def test_get_bit_depth(self):
self.assertEqual(utils.get_bit_depth("Byte"), "u08")
self.assertEqual(utils.get_bit_depth("UInt16"), "u16")
self.assertEqual(utils.get_bit_depth("Float32"), "f32")
self.assertEqual(utils.get_bit_depth("Uint16"), None) # function logs error, and returns None
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
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")
image_list2.append(newname)
else:
image_list2.append(srcfp)
image_list = list(set(image_list2))
logger.info('Number of src images: {}'.format(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, "%s_%s%s%d%s" %
(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: {}'.format(i))
## Run tasks
if len(task_queue) > 0:
image_pair = ImagePair(srcfp, spatial_ref)
except RuntimeError, e:
logger.error(e)
else:
logger.info("Image: {}, Sensor: {}".format(image_pair.mul_srcfn,
image_pair.sensor))
pair_list.append(image_pair)
logger.info('Number of src image pairs: {}'.format(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: {}'.format(i))
def exec_pansharpen(image_pair, pansh_dstfp, args):
dstdir = os.path.dirname(pansh_dstfp)
#### Get working dir
if args.wd is not None:
wd = args.wd
else:
wd = dstdir
if not os.path.isdir(wd):
try:
os.makedirs(wd)
except OSError:
pass
logger.info("Working Dir: %s" % wd)
#### Identify name pattern
print "Multispectral image: %s" % image_pair.mul_srcfp
print "Panchromatic image: %s" % image_pair.pan_srcfp
if args.dem is not None:
dem_arg = '-d "%s" ' % args.dem
else:
dem_arg = ""
bittype = utils.get_bit_depth(args.outtype)
pan_basename = os.path.splitext(image_pair.pan_srcfn)[0]
mul_basename = os.path.splitext(image_pair.mul_srcfn)[0]
pan_local_dstfp = os.path.join(
wd, "{}_{}{}{}.tif".format(pan_basename, bittype, args.stretch,
args.epsg))
mul_local_dstfp = os.path.join(
wd, "{}_{}{}{}.tif".format(mul_basename, bittype, args.stretch,
args.epsg))
pan_dstfp = os.path.join(
dstdir, "{}_{}{}{}.tif".format(pan_basename, bittype, args.stretch,
args.epsg))
mul_dstfp = os.path.join(
dstdir, "{}_{}{}{}.tif".format(mul_basename, bittype, args.stretch,
args.epsg))
pansh_tempfp = os.path.join(
wd, "{}_{}{}{}_pansh_temp.tif".format(mul_basename, bittype,
args.stretch, args.epsg))
pansh_local_dstfp = os.path.join(
wd, "{}_{}{}{}_pansh.tif".format(mul_basename, bittype, args.stretch,
args.epsg))
pansh_xmlfp = os.path.join(
dstdir, "{}_{}{}{}_pansh.xml".format(mul_basename, bittype,
args.stretch, args.epsg))
mul_xmlfp = os.path.join(
dstdir, "{}_{}{}{}.xml".format(mul_basename, bittype, args.stretch,
args.epsg))
if not os.path.isdir(wd):
os.makedirs(wd)
#### Ortho pan
logger.info("Orthorectifying panchromatic image")
if not os.path.isfile(pan_dstfp) and not os.path.isfile(pan_local_dstfp):
ortho_functions.process_image(image_pair.pan_srcfp, pan_dstfp, args,
image_pair.intersection_geom)
if not os.path.isfile(pan_local_dstfp) and os.path.isfile(pan_dstfp):
shutil.copy2(pan_dstfp, pan_local_dstfp)
logger.info("Orthorectifying multispectral image")
#### Ortho multi
if not os.path.isfile(mul_dstfp) and not os.path.isfile(mul_local_dstfp):
## If resolution is specified in the command line, assume it's intended for the pansharpened image
## and multiply the multi by 4
if args.resolution:
args.resolution = args.resolution * 4.0
ortho_functions.process_image(image_pair.mul_srcfp, mul_dstfp, args,
image_pair.intersection_geom)
if not os.path.isfile(mul_local_dstfp) and os.path.isfile(mul_dstfp):
shutil.copy2(mul_dstfp, mul_local_dstfp)
#### Pansharpen
logger.info("Pansharpening multispectral image")
if os.path.isfile(pan_local_dstfp) and os.path.isfile(mul_local_dstfp):
if not os.path.isfile(pansh_local_dstfp):
cmd = 'gdal_pansharpen.py -co BIGTIFF=IF_SAFER -co COMPRESS=LZW -co TILED=YES "{}" "{}" "{}"'.format(
pan_local_dstfp, mul_local_dstfp, pansh_local_dstfp)
