Merge branch 'insarlab:main' into add_diff_resampling

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ fail_fast: true
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: "v4.6.0"
+    rev: "v5.0.0"
     hooks:
       - id: check-added-large-files
         args: ['--maxkb=20']
@@ -36,7 +36,7 @@ repos:
                '--combine-as']
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: "v3.17.0"
+    rev: "v3.19.0"
     hooks:
       - id: pyupgrade
         name: modernize python

docs/dir_structure.md

@@ -8,12 +8,24 @@ $DATA_DIR/GalapagosSenDT128
 │   ├── 20141213_20141225
 │   │   └── 20141213_20141225.txt
 │   └── ...
-├── reference
-│   ├── data.rsc    #generated by prep_isce.py
-│   ├── IW1
-│   ├── IW1.xml
-│   ├── IW2
-│   └── IW2.xml
+├── ion
+│   ├── 20141213_20141225
+|   │   ├── ion_cal
+|   |   |   ├── filt.ion
+|   |   |   ├── filt.ion.vrt
+|   |   |   ├── filt.ion.xml
+|   |   |   ├── raw_no_projection.cor
+|   |   |   ├── raw_no_projection.cor.vrt
+|   |   |   ├── raw_no_projection.cor.xml
+|   |   |   ├── ...
+|   |   └── ...
+|   ├── 20141213_20150307
+|   └── ...
+├── ion_dates
+|   ├── 20141213.ion
+|   ├── 20141213.ion.vrt
+|   ├── 20141213.ion.xml
+|   └── ...
 ├── merged
 │   ├── geom_reference
 │   │   ├── hgt.rdr
@@ -55,6 +67,12 @@ $DATA_DIR/GalapagosSenDT128
 │       │   ├── ...
 │       ├── 20141213_20150307
 │       └── ...
+├── reference
+│   ├── data.rsc    #generated by prep_isce.py
+│   ├── IW1
+│   ├── IW1.xml
+│   ├── IW2
+│   └── IW2.xml
 ├── secondarys
 │   ├── 20141225
 │   │   ├── IW1
@@ -78,6 +96,9 @@ mintpy.load.baselineDir      = $DATA_DIR/GalapagosSenDT128/baselines
 mintpy.load.unwFile          = $DATA_DIR/GalapagosSenDT128/merged/interferograms/*/filt_*.unw
 mintpy.load.corFile          = $DATA_DIR/GalapagosSenDT128/merged/interferograms/*/filt_*.cor
 mintpy.load.connCompFile     = $DATA_DIR/GalapagosSenDT128/merged/interferograms/*/filt_*.unw.conncomp
+##---------ionosphere stack (optional):
+mintpy.load.ionUnwFile       = $DATA_DIR/GalapagosSenDT128/ion/*/ion_cal/filt.ion
+mintpy.load.ionCorFile       = $DATA_DIR/GalapagosSenDT128/ion/*/ion_cal/raw_no_projection.cor
 ##---------geometry datasets:
 mintpy.load.demFile          = $DATA_DIR/GalapagosSenDT128/merged/geom_reference/hgt.rdr
 mintpy.load.lookupYFile      = $DATA_DIR/GalapagosSenDT128/merged/geom_reference/lat.rdr
@@ -187,6 +208,8 @@ mintpy.load.baselineDir      = $DATA_DIR/KirishimaAlosAT424/baselines
 mintpy.load.unwFile          = $DATA_DIR/KirishimaAlosAT424/Igrams/*/filt_*.unw
 mintpy.load.corFile          = $DATA_DIR/KirishimaAlosAT424/Igrams/*/filt_*.cor
 mintpy.load.connCompFile     = $DATA_DIR/KirishimaAlosAT424/Igrams/*/filt_*.unw.conncomp
+##---------ionosphere stack (optional):
+mintpy.load.ionUnwFile       = $DATA_DIR/KirishimaAlosAT424/ionosphere/*/iono*.filt
 ##---------geometry datasets:
 mintpy.load.demFile          = $DATA_DIR/KirishimaAlosAT424/geom_reference/hgt.rdr
 mintpy.load.lookupYFile      = $DATA_DIR/KirishimaAlosAT424/geom_reference/lat.rdr
@@ -294,6 +317,9 @@ mintpy.load.baselineDir      = $DATA_DIR/NCalAlos2DT169/baseline
 mintpy.load.unwFile          = $DATA_DIR/NCalAlos2DT169/pairs/*-*/insar/filt_*-*_5rlks_28alks.unw
 mintpy.load.corFile          = $DATA_DIR/NCalAlos2DT169/pairs/*-*/insar/*-*_5rlks_28alks.cor
 mintpy.load.connCompFile     = $DATA_DIR/NCalAlos2DT169/pairs/*-*/insar/filt_*-*_5rlks_28alks.unw.conncomp
+##---------ionosphere stack (optional):
+mintpy.load.ionUnwFile       = $DATA_DIR/NCalAlos2DT169/pairs_ion/*-*/ion/ion_cal/filt_ion_*.ion
+mintpy.load.ionCorFile       = $DATA_DIR/NCalAlos2DT169/pairs_ion/*-*/ion/ion_cal/diff_*.cor
 ##---------geometry datasets:
 mintpy.load.demFile          = $DATA_DIR/NCalAlos2DT169/dates_res*/150408/insar/*_5rlks_28alks.hgt
 mintpy.load.lookupYFile      = $DATA_DIR/NCalAlos2DT169/dates_res*/150408/insar/*_5rlks_28alks.lat

