Revision 41d291a6
Added by Adam Wilson almost 11 years ago
| climate/procedures/ee.MOD09.py | ||
|---|---|---|
| 12 | 12 |
import wget |
| 13 | 13 |
import os |
| 14 | 14 |
import sys |
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from subprocess import call |
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| 15 |
import subprocess |
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import time |
|
| 16 | 17 |
|
| 17 | 18 |
import logging |
| 18 | 19 |
logging.basicConfig(filename='error.log',level=logging.DEBUG) |
| 19 | 20 |
|
| 20 | 21 |
def Usage(): |
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print('Usage: ee.MOD9.py -projwin ulx uly lrx lry -year year -month month -regionname 1')
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|
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print('Usage: ee.MOD9.py -projwin ulx uly urx ury lrx lry llx lly -year year -month month -regionname 1')
|
|
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sys.exit( 1 ) |
| 23 | 24 |
|
| 24 | 25 |
ulx = float(sys.argv[2]) |
| 25 | 26 |
uly = float(sys.argv[3]) |
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lrx = float(sys.argv[4]) |
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lry = float(sys.argv[5]) |
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year = int(sys.argv[7]) |
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month = int(sys.argv[9]) |
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regionname = str(sys.argv[11]) |
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urx = float(sys.argv[4]) |
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ury = float(sys.argv[5]) |
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lrx = float(sys.argv[6]) |
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lry = float(sys.argv[7]) |
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llx = float(sys.argv[8]) |
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lly = float(sys.argv[9]) |
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year = int(sys.argv[11]) |
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month = int(sys.argv[13]) |
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regionname = str(sys.argv[15]) |
|
| 32 | 36 |
#``` |
| 33 | 37 |
#ulx=-159 |
| 34 | 38 |
#uly=20 |
| ... | ... | |
| 41 | 45 |
output=regionname+'_'+str(year)+'_'+str(month) |
| 42 | 46 |
|
| 43 | 47 |
## set working directory (where files will be downloaded) |
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os.chdir('/mnt/data2/projects/cloud/mod09')
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cwd='/mnt/data2/projects/cloud/mod09/' |
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## Wget always starts with a temporary file called "download", so move to a subdirectory to |
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## prevent overwrting when parallel downloading |
|
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if not os.path.exists(cwd+output): |
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os.makedirs(cwd+output) |
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os.chdir(cwd+output) |
|
| 45 | 54 |
|
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# output filename |
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unzippedfilename=output+".mod09.tif" |
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# Check if file already exists and continue if so... |
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if(os.path.exists(unzippedfilename)): |
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sys.exit("File exists:"+output)
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|
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## initialize GEE |
|
| 46 | 62 |
MY_SERVICE_ACCOUNT = '511722844190@developer.gserviceaccount.com' # replace with your service account |
| 47 | 63 |
MY_PRIVATE_KEY_FILE = '/home/adamw/EarthEngine-privatekey.p12' # replace with you private key file path |
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|
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| 49 | 64 |
ee.Initialize(ee.ServiceAccountCredentials(MY_SERVICE_ACCOUNT, MY_PRIVATE_KEY_FILE)) |
| 50 | 65 |
|
| 51 | 66 |
## set map center to speed up viewing |
| ... | ... | |
| 57 | 72 |
# added the >0.5 because some values are coming out >1. Need to look into this further as they should be bounded 0-1... |
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#//////////////////////////////////////////////////// |
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|
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# output filename |
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unzippedfilename=output+".mod09.tif" |
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# Check if file already exists and continue if so... |
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if(os.path.exists(unzippedfilename)): |
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sys.exit("File exists:"+output)
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##################################################### |
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# Processing Function |
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# MOD09 internal cloud flag for this year-month |
| ... | ... | |
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###################################################### |
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|
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## define region for download |
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region=[ulx,lry], [ulx, uly], [lrx, uly], [lrx, lry] #h11v08
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|
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region=[llx, lly],[lrx, lry],[urx, ury],[ulx,uly] #h11v08
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| 84 | 90 |