taskhandler.exec_cmd(cmd)
else:
print "Pan or Multi warped image does not exist\n\t%s\n\t%s" % (
pan_local_dstfp, mul_local_dstfp)
#### Make pyramids
if os.path.isfile(pansh_local_dstfp):
cmd = 'gdaladdo "%s" 2 4 8 16' % (pansh_local_dstfp)
taskhandler.exec_cmd(cmd)
## Copy warped multispectral xml to pansharpened output
shutil.copy2(mul_xmlfp, pansh_xmlfp)
#### Copy pansharpened output
if wd <> dstdir:
for local_path, dst_path in [(pansh_local_dstfp, pansh_dstfp),
(pan_local_dstfp, pan_dstfp),
(mul_local_dstfp, mul_dstfp)]:
if os.path.isfile(local_path) and not os.path.isfile(dst_path):
shutil.copy2(local_path, dst_path)
#### Delete Temp Files
wd_files = [pansh_local_dstfp, pan_local_dstfp, mul_local_dstfp]
if not args.save_temps:
if wd <> dstdir:
for f in wd_files:
try:
os.remove(f)
except Exception, e:
logger.warning('Could not remove %s: %s' %
(os.path.basename(f), e))
def exec_pansharpen(image_pair, pansh_dstfp, args):
dstdir = os.path.dirname(pansh_dstfp)
#### Get working dir
if args.wd is not None:
wd = args.wd
else:
wd = dstdir
if not os.path.isdir(wd):
try:
os.makedirs(wd)
except OSError:
pass
logger.info("Working Dir: %s", wd)
#### Identify name pattern
print("Multispectral image: {}".format(image_pair.mul_srcfp))
print("Panchromatic image: {}".format(image_pair.pan_srcfp))
if args.dem is not None:
dem_arg = '-d "{}" '.format(args.dem)
else:
dem_arg = ""
bittype = utils.get_bit_depth(args.outtype)
pan_basename = os.path.splitext(image_pair.pan_srcfn)[0]
mul_basename = os.path.splitext(image_pair.mul_srcfn)[0]
pan_local_dstfp = os.path.join(wd, "{}_{}{}{}.tif".format(pan_basename, bittype, args.stretch, args.epsg))
mul_local_dstfp = os.path.join(wd, "{}_{}{}{}.tif".format(mul_basename, bittype, args.stretch, args.epsg))
pan_dstfp = os.path.join(dstdir, "{}_{}{}{}.tif".format(pan_basename, bittype, args.stretch, args.epsg))
mul_dstfp = os.path.join(dstdir, "{}_{}{}{}.tif".format(mul_basename, bittype, args.stretch, args.epsg))
pansh_tempfp = os.path.join(wd, "{}_{}{}{}_pansh_temp.tif".format(mul_basename, bittype, args.stretch, args.epsg))
pansh_local_dstfp = os.path.join(wd, "{}_{}{}{}_pansh.tif".format(mul_basename, bittype, args.stretch, args.epsg))
pansh_xmlfp = os.path.join(dstdir, "{}_{}{}{}_pansh.xml".format(mul_basename, bittype, args.stretch, args.epsg))
mul_xmlfp = os.path.join(dstdir, "{}_{}{}{}.xml".format(mul_basename, bittype, args.stretch, args.epsg))
if not os.path.isdir(wd):
os.makedirs(wd)
#### Ortho pan
logger.info("Orthorectifying panchromatic image")
if not os.path.isfile(pan_dstfp) and not os.path.isfile(pan_local_dstfp):
ortho_functions.process_image(image_pair.pan_srcfp, pan_dstfp, args, image_pair.intersection_geom)
if not os.path.isfile(pan_local_dstfp) and os.path.isfile(pan_dstfp):
shutil.copy2(pan_dstfp, pan_local_dstfp)
logger.info("Orthorectifying multispectral image")
#### Ortho multi
if not os.path.isfile(mul_dstfp) and not os.path.isfile(mul_local_dstfp):
## If resolution is specified in the command line, assume it's intended for the pansharpened image
## and multiply the multi by 4
if args.resolution:
args.resolution = args.resolution * 4.0
ortho_functions.process_image(image_pair.mul_srcfp, mul_dstfp, args, image_pair.intersection_geom)
if not os.path.isfile(mul_local_dstfp) and os.path.isfile(mul_dstfp):
shutil.copy2(mul_dstfp, mul_local_dstfp)
#### Pansharpen
## get system info for program extension
if platform.system() == 'Windows':
py_ext = ''
else:
py_ext = '.py'
logger.info("Pansharpening multispectral image")
if os.path.isfile(pan_local_dstfp) and os.path.isfile(mul_local_dstfp):
if not os.path.isfile(pansh_local_dstfp):
cmd = 'gdal_pansharpen{} -co BIGTIFF=IF_SAFER -co COMPRESS=LZW -co TILED=YES "{}" "{}" "{}"'.\
format(py_ext, pan_local_dstfp, mul_local_dstfp, pansh_local_dstfp)
