def main():
#### Set Up Arguments
parent_parser, pos_arg_keys = ortho_functions.buildParentArgumentParser()
parser = argparse.ArgumentParser(
parents=[parent_parser],
description="Run/submit batch image ortho and conversion tasks")
parser.add_argument("--pbs",
action='store_true',
default=False,
help="submit tasks to PBS")
parser.add_argument("--slurm",
action='store_true',
default=False,
help="submit tasks to SLURM")
parser.add_argument(
"--parallel-processes",
type=int,
default=1,
help="number of parallel processes to spawn (default 1)")
parser.add_argument(
"--qsubscript",
help=
"submission script to use in PBS/SLURM submission (PBS default is qsub_ortho.sh, SLURM "
"default is slurm_ortho.py, in script root folder)")
parser.add_argument(
"-l", help="PBS resources requested (mimicks qsub syntax, PBS only)")
parser.add_argument("--dryrun",
action='store_true',
default=False,
help='print actions without executing')
#### Parse Arguments
args = parser.parse_args()
scriptpath = os.path.abspath(sys.argv[0])
src = os.path.abspath(args.src)
dstdir = os.path.abspath(args.dst)
#### Validate Required Arguments
if os.path.isdir(src):
srctype = 'dir'
elif os.path.isfile(src) and os.path.splitext(src)[1].lower() == '.txt':
srctype = 'textfile'
elif os.path.isfile(src) and os.path.splitext(
src)[1].lower() in ortho_functions.exts:
srctype = 'image'
elif os.path.isfile(src.replace('msi', 'blu')) and os.path.splitext(
src)[1].lower() in ortho_functions.exts:
srctype = 'image'
else:
parser.error(
"Error arg1 is not a recognized file path or file type: {}".format(
src))
if not os.path.isdir(dstdir):
parser.error("Error arg2 is not a valid file path: {}".format(dstdir))
## Verify qsubscript
if args.pbs or args.slurm:
if args.qsubscript is None:
if args.pbs:
qsubpath = os.path.join(os.path.dirname(scriptpath),
'qsub_ortho.sh')
if args.slurm:
qsubpath = os.path.join(os.path.dirname(scriptpath),
'slurm_ortho.sh')
else:
qsubpath = os.path.abspath(args.qsubscript)
if not os.path.isfile(qsubpath):
parser.error("qsub script path is not valid: {}".format(qsubpath))
## Verify processing options do not conflict
if args.pbs and args.slurm:
parser.error("Options --pbs and --slurm are mutually exclusive")
if (args.pbs or args.slurm) and args.parallel_processes > 1:
parser.error(
"HPC Options (--pbs or --slurm) and --parallel-processes > 1 are mutually exclusive"
)
#### Verify EPSG
try:
spatial_ref = utils.SpatialRef(args.epsg)
except RuntimeError as e:
parser.error(e)
#### Verify that dem and ortho_height are not both specified
if args.dem is not None and args.ortho_height is not None:
parser.error(
"--dem and --ortho_height options are mutually exclusive. Please choose only one."
)
#### Test if DEM exists
if args.dem:
if not os.path.isfile(args.dem):
parser.error("DEM does not exist: {}".format(args.dem))
#### Set up console logging handler
lso = logging.StreamHandler()
lso.setLevel(logging.INFO)
formatter = logging.Formatter('%(asctime)s %(levelname)s- %(message)s',
'%m-%d-%Y %H:%M:%S')
lso.setFormatter(formatter)
logger.addHandler(lso)
#### Get args ready to pass to task handler
arg_keys_to_remove = ('l', 'qsubscript', 'dryrun', 'pbs', 'slurm',
'parallel_processes')
arg_str_base = taskhandler.convert_optional_args_to_string(
args, pos_arg_keys, arg_keys_to_remove)
## Identify source images
if srctype == 'dir':
image_list1 = utils.find_images(src, False, ortho_functions.exts)
elif srctype == 'textfile':
image_list1 = utils.find_images(src, True, ortho_functions.exts)
else:
image_list1 = [src]
## Group Ikonos
image_list2 = []
for srcfp in image_list1:
srcdir, srcfn = os.path.split(srcfp)
if "IK01" in srcfn and sum(
[b in srcfn for b in ortho_functions.ikMsiBands]) > 0:
for b in ortho_functions.ikMsiBands:
if b in srcfn:
newname = os.path.join(srcdir, srcfn.replace(b, "msi"))
break
image_list2.append(newname)
else:
image_list2.append(srcfp)
image_list = list(set(image_list2))
logger.info('Number of src images: %i', len(image_list))
## Build task queue
i = 0
task_queue = []
for srcfp in image_list:
srcdir, srcfn = os.path.split(srcfp)
dstfp = os.path.join(
dstdir, "{}_{}{}{}{}".format(
os.path.splitext(srcfn)[0], utils.get_bit_depth(args.outtype),
args.stretch, spatial_ref.epsg,
ortho_functions.formats[args.format]))
done = os.path.isfile(dstfp)
if done is False:
i += 1
task = taskhandler.Task(
srcfn, 'Or{:04g}'.format(i), 'python',
'{} {} {} {}'.format(scriptpath, arg_str_base, srcfp, dstdir),
ortho_functions.process_image, [srcfp, dstfp, args])
task_queue.append(task)
logger.info('Number of incomplete tasks: %i', i)
## Run tasks
if len(task_queue) > 0:
logger.info("Submitting Tasks")
if args.pbs:
l = "-l {}".format(args.l) if args.l else ""
try:
task_handler = taskhandler.PBSTaskHandler(qsubpath, l)
except RuntimeError as e:
logger.error(e)
else:
if not args.dryrun:
task_handler.run_tasks(task_queue)
elif args.slurm:
try:
task_handler = taskhandler.SLURMTaskHandler(qsubpath)
except RuntimeError as e:
logger.error(e)
else:
if not args.dryrun:
task_handler.run_tasks(task_queue)
elif args.parallel_processes > 1:
try:
task_handler = taskhandler.ParallelTaskHandler(
args.parallel_processes)
