From e3cd68ff4370ecfbdc2153f6fe8ea7a648a5404f Mon Sep 17 00:00:00 2001
From: tkerr1 <theodoremkerr@gmail.com>
Date: Mon, 1 Nov 2021 15:23:30 +0000
Subject: [PATCH] Working on NCEO cell error
---
.../forest_biomass_summary_DRC_output.ipynb | 86 ++++++++-----------
1 file changed, 38 insertions(+), 48 deletions(-)
diff --git a/country_outputs/forest_biomass_summary_DRC_output.ipynb b/country_outputs/forest_biomass_summary_DRC_output.ipynb
index 7bdc970..0732493 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": "domestic-poverty",
+ "id": "understood-error",
"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": "unlimited-minnesota",
+ "id": "imperial-navigation",
"metadata": {},
"source": [
"#### Install these R packages first, and load them into the R session. Source R script with support functions."
@@ -27,13 +27,8 @@
{
"cell_type": "code",
"execution_count": 1,
- "id": "exterior-nightmare",
- "metadata": {
- "collapsed": true,
- "jupyter": {
- "outputs_hidden": true
- }
- },
+ "id": "published-basin",
+ "metadata": {},
"outputs": [
{
"name": "stderr",
@@ -119,7 +114,7 @@
"\n",
"Attaching package ff\n",
"\n",
- "- getOption(\"fftempdir\")==\"/tmp/RtmpPRaI0t/ff\"\n",
+ "- getOption(\"fftempdir\")==\"/tmp/RtmpO8dWrM/ff\"\n",
"\n",
"\n",
"- getOption(\"ffextension\")==\"ff\"\n",
@@ -168,13 +163,9 @@
"\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",
- "Warning message:\n",
- "“dependency ‘nws’ is not availableâ€\n",
- "also installing the dependencies ‘Rmpi’, ‘rlecuyer’\n",
+ "also installing the dependency ‘rlecuyer’\n",
"\n",
"\n",
- "Warning message in install.packages(x, dependencies = TRUE):\n",
- "“installation of package ‘Rmpi’ had non-zero exit statusâ€\n",
"Updating HTML index of packages in '.Library'\n",
"\n",
"Making 'packages.html' ...\n",
@@ -209,7 +200,7 @@
},
{
"cell_type": "markdown",
- "id": "united-district",
+ "id": "amino-hometown",
"metadata": {},
"source": [
"#### Set the path to the CCI Biomass data folder & read in world countries shapefile"
@@ -218,7 +209,7 @@
{
"cell_type": "code",
"execution_count": 2,
- "id": "searching-deployment",
+ "id": "frank-wings",
"metadata": {},
"outputs": [
{
@@ -261,7 +252,7 @@
},
{
"cell_type": "markdown",
- "id": "fifteen-wedding",
+ "id": "contained-status",
"metadata": {},
"source": [
"#### Generate 10x10 degree WGS84 grid that the CCI Biomass and Hansen Forest Cover products are tiled on"
@@ -270,7 +261,7 @@
{
"cell_type": "code",
"execution_count": 3,
- "id": "sacred-rings",
+ "id": "synthetic-tucson",
"metadata": {},
"outputs": [
{
@@ -292,7 +283,7 @@
},
{
"cell_type": "markdown",
- "id": "german-device",
+ "id": "formal-language",
"metadata": {},
"source": [
"#### Print out country names in Africa to select from"
@@ -300,8 +291,8 @@
},
{
"cell_type": "code",
- "execution_count": 6,
- "id": "developmental-aruba",
+ "execution_count": 4,
+ "id": "harmful-covering",
"metadata": {},
"outputs": [
{
@@ -609,7 +600,7 @@
},
{
"cell_type": "markdown",
- "id": "bigger-racing",
+ "id": "passing-aircraft",
"metadata": {},
"source": [
"#### Select a country in Africa to plot with corresponding data tiles"
@@ -617,8 +608,8 @@
},
{
"cell_type": "code",
- "execution_count": 7,
- "id": "chronic-packing",
+ "execution_count": 5,
+ "id": "behavioral-antique",
"metadata": {},
"outputs": [
{
@@ -677,8 +668,8 @@
},
{
"cell_type": "code",
- "execution_count": 8,
- "id": "likely-reflection",
+ "execution_count": 6,
+ "id": "ideal-transfer",
"metadata": {},
"outputs": [],
"source": [
@@ -688,7 +679,7 @@
},
{
"cell_type": "markdown",
- "id": "emotional-consistency",
+ "id": "amateur-glenn",
"metadata": {},
"source": [
"#### Read in the CCI Biomass data for this AOI from the downloaded CCI Biomass tiles, mosaicing multiple tiles as necessary"
@@ -696,8 +687,8 @@
},
{
"cell_type": "code",
- "execution_count": 9,
- "id": "honey-stewart",
+ "execution_count": 7,
+ "id": "interesting-adrian",
"metadata": {},
"outputs": [
{
@@ -708,7 +699,7 @@
"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_2021-10-25_142438_1337_91161.tif \n",
+ "source : r_tmp_2021-11-01_145918_845_65258.tif \n",
"names : agbd_2020, agbd_sd_2020 \n",
"min values : 0, 0 \n",
"max values : 552, 1068 \n"
@@ -725,7 +716,7 @@
},
{
"cell_type": "markdown",
- "id": "careful-delivery",
+ "id": "needed-return",
"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."
