Merge pull request #93 from ASFHyP3/develop

Release upgrade to autoRIFT 1.3.0
ASFHyP3 · Jun 2, 2021 · 99bd90a · 99bd90a
2 parents 4d2b627 + 8d47096
commit 99bd90a
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [PEP 440](https://www.python.org/dev/peps/pep-0440/)
 and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.6.0](https://github.com/ASFHyP3/hyp3-autorift/compare/v0.5.2...v0.6.0)
+
+### Changed
+* Upgraded autoRIFT to [v1.3.0](https://github.com/leiyangleon/autoRIFT/releases/tag/v1.3.0)
+  and [ISCE2 v2.5.1 built with autoRIFT v1.3.0](https://anaconda.org/hyp3/isce2)
+
 ## [0.5.2](https://github.com/ASFHyP3/hyp3-autorift/compare/v0.5.1...v0.5.2)
 
 ### Changed

diff --git a/conda-env.yml b/conda-env.yml
@@ -24,8 +24,8 @@ dependencies:
   # For running
   - gdal>=3
   - hyp3lib=1.6.7
-  - isce2=2.5.1.dev5
-  - autorift=1.2.0
+  - isce2=2.5.1.dev6
+  - autorift=1.3.0
   - boto3
   - matplotlib-base
   - netCDF4

diff --git a/hyp3_autorift/netcdf_output.py b/hyp3_autorift/netcdf_output.py
@@ -47,16 +47,16 @@ def netCDF_packaging(VX, VY, DX, DY, INTERPMASK, CHIPSIZEX, CHIPSIZEY, SSM, SSM1
 
     if pair_type is 'radar':
         VR = DX * rangePixelSize / dt * 365.0 * 24.0 * 3600.0
-        VA = (-DY) * azimuthPixelSize / dt * 365.0 * 24.0 * 3600.0
+        VA = (DY) * azimuthPixelSize / dt * 365.0 * 24.0 * 3600.0
         VR = VR.astype(np.float32)
         VA = VA.astype(np.float32)
 
 
         vr_mean_shift = dx_mean_shift * rangePixelSize / dt * 365.0 * 24.0 * 3600.0
-        va_mean_shift = (-dy_mean_shift) * azimuthPixelSize / dt * 365.0 * 24.0 * 3600.0
+        va_mean_shift = (dy_mean_shift) * azimuthPixelSize / dt * 365.0 * 24.0 * 3600.0
 
         vr_mean_shift1 = dx_mean_shift1 * rangePixelSize / dt * 365.0 * 24.0 * 3600.0
-        va_mean_shift1 = (-dy_mean_shift1) * azimuthPixelSize / dt * 365.0 * 24.0 * 3600.0
+        va_mean_shift1 = (dy_mean_shift1) * azimuthPixelSize / dt * 365.0 * 24.0 * 3600.0
 
         # create the (slope parallel & reference) flow-based range-projected result
         alpha_sp = DX / (offset2vy_2 / (offset2vx_1 * offset2vy_2 - offset2vx_2 * offset2vy_1) * (-SX) - offset2vx_2 / (offset2vx_1 * offset2vy_2 - offset2vx_2 * offset2vy_1) * (-SY))
@@ -199,7 +199,7 @@ def netCDF_packaging(VX, VY, DX, DY, INTERPMASK, CHIPSIZEX, CHIPSIZEY, SSM, SSM1
     nc_outfile.setncattr('references', references)
 
     varname='img_pair_info'
-    datatype=np.dtype('S1')
+    datatype='U1'
     dimensions=()
     FillValue=None
 
@@ -242,9 +242,9 @@ def netCDF_packaging(VX, VY, DX, DY, INTERPMASK, CHIPSIZEX, CHIPSIZEY, SSM, SSM1
 
     if (srs.GetAttrValue('PROJECTION') == 'Polar_Stereographic'):
 
-        mapping_name='Polar_Stereographic'
+        mapping_name='mapping'
         grid_mapping='polar_stereographic'  # need to set this as an attribute for the image variables
-        datatype=np.dtype('S1')
+        datatype='U1'
         dimensions=()
         FillValue=None
 
@@ -267,9 +267,9 @@ def netCDF_packaging(VX, VY, DX, DY, INTERPMASK, CHIPSIZEX, CHIPSIZEY, SSM, SSM1
 
     elif (srs.GetAttrValue('PROJECTION') == 'Transverse_Mercator'):
 
-        mapping_name='UTM_projection'
+        mapping_name='mapping'
         grid_mapping='universal_transverse_mercator'  # need to set this as an attribute for the image variables
-        datatype=np.dtype('S1')
+        datatype='U1'
         dimensions=()
         FillValue=None
 
@@ -350,10 +350,15 @@ def netCDF_packaging(VX, VY, DX, DY, INTERPMASK, CHIPSIZEX, CHIPSIZEY, SSM, SSM1
     else:
         var.setncattr('stable_shift_slow',np.nan)
 
