replace xml.etree with defusedxml for ElementTree

docs/README.md

@@ -82,7 +82,7 @@ ts_data, meta = readfile.read('timeseries_ERA5_ramp_demErr.h5')
 
 ### 3. [Documentation](https://mintpy.readthedocs.io/) ###
 
-Detailed algorithms implemented in the software are described in [Yunjun et al. (2019)](https://doi.org/10.1016/j.cageo.2019.104331).
+Algorithms implemented in the software are described in details in [Yunjun et al. (2019)](https://doi.org/10.1016/j.cageo.2019.104331).
 
 + [Tutorials in Jupyter Notebook](https://github.com/insarlab/MintPy-tutorial)
 + [Example datasets](./demo_dataset.md)

docs/conda.txt

@@ -4,6 +4,7 @@ cdsapi
 cvxopt
 dask>=1.0
 dask-jobqueue>=0.3
+defusedxml
 ecCodes
 h5py
 lxml

docs/conda_env.yml

@@ -14,6 +14,7 @@ dependencies:
   - cvxopt
   - dask>=1.0
   - dask-jobqueue>=0.3
+  - defusedxml
   - ecCodes
   - h5py
   - lxml

docs/ports.txt

@@ -70,6 +70,7 @@ swig
 swig-python
 gdal +expat +geos +hdf5 +netcdf +openjpeg +postgresql95 +sqlite3
 py37-cython
+py37-defusedxml
 py37-mpi4py +gcc7 +openmpi
 py37-numpy +gcc7 +openblas
 py37-scipy +gcc7 +openblas

docs/requirements.txt

@@ -1,6 +1,7 @@
 cvxopt
 dask>=1.0
 dask-jobqueue>=0.3
+defusedxml
 h5py
 lxml
 matplotlib

mintpy/dem_gsi.py

@@ -126,7 +126,7 @@ def write_dem_file(SNWE, dem_file, grid_dir):
     return meta
 
 
-def write_rsc_file(meta, out_file):
+def write_rsc_file(meta, fname):
     # initiate meta dict
     rsc = dict()
     rsc['FILE_LENGTH'] = meta.length
@@ -148,12 +148,15 @@ def write_rsc_file(meta, out_file):
     rsc['PROJECTION'] = 'LATLON'
     rsc['DATE12'] = '111111-222222'
     rsc['DATA_TYPE'] = 'int16'
+
     # write rsc file
-    writefile.write_roipac_rsc(rsc, out_file, print_msg=True)
-    return out_file
+    rsc_file = fname + '.rsc'
+    writefile.write_roipac_rsc(rsc, rsc_file, print_msg=True)
+
+    return rsc_file
 
 
-def write_vrt_file(meta, out_file):
+def write_vrt_file(meta, fname):
     # initiate vrt string
     vrt_str = """<VRTDataset rasterXSize="{w}" rasterYSize="{l}">
     <SRS>EPSG:4326</SRS>
@@ -176,40 +179,74 @@ def write_vrt_file(meta, out_file):
            lo=2*meta.width)
 
     # write to vrt file
-    with open(out_file, 'w') as f:
+    vrt_file = fname + '.vrt'
+    with open(vrt_file, 'w') as f:
         f.write(vrt_str)
-    print('write {}'.format(out_file))
-    return out_file
+    print('write {}'.format(vrt_file))
+
+    return vrt_file
+
+
+def write_isce_metadata(meta, fname):
+    """
+    Write metadata files in ISCE format (.vrt and .xml files)
+    """
+    import isce
+    import isceobj
+
+    # create isce object for xml file
+    img = isceobj.createDemImage()
+    img.setFilename(os.path.abspath(fname))
+    img.setWidth(meta.width)
+    img.setLength(meta.length)
+    img.setAccessMode('READ')
+    img.bands = 1
+    img.dataType = 'SHORT'
+    img.scheme = 'BIP'
+    img.reference = 'WGS84'
+
+    img.firstLatitude  = meta.north + meta.lat_step / 2.
+    img.firstLongitude = meta.west + meta.lon_step / 2.
+    img.deltaLatitude  = meta.lat_step
+    img.deltaLongitude = meta.lon_step
+
+    # write to xml file
+    xml_file = fname + '.xml'
+    img.dump(xml_file)
+
+    return xml_file
 
 
 def add_reference_datum(xml_file):
+    """
+    Example of modifying an existing XML file
+    """
+
     import xml.etree.ElementTree as ET
     from xml.dom import minidom
     print('add <reference> info to xml file: {}'.format(os.path.basename(xml_file)))
-    tree = ET.parse(xml_file)
-    root = tree.getroot()
 
