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Commit cecbab82 authored by Valentin Genin's avatar Valentin Genin
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Add new schema json for SAR_MultiSlc.py

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json_schemas/schema_MultiSlc.json 0 → 100644
+ 132
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View file @ cecbab82
{
"$schema": "http://json-schema.org/schema#",
"title": "JSON SCHEMA for MultiSlc",
"description": "JSON organization for the script SAR_MultiSlc.py",
"type": "object",
"allOf": [{"required": ["Global", "Pre_Processing", "Metadata_Correction", "DIn_SAR"]}],
"properties":
{
"Global":
{
"type": "object",
"properties":
{
"in":
{
"type": "object",
"required": ["SRTM_Shapefile", "SRTM_Path", "Geoid", "Master_Image", "Start_Date",
"End_Date", "Input_Path"],
"additionalProperties": false,
"properties": {"SRTM_Shapefile": {"type": "string"},
"SRTM_Path": {"type": "string"},
"Geoid": {"type": "string"},
"Master_Image": {"type": "string"},
"Start_Date": {"type": "string"},
"End_Date": {"type": "string"},
"Exclude": {"type": "string", "default": "-9999"},
"Input_Path": {"type": "string"}}
},
"out":
{
"type": "object",
"required": ["Output_Path"],
"additionalProperties": false,
"properties": {"Output_Path": {"type": "string"}}
},
"parameter":
{
"type": "object",
"additionalProperties": false,
"properties": {"clean": {"type": "boolean", "default": true},
"optram": {"type": "number", "default": 4000}}
}
},
"additionalProperties": false,
"required": ["in", "out"]
},
"Pre_Processing":
{
"type": "object",
"properties":
{
"out":
{
"type": "object",
"required": ["doppler_file"],
"additionalProperties": false,
"properties": {"doppler_file": {"type": "string"}}
},
"parameter":
{
"type": "object",
"required": ["ML_gain"],
"additionalProperties": false,
"properties": {"ML_ran": {"type": "number", "default" : 3},
"ML_azi": {"type": "number", "default" : 3},
"ML_gain": {"type": "number"}}
}
},
"additionalProperties": false,
"required": ["out", "parameter"]
},
"Metadata_Correction":
{
"type": "object",
"properties":
{
"out":
{
"type": "object",
"required": ["fine_metadata_file"],
"additionalProperties": false,
"properties": {"fine_metadata_file": {"type": "string"}}
},
"parameter":
{
"type": "object",
"required": ["activate", "GridStep_range", "GridStep_azimut"],
"additionalProperties": false,
"properties": {"activate": {"type": "boolean"},
"GridStep_range": {"type": "number"},
"GridStep_azimut": {"type": "number"}}
}
},
"additionalProperties": false,
"required": ["out", "parameter"]
},
"DIn_SAR":
{
"type": "object",
"properties":
{
"parameter":
{
"type": "object",
"required": ["GridStep_range", "GridStep_azimut", "Grid_Threshold", "Grid_Gap",
"Interferogram_gain"],
"additionalProperties": false,
"properties": {"GridStep_range": {"type": "number"},
"GridStep_azimut": {"type": "number"},
"Grid_Threshold": {"type": "number"},
"Grid_Gap": {"type": "number"},
"Interferogram_gain": {"type": "number"},
"Activate_Interferogram": {"type": "string", "default": "yes"},
"Activate_Ortho": {"type": "string"},
"Spacingxy": {"type": "number", "default": 0.0001},
"roi": {"type": "string"}
}
}
},
"additionalProperties": false,
"required": ["parameter"]
}
}
}
python_src/SAR_MultiSlc.py
+ 65
− 84
View file @ cecbab82
......@@ -66,45 +66,6 @@ if __name__ == "__main__":
parser.add_argument("configfile",
help="""input conguration file for the
application DiapOTB""")
parser.add_argument("-d", "--start_date", dest="start_date",
action="store", help="start date, fmt('20151222')",
default=None)
parser.add_argument("-f", "--end_date", dest="end_date", action="store",
help="end date, fmt('20151223')", default=None)
parser.add_argument("-m", "--master", dest="master", action="store",
help="master image, fmt (.tiff or .h5)", default=None)
parser.add_argument("-e", "--exclude", dest="exclude", nargs="+",
action="store", help=""""excluded date(s) from the time
serie, exemple('20151221 20160114')""", default="-9999")
parser.add_argument("-roi", "--roi", dest="roi", nargs="+", action="store",
help=""""Define the lat lng ROI coordinates,
fmt('ulx uly lrx lry'), ex: -roi 2.44115 48.96126
2.44176 48.95927""", default=None)
parser.add_argument("-i", "--interferogram", dest="interferogram",
action="store", help=""" Simply write ' -i no ' to
deactivate interferogram output. Activated by default.
