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workflow_HRSI_vDISC.py
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# 9/18/2018: adding the four dg_stereo arguments (subpixKern, erodeSize, corrKern, corrTime) to the command line in query to be received here. these will be passed to dg_stereo along with other hardcoded vars
#!/usr/local/other/SLES11.3/miniconda/4.0.5/gcc-5.3-sp3/bin/python
###############################################
# Import and function definitions
import os, sys, osgeo, time, glob, platform, subprocess as subp
from timeit import default_timer as timer
from time import gmtime, strftime
from shutil import copyfile
def find_elapsed_time(start, end): # take two timer() objects and find elapsed time between them, in minutes
elapsed_min = (end-start)/60
return float(elapsed_min)
def run_asp(
pairname,
batchID,
ASPdir,
preLogTextFile,
subpixKern,
erodeSize,
corrKern,
corrTime,
stereoDef='/discover/nobackup/projects/boreal_nga/code/stereo.default',
searchExtList=['.ntf','.tif','.NTF','.TIF']
):
#n #8 shouldnt really need any of this. Variables needed:
# pairname; batchID; prelog text file (eh)
# imageDir is /discover/.../ASP/batch/pairname -- imageDir is now the outDir AND inDir
# batchDir is /discover/.../ASP/batch
# ddir is /discover/.../ASP/
batchDir = os.path.join(ASPdir, 'batch{}'.format(batchID))
imageDir = os.path.join(batchDir, pairname)
ddir = os.path.split(ASPdir)[0] # strip off ASP to get boreal_nga
stereoCode = os.path.join(ddir, 'code', 'evhr', 'dg_stereo.sh') # now strip off ASP (outdir name) and get code dir
start_main = timer()
#T:
print ddir
print batchDir
print imageDir
print stereoCode
# hardcode stuff for now
nodeName = platform.node()
test = False
# also need to read preLogText file into list
with open(preLogTextFile, 'r') as tf:
preLogText = tf.read()
# For logging on the fly
logdir = os.path.join(ddir, 'Logs')
os.system('mkdir -p {}'.format(logdir)) # make log dir if it doesn't exist
start_time = strftime("%Y%m%d-%H%M%S")
lfile = os.path.join(logdir, 'batch{}__{}__{}_{}_Log.txt'.format(batchID, pairname, start_time, nodeName)) #* 2/8: putting date/time before node so it's in chrono order
so = se = open(lfile, 'w', 0) # open our log file
sys.stdout = os.fdopen(sys.stdout.fileno(), 'w', 0) # re-open stdout without buffering
os.dup2(so.fileno(), sys.stdout.fileno()) # redirect stdout and stderr to the log file opened above
os.dup2(se.fileno(), sys.stderr.fileno())
# print some things to the log file
print "--LOGFILE------------------"
print(lfile)
print "\n"
print "--PYTHON FILE-----------"
print os.path.basename(__file__)
print "\n"
# print input parameters to log file:
print '-------pair parameters:-------'
print 'test = {}'.format(test)
print 'batchID = {}'.format(batchID)
print 'imageDir = {}'.format(imageDir)
print '\nBEGIN: {}\n\n'.format(start_time)
print "########################################\nQuery Log:\n{}\n########################################\n".format(preLogText)
#command = 'bash {} {} false false {}'.format(stereoCode, pairname, batchDir) # false for ADAPT and false for MAP -- OLD COMMAND
"""Command above is what we've been using. Parameters below are what Paul wants to run with ANDES mini for new dg_stereo (6/1/2018):
pairname=$1
TEST=false
ADAPT=false
MAP=false
RUN_PSTEREO=false
batch_name='batch_andesmini'
rpcdem=''
NODES=false
nodeslist=''
SGM=false
subpixk=25
erode_max_size=1024
"""
# 9/18/2018 - last 4 variables (change from batch to batch) are now being passed from query command line
# these variables more or less stay the same between runs:
test_p = 'false'
adapt_p = 'false'
map_p = 'false'
runStereo_p = 'true' # temp for test SGM batch 1/10/2019 pstereo = true from now
batch_p = 'batch{}'.format(batchID)
rpc_p = ''
nodes_p = 'false'
nodesList_p = ''
sgm_p = 'true' # temp for test SGM batch 1/10/2019 SGM = true from now
# print params to log
print "Calling {} to perform stereo...".format(stereoCode)
print " Parameters for dg_stereo.sh :" #false false {}\n\n".format(pairname, batchDir)
print " pairname: {}".format(pairname)
print " TEST: {}".format(test_p)
print " ADAPT: {}".format(adapt_p)
print " MAP: {}".format(map_p)
print " RUN_PSTEREO: {}".format(runStereo_p)
print " batch_name: {}".format(batchID)
print " rpcdem: {}".format(rpc_p)
print " NODES: {}".format(nodes_p)
print " nodeslist: {}".format(nodesList_p)
print " SGM: {}".format(sgm_p)
print " subpix_kern: {}".format(subpixKern)
print " erode_max_size: {}".format(erodeSize)
print " corr_kern: {}".format(corrKern)
print " corr_time: {}\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n".format(corrTime)
command = 'bash {} {} {} {} {} {} {} "{}" {} "{}" {} {} {} {} {}'.format(stereoCode, pairname, test_p, adapt_p, map_p, runStereo_p, batch_p, rpc_p, nodes_p, nodesList_p, sgm_p, subpixKern, erodeSize, corrKern, corrTime)
#subp.check_output([command])
print 'Command: {}\n'.format(command)
os.system(command) # try this for now
# also move the slurm.out file(s) to outASP/slurmOuts/batchID and rename them to the pairname_slurm.out
# loop through all slurm files in pairname directory and rename/copy them to outSlurm dir -- if we are rerunning a pair process it will just name/recopy the slurm.out files to outSlurm
inSlurmGlob = glob.glob(os.path.join(imageDir, 'slurm*out')) # list of all slurm files in pairname dir
## print inSlurmGlob #T
outSlurmDir = os.path.join(ddir, 'outSlurm') # doing just one big dir for outSlurm now. files will have batch names in them though
os.system('mkdir -p {}'.format(outSlurmDir))
print ''
for inSlurm in inSlurmGlob: # loop through slurm files
outSlurm = os.path.join(outSlurmDir, os.path.basename(inSlurm).replace("slurm", "batch{}__{}__slurm".format(batchID, pairname)))
print " Copying outSlurm file {} to a new name {}".format(inSlurm, outSlurm)
os.system('cp {} {}'.format(inSlurm, outSlurm)) # review this after we are sure it works
print "\n Adding pair {} to completedPairs text file and recording run time information to spreadsheet".format(pairname)
#chmod on all the xml's in the imageDir
print " \n Running chmod on {}".format(os.path.join(imageDir, '*xml'))
os.system('chmod 777 {}'.format(os.path.join(imageDir, '*xml')))
#* check for the final ovr file and if it exists, add pair to list
finalFile = os.path.join(imageDir, '{}_ortho.tif.ovr'.format(pairname))
## print finalFile #T
if os.path.isfile(finalFile):
comp_pair_dir = os.path.join(ddir, 'batchSummary')
os.system('mkdir -p {}'.format(comp_pair_dir))
completed_pairs_txt = os.path.join(comp_pair_dir, 'batch{}_completedPairs.txt'.format(batchID))
with open (completed_pairs_txt, 'a') as cp:
cp.write('{}\n'.format(pairname))
else: print "\n Final ovr file ({}) does not exist. Something went wrong, please check the log.".format(finalFile)
end_main = timer()
total_time = find_elapsed_time(start_main, end_main)
# copy the python log to pairname dir
copyfile(lfile, lfile.replace(logdir, imageDir))
# add some info to the run_times csv for NCCS
# then print batchID, pairname, total_time (minutes and hours) to csv
## strip1size = round(os.path.getsize(fullPathStrips[0])/1024.0/1024/1024, 3) #* PC_tif here instead
## strip2size = round(os.path.getsize(fullPathStrips[1])/1024.0/1024/1024, 3)
# get the size of the out-PC file:
outPC = os.path.join(imageDir, 'out-PC.tif')
PCsize_GB = round(os.path.getsize(outPC)/1024.0/1024/1024, 3)
run_times_csv = os.path.join(ddir, 'run_times.csv')
with open(run_times_csv, 'a') as rt:
rt.write('{}, {}, {}, {}, {}, {}\n'.format(batchID, pairname, total_time, (total_time/60), PCsize_GB, nodeName))
print("\n\n-----------------------------")
print("\n\t ")
print("Finished processing {}".format(pairname))
print 'End time: {}'.format(strftime("%Y%m%d-%H%M%S"))
print "Elapsed time = {} minutes".format(round(total_time, 3))
print("\n\t ")
print("-----------------------------\n\n")
## # try to close the out/err files-- http://stackoverflow.com/questions/7955138/addressing-sys-excepthook-error-in-bash-script
## try:
## sys.stdout.close()
## except:
## pass
## try:
## sys.stderr.close()
## except:
## pass
if __name__ == "__main__":
#import sys
# get variables being passed along from query_db and run_asp with them
# args:
# pairname, batchID, ASPdir, prelogtextFile, subpixKern, erodeSize, corrKern, corrTime
run_asp( sys.argv[1], sys.argv[2], sys.argv[3], sys.argv[4], sys.argv[5], sys.argv[6], sys.argv[7], sys.argv[8])#, sys.argv[5], sys.argv[6], sys.argv[7], sys.argv[8], sys.argv[9], sys.argv[10], sys.argv[11], sys.argv[12], sys.argv[13] ) # 13 arguments (plus python script)