From 43ff219882f1dd718f70a8d701b7e0365d4f94b4 Mon Sep 17 00:00:00 2001
From: tkerr1 <theodoremkerr@gmail.com>
Date: Fri, 3 Dec 2021 02:02:19 +0000
Subject: [PATCH] Added some cells to resolve the disk overutilization issue
---
.../forest_biomass_summary_DRC_output.ipynb | 223 ++++++++++--------
1 file changed, 128 insertions(+), 95 deletions(-)
diff --git a/country_outputs/forest_biomass_summary_DRC_output.ipynb b/country_outputs/forest_biomass_summary_DRC_output.ipynb
index fa86cef..fe7f8c8 100644
--- a/country_outputs/forest_biomass_summary_DRC_output.ipynb
+++ b/country_outputs/forest_biomass_summary_DRC_output.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "markdown",
- "id": "narrow-lodge",
+ "id": "working-vision",
"metadata": {},
"source": [
"# ESA Biomass Climate Change Initiative global forest aboveground biomass dataset v2.0 2010, 2017, 2018\n",
@@ -18,7 +18,7 @@
},
{
"cell_type": "markdown",
- "id": "answering-provision",
+ "id": "infectious-divorce",
"metadata": {},
"source": [
"#### Install these R packages first, and load them into the R session. Source R script with support functions."
@@ -27,7 +27,7 @@
{
"cell_type": "code",
"execution_count": 1,
- "id": "ordered-novel",
+ "id": "killing-april",
"metadata": {},
"outputs": [
{
@@ -54,6 +54,16 @@
"\n",
"Loading required package: rgeos\n",
"\n",
+ "Warning message in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :\n",
+ "“there is no package called ‘rgeos’â€\n",
+ "also installing the dependencies ‘foreign’, ‘maptools’, ‘maps’\n",
+ "\n",
+ "\n",
+ "Updating HTML index of packages in '.Library'\n",
+ "\n",
+ "Making 'packages.html' ...\n",
+ " done\n",
+ "\n",
"rgeos version: 0.5-8, (SVN revision 679)\n",
" GEOS runtime version: 3.9.1-CAPI-1.14.2 \n",
" Please note that rgeos will be retired by the end of 2023,\n",
@@ -65,13 +75,28 @@
"\n",
"Loading required package: geosphere\n",
"\n",
+ "Warning message in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :\n",
+ "“there is no package called ‘geosphere’â€\n",
+ "Updating HTML index of packages in '.Library'\n",
+ "\n",
+ "Making 'packages.html' ...\n",
+ " done\n",
+ "\n",
"Loading required package: RColorBrewer\n",
"\n",
"Loading required package: gdalUtils\n",
"\n",
"Loading required package: ff\n",
"\n",
- "Loading required package: bit\n",
+ "Warning message in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :\n",
+ "“there is no package called ‘ff’â€\n",
+ "also installing the dependency ‘biglm’\n",
+ "\n",
+ "\n",
+ "Updating HTML index of packages in '.Library'\n",
+ "\n",
+ "Making 'packages.html' ...\n",
+ " done\n",
"\n",
"\n",
"Attaching package: ‘bit’\n",
@@ -89,7 +114,7 @@
"\n",
"Attaching package ff\n",
"\n",
- "- getOption(\"fftempdir\")==\"/tmp/RtmpMbrE16/ff\"\n",
+ "- getOption(\"fftempdir\")==\"/tmp/RtmpWvIQu8/ff\"\n",
"\n",
"\n",
"- getOption(\"ffextension\")==\"ff\"\n",
@@ -136,6 +161,16 @@
"\n",
"Loading required package: snow\n",
"\n",
+ "Warning message in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :\n",
+ "“there is no package called ‘snow’â€\n",
+ "also installing the dependency ‘rlecuyer’\n",
+ "\n",
+ "\n",
+ "Updating HTML index of packages in '.Library'\n",
+ "\n",
