From e63c852ed38f957019f511e0d549dea0d7df0be5 Mon Sep 17 00:00:00 2001
From: nehajo88 <nehajo88@gmail.com>
Date: Tue, 7 Feb 2023 18:08:18 +0000
Subject: [PATCH] Allowing GEDI total calculations
---
.../Country_summaries_DPS-checkpoint.R | 3 +-
.../run_country_summaries-checkpoint.ipynb | 147 +++++++++---------
country_summaries/dps/Country_summaries_DPS.R | 1 +
.../dps/run_country_summaries.ipynb | 147 +++++++++---------
4 files changed, 155 insertions(+), 143 deletions(-)
diff --git a/country_summaries/dps/.ipynb_checkpoints/Country_summaries_DPS-checkpoint.R b/country_summaries/dps/.ipynb_checkpoints/Country_summaries_DPS-checkpoint.R
index 5db34ec..d8ad550 100644
--- a/country_summaries/dps/.ipynb_checkpoints/Country_summaries_DPS-checkpoint.R
+++ b/country_summaries/dps/.ipynb_checkpoints/Country_summaries_DPS-checkpoint.R
@@ -8,7 +8,7 @@
# Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R GHA /projects/my-public-bucket/Data/Country_boundaries/GEDI_countries_Dubayah_individual/ne_10m_a_1_GHA.gpkg CCI,GEDI,NCEO /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
-# Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 2104 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_2104.gpkg CCI,GEDI,NCEO /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_clipped/2104_CCI_AOImasked.tif /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
+# Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 2104 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_2104.gpkg CCI,GEDI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_clipped/2104_CCI_AOImasked.tif /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
################################# DESCRIPTION OF ARGUMENTS ############################################
# args[1] = Country eco3 code
@@ -322,6 +322,7 @@ overlay_products <- function(Out_folder,maps,maps_AOImasked,coarsest_res,CI_map_
agb_for_CI_comparison[(agb_for_CI_comparison != 0) & (agb_for_CI_comparison != 1)] <- -1
plot(agb_for_CI_comparison,col = pal2(3),main=paste0(maps[i]," AGBD ", eval(parse(text=paste0(maps[i],"_year"))), ' within 95% CI of ', maps[coarsest_res[1]]," AGBD ", eval(parse(text=paste0(maps[coarsest_res[1]],"_year")))),legend=FALSE,cex.main=0.8)
legend("topright", inset=c(-0.4, 0), xpd=TRUE, legend=c("FALSE", "TRUE", "NoData"), fill=c("red", "green", "gray"),bty="n",border=c("black", "black", "black"), cex=1)
+ writeRaster(agb_for_CI_comparison,file.path(Out_folder,paste0(eco3,'_GEDI_95CI_CCI_is_TF.tif')),datatype="INT1U",format="GTiff",options=c("COMPRESS=DEFLATE","PREDICTOR=2","ZLEVEL=9"),overwrite=TRUE)
if (file.exists(output_warps)){file.remove(output_warps)}
}
}
diff --git a/country_summaries/dps/.ipynb_checkpoints/run_country_summaries-checkpoint.ipynb b/country_summaries/dps/.ipynb_checkpoints/run_country_summaries-checkpoint.ipynb
index b4a51bd..7bd39f2 100644
--- a/country_summaries/dps/.ipynb_checkpoints/run_country_summaries-checkpoint.ipynb
+++ b/country_summaries/dps/.ipynb_checkpoints/run_country_summaries-checkpoint.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": 1,
- "id": "alternative-midwest",
+ "id": "antique-blend",
"metadata": {},
"outputs": [
{
@@ -26,7 +26,7 @@
},
{
"cell_type": "markdown",
- "id": "raised-walker",
+ "id": "affecting-accuracy",
"metadata": {},
"source": [
"# Launch DPS for Country_summaries_DPS.R"
@@ -35,7 +35,7 @@
{
"cell_type": "code",
"execution_count": 34,
- "id": "democratic-shock",
+ "id": "abroad-grove",
"metadata": {},
"outputs": [
{
@@ -253,7 +253,7 @@
},
{
"cell_type": "markdown",
- "id": "analyzed-cabin",
+ "id": "adult-integrity",
"metadata": {},
"source": [
"## COMMIT ALL CHANGES and REGISTER ALGORITHM FROM TERMINAL"
@@ -261,18 +261,18 @@
},
{
"cell_type": "markdown",
- "id": "white-clearing",
+ "id": "coordinate-dragon",
"metadata": {},
"source": [
"conda activate r-with-gdal\n",
"cd biomass_harmonization/\n",
"git add country_summaries/dps\n",
- "git commit -m 'moving to ecoregions and CCI 2018'\n",
- "git tag -f AGB_ecoregions\n",
+ "git commit -m 'Allowing GEDI total calculations'\n",
+ "git tag -f AGB_ecoregions_PART2\n",
"\n",
- "git push origin -f AGB_ecoregions\n",
+ "git push origin -f AGB_ecoregions_PART2\n",
"git push\n",
- "git push origin -f AGB_ecoregions\n",
+ "git push origin -f AGB_ecoregions_PART2\n",
"\n",
"conda activate base\n",
"python /projects/register-algorithm /projects/biomass_harmonization/country_summaries/dps/algorithm_config.yaml\n",
@@ -281,7 +281,7 @@
},
{
"cell_type": "markdown",
- "id": "competent-rogers",
+ "id": "classical-monthly",
"metadata": {},
"source": [
"## CREATE LISTS OF 500 DPS JOBS one by one"
@@ -289,8 +289,8 @@
},
{
"cell_type": "code",
- "execution_count": 13,
- "id": "valuable-senior",
+ "execution_count": 55,
+ "id": "hispanic-allah",
"metadata": {},
"outputs": [
{
@@ -317,7 +317,7 @@
},
{
"cell_type": "markdown",
- "id": "breeding-threat",
+ "id": "practical-electricity",
"metadata": {},
"source": [
"## Run DPS jobs\n"
@@ -326,8 +326,13 @@
{
"cell_type": "code",
"execution_count": 6,
- "id": "dying-momentum",
- "metadata": {},
+ "id": "metric-commerce",
+ "metadata": {
+ "collapsed": true,
+ "jupyter": {
+ "outputs_hidden": true
+ }
+ },
"outputs": [
{
"name": "stdout",
@@ -367,10 +372,10 @@
"# Aus and Oceania: ['9736','7621','8966','9729','9230','7108','8819','8797','9049','9250','7410','9278','9218','8837','9214','9110','9016','7172','9235','9206','8722','9728','9254','8889','9266','3369','9730','9199','7099','9726','9737','9725','9017','9274','9034','7104','9445','9355','9367','7855','7612','9461','9738','8885','9261','9293','9449','9437','9455','6684','7107','9074','9462','9368','9162','9323','8265','9727','9479','7922','8729','8266','8639','8017','8970','9369','8564','7202','3912','8144','8936','8689','9288','7190','9316','7443','3096','7867','8918','8524','7002','8339','7370','7035','9220','7223','7861','7936','9160','9411','9739','8008','7450','9408','9028','8942','8318','7106','8978','9044','8161','9360','7036','8149','8932','8512','9193','9031','8734','9354','9229','9464','9208','7886','8583','3368','8875','9735','9424','8949','8867','9039','7162','9406','9076','9006','6940','9029','8618','8092','8829','8712','7875','9372','7071','8846','7226','9399','9248','6992','7033','6690','9379','8037','7447','8438','7870','9395','8716','9371','9392','8070','9485','3364','8702','6995','6934','8864','9246','9393','9400','9245','8683','8834','9396','8740','8522','6682','9447','9165','9243','7219','9397','8167','9376','9002','7617','8953','8884','8603','8619','7220','8747','6683','8964','8984','9384','9027','8058','9401','8677','7991','9443','9383','8148','8738','8602','8891','9163','8229','9093','9389','7201','6996','7380','9436','7082','9205','9500','8854','7440','8730','8546','9428','9434','9072','9431','8257','7216','6945','7392','9042','8662','8742','9458','9398','8137','8839','8883','8242','8021','6710','8552','9085','8782','9051','7381','7854','8748','9223','8754','9061','7596','7222','7873','9484','9405','8865','8760