def save_image(self,input_template,outname,size):
im = Image()
im.load(input_template + '.xml')
latstart = size['lat']['val']
lonstart = size['lon']['val']
latsize = size['lat']['size']
lonsize = size['lon']['size']
latdelta = size['lat']['delta']
londelta = size['lon']['delta']
im.filename = outname
im.coord2.coordStart = latstart
im.coord2.coordSize = latsize
im.coord2.coordDelta = latdelta
im.coord2.coordEnd = latstart + latsize*latdelta
im.coord1.coordStart = lonstart
im.coord1.coordSize = lonsize
im.coord1.coordDelta = londelta
im.coord1.coordEnd = lonstart + lonsize*londelta
im.renderHdr()
def get_image(fname):
im = Image()
im.load(fname)
return im
def main():
"""HySDS PGE wrapper for TopsInSAR interferogram generation."""
# save cwd (working directory)
cwd = os.getcwd()
# get context
ctx_file = os.path.abspath('_context.json')
if not os.path.exists(ctx_file):
raise RuntimeError("Failed to find _context.json.")
with open(ctx_file) as f:
ctx = json.load(f)
logger.info("ctx: {}".format(json.dumps(ctx, indent=2)))
master_safe_dirs = []
for i in ctx['master_zip_file']:
master_safe_dirs.append(i.replace(".zip", ".SAFE"))
slave_safe_dirs = []
for i in ctx['slave_zip_file']:
slave_safe_dirs.append(i.replace(".zip", ".SAFE"))
# unzip SAFE dirs
master_safe_dirs = []
for i in ctx['master_zip_file']:
logger.info("Unzipping {}.".format(i))
with ZipFile(i, 'r') as zf:
zf.extractall()
logger.info("Removing {}.".format(i))
try:
os.unlink(i)
except:
pass
master_safe_dirs.append(i.replace(".zip", ".SAFE"))
slave_safe_dirs = []
for i in ctx['slave_zip_file']:
logger.info("Unzipping {}.".format(i))
with ZipFile(i, 'r') as zf:
zf.extractall()
logger.info("Removing {}.".format(i))
try:
os.unlink(i)
except:
pass
slave_safe_dirs.append(i.replace(".zip", ".SAFE"))
#bbox only needed to create dem and not if dem provided
if 'dem_urls' not in ctx:
# get union bbox
logger.info("Determining envelope bbox from SLC swaths.")
bbox_json = "bbox.json"
bbox_cmd_tmpl = "{}/get_union_bbox.sh -o {} *.SAFE/annotation/s1?-iw{}-slc-{}-*.xml"
check_call(bbox_cmd_tmpl.format(BASE_PATH, bbox_json, ctx['swathnum'],
"hh"),
shell=True)
with open(bbox_json) as f:
bbox = json.load(f)['envelope']
logger.info("bbox: {}".format(bbox))
# get id base
id_base = ctx['id']
logger.info("Product base ID: {}".format(id_base))
# get dataset version and set dataset ID
version = get_version()
id = "{}-{}-{}".format(
id_base, version,
re.sub("[^a-zA-Z0-9_]", "_",
ctx.get("context", {}).get("dataset_tag", "standard")))
# get endpoint configurations
uu = UrlUtils()
es_url = uu.rest_url
es_index = "{}_{}_s1-ifg".format(uu.grq_index_prefix, version)
# check if interferogram already exists
logger.info("GRQ url: {}".format(es_url))
logger.info("GRQ index: {}".format(es_index))
logger.info("Product ID for version {}: {}".format(version, id))
#TAGREMOVE
#this part needs to be adapted for offest products, probably just need to add
#the dataset_tag to _context.json
if ifg_exists(es_url, es_index, id):
logger.info("{} interferogram for {}".format(version, id_base) +
" was previously generated and exists in GRQ database.")
