From 9c9e349467338b7b4568fb3339e4109dfa3e4aa9 Mon Sep 17 00:00:00 2001
From: tkerr1 <theodoremkerr@gmail.com>
Date: Wed, 1 Dec 2021 21:30:29 +0000
Subject: [PATCH] Finalized everything and changed the zlim for the CCI plots
---
.../forest_biomass_summary_DRC_output.ipynb | 211 ++++++------------
1 file changed, 73 insertions(+), 138 deletions(-)
diff --git a/country_outputs/forest_biomass_summary_DRC_output.ipynb b/country_outputs/forest_biomass_summary_DRC_output.ipynb
index b13a8a7..ae71c3f 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": "bronze-organization",
+ "id": "worse-devon",
"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": "shaped-prison",
+ "id": "passing-cannon",
"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": "swiss-modem",
+ "id": "thick-farming",
"metadata": {},
"outputs": [
{
@@ -114,7 +114,7 @@
"\n",
"Attaching package ff\n",
"\n",
- "- getOption(\"fftempdir\")==\"/tmp/RtmpKu4r1p/ff\"\n",
+ "- getOption(\"fftempdir\")==\"/tmp/RtmpV2y1W7/ff\"\n",
"\n",
"\n",
"- getOption(\"ffextension\")==\"ff\"\n",
@@ -200,7 +200,7 @@
},
{
"cell_type": "markdown",
- "id": "historic-liberty",
+ "id": "conditional-mount",
"metadata": {},
"source": [
"#### Set the path to the CCI, JPL, and NCEO Biomass data folders & read in world countries shapefile"
@@ -209,7 +209,7 @@
{
"cell_type": "code",
"execution_count": 2,
- "id": "built-thousand",
+ "id": "former-governor",
"metadata": {},
"outputs": [
{
@@ -243,7 +243,7 @@
},
{
"cell_type": "markdown",
- "id": "lasting-entry",
+ "id": "premier-rental",
"metadata": {},
"source": [
"#### Generate 10x10 degree WGS84 grid that the CCI Biomass and Hansen Forest Cover products are tiled on"
@@ -252,7 +252,7 @@
{
"cell_type": "code",
"execution_count": 3,
- "id": "laden-crest",
+ "id": "visible-newman",
"metadata": {},
"outputs": [
{
@@ -274,7 +274,7 @@
},
{
"cell_type": "markdown",
- "id": "owned-narrow",
+ "id": "isolated-montgomery",
"metadata": {},
"source": [
"#### Print out country names in Africa to select from"
@@ -283,7 +283,7 @@
{
"cell_type": "code",
"execution_count": 4,
- "id": "needed-software",
+ "id": "foster-institution",
"metadata": {},
"outputs": [
{
@@ -591,7 +591,7 @@
},
{
"cell_type": "markdown",
- "id": "recognized-causing",
+ "id": "discrete-england",
"metadata": {},
"source": [
"#### Select a country in Africa to plot with corresponding data tiles"
@@ -600,7 +600,7 @@
{
"cell_type": "code",
"execution_count": 5,
- "id": "visible-lightning",
+ "id": "imported-haven",
"metadata": {},
"outputs": [
{
@@ -660,7 +660,7 @@
{
"cell_type": "code",
"execution_count": 6,
- "id": "special-lithuania",
+ "id": "oriented-planner",
"metadata": {},
"outputs": [],
"source": [
@@ -670,7 +670,7 @@
},
{
"cell_type": "markdown",
- "id": "republican-plastic",
+ "id": "soviet-merchandise",
"metadata": {},
"source": [
"#### Read in the CCI Biomass data for this AOI from the downloaded CCI Biomass tiles, mosaicing multiple tiles as necessary"
@@ -678,28 +678,10 @@
},
{
"cell_type": "code",
- "execution_count": 11,
- "id": "driving-universe",
+ "execution_count": 7,
+ "id": "suited-computer",
"metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "class : RasterBrick \n",
- "dimensions : 21188, 21454, 454567352, 2 (nrow, ncol, ncell, nlayers)\n",
- "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_2021-11-29_195041_783_44667.tif \n",
- "names : agbd_2020, agbd_sd_2020 \n",
- "min values : 0, 0 \n",
- "max values : 552, 1068 \n"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
+ "outputs": [],
"source": [
"cci <- readCCI(data_folder=cci_folder, year=\"2020\", version=3, aoi=aoi)\n",
"cci"
@@ -707,7 +689,7 @@
},
{
"cell_type": "markdown",
- "id": "numeric-omaha",
+ "id": "ceramic-anchor",
"metadata": {},
"source": [
"#### Plot the CCI AGBD for 2020"
@@ -716,16 +698,16 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "regular-ethics",
+ "id": "intense-palmer",
"metadata": {},
"outputs": [],
"source": [
- "plot(cci$agbd_2020, main=\"CCI AGBD 2020\", zlim=c(0,250)); plot(aoi, add=T)"
+ "plot(cci$agbd_2020, main=\"CCI AGBD 2020\", zlim=c(0,300)); plot(aoi, add=T)"
]
},
{
"cell_type": "markdown",
- "id": "robust-costa",
+ "id": "stylish-iceland",
"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."