+ "Making 'packages.html' ...\n",
+ " done\n",
+ "\n",
"\n",
"Attaching package: ‘snow’\n",
"\n",
@@ -165,7 +200,7 @@
},
{
"cell_type": "markdown",
- "id": "assigned-mining",
+ "id": "juvenile-synthesis",
"metadata": {},
"source": [
"#### Set the path to the CCI, JPL, and NCEO Biomass data folders & read in world countries shapefile"
@@ -174,7 +209,7 @@
{
"cell_type": "code",
"execution_count": 2,
- "id": "homeless-blade",
+ "id": "experimental-dynamics",
"metadata": {},
"outputs": [
{
@@ -208,7 +243,7 @@
},
{
"cell_type": "markdown",
- "id": "vietnamese-calcium",
+ "id": "rocky-warning",
"metadata": {},
"source": [
"#### Generate 10x10 degree WGS84 grid that the CCI Biomass and Hansen Forest Cover products are tiled on"
@@ -217,7 +252,7 @@
{
"cell_type": "code",
"execution_count": 3,
- "id": "southeast-johnston",
+ "id": "decent-leadership",
"metadata": {},
"outputs": [
{
@@ -239,7 +274,7 @@
},
{
"cell_type": "markdown",
- "id": "fewer-dutch",
+ "id": "organized-dealing",
"metadata": {},
"source": [
"#### Print out country names in Africa to select from"
@@ -248,7 +283,7 @@
{
"cell_type": "code",
"execution_count": 4,
- "id": "intensive-assault",
+ "id": "smooth-burner",
"metadata": {},
"outputs": [
{
@@ -556,7 +591,7 @@
},
{
"cell_type": "markdown",
- "id": "different-serum",
+ "id": "prescription-accordance",
"metadata": {},
"source": [
"#### Select a country in Africa to plot with corresponding data tiles"
@@ -565,7 +600,7 @@
{
"cell_type": "code",
"execution_count": 5,
- "id": "operating-beatles",
+ "id": "isolated-preference",
"metadata": {},
"outputs": [
{
@@ -625,7 +660,7 @@
{
"cell_type": "code",
"execution_count": 6,
- "id": "medium-medication",
+ "id": "conditional-command",
"metadata": {},
"outputs": [],
"source": [
@@ -635,7 +670,7 @@
},
{
"cell_type": "markdown",
- "id": "other-governor",
+ "id": "historic-serum",
"metadata": {},
"source": [
"#### Read in the CCI Biomass data for this AOI from the downloaded CCI Biomass tiles, mosaicing multiple tiles as necessary"
@@ -644,7 +679,7 @@
{
"cell_type": "code",
"execution_count": 7,
- "id": "scheduled-arlington",
+ "id": "continental-check",
"metadata": {},
"outputs": [
{
@@ -655,7 +690,7 @@
"resolution : 0.0008888889, 0.0008888889 (x, y)\n",
"extent : 12.21067, 31.28089, -13.45867, 5.375111 (xmin, xmax, ymin, ymax)\n",
"crs : +proj=longlat +datum=WGS84 +no_defs \n",
- "source : r_tmp_2021-12-02_165408_9245_93637.tif \n",
+ "source : r_tmp_2021-12-03_014403_789_64087.tif \n",
"names : agbd_2020, agbd_sd_2020 \n",
"min values : 0, 0 \n",
"max values : 552, 1068 \n"
@@ -672,7 +707,7 @@
},
{
"cell_type": "markdown",
- "id": "immediate-playlist",
+ "id": "occupied-spectrum",
"metadata": {},
"source": [
"#### Plot the CCI AGBD for 2020"
@@ -681,7 +716,7 @@
{
"cell_type": "code",
"execution_count": 8,
- "id": "expired-doctrine",
+ "id": "separate-american",
"metadata": {},
"outputs": [
{
@@ -706,7 +741,7 @@
},
{
"cell_type": "markdown",
- "id": "scientific-screening",
+ "id": "pretty-portal",
"metadata": {},
"source": [
"#### Read in the NCEO Biomass data for this AOI from the downloaded data. NCEO data is stored as a single file for the continent of Africa, rather than multiple tiles."