# cleanup SAFE dirs
for i in chain(master_safe_dirs, slave_safe_dirs):
logger.info("Removing {}.".format(i))
try:
shutil.rmtree(i)
except:
pass
return 0
# get DEM configuration
dem_type = ctx.get("context", {}).get("dem_type", "SRTM+v3")
srtm_dem_url = uu.dem_url
ned1_dem_url = uu.ned1_dem_url
ned13_dem_url = uu.ned13_dem_url
dem_user = uu.dem_u
dem_pass = uu.dem_p
# download project specific DEM
if 'dem_urls' in ctx:
s = requests.session()
#assume that the first is the data and the second the metadata
download_file(ctx['dem_urls'][0], session=s)
download_file(ctx['dem_urls'][1], session=s)
dem_file = os.path.basename(ctx['dem_urls'][0])
else:
# get DEM bbox
dem_S, dem_N, dem_W, dem_E = bbox
dem_S = int(math.floor(dem_S))
dem_N = int(math.ceil(dem_N))
dem_W = int(math.floor(dem_W))
dem_E = int(math.ceil(dem_E))
if dem_type == "SRTM+v3":
dem_url = srtm_dem_url
dem_cmd = [
"{}/applications/dem.py".format(os.environ['ISCE_HOME']), "-a",
"stitch", "-b", "{} {} {} {}".format(dem_S, dem_N, dem_W,
dem_E), "-r", "-s", "1",
"-f", "-x", "-c", "-n", dem_user, "-w", dem_pass, "-u", dem_url
]
dem_cmd_line = " ".join(dem_cmd)
logger.info("Calling dem.py: {}".format(dem_cmd_line))
check_call(dem_cmd_line, shell=True)
dem_file = glob("*.dem.wgs84")[0]
else:
if dem_type == "NED1": dem_url = ned1_dem_url
elif dem_type.startswith("NED13"): dem_url = ned13_dem_url
else: raise RuntimeError("Unknown dem type %s." % dem_type)
if dem_type == "NED13-downsampled": downsample_option = "-d 33%"
else: downsample_option = ""
dem_cmd = [
"{}/ned_dem.py".format(BASE_PATH), "-a", "stitch", "-b",
"{} {} {} {}".format(dem_S, dem_N, dem_W, dem_E),
downsample_option, "-u", dem_user, "-p", dem_pass, dem_url
]
dem_cmd_line = " ".join(dem_cmd)
logger.info("Calling ned_dem.py: {}".format(dem_cmd_line))
check_call(dem_cmd_line, shell=True)
dem_file = "stitched.dem"
logger.info("Using DEM file: {}".format(dem_file))
# fix file path in DEM xml
fix_cmd = [
"{}/applications/fixImageXml.py".format(os.environ['ISCE_HOME']), "-i",
dem_file, "--full"
]
fix_cmd_line = " ".join(fix_cmd)
logger.info("Calling fixImageXml.py: {}".format(fix_cmd_line))
check_call(fix_cmd_line, shell=True)
# download auciliary calibration files
aux_cmd = [
#"{}/fetchCal.py".format(BASE_PATH), "-o", "aux_cal"
"{}/fetchCalES.py".format(BASE_PATH),
"-o",
"aux_cal"
]
aux_cmd_line = " ".join(aux_cmd)
#logger.info("Calling fetchCal.py: {}".format(aux_cmd_line))
logger.info("Calling fetchCalES.py: {}".format(aux_cmd_line))
check_call(aux_cmd_line, shell=True)
# create initial input xml
xml_file = "topsApp.xml"
create_input_xml_offset(
os.path.join(BASE_PATH, 'topsApp_offset.xml.tmpl'), xml_file,
str(master_safe_dirs), str(slave_safe_dirs), ctx['master_orbit_file'],
ctx['slave_orbit_file'], dem_file, ctx['swathnum'],
ctx['ampcor_skip_width'], ctx['ampcor_skip_height'],
ctx['ampcor_src_win_width'], ctx['ampcor_src_win_height'],
ctx['ampcor_src_width'], ctx['ampcor_src_height'])
# run topsApp for offset
topsapp_cmd = ["topsApp.py", "--steps"]
topsapp_cmd_line = " ".join(topsapp_cmd)
logger.info("Calling topsApp.py for offest: {}".format(topsapp_cmd_line))
check_call(topsapp_cmd_line, shell=True)
# create product directory
prod_dir = id
os.makedirs(prod_dir, 0o755)
# create merged directory in product
prod_merged_dir = os.path.join(prod_dir, 'merged')
os.makedirs(prod_merged_dir, 0o755)
# generate GDAL (ENVI) headers and move to product directory
raster_prods = ('merged/dense_offsets.bil', 'merged/dense_offsets_snr.bil',
'merged/filt_dense_offsets.bil', 'merged/los.rdr')