Returns: Interferogram.tif""", default="yes")
parser.add_argument("-o", "--ortho", dest="ortho",
action="store", help=""" Simply write ' -o yes ' to
activate Orthorectified interferogram output. If activated,
returns: Ortho_Interferogram.tif""", default=None)
parser.add_argument("-l", "--light", dest="light", action="store",
help="""" -l no' to deactivate. If activated, returns a
light version: Interferogram.tif + Coregistrated.tif +
Concatenated (deramped, and multilooked) bursts.tif""",
default="yes")
parser.add_argument("-ram", "--optram", dest="optram",
action="store", help="""Available RAM (mb),
by default value is 4OOO""",
default="4000")
parser.add_argument("-spacingxy", "--spacingxy", dest="spacingxy",
action="store", help="""Set the spatial resolution
for OrthoRectification in degrees,
Default value is 0.0001""",
default="0.0001")
parser.add_argument("-ml", "--multilook", dest="multi", nargs="+", action="store",
help=""""Set the range and azimuth (in this order) you want
for the multilook. Default is 3 3""", default='3' '3')
args = parser.parse_args()
print(args.configfile)
......@@ -112,61 +73,63 @@ if __name__ == "__main__":
func_utils.init_logger()
# ====== Read and Load the configuration file
dataConfig = func_utils.load_configfile(args.configfile)
dataConfig = func_utils.load_configfile(args.configfile, mode="multi_S1")
# ====== Get dictionaries
dict_Global = dataConfig['Global']
dict_PreProcessing = dataConfig['Pre_Processing']
dict_Metadata_Correction = dataConfig['Metadata_Correction']
dict_DInSAR = dataConfig['DIn_SAR']
# ====== Check extension (if .h5 => HDF5 file => Cosmo Sensor)
master_ext = args.master.split(".")[-1:]
master_ext = dict_Global['in']['Master_Image'].split(".")[-1:]
# ====== Get elements from configuration file
# ====== Global
srtm_shapefile = dict_Global['in']['SRTM_Shapefile']
hgts_path = dict_Global['in']['SRTM_Path']
geoid_path = dict_Global['in']['Geoid']
output_dir = dict_Global['out']['Output_Path']
# =================================
# Get elements from users arguments
# =================================
if not os.path.exists(output_dir):
print("The output directory does not exist and will be created")
os.makedirs(output_dir)
else :
print("The output directory exists. Some files can be overwritten")
# ====== Set the variables names
iso_start, iso_end = func_utils.argDates_to_isoDates(args.start_date, args.end_date)
start_time = int(args.start_date)
end_time = int(args.end_date)
master_Image_base = args.master
iso_start, iso_end = func_utils.argDates_to_isoDates(dict_Global['in']['Start_Date'], dict_Global['in']['End_Date'])
start_time = int(dict_Global['in']['Start_Date'])
end_time = int(dict_Global['in']['End_Date'])
master_Image_base = dict_Global['in']['Master_Image']
master_Image = ""
pol = ""
spacingxy = args.spacingxy
exclude = args.exclude
roi = args.roi
light_version = args.light
exclude = "-9999"
if 'Exclude' in dict_Global['in']:
exclude = dict_Global['in']['Exclude']
light_version = dict_Global['parameter']['clean']
relative_orbit = ""
manifest = ""
light_version = True
ram = 4000
if 'parameter' in dict_Global:
if 'optram' in dict_Global['parameter']:
ram = dict_Global['parameter']['ram']
if 'clean' in dict_Global['parameter']:
light_version = dict_Global['parameter']['clean']
if master_ext[0] == "h5" : # Cosmo case
master_Image = func_utils.get_imgFromDir(args.master)
master_Image = func_utils.get_imgFromDir(dict_Global['in']['Master_Image'], dict_Global['in']['Input_Path'])
master_date = master_Image_base.split("_")[8][:8]
pol = master_Image_base.split("_")[5]
else : #S1 SM case
master_Image = func_utils.get_imgFromSAFE(args.master)
master_Image = func_utils.get_imgFromSAFE(dict_Global['in']['Master_Image'], dict_Global['in']['Input_Path'])
master_date = master_Image_base.split("-")[4].split("t")[0]
pol = master_Image_base.split("-")[3]