@@ -733,34 +715,10 @@
},
{
"cell_type": "code",
- "execution_count": 12,
- "id": "spanish-permission",
+ "execution_count": null,
+ "id": "approximate-swiss",
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "[1] \"/projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif\"\n"
- ]
- },
- {
- "ename": "ERROR",
- "evalue": "Error in rgdal::getRasterData(object@file@con, offset = offs, region.dim = reg, : Failure during raster IO\n\n",
- "output_type": "error",
- "traceback": [
- "Error in rgdal::getRasterData(object@file@con, offset = offs, region.dim = reg, : Failure during raster IO\n\nTraceback:\n",
- "1. crop(stack(filenames_nceo), aoi)",
- "2. crop(stack(filenames_nceo), aoi)",
- "3. .local(x, y, ...)",
- "4. getValuesBlock(x, row = tr$row[i] + row1 - 1, nrows = tr$nrows[i], \n . col1, nc)",
- "5. getValuesBlock(x, row = tr$row[i] + row1 - 1, nrows = tr$nrows[i], \n . col1, nc)",
- "6. .local(x, ...)",
- "7. .readRasterLayerValues(xx, row, nrows, col, ncols)",
- "8. rgdal::getRasterData(object@file@con, offset = offs, region.dim = reg, \n . band = object@data@band)"
- ]
- }
- ],
+ "outputs": [],
"source": [
"nceo_file <- 'AGB_map_2017v0m.tif'\n",
"# nceo_sd_file <- 'SD_map_2017v0m.tif'\n",
@@ -786,7 +744,7 @@
},
{
"cell_type": "markdown",
- "id": "acute-complex",
+ "id": "excess-customer",
"metadata": {},
"source": [
"#### Plot the NCEO AGBD for 2017"
@@ -795,7 +753,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "natural-tuner",
+ "id": "representative-detective",
"metadata": {},
"outputs": [],
"source": [
@@ -805,7 +763,7 @@
},
{
"cell_type": "markdown",
- "id": "major-definition",
+ "id": "delayed-functionality",
"metadata": {},
"source": [
"#### Read in the JPL Biomass data for this AOI"
@@ -814,7 +772,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "stock-toolbox",
+ "id": "freelance-solid",
"metadata": {},
"outputs": [],
"source": [
@@ -848,7 +806,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "tender-juice",
+ "id": "satisfied-picnic",
"metadata": {},
"outputs": [],
"source": [
@@ -862,7 +820,7 @@
},
{
"cell_type": "markdown",
- "id": "sharp-blood",
+ "id": "cultural-columbia",
"metadata": {},
"source": [
"#### Plot the JPL AGBD for 2020"
@@ -870,40 +828,17 @@
},
{
"cell_type": "code",
- "execution_count": 4,
- "id": "fewer-issue",
+ "execution_count": null,
+ "id": "valuable-performer",
"metadata": {},
- "outputs": [
- {
- "ename": "ERROR",
- "evalue": "Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'jpl_corr' not found\n",
- "output_type": "error",
- "traceback": [
- "Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'jpl_corr' not found\nTraceback:\n",
- "1. plot(jpl_corr$agbd_2020, main = \"JPL AGBD 2020\", zlim = c(0, \n . 500))",
- "2. .handleSimpleError(function (cond) \n . .Internal(C_tryCatchHelper(addr, 1L, cond)), \"object 'jpl_corr' not found\", \n . base::quote(plot(jpl_corr$agbd_2020, main = \"JPL AGBD 2020\", \n . zlim = c(0, 500))))",
- "3. h(simpleError(msg, call))"
- ]
- },
- {
- "ename": "ERROR",
- "evalue": "Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'aoi' not found\n",
- "output_type": "error",
- "traceback": [
- "Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'aoi' not found\nTraceback:\n",
- "1. plot(aoi, add = T)",
- "2. .handleSimpleError(function (cond) \n . .Internal(C_tryCatchHelper(addr, 1L, cond)), \"object 'aoi' not found\", \n . base::quote(plot(aoi, add = T)))",
- "3. h(simpleError(msg, call))"
- ]
- }
- ],
+ "outputs": [],
"source": [
"plot(jpl_corr$agbd_2020, main=\"JPL AGBD 2020\", zlim=c(0,500)); plot(aoi, add=T)"
]
},
{
"cell_type": "markdown",
- "id": "plastic-making",
+ "id": "elder-pickup",
"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."