strregion=str(list(region)) |
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# Next few lines for testing only |
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# print info to confirm there is data |
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print(data.getInfo()) |
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|
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## print a status update |
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print(output+' Processing.... Coords:'+strregion) |
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| 92 | 91 |
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| 93 | 92 |
# add to plot to confirm it's working |
| 94 | 93 |
#ee.mapclient.addToMap(data, {'range': '0,100'}, 'MOD09')
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#``` |
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# TODO: |
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# use MODIS projection |
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# build the URL and name the object (so that when it's unzipped we know what it is!) |
| 101 | 96 |
path =mod09a.getDownloadUrl({
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'crs': 'SR-ORG:6974', # MODIS Sinusoidal |
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'scale': '926.625433055833', # MODIS ~1km |
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'name': output, # name the file (otherwise it will be a uninterpretable hash) |
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'scale': 926, # resolution in meters |
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'crs': 'EPSG:4326', #4326 # projection |
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'region': strregion # region defined above |
| 106 | 101 |
}); |
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# Sometimes EE will serve a corrupt zipped file with no error |
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# to check this, use a while loop that keeps going till there is an unzippable file. |
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# This has the potential for an infinite loop... |
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#if(not(os.path.exists(output+".tif"))): |
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# download with wget |
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print("Downloading "+output)
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wget.download(path) |
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#call(["wget"+path,shell=T]) |
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# try to unzip it |
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print("Unzipping "+output)
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zipstatus=call("unzip "+output+".zip",shell=True)
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# if file doesn't exists or it didn't unzip, remove it and try again |
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if(zipstatus==9): |
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sys.exit("File exists:"+output)
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# print("ERROR: "+output+" unzip-able")
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# os.remove(output+".zip") |
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# print info to confirm there is data |
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#print(data.getInfo()) |
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print(' Processing.... '+output+' Coords:'+strregion)
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#test=wget.download(path) |
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test=subprocess.call(['-c','-q','--timeout=0','--ignore-length','--no-http-keep-alive','-O','mod09.zip',path],executable='wget') |
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print('download sucess for'+output+': '+str(test))
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## Sometimes EE will serve a corrupt zipped file with no error |
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# try to unzip it |
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zipstatus=subprocess.call("unzip -o mod09.zip",shell=True)
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if zipstatus==0: #if sucessful, quit |
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os.remove("mod09.zip")
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sys.exit("Finished: "+output)
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# if file doesn't exists or it didn't unzip, try again |
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if zipstatus!=0: |
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print("Zip Error for: "+output+"... Trying again (#2)")
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time.sleep(15) |
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test=subprocess.call(['-c','-q','--timeout=0','--ignore-length','--no-http-keep-alive','-O','mod09.zip',path],executable='wget') |
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zipstatus=subprocess.call("unzip -o mod09.zip",shell=True)
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if zipstatus==0: #if sucessful, quit |
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os.remove("mod09.zip")
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sys.exit("Finished: "+output)
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# if file doesn't exists or it didn't unzip, try again |
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if zipstatus!=0: |
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print("Zip Error for: "+output+"... Trying again (#3)")
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time.sleep(30) |
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test=subprocess.call(['-c','-q','--timeout=0','--ignore-length','--no-http-keep-alive','-O','mod09.zip',path],executable='wget') |