     # get property element for reference
-    ref = ET.Element("property")
-    ref.attrib = {'name': 'reference'}
+    ref = ET.Element("property", attrib={'name': 'reference'})
 
-    elm1 = ET.Element("value")
-    elm1.text = "WGS84"
-    ref.append(elm1)
+    val = ET.SubElement(ref, "value")
+    val.text = "WGS84"
 
-    elm1 = ET.Element("doc")
-    elm1.text = "Geodetic datum"
-    ref.append(elm1)
-
-    ref = ET.fromstring(minidom.parseString(ET.tostring(ref)).toprettyxml(indent="    "))
+    doc = ET.SubElement(ref, "doc")
+    doc.text = "Geodetic datum"
+
+    # pretty xml
+    ref_str = minidom.parseString(ET.tostring(ref)).toprettyxml(indent="    ")
+    ref = ET.fromstring(ref_str)
 
     # write back to xml file
+    tree = ET.parse(xml_file)
+    root = tree.getroot()
     root.append(ref)
     tree.write(xml_file)
     return xml_file
 
 
-
 ##################################################################################################
 def main(iargs=None):
     inps = cmd_line_parse(iargs)
@@ -219,24 +256,11 @@ def main(iargs=None):
                           grid_dir=inps.grid_dir)
 
     # rsc file for roipac
-    write_rsc_file(meta, out_file='{}.rsc'.format(inps.outfile))
-
-    # vrt file for gdal
-    write_vrt_file(meta, out_file='{}.vrt'.format(inps.outfile))
-
-    # vrt file to xml file
-    try:
-        print('generate {}.xml file using ISCE command'.format(inps.outfile))
-        cmd = 'gdal2isce_xml.py -i {}.vrt'.format(inps.outfile)
-        print(cmd)
-        os.system(cmd)
+    write_rsc_file(meta, inps.outfile)
 
-    except RuntimeError:
-        raise RuntimeError('$ISCE_HOME/applications/gdal2isce_xml.py command not found!')
+    # vrt/xml file for isce
+    write_isce_metadata(meta, inps.outfile)
 
-    # DEHM from GSI is already in ellipsoid, add the information to xml file
-    if os.path.isfile(inps.outfile+'.xml'):
-        add_reference_datum(inps.outfile+'.xml')
     return
 
 

mintpy/utils/readfile.py

@@ -10,7 +10,7 @@
 import os
 import re
 import warnings
-import xml.etree.ElementTree as ET
+import defusedxml.ElementTree as ET
 
 import h5py
 import json
@@ -960,12 +960,11 @@ def read_isce_xml(fname, standardize=True):
         # in form: root/component coordinate*/property name/value
         for coord_name, prefix in zip(['coordinate1', 'coordinate2'], ['X', 'Y']):
             child = root.find("./component[@name='{}']".format(coord_name))
-            if ET.iselement(child):
-                v_step  = float(child.find("./property[@name='delta']").find('value').text)
-                v_first = float(child.find("./property[@name='startingvalue']").find('value').text)
-                if abs(v_step) < 1. and abs(v_step) > 1e-7:
-                    xmlDict['{}_STEP'.format(prefix)] = v_step
-                    xmlDict['{}_FIRST'.format(prefix)] = v_first - v_step / 2.
+            v_step  = float(child.find("./property[@name='delta']").find('value').text)
+            v_first = float(child.find("./property[@name='startingvalue']").find('value').text)
+            if abs(v_step) < 1. and abs(v_step) > 1e-7:
+                xmlDict['{}_STEP'.format(prefix)] = v_step
+                xmlDict['{}_FIRST'.format(prefix)] = v_first - v_step / 2.
 
     # PAMDataset, e.g. hgt.rdr.aux.xml
     elif root.tag == 'PAMDataset':
@@ -1006,16 +1005,16 @@ def read_envi_hdr(fname, standardize=True):
 
 
 def read_gdal_vrt(fname, standardize=True):
-    """Read GDAL .vrt file into a python dict structure
+    """Read GDAL .vrt file into a python dict structure using gdal
 
     Modified from $ISCE_HOME/applications/gdal2isce_xml.gdal2isce_xml() written by David Bekaert.
     """
-
-    # read dataset using gdal
     try:
         import gdal
     except ImportError:
         raise ImportError('Cannot import gdal!')
+
+    # read dataset using gdal
     ds = gdal.Open(fname, gdal.GA_ReadOnly)
 
     atr = {}