docs/google_earth.md

@@ -2,7 +2,7 @@ MintPy use [pyKML](https://pythonhosted.org/pykml/) to generate KMZ (Keyhole Mar
 
 ### 1. Displacement time-series ###
 
-`save_kmz_timeseries.py` takes 3D displacement time-series file and outputs a KMZ file with interactive time-seires plot.
+`save_kmz_timeseries.py` takes 3D displacement time-series file and outputs a KMZ file with interactive time-series plot.
 
 <p align="center">
   <img src="https://insarlab.github.io/figs/docs/mintpy/GoogleEarth-FernandinaSenD128-TS.jpg">

src/mintpy/cli/modify_network.py

@@ -121,9 +121,12 @@ def cmd_line_parse(iargs=None):
     inps.excludeIfgIndex = read_input_index_list(inps.excludeIfgIndex, stackFile=inps.file)
 
     # check: --ex-date(12) options
+    # and ignore , in the inputs
     if inps.excludeDate:
-        inps.exlcudeDate = ptime.yyyymmdd(inps.excludeDate)
+        inps.excludeDate = ' '.join(inps.excludeDate).replace(',', ' ').split()
+        inps.excludeDate = ptime.yyyymmdd(inps.excludeDate)
     if inps.excludeDate12:
+        inps.excludeDat12e = ' '.join(inps.excludeDate12).replace(',', ' ').split()
         inps.excludeDate12 = ptime.yyyymmdd_date12(inps.excludeDate12)
 
     # check: -t / --template option

src/mintpy/defaults/mintpy.yaml

@@ -67,7 +67,7 @@ jobqueue:
     death-timeout: 60           # Number of seconds to wait if a worker can not find a scheduler
     local-directory: null       # Location of fast local storage like /scratch or $TMPDIR
 
-    # LSF resource manager options
+    # Slurm resource manager options
     shebang: "#!/usr/bin/env bash"
     queue: null
     project: null

src/mintpy/objects/gnss.py

@@ -71,7 +71,8 @@ def search_gnss(SNWE, start_date=None, end_date=None, source='UNR', site_list_fi
 
     # ensure that site data formatting is consistent
     sites['site'] = np.array([site.upper() for site in sites['site']])
-    sites['lon'][sites['lon'] > 180] -= 360         # ensure lon values in (-180, 180]
+    # ensure longitude values in (-180, 180]
+    sites['lon'] = ut.standardize_longitude(sites['lon'], limit='-180to180')
     vprint(f'load {len(sites["site"]):d} GNSS sites with fields: {" ".join(sites.keys())}')
 
     # limit in space
@@ -867,6 +868,9 @@ def get_site_lat_lon(self, print_msg=False) -> (float, float):
 
         data = np.loadtxt(self.file, dtype=bytes, skiprows=1, max_rows=10)
         self.site_lat, self.site_lon = data[0, 20:22].astype(float)
+        # ensure longitude in the range of (-180, 180]
+        self.site_lon = ut.standardize_longitude(self.site_lon, limit='-180to180')
+
         return self.site_lat, self.site_lon
 