except RuntimeError as e:
logger.error(e)
else:
logger.info("Number of child processes to spawn: %i",
task_handler.num_processes)
if not args.dryrun:
task_handler.run_tasks(task_queue)
else:
results = {}
for task in task_queue:
src, dstfp, task_arg_obj = task.method_arg_list
#### Set up processing log handler
logfile = os.path.splitext(dstfp)[0] + ".log"
lfh = logging.FileHandler(logfile)
lfh.setLevel(logging.DEBUG)
formatter = logging.Formatter(
'%(asctime)s %(levelname)s- %(message)s',
'%m-%d-%Y %H:%M:%S')
lfh.setFormatter(formatter)
logger.addHandler(lfh)
if not args.dryrun:
results[task.name] = task.method(src, dstfp, task_arg_obj)
#### remove existing file handler
logger.removeHandler(lfh)
#### Print Images with Errors
for k, v in results.items():
if v != 0:
logger.warning("Failed Image: %s", k)
logger.info("Done")
else:
logger.info("No images found to process")
def main():
#### Set Up Arguments
parser = argparse.ArgumentParser(
description="Sumbit/run batch mosaic tasks")
parser.add_argument(
"src", help="textfile or directory of input rasters (tif only)")
parser.add_argument("mosaicname",
help="output mosaic name excluding extension")
pos_arg_keys = ["src", "mosaicname"]
parser.add_argument(
"-r",
"--resolution",
nargs=2,
type=float,
help=
"output pixel resolution -- xres yres (default is same as first input file)"
)
parser.add_argument(
"-e",
"--extent",
nargs=4,
type=float,
help=
"extent of output mosaic -- xmin xmax ymin ymax (default is union of all inputs)"
)
parser.add_argument(
"-t",
"--tilesize",
nargs=2,
type=float,
help=
"tile size in coordinate system units -- xsize ysize (default is 40,000 times output "
"resolution)")
parser.add_argument(
"--force-pan-to-multi",
action="store_true",
default=False,
help="if output is multiband, force script to also use 1 band images")
parser.add_argument(
"-b",
"--bands",
type=int,
help=
"number of output bands( default is number of bands in the first image)"
)
parser.add_argument(
"--tday",
help=
"month and day of the year to use as target for image suitability ranking -- 04-05"
)
parser.add_argument(
"--tyear",
help=
"year (or year range) to use as target for image suitability ranking -- 2017 or 2015-2017"
)
parser.add_argument(
"--nosort",
action="store_true",
default=False,
help=
"do not sort images by metadata. script uses the order of the input textfile or directory "
"(first image is first drawn). Not recommended if input is a directory; order will be "
"random")
parser.add_argument(
"--use-exposure",
action="store_true",
default=False,
help="use exposure settings in metadata to inform score")
parser.add_argument(
"--exclude",
help=
"file of file name patterns (text only, no wildcards or regexs) to exclude"
)
parser.add_argument(
"--max-cc",
type=float,
default=0.2,
help="maximum fractional cloud cover (0.0-1.0, default 0.5)")
parser.add_argument(
"--include-all-ms",
action="store_true",
default=False,
help=
"include all multispectral imagery, even if the imagery has differing numbers of bands"
)
parser.add_argument(
"--min-contribution-area",
type=int,
default=20000000,
help=
"minimum area contribution threshold in target projection units (default=20000000). "
"Higher values remove more image slivers from the resulting mosaic")
parser.add_argument(
"--median-remove",
action="store_true",
default=False,
help=
"subtract the median from each input image before forming the mosaic in order to correct "
"for contrast")
parser.add_argument(
"--allow-invalid-geom",
action="store_true",
default=False,
help=
"normally, if 1 or more images has a invalid geometry, a tile will not be created. this "
"option will attempt to create a mosaic with the remaining valid geometries, if any."
)
parser.add_argument(
"--mode",
choices=mosaic.MODES,
default="ALL",
help=
" mode: ALL- all steps (default), SHP- create shapefiles, MOSAIC- create tiled tifs, "
"TEST- create log only")
parser.add_argument("--wd",
help="scratch space (default is mosaic directory)")
parser.add_argument("--component-shp",
action="store_true",
default=False,
help="create shp of all componenet images")
parser.add_argument(
"--cutline-step",
type=int,
default=2,
help="cutline calculator pixel skip interval (default=2)")
parser.add_argument(
"--calc-stats",
action="store_true",
default=False,
help="calculate image stats and record them in the index")
parser.add_argument("--gtiff-compression",
choices=mosaic.GTIFF_COMPRESSIONS,
default="lzw",
help="GTiff compression type. Default=lzw ({})".format(
",".join(mosaic.GTIFF_COMPRESSIONS)))
parser.add_argument("--pbs",
action='store_true',
default=False,
help="submit tasks to PBS")
parser.add_argument("--slurm",
action='store_true',
default=False,
help="submit tasks to SLURM")
parser.add_argument(
"--parallel-processes",
type=int,
default=1,
help="number of parallel processes to spawn (default 1)")
parser.add_argument(
"--qsubscript",
help=
"submission script to use in PBS/SLURM submission (PBS default is qsub_mosaic.sh, SLURM "
"default is slurm_mosaic.py, in script root folder)")
parser.add_argument(
"-l",
help=
"PBS resources requested (mimicks qsub syntax). Use only on HPC systems."
