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Update: documentation
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‎doc/doc.ipynb‎

Lines changed: 41 additions & 81 deletions
Original file line numberDiff line numberDiff line change
@@ -143,7 +143,7 @@
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" data=data.mean(dims),\n",
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" title=title,\n",
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" fn=f\"map-mean-{title}\",\n",
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" plot_size=(7.2, 3.6),\n",
146+
" plot_size=(9.6, 3.6),\n",
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" cbar_label=\"mean normalized error\",\n",
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" vmin=vmin,\n",
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" vmax=vmax,\n",
@@ -173,7 +173,7 @@
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" data=data.std(dims),\n",
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" title=title,\n",
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" fn=f\"map-std-{title}\",\n",
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" plot_size=(7.2, 3.6),\n",
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" plot_size=(9.6, 3.6),\n",
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" cbar_label=\"std. dev. normalized errors\",\n",
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" vmin=vmin,\n",
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" vmax=vmax,\n",
@@ -203,7 +203,7 @@
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" data=(data.max(dim=dims) - data.min(dim=dims)),\n",
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" title=title,\n",
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" fn=f\"map-range-{title}\",\n",
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" plot_size=(7.2, 3.6),\n",
206+
" plot_size=(9.6, 3.6),\n",
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" cbar_label=\"range of normalized errors\",\n",
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" vmin=vmin,\n",
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" vmax=vmax,\n",
@@ -234,7 +234,7 @@
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" chunks={\"time\": 12},\n",
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" combine=\"nested\",\n",
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" concat_dim=\"i\",\n",
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").transpose(\"time\", \"i\", \"latitude\", \"longitude\")"
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").transpose(\"i\", \"time\", \"latitude\", \"longitude\")"
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]
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},
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{
@@ -297,8 +297,8 @@
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"outputs": [],
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"source": [
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"def xu(ds, v, a):\n",
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" x = ds[v][:, 0]\n",
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" u = ds[a[\"uncertainty\"]][:, 0] / a.get(\"coverage\", 1.0)\n",
300+
" x = ds[v][0]\n",
301+
" u = ds[a[\"uncertainty\"]][0] / a.get(\"coverage\", 1.0)\n",
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" if a.get(\"relative\", False):\n",
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" u = u * x\n",
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" return x, u"
@@ -313,7 +313,7 @@
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"source": [
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"for v, a in config.items():\n",
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" x, u = xu(ds, v, a)\n",
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" res = (ds[v][:, 1:] - x) / u\n",
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" res = (ds[v][1:] - x) / u\n",
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" plot_histogram(\n",
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" res,\n",
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" title=a[\"name\"],\n",
@@ -366,7 +366,7 @@
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" chunks={\"lat\": 1080, \"lon\": 1080},\n",
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" combine=\"nested\",\n",
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" concat_dim=\"i\",\n",
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").transpose(\"time\", \"i\", \"lat\", \"lon\")"
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")"
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]
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},
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{
@@ -477,36 +477,6 @@
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" \"bias\": \"aph_665_bias\",\n",
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" \"rmsd\": \"aph_665_rmsd\",\n",
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" },\n",
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" \"atot_412\": {\n",
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" \"name\": \"Total absorption coefficient (412 nm)\",\n",
482-
" \"bias\": \"aph_412_bias\",\n",
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" \"rmsd\": \"aph_412_rmsd\",\n",
484-
" },\n",
485-
" \"atot_443\": {\n",
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" \"name\": \"Total absorption coefficient (443 nm)\",\n",
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" \"bias\": \"aph_443_bias\",\n",
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" \"rmsd\": \"aph_443_rmsd\",\n",
489-
" },\n",
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" \"atot_490\": {\n",
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" \"name\": \"Total absorption coefficient (490 nm)\",\n",
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" \"bias\": \"aph_490_bias\",\n",
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" \"rmsd\": \"aph_490_rmsd\",\n",
494-
" },\n",
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" \"atot_510\": {\n",
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" \"name\": \"Total absorption coefficient (510 nm)\",\n",
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" \"bias\": \"aph_510_bias\",\n",
498-
" \"rmsd\": \"aph_510_rmsd\",\n",
499-
" },\n",
500-
" \"atot_560\": {\n",
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" \"name\": \"Total absorption coefficient (560 nm)\",\n",
502-
" \"bias\": \"aph_560_bias\",\n",
503-
" \"rmsd\": \"aph_560_rmsd\",\n",
504-
" },\n",
505-
" \"atot_665\": {\n",
506-
" \"name\": \"Total absorption coefficient (665 nm)\",\n",
507-
" \"bias\": \"aph_665_bias\",\n",
508-
" \"rmsd\": \"aph_665_rmsd\",\n",
509-
" },\n",
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" \"kd_490\": {\n",
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" \"name\": \"Attenuation coefficent (490 nm)\",\n",
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" \"bias\": \"kd_490_bias\",\n",
@@ -546,7 +516,7 @@
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"source": [
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"for v, a in config.items():\n",
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" x, u = xu(ds, v, a)\n",
549-
" res = (ds[v][0, 1:] - x) / u\n",
519+
" res = (ds[v][1:, 0] - x) / u\n",
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" plot_histogram(\n",
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" res,\n",
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" title=a[\"name\"],\n",
@@ -614,7 +584,7 @@
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" chunks={\"lat\": 1800, \"lon\": 3600},\n",
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" combine=\"nested\",\n",
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" concat_dim=\"i\",\n",
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").transpose(\"time\", \"i\", \"lat\", \"lon\")"
587+
")"
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]
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},
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{
@@ -633,18 +603,6 @@
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"id": "27",
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"metadata": {},
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"outputs": [],
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"source": [
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"ds_mean = ds.isel(i=0)\n",
638-
"ds_std = (ds - ds_mean).std(dim=\"i\")\n",
639-
"ds_target = "
640-
]
641-
},
642-
{
643-
"cell_type": "code",
644-
"execution_count": null,
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"id": "28",
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"metadata": {},
647-
"outputs": [],
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"source": [
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"config = {\n",
