-
Notifications
You must be signed in to change notification settings - Fork 2
/
workflow_HRSI_vDISC.py
executable file
·215 lines (176 loc) · 9.26 KB
/
workflow_HRSI_vDISC.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
#!/usr/bin/env python
# 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
###############################################
# 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,
SGM,
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 - 3/7/2019: this is now a parameter passed down from query step --> SGM
# 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)
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, 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, SGM, 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[9])#, 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)