manifest = master_Image.split("measurement")[0]+"/manifest.safe"
relative_orbit = func_utils.get_relative_orbit(manifest)
version_interferogram = args.interferogram
ortho_interferogram = args.ortho
if roi:
ortho_interferogram = "yes"
print("ortho_interferogram", ortho_interferogram)
ram = args.optram
rng,azi = args.multi
# ====== Get dictionaries
dict_Global = dataConfig['Global']
dict_PreProcessing = dataConfig['Pre_Processing']
dict_Metadata_Correction = dataConfig['Metadata_Correction']
dict_DInSAR = dataConfig['DIn_SAR']
# ====== Get elements from configuration file
# ====== Global
srtm_shapefile = dict_Global['in']['SRTMShapefile']
hgts_path = dict_Global['in']['Datalake']
geoid_path = dict_Global['in']['Geoid']
satellite = "default"
mode = "default"
......@@ -175,6 +138,12 @@ if __name__ == "__main__":
mode = dict_Global['sensor']['mode']
# ====== Pre_Processing
rng = 3
azi = 3
if "ML_ran" in dict_PreProcessing['parameter']:
rng = dict_PreProcessing['parameter'].get('ML_ran')
if "ML_azi" in dict_PreProcessing['parameter']:
azi = dict_PreProcessing['parameter'].get('ML_azi')
ml_range = int(rng)
ml_azimut = int(azi)
ml_gain = dict_PreProcessing['parameter']['ML_gain']
......@@ -192,13 +161,23 @@ if __name__ == "__main__":
fine_metadata_file = dict_Metadata_Correction['out']['fine_metadata_file']
# ====== DIn_SAR
spacingxy = 0.0001
if "Spacingxy" in dict_DInSAR['parameter']:
spacingxy = dict_DInSAR['parameter']['Spacingxy']
roi = None
if 'roi' in dict_DInSAR['parameter']:
roi = dict_DInSAR['parameter']['roi']
version_interferogram = dict_DInSAR['parameter']['Activate_Interferogram']
ortho_interferogram = None
if 'Activate_Ortho' in dict_DInSAR['parameter']:
ortho_interferogram = dict_DInSAR['parameter']['Activate_Ortho']
if roi:
ortho_interferogram = "yes"
print("ortho_interferogram", ortho_interferogram)
geoGrid_gridstep_range = dict_DInSAR['parameter']['GridStep_range']
geoGrid_gridstep_azimut = dict_DInSAR['parameter']['GridStep_azimut']
geoGrid_threshold = dict_DInSAR['parameter']['Grid_Threshold']
if not master_ext[0] == "h5":
geoGrid_gap = dict_DInSAR['parameter']['Grid_Gap_S1']
else:
geoGrid_gap = dict_DInSAR['parameter']['Grid_Gap_Co']
geoGrid_gap = dict_DInSAR['parameter']['Grid_Gap']
ml_geoGrid_range = ml_range
ml_geoGrid_azimut = ml_azimut
gain_interfero = dict_DInSAR['parameter']['Interferogram_gain']
......@@ -213,8 +192,10 @@ if __name__ == "__main__":
func_utils.check_ifExist(master_Image)
# ====== Create global folder with starting and ending dates + master date
output_glob = "./output_{}_to_{}_m_{}".format(start_time, end_time,
master_date)
# output_glob = "./output_{}_to_{}_m_{}".format(start_time, end_time,
# master_date)
output_glob = "{}/output_{}_to_{}_m_{}".format(output_dir, start_time,
end_time, master_date)
if not os.path.exists(output_glob):
os.makedirs(output_glob)
......@@ -258,7 +239,7 @@ if __name__ == "__main__":
# =============================
# ====== Get the list of GTiff corresponding to dates
tiff_list = func_utils.get_AllTiff(pol=pol, ext=master_ext[0])
tiff_list = func_utils.get_AllTiff(pol=pol, ext=master_ext[0], searchDir=dict_Global["in"]["Input_Path"])
tiff_dates = func_utils.get_Tiff_WithDates(start_time, end_time, exclude, tiff_list, master_ext[0])
counter = 0
......@@ -268,9 +249,9 @@ if __name__ == "__main__":
slave_Image_base = i
slave_Image = ""
if not master_ext[0] == "h5" :
slave_Image = func_utils.get_imgFromSAFE(slave_Image_base)
slave_Image = func_utils.get_imgFromSAFE(slave_Image_base, searchDir=dict_Global["in"]["Input_Path"])
else :
slave_Image = func_utils.get_imgFromDir(slave_Image_base)
slave_Image = func_utils.get_imgFromDir(slave_Image_base, searchDir=dict_Global["in"]["Input_Path"])
slave_date = func_utils.get_Date(i, master_ext[0])
counter += 1
output_dir = output_glob + "/{}_m_{}_s".format(master_date, slave_date)
......