)
parser.add_argument(
"--log",
help="file to log progress (default is <output dir>\{}".format(
default_logfile))
parser.add_argument("--version",
action='version',
version="imagery_utils v{}".format(
utils.package_version))
#### Parse Arguments
args = parser.parse_args()
scriptpath = os.path.abspath(sys.argv[0])
inpath = os.path.abspath(args.src)
mosaicname = os.path.abspath(args.mosaicname)
mosaicname = os.path.splitext(mosaicname)[0]
mosaic_dir = os.path.dirname(mosaicname)
tile_builder_script = os.path.join(os.path.dirname(scriptpath),
'pgc_mosaic_build_tile.py')
## Verify qsubscript
if args.pbs or args.slurm:
if args.qsubscript is None:
if args.pbs:
qsubpath = os.path.join(os.path.dirname(scriptpath),
'qsub_mosaic.sh')
if args.slurm:
qsubpath = os.path.join(os.path.dirname(scriptpath),
'slurm_mosaic.sh')
else:
qsubpath = os.path.abspath(args.qsubscript)
if not os.path.isfile(qsubpath):
parser.error("qsub script path is not valid: {}".format(qsubpath))
## Verify processing options do not conflict
if args.pbs and args.slurm:
parser.error("Options --pbs and --slurm are mutually exclusive")
#### Validate Arguments
if os.path.isfile(inpath):
bTextfile = True
elif os.path.isdir(inpath):
bTextfile = False
else:
parser.error(
"Arg1 is not a valid file path or directory: {}".format(inpath))
#### Validate target day option
if args.tday is not None:
try:
m = int(args.tday.split("-")[0])
d = int(args.tday.split("-")[1])
td = date(2000, m, d)
except ValueError:
parser.error("Target day must be in mm-dd format (i.e 04-05)")
sys.exit(1)
else:
m = 0
d = 0
#### Validate target year/year range option
if args.tyear is not None:
if len(str(args.tyear)) == 4:
## ensure single year is valid
try:
tyear_test = datetime(year=args.tyear, month=1, day=1)
except ValueError:
parser.error("Supplied year {0} is not valid".format(
args.tyear))
sys.exit(1)
elif len(str(args.tyear)) == 9:
if '-' in args.tyear:
## decouple range and build year
yrs = args.tyear.split('-')
yrs_range = range(int(yrs[0]), int(yrs[1]) + 1)
for yy in yrs_range:
try:
tyear_test = datetime(year=yy, month=1, day=1)
except ValueError:
parser.error(
"Supplied year {0} in range {1} is not valid".
format(yy, args.tyear))
sys.exit(1)
else:
parser.error(
"Supplied year range {0} is not valid; should be like: 2015 OR 2015-2017"
.format(args.tyear))
sys.exit(1)
else:
parser.error(
"Supplied year {0} is not valid, or its format is incorrect; should be 4 digits for single "
"year (e.g., 2017), eight digits and dash for range (e.g., 2015-2017)"
.format(args.tyear))
sys.exit(1)
#### Get exclude list if specified
if args.exclude is not None:
if not os.path.isfile(args.exclude):
parser.error("Value for option --exclude-list is not a valid file")
## Build tasks
task_queue = []
#### Create task for mosaic
arg_keys_to_remove = ('l', 'qsubscript', 'pbs', 'slurm')
mos_arg_str = taskhandler.convert_optional_args_to_string(
args, pos_arg_keys, arg_keys_to_remove)
cmd = r'{} {} {} {}'.format(scriptpath, mos_arg_str, inpath, mosaicname)
task = taskhandler.Task('Mosaic {}'.format(os.path.basename(mosaicname)),
'Mos{:04g}'.format(1), 'python', cmd)
task_queue.append(task)
#logger.info(task_queue)
if len(task_queue) > 0:
if args.pbs:
l = "-l {}".format(args.l) if args.l else ""
try:
task_handler = taskhandler.PBSTaskHandler(qsubpath, l)
except RuntimeError as e:
logger.error(e)
else:
task_handler.run_tasks(task_queue)
elif args.slurm:
try:
task_handler = taskhandler.SLURMTaskHandler(qsubpath)
except RuntimeError as e:
logger.error(e)
else:
task_handler.run_tasks(task_queue)
else:
try:
run_mosaic(tile_builder_script, inpath, mosaicname, mosaic_dir,
args, pos_arg_keys)
except RuntimeError as e:
logger.error(e)
else:
logger.info("No tasks to process")
def main():
parser = argparse.ArgumentParser()
#### Set Up Options
parser.add_argument("src", help="source directory or image")
parser.add_argument("--dstdir", help="dstination directory")
parser.add_argument("-o",
"--overwrite",
action="store_true",
default=False,
help="overwrite existing files if present")
parser.add_argument("--pbs",
action='store_true',
default=False,
help="submit tasks to PBS")
parser.add_argument("--slurm",
action='store_true',
default=False,
help="submit tasks to SLURM")
parser.add_argument(
"--parallel-processes",
type=int,
default=1,
help="number of parallel processes to spawn (default 1)")
parser.add_argument(
"--qsubscript",
help=
"qsub script to use in scheduler submission (PBS default is qsub_resample.sh, SLURM default is slurm_resample.sh)"
)
parser.add_argument("--dryrun",
action="store_true",
default=False,
help="print actions without executing")
pos_arg_keys = ['src']
#### Parse Arguments
args = parser.parse_args()
scriptpath = os.path.abspath(sys.argv[0])
src = os.path.abspath(args.src)
#### Validate Required Arguments
if not os.path.isdir(src) and not os.path.isfile(src):
parser.error('src must be avalid directory or file')
## Verify qsubscript
if args.pbs or args.slurm:
if args.qsubscript is None:
if args.pbs:
qsubpath = os.path.join(os.path.dirname(scriptpath),
'qsub_resample.sh')
if args.slurm:
qsubpath = os.path.join(os.path.dirname(scriptpath),
'slurm_resample.sh')
else:
qsubpath = os.path.abspath(args.qsubscript)
if not os.path.isfile(qsubpath):
parser.error("qsub script path is not valid: %s" % qsubpath)
## Verify processing options do not conflict
if args.pbs and args.slurm:
parser.error("Options --pbs and --slurm are mutually exclusive")
if (args.pbs or args.slurm) and args.parallel_processes > 1:
parser.error(
"HPC Options (--pbs or --slurm) and --parallel-processes > 1 are mutually exclusive"
)
#### Set up console logging handler
lso = logging.StreamHandler()
lso.setLevel(logging.INFO)
formatter = logging.Formatter('%(asctime)s %(levelname)s- %(message)s',
'%m-%d-%Y %H:%M:%S')
lso.setFormatter(formatter)
logger.addHandler(lso)
#### Get args ready to pass to task handler
arg_keys_to_remove = ('qsubscript', 'dryrun', 'pbs', 'slurm',
'parallel_processes')
arg_str_base = taskhandler.convert_optional_args_to_string(
args, pos_arg_keys, arg_keys_to_remove)
task_queue = []
i = 0
logger.info("Searching for SETSM rasters")
if os.path.isfile(src):
if src.endswith(('dem.tif', 'matchtag.tif', 'ortho.tif')):
srcfp = src
regfp = srcfp.replace('dem.tif', 'reg.txt').replace(
'matchtag.tif', 'reg.txt').replace('ortho.tif', 'reg.txt')
if not os.path.isfile(regfp):
logger.info("No regfile found for {}".format(src))
else:
if args.dstdir:
dstfp = "{}_reg.tif".format(
os.path.join(
args.dstdir,
os.path.basename(os.path.splitext(srcfp)[0])))
else:
dstfp = "{}_reg.tif".format(os.path.splitext(srcfp)[0])
if not os.path.isfile(dstfp):
i += 1
task = taskhandler.Task(
os.path.basename(srcfp), 'Reg{:04g}'.format(i),
'python', '{} {} {}'.format(scriptpath, arg_str_base,
srcfp), apply_reg,
[srcfp, args])
task_queue.append(task)
else:
for root, dirs, files in os.walk(src):
for f in files:
if f.endswith(('dem.tif', 'matchtag.tif', 'ortho.tif')):
srcfp = os.path.join(root, f)
regfp = srcfp.replace('dem.tif', 'reg.txt').replace(
'matchtag.tif',
'reg.txt').replace('ortho.tif', 'reg.txt')
if not os.path.isfile(regfp):
logger.info("No regfile found for {}".format(srcfp))
else:
if args.dstdir:
dstfp = "{}_reg.tif".format(
os.path.join(
args.dstdir,
os.path.basename(
os.path.splitext(srcfp)[0])))
else:
dstfp = "{}_reg.tif".format(
os.path.splitext(srcfp)[0])
if not os.path.isfile(dstfp):
i += 1
task = taskhandler.Task(
f, 'Reg{:04g}'.format(i), 'python',
'{} {} {}'.format(scriptpath, arg_str_base,
srcfp), apply_reg,
[srcfp, args])
task_queue.append(task)
logger.info('Number of incomplete tasks: {}'.format(i))
if len(task_queue) > 0:
logger.info("Submitting Tasks")
if args.pbs:
try:
task_handler = taskhandler.PBSTaskHandler(qsubpath)
except RuntimeError as e:
logger.error(e)
else:
if not args.dryrun:
task_handler.run_tasks(task_queue)
elif args.slurm:
try:
task_handler = taskhandler.SLURMTaskHandler(qsubpath)
except RuntimeError as e:
logger.error(e)
else:
if not args.dryrun:
task_handler.run_tasks(task_queue)
elif args.parallel_processes > 1:
try:
task_handler = taskhandler.ParallelTaskHandler(
args.parallel_processes)
except RuntimeError as e:
logger.error(e)
else:
logger.info("Number of child processes to spawn: {0}".format(
task_handler.num_processes))
if not args.dryrun:
task_handler.run_tasks(task_queue)
else:
for task in task_queue:
src, task_arg_obj = task.method_arg_list
#### Set up processing log handler
if args.dstdir:
logfile = "{}.log".format(
os.path.join(
args.dstdir,
os.path.basename(os.path.splitext(src)[0])))
else:
logfile = os.path.splitext(src)[0] + ".log"
lfh = logging.FileHandler(logfile)
lfh.setLevel(logging.DEBUG)
formatter = logging.Formatter(
'%(asctime)s %(levelname)s- %(message)s',
'%m-%d-%Y %H:%M:%S')
lfh.setFormatter(formatter)
logger.addHandler(lfh)
if not args.dryrun:
task.method(src, task_arg_obj)
#### remove existing file handler
logger.removeHandler(lfh)
else:
logger.info("No tasks found to process")
## Run tasks
if len(task_queue) > 0:
logger.info("Submitting Tasks")
if args.pbs:
l = "-l {}".format(args.l) if args.l else ""
try:
task_handler = taskhandler.PBSTaskHandler(qsubpath, l)
except RuntimeError, e:
logger.error(e)
else:
if not args.dryrun:
task_handler.run_tasks(task_queue)
elif args.slurm:
try:
task_handler = taskhandler.SLURMTaskHandler(qsubpath)
except RuntimeError, e:
logger.error(e)
else:
if not args.dryrun:
task_handler.run_tasks(task_queue)
elif args.parallel_processes > 1:
try:
task_handler = taskhandler.ParallelTaskHandler(
args.parallel_processes)
except RuntimeError, e:
logger.error(e)
else:
logger.info("Number of child processes to spawn: {0}".format(
task_handler.num_processes))
def main():
#### Set Up Arguments
parent_parser, pos_arg_keys = ortho_functions.buildParentArgumentParser()
parser = argparse.ArgumentParser(
parents=[parent_parser],
description="Run/submit batch image ortho and conversion tasks")
parser.add_argument("--pbs",
action='store_true',
default=False,
help="submit tasks to PBS")
parser.add_argument("--slurm",
action='store_true',
default=False,
help="submit tasks to SLURM")
parser.add_argument(
"--tasks-per-job",
type=int,
help=
"Number of tasks to bundle into a single job. (requires --pbs or --slurm option) (Warning:"
" a higher number of tasks per job may require modification of default wallclock limit.)"
