def test_args(self):
positional_arg_keys = ['positional']
arg_keys_to_remove = ['toremove', 'to_remove']
arg_str = utils.convert_optional_args_to_string(self.args, positional_arg_keys, arg_keys_to_remove)
self.assertIn('--tuple item1 item2', arg_str)
self.assertIn('--list item1 item2', arg_str)
self.assertIn('--boolean', arg_str)
self.assertIn('--multi-word-key multi-word-key', arg_str)
self.assertNotIn('positional', arg_str)
self.assertNotIn('toremove', arg_str)
self.assertNotIn('to-remove', arg_str)
self.assertNotIn('to_remove', arg_str)
def main():
#### Set Up Arguments
parent_parser = mosaic.buildMosaicParentArgumentParser()
parser = argparse.ArgumentParser(
parents=[parent_parser],
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("--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("--gtiff-compression", choices=mosaic.GTIFF_COMPRESSIONS, default="lzw",
help="GTiff compression type. Default=lzw (%s)"%(",".join(mosaic.GTIFF_COMPRESSIONS)))
parser.add_argument("--pbs", action='store_true', default=False,
help="submit tasks to PBS")
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 cluster job submission (default is <script_dir>/%s)" %default_qsub_script)
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>\%s" %default_logfile)
#### 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)
cutline_builder_script = os.path.join(os.path.dirname(scriptpath),'pgc_mosaic_build_cutlines.py')
tile_builder_script = os.path.join(os.path.dirname(scriptpath),'pgc_mosaic_build_tile.py')
## Verify qsubscript
if args.qsubscript is None:
qsubpath = os.path.join(os.path.dirname(scriptpath),default_qsub_script)
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.parallel_processes > 1:
parser.error("Options --pbs and --parallel-processes > 1 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: %s" %inpath)
if not os.path.isdir(mosaic_dir):
os.makedirs(mosaic_dir)
if not os.path.isfile(qsubpath):
parser.error("Arg3 is not a valid file path: %s" %qsubpath)
#### 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:
logger.error("Target day must be in mm-dd format (i.e 04-05)")
sys.exit(1)
else:
m = 0
d = 0
#### Configure Logger
if args.log is not None:
logfile = os.path.abspath(args.log)
else:
logfile = os.path.join(mosaic_dir,default_logfile)
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)
lsh = logging.StreamHandler()
lsh.setLevel(logging.INFO)
formatter = logging.Formatter('%(asctime)s %(levelname)s- %(message)s','%m-%d-%Y %H:%M:%S')
lsh.setFormatter(formatter)
logger.addHandler(lsh)
#### 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")
f = open(args.exclude, 'r')
exclude_list = set([line.rstrip() for line in f.readlines()])
else:
exclude_list = set()
#### Get Images
#logger.info("Reading input images")
xs = []
ys = []
image_list = utils.find_images_with_exclude_list(inpath, bTextfile, mosaic.EXTS, exclude_list)
if len(image_list) == 0:
logger.error("No images found in input file or directory: %s" %inpath)
sys.exit()
else:
logger.info("%i existing images found" %len(image_list))
#### gather image info list
logger.info("Getting image info")
imginfo_list = [mosaic.ImageInfo(image,"IMAGE") for image in image_list]
#### Get mosaic parameters
logger.info("Setting mosaic parameters")
params = mosaic.getMosaicParameters(imginfo_list[0],args)
#### Remove images that do not match ref
logger.info("Applying attribute filter")
imginfo_list2 = mosaic.filterMatchingImages(imginfo_list,params)
if len(imginfo_list2) == 0:
logger.error("No valid images found. Check input filter parameters.")
