and _goodness_ of pairings"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "trajectories[!, [:uuid, :passtime, :area_mismatch, :corr]]"
    ]
   }
  ],