 
@@ -987,8 +991,9 @@ def get_site_lat_lon(self, print_msg=False) -> (float, float):
             # longitude
             lon_line = [x for x in lines if x.startswith('# East Longitude')][0].strip('\n')
             self.site_lon = float(lon_line.split()[-1])
-            # ensure longitude in the range of (-180, 180]
-            self.site_lon -= 0 if self.site_lon <= 180 else 360
+
+        # ensure longitude in the range of (-180, 180]
+        self.site_lon = ut.standardize_longitude(self.site_lon, limit='-180to180')
 
         return self.site_lat, self.site_lon
 
@@ -1094,6 +1099,8 @@ def get_site_lat_lon(self, print_msg=False) -> (float, float):
         # format
         self.site_lat = float(site_lat)
         self.site_lon = float(site_lon)
+        # ensure longitude in the range of (-180, 180]
+        self.site_lon = ut.standardize_longitude(self.site_lon, limit='-180to180')
 
         if print_msg == True:
             print(f'\t{self.site_lat:f}, {self.site_lon:f}')
@@ -1185,7 +1192,11 @@ def get_site_lat_lon(self, print_msg=False) -> (str, str):
         """
         sites = read_GENERIC_site_list('GenericList.txt')
         ind = sites['site'].tolist().index(self.site)
-        return sites['lat'][ind], sites['lon'][ind]
+        site_lat, site_lon = sites['lat'][ind], sites['lon'][ind]
+        # ensure longitude in the range of (-180, 180]
+        site_lon = ut.standardize_longitude(site_lon, limit='-180to180')
+
+        return site_lat, site_lon
 
 
     def read_displacement(self, start_date=None, end_date=None, print_msg=True, display=False):

src/mintpy/utils/readfile.py

@@ -724,7 +724,7 @@ def read_binary_file(fname, datasetName=None, box=None, xstep=1, ystep=1):
             cpx_band = 'magnitude'
 
         elif fext in ['.mli', '.rmli']:
-            byte_order = 'little-endian'
+            byte_order = 'little-endian'   # big-endian
 
     # SNAP
     # BEAM-DIMAP data format

src/mintpy/utils/utils0.py

@@ -267,6 +267,30 @@ def touch(fname_list, times=None):
 
 
 ################################## Coordinate ##########################################
+def standardize_longitude(lon, limit='-180to180'):
+    """Normalize the longitude value range into (-180, 180] or [0, 360).
+
+    Parameters: lon   - float / np.ndarray, longitude in degree
+                limit - str, -180to180 or 0to360
+    Returns:    lon   - float / np.ndarray, longitude in degree
+    """
+    lon = np.asarray(lon)
+
+    # ensure data within (-180, 360)
+    lon = np.where(lon >= 360, lon - 360, lon)
+    lon = np.where(lon <= -180, lon + 360, lon)
+
+    # range option 1: ensure data within (-180, 180]
+    if limit == '-180to180':
+        lon = np.where(lon > 180, lon - 360, lon)
+
+    # range option 2: ensure data within [0, 360)
+    elif limit == '0to360' and np.nanmin(lon) < 0:
+        lon = np.where(lon < 0, lon + 360, lon)
+
+    return float(lon) if np.isscalar(lon) else lon
+
+
 def utm_zone2epsg_code(utm_zone):
     """Convert UTM Zone string to EPSG code.
 

src/mintpy/view.py

@@ -206,13 +206,13 @@ def check_map_projection(inps, metadata, print_msg=True):
         msg = 'initiate cartopy map projection: '
         if inps.coord_unit.startswith('deg'):
             inps.map_proj_obj = ccrs.PlateCarree()
-            vprint(msg + 'PlateCarree')
+            print(msg + 'PlateCarree')
 
         elif inps.coord_unit.startswith('meter'):
             if 'UTM_ZONE' in metadata.keys():
                 utm_zone = metadata['UTM_ZONE']
                 inps.map_proj_obj = ccrs.UTM(utm_zone)
-                vprint(msg + f'UTM zone {utm_zone}')
+                print(msg + f'UTM zone {utm_zone}')
 
                 # check --lalo-label (works for PlateCarree only)
                 if inps.lalo_label:
@@ -1652,9 +1652,15 @@ def plot(self):
             no_data_val = readfile.get_no_data_value(self.file)
             if self.no_data_value is not None:
                 vprint(f'masking pixels with NO_DATA_VALUE of {self.no_data_value}')
+                # convert integer to floating to enable masking with nan
+                if np.issubdtype(data.dtype, np.integer):
+                    data = np.array(data, np.float32)
                 data[data == self.no_data_value] = np.nan
             elif no_data_val is not None and not np.isnan(no_data_val):
                 vprint(f'masking pixels with NO_DATA_VALUE of {no_data_val}')
+                # convert integer to floating to enable masking with nan
+                if np.issubdtype(data.dtype, np.integer):
+                    data = np.array(data, np.float32)
                 data[data == no_data_val] = np.nan
 
             # update/save mask info