)
parser.add_argument(
'--scratch',
default=ARGDEF_SCRATCH,
help="Scratch space to build task bundle text files. (default={})".
format(ARGDEF_SCRATCH))
parser.add_argument(
"--parallel-processes",
type=int,
default=1,
help="number of parallel processes to spawn (default 1)")
parser.add_argument(
"--qsubscript",
help=
"submission script to use in PBS/SLURM submission (PBS default is qsub_ortho.sh, SLURM "
"default is slurm_ortho.py, in script root folder)")
parser.add_argument(
"-l", help="PBS resources requested (mimicks qsub syntax, PBS only)")
parser.add_argument("--dryrun",
action='store_true',
default=False,
help='print actions without executing')
#### Parse Arguments
args = parser.parse_args()
scriptpath = os.path.abspath(sys.argv[0])
src = os.path.abspath(args.src)
dstdir = os.path.abspath(args.dst)
scratch = os.path.abspath(args.scratch)
bittype = utils.get_bit_depth(args.outtype)
#### Validate Required Arguments
if os.path.isdir(src):
srctype = 'dir'
elif os.path.isfile(src) and os.path.splitext(src)[1].lower() == '.txt':
srctype = 'textfile'
elif os.path.isfile(src) and os.path.splitext(
src)[1].lower() in ortho_functions.exts:
srctype = 'image'
elif os.path.isfile(src.replace('msi', 'blu')) and os.path.splitext(
src)[1].lower() in ortho_functions.exts:
srctype = 'image'
else:
parser.error(
"Error arg1 is not a recognized file path or file type: {}".format(
src))
if not os.path.isdir(dstdir):
parser.error("Error arg2 is not a valid file path: {}".format(dstdir))
## Verify qsubscript
if args.pbs or args.slurm:
if args.qsubscript is None:
if args.pbs:
qsubpath = os.path.join(os.path.dirname(scriptpath),
'qsub_ortho.sh')
if args.slurm:
qsubpath = os.path.join(os.path.dirname(scriptpath),
'slurm_ortho.sh')
else:
qsubpath = os.path.abspath(args.qsubscript)
if not os.path.isfile(qsubpath):
parser.error("qsub script path is not valid: {}".format(qsubpath))
## Verify processing options do not conflict
requested_threads = ortho_functions.ARGDEF_CPUS_AVAIL if args.threads == "ALL_CPUS" else args.threads
if args.pbs and args.slurm:
parser.error("Options --pbs and --slurm are mutually exclusive")
if (args.pbs or args.slurm) and args.parallel_processes > 1:
parser.error(
"HPC Options (--pbs or --slurm) and --parallel-processes > 1 are mutually exclusive"
)
if (args.pbs or args.slurm) and requested_threads > 1:
parser.error(
"HPC Options (--pbs or --slurm) and --threads > 1 are mutually exclusive"
)
if requested_threads < 1:
parser.error(
"--threads count must be positive, nonzero integer or ALL_CPUS")
if args.parallel_processes > 1:
total_proc_count = requested_threads * args.parallel_processes
if total_proc_count > ortho_functions.ARGDEF_CPUS_AVAIL:
parser.error(
"the (threads * number of processes requested) ({0}) exceeds number of available threads "
"({1}); reduce --threads and/or --parallel-processes count".
format(total_proc_count, ortho_functions.ARGDEF_CPUS_AVAIL))
if args.tasks_per_job:
if not (args.pbs or args.slurm):
parser.error(
"--tasks-per-job option requires the (--pbs or --slurm) option"
)
if not os.path.isdir(args.scratch):
print("Creating --scratch directory: {}".format(args.scratch))
os.makedirs(args.scratch)
#### Verify EPSG
try:
spatial_ref = utils.SpatialRef(args.epsg)
except RuntimeError as e:
parser.error(e)
#### Verify that dem and ortho_height are not both specified
if args.dem is not None and args.ortho_height is not None:
parser.error(
"--dem and --ortho_height options are mutually exclusive. Please choose only one."
)
#### Test if DEM exists
if args.dem:
if not os.path.isfile(args.dem):
parser.error("DEM does not exist: {}".format(args.dem))
if args.l is None:
if args.dem.endswith('.vrt'):
total_dem_filesz_gb = 0.0
tree = ET.parse(args.dem)
root = tree.getroot()
for sourceFilename in root.iter('SourceFilename'):
dem_filename = sourceFilename.text
if not os.path.isfile(dem_filename):
parser.error(
"VRT DEM component raster does not exist: {}".
