Merge branch 'master' into BLM

.cmake/TargetX11.cmake

@@ -5,6 +5,9 @@ set(components
 
 find_package(X11 COMPONENTS ${components})
 
+# The X11::{component} targets only exist for CMake ≥ 3.14,
+# so we create them here for backwards compatibility.
+
 if(X11_FOUND)
 
     # make X11 look like a regular find_package component
@@ -13,11 +16,9 @@ if(X11_FOUND)
     list(APPEND components X11)
 
     foreach(component ${components})
-        message("${component} include = ${X11_${component}_INCLUDE_PATH}")
+        if(X11_${component}_FOUND AND
-        if(X11_${component}_FOUND)
+           NOT TARGET X11::${component})
-            if(NOT TARGET X11::${component})
+            add_library(X11::${component} IMPORTED INTERFACE)
-                add_library(X11::${component} IMPORTED INTERFACE)
-            endif()
             target_link_libraries(X11::${component}
                 INTERFACE ${X11_${component}_LIB})
             target_include_directories(X11::${component} SYSTEM

.cmake/isce2_buildflags.cmake

@@ -14,13 +14,15 @@ set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED y)
 set(CMAKE_CXX_EXTENSIONS n)
 
-# TODO (fix RPATHs)
+include(GNUInstallDirs)
-# We have to hack our RPATHs a bit for these shared libraries to be
+
-# loaded by others on the install-side. Maybe these libraries should
+# add automatically determined parts of the RPATH, which point to directories
-# be combined and/or installed to a common ISCE2 lib directory.
+# outside of the build tree, to the install RPATH
-# Is there a semantic way to propagate their RPATHs
-# without using these global variables?
 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON)
-list(APPEND CMAKE_INSTALL_RPATH
+
-    ${CMAKE_INSTALL_PREFIX}/${ISCE2_PKG}/components/isceobj/Util
+# the RPATH to be used when installing, but only if it's not a system directory
-    )
+set(abs_libdir ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR})
+list(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES ${abs_libdir} isSystemDir)
+if("${isSystemDir}" STREQUAL "-1")
+    list(APPEND CMAKE_INSTALL_RPATH ${abs_libdir})
+endif()

.cmake/isce2_helpers.cmake

@@ -50,22 +50,16 @@ endfunction()
 # Note that it first checks if a provided file is a target,
 # and if so, installs it as a TARGET instead. Make sure your
 # filenames and target names don't have any overlap!
-
 function(InstallSameDir)
-mark_as_advanced(isce2_bin_base)
     foreach(name ${ARGN})
         if(TARGET ${name})
             set(installtype TARGETS)
         else()
             set(installtype FILES)
         endif()
-        file(RELATIVE_PATH path ${isce2_bin_dir} ${CMAKE_CURRENT_BINARY_DIR})
+        file(RELATIVE_PATH path ${isce2_BINARY_DIR} ${CMAKE_CURRENT_BINARY_DIR})
         install(${installtype} ${name}
                 DESTINATION ${ISCE2_PKG}/${path}
                 )
     endforeach()
 endfunction()
-# We use this instead of CMAKE_BINARY_DIR to handle
-# cases where isce2 is added as a subdirectory
-set(isce2_bin_dir ${CMAKE_CURRENT_BINARY_DIR} CACHE PATH
-    "ISCE2 root build directory")

CMakeLists.txt

@@ -2,15 +2,19 @@ cmake_minimum_required(VERSION 3.12 FATAL_ERROR)
 
 project(isce2 LANGUAGES C CXX Fortran)
 
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/.cmake)
+
 include(CheckLanguage)
 check_language(CUDA)
 if(CMAKE_CUDA_COMPILER)
+    set(CMAKE_CUDA_STANDARD 11)
+    set(CMAKE_CUDA_STANDARD_REQUIRED TRUE)
     enable_language(CUDA)
+    find_package(CUDAToolkit) # TODO added in cmake 3.17 - copy this module
 endif()
 
-list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/.cmake)
+find_package(Python 3.5 REQUIRED COMPONENTS Interpreter Development
-
+                        OPTIONAL_COMPONENTS NumPy)
-find_package(Python 3.5 REQUIRED COMPONENTS Interpreter Development)
 find_package(FFTW REQUIRED)
 find_package(Motif)
 find_package(OpenMP REQUIRED COMPONENTS C CXX Fortran)

README.md

@@ -33,8 +33,10 @@ TERRASARX, and UAVSAR.
    - [Note On 'python3' Exectuable Convention](#python3-convention)
    - [License required for dependencies to enable some workflows in ISCE](#license-required-for-dependencies-to-enable-some-workflows-in-isce)
 2. [Building ISCE](#building-isce)
-   - [Configuration control: SCONS\_CONFIG\_DIR and SConfigISCE](#configuration-control)
+   - [SCons](#scons-recommended)
-   - [Install ISCE](#install-isce)
+     - [Configuration control: SCONS\_CONFIG\_DIR and SConfigISCE](#configuration-control)
+     - [Install ISCE](#install-isce)
+   - [CMake](#cmake-experimental)
    - [Setup Your Environment](#setup-your-environment)
 3. [Running ISCE](#running-isce)
    - [Running ISCE from the command line](#running-isce-from-the-command-line)
@@ -192,7 +194,9 @@ the older data with the same workflows available in this open source release.
 
 ## Building ISCE
 
-### Configuration control
+### SCons (recommended)
+
+#### Configuration control
 
 Scons requires that configuration information be present in a directory
 specified by the environment variable SCONS\_CONFIG\_DIR.  First, create a
@@ -252,7 +256,7 @@ and the install files.  Also, in the following the capitalization of 'isce' as
 lower case does matter.  This is the case-sensitive package name that Python
 code uses for importing isce.
 
-### Install ISCE
+#### Install ISCE
 
 cd isce
 scons install
@@ -273,7 +277,7 @@ This will build the necessary components and install them into the location
 specified in the configuration file as PRJ\_SCONS\_INSTALL.
 
 
-#### Note about compiling ISCE after an unsuccessful build.
+##### Note about compiling ISCE after an unsuccessful build.
 
 When building ISCE, scons will check the list of header files and libraries that
 ISCE requires.  Scons will cache the results of this dependency checking.  So,
@@ -290,6 +294,47 @@ directory containing the SConstruct file):
 
 and then try "scons install" again.
 
+### CMake (experimental)
+Make sure you have the following prerequisites:