@@ -715,7 +750,7 @@
{
"cell_type": "code",
"execution_count": 9,
- "id": "limiting-alexander",
+ "id": "peaceful-parallel",
"metadata": {},
"outputs": [
{
@@ -733,7 +768,7 @@
"resolution : 0.0008983153, 0.0008983153 (x, y)\n",
"extent : 12.2108, 31.28024, -13.45856, 5.375519 (xmin, xmax, ymin, ymax)\n",
"crs : +proj=longlat +datum=WGS84 +no_defs \n",
- "source : r_tmp_2021-12-02_165730_9245_75779.grd \n",
+ "source : r_tmp_2021-12-03_014816_789_46965.grd \n",
"names : agbd_2017 \n",
"min values : 0 \n",
"max values : 730 \n"
@@ -768,7 +803,7 @@
},
{
"cell_type": "markdown",
- "id": "boxed-electricity",
+ "id": "matched-focus",
"metadata": {},
"source": [
"#### Plot the NCEO AGBD for 2017"
@@ -777,7 +812,7 @@
{
"cell_type": "code",
"execution_count": 10,
- "id": "built-worry",
+ "id": "numerical-punch",
"metadata": {},
"outputs": [
{
@@ -803,7 +838,7 @@
},
{
"cell_type": "markdown",
- "id": "atlantic-installation",
+ "id": "derived-timer",
"metadata": {},
"source": [
"#### Read in the JPL Biomass data for this AOI"
@@ -812,7 +847,7 @@
{
"cell_type": "code",
"execution_count": 11,
- "id": "cutting-paint",
+ "id": "obvious-lewis",
"metadata": {},
"outputs": [
{
@@ -830,7 +865,7 @@
"resolution : 0.0008983153, 0.0008983153 (x, y)\n",
"extent : 12.2108, 31.28024, -13.45856, 5.375519 (xmin, xmax, ymin, ymax)\n",
"crs : +proj=longlat +datum=WGS84 +no_defs \n",
- "source : r_tmp_2021-12-02_165819_9245_94988.grd \n",
+ "source : r_tmp_2021-12-03_014936_789_16723.grd \n",
"names : agbd_2020 \n",
"min values : 0 \n",
"max values : 24186 \n"
@@ -871,7 +906,7 @@
{
"cell_type": "code",
"execution_count": 12,
- "id": "offshore-russia",
+ "id": "unlimited-volume",
"metadata": {},
"outputs": [
{
@@ -882,7 +917,7 @@
"resolution : 0.0008983153, 0.0008983153 (x, y)\n",
"extent : 12.2108, 31.28024, -13.45856, 5.375519 (xmin, xmax, ymin, ymax)\n",
"crs : +proj=longlat +datum=WGS84 +no_defs \n",
- "source : r_tmp_2021-12-02_170249_9245_84317.grd \n",
+ "source : r_tmp_2021-12-03_015433_789_81839.grd \n",
"names : agbd_2020 \n",
"values : 0, 1997.5 (min, max)\n"
]
@@ -902,7 +937,7 @@
},
{
"cell_type": "markdown",
- "id": "fleet-brave",
+ "id": "essential-sarah",
"metadata": {},
"source": [
"#### Plot the JPL AGBD for 2020"
@@ -911,7 +946,7 @@
{
"cell_type": "code",
"execution_count": 13,
- "id": "banned-colony",
+ "id": "favorite-korean",
"metadata": {},
"outputs": [
{
@@ -936,7 +971,7 @@
},
{
"cell_type": "markdown",
- "id": "endangered-layout",
+ "id": "wooden-drinking",
"metadata": {},
"source": [
"#### Read in forest cover raster. Currently using 30% forest cover from Hansen product. The cover rasters have been resampled to the resolutions of CCI Biomass, JPL Biomass, and NCEO Biomass for use as a forest cover mask."