format(dem_filename))
dem_filesz_gb = os.path.getsize(
dem_filename) / 1024.0 / 1024 / 1024
total_dem_filesz_gb += dem_filesz_gb
dem_filesz_gb = total_dem_filesz_gb
else:
dem_filesz_gb = os.path.getsize(
args.dem) / 1024.0 / 1024 / 1024
pbs_req_mem_gb = int(max(math.ceil(dem_filesz_gb) + 2, 4))
args.l = 'mem={}gb'.format(pbs_req_mem_gb)
#### Set up console logging handler
lso = logging.StreamHandler()
lso.setLevel(logging.DEBUG)
formatter = logging.Formatter('%(asctime)s %(levelname)s- %(message)s',
'%m-%d-%Y %H:%M:%S')
lso.setFormatter(formatter)
logger.addHandler(lso)
#### Handle thread count that exceeds system limits
if requested_threads > ortho_functions.ARGDEF_CPUS_AVAIL:
logger.info(
"threads requested ({0}) exceeds number available on system ({1}), setting thread count to "
"'ALL_CPUS'".format(requested_threads,
ortho_functions.ARGDEF_CPUS_AVAIL))
args.threads = 'ALL_CPUS'
#### Get args ready to pass to task handler
arg_keys_to_remove = ('l', 'qsubscript', 'dryrun', 'pbs', 'slurm',
'parallel_processes', 'tasks_per_job')
arg_str_base = taskhandler.convert_optional_args_to_string(
args, pos_arg_keys, arg_keys_to_remove)
## Identify source images
if srctype == 'dir':
image_list1 = utils.find_images(src, False, ortho_functions.exts)
elif srctype == 'textfile':
image_list1 = utils.find_images(src, True, ortho_functions.exts)
else:
image_list1 = [src]
## Group Ikonos
image_list2 = []
for srcfp in image_list1:
srcdir, srcfn = os.path.split(srcfp)
if "IK01" in srcfn and sum(
[b in srcfn for b in ortho_functions.ikMsiBands]) > 0:
for b in ortho_functions.ikMsiBands:
if b in srcfn:
newname = os.path.join(srcdir, srcfn.replace(b, "msi"))
break
image_list2.append(newname)
else:
image_list2.append(srcfp)
image_list = list(set(image_list2))
logger.info('Number of src images: %i', len(image_list))
## Build task queue
i = 0
images_to_process = []
for srcfp in image_list:
srcdir, srcfn = os.path.split(srcfp)
dstfp = os.path.join(
dstdir, "{}_{}{}{}{}".format(
os.path.splitext(srcfn)[0], bittype, args.stretch,
spatial_ref.epsg, ortho_functions.formats[args.format]))
done = os.path.isfile(dstfp)
if done is False:
i += 1
images_to_process.append(srcfp)
logger.info('Number of incomplete tasks: %i', i)
if len(images_to_process) == 0:
logger.info("No images found to process")
sys.exit(0)
task_queue = []
if args.tasks_per_job and args.tasks_per_job > 1:
task_srcfp_list = utils.write_task_bundles(images_to_process,
args.tasks_per_job, scratch,
'Or_src')
else:
task_srcfp_list = images_to_process
for job_count, srcfp in enumerate(task_srcfp_list, 1):
srcdir, srcfn = os.path.split(srcfp)
if task_srcfp_list is images_to_process:
dstfp = os.path.join(
dstdir, "{}_{}{}{}{}".format(
os.path.splitext(srcfn)[0], bittype, args.stretch,
spatial_ref.epsg, ortho_functions.formats[args.format]))
else:
dstfp = None
task = taskhandler.Task(
srcfn, 'Or{:04g}'.format(job_count), 'python',
'{} {} {} {}'.format(argval2str(scriptpath), arg_str_base,
argval2str(srcfp), argval2str(dstdir)),
ortho_functions.process_image, [srcfp, dstfp, args])
task_queue.append(task)
## Run tasks
if len(task_queue) > 0:
logger.info("Submitting Tasks")
if args.pbs:
l = "-l {}".format(args.l) if args.l else ""
try:
task_handler = taskhandler.PBSTaskHandler(qsubpath, l)
except RuntimeError as e:
logger.error(e)
else:
if not args.dryrun:
task_handler.run_tasks(task_queue, dryrun=args.dryrun)
elif args.slurm:
try:
task_handler = taskhandler.SLURMTaskHandler(qsubpath)
except RuntimeError as e:
logger.error(e)
else:
if not args.dryrun:
task_handler.run_tasks(task_queue)
elif args.parallel_processes > 1:
try:
task_handler = taskhandler.ParallelTaskHandler(
args.parallel_processes)
except RuntimeError as e:
logger.error(e)
else:
logger.info("Number of child processes to spawn: %i",
task_handler.num_processes)
if not args.dryrun:
task_handler.run_tasks(task_queue)
else:
results = {}
for task in task_queue:
src, dstfp, task_arg_obj = task.method_arg_list
#### Set up processing log handler
logfile = os.path.splitext(dstfp)[0] + ".log"
lfh = logging.FileHandler(logfile)
lfh.setLevel(logging.DEBUG)
formatter = logging.Formatter(
'%(asctime)s %(levelname)s- %(message)s',
'%m-%d-%Y %H:%M:%S')
lfh.setFormatter(formatter)
logger.addHandler(lfh)
if not args.dryrun:
results[task.name] = task.method(src, dstfp, task_arg_obj)
#### remove existing file handler
logger.removeHandler(lfh)
#### Print Images with Errors
for k, v in results.items():
if v != 0:
logger.warning("Failed Image: %s", k)
logger.info("Done")
else:
logger.info("No images found to process")
def main():
#### Set Up Arguments
parent_parser, pos_arg_keys = ortho_functions.buildParentArgumentParser()
parser = argparse.ArgumentParser(
parents=[parent_parser],
description="Run/Submit batch pansharpening in parallel")
parser.add_argument("--pbs",
action='store_true',
default=False,
help="submit tasks to PBS")
parser.add_argument("--slurm",
action='store_true',
default=False,
help="submit tasks to SLURM")
parser.add_argument(
"--parallel-processes",
type=int,
default=1,
help="number of parallel processes to spawn (default 1)")
parser.add_argument(
"--qsubscript",
help=
"submission script to use in PBS/SLURM submission (PBS default is qsub_pansharpen.sh, "
"SLURM default is slurm_pansharpen.py, in script root folder)")
parser.add_argument(