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" \"analysed_sst\": {\n",
@@ -658,7 +616,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "29",
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"id": "28",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -671,13 +629,13 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "30",
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"id": "29",
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"metadata": {},
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"outputs": [],
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"source": [
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"for v, a in config.items():\n",
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" x, u = xu(ds, v, a)\n",
680-
" res = (ds[v][0, 1:] - x) / u\n",
638+
" res = (ds[v][1:, 0] - x) / u\n",
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" plot_histogram(\n",
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" res,\n",
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" title=a[\"name\"],\n",
@@ -717,7 +675,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "31",
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"id": "30",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -726,35 +684,33 @@
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},
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{
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"cell_type": "markdown",
729-
"id": "32",
730-
"metadata": {
731-
"jp-MarkdownHeadingCollapsed": true
732-
},
687+
"id": "31",
688+
"metadata": {},
733689
"source": [
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"# GLORYS"
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]
736692
},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "33",
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"id": "32",
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"metadata": {},
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"outputs": [],
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"source": [
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"ds = xr.open_mfdataset(\n",
745701
" \"./mercatorglorys12v1_gl12_mean_200001.*.nc\",\n",
746702
" engine=\"h5netcdf\",\n",
747703
" mask_and_scale=True,\n",
748-
" chunks={\"depth\": 10, \"latitude\": 511, \"lon\": 1080},\n",
704+
" chunks={\"latitude\": 2041, \"lon\": 2160, \"depth\": 1},\n",
749705
" combine=\"nested\",\n",
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" concat_dim=\"i\",\n",
751-
").transpose(\"time\", \"i\", \"depth\", \"latitude\", \"longitude\")"
707+
")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "34",
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"id": "33",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -764,7 +720,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "35",
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"id": "34",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -779,7 +735,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "36",
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"id": "35",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -792,13 +748,13 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "37",
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"id": "36",
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"metadata": {},
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"outputs": [],
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"source": [
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"for v, a in config.items():\n",
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" x, u = xu(ds, v, a)\n",
801-
" res = (ds[v][0, 1:, 0] - x) / u\n",
757+
" res = (ds[v][1:, 0, 0] - x) / u\n",
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" plot_histogram(\n",
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" res,\n",
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" title=a[\"name\"],\n",
@@ -838,7 +794,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "38",
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"id": "37",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -847,7 +803,7 @@
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},
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{
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"cell_type": "markdown",
850-
"id": "39",
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"id": "38",
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"metadata": {},
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"source": [
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"# ESA SCOPE PP parameters"
@@ -856,23 +812,23 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "40",
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"id": "39",
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"metadata": {},
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"outputs": [],
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"source": [
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"ds = xr.open_mfdataset(\n",
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" \"./PE_mro_mean_error_prv_4km_120p_spring_cor.*.nc\",\n",
865821
" engine=\"h5netcdf\",\n",
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" chunks={\"latitude\": 2160, \"lon\": 2160},\n",
822+
" chunks={\"lat\": 1440, \"lon\": 1440},\n",
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" combine=\"nested\",\n",
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" concat_dim=\"i\",\n",
869-
").transpose(\"i\", \"lat\", \"lon\")"
825+
")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "41",
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"id": "40",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -882,19 +838,17 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "42",
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"id": "41",
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"metadata": {},
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"outputs": [],
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"source": [
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"config = {\n",
890846
" \"alphaB\": {\n",
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" \"uncertainty\": \"alphaB_unc\",\n",
892-
" \"distribution\": \"lognormal\",\n",
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" \"name\": \"Initial slope of photosynthesis-irradiance curve\",\n",
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" },\n",
895850
" \"PmB\": {\n",
896851
" \"uncertainty\": \"PmB_unc\",\n",
897-
" \"distribution\": \"normal\",\n",
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" \"name\": \"Assimilation number of photosynthesis-irradiance curve\",\n",
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" }\n",
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"}"
@@ -903,7 +857,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "43",
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"id": "42",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -916,7 +870,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "44",
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"id": "43",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -946,23 +900,29 @@
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" res,\n",
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" dims=[\"i\"],\n",
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" title=a[\"name\"],\n",
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" x=\"lon\",\n",
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" y=\"lat\",\n",
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" )\n",
950906
" plot_std(\n",
951907
" res,\n",
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" dims=[\"i\"],\n",
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" title=a[\"name\"],\n",
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" x=\"lon\",\n",
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" y=\"lat\",\n",
954912
" )\n",
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" plot_range(\n",
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" res,\n",
957915
" dims=[\"i\"],\n",
958916
" title=a[\"name\"],\n",
917+
" x=\"lon\",\n",
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" y=\"lat\",\n",
959919
" )"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "45",
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"id": "44",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -972,7 +932,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "46",
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"id": "45",
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"metadata": {},
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"outputs": [],
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"source": []

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