@@ -945,7 +980,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "smooth-decade",
+ "id": "deadly-closure",
"metadata": {},
"outputs": [],
"source": [
@@ -956,7 +991,7 @@
},
{
"cell_type": "markdown",
- "id": "urban-stick",
+ "id": "crazy-buffer",
"metadata": {},
"source": [
"#### Create 30% cover forest threshold mask for CCI"
@@ -965,7 +1000,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "steady-bones",
+ "id": "alpha-candidate",
"metadata": {},
"outputs": [],
"source": [
@@ -978,7 +1013,7 @@
},
{
"cell_type": "markdown",
- "id": "marine-silver",
+ "id": "strategic-pennsylvania",
"metadata": {},
"source": [
"#### Create 30% cover forest threshold mask for JPL"
@@ -987,7 +1022,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "canadian-crack",
+ "id": "quality-durham",
"metadata": {},
"outputs": [],
"source": [
@@ -1000,7 +1035,7 @@
},
{
"cell_type": "markdown",
- "id": "guided-terrace",
+ "id": "forward-diana",
"metadata": {},
"source": [
"#### Create 30% cover forest threshold mask for NCEO"
@@ -1009,7 +1044,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "typical-philip",
+ "id": "sophisticated-wound",
"metadata": {},
"outputs": [],
"source": [
@@ -1023,7 +1058,7 @@
{
"cell_type": "code",
"execution_count": 28,
- "id": "strategic-taste",
+ "id": "pregnant-wrist",
"metadata": {},
"outputs": [],
"source": [
@@ -1034,7 +1069,7 @@
},
{
"cell_type": "markdown",
- "id": "advisory-america",
+ "id": "injured-cliff",
"metadata": {},
"source": [
"### Checkpoint: Write out and read in Forest cover threshold mask for CCI and JPL"
@@ -1043,7 +1078,7 @@
{
"cell_type": "code",
"execution_count": 29,
- "id": "entertaining-blame",
+ "id": "derived-acrobat",
"metadata": {},
"outputs": [],
"source": [
@@ -1062,7 +1097,7 @@
{
"cell_type": "code",
"execution_count": 14,
- "id": "solid-terrace",
+ "id": "fabulous-finance",
"metadata": {},
"outputs": [],
"source": [
@@ -1084,7 +1119,7 @@
},
{
"cell_type": "markdown",
- "id": "amber-cursor",
+ "id": "intense-notice",
"metadata": {},
"source": [
"#### Apply the forest cover threshold mask to CCI, JPL, and NCEO"
@@ -1093,7 +1128,7 @@
{
"cell_type": "code",
"execution_count": 15,
- "id": "smart-spice",
+ "id": "north-capacity",
"metadata": {},
"outputs": [
{
@@ -1121,7 +1156,7 @@
{
"cell_type": "code",
"execution_count": 16,
- "id": "olive-onion",
+ "id": "isolated-trigger",
"metadata": {},
"outputs": [
{
@@ -1179,7 +1214,7 @@
{
"cell_type": "code",
"execution_count": 17,
- "id": "talented-emphasis",
+ "id": "democratic-integration",
"metadata": {},
"outputs": [
{
@@ -1207,7 +1242,7 @@
{
"cell_type": "code",
"execution_count": 18,
- "id": "marine-theology",
+ "id": "legitimate-lesbian",
"metadata": {},
"outputs": [
{
@@ -1265,7 +1300,7 @@
{
"cell_type": "code",
"execution_count": 20,
- "id": "spare-istanbul",
+ "id": "wound-space",
"metadata": {},
"outputs": [
{
@@ -1293,7 +1328,7 @@
{
"cell_type": "code",
"execution_count": 21,
- "id": "traditional-record",
+ "id": "exempt-lafayette",
"metadata": {},
"outputs": [
{
@@ -1350,7 +1385,7 @@
},
{
"cell_type": "markdown",
- "id": "suited-desperate",
+ "id": "limited-switzerland",
"metadata": {},
"source": [
"### Checkpoint: Write out and read in Forest only biomass for CCI, JPL, and NCEO"
@@ -1359,7 +1394,7 @@
{
"cell_type": "code",
"execution_count": 22,
- "id": "polished-regular",
+ "id": "promising-papua",
"metadata": {},
"outputs": [],
"source": [
@@ -1377,32 +1412,10 @@
},
{
"cell_type": "code",
- "execution_count": 25,
- "id": "voluntary-fence",
+ "execution_count": 15,
+ "id": "heated-devon",
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Error in .local(.Object, ...) : \n",
- "\n"
- ]
- },
- {
- "ename": "ERROR",
- "evalue": "Error in .rasterObjectFromFile(x, band = band, objecttype = \"RasterLayer\", : Cannot create a RasterLayer object from this file. (file does not exist)\n",
- "output_type": "error",
- "traceback": [
- "Error in .rasterObjectFromFile(x, band = band, objecttype = \"RasterLayer\", : Cannot create a RasterLayer object from this file. (file does not exist)\nTraceback:\n",