sys.exit()
else:
logger.info("%i images match filter" %len(imginfo_list2))
#### if extent is specified, build tile params and compare extent to input image geom
if args.extent:
imginfo_list3 = mosaic.filter_images_by_geometry(imginfo_list2, params)
#### else set extent after image geoms computed
else:
#### Get geom for each image
imginfo_list3 = []
for iinfo in imginfo_list2:
if iinfo.geom is not None:
xs = xs + iinfo.xs
ys = ys + iinfo.ys
imginfo_list3.append(iinfo)
else: # remove from list if no geom
logger.debug("Null geometry for image: %s" %iinfo.srcfn)
params.xmin = min(xs)
params.xmax = max(xs)
params.ymin = min(ys)
params.ymax = max(ys)
poly_wkt = 'POLYGON (( %f %f, %f %f, %f %f, %f %f, %f %f ))' %(params.xmin,params.ymin,params.xmin,params.ymax,params.xmax,params.ymax,params.xmax,params.ymin,params.xmin,params.ymin)
params.extent_geom = ogr.CreateGeometryFromWkt(poly_wkt)
#### Check number of remaining images
num_images = len(imginfo_list3)
if num_images > 0:
logger.info("%d of %d input images intersect mosaic extent" %(num_images,len(image_list)))
logger.info("Mosaic parameters: resolution %f x %f, tilesize %f x %f, extent %f %f %f %f" %(params.xres,params.yres,params.xtilesize,params.ytilesize,params.xmin,params.xmax,params.ymin,params.ymax))
else:
logger.error("No valid images found")
sys.exit(0)
## Sort images by score
logger.info("Reading image metadata and determining sort order")
for iinfo in imginfo_list3:
iinfo.getScore(params)
#### Sort by score
if not args.nosort:
imginfo_list3.sort(key=lambda x: x.score)
#### Write all intersects file
intersects_all = []
for iinfo in imginfo_list3:
if params.extent_geom.Intersect(iinfo.geom) is True:
if iinfo.score > 0:
intersects_all.append(iinfo)
elif args.nosort:
intersects_all.append(iinfo)
else:
logger.debug("Image has an invalid score: %s --> %i" %(iinfo.srcfp, iinfo.score))
else:
logger.debug("Image does not intersect mosaic extent: %s" %iinfo.srcfp) ### this line should never be needed. non-intersecting images should be removed earlier if extent is provided, otherwise all images are in the extent.
aitpath = mosaicname+"_intersects.txt"
ait = open(aitpath,"w")
intersects_fps = [intersect.srcfp for intersect in intersects_all]
ait.write(string.join(intersects_fps,"\n"))
ait.close()
## Create tiles
logger.info("Creating tiles")
tiles = []
xtiledim = math.ceil((params.xmax-params.xmin)/params.xtilesize)
ytiledim = math.ceil((params.ymax-params.ymin)/params.ytilesize)
logger.info("Tiles: %d rows, %d columns" %(ytiledim,xtiledim))
xtdb = len(str(int(xtiledim)))
ytdb = len(str(int(ytiledim)))
i = 1
for x in mosaic.drange(params.xmin,params.xmax,params.xtilesize): # Columns
if x+params.xtilesize > params.xmax:
x2 = params.xmax
else:
x2 = x+params.xtilesize
j = 1
for y in mosaic.drange(params.ymin,params.ymax,params.ytilesize): # Rows
if y+params.ytilesize > params.ymax:
y2 = params.ymax
else:
y2 = y+params.ytilesize
tilename = "%s_%s_%s.tif" %(mosaicname,mosaic.buffernum(j,ytdb),mosaic.buffernum(i,xtdb))
tile = mosaic.TileParams(x,x2,y,y2,j,i,tilename)
tiles.append(tile)
j += 1
i += 1
num_tiles = len(tiles)
#### Write shapefile of tiles
if args.mode == "ALL" or args.mode == "SHP":
shp = mosaicname + "_tiles.shp"
if os.path.isfile(shp):
logger.info("Tiles shapefile already exists: %s" %os.path.basename(shp))
else:
logger.info("Creating shapefile of tiles: %s" %os.path.basename(shp))
fields = [('ROW', ogr.OFTInteger, 4),
('COL', ogr.OFTInteger, 4),
("TILENAME", ogr.OFTString, 100),
('TILEPATH', ogr.OFTString, 254),
('XMIN', ogr.OFTReal, 0),
('XMAX', ogr.OFTReal, 0),
('YMIN', ogr.OFTReal, 0),
('YMAX', ogr.OFTReal, 0)]
OGR_DRIVER = "ESRI Shapefile"