@@ -733,8 +724,8 @@
},
{
"cell_type": "code",
- "execution_count": 13,
- "id": "fatty-activation",
+ "execution_count": 9,
+ "id": "sudden-veteran",
"metadata": {},
"outputs": [
{
@@ -753,7 +744,7 @@
"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_2021-10-25_145108_1337_50743.grd \n",
+ "source : r_tmp_2021-11-01_151612_845_75868.grd \n",
"names : agbd_2017, agbd_sd_2017 \n",
"min values : 0, 0 \n",
"max values : 730, 310 \n"
@@ -771,14 +762,13 @@
"filenames_nceo <- c(file.path(nceo_data_folder, file_name), file.path(nceo_data_folder, file_name_sd))\n",
"print(filenames_nceo)\n",
"\n",
- "\n",
+ "filename <- \"\"\n",
"\n",
"tile_stack <- crop(stack(filenames_nceo), aoi)#, datatype=\"INT1U\", format='GTiff', options=\"COMPRESS=LZW\")\n",
"\n",
"names(tile_stack) <- band_names_nceo\n",
"tile_stacks <- list(tile_stack)\n",
"\n",
- "\n",
"tile_mosaic <- tile_stacks[[1]]\n",
" if (filename != '') {\n",
" tile_mosaic <- writeRaster(tile_mosaic, filename=filename, \n",
@@ -796,7 +786,7 @@
{
"cell_type": "code",
"execution_count": 14,
- "id": "hawaiian-bargain",
+ "id": "intelligent-russell",
"metadata": {},
"outputs": [
{
@@ -846,7 +836,7 @@
},
{
"cell_type": "markdown",
- "id": "caroline-infrared",
+ "id": "developmental-natural",
"metadata": {},
"source": [
"#### Calculate total aboveground biomass and average aboveground biomass density for 2017 CCI and NCEO biomass for the selected country"
@@ -855,7 +845,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "sophisticated-photographer",
+ "id": "cooperative-field",
"metadata": {},
"outputs": [],
"source": [
@@ -999,7 +989,7 @@
},
{
"cell_type": "markdown",
- "id": "continuing-crest",
+ "id": "simplified-format",
"metadata": {},
"source": [
"#### Print out basic forest aboveground biomass statistics for the selected country\n",
@@ -1009,7 +999,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "professional-vertical",
+ "id": "later-budapest",
"metadata": {},
"outputs": [],
"source": [
@@ -1020,7 +1010,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "premier-wallace",
+ "id": "normal-princeton",
"metadata": {},
"outputs": [],
"source": [
@@ -1054,7 +1044,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "statutory-chess",
+ "id": "rapid-request",
"metadata": {},
"outputs": [],
"source": [
@@ -1065,7 +1055,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "dedicated-grass",
+ "id": "ultimate-woman",
"metadata": {},
"outputs": [],
"source": [
@@ -1075,7 +1065,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "signal-tractor",
+ "id": "portable-framing",
"metadata": {},
"outputs": [],
"source": [
@@ -1085,7 +1075,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "focal-trunk",
+ "id": "hybrid-tattoo",
"metadata": {},
"outputs": [],
"source": []
@@ -1093,7 +1083,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "several-spokesman",
+ "id": "ceramic-paradise",
"metadata": {},
"outputs": [],
"source": []
--
GitLab