"-l", help="PBS resources requested (mimicks qsub syntax, PBS only)")
parser.add_argument("--dryrun",
action="store_true",
default=False,
help="print actions without executing")
#### Parse Arguments
args = parser.parse_args()
scriptpath = os.path.abspath(sys.argv[0])
src = os.path.abspath(args.src)
dstdir = os.path.abspath(args.dst)
#### Validate Required Arguments
if os.path.isdir(src):
srctype = 'dir'
elif os.path.isfile(src) and os.path.splitext(src)[1].lower() == '.txt':
srctype = 'textfile'
elif os.path.isfile(src) and os.path.splitext(
src)[1].lower() in ortho_functions.exts:
srctype = 'image'
elif os.path.isfile(src.replace('msi', 'blu')) and os.path.splitext(
src)[1].lower() in ortho_functions.exts:
srctype = 'image'
else:
parser.error(
"Error arg1 is not a recognized file path or file type: {}".format(
src))
if not os.path.isdir(dstdir):
parser.error("Error arg2 is not a valid file path: {}".format(dstdir))
# Verify qsubscript
if args.pbs or args.slurm:
if args.qsubscript is None:
if args.pbs:
qsubpath = os.path.join(os.path.dirname(scriptpath),
'qsub_pansharpen.sh')
if args.slurm:
qsubpath = os.path.join(os.path.dirname(scriptpath),
'slurm_pansharpen.sh')
else:
qsubpath = os.path.abspath(args.qsubscript)
if not os.path.isfile(qsubpath):
parser.error("qsub script path is not valid: {}".format(qsubpath))
### Verify processing options do not conflict
if args.pbs and args.slurm:
parser.error("Options --pbs and --slurm are mutually exclusive")
if (args.pbs or args.slurm) and args.parallel_processes > 1:
parser.error(
"HPC Options (--pbs or --slurm) and --parallel-processes > 1 are mutually exclusive"
)
#### Verify EPSG
try:
spatial_ref = utils.SpatialRef(args.epsg)
except RuntimeError as e:
parser.error(e)
## Check GDAL version (2.1.0 minimum)
gdal_version = gdal.VersionInfo()
try:
if int(gdal_version) < 2010000:
parser.error(
"gdal_pansharpen requires GDAL version 2.1.0 or higher")
except ValueError:
parser.error("Cannot parse GDAL version: {}".format(gdal_version))
#### Set up console logging handler
lso = logging.StreamHandler()
lso.setLevel(logging.DEBUG)
formatter = logging.Formatter('%(asctime)s %(levelname)s- %(message)s',
'%m-%d-%Y %H:%M:%S')
lso.setFormatter(formatter)
logger.addHandler(lso)
#### Get args ready to pass to task handler
arg_keys_to_remove = ('l', 'qsubscript', 'dryrun', 'pbs', 'slurm',
'parallel_processes')
arg_str_base = taskhandler.convert_optional_args_to_string(
args, pos_arg_keys, arg_keys_to_remove)
## Identify source images
if srctype == 'dir':
image_list1 = utils.find_images(src, False, ortho_functions.exts)
elif srctype == 'textfile':
image_list1 = utils.find_images(src, True, ortho_functions.exts)
else:
image_list1 = [src]
pair_list = []
for srcfp in image_list1:
#print(srcfp)
try:
image_pair = ImagePair(srcfp, spatial_ref)
except RuntimeError as e:
logger.error(e)
else:
logger.info("Image: %s, Sensor: %s", image_pair.mul_srcfn,
image_pair.sensor)
pair_list.append(image_pair)
logger.info('Number of src image pairs: %i', len(pair_list))
## Build task queue
i = 0
task_queue = []
for image_pair in pair_list:
bittype = utils.get_bit_depth(args.outtype)
pansh_dstfp = os.path.join(
dstdir, "{}_{}{}{}_pansh.tif".format(
os.path.splitext(image_pair.mul_srcfn)[0], bittype,
args.stretch, args.epsg))
if not os.path.isfile(pansh_dstfp):
i += 1
task = taskhandler.Task(
image_pair.mul_srcfn, 'Psh{:04g}'.format(i), 'python',
'{} {} {} {}'.format(scriptpath, arg_str_base,
image_pair.mul_srcfp, dstdir),
exec_pansharpen, [image_pair, pansh_dstfp, args])
task_queue.append(task)
logger.info('Number of incomplete tasks: %i', i)
## Run tasks
if len(task_queue) > 0:
logger.info("Submitting Tasks")
if args.pbs:
l = "-l {}".format(args.l) if args.l else ""
try:
task_handler = taskhandler.PBSTaskHandler(qsubpath, l)
except RuntimeError as e:
logger.error(e)
else:
if not args.dryrun:
task_handler.run_tasks(task_queue)
elif args.slurm:
try:
task_handler = taskhandler.SLURMTaskHandler(qsubpath)
except RuntimeError as e:
logger.error(e)
else:
if not args.dryrun:
task_handler.run_tasks(task_queue)
elif args.parallel_processes > 1:
try:
task_handler = taskhandler.ParallelTaskHandler(
args.parallel_processes)
except RuntimeError as e:
logger.error(e)
else:
logger.info("Number of child processes to spawn: %i",
task_handler.num_processes)
if not args.dryrun:
task_handler.run_tasks(task_queue)
else:
results = {}
lfh = None
for task in task_queue:
src, dstfp, task_arg_obj = task.method_arg_list
#### Set up processing log handler
logfile = os.path.splitext(dstfp)[0] + ".log"
lfh = logging.FileHandler(logfile)
lfh.setLevel(logging.DEBUG)
formatter = logging.Formatter(
'%(asctime)s %(levelname)s- %(message)s',
'%m-%d-%Y %H:%M:%S')
lfh.setFormatter(formatter)
logger.addHandler(lfh)
if not args.dryrun:
results[task.name] = task.method(src, dstfp, task_arg_obj)
#### remove existing file handler
logger.removeHandler(lfh)
#### remove existing file handler
logger.removeHandler(lfh)
#### Print Images with Errors
for k, v in results.items():
if v != 0:
logger.warning("Failed Image: %s", k)
logger.info("Done")
else:
logger.info("No images found to process")
def main():
#### Set Up Arguments
parser = argparse.ArgumentParser(
description="Run/Submit batch ndvi calculation in parallel"
)
parser.add_argument("src", help="source image, text file, or directory")