for i in raster_prods:
# radar-coded products
call_noerr("isce2gis.py envi -i {}".format(i))
#call_noerr("gdal_translate {} {}.tif".format(i, i))
gdal_xml = "{}.xml".format(i)
gdal_hdr = "{}.hdr".format(i)
#gdal_tif = "{}.tif".format(i)
gdal_vrt = "{}.vrt".format(i)
if os.path.exists(i): shutil.move(i, prod_merged_dir)
else: logger.warn("{} wasn't generated.".format(i))
if os.path.exists(gdal_xml): shutil.move(gdal_xml, prod_merged_dir)
else: logger.warn("{} wasn't generated.".format(gdal_xml))
if os.path.exists(gdal_hdr): shutil.move(gdal_hdr, prod_merged_dir)
else: logger.warn("{} wasn't generated.".format(gdal_hdr))
#if os.path.exists(gdal_tif): shutil.move(gdal_tif, prod_merged_dir)
#else: logger.warn("{} wasn't generated.".format(gdal_tif))
if os.path.exists(gdal_vrt): shutil.move(gdal_vrt, prod_merged_dir)
else: logger.warn("{} wasn't generated.".format(gdal_vrt))
# geo-coded products
j = "{}.geo".format(i)
if not os.path.exists(j): continue
call_noerr("isce2gis.py envi -i {}".format(j))
#call_noerr("gdal_translate {} {}.tif".format(j, j))
gdal_xml = "{}.xml".format(j)
gdal_hdr = "{}.hdr".format(j)
#gdal_tif = "{}.tif".format(j)
gdal_vrt = "{}.vrt".format(j)
if os.path.exists(j): shutil.move(j, prod_merged_dir)
else: logger.warn("{} wasn't generated.".format(j))
if os.path.exists(gdal_xml): shutil.move(gdal_xml, prod_merged_dir)
else: logger.warn("{} wasn't generated.".format(gdal_xml))
if os.path.exists(gdal_hdr): shutil.move(gdal_hdr, prod_merged_dir)
else: logger.warn("{} wasn't generated.".format(gdal_hdr))
#if os.path.exists(gdal_tif): shutil.move(gdal_tif, prod_merged_dir)
#else: logger.warn("{} wasn't generated.".format(gdal_tif))
if os.path.exists(gdal_vrt): shutil.move(gdal_vrt, prod_merged_dir)
else: logger.warn("{} wasn't generated.".format(gdal_vrt))
# save other files to product directory
shutil.copyfile("_context.json",
os.path.join(prod_dir, "{}.context.json".format(id)))
shutil.copyfile("topsApp.xml", os.path.join(prod_dir, "topsApp.xml"))
shutil.copyfile("fine_interferogram/IW{}.xml".format(ctx['swathnum']),
os.path.join(prod_dir, "fine_interferogram.xml"))
shutil.copyfile("master/IW{}.xml".format(ctx['swathnum']),
os.path.join(prod_dir, "master.xml"))
shutil.copyfile("slave/IW{}.xml".format(ctx['swathnum']),
os.path.join(prod_dir, "slave.xml"))
if os.path.exists('topsProc.xml'):
shutil.copyfile("topsProc.xml", os.path.join(prod_dir, "topsProc.xml"))
if os.path.exists('isce.log'):
shutil.copyfile("isce.log", os.path.join(prod_dir, "isce.log"))
# move PICKLE to product directory
shutil.move('PICKLE', prod_dir)
# create browse images
os.chdir(prod_merged_dir)
mdx_path = "{}/bin/mdx".format(os.environ['ISCE_HOME'])
from utils.createImage import createImage
from isceobj.Image.Image import Image
offset_file = "dense_offsets.bil.geo"
snr_file = "dense_offsets_snr.bil.geo"
im = Image()
im.load(offset_file + '.xml')
mdx_args = '-s %d -r4 -rtlr %d -cmap cmy -wrap 10' % (im.width,
4 * im.width)
#unwrapped image at different rates
createImage("{} -P {} {}".format(mdx_path, offset_file, mdx_args),
'dense_offsets_az.bil.geo')
mdx_args = '-s %d -r4 -rhdr %d -cmap cmy -wrap 10' % (im.width,
4 * im.width)
#unwrapped image at different rates
createImage("{} -P {} {}".format(mdx_path, offset_file, mdx_args),
'dense_offsets_rn.bil.geo')
mdx_args = '-s %d -r4 -clpmin 0 -clpmax 10 -cmap cmy -wrap 12' % (
im.width, )
#unwrapped image at different rates
createImage("{} -P {} {}".format(mdx_path, snr_file, mdx_args), snr_file)
# move all browse images to root of product directory
call_noerr("mv -f *.png ..")