ogrDriver = ogr.GetDriverByName(OGR_DRIVER)
if ogrDriver is None:
logger.error("OGR: Driver %s is not available" % OGR_DRIVER)
sys.exit(-1)
if os.path.isfile(shp):
ogrDriver.DeleteDataSource(shp)
vds = ogrDriver.CreateDataSource(shp)
if vds is None:
logger.error("Could not create shp")
sys.exit(-1)
shpd, shpn = os.path.split(shp)
shpbn, shpe = os.path.splitext(shpn)
rp = osr.SpatialReference()
rp.ImportFromWkt(params.proj)
lyr = vds.CreateLayer(shpbn, rp, ogr.wkbPolygon)
if lyr is None:
logger.error("ERROR: Failed to create layer: %s" % shpbn)
sys.exit(-1)
for fld, fdef, flen in fields:
field_defn = ogr.FieldDefn(fld, fdef)
if fdef == ogr.OFTString:
field_defn.SetWidth(flen)
if lyr.CreateField(field_defn) != 0:
logger.error("ERROR: Failed to create field: %s" % fld)
for t in tiles:
feat = ogr.Feature(lyr.GetLayerDefn())
feat.SetField("TILENAME",os.path.basename(t.name))
feat.SetField("TILEPATH",t.name)
feat.SetField("ROW",t.j)
feat.SetField("COL",t.i)
feat.SetField("XMIN",t.xmin)
feat.SetField("XMAX",t.xmax)
feat.SetField("YMIN",t.ymin)
feat.SetField("YMAX",t.ymax)
feat.SetGeometry(t.geom)
if lyr.CreateFeature(feat) != 0:
logger.error("ERROR: Could not create feature for tile %s" % tile)
feat.Destroy()
## Build tasks
task_queue = []
#### Create task for shapefile of mosaic components
if args.component_shp is True:
arg_keys_to_remove = (
'l',
'qsubscript',
'parallel_processes',
'log',
'gtiff_compression',
'mode',
'extent',
'resolution',
'pbs',
'wd'
)
shp_arg_str = utils.convert_optional_args_to_string(args, pos_arg_keys, arg_keys_to_remove)
comp_shp = mosaicname + "_components.shp"
if os.path.isfile(comp_shp):
logger.info("Components shapefile already exists: %s" %os.path.basename(comp_shp))
else:
logger.info("Processing components: %s" %os.path.basename(comp_shp))
## Make task and add to queue
cmd = '{} --cutline-step 512 {} -e {} {} {} {} {} {}'.format(
cutline_builder_script,
shp_arg_str,
params.xmin,
params.xmax,
params.ymin,
params.ymax,
comp_shp,
aitpath
)
task = utils.Task(
'Components',
'Components',
'python',
cmd
)
if args.mode == "ALL" or args.mode == "SHP":
logger.debug(cmd)
task_queue.append(task)
#### Create task for shapefile of image cutlines
shp = mosaicname + "_cutlines.shp"
arg_keys_to_remove = (
'l',
'qsubscript',
'parallel_processes',
'log',
'gtiff_compression',
'mode',
'extent',
'resolution',
'component_shp',
'pbs',
'wd'
)
shp_arg_str = utils.convert_optional_args_to_string(args, pos_arg_keys, arg_keys_to_remove)
if os.path.isfile(shp):
logger.info("Cutlines shapefile already exists: %s" %os.path.basename(shp))
else:
logger.info("Processing cutlines: %s" %os.path.basename(shp))
## Make task and add to queue
cmd = '{} {} -e {} {} {} {} {} {}'.format(
cutline_builder_script,
shp_arg_str,
params.xmin,
params.xmax,
params.ymin,
params.ymax,
shp,
aitpath
)
task = utils.Task(
'Cutlines',
'Cutlines',
'python',
cmd
)
if args.mode == "ALL" or args.mode == "SHP":
logger.debug(cmd)
task_queue.append(task)
#### Create task for each tile
arg_keys_to_remove = (
'l',
'qsubscript',
'parallel_processes',
'log',
'mode',
'extent',
'resolution',
'bands',
'component_shp',
'pbs'
)
tile_arg_str = utils.convert_optional_args_to_string(args, pos_arg_keys, arg_keys_to_remove)
logger.debug("Identifying components of {0} subtiles".format(num_tiles))
i = 0
for t in tiles:
logger.debug("Identifying components of tile %d of %d: %s" %(i,num_tiles,os.path.basename(t.name)))
#### determine which images in each tile - create geom and query image geoms
logger.debug("Running intersect with imagery")
intersects = []
for iinfo in intersects_all:
if t.geom.Intersect(iinfo.geom) is True:
if iinfo.score > 0:
logger.debug("intersects tile: %s - score %f" %(iinfo.srcfn,iinfo.score))
intersects.append(iinfo.srcfp)
elif args.nosort:
logger.debug("intersects tile: %s - score %f" %(iinfo.srcfn,iinfo.score))
intersects.append(iinfo.srcfp)
else:
logger.warning("Invalid score: %s --> %i" %(iinfo.srcfp, iinfo.score))
#### If any images are in the tile, mosaic them
if len(intersects) > 0:
tile_basename = os.path.basename(os.path.splitext(t.name)[0])
itpath = os.path.join(mosaic_dir,tile_basename+"_intersects.txt")
it = open(itpath,"w")
it.write(string.join(intersects,"\n"))
it.close()
#### Submit QSUB job
logger.debug("Building mosaicking job for tile: %s" %os.path.basename(t.name))
if not os.path.isfile(t.name):
cmd = r'{} {} -e {} {} {} {} -r {} {} -b {} {} {}'.format(
tile_builder_script,
tile_arg_str,
t.xmin,
t.xmax,
t.ymin,
t.ymax,
params.xres,
params.yres,
params.bands,
t.name,
itpath
)
task = utils.Task(
'Tile {0}'.format(os.path.basename(t.name)),
'Mosaic{:04g}'.format(i),
'python',
cmd
)
if args.mode == "ALL" or args.mode == "MOSAIC":
logger.debug(cmd)
task_queue.append(task)
else:
logger.info("Tile already exists: %s" %os.path.basename(t.name))
i += 1
logger.info("Submitting Tasks")
#logger.info(task_queue)
if len(task_queue) > 0:
if args.pbs:
if args.l:
task_handler = utils.PBSTaskHandler(qsubpath, "-l {}".format(args.l))
else:
task_handler = utils.PBSTaskHandler(qsubpath)
task_handler.run_tasks(task_queue)
else:
task_handler = utils.ParallelTaskHandler(args.parallel_processes)
if task_handler.num_processes > 1:
logger.info("Number of child processes to spawn: {0}".format(task_handler.num_processes))
task_handler.run_tasks(task_queue)
logger.info("Done")
else:
logger.info("No tasks to process")
#### Test if DEM exists
if args.dem:
if not os.path.isfile(args.dem):
parser.error("DEM does not exist: %s" %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', 'parallel_processes')
arg_str_base = utils.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:
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("--parallel-processes", type=int, default=1,
help="number of parallel processes to spawn (default 1)")
parser.add_argument("-l", help="PBS resources requested (mimicks qsub syntax)")
parser.add_argument("--qsubscript",
help="qsub script to use in cluster job submission (default is qsub_ndvi.sh in script root folder)")
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: %s" %(src))
if not os.path.isdir(dstdir):
parser.error("Error arg2 is not a valid file path: %s" %(dstdir))
## Verify qsubscript
if args.qsubscript is None:
qsubpath = os.path.join(os.path.dirname(scriptpath),'qsub_ndvi.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.parallel_processes > 1:
parser.error("Options --pbs 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', 'parallel_processes', 'dryrun')
arg_str = utils.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 = utils.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: {}'.format(i))
## Run tasks
if len(task_queue) > 0:
logger.info("Submitting Tasks")
if args.pbs:
if args.l:
task_handler = utils.PBSTaskHandler(qsubpath, "-l {}".format(args.l))
else:
task_handler = utils.PBSTaskHandler(qsubpath)
if not args.dryrun:
task_handler.run_tasks(task_queue)
elif args.parallel_processes > 1:
task_handler = utils.ParallelTaskHandler(args.parallel_processes)
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:
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)
#### Print Images with Errors
for k,v in results.iteritems():
if v != 0:
logger.warning("Failed Image: {}".format(k))
logger.info("Done")
else:
logger.info("No images found to process")