python_src/utils/func_utils.py
+ 18
− 13
View file @ cecbab82
......@@ -156,9 +156,12 @@ def load_configfile(configfile, mode="Others"):
schema_json = "schema_S1SM.json"
if mode == "S1_IW":
schema_json = "schema_S1IW.json"
elif mode == "multi_S1":
schema_json = "schema_MultiSlc.json"
# Load schema (into DiapOTB install)
diapOTB_install = os.getenv('DIAPOTB_INSTALL')
print(diapOTB_install)
if diapOTB_install is not None and os.path.exists(diapOTB_install):
schemas_path = os.path.join(diapOTB_install, "json_schemas")
if os.path.exists(schemas_path):
......@@ -221,27 +224,29 @@ def getDEMInformation(dem):
### Functions for image/file selection
def get_imgFromSAFE(arg):
def get_imgFromSAFE(arg, searchDir="."):
"""
Retrive selected image from a SAFE directory
"""
img = []
for root, dirs, files in os.walk("."):
for root, dirs, files in os.walk(searchDir):
for i in (i for i in files if i == arg):
img.append(os.path.join(os.getcwd()+root.split(".")[1] +
".SAFE/measurement/"+(i)))
# img.append(os.path.join(os.getcwd()+root.split(".")[1] +
# ".SAFE/measurement/"+(i)))
img.append(os.path.join(root+"/measurement/", i))
img = str("".join(img))
return img
def get_imgFromDir(arg):
def get_imgFromDir(arg, searchDir="."):
"""
Retrive selected image from a directory (for Cosmo sensor)
"""
img = []
for root, dirs, files in os.walk("."):
for root, dirs, files in os.walk(searchDir):
for i in (i for i in files if i == arg):
img.append(os.path.join(os.getcwd()+root.split(".")[1] +
"/"+(i)))
# img.append(os.path.join(os.getcwd()+root.split(".")[1] +
# "/"+(i)))
img.append(os.path.join(root, i))
img = str("".join(img))
return img
......@@ -286,31 +291,31 @@ def check_srtm_coverage(inSHP_Geometry, SRTM):
needed_srtm_tiles = srtm_tiles
return needed_srtm_tiles
def get_AllTiff(pol, iw="", ext=""):
def get_AllTiff(pol, iw="", ext="", searchDir="."):
"""
Get all tiff from an input directory
"""
TiffList = []
if not iw == "" :
for root, dirs, files in os.walk("."):
for root, dirs, files in os.walk(searchDir):
for i in (i for i in files): # if i != inTIF):
if i.endswith(".tiff") and pol == i.split("-")[3]:
if iw == i.split("-")[1]:
TiffList.append(i)
else :
if ext == "h5":
for root, dirs, files in os.walk("."):
for root, dirs, files in os.walk(searchDir):
for i in (i for i in files): # if i != inTIF):
if i.endswith(".h5") and pol == i.split("_")[5]:
TiffList.append(i)
if not ext == "h5":
for root, dirs, files in os.walk("."):
for root, dirs, files in os.walk(searchDir):
for i in (i for i in files): # if i != inTIF):
if i.endswith(".tiff") and pol == i.split("-")[3]:
TiffList.append(i)
print(TiffList)
return TiffList
def get_AllFilesWithExt(searchDir, ext) :
......
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