# chdir back up to work directory
os.chdir(cwd)
# extract metadata from master
met_file = os.path.join(prod_dir, "{}.met.json".format(id))
extract_cmd_path = os.path.abspath(
os.path.join(BASE_PATH, '..', '..', 'frameMetadata', 'sentinel'))
#TAGREMOVE
#return
extract_cmd_tmpl = "{}/extractMetadata_s1.sh -i {}/annotation/s1?-iw{}-slc-{}-*.xml -o {}"
check_call(extract_cmd_tmpl.format(extract_cmd_path, master_safe_dirs[0],
ctx['swathnum'], "hh", met_file),
shell=True)
# add master/slave ids and orbits to met JSON (per ASF request)
master_ids = [i.replace(".zip", "") for i in ctx['master_zip_file']]
slave_ids = [i.replace(".zip", "") for i in ctx['slave_zip_file']]
master_rt = parse(os.path.join(prod_dir, "master.xml"))
master_orbit_number = eval(
master_rt.xpath('.//property[@name="orbitnumber"]/value/text()')[0])
slave_rt = parse(os.path.join(prod_dir, "slave.xml"))
slave_orbit_number = eval(
slave_rt.xpath('.//property[@name="orbitnumber"]/value/text()')[0])
with open(met_file) as f:
md = json.load(f)
md['master_scenes'] = master_ids
md['slave_scenes'] = slave_ids
md['orbitNumber'] = [master_orbit_number, slave_orbit_number]
md['dataset_type'] = 'offset'
#fix to make platform metadata consistent
if 'platform' in md:
if md['platform'] == 'S1A':
md['platform'] = 'Sentinel-1A'
if md['platform'] == 'S1B':
md['platform'] = 'Sentinel-1B'
if 'orbit' in md: del md['orbit'] #FIX FOR INVALID ORBIT METADATA
if ctx.get('stitch_subswaths_xt', False): md['swath'] = [1, 2, 3]
#md['esd_threshold'] = esd_coh_th if do_esd else -1. # add ESD coherence threshold
# add range_looks and azimuth_looks to metadata for stitching purposes
md['azimuth_looks'] = int(ctx['azimuth_looks'])
md['range_looks'] = int(ctx['range_looks'])
# add dem_type
md['dem_type'] = dem_type
# write met json
with open(met_file, 'w') as f:
json.dump(md, f, indent=2)
# generate dataset JSON
ds_file = os.path.join(prod_dir, "{}.dataset.json".format(id))
create_dataset_json(id, version, met_file, ds_file)
# move merged products to root of product directory
#call_noerr("mv -f {}/* {}".format(prod_merged_dir, prod_dir))
#shutil.rmtree(prod_merged_dir)
# write PROV-ES JSON
#${BASE_PATH}/create_prov_es-create_interferogram.sh $id $project $master_orbit_file $slave_orbit_file \
# ${dem_file}.xml $dem_file $WORK_DIR \
# ${id}/${id}.prov_es.json > create_prov_es.log 2>&1
# clean out SAFE directories and DEM files
for i in chain(master_safe_dirs, slave_safe_dirs):
shutil.rmtree(i)
for i in glob("dem*"):
os.unlink(i)
import matplotlib.pyplot as plt
# import xml.etree.ElementTree as ET
def getImageSize(infile):
ds = gdal.Open(infile + ".vrt")
b = ds.GetRasterBand(1)
return b.XSize, b.YSize
if __name__ == '__main__':
listFile = "/media/jiechencyz/Experiments_1/P120_Lena_stackProcess/merged/interferograms/unw_list"
with open(listFile, 'r') as fileHandle:
try:
for fileName in fileHandle:
fileName = fileName.rstrip()
imageWidth, imageLength = getImageSize(fileName)
unw = ts.load_mmap(fileName, imageWidth, imageLength, quiet=True, map='BIL',
nchannels=2, channel=2, conv=False)
# print(unw[1000:1004, 1000:1005])
# print(getImageSize(fileName))
finally:
fileHandle.close()
obj = Image()
obj.load(fileName + ".xml")
obj.setAccessMode('read')
obj.createImage()
imageOut = obj.memMap('r', 1)
plt.imshow(imageOut, cmap='jet', vmin=-60, vmax=-30)
plt.colorbar()
plt.show()