-
-    var.setncattr('vx_error_mask',int(round(vx_error_mask*10))/10)
+    if stable_count != 0:
+        var.setncattr('vx_error_mask',int(round(vx_error_mask*10))/10)
+    else:
+        var.setncattr('vx_error_mask',np.nan)
     var.setncattr('vx_error_mask_description','RMSE over stable surfaces, stationary or slow-flowing surfaces with velocity < 15 m/yr identified from an external mask')
-    var.setncattr('vx_error_slow',int(round(vx_error_slow*10))/10)
+    if stable_count1 != 0:
+        var.setncattr('vx_error_slow',int(round(vx_error_slow*10))/10)
+    else:
+        var.setncattr('vx_error_slow',np.nan)
     var.setncattr('vx_error_slow_description','RMSE over slowest 25% of retrieved velocities')
     var.setncattr('vx_error_modeled',int(round(vx_error_mod*10))/10)
     var.setncattr('vx_error_modeled_description','1-sigma error calculated using a modeled error-dt relationship')
@@ -425,10 +430,15 @@ def netCDF_packaging(VX, VY, DX, DY, INTERPMASK, CHIPSIZEX, CHIPSIZEY, SSM, SSM1
     else:
         var.setncattr('stable_shift_slow',np.nan)
 
-
-    var.setncattr('vy_error_mask',int(round(vy_error_mask*10))/10)
+    if stable_count != 0:
+        var.setncattr('vy_error_mask',int(round(vy_error_mask*10))/10)
+    else:
+        var.setncattr('vy_error_mask',np.nan)
     var.setncattr('vy_error_mask_description','RMSE over stable surfaces, stationary or slow-flowing surfaces with velocity < 15 m/yr identified from an external mask')
-    var.setncattr('vy_error_slow',int(round(vy_error_slow*10))/10)
+    if stable_count1 != 0:
+        var.setncattr('vy_error_slow',int(round(vy_error_slow*10))/10)
+    else:
+        var.setncattr('vy_error_slow',np.nan)
     var.setncattr('vy_error_slow_description','RMSE over slowest 25% of retrieved velocities')
     var.setncattr('vy_error_modeled',int(round(vy_error_mod*10))/10)
     var.setncattr('vy_error_modeled_description','1-sigma error calculated using a modeled error-dt relationship')
@@ -546,10 +556,15 @@ def netCDF_packaging(VX, VY, DX, DY, INTERPMASK, CHIPSIZEX, CHIPSIZEY, SSM, SSM1
         else:
             var.setncattr('stable_shift_slow',np.nan)
 
-
-        var.setncattr('vr_error_mask',int(round(vr_error_mask*10))/10)
+        if stable_count != 0:
+            var.setncattr('vr_error_mask',int(round(vr_error_mask*10))/10)
+        else:
+            var.setncattr('vr_error_mask',np.nan)
         var.setncattr('vr_error_mask_description','RMSE over stable surfaces, stationary or slow-flowing surfaces with velocity < 15 m/yr identified from an external mask')
-        var.setncattr('vr_error_slow',int(round(vr_error_slow*10))/10)
+        if stable_count1 != 0:
+            var.setncattr('vr_error_slow',int(round(vr_error_slow*10))/10)
+        else:
+            var.setncattr('vr_error_slow',np.nan)
         var.setncattr('vr_error_slow_description','RMSE over slowest 25% of retrieved velocities')
         var.setncattr('vr_error_modeled',int(round(vr_error_mod*10))/10)
         var.setncattr('vr_error_modeled_description','1-sigma error calculated using a modeled error-dt relationship')
@@ -619,10 +634,15 @@ def netCDF_packaging(VX, VY, DX, DY, INTERPMASK, CHIPSIZEX, CHIPSIZEY, SSM, SSM1
         else:
             var.setncattr('stable_shift_slow',np.nan)
 
-
-        var.setncattr('va_error_mask',int(round(va_error_mask*10))/10)
+        if stable_count != 0:
+            var.setncattr('va_error_mask',int(round(va_error_mask*10))/10)
+        else:
+            var.setncattr('va_error_mask',np.nan)
         var.setncattr('va_error_mask_description','RMSE over stable surfaces, stationary or slow-flowing surfaces with velocity < 15 m/yr identified from an external mask')
-        var.setncattr('va_error_slow',int(round(va_error_slow*10))/10)
+        if stable_count1 != 0:
+            var.setncattr('va_error_slow',int(round(va_error_slow*10))/10)
+        else:
+            var.setncattr('va_error_slow',np.nan)
         var.setncattr('va_error_slow_description','RMSE over slowest 25% of retrieved velocities')
         var.setncattr('va_error_modeled',int(round(va_error_mod*10))/10)
         var.setncattr('va_error_modeled_description','1-sigma error calculated using a modeled error-dt relationship')
@@ -774,10 +794,15 @@ def netCDF_packaging(VX, VY, DX, DY, INTERPMASK, CHIPSIZEX, CHIPSIZEY, SSM, SSM1
         else:
             var.setncattr('stable_shift_slow',np.nan)
 