','8849','8799','6307','8623','9113','9221','9216','8733','9494','8732','8811','8841','8580','7382','8156','3575','8957','8958','9012','9010','7092','8952','8255','9098','3367','8826','6677','8182','8789','8690','9377','7400','8946','9497','8526','9375','9041','7923','9035','9053','8009','9482','9492','8840','7598','9463','9161','8105','7174','8765','8033','8752','8965','7090','8228','7449','8157','8631','9075','8842','7224','9201','7069','7073','8956','7212','9095','8317','9204','8159','7103','8783','8995','7156','6942','9373','7467','9380','7561','8951','7394','8866','7848','7925','7913','7975','9387','7825','9475','5828','6651','8594','8614','7765','9407','8507','8862','8887','6674','9477','7225','9026','6630','6946','8888','8697','9470','7615','8753','9057','9166','8419','8024','4434','8703','7458','8110','7030','8725','9385','8724','7011','7077','8708','8756','7593','9496','9425','9491','8492','7391','9415','9071','3376','9402','7032','8571','7620','9101','8895','6311','8989','9478','7086','8838','7603','9451','9077','8562','9386','7955','7614','8817','7021','8743','8696','8948','9456','9169','8023','8169','9138','8982','8565','8165','8975','7068','9501','8750','6314','8066','9391','7686','7464','8458','8727','8700','9351','7093','6979','7076','9140','7585','9403','8991','9495','9362','7605','8844','8869','8515','8588','9139','9421','8717','9055','7398','7101','3574','8739','8657','8065','8994','8726','6681','3083','8976','7583','8719','9410','8634','8872','8041','7857','7028','9167','7602','8845','9196','8640','9498','7397','7423','8851','8939','7883','8135','8971','6994','8962','9440','8670','7515','7221','8766','9460','7102','8914','7196','7507','8150','8411','6943','8606','8751','9370','9457','7599','3372','7939','8598','3373','3370','6980','8992','8847','8234','9378','8020','8786','6658','9404','9409','8901','9467','9488','8704','7377','7881','7218','9081','9102','9480','7680','8609','3371','9202','8758','8969','8701','7034','8633','8721','9363','6678','9225','8807','9471','7869','7396','9390','6993','6702','7590','7040','9486','9412','9186','7896','8723','9499','7388','9469','7866','7399','8151','6290','8241','8032','8900','9481','7078','7213','7095','6292','7582','7070','9483','9493','3094','9489','9419','6657','9473','7408','8759','8718','9454','8418','9422','8744','9429','9453','7023','9388','9459','8749','7868','9048','8954','3557','8337','8737','7519','9490','8396','3560','7668','8794','8967','8945','8651','8741','8899','8812','7217','7872','7105','9438','8853','7915','8715','7214','6999','7072','9448','9172','7043','7087','8968','9487','9364','9089','8993','8735','7228','7792','9435','8980','7412','8973','7227','6679','7891','8910','7475','9159','9164','9381','9423','9452','9472','9394','7176','7435','9439','8985','8172','7390','9427','8937','8163','9194','7409','7079','8755','8746','8983','9417','7845','9197','7215','8162','9173','8810','8649','9474','3565','9215','8480','8714','8736','9030','8987','8334','9446','8904','8166','9416','7100','7763','9476','7871','7849','9444','7938','9079','9382','8472','9195','9374','3084','9087','9365','7933','7893','9426','8745','7690','8775','8170','7004','7094','7755','8906','6647','7433','8981','7924','9094','4753','8798','3092','7592','9418','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"# INPUT_FILE_LIST = 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"# DPS_group_MEX = ['10392','10350','10409','10221','10430','10512','10270','10398','10003','10413','10034','10167','10194','10079','10554','10423','10163','10248','10174','10106','10391','10161','10369','10510','10330','10081','10066','10239','10276','10227','10298','10213','10502','10210','10319','10577','10438','10138','10342','10394','10232','10234','10314','10400','10289','10557','10526','10035','10178','10222','10572','10100','10407','10228','10054','10206','10037','10224','10132','10485','10397','10556','10592','10574','10112','10318','10581','10097','10590','10094','10563','10147','10123','10578','10027','10405','10544','10586','10547','10433','10447','10148','10291','10425','10162','10545','10093','10255','10062','10474','10403','10164','10521','10177','10275','10263','10576','10435','10553','10247','10359','10472','10230','10280','10165','10104','10504','10427','10218','10331','10589','10036','10159','10168','10441','10470','10434','10014','10190','10386','10046','10334','10152','10048','10465','10102','10481','10458','10499','10300','10508','10188','10189','10517','10110','10299','10169','10466','10278','10362','10442','10475','10546','10129','10390','10387','10328','10015','10182','10284','10399','10196','10173','10166','10448','10575','10144','10498','10415','10582','10226','10051','10372','10532','10155','10023','10022','10091','10530','10208','10201','10266','10114','10529','10358','10537','10357','10158','10351','10552','10515','10579','10010','10063','10004','10116','10356','10154','10437','10176','10236','10524','10267','10329','10085','10419','10503','10029','10469','10480','10335','10065','10349','10271','10149','10070','10107','10175','10229','10523','10567','10462','10360','10235','10080','10303','10528','10067','10489','10197','10417','10573','10137','10549','10411','10340','10099','10463','10453','10422','10378','10587','10262','10117','10346','10126','10476','10074','10238','10136','10028','10170','10131','10562','10431','10056','10181','10317','10428','10008','10491','10265','10288','10444','10571','10373','10030','10083','10257','10032','10497','10325','10204','10534','10446','10408','10332','10286','10073','10241','10045','10580']\n",
- "DPS_group_PER = ['1','2','3','4','5','6'] #1','2','3','4','5',\n",
- "DPS_group_PER = ['20001','20002','20003','20004','20005','20006','20007','20008','20009'] #1','2','3','4','5',\n",
+ "# DPS_group_PER = ['1','2','3','4','5','6'] #1','2','3','4','5',\n",
+ "# DPS_group_PER = ['20001','20002','20003','20004','20005','20006','20007','20008','20009'] #1','2','3','4','5',\n",
" \n",
- "INPUT_FILE_LIST = DPS_group_PER\n",
+ "INPUT_FILE_LIST = DPS_group_0\n",
"INPUT_MAP_LIST = ['CCI','GEDI','NCEO']\n",
"submit_results_df_list = []\n",
"len_input_list = len(INPUT_FILE_LIST)\n",
@@ -380,7 +385,7 @@
"NCEO_file_location = \"https://maap-ops-workspace.s3.us-west-2.amazonaws.com/shared/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif\"\n",
"\n",
"for i, INPUT_TILE_NUM in enumerate(INPUT_FILE_LIST):\n",
- " if not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/' + INPUT_TILE_NUM + '_AGB_products_stats.txt'):\n",
+ " if not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/' + INPUT_TILE_NUM + '_AGB_products_stats.txt'):\n",
" print(\"CURRENTLY PROCESSING \" + INPUT_TILE_NUM)\n",
" Local_GPKG = \"/projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_\" + INPUT_TILE_NUM + \".gpkg\"\n",
"# Local_GPKG = \"/projects/my-public-bucket/Data/Country_biomes/PERU/DPS_run_\" + INPUT_TILE_NUM + \".gpkg\" ###### PERUUUUUU ################\n",
@@ -391,7 +396,7 @@
"\n",