@@ -912,7 +847,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "funny-tournament",
+ "id": "brave-funeral",
"metadata": {},
"outputs": [],
"source": [
@@ -923,7 +858,7 @@
},
{
"cell_type": "markdown",
- "id": "growing-center",
+ "id": "impressed-header",
"metadata": {},
"source": [
"#### Create 30% cover forest threshold mask for CCI"
@@ -932,7 +867,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "chinese-travel",
+ "id": "smooth-repair",
"metadata": {},
"outputs": [],
"source": [
@@ -945,7 +880,7 @@
},
{
"cell_type": "markdown",
- "id": "permanent-recognition",
+ "id": "mathematical-performance",
"metadata": {},
"source": [
"#### Create 30% cover forest threshold mask for JPL"
@@ -954,7 +889,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "joint-correction",
+ "id": "religious-mitchell",
"metadata": {},
"outputs": [],
"source": [
@@ -967,7 +902,7 @@
},
{
"cell_type": "markdown",
- "id": "impossible-estate",
+ "id": "moral-nigeria",
"metadata": {},
"source": [
"#### Create 30% cover forest threshold mask for NCEO"
@@ -976,7 +911,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "demographic-mobile",
+ "id": "convinced-appeal",
"metadata": {},
"outputs": [],
"source": [
@@ -990,7 +925,7 @@
{
"cell_type": "code",
"execution_count": 28,
- "id": "center-toronto",
+ "id": "mobile-fashion",
"metadata": {},
"outputs": [],
"source": [
@@ -1001,7 +936,7 @@
},
{
"cell_type": "markdown",
- "id": "aging-mortality",
+ "id": "adult-begin",
"metadata": {},
"source": [
"### Checkpoint: Write out and read in Forest cover threshold mask for CCI and JPL"
@@ -1010,7 +945,7 @@
{
"cell_type": "code",
"execution_count": 29,
- "id": "facial-bermuda",
+ "id": "therapeutic-shoot",
"metadata": {},
"outputs": [],
"source": [
@@ -1029,7 +964,7 @@
{
"cell_type": "code",
"execution_count": 8,
- "id": "according-richards",
+ "id": "sound-muslim",
"metadata": {},
"outputs": [],
"source": [
@@ -1051,7 +986,7 @@
},
{
"cell_type": "markdown",
- "id": "purple-error",
+ "id": "mediterranean-phone",
"metadata": {},
"source": [
"#### Apply the forest cover threshold mask to CCI, JPL, and NCEO"
@@ -1060,7 +995,7 @@
{
"cell_type": "code",
"execution_count": 9,
- "id": "pharmaceutical-oxygen",
+ "id": "rental-chapel",
"metadata": {},
"outputs": [
{
@@ -1088,7 +1023,7 @@
{
"cell_type": "code",
"execution_count": 10,
- "id": "killing-apache",
+ "id": "martial-private",
"metadata": {},
"outputs": [
{
@@ -1138,15 +1073,15 @@
}
],
"source": [
- "plot(cci$agbd_2020, zlim=c(0,500), main=\"CCI biomass\"); plot(aoi, add=T)\n",
+ "plot(cci$agbd_2020, zlim=c(0,300), main=\"CCI biomass\"); plot(aoi, add=T)\n",
"plot(gfc_cci_thresholded$forest2020, main=\"forest mask\"); plot(aoi, add=T)\n",
- "plot(cci_thresholded$agbd_2020, zlim=c(0,500), main=\"CCI masked\"); plot(aoi, add=T)"
+ "plot(cci_thresholded$agbd_2020, zlim=c(0,300), main=\"CCI masked\"); plot(aoi, add=T)"
]
},
{
"cell_type": "code",
"execution_count": 15,
- "id": "secure-dating",
+ "id": "distant-newman",
"metadata": {},
"outputs": [
{
@@ -1174,7 +1109,7 @@
{
"cell_type": "code",
"execution_count": 16,
- "id": "placed-handbook",
+ "id": "written-harris",
"metadata": {},
"outputs": [
{
@@ -1232,7 +1167,7 @@
{
"cell_type": "code",
"execution_count": 17,
- "id": "bibliographic-event",
+ "id": "regulation-entry",
"metadata": {},
"outputs": [
{
@@ -1260,7 +1195,7 @@
{
"cell_type": "code",
"execution_count": 18,
- "id": "spread-assets",
+ "id": "systematic-violation",
"metadata": {},
"outputs": [
{
@@ -1317,7 +1252,7 @@
},
{
"cell_type": "markdown",
- "id": "romance-shannon",
+ "id": "worldwide-edinburgh",
"metadata": {},
"source": [
"### Checkpoint: Write out and read in Forest only biomass for CCI, JPL, and NCEO"