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# try again #4 |
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zipstatus=subprocess.call("unzip -o mod09.zip",shell=True)
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if zipstatus==0: #if sucessful, quit |
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os.remove("mod09.zip")
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sys.exit("Finished: "+output)
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# if file doesn't exists or it didn't unzip, try again |
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if zipstatus!=0: |
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print("Zip Error for: "+output+"... Trying again (#4)")
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time.sleep(30) |
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test=subprocess.call(['-c','-q','--timeout=0','--ignore-length','--no-http-keep-alive','-O','mod09.zip',path],executable='wget') |
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zipstatus=subprocess.call("unzip -o mod09.zip",shell=True)
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if zipstatus==0: #if sucessful, quit |
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os.remove("mod09.zip")
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sys.exit("Finished: "+output)
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## delete the zipped file (the unzipped version is kept) |
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os.remove(output+".zip") |
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print(output+' Finished!') |
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os.remove("mod09.zip")
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sys.exit("Zip Error for: "+output)
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|
| climate/procedures/ee_compile.R | ||
|---|---|---|
| 3 | 3 |
setwd("~/acrobates/adamw/projects/cloud")
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library(raster) |
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library(doMC) |
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registerDoMC(4) |
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beginCluster(4) |
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library(multicore) |
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library(foreach) |
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#library(doMPI) |
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registerDoMC(10) |
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#beginCluster(4) |
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| 9 | 11 |
|
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tempdir="tmp" |
| 11 | 13 |
if(!file.exists(tempdir)) dir.create(tempdir) |
| ... | ... | |
| 14 | 16 |
## Load list of tiles |
| 15 | 17 |
tiles=read.table("tile_lat_long_10d.txt",header=T)
|
| 16 | 18 |
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jobs=expand.grid(tile=tiles$Tile,year=2000:2012,month=1:12) |
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jobs[,c("ULX","ULY","LRX","LRY")]=tiles[match(jobs$tile,tiles$Tile),c("ULX","ULY","LRX","LRY")]
|
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### Build Tiles |
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|
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## bin sizes |
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ybin=30 |
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xbin=30 |
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tiles=expand.grid(ulx=seq(-180,180-xbin,by=xbin),uly=seq(90,-90+ybin,by=-ybin)) |
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tiles$h=factor(tiles$ulx,labels=paste("h",sprintf("%02d",1:length(unique(tiles$ulx))),sep=""))
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tiles$v=factor(tiles$uly,labels=paste("v",sprintf("%02d",1:length(unique(tiles$uly))),sep=""))
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tiles$tile=paste(tiles$h,tiles$v,sep="") |
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tiles$urx=tiles$ulx+xbin |
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tiles$ury=tiles$uly |
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tiles$lrx=tiles$ulx+xbin |
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tiles$lry=tiles$uly-ybin |
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tiles$llx=tiles$ulx |
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tiles$lly=tiles$uly-ybin |
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tiles$cy=(tiles$uly+tiles$lry)/2 |
|
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tiles$cx=(tiles$ulx+tiles$urx)/2 |
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tiles=tiles[,c("tile","h","v","ulx","uly","urx","ury","lrx","lry","llx","lly","cx","cy")]
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| 38 |
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jobs=expand.grid(tile=tiles$tile,year=2000:2012,month=1:12) |
|
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jobs[,c("ulx","uly","urx","ury","lrx","lry","llx","lly")]=tiles[match(jobs$tile,tiles$tile),c("ulx","uly","urx","ury","lrx","lry","llx","lly")]
|
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| 41 |
|
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## drop Janurary 2000 from list (pre-modis) |
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jobs=jobs[!(jobs$year==2000&jobs$month==1),] |
|
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#jobs=jobs[jobs$month==1,] |
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| 19 | 46 |
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| 20 | 47 |
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jobs=jobs[jobs$month==1,]
|
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#jobs=jobs[jobs$month==7,]
|
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| 22 | 49 |
## Run the python downloading script |
| 23 | 50 |