-
-        var.setncattr('vxp_error_mask',int(round(vxp_error_mask*10))/10)
+        if stable_count_p != 0:
+            var.setncattr('vxp_error_mask',int(round(vxp_error_mask*10))/10)
+        else:
+            var.setncattr('vxp_error_mask',np.nan)
         var.setncattr('vxp_error_mask_description','RMSE over stable surfaces, stationary or slow-flowing surfaces with velocity < 15 m/yr identified from an external mask')
-        var.setncattr('vxp_error_slow',int(round(vxp_error_slow*10))/10)
+        if stable_count1_p != 0:
+            var.setncattr('vxp_error_slow',int(round(vxp_error_slow*10))/10)
+        else:
+            var.setncattr('vxp_error_slow',np.nan)
         var.setncattr('vxp_error_slow_description','RMSE over slowest 25% of retrieved velocities')
         var.setncattr('vxp_error_modeled',int(round(vxp_error_mod*10))/10)
         var.setncattr('vxp_error_modeled_description','1-sigma error calculated using a modeled error-dt relationship')
@@ -849,10 +874,15 @@ def netCDF_packaging(VX, VY, DX, DY, INTERPMASK, CHIPSIZEX, CHIPSIZEY, SSM, SSM1
         else:
             var.setncattr('stable_shift_slow',np.nan)
 
-
-        var.setncattr('vyp_error_mask',int(round(vyp_error_mask*10))/10)
+        if stable_count_p != 0:
+            var.setncattr('vyp_error_mask',int(round(vyp_error_mask*10))/10)
+        else:
+            var.setncattr('vyp_error_mask',np.nan)
         var.setncattr('vyp_error_mask_description','RMSE over stable surfaces, stationary or slow-flowing surfaces with velocity < 15 m/yr identified from an external mask')
-        var.setncattr('vyp_error_slow',int(round(vyp_error_slow*10))/10)
+        if stable_count1_p != 0:
+            var.setncattr('vyp_error_slow',int(round(vyp_error_slow*10))/10)
+        else:
+            var.setncattr('vyp_error_slow',np.nan)
         var.setncattr('vyp_error_slow_description','RMSE over slowest 25% of retrieved velocities')
         var.setncattr('vyp_error_modeled',int(round(vyp_error_mod*10))/10)
         var.setncattr('vyp_error_modeled_description','1-sigma error calculated using a modeled error-dt relationship')
@@ -957,7 +987,7 @@ def netCDF_packaging(VX, VY, DX, DY, INTERPMASK, CHIPSIZEX, CHIPSIZEY, SSM, SSM1
     varname='interp_mask'
     datatype=np.dtype('uint8')
     dimensions=('y','x')
-    FillValue=None
+    FillValue=0
     var = nc_outfile.createVariable(varname,datatype,dimensions, fill_value=FillValue, zlib=True, complevel=2, shuffle=True, chunksizes=ChunkSize)
 
     var.setncattr('standard_name','interpolated_value_mask')

diff --git a/hyp3_autorift/process.py b/hyp3_autorift/process.py
@@ -178,6 +178,10 @@ def process(reference: str, secondary: str, parameter_file: str = DEFAULT_PARAME
         gdal.SetConfigOption('GDAL_DISABLE_READDIR_ON_OPEN', 'EMPTY_DIR')
         gdal.SetConfigOption('AWS_REQUEST_PAYER', 'requester')
         gdal.SetConfigOption('AWS_REGION', 'eu-central-1')
+        # Also set for new CXX threads in Geogrid/autoRIFT
+        os.environ['GDAL_DISABLE_READDIR_ON_OPEN'] = 'EMPTY_DIR'
+        os.environ['AWS_REQUEST_PAYER'] = 'requester'
+        os.environ['AWS_REGION'] = 'eu-central-1'
 
         reference_metadata = get_s2_metadata(reference)
         reference_path = reference_metadata['assets'][band]['href'].replace('s3://', '/vsis3/')
@@ -193,6 +197,10 @@ def process(reference: str, secondary: str, parameter_file: str = DEFAULT_PARAME
         gdal.SetConfigOption('GDAL_DISABLE_READDIR_ON_OPEN', 'EMPTY_DIR')
         gdal.SetConfigOption('AWS_REQUEST_PAYER', 'requester')
         gdal.SetConfigOption('AWS_REGION', 'us-west-2')
+        # Also set for new CXX threads in Geogrid/autoRIFT
+        os.environ['GDAL_DISABLE_READDIR_ON_OPEN'] = 'EMPTY_DIR'
+        os.environ['AWS_REQUEST_PAYER'] = 'requester'
+        os.environ['AWS_REGION'] = 'us-west-2'
 
         if band == 'B08':
             band = 'B8'