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minor changes in script to get it running on my device

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Timon 2024-03-04 12:15:23 +01:00
parent 07a54eab25
commit 86f4a49d30
3 changed files with 50 additions and 37 deletions
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69
python_app/Chemba_download.ipynb
View file

@ -2,7 +2,7 @@
"cells": [ "cells": [
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 2, "execution_count": 1,
"id": "b7ca7102-5fd9-481f-90cd-3ba60e288649", "id": "b7ca7102-5fd9-481f-90cd-3ba60e288649",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
@ -296,9 +296,6 @@
"text": [ "text": [
"Monthly time windows:\n", "Monthly time windows:\n",
"\n", "\n",
"2024-02-03\n",
"2024-02-04\n",
"2024-02-05\n",
"2024-02-06\n", "2024-02-06\n",
"2024-02-07\n", "2024-02-07\n",
"2024-02-08\n", "2024-02-08\n",
@ -323,7 +320,10 @@
"2024-02-27\n", "2024-02-27\n",
"2024-02-28\n", "2024-02-28\n",
"2024-02-29\n", "2024-02-29\n",
"2024-03-01\n" "2024-03-01\n",
"2024-03-02\n",
"2024-03-03\n",
"2024-03-04\n"
] ]
} }
], ],
@ -433,12 +433,6 @@
"name": "stdout", "name": "stdout",
"output_type": "stream", "output_type": "stream",
"text": [ "text": [
" East downloaded 2024-02-03\n",
" West downloaded 2024-02-03\n",
" East downloaded 2024-02-04\n",
" West downloaded 2024-02-04\n",
" East downloaded 2024-02-05\n",
" West downloaded 2024-02-05\n",
" East downloaded 2024-02-06\n", " East downloaded 2024-02-06\n",
" West downloaded 2024-02-06\n", " West downloaded 2024-02-06\n",
" East downloaded 2024-02-07\n", " East downloaded 2024-02-07\n",
@ -488,7 +482,13 @@
" East downloaded 2024-02-29\n", " East downloaded 2024-02-29\n",
" West downloaded 2024-02-29\n", " West downloaded 2024-02-29\n",
" East downloaded 2024-03-01\n", " East downloaded 2024-03-01\n",
" West downloaded 2024-03-01\n" " West downloaded 2024-03-01\n",
" East downloaded 2024-03-02\n",
" West downloaded 2024-03-02\n",
" East downloaded 2024-03-03\n",
" West downloaded 2024-03-03\n",
" East downloaded 2024-03-04\n",
" West downloaded 2024-03-04\n"
] ]
} }
], ],
@ -499,7 +499,7 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 13, "execution_count": 14,
"id": "68db3c15-6f94-432e-b315-c329e4251b21", "id": "68db3c15-6f94-432e-b315-c329e4251b21",
"metadata": { "metadata": {
"tags": [] "tags": []
@ -509,21 +509,34 @@
"name": "stdout", "name": "stdout",
"output_type": "stream", "output_type": "stream",
"text": [ "text": [
"['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-03\\\\ad6499018e56b5e1924aa019ccfc6419/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-03\\\\d402cfafa9a6ae7d7d658652bf0efc8b/response.tiff']\n" "['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-06\\\\2cb2971fef19fb55e127e60ec59b400f/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-06\\\\ea7fbec090549628be3a22a314aa6a80/response.tiff']\n",
] "['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-07\\\\404537649ccd9d80105af5eddbc67ae3/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-07\\\\656e1f90cbeaebdd0beb773ea9c632b5/response.tiff']\n",
}, "['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-08\\\\78af404d33e4a7a8a7c63dd7266e9940/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-08\\\\a58815b1793822e2be090555991c070f/response.tiff']\n",
{ "['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-09\\\\b5f8af8311ec9839c6837bd702ff704f/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-09\\\\e80afe76517b3b227f9145b0b5441d47/response.tiff']\n",
"ename": "ValueError", "['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-10\\\\4280add6cbff9b32b7e56203840be60c/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-10\\\\6a3cb421bfe72d6f1e83e0a4d6a35b74/response.tiff']\n",