#system("~/acrobates/adamw/projects/environmental-layers/climate/procedures/ee.MOD09.py -projwin -159 20 -154.5 18.5 -year 2001 -month 6 -region test")
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i=6715 |
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testtiles=c("h02v07","h02v06","h02v08","h03v07","h03v06")
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todo=which(jobs$tile%in%testtiles) |
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todo=todo[1:3] |
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i=1 |
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#testtiles=c("h02v07","h02v06","h02v08","h03v07","h03v06","h03v08")
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#todo=which(jobs$tile%in%testtiles) |
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#todo=todo[1:3] |
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#todo=1 |
|
| 28 | 56 |
todo=1:nrow(jobs) |
| 29 |
#todo=todo[500:503] |
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mclapply(todo,function(i) |
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system(paste("~/acrobates/adamw/projects/environmental-layers/climate/procedures/ee.MOD09.py -projwin ",jobs$ULX[i]," ",jobs$ULY[i]," ",jobs$LRX[i]," ",jobs$LRY[i],
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| 32 |
" -year ",jobs$year[i]," -month ",jobs$month[i]," -region ",jobs$tile[i],sep="")),mc.cores=1) |
|
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|
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checkcomplete=T |
|
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if(checkcomplete&exists("df")){ #if desired (and "df" exists from below) drop complete date-tiles
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| 60 |
todo=which(!paste(jobs$tile,jobs$year,jobs$month)%in%paste(df$region,df$year,df$month)) |
|
| 61 |
} |
|
| 62 |
|
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| 63 |
writeLines(paste("Tiling options will produce",nrow(tiles),"tiles and ",nrow(jobs),"tile-months. Current todo list is ",length(todo)))
|
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| 64 |
|
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| 65 |
foreach(i=todo) %dopar%{
|
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| 66 |
system(paste("python ~/acrobates/adamw/projects/environmental-layers/climate/procedures/ee.MOD09.py -projwin ",
|
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| 67 |
jobs$ulx[i]," ",jobs$uly[i]," ",jobs$urx[i]," ",jobs$ury[i]," ",jobs$lrx[i]," ",jobs$lry[i]," ",jobs$llx[i]," ",jobs$lly[i]," ", |
|
| 68 |
" -year ",jobs$year[i]," -month ",jobs$month[i]," -region ",jobs$tile[i],sep="")) |
|
| 69 |
} |
|
| 33 | 70 |
|
| 34 | 71 |
|
| 35 | 72 |
## Get list of available files |
| 36 |
df=data.frame(path=list.files("/mnt/data2/projects/cloud/mod09",pattern="*.tif$",full=T),stringsAsFactors=F)
|
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| 73 |
df=data.frame(path=list.files("/mnt/data2/projects/cloud/mod09",pattern="*.tif$",full=T,recur=T),stringsAsFactors=F)
|
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| 37 | 74 |
df[,c("region","year","month")]=do.call(rbind,strsplit(basename(df$path),"_|[.]"))[,c(1,2,3)]
|
| 38 | 75 |
df$date=as.Date(paste(df$year,"_",df$month,"_15",sep=""),"%Y_%m_%d") |
| 39 | 76 |
|
| 77 |
## add stats to test for missing data |
|
| 78 |
addstats=F |
|
| 79 |
if(addstats){
|
|
| 80 |
df[,c("max","min","mean","sd")]=do.call(rbind.data.frame,mclapply(1:nrow(df),function(i) as.numeric(sub("^.*[=]","",grep("STATISTICS",system(paste("gdalinfo -stats",df$path[i]),inter=T),value=T)))))
|
|
| 81 |
table(df$sd==0) |
|
| 82 |
} |
|
| 83 |
|
|
| 40 | 84 |
## subset to testtiles? |
| 41 | 85 |
#df=df[df$region%in%testtiles,] |
| 42 |
df=df[df$month==1,] |
|
| 86 |
#df=df[df$month==1,]
|
|
| 43 | 87 |
table(df$year,df$month) |
| 44 | 88 |
|
| 45 | 89 |
## drop some if not complete |
| 46 |
#df=df[df$year<=2009,]
|
|
| 90 |
df=df[df$month==1&df$year%in%c(2001:2002,2005),]
|
|
| 47 | 91 |
rerun=T # set to true to recalculate all dates even if file already exists |
| 48 | 92 |
|
| 49 | 93 |
## Loop over existing months to build composite netcdf files |
| ... | ... | |
| 51 | 95 |
## get date |
| 52 | 96 |
print(date) |
| 53 | 97 |
## Define output and check if it already exists |
| 98 |
tffile=paste(tempdir,"/mod09_",date,".tif",sep="") |
|
| 54 | 99 |
ncfile=paste(tempdir,"/mod09_",date,".nc",sep="") |
| 55 | 100 |
if(!rerun&file.exists(ncfile)) next |
| 56 | 101 |
## merge regions to a new netcdf file |
| 57 |
system(paste("gdal_merge.py -o ",ncfile," -n -32768 -of netCDF -ot Int16 ",paste(df$path[df$date==date],collapse=" ")))
|
|
| 102 |
# system(paste("gdal_merge.py -tap -init 5 -o ",ncfile," -n -32768.000 -of netCDF -ot Int16 ",paste(df$path[df$date==date],collapse=" ")))
|
|
| 103 |
system(paste("gdal_merge.py -o ",tffile," -init -32768 -n -32768.000 -ot Int16 ",paste(df$path[df$date==date],collapse=" ")))
|
|
| 104 |
system(paste("gdal_translate -of netCDF ",tffile," ",ncfile," -ot Int16 "))
|
|
| 105 |
file.remove(tffile) |
|
| 58 | 106 |
system(paste("ncecat -O -u time ",ncfile," ",ncfile,sep=""))
|
| 59 | 107 |
## create temporary nc file with time information to append to MOD06 data |
| 60 | 108 |
cat(paste("
|
| ... | ... | |
| 102 | 150 |
|
| 103 | 151 |
### generate the monthly mean and sd |
| 104 | 152 |
#system(paste("cdo -P 10 -O merge -ymonmean data/mod09.nc -chname,CF,CF_sd -ymonstd data/mod09.nc data/mod09_clim.nc"))
|
| 105 |
system(paste("cdo -O -ymonmean data/mod09.nc data/mod09_clim_mean.nc"))
|
|
| 153 |
xosystem(paste("cdo -O -ymonmean data/mod09.nc data/mod09_clim_mean.nc"))
|
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| 106 | 154 |
system(paste("cdo -O -chname,CF,CF_sd -ymonstd data/mod09.nc data/mod09_clim_sd.nc"))
|
| 107 | 155 |
|
| 108 | 156 |
# Overall mean |
Also available in: Unified diff
Added multiple tries to python GEE script