taskhandler.exec_cmd(cmd)
else:
print("Pan or Multi warped image does not exist\n\t{}\n\t{}").format(pan_local_dstfp, mul_local_dstfp)
#### Make pyramids
if os.path.isfile(pansh_local_dstfp):
cmd = 'gdaladdo -r {} "{}" 2 4 8 16'.format(args.pyramid_type, pansh_local_dstfp)
taskhandler.exec_cmd(cmd)
## Copy warped multispectral xml to pansharpened output
shutil.copy2(mul_xmlfp, pansh_xmlfp)
#### Copy pansharpened output
if wd != dstdir:
for local_path, dst_path in [(pansh_local_dstfp, pansh_dstfp), (pan_local_dstfp, pan_dstfp),
(mul_local_dstfp, mul_dstfp)]:
if os.path.isfile(local_path) and not os.path.isfile(dst_path):
shutil.copy2(local_path, dst_path)
#### Delete Temp Files
wd_files = [
pansh_local_dstfp,
pan_local_dstfp,
mul_local_dstfp
]
if not args.save_temps:
if wd != dstdir:
for f in wd_files:
try:
os.remove(f)
except Exception as e:
logger.warning('Could not remove %s: %s', os.path.basename(f), e)
if os.path.isfile(pansh_dstfp):
return 0
else:
return 0
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
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")
image_list2.append(newname)
else:
image_list2.append(srcfp)
image_list = list(set(image_list2))
logger.info('Number of src images: {}'.format(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,"%s_%s%s%d%s" %(
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 = utils.Task(
srcfn,
'Ortho{:04g}'.format(i),
'python',
'{} {} {} {}'.format(scriptpath, arg_str_base, srcfp, dstdir),
ortho_functions.process_image,
[srcfp, dstfp, args]
def exec_pansharpen(image_pair, pansh_dstfp, args):
dstdir = os.path.dirname(pansh_dstfp)
#### Get working dir
if args.wd is not None:
wd = args.wd
else:
wd = dstdir
if not os.path.isdir(wd):
try:
os.makedirs(wd)
except OSError:
pass
logger.info("Working Dir: %s", wd)
#### Identify name pattern
print("Multispectral image: {}".format(image_pair.mul_srcfp))
print("Panchromatic image: {}".format(image_pair.pan_srcfp))
if args.dem is not None:
dem_arg = '-d "{}" '.format(args.dem)
else:
dem_arg = ""
bittype = utils.get_bit_depth(args.outtype)
pan_basename = os.path.splitext(image_pair.pan_srcfn)[0]
mul_basename = os.path.splitext(image_pair.mul_srcfn)[0]
pan_local_dstfp = os.path.join(
wd, "{}_{}{}{}.tif".format(pan_basename, bittype, args.stretch,
args.epsg))
mul_local_dstfp = os.path.join(
wd, "{}_{}{}{}.tif".format(mul_basename, bittype, args.stretch,
args.epsg))
pan_dstfp = os.path.join(
dstdir, "{}_{}{}{}.tif".format(pan_basename, bittype, args.stretch,
args.epsg))
mul_dstfp = os.path.join(
dstdir, "{}_{}{}{}.tif".format(mul_basename, bittype, args.stretch,
args.epsg))
pansh_tempfp = os.path.join(
wd, "{}_{}{}{}_pansh_temp.tif".format(mul_basename, bittype,
args.stretch, args.epsg))
pansh_local_dstfp = os.path.join(
wd, "{}_{}{}{}_pansh.tif".format(mul_basename, bittype, args.stretch,
args.epsg))
pansh_xmlfp = os.path.join(
dstdir, "{}_{}{}{}_pansh.xml".format(mul_basename, bittype,
args.stretch, args.epsg))
mul_xmlfp = os.path.join(
dstdir, "{}_{}{}{}.xml".format(mul_basename, bittype, args.stretch,
args.epsg))
if not os.path.isdir(wd):
os.makedirs(wd)
#### Ortho pan
logger.info("Orthorectifying panchromatic image")
if not os.path.isfile(pan_dstfp) and not os.path.isfile(pan_local_dstfp):
ortho_functions.process_image(image_pair.pan_srcfp, pan_dstfp, args,
image_pair.intersection_geom)
if not os.path.isfile(pan_local_dstfp) and os.path.isfile(pan_dstfp):
shutil.copy2(pan_dstfp, pan_local_dstfp)
logger.info("Orthorectifying multispectral image")
#### Ortho multi
if not os.path.isfile(mul_dstfp) and not os.path.isfile(mul_local_dstfp):
## If resolution is specified in the command line, assume it's intended for the pansharpened image
## and multiply the multi by 4
if args.resolution:
args.resolution = args.resolution * 4.0