" ############################## MAKE AN EXCEPTION FOR CCI MAPS, FIRST MOSAIC AND CLIP TILES BEFORE THE DPS JOB BEGINS #######################################\n",
" if 'CCI' in INPUT_MAP_LIST:\n",
- " CCI_clip_folder = '/projects/my-public-bucket/Data/Biomass_maps/CCI_clipped_PERU'\n",
+ " CCI_clip_folder = '/projects/my-public-bucket/Data/Biomass_maps/CCI_clipped'\n",
" if not os.path.exists(os.path.join(CCI_clip_folder,INPUT_TILE_NUM +'_CCI_AOImasked.tif')):# and not os.path.exists(os.path.join(CCI_clip_folder,INPUT_TILE_NUM +'_location.jpeg')): \n",
" print(\"We are going to need to mosaic and clip CCI tiles for \" + INPUT_TILE_NUM)\n",
" print(\"This may take a while. Check this folder for results: \" + CCI_clip_folder + \". The output GeoTIFF will be added to the DPS job as an input param for CCI_file_location\")\n",
@@ -403,7 +408,7 @@
" CCI_file_location = \"https://maap-ops-workspace.s3.us-west-2.amazonaws.com/shared/nehajo88/Data/Biomass_maps/CCI_clipped/\" + INPUT_TILE_NUM +'_CCI_AOImasked.tif'\n",
" else: \n",
" print(\"CCI file has already been clipped and saved for \" + INPUT_TILE_NUM)\n",
- " CCI_file_location = \"https://maap-ops-workspace.s3.us-west-2.amazonaws.com/shared/nehajo88/Data/Biomass_maps/CCI_clipped_PERU/\" + INPUT_TILE_NUM +'_CCI_AOImasked.tif'\n",
+ " CCI_file_location = \"https://maap-ops-workspace.s3.us-west-2.amazonaws.com/shared/nehajo88/Data/Biomass_maps/CCI_clipped/\" + INPUT_TILE_NUM +'_CCI_AOImasked.tif'\n",
"\n",
" ############################## BEGIN DPS JOB ##################################################################################################################### \n",
" INPUT_Country_shapefile = 'https://maap-ops-workspace.s3.us-west-2.amazonaws.com/shared/nehajo88/Data/WWF_NE_ecoregions/DPS_run_' + INPUT_TILE_NUM + '.gpkg'\n",
@@ -432,7 +437,7 @@
" submit_result = maap.submitJob(\n",
" identifier=IDENTIFIER,\n",
" algo_id=ALGO_ID,\n",
- " version='AGB_ecoregions',\n",
+ " version='AGB_ecoregions_PART2',\n",
" username=USER, # username needs to be the same as whoever created the workspace\n",
" queue=WORKER_TYPE,\n",
" **in_param_dict\n",
@@ -462,7 +467,7 @@
},
{
"cell_type": "markdown",
- "id": "detected-comfort",
+ "id": "exterior-tracker",
"metadata": {},
"source": [
"## Assess DPS Results"
@@ -471,7 +476,7 @@
{
"cell_type": "code",
"execution_count": 13,
- "id": "textile-builder",
+ "id": "detected-devices",
"metadata": {},
"outputs": [
{
@@ -515,7 +520,7 @@
},
{
"cell_type": "markdown",
- "id": "literary-setup",
+ "id": "permanent-creation",
"metadata": {},
"source": [
"## MOVE ALL RESULTS INTO ONE FOLDER"
@@ -524,7 +529,7 @@
{
"cell_type": "code",
"execution_count": 14,
- "id": "controlling-server",
+ "id": "australian-connecticut",
"metadata": {
"collapsed": true,
"jupyter": {
@@ -546,40 +551,40 @@
}
],
"source": [
- "if not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/'): \n",
- " os.makedirs('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/')\n",
+ "if not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/'): \n",
+ " os.makedirs('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/')\n",
" \n",
- "SUMMARY_files_tifs = glob.glob('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/2023/**/*.tif', recursive=True)\n",
+ "SUMMARY_files_tifs = glob.glob('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/2023/**/*.tif', recursive=True)\n",
"print(\"Moving files in SUMMARY_files_tifs\")\n",
"for each_file in SUMMARY_files_tifs:\n",
- " if os.path.exists(each_file) and not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/' + os.path.basename(each_file)): \n",
- " shutil.move(each_file, '/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled')\n",
+ " if os.path.exists(each_file) and not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/' + os.path.basename(each_file)): \n",
+ " shutil.move(each_file, '/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled')\n",
" else: \n",
- " if os.path.exists(each_file) and os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/' + os.path.basename(each_file)): \n",
+ " if os.path.exists(each_file) and os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/' + os.path.basename(each_file)): \n",
" os.remove(each_file)\n",
" \n",
- "SUMMARY_files_jpegs = glob.glob('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/2023/**/*.jpeg', recursive=True)\n",
+ "SUMMARY_files_jpegs = glob.glob('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/2023/**/*.jpeg', recursive=True)\n",
"print(\"Moving files in SUMMARY_files_jpegs\")\n",
"for each_file in SUMMARY_files_jpegs:\n",
- " if os.path.exists(each_file) and not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/' + os.path.basename(each_file)): \n",
- " shutil.move(each_file, '/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled')\n",
+ " if os.path.exists(each_file) and not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/' + os.path.basename(each_file)): \n",
+ " shutil.move(each_file, '/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled')\n",
" else: \n",
- " if os.path.exists(each_file) and os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/' + os.path.basename(each_file)): \n",
+ " if os.path.exists(each_file) and os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/' + os.path.basename(each_file)): \n",
" os.remove(each_file)\n",
" \n",
- "SUMMARY_files_txts = glob.glob('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/2023/**/*_AGB_products_stats.txt', recursive=True)\n",
+ "SUMMARY_files_txts = glob.glob('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/2023/**/*_AGB_products_stats.txt', recursive=True)\n",
"print(\"Moving files in SUMMARY_files_txts\")\n",
"for each_file in SUMMARY_files_txts:\n",
- " if os.path.exists(each_file) and not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/' + os.path.basename(each_file)): \n",
- " shutil.move(each_file, '/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled')\n",
+ " if os.path.exists(each_file) and not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/' + os.path.basename(each_file)): \n",
+ " shutil.move(each_file, '/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled')\n",
" else: \n",
- " if os.path.exists(each_file) and os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/' + os.path.basename(each_file)): \n",
+ " if os.path.exists(each_file) and os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/' + os.path.basename(each_file)): \n",
" os.remove(each_file)"
]
},
{
"cell_type": "markdown",
- "id": "suited-chocolate",
+ "id": "choice-christmas",
"metadata": {},
"source": [
"### COMPILE ALL OUTPUT STAT FILES INTO ONE"
@@ -588,7 +593,7 @@
{
"cell_type": "code",
"execution_count": 15,
- "id": "happy-legislature",
+ "id": "novel-berkeley",
"metadata": {},
"outputs": [],
"source": [
@@ -611,7 +616,7 @@
},
{
"cell_type": "markdown",
- "id": "heavy-aaron",
+ "id": "finnish-rugby",
"metadata": {},
"source": [
"### QUESTION: DO THE ECOREGION -MEANS OF THE VARIOUS PRODUCTS AT DIFFER SIGNIFICANTLY BY BIOME, \n",