- "1. raster(x = filename)",
- "2. raster(x = filename)",
- "3. .local(x, ...)",
- "4. .rasterObjectFromFile(x, band = band, objecttype = \"RasterLayer\", \n . ...)",
- "5. stop(\"Cannot create a RasterLayer object from this file. (file does not exist)\")"
- ]
- }
- ],
+ "outputs": [],
"source": [
"threshold_folder = \"/projects/shared-buckets/tkerr1/data/gfc_threshold\"\n",
"\n",
@@ -1422,7 +1435,7 @@
},
{
"cell_type": "markdown",
- "id": "reported-warrior",
+ "id": "sporting-profit",
"metadata": {},
"source": [
"#### Mask to country shape"
@@ -1430,8 +1443,8 @@
},
{
"cell_type": "code",
- "execution_count": 24,
- "id": "proper-singles",
+ "execution_count": 16,
+ "id": "entertaining-station",
"metadata": {},
"outputs": [
{
@@ -1456,17 +1469,37 @@
],
"source": [
"cci_masked <- mask(cci_thresholded, aoi, updatevalue=NA)\n",
+ "\n",
+ "names(cci_masked) <- c('agbd_2020')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "immune-chicken",
+ "metadata": {},
+ "outputs": [],
+ "source": [
"jpl_masked <- mask(jpl_thresholded, aoi, updatevalue=NA)\n",
+ "\n",
+ "names(jpl_masked) <- c('agbd_2020')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "practical-adoption",
+ "metadata": {},
+ "outputs": [],
+ "source": [
"nceo_masked <- mask(nceo_thresholded, aoi, updatevalue=NA)\n",
"\n",
- "names(cci_masked) <- c('agbd_2020')\n",
- "names(jpl_masked) <- c('agbd_2020')\n",
"names(nceo_masked) <- c('agbd_2020')"
]
},
{
"cell_type": "markdown",
- "id": "executive-struggle",
+ "id": "julian-bhutan",
"metadata": {},
"source": [
"#### Plot forest biomass map and histogram of biomass density for CCI, JPL, and NCEO"
@@ -1475,7 +1508,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "individual-liverpool",
+ "id": "informational-gates",
"metadata": {},
"outputs": [],
"source": [
@@ -1507,7 +1540,7 @@
},
{
"cell_type": "markdown",
- "id": "tired-cable",
+ "id": "physical-scientist",
"metadata": {},
"source": [
"#### Calculate total aboveground biomass and average aboveground biomass density for 2020 CCI and JPL biomass for the selected country"
@@ -1516,7 +1549,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "norman-ordinary",
+ "id": "double-poster",
"metadata": {},
"outputs": [],
"source": [
@@ -1527,7 +1560,7 @@
},
{
"cell_type": "markdown",
- "id": "practical-gambling",
+ "id": "accepted-influence",
"metadata": {},
"source": [
"#### Print out basic forest aboveground biomass statistics for the selected country\n"
@@ -1536,7 +1569,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "dominant-roulette",
+ "id": "fixed-conference",
"metadata": {},
"outputs": [],
"source": [
@@ -1560,7 +1593,7 @@
},
{
"cell_type": "markdown",
- "id": "apparent-aaron",
+ "id": "needed-cursor",
"metadata": {},
"source": [
"## The following is old code I'm keeping here for reference purposes"
@@ -1568,7 +1601,7 @@
},
{
"cell_type": "markdown",
- "id": "constant-fossil",
+ "id": "secret-aircraft",
"metadata": {},
"source": [
"#### Calculate total aboveground biomass and average aboveground biomass density for 2020 CCI and NCEO biomass for the selected country"
@@ -1577,7 +1610,7 @@
{
"cell_type": "code",
"execution_count": 23,
- "id": "expected-association",
+ "id": "naval-disability",
"metadata": {
"collapsed": true,
"jupyter": {
@@ -1789,7 +1822,7 @@
},
{
"cell_type": "markdown",
- "id": "second-dancing",
+ "id": "adaptive-parcel",
"metadata": {},
"source": [
"#### Print out basic forest aboveground biomass statistics for the selected country\n",
@@ -1799,7 +1832,7 @@
{
"cell_type": "code",
"execution_count": 24,
- "id": "going-garbage",
+ "id": "global-preservation",
"metadata": {},
"outputs": [
{
@@ -1829,7 +1862,7 @@
{
"cell_type": "code",
"execution_count": 26,
- "id": "assigned-graphics",
+ "id": "floating-discipline",
"metadata": {},
"outputs": [
{
@@ -1876,7 +1909,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "reported-cooperation",
+ "id": "congressional-equivalent",
"metadata": {},
"outputs": [],
"source": []
--
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