ortho_functions.process_image(image_pair.mul_srcfp, mul_dstfp, args,
image_pair.intersection_geom)
if not os.path.isfile(mul_local_dstfp) and os.path.isfile(mul_dstfp):
shutil.copy2(mul_dstfp, mul_local_dstfp)
#### Pansharpen
## get system info for program extension
if platform.system() == 'Windows':
py_ext = ''
else:
py_ext = '.py'
pan_threading = ''
if hasattr(args, 'threads'):
if args.threads != 1:
pan_threading = '-threads {}'.format(args.threads)
logger.info("Pansharpening multispectral image")
if os.path.isfile(pan_local_dstfp) and os.path.isfile(mul_local_dstfp):
if not os.path.isfile(pansh_local_dstfp):
cmd = 'gdal_pansharpen{} -co BIGTIFF=IF_SAFER -co COMPRESS=LZW -co TILED=YES {} "{}" "{}" "{}"'.\
format(py_ext, pan_threading, pan_local_dstfp, mul_local_dstfp, pansh_local_dstfp)
taskhandler.exec_cmd(cmd)
else:
logger.warning(
"Pan or Multi warped image does not exist\n\t{}\n\t{}".format(
pan_local_dstfp, mul_local_dstfp))
#### Make pyramids
if os.path.isfile(pansh_local_dstfp):
cmd = 'gdaladdo -r {} "{}" 2 4 8 16'.format(args.pyramid_type,
pansh_local_dstfp)
taskhandler.exec_cmd(cmd)
## Copy warped multispectral xml to pansharpened output
shutil.copy2(mul_xmlfp, pansh_xmlfp)
#### Copy pansharpened output
if wd != dstdir:
for local_path, dst_path in [(pansh_local_dstfp, pansh_dstfp),
(pan_local_dstfp, pan_dstfp),
(mul_local_dstfp, mul_dstfp)]:
if os.path.isfile(local_path) and not os.path.isfile(dst_path):
shutil.copy2(local_path, dst_path)
#### Delete Temp Files
wd_files = [pansh_local_dstfp, pan_local_dstfp, mul_local_dstfp]
if not args.save_temps:
if wd != dstdir:
for f in wd_files:
try:
os.remove(f)
except Exception as e:
logger.warning('Could not remove %s: %s',
os.path.basename(f), e)
if os.path.isfile(pansh_dstfp):
return 0
else:
return 0
def test_get_bit_depth(self):
self.assertEqual(utils.get_bit_depth("Byte"), "u08")
self.assertEqual(utils.get_bit_depth("UInt16"), "u16")
self.assertEqual(utils.get_bit_depth("Float32"), "f32")
self.assertEqual(utils.get_bit_depth("Uint16"), None) # function logs error, and returns None
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)
#### 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")
if args.tasks_per_job:
if not (args.pbs or args.slurm):
parser.error("--jobs-per-task 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))
#### 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', '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],
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
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)
tm = datetime.now()
job_count = 0
image_count = 0
scenes_in_job_count = 0
task_queue = []
for srcfp in images_to_process:
image_count += 1
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]
))
if args.tasks_per_job:
# bundle tasks into text files in the dst dir and pass the text file in as src
scenes_in_job_count += 1
src_txt = os.path.join(scratch, 'Or_src_{}_{}.txt'.format(tm.strftime("%Y%m%d%H%M%S"), job_count + 1))
if scenes_in_job_count == 1:
# remove text file if dst already exists
try:
os.remove(src_txt)
except OSError:
pass
if scenes_in_job_count <= args.tasks_per_job:
# add to txt file
fh = open(src_txt, 'a')
fh.write("{}\n".format(srcfp))
fh.close()
if scenes_in_job_count == args.tasks_per_job or image_count == len(images_to_process):
scenes_in_job_count = 0
job_count += 1
task = taskhandler.Task(
srcfn,
'Or{:04g}'.format(job_count),
'python',
'{} {} {} {}'.format(scriptpath, arg_str_base, src_txt, dstdir),
ortho_functions.process_image,
[srcfp, dstfp, args]
)
task_queue.append(task)
else:
job_count += 1
task = taskhandler.Task(
srcfn,
'Or{:04g}'.format(job_count),
'python',
'{} {} {} {}'.format(scriptpath, arg_str_base, srcfp, 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)
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")