@@ -621,7 +626,7 @@
{
"cell_type": "code",
"execution_count": 95,
- "id": "ordinary-hearing",
+ "id": "disturbed-tissue",
"metadata": {
"collapsed": true,
"jupyter": {
@@ -798,7 +803,7 @@
},
{
"cell_type": "markdown",
- "id": "modified-austria",
+ "id": "requested-grammar",
"metadata": {},
"source": [
"### PLOT WHERE ECOREGIONS (AND BIOMES) DIFFER (before grouping them - this is to check if all expected ecoregions have processed)"
@@ -807,7 +812,7 @@
{
"cell_type": "code",
"execution_count": 3,
- "id": "ideal-perspective",
+ "id": "understood-indication",
"metadata": {},
"outputs": [
{
@@ -861,7 +866,7 @@
},
{
"cell_type": "markdown",
- "id": "economic-harmony",
+ "id": "anonymous-justice",
"metadata": {},
"source": [
"### PLOT WHERE ECOREGIONS (AND BIOMES) DIFFER (after grouping them)"
@@ -870,7 +875,7 @@
{
"cell_type": "code",
"execution_count": 29,
- "id": "alternative-austria",
+ "id": "lasting-performance",
"metadata": {},
"outputs": [
{
@@ -973,7 +978,7 @@
{
"cell_type": "code",
"execution_count": 33,
- "id": "ignored-sacramento",
+ "id": "present-covering",
"metadata": {},
"outputs": [],
"source": [
@@ -1000,7 +1005,7 @@
{
"cell_type": "code",
"execution_count": 335,
- "id": "informative-jordan",
+ "id": "sunrise-showcase",
"metadata": {},
"outputs": [
{
@@ -1130,7 +1135,7 @@
},
{
"cell_type": "markdown",
- "id": "portuguese-induction",
+ "id": "conscious-calgary",
"metadata": {},
"source": [
"### QUESTION: DO THE AGB-DIFFERENCES IN THE PRODUCTS ALSO DIFFER BY CONTINENT? \n",
@@ -1140,7 +1145,7 @@
{
"cell_type": "code",
"execution_count": 28,
- "id": "current-folder",
+ "id": "alien-liberia",
"metadata": {},
"outputs": [
{
@@ -1198,7 +1203,7 @@
},
{
"cell_type": "markdown",
- "id": "pleasant-exhibit",
+ "id": "mighty-sharp",
"metadata": {},
"source": [
"### VISUALIZE THIS DIFFERENCE BY PLOTTING BIOME MEANS IN ALL CONTINENTS"
@@ -1207,7 +1212,7 @@
{
"cell_type": "code",
"execution_count": 30,
- "id": "white-amendment",
+ "id": "technological-knowing",
"metadata": {},
"outputs": [
{
@@ -1280,7 +1285,7 @@
},
{
"cell_type": "markdown",
- "id": "adverse-actor",
+ "id": "supposed-shoot",
"metadata": {},
"source": [
"## MEXICO NFI AND AGB MAP VALIDATION"
@@ -1289,7 +1294,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "ethical-republican",
+ "id": "inner-jacksonville",
"metadata": {},
"outputs": [],
"source": [
@@ -1326,7 +1331,7 @@
{
"cell_type": "code",
"execution_count": 238,
- "id": "searching-release",
+ "id": "rapid-damages",
"metadata": {},
"outputs": [],
"source": [
@@ -1357,7 +1362,7 @@
{
"cell_type": "code",
"execution_count": 5,
- "id": "phantom-passion",
+ "id": "regional-brunswick",
"metadata": {
"collapsed": true,
"jupyter": {
@@ -2303,7 +2308,7 @@
{
"cell_type": "code",
"execution_count": 53,
- "id": "arabic-ordinary",
+ "id": "crude-respect",
"metadata": {},
"outputs": [
{
@@ -2469,7 +2474,7 @@
{
"cell_type": "code",
"execution_count": 15,
- "id": "pressed-motion",
+ "id": "reasonable-stuart",
"metadata": {},
"outputs": [
{
@@ -2666,7 +2671,7 @@
{
"cell_type": "code",
"execution_count": 54,
- "id": "sixth-friday",
+ "id": "intense-brown",
"metadata": {},
"outputs": [
{
@@ -2812,7 +2817,7 @@
{
"cell_type": "code",
"execution_count": 18,
- "id": "material-radical",
+ "id": "funky-tattoo",
"metadata": {},
"outputs": [
{
@@ -2926,7 +2931,7 @@
{
"cell_type": "code",
"execution_count": 9,
- "id": "experimental-shield",
+ "id": "interim-thinking",
"metadata": {},
"outputs": [
{
@@ -3045,7 +3050,7 @@
},
{
"cell_type": "markdown",
- "id": "persistent-albania",
+ "id": "understood-dimension",
"metadata": {},
"source": [
"## PERU NFI AND AGB MAP VALIDATION"
@@ -3054,7 +3059,7 @@
{
"cell_type": "code",
"execution_count": 79,
- "id": "determined-japanese",
+ "id": "architectural-scanning",
"metadata": {},
"outputs": [],
"source": [
@@ -3092,7 +3097,7 @@
{
"cell_type": "code",
"execution_count": 10,
- "id": "western-windsor",
+ "id": "severe-municipality",
"metadata": {},
"outputs": [
{
@@ -3289,7 +3294,7 @@
{
"cell_type": "code",
"execution_count": 14,
- "id": "funded-hawaii",
+ "id": "protecting-bargain",
"metadata": {
"collapsed": true,
"jupyter": {
@@ -3489,7 +3494,7 @@
},
{
"cell_type": "markdown",
- "id": "later-distance",
+ "id": "dominican-mobile",
"metadata": {},
"source": [
"## SPAIN NFI AND AGB MAP VALIDATION"
@@ -3498,7 +3503,7 @@
{
"cell_type": "code",
"execution_count": 16,
- "id": "rubber-violence",
+ "id": "secret-holmes",
"metadata": {},
"outputs": [],
"source": [
@@ -3535,7 +3540,7 @@
{
"cell_type": "code",
"execution_count": 20,
- "id": "finnish-nicholas",
+ "id": "small-rescue",
"metadata": {},
"outputs": [
{
@@ -4033,7 +4038,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "large-favorite",
+ "id": "functioning-concert",
"metadata": {},
"outputs": [],
"source": []
diff --git a/country_summaries/dps/Country_summaries_DPS.R b/country_summaries/dps/Country_summaries_DPS.R
index 9a0046b..d8ad550 100644
--- a/country_summaries/dps/Country_summaries_DPS.R
+++ b/country_summaries/dps/Country_summaries_DPS.R
@@ -322,6 +322,7 @@ overlay_products <- function(Out_folder,maps,maps_AOImasked,coarsest_res,CI_map_
agb_for_CI_comparison[(agb_for_CI_comparison != 0) & (agb_for_CI_comparison != 1)] <- -1
plot(agb_for_CI_comparison,col = pal2(3),main=paste0(maps[i]," AGBD ", eval(parse(text=paste0(maps[i],"_year"))), ' within 95% CI of ', maps[coarsest_res[1]]," AGBD ", eval(parse(text=paste0(maps[coarsest_res[1]],"_year")))),legend=FALSE,cex.main=0.8)
legend("topright", inset=c(-0.4, 0), xpd=TRUE, legend=c("FALSE", "TRUE", "NoData"), fill=c("red", "green", "gray"),bty="n",border=c("black", "black", "black"), cex=1)
+ writeRaster(agb_for_CI_comparison,file.path(Out_folder,paste0(eco3,'_GEDI_95CI_CCI_is_TF.tif')),datatype="INT1U",format="GTiff",options=c("COMPRESS=DEFLATE","PREDICTOR=2","ZLEVEL=9"),overwrite=TRUE)
if (file.exists(output_warps)){file.remove(output_warps)}
}
}
diff --git a/country_summaries/dps/run_country_summaries.ipynb b/country_summaries/dps/run_country_summaries.ipynb
index b4a51bd..7bd39f2 100644
--- a/country_summaries/dps/run_country_summaries.ipynb
+++ b/country_summaries/dps/run_country_summaries.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": 1,
- "id": "alternative-midwest",
+ "id": "antique-blend",
"metadata": {},
"outputs": [
{
@@ -26,7 +26,7 @@
},
{
"cell_type": "markdown",
- "id": "raised-walker",
+ "id": "affecting-accuracy",
"metadata": {},
"source": [
"# Launch DPS for Country_summaries_DPS.R"
@@ -35,7 +35,7 @@
{
"cell_type": "code",
"execution_count": 34,
- "id": "democratic-shock",
+ "id": "abroad-grove",
"metadata": {},
"outputs": [
{
@@ -253,7 +253,7 @@
},
{
"cell_type": "markdown",
- "id": "analyzed-cabin",
+ "id": "adult-integrity",
"metadata": {},
"source": [
"## COMMIT ALL CHANGES and REGISTER ALGORITHM FROM TERMINAL"
@@ -261,18 +261,18 @@
},
{
"cell_type": "markdown",
- "id": "white-clearing",
+ "id": "coordinate-dragon",
"metadata": {},
"source": [
"conda activate r-with-gdal\n",
"cd biomass_harmonization/\n",
"git add country_summaries/dps\n",
- "git commit -m 'moving to ecoregions and CCI 2018'\n",
- "git tag -f AGB_ecoregions\n",
+ "git commit -m 'Allowing GEDI total calculations'\n",
+ "git tag -f AGB_ecoregions_PART2\n",
"\n",
- "git push origin -f AGB_ecoregions\n",
+ "git push origin -f AGB_ecoregions_PART2\n",
"git push\n",
- "git push origin -f AGB_ecoregions\n",
+ "git push origin -f AGB_ecoregions_PART2\n",
"\n",
"conda activate base\n",
"python /projects/register-algorithm /projects/biomass_harmonization/country_summaries/dps/algorithm_config.yaml\n",
@@ -281,7 +281,7 @@
},
{
"cell_type": "markdown",
- "id": "competent-rogers",
+ "id": "classical-monthly",
"metadata": {},
"source": [
"## CREATE LISTS OF 500 DPS JOBS one by one"
@@ -289,8 +289,8 @@
},
{
"cell_type": "code",
- "execution_count": 13,
- "id": "valuable-senior",
+ "execution_count": 55,
+ "id": "hispanic-allah",
"metadata": {},
"outputs": [
{
@@ -317,7 +317,7 @@
},
{
"cell_type": "markdown",
- "id": "breeding-threat",
+ "id": "practical-electricity",
"metadata": {},
"source": [
"## Run DPS jobs\n"
@@ -326,8 +326,13 @@
{
"cell_type": "code",
"execution_count": 6,
- "id": "dying-momentum",
- "metadata": {},
+ "id": "metric-commerce",
+ "metadata": {
+ "collapsed": true,
+ "jupyter": {
+ "outputs_hidden": true
+ }
+ },
"outputs": [
{
"name": "stdout",
@@ -367,10 +372,10 @@
"# Aus and Oceania: ['9736','7621','8966','9729','9230','7108','8819','8797','9049','9250','7410','9278','9218','8837','9214','9110','9016','7172','9235','9206','8722','9728','9254','8889','9266','3369','9730','9199','7099','9726','9737','9725','9017','9274','9034','7104','9445','9355','9367','7855','7612','9461','9738','8885','9261','9293','9449','9437','9455','6684','7107','9074','9462','9368','9162','9323','8265','9727','9479','7922','8729','8266','8639','8017','8970','9369','8564','7202','3912','8144','8936','8689','9288','7190','9316','7443','3096','7867','8918','8524','7002','8339','7370','7035','9220','7223','7861','7936','9160','9411','9739','8008','7450','9408','9028','8942','8318','7106','8978','9044','8161','9360','7036','8149','8932','8512','9193','9031','8734','9354','9229','9464','9208','7886','8583','3368','8875','9735','9424','8949','8867','9039','7162','9406','9076','9006','6940','9029','8618','8092','8829','8712','7875','9372','7071','8846','7226','9399','9248','6992','7033','6690','9379','8037','7447','8438','7870','9395','8716','9371','9392','8070','9485','3364','8702','6995','6934','8864','9246','9393','9400','9245','8683','8834','9396','8740','8522','6682','9447','9165','9243','7219','9397','8167','9376','9002','7617','8953','8884','8603','8619','7220','8747','6683','8964','8984','9384','9027','8058','9401','8677','7991','9443','9383','8148','8738','8602','8891','9163','8229','9093','9389','7201','6996','7380','9436','7082','9205','9500','8854','7440','8730','8546','9428','9434','9072','9431','8257','7216','6945','7392','9042','8662','8742','9458','9398','8137','8839','8883','8242','8021','6710','8552','9085','8782','9051','7381','7854','8748','9223','8754','9061','7596','7222','7873','9484','9405','8865','8760','8849','8799','6307','8623','9113','9221','9216','8733','9494','8732','8811','8841','8580','7382','8156','3575','8957','8958','9012','9010','7092','8952','8255','9098','3367','8826','6677','8182','8789','8690','9377','7400','8946','9497','8526','9375','9041','7923','9035','9053','8009','9482','9492','8840','7598','9463','9161','8105','7174','8765','8033','8752','8965','7090','8228','7449','8157','8631','9075','8842','7224','9201','7069','7073','8956','7212','9095','8317','9204','8159','7103','8783','8995','7156','6942','9373','7467','9380','7561','8951','7394','8866','7848','7925','7913','7975','9387','7825','9475','5828','6651','8594','8614','7765','9407','8507','8862','8887','6674','9477','7225','9026','6630','6946','8888','8697','9470','7615','8753','9057','9166','8419','8024','4434','8703','7458','8110','7030','8725','9385','8724','7011','7077','8708','8756','7593','9496','9425','9491','8492','7391','9415','9071','3376','9402','7032','8571','7620','9101','8895','6311','8989','9478','7086','8838','7603','9451','9077','8562','9386','7955','7614','8817','7021','8743','8696','8948','9456','9169','8023','8169','9138','8982','8565','8165','8975','7068','9501','8750','6314','8066','9391','7686','7464','8458','8727','8700','9351','7093','6979','7076','9140','7585','9403','8991','9495','9362','7605','8844','8869','8515','8588','9139','9421','8717','9055','7398','7101','3574','8739','8657','8065','8994','8726','6681','3083','8976','7583','8719','9410','8634','8872','8041','7857','7028','9167','7602','8845','9196','8640','9498','7397','7423','8851','8939','7883','8135','8971','6994','8962','9440','8670','7515','7221','8766','9460','7102','8914','7196','7507','8150','8411','6943','8606','8751','9370','9457','7599','3372','7939','8598','3373','3370','6980','8992','8847','8234','9378','8020','8786','6658','9404','9409','8901','9467','9488','8704','7377','7881','7218','9081','9102','9480','7680','8609','3371','9202','8758','8969','8701','7034','8633','8721','9363','6678','9225','8807','9471','7869','7396','9390','6993','6702','7590','7040','9486','9412','9186','7896','8723','9499','7388','9469','7866','7399','8151','6290','8241','8032','8900','9481','7078','7213','7095','6292','7582','7070','9483','9493','3094','9489','9419','6657','9473','7408','8759','8718','9454','8418','9422','8744','9429','9453','7023','9388','9459','8749','7868','9048','8954','3557','8337','8737','7519','9490','8396','3560','7668','8794','8967','8945','8651','8741','8899','8812','7217','7872','7105','9438','8853','7915','8715','7214','6999','7072','9448','9172','7043','7087','8968','9487','9364','9089','8993','8735','7228','7792','9435','8980','7412','8973','7227','6679','7891','8910','7475','9159','9164','9381','9423','9452','9472','9394','7176','7435','9439','8985','8172','7390','9427','8937','8163','9194','7409','7079','8755','8746','8983','9417','7845','9197','7215','8162','9173','8810','8649','9474','3565','9215','8480','8714','8736','9030','8987','8334','9446','8904','8166','9416','7100','7763','9476','7871','7849','9444','7938','9079','9382','8472','9195','9374','3084','9087','9365','7933','7893','9426','8745','7690','8775','8170','7004','7094','7755','8906','6647','7433','8981','7924','9094','4753','8798','3092','7592','9418','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"# INPUT_FILE_LIST = ['9736','7621','8966','9729','9230','7108','8819','8797','9049','9250','7410','9278','9218','8837','9214','9110','9016','7172','9235','9206','8722','9728','9254','8889','9266','3369','9730','9199','7099','9726','9737','9725','9017','9274','9034','7104','9445','9355','9367','7855','7612','9461','9738','8885','9261','9293','9449','9437','9455','6684','7107','9074','9462','9368','9162','9323','8265','9727','9479','7922','8729','8266','8639','8017','8970','9369','8564','7202','3912','8144','8936','8689','9288','7190','9316','7443','3096','7867','8918','8524','7002','8339','7370','7035','9220','7223','7861','7936','9160','9411','9739','8008','7450','9408','9028','8942','8318','7106','8978','9044','8161','9360','7036','8149','8932','8512','9193','9031','8734','9354','9229','9464','9208','7886','8583','3368','8875','9735','9424','8949','8867','9039','7162','9406','9076','9006','6940','9029','8618','8092','8829','8712','7875','9372','7071','8846','7226','9399','9248','6992','7033','6690','9379','8037','7447','8438','7870','9395','8716','9371','9392','8070','9485','3364','8702','6995','6934','8864','9246','9393','9400','9245','8683','8834','9396','8740','8522','6682','9447','9165','9243','7219','9397','8167','9376','9002','7617','8953','8884','8603','8619','7220','8747','6683','8964','8984','9384','9027','8058','9401','8677','7991','9443','9383','8148','8738','8602','8891','9163','8229','9093','9389','7201','6996','7380','9436','7082','9205','9500','8854','7440','8730','8546','9428','9434','9072','9431','8257','7216','6945','7392','9042','8662','8742','9458','9398','8137','8839','8883','8242','8021','6710','8552','9085','8782','9051','7381','7854','8748','9223','8754','9061','7596','7222','7873','9484','9405','8865','8760','8849','8799','6307','8623','9113','9221','9216','8733','9494','8732','8811','8841','8580','7382','8156','3575','8957','8958','9012','9010','7092','8952','8255','9098','3367','8826','6677','8182','8789','8690','9377','7400','8946','9497','8526','9375','9041','7923','9035','9053','8009','9482','9492','8840','7598','9463','9161','8105','7174','8765','8033','8752','8965','7090','8228','7449','8157','8631','9075','8842','7224','9201','7069','7073','8956','7212','9095','8317','9204','8159','7103','8783','8995','7156','6942','9373','7467','9380','7561','8951','7394','8866','7848','7925','7913','7975','9387','7825','9475','5828','6651','8594','8614','7765','9407','8507','8862','8887','6674','9477','7225','9026','6630','6946','8888','8697','9470','7615','8753','9057','9166','8419','8024','4434','8703','7458','8110','7030','8725','9385','8724','7011','7077','8708','8756','7593','9496','9425','9491','8492','7391','9415','9071','3376','9402','7032','8571','7620','9101','8895','6311','8989','9478','7086','8838','7603','9451','9077','8562','9386','7955','7614','8817','7021','8743','8696','8948','9456','9169','8023','8169','9138','8982','8565','8165','8975','7068','9501','8750','6314','8066','9391','7686','7464','8458','8727','8700','9351','7093','6979','7076','9140','7585','9403','8991','9495','9362','7605','8844','8869','8515','8588','9139','9421','8717','9055','7398','7101','3574','8739','8657','8065','8994','8726','6681','3083','8976','7583','8719','9410','8634','8872','8041','7857','7028','9167','7602','8845','9196','8640','9498','7397','7423','8851','8939','7883','8135','8971','6994','8962','9440','8670','7515','7221','8766','9460','7102','8914','7196','7507','8150','8411','6943','8606','8751','9370','9457','7599','3372','7939','8598','3373','3370','6980','8992','8847','8234','9378','8020','8786','6658','9404','9409','8901','9467','9488','8704','7377','7881','7218','9081','9102','9480','7680','8609','3371','9202','8758','8969','8701','7034','8633','8721','9363','6678','9225','8807','9471','7869','7396','9390','6993','6702','7590','7040','9486','9412','9186','7896','8723','9499','7388','9469','7866','7399','8151','6290','8241','8032','8900','9481','7078','7213','7095','6292','7582','7070','9483','9493','3094','9489','9419','6657','9473','7408','8759','8718','9454','8418','9422','8744','9429','9453','7023','9388','9459','8749','7868','9048','8954','3557','8337','8737','7519','9490','8396','3560','7668','8794','8967','8945','8651','8741','8899','8812','7217','7872','7105','9438','8853','7915','8715','7214','6999','7072','9448','9172','7043','7087','8968','9487','9364','9089','8993','8735','7228','7792','9435','8980','7412','8973','7227','6679','7891','8910','7475','9159','9164','9381','9423','9452','9472','9394','7176','7435','9439','8985','8172','7390','9427','8937','8163','9194','7409','7079','8755','8746','8983','9417','7845','9197','7215','8162','9173','8810','8649','9474','3565','9215','8480','8714','8736','9030','8987','8334','9446','8904','8166','9416','7100','7763','9476','7871','7849','9444','7938','9079','9382','8472','9195','9374','3084','9087','9365','7933','7893','9426','8745','7690','8775','8170','7004','7094','7755','8906','6647','7433','8981','7924','9094','4753','8798','3092','7592','9418','8963','7756','9096','9171','7170','9420','8977','7513','9366','9430','8955','8908','3090','7166','8959','9466','6650','7411','7636','3093','8950','7403','7632','6649','7003','7084','9189','7525','9468','7850','7434','7666','8171','7890','9086','8590','7047','9001','7663','7528','7158','9137','9450','8940','7762','6313','7757','6312','7046','7512','6673','8990','8998','8915','7934','8907','7448','7565','7673','7088','7466','8905','9441','7402','7446','9084','9222','9080','7930','9413','7089','7097','6309','7476','6998','9088','9097','7932','9106','7889','7179','8902','8974','7529','9228','9092','6310','8890','6316','7413','7083','9465','9336','9143','9188','9442','9433','7085','9141','8897','6315','7444','8896','7888','7445','7559','7091','9090','9414','7178','8898','7453','9033','9432','9170','7935','8894','8903','9091','7098','7407','9187','6997','7211','7177','7096','9105','7595','9133','9104','9099','9082','7452','9344','9342','9032']\n",
"# DPS_group_MEX = ['10392','10350','10409','10221','10430','10512','10270','10398','10003','10413','10034','10167','10194','10079','10554','10423','10163','10248','10174','10106','10391','10161','10369','10510','10330','10081','10066','10239','10276','10227','10298','10213','10502','10210','10319','10577','10438','10138','10342','10394','10232','10234','10314','10400','10289','10557','10526','10035','10178','10222','10572','10100','10407','10228','10054','10206','10037','10224','10132','10485','10397','10556','10592','10574','10112','10318','10581','10097','10590','10094','10563','10147','10123','10578','10027','10405','10544','10586','10547','10433','10447','10148','10291','10425','10162','10545','10093','10255','10062','10474','10403','10164','10521','10177','10275','10263','10576','10435','10553','10247','10359','10472','10230','10280','10165','10104','10504','10427','10218','10331','10589','10036','10159','10168','10441','10470','10434','10014','10190','10386','10046','10334','10152','10048','10465','10102','10481','10458','10499','10300','10508','10188','10189','10517','10110','10299','10169','10466','10278','10362','10442','10475','10546','10129','10390','10387','10328','10015','10182','10284','10399','10196','10173','10166','10448','10575','10144','10498','10415','10582','10226','10051','10372','10532','10155','10023','10022','10091','10530','10208','10201','10266','10114','10529','10358','10537','10357','10158','10351','10552','10515','10579','10010','10063','10004','10116','10356','10154','10437','10176','10236','10524','10267','10329','10085','10419','10503','10029','10469','10480','10335','10065','10349','10271','10149','10070','10107','10175','10229','10523','10567','10462','10360','10235','10080','10303','10528','10067','10489','10197','10417','10573','10137','10549','10411','10340','10099','10463','10453','10422','10378','10587','10262','10117','10346','10126','10476','10074','10238','10136','10028','10170','10131','10562','10431','10056','10181','10317','10428','10008','10491','10265','10288','10444','10571','10373','10030','10083','10257','10032','10497','10325','10204','10534','10446','10408','10332','10286','10073','10241','10045','10580']\n",
- "DPS_group_PER = ['1','2','3','4','5','6'] #1','2','3','4','5',\n",
- "DPS_group_PER = ['20001','20002','20003','20004','20005','20006','20007','20008','20009'] #1','2','3','4','5',\n",
+ "# DPS_group_PER = ['1','2','3','4','5','6'] #1','2','3','4','5',\n",
+ "# DPS_group_PER = ['20001','20002','20003','20004','20005','20006','20007','20008','20009'] #1','2','3','4','5',\n",
" \n",
- "INPUT_FILE_LIST = DPS_group_PER\n",
+ "INPUT_FILE_LIST = DPS_group_0\n",
"INPUT_MAP_LIST = ['CCI','GEDI','NCEO']\n",
"submit_results_df_list = []\n",
"len_input_list = len(INPUT_FILE_LIST)\n",
@@ -380,7 +385,7 @@
"NCEO_file_location = \"https://maap-ops-workspace.s3.us-west-2.amazonaws.com/shared/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif\"\n",
"\n",
"for i, INPUT_TILE_NUM in enumerate(INPUT_FILE_LIST):\n",
- " if not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/' + INPUT_TILE_NUM + '_AGB_products_stats.txt'):\n",
+ " if not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/' + INPUT_TILE_NUM + '_AGB_products_stats.txt'):\n",
" print(\"CURRENTLY PROCESSING \" + INPUT_TILE_NUM)\n",
" Local_GPKG = \"/projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_\" + INPUT_TILE_NUM + \".gpkg\"\n",
"# Local_GPKG = \"/projects/my-public-bucket/Data/Country_biomes/PERU/DPS_run_\" + INPUT_TILE_NUM + \".gpkg\" ###### PERUUUUUU ################\n",
@@ -391,7 +396,7 @@
"\n",
" ############################## MAKE AN EXCEPTION FOR CCI MAPS, FIRST MOSAIC AND CLIP TILES BEFORE THE DPS JOB BEGINS #######################################\n",
" if 'CCI' in INPUT_MAP_LIST:\n",
- " CCI_clip_folder = '/projects/my-public-bucket/Data/Biomass_maps/CCI_clipped_PERU'\n",
+ " CCI_clip_folder = '/projects/my-public-bucket/Data/Biomass_maps/CCI_clipped'\n",
" if not os.path.exists(os.path.join(CCI_clip_folder,INPUT_TILE_NUM +'_CCI_AOImasked.tif')):# and not os.path.exists(os.path.join(CCI_clip_folder,INPUT_TILE_NUM +'_location.jpeg')): \n",
" print(\"We are going to need to mosaic and clip CCI tiles for \" + INPUT_TILE_NUM)\n",
" print(\"This may take a while. Check this folder for results: \" + CCI_clip_folder + \". The output GeoTIFF will be added to the DPS job as an input param for CCI_file_location\")\n",
@@ -403,7 +408,7 @@
" CCI_file_location = \"https://maap-ops-workspace.s3.us-west-2.amazonaws.com/shared/nehajo88/Data/Biomass_maps/CCI_clipped/\" + INPUT_TILE_NUM +'_CCI_AOImasked.tif'\n",
" else: \n",
" print(\"CCI file has already been clipped and saved for \" + INPUT_TILE_NUM)\n",
- " CCI_file_location = \"https://maap-ops-workspace.s3.us-west-2.amazonaws.com/shared/nehajo88/Data/Biomass_maps/CCI_clipped_PERU/\" + INPUT_TILE_NUM +'_CCI_AOImasked.tif'\n",
+ " CCI_file_location = \"https://maap-ops-workspace.s3.us-west-2.amazonaws.com/shared/nehajo88/Data/Biomass_maps/CCI_clipped/\" + INPUT_TILE_NUM +'_CCI_AOImasked.tif'\n",
"\n",
" ############################## BEGIN DPS JOB ##################################################################################################################### \n",
" INPUT_Country_shapefile = 'https://maap-ops-workspace.s3.us-west-2.amazonaws.com/shared/nehajo88/Data/WWF_NE_ecoregions/DPS_run_' + INPUT_TILE_NUM + '.gpkg'\n",
@@ -432,7 +437,7 @@
" submit_result = maap.submitJob(\n",
" identifier=IDENTIFIER,\n",
" algo_id=ALGO_ID,\n",
- " version='AGB_ecoregions',\n",
+ " version='AGB_ecoregions_PART2',\n",
" username=USER, # username needs to be the same as whoever created the workspace\n",
" queue=WORKER_TYPE,\n",
" **in_param_dict\n",
@@ -462,7 +467,7 @@
},
{
"cell_type": "markdown",
- "id": "detected-comfort",
+ "id": "exterior-tracker",
"metadata": {},
"source": [
"## Assess DPS Results"
@@ -471,7 +476,7 @@
{
"cell_type": "code",
"execution_count": 13,
- "id": "textile-builder",
+ "id": "detected-devices",
"metadata": {},
"outputs": [
{
@@ -515,7 +520,7 @@
},
{
"cell_type": "markdown",
- "id": "literary-setup",
+ "id": "permanent-creation",
"metadata": {},
"source": [
"## MOVE ALL RESULTS INTO ONE FOLDER"
@@ -524,7 +529,7 @@
{
"cell_type": "code",
"execution_count": 14,
- "id": "controlling-server",
+ "id": "australian-connecticut",
"metadata": {
"collapsed": true,
"jupyter": {
@@ -546,40 +551,40 @@
}
],
"source": [
- "if not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/'): \n",
- " os.makedirs('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/')\n",
+ "if not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/'): \n",
+ " os.makedirs('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/')\n",
" \n",
- "SUMMARY_files_tifs = glob.glob('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/2023/**/*.tif', recursive=True)\n",
+ "SUMMARY_files_tifs = glob.glob('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/2023/**/*.tif', recursive=True)\n",
"print(\"Moving files in SUMMARY_files_tifs\")\n",
"for each_file in SUMMARY_files_tifs:\n",
- " if os.path.exists(each_file) and not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/' + os.path.basename(each_file)): \n",
- " shutil.move(each_file, '/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled')\n",
+ " if os.path.exists(each_file) and not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/' + os.path.basename(each_file)): \n",
+ " shutil.move(each_file, '/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled')\n",
" else: \n",
- " if os.path.exists(each_file) and os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/' + os.path.basename(each_file)): \n",
+ " if os.path.exists(each_file) and os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/' + os.path.basename(each_file)): \n",
" os.remove(each_file)\n",
" \n",
- "SUMMARY_files_jpegs = glob.glob('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/2023/**/*.jpeg', recursive=True)\n",
+ "SUMMARY_files_jpegs = glob.glob('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/2023/**/*.jpeg', recursive=True)\n",
"print(\"Moving files in SUMMARY_files_jpegs\")\n",
"for each_file in SUMMARY_files_jpegs:\n",
- " if os.path.exists(each_file) and not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/' + os.path.basename(each_file)): \n",
- " shutil.move(each_file, '/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled')\n",
+ " if os.path.exists(each_file) and not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/' + os.path.basename(each_file)): \n",
+ " shutil.move(each_file, '/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled')\n",
" else: \n",
- " if os.path.exists(each_file) and os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/' + os.path.basename(each_file)): \n",
+ " if os.path.exists(each_file) and os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/' + os.path.basename(each_file)): \n",
" os.remove(each_file)\n",
" \n",
- "SUMMARY_files_txts = glob.glob('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/2023/**/*_AGB_products_stats.txt', recursive=True)\n",
+ "SUMMARY_files_txts = glob.glob('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/2023/**/*_AGB_products_stats.txt', recursive=True)\n",
"print(\"Moving files in SUMMARY_files_txts\")\n",
"for each_file in SUMMARY_files_txts:\n",
- " if os.path.exists(each_file) and not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/' + os.path.basename(each_file)): \n",
- " shutil.move(each_file, '/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled')\n",
+ " if os.path.exists(each_file) and not os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/' + os.path.basename(each_file)): \n",
+ " shutil.move(each_file, '/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled')\n",
" else: \n",
- " if os.path.exists(each_file) and os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions/Outputs_compiled/' + os.path.basename(each_file)): \n",
+ " if os.path.exists(each_file) and os.path.exists('/projects/my-private-bucket/dps_output/run_country_summaries_ubuntu/AGB_ecoregions_PART2/Outputs_compiled/' + os.path.basename(each_file)): \n",
" os.remove(each_file)"
]
},
{
"cell_type": "markdown",
- "id": "suited-chocolate",
+ "id": "choice-christmas",
"metadata": {},
"source": [
"### COMPILE ALL OUTPUT STAT FILES INTO ONE"
@@ -588,7 +593,7 @@
{
"cell_type": "code",
"execution_count": 15,
- "id": "happy-legislature",
+ "id": "novel-berkeley",
"metadata": {},
"outputs": [],
"source": [
@@ -611,7 +616,7 @@
},
{
"cell_type": "markdown",
- "id": "heavy-aaron",
+ "id": "finnish-rugby",
"metadata": {},
"source": [
"### QUESTION: DO THE ECOREGION -MEANS OF THE VARIOUS PRODUCTS AT DIFFER SIGNIFICANTLY BY BIOME, \n",
@@ -621,7 +626,7 @@
{
"cell_type": "code",
"execution_count": 95,
- "id": "ordinary-hearing",
+ "id": "disturbed-tissue",
"metadata": {
"collapsed": true,
"jupyter": {
@@ -798,7 +803,7 @@
},
{
"cell_type": "markdown",
- "id": "modified-austria",
+ "id": "requested-grammar",
"metadata": {},
"source": [
"### PLOT WHERE ECOREGIONS (AND BIOMES) DIFFER (before grouping them - this is to check if all expected ecoregions have processed)"
@@ -807,7 +812,7 @@
{
"cell_type": "code",
"execution_count": 3,
- "id": "ideal-perspective",
+ "id": "understood-indication",
"metadata": {},
"outputs": [
{
@@ -861,7 +866,7 @@
},
{
"cell_type": "markdown",
- "id": "economic-harmony",
+ "id": "anonymous-justice",
"metadata": {},
"source": [
"### PLOT WHERE ECOREGIONS (AND BIOMES) DIFFER (after grouping them)"
@@ -870,7 +875,7 @@
{
"cell_type": "code",
"execution_count": 29,
- "id": "alternative-austria",
+ "id": "lasting-performance",
"metadata": {},
"outputs": [
{
@@ -973,7 +978,7 @@
{
"cell_type": "code",
"execution_count": 33,
- "id": "ignored-sacramento",
+ "id": "present-covering",
"metadata": {},
"outputs": [],
"source": [
@@ -1000,7 +1005,7 @@
{
"cell_type": "code",
"execution_count": 335,
- "id": "informative-jordan",
+ "id": "sunrise-showcase",
"metadata": {},
"outputs": [
{
@@ -1130,7 +1135,7 @@
},
{
"cell_type": "markdown",
- "id": "portuguese-induction",
+ "id": "conscious-calgary",
"metadata": {},
"source": [
"### QUESTION: DO THE AGB-DIFFERENCES IN THE PRODUCTS ALSO DIFFER BY CONTINENT? \n",
@@ -1140,7 +1145,7 @@
{
"cell_type": "code",
"execution_count": 28,
- "id": "current-folder",
+ "id": "alien-liberia",
"metadata": {},
"outputs": [
{
@@ -1198,7 +1203,7 @@
},
{
"cell_type": "markdown",
- "id": "pleasant-exhibit",
+ "id": "mighty-sharp",
"metadata": {},
"source": [
"### VISUALIZE THIS DIFFERENCE BY PLOTTING BIOME MEANS IN ALL CONTINENTS"
@@ -1207,7 +1212,7 @@
{
"cell_type": "code",
"execution_count": 30,
- "id": "white-amendment",
+ "id": "technological-knowing",
"metadata": {},
"outputs": [
{
@@ -1280,7 +1285,7 @@
},
{
"cell_type": "markdown",
- "id": "adverse-actor",
+ "id": "supposed-shoot",
"metadata": {},
"source": [
"## MEXICO NFI AND AGB MAP VALIDATION"
@@ -1289,7 +1294,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "ethical-republican",
+ "id": "inner-jacksonville",
"metadata": {},
"outputs": [],
"source": [
@@ -1326,7 +1331,7 @@
{
"cell_type": "code",
"execution_count": 238,
- "id": "searching-release",
+ "id": "rapid-damages",
"metadata": {},
"outputs": [],
"source": [
@@ -1357,7 +1362,7 @@
{
"cell_type": "code",
"execution_count": 5,
- "id": "phantom-passion",
+ "id": "regional-brunswick",
"metadata": {
"collapsed": true,
"jupyter": {
@@ -2303,7 +2308,7 @@
{
"cell_type": "code",
"execution_count": 53,
- "id": "arabic-ordinary",
+ "id": "crude-respect",
"metadata": {},
"outputs": [
{
@@ -2469,7 +2474,7 @@
{
"cell_type": "code",
"execution_count": 15,
- "id": "pressed-motion",
+ "id": "reasonable-stuart",
"metadata": {},
"outputs": [
{
@@ -2666,7 +2671,7 @@
{
"cell_type": "code",
"execution_count": 54,
- "id": "sixth-friday",
+ "id": "intense-brown",
"metadata": {},
"outputs": [
{
@@ -2812,7 +2817,7 @@
{
"cell_type": "code",
"execution_count": 18,
- "id": "material-radical",
+ "id": "funky-tattoo",
"metadata": {},
"outputs": [
{
@@ -2926,7 +2931,7 @@
{
"cell_type": "code",
"execution_count": 9,
- "id": "experimental-shield",
+ "id": "interim-thinking",
"metadata": {},
"outputs": [
{
@@ -3045,7 +3050,7 @@
},
{
"cell_type": "markdown",
- "id": "persistent-albania",
+ "id": "understood-dimension",
"metadata": {},
"source": [
"## PERU NFI AND AGB MAP VALIDATION"
@@ -3054,7 +3059,7 @@
{
"cell_type": "code",
"execution_count": 79,
- "id": "determined-japanese",
+ "id": "architectural-scanning",
"metadata": {},
"outputs": [],
"source": [
@@ -3092,7 +3097,7 @@
{
"cell_type": "code",
"execution_count": 10,
- "id": "western-windsor",
+ "id": "severe-municipality",
"metadata": {},
"outputs": [
{
@@ -3289,7 +3294,7 @@
{
"cell_type": "code",
"execution_count": 14,
- "id": "funded-hawaii",
+ "id": "protecting-bargain",
"metadata": {
"collapsed": true,
"jupyter": {
@@ -3489,7 +3494,7 @@
},
{
"cell_type": "markdown",
- "id": "later-distance",
+ "id": "dominican-mobile",
"metadata": {},
"source": [
"## SPAIN NFI AND AGB MAP VALIDATION"
@@ -3498,7 +3503,7 @@
{
"cell_type": "code",
"execution_count": 16,
- "id": "rubber-violence",
+ "id": "secret-holmes",
"metadata": {},
"outputs": [],
"source": [
@@ -3535,7 +3540,7 @@
{
"cell_type": "code",
"execution_count": 20,
- "id": "finnish-nicholas",
+ "id": "small-rescue",
"metadata": {},
"outputs": [
{
@@ -4033,7 +4038,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "large-favorite",
+ "id": "functioning-concert",
"metadata": {},
"outputs": [],
"source": []
--
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