@@ -1326,7 +1261,7 @@
{
"cell_type": "code",
"execution_count": 19,
- "id": "authentic-raleigh",
+ "id": "chubby-black",
"metadata": {},
"outputs": [],
"source": [
@@ -1345,7 +1280,7 @@
{
"cell_type": "code",
"execution_count": 7,
- "id": "waiting-canyon",
+ "id": "thermal-brook",
"metadata": {},
"outputs": [],
"source": [
@@ -1367,7 +1302,7 @@
},
{
"cell_type": "markdown",
- "id": "surprising-resolution",
+ "id": "liberal-reynolds",
"metadata": {},
"source": [
"#### Mask to country shape"
@@ -1376,7 +1311,7 @@
{
"cell_type": "code",
"execution_count": 8,
- "id": "blank-browse",
+ "id": "impaired-president",
"metadata": {},
"outputs": [],
"source": [
@@ -1391,7 +1326,7 @@
},
{
"cell_type": "markdown",
- "id": "controlling-testimony",
+ "id": "african-floating",
"metadata": {},
"source": [
"#### Plot forest biomass map and histogram of biomass density for CCI, JPL, and NCEO"
@@ -1400,7 +1335,7 @@
{
"cell_type": "code",
"execution_count": 9,
- "id": "experienced-essay",
+ "id": "expanded-module",
"metadata": {},
"outputs": [
{
@@ -1438,7 +1373,7 @@
"par(mfrow=c(2,2), mai=c(0.5,0.5,0.5,0.5))\n",
"options(repr.plot.width=15, repr.plot.height=15)\n",
"\n",
- "plot(cci_masked$agbd_2020, main=\"CCI AGBD 2020 (cover>30%)\", zlim=c(0,500) ); plot(aoi, add=T)\n",
+ "plot(cci_masked$agbd_2020, main=\"CCI AGBD 2020 (cover>30%)\", zlim=c(0,300) ); plot(aoi, add=T)\n",
"\n",
"val.cci2020 <- ff(getValues(cci_masked$agbd_2020))\n",
"hist(val.cci2020[,3][val.cci2020[,3]>0], freq=F,\n",
@@ -1463,7 +1398,7 @@
},
{
"cell_type": "markdown",
- "id": "irish-genome",
+ "id": "robust-cartoon",
"metadata": {},
"source": [
"#### Calculate total aboveground biomass and average aboveground biomass density for 2020 CCI and JPL biomass for the selected country"
@@ -1472,7 +1407,7 @@
{
"cell_type": "code",
"execution_count": 13,
- "id": "urban-approval",
+ "id": "recognized-spice",
"metadata": {},
"outputs": [
{
@@ -1508,7 +1443,7 @@
},
{
"cell_type": "markdown",
- "id": "presidential-zoning",
+ "id": "endless-withdrawal",
"metadata": {},
"source": [
"#### Print out basic forest aboveground biomass statistics for the selected country\n"
@@ -1517,7 +1452,7 @@
{
"cell_type": "code",
"execution_count": 14,
- "id": "balanced-textbook",
+ "id": "political-narrative",
"metadata": {},
"outputs": [
{
@@ -1556,7 +1491,7 @@
},
{
"cell_type": "markdown",
- "id": "selected-acoustic",
+ "id": "normal-bahrain",
"metadata": {},
"source": [
"## The following is old code I'm keeping here for reference purposes"
@@ -1564,7 +1499,7 @@
},
{
"cell_type": "markdown",
- "id": "thrown-framework",
+ "id": "committed-coupon",
"metadata": {},
"source": [
"#### Calculate total aboveground biomass and average aboveground biomass density for 2020 CCI and NCEO biomass for the selected country"
@@ -1573,7 +1508,7 @@
{
"cell_type": "code",
"execution_count": 23,
- "id": "imperial-endorsement",
+ "id": "unlikely-tuition",
"metadata": {
"collapsed": true,
"jupyter": {
@@ -1785,7 +1720,7 @@
},
{
"cell_type": "markdown",
- "id": "exempt-sandwich",
+ "id": "wooden-welding",
"metadata": {},
"source": [
"#### Print out basic forest aboveground biomass statistics for the selected country\n",
@@ -1795,7 +1730,7 @@
{
"cell_type": "code",
"execution_count": 24,
- "id": "fabulous-president",
+ "id": "historical-windsor",
"metadata": {},
"outputs": [
{
@@ -1825,7 +1760,7 @@
{
"cell_type": "code",
"execution_count": 26,
- "id": "electoral-potato",
+ "id": "signed-easter",
"metadata": {},
"outputs": [
{
@@ -1872,7 +1807,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "hundred-official",
+ "id": "demographic-mexican",
"metadata": {},
"outputs": [],
"source": []
--
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