"evalue": "Received a NULL pointer.", "['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-11\\\\ce6d23ba70336ceb47b36b7ac54a5fa6/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-11\\\\d6255d2b8f966beece2ee91f86eb1376/response.tiff']\n",
"output_type": "error", "['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-12\\\\6df3e48f4e103d1f984e6f331bd20d36/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-12\\\\db8bab81aa54f14b78ce40d9bd484b67/response.tiff']\n",
"traceback": [ "['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-13\\\\c1a0dadbea9723a10511f9e8ad55484f/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-13\\\\ceeb939ee7bc791dbcacadd68ae43963/response.tiff']\n",
"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", "['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-14\\\\05fab2afd14dde5956b68064eabb5584/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-14\\\\3cf514cf1796cb7ffdb74fd2cd1fa557/response.tiff']\n",
"\u001b[1;31mValueError\u001b[0m Traceback (most recent call last)", "['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-15\\\\25bca4ee6801370a109efd9928b6bad2/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-15\\\\77c29bad384c037085362a8b4e97b823/response.tiff']\n",
"Cell \u001b[1;32mIn [13], line 2\u001b[0m\n\u001b[0;32m 1\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m slot \u001b[38;5;129;01min\u001b[39;00m slots:\n\u001b[1;32m----> 2\u001b[0m \u001b[43mmerge_files\u001b[49m\u001b[43m(\u001b[49m\u001b[43mslot\u001b[49m\u001b[43m)\u001b[49m\n", "['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-16\\\\385d81eb553a3b080e1c840199b7d8ad/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-16\\\\f5a9ca774ee072d83ec449b47fb11398/response.tiff']\n",
"Cell \u001b[1;32mIn [11], line 36\u001b[0m, in \u001b[0;36mmerge_files\u001b[1;34m(slot)\u001b[0m\n\u001b[0;32m 33\u001b[0m vrt_all \u001b[38;5;241m=\u001b[39m gdal\u001b[38;5;241m.\u001b[39mBuildVRT(folder_for_virtual_raster, file_list)\n\u001b[0;32m 35\u001b[0m \u001b[38;5;66;03m# Convert to JPEG\u001b[39;00m\n\u001b[1;32m---> 36\u001b[0m \u001b[43mgdal\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mTranslate\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfolder_for_merged_tifs\u001b[49m\u001b[43m,\u001b[49m\u001b[43mfolder_for_virtual_raster\u001b[49m\u001b[43m)\u001b[49m\n", "['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-17\\\\5326b5d776ba3310e5be7ca523c2832d/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-17\\\\6002c8b4be4344e1a427993a1c8f07ee/response.tiff']\n",
"File \u001b[1;32m~\\anaconda3\\lib\\site-packages\\osgeo\\gdal.py:491\u001b[0m, in \u001b[0;36mTranslate\u001b[1;34m(destName, srcDS, **kwargs)\u001b[0m\n\u001b[0;32m 488\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(srcDS, \u001b[38;5;28mstr\u001b[39m):\n\u001b[0;32m 489\u001b[0m srcDS \u001b[38;5;241m=\u001b[39m Open(srcDS)\n\u001b[1;32m--> 491\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mTranslateInternal\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdestName\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msrcDS\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mopts\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcallback\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcallback_data\u001b[49m\u001b[43m)\u001b[49m\n", "['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-18\\\\0fbdec0a57e4d0b7d4f4f4e375559007/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-18\\\\a3a6cbc00e10f12fd51bdea81aea0927/response.tiff']\n",
"File \u001b[1;32m~\\anaconda3\\lib\\site-packages\\osgeo\\gdal.py:4674\u001b[0m, in \u001b[0;36mTranslateInternal\u001b[1;34m(*args)\u001b[0m\n\u001b[0;32m 4672\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mTranslateInternal\u001b[39m(\u001b[38;5;241m*\u001b[39margs):\n\u001b[0;32m 4673\u001b[0m \u001b[38;5;124;03m\"\"\"TranslateInternal(char const * dest, Dataset dataset, GDALTranslateOptions translateOptions, GDALProgressFunc callback=0, void * callback_data=None) -> Dataset\"\"\"\u001b[39;00m\n\u001b[1;32m-> 4674\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43m_gdal\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mTranslateInternal\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m)\u001b[49m\n", "['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-19\\\\0e07cff0d010befc4b61b2bcc1505e14/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-19\\\\77ebfbc4b72521a8ee8ed0644694a4d8/response.tiff']\n",
"\u001b[1;31mValueError\u001b[0m: Received a NULL pointer." "['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-20\\\\954b99cae830de20b481c1c095fa8fec/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-20\\\\de49a1ae7fc7cce6bbb51307b51421a7/response.tiff']\n",
"['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-21\\\\22aac7ab7fe69e51dc2234c0a9ef2b78/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-21\\\\c703f5c937fe7d31c01e5dc0e1f1b3c6/response.tiff']\n",
"['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-22\\\\4cc6c6c928fbe9261b235a1a2bd82988/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-22\\\\6eee415cdc80617dbcbe376854d7c638/response.tiff']\n",
"['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-23\\\\a71078194fb9344dfa8d1254b34a8972/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-23\\\\f4c483ff844754609c15946f39062af0/response.tiff']\n",
"['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-24\\\\948621c2612a3623fe0a8c6f2e232d4c/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-24\\\\b5453c78662b27e0e31d3246e63d54ef/response.tiff']\n",
"['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-25\\\\09034667d9d66ad95bb45114be61c294/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-25\\\\153a5ff825431397c8c3d98b0cb7f8e0/response.tiff']\n",
"['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-26\\\\812fa312f85f5645979751acbfdb4137/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-26\\\\bea202027ff912b58ea0de56ecd60559/response.tiff']\n",
"['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-27\\\\1a5ef1a23663df92e3d6ea0cd4e566be/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-27\\\\d4cbaea4023bc70fa32512e73c74130a/response.tiff']\n",
"['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-28\\\\1e84c7daad84245d60c0117309786237/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-28\\\\76ef1594ab86e53afc8cfe62f1add323/response.tiff']\n",
"['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-29\\\\08baa805ee5178e3b20ff5f04f1481c6/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-02-29\\\\1322ca6b580917bb3e481d322e483f2b/response.tiff']\n",
"['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-03-01\\\\64455452d2ff2d41bae9e25445244dec/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-03-01\\\\e83cbe6c52f505b9d632a6427db1deb8/response.tiff']\n",
"['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-03-02\\\\b02488afaa37d33ce11b212702c48d61/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-03-02\\\\f7f75ecaae4a20c23fb170b2cfc3609c/response.tiff']\n",
"['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-03-03\\\\c3403f247cbe040895abec576582dc9e/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-03-03\\\\f20b352771e5ed34c2482680106f5514/response.tiff']\n",
"['..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-03-04\\\\a2f45492c5e7994ce6a3959eb6a0822d/response.tiff', '..\\\\laravel_app\\\\storage\\\\app\\\\chemba\\\\single_images\\\\2024-03-04\\\\f89199ceb4c461225686bb7176935986/response.tiff']\n"
] ]
} }
], ],

3
r_app/2_CI_data_prep.R
View file

@ -29,7 +29,8 @@ if (is.na(weeks_ago)) {
} }
# laravel_storage_dir <- here("../laravel_app/storage/app") # laravel_storage_dir <- here("../laravel_app/storage/app")
laravel_storage_dir <- here("/laravel_app/storage/app") here("C:/Users/timon/Resilience BV/4020 SCane ESA DEMO - Documenten/General/4020 SCDEMO Team/4020 TechnicalData/WP2/smartcane")
laravel_storage_dir <- here("laravel_app/storage/app")
#preparing directories #preparing directories
planet_tif_folder <- here(laravel_storage_dir, "chemba/merged_tif") planet_tif_folder <- here(laravel_storage_dir, "chemba/merged_tif")

15
r_app/CI_report_dashboard_planet.Rmd
View file

@ -82,9 +82,9 @@ week_minus_2 <- sprintf("%02d", week(today_minus_2))
week_minus_3 <- sprintf("%02d", week(today_minus_3)) week_minus_3 <- sprintf("%02d", week(today_minus_3))
year = year(today) year = year(today)
year_2 = year(today_minus_1) year_1 = year(today_minus_1)
year_3 = year(today_minus_2) year_2 = year(today_minus_2)
year_4 = year(today_minus_3) year_3 = year(today_minus_3)
``` ```
@ -107,11 +107,10 @@ This PDF-dashboard shows the status of your fields on a weekly basis. We will sh
CI_quadrant <- readRDS(here(cumulative_CI_vals_dir,"All_pivots_Cumulative_CI_quadrant_year_v2.rds"))# %>% CI_quadrant <- readRDS(here(cumulative_CI_vals_dir,"All_pivots_Cumulative_CI_quadrant_year_v2.rds"))# %>%
# rename(pivot_quadrant = Field) # rename(pivot_quadrant = Field)
message("STOP - check ci name in layer")
CI <- brick(here(weekly_CI_mosaic, paste0("week_",week, "_", year, ".tif"))) %>% subset("CI") CI <- brick(here(weekly_CI_mosaic, paste0("week_",week, "_", year, ".tif"))) %>% subset("CI")
CI_m1 <- brick(here(weekly_CI_mosaic, paste0("week_",week_minus_1, "_", year_2, ".tif"))) %>% subset("CI") CI_m1 <- brick(here(weekly_CI_mosaic, paste0("week_",week_minus_1, "_", year_1, ".tif"))) %>% subset("CI")
CI_m2 <- brick(here(weekly_CI_mosaic, paste0("week_",week_minus_2, "_", year_3, ".tif"))) %>% subset("CI") CI_m2 <- brick(here(weekly_CI_mosaic, paste0("week_",week_minus_2, "_", year_2, ".tif"))) %>% subset("CI")
CI_m3 <- brick(here(weekly_CI_mosaic, paste0("week_",week_minus_3, "_", year_4, ".tif"))) %>% subset("CI") CI_m3 <- brick(here(weekly_CI_mosaic, paste0("week_",week_minus_3, "_", year_3, ".tif"))) %>% subset("CI")
# last_week_dif_raster <- ((CI - CI_m1) / CI_m1) * 100 # last_week_dif_raster <- ((CI - CI_m1) / CI_m1) * 100
last_week_dif_raster_abs <- (CI - CI_m1) last_week_dif_raster_abs <- (CI - CI_m1)
@ -234,7 +233,7 @@ ci_plot <- function(pivotName){
singlePivot_m1 <- CI_m1 %>% crop(., pivotShape) %>% mask(., pivotShape) singlePivot_m1 <- CI_m1 %>% crop(., pivotShape) %>% mask(., pivotShape)
singlePivot_m2 <- CI_m2 %>% crop(., pivotShape) %>% mask(., pivotShape) singlePivot_m2 <- CI_m2 %>% crop(., pivotShape) %>% mask(., pivotShape)
singlePivot_m3 <- CI_m3 %>% crop(., pivotShape) %>% mask(., pivotShape) # singlePivot_m3 <- CI_m3 %>% crop(., pivotShape) %>% mask(., pivotShape)
abs_CI_last_week <- last_week_dif_raster_abs %>% crop(., pivotShape) %>% mask(., pivotShape) abs_CI_last_week <- last_week_dif_raster_abs %>% crop(., pivotShape) %>% mask(., pivotShape)
abs_CI_three_week <- three_week_dif_raster_abs %>% crop(., pivotShape) %>% mask(., pivotShape) abs_CI_three_week <- three_week_dif_raster_abs %>% crop(., pivotShape) %>% mask(., pivotShape)