parser.add_argument("dst", help="destination directory")
pos_arg_keys = ["src", "dst"]
parser.add_argument("-t", "--outtype", choices=outtypes, default='Float32',
help="output data type (for Int16, output values are scaled from -1000 to 1000)")
parser.add_argument("-s", "--save-temps", action="store_true", default=False,
help="save temp files")
parser.add_argument("--wd",
help="local working directory for cluster jobs (default is dst dir)")
parser.add_argument("--pbs", action='store_true', default=False,
help="submit tasks to PBS")
parser.add_argument("--slurm", action='store_true', default=False,
help="submit tasks to SLURM")
parser.add_argument("--parallel-processes", type=int, default=1,
help="number of parallel processes to spawn (default 1)")
parser.add_argument("--qsubscript",
help="submission script to use in PBS/SLURM submission (PBS default is qsub_ndvi.sh, SLURM "
"default is slurm_ndvi.py, in script root folder)")
parser.add_argument("-l", help="PBS resources requested (mimicks qsub syntax, PBS only)")
parser.add_argument("--dryrun", action="store_true", default=False,
help="print actions without executing")
parser.add_argument("--version", action='version', version="imagery_utils v{}".format(utils.package_version))
#### Parse Arguments
args = parser.parse_args()
scriptpath = os.path.abspath(sys.argv[0])
src = os.path.abspath(args.src)
dstdir = os.path.abspath(args.dst)
#### Validate Required Arguments
if os.path.isdir(src):
srctype = 'dir'
elif os.path.isfile(src) and os.path.splitext(src)[1].lower() == '.txt':
srctype = 'textfile'
elif os.path.isfile(src) and os.path.splitext(src)[1].lower() in ortho_functions.exts:
srctype = 'image'
elif os.path.isfile(src.replace('msi', 'blu')) and os.path.splitext(src)[1].lower() in ortho_functions.exts:
srctype = 'image'
else:
parser.error("Error arg1 is not a recognized file path or file type: {}".format(src))
if not os.path.isdir(dstdir):
parser.error("Error arg2 is not a valid file path: {}".format(dstdir))
## Verify qsubscript
if args.pbs or args.slurm:
if args.qsubscript is None:
if args.pbs:
qsubpath = os.path.join(os.path.dirname(scriptpath), 'qsub_ndvi.sh')
if args.slurm:
qsubpath = os.path.join(os.path.dirname(scriptpath), 'slurm_ndvi.sh')
else:
qsubpath = os.path.abspath(args.qsubscript)
if not os.path.isfile(qsubpath):
parser.error("qsub script path is not valid: {}".format(qsubpath))
## Verify processing options do not conflict
if args.pbs and args.slurm:
parser.error("Options --pbs and --slurm are mutually exclusive")
if (args.pbs or args.slurm) and args.parallel_processes > 1:
parser.error("HPC Options (--pbs or --slurm) and --parallel-processes > 1 are mutually exclusive")
#### Set concole logging handler
lso = logging.StreamHandler()
lso.setLevel(logging.DEBUG)
formatter = logging.Formatter('%(asctime)s %(levelname)s- %(message)s', '%m-%d-%Y %H:%M:%S')
lso.setFormatter(formatter)
logger.addHandler(lso)
#### Get args ready to pass to task handler
arg_keys_to_remove = ('l', 'qsubscript', 'pbs', 'slurm', 'parallel_processes', 'dryrun')
arg_str = taskhandler.convert_optional_args_to_string(args, pos_arg_keys, arg_keys_to_remove)
## Identify source images
if srctype == 'dir':
image_list = utils.find_images(src, False, ortho_functions.exts)
elif srctype == 'textfile':
image_list = utils.find_images(src, True, ortho_functions.exts)
else:
image_list = [src]
logger.info('Number of src images: %i', len(image_list))
## Build task queue
i = 0
task_queue = []
for srcfp in image_list:
srcdir, srcfn = os.path.split(srcfp)
bn, ext = os.path.splitext(srcfn)
dstfp = os.path.join(dstdir, bn + '_ndvi.tif')
if not os.path.isfile(dstfp):
i += 1
task = taskhandler.Task(
srcfn,
'NDVI{:04g}'.format(i),
'python',
'{} {} {} {}'.format(scriptpath, arg_str, srcfp, dstdir),
calc_ndvi,
[srcfp, dstfp, args]
)
task_queue.append(task)
logger.info('Number of incomplete tasks: %i', i)
## Run tasks
if len(task_queue) > 0:
logger.info("Submitting Tasks")
if args.pbs:
l = "-l {}".format(args.l) if args.l else ""
try:
task_handler = taskhandler.PBSTaskHandler(qsubpath, l)
except RuntimeError as e:
logger.error(e)
else:
if not args.dryrun:
task_handler.run_tasks(task_queue)
elif args.slurm:
try:
task_handler = taskhandler.SLURMTaskHandler(qsubpath)
except RuntimeError as e:
logger.error(e)
else:
if not args.dryrun:
task_handler.run_tasks(task_queue)
elif args.parallel_processes > 1:
try:
task_handler = taskhandler.ParallelTaskHandler(args.parallel_processes)
except RuntimeError as e:
logger.error(e)
else:
logger.info("Number of child processes to spawn: %i", task_handler.num_processes)
if not args.dryrun:
task_handler.run_tasks(task_queue)
else:
results = {}
for task in task_queue:
srcfp, dstfp, task_arg_obj = task.method_arg_list
#### Set up processing log handler
logfile = os.path.splitext(dstfp)[0] + ".log"
lfh = logging.FileHandler(logfile)
lfh.setLevel(logging.DEBUG)
formatter = logging.Formatter('%(asctime)s %(levelname)s- %(message)s', '%m-%d-%Y %H:%M:%S')
lfh.setFormatter(formatter)
logger.addHandler(lfh)
if not args.dryrun:
results[task.name] = task.method(srcfp, dstfp, task_arg_obj)
#### remove existing file handler
logger.removeHandler(lfh)
#### Print Images with Errors
for k, v in results.items():
if v != 0:
logger.warning("Failed Image: %s", k)
logger.info("Done")
else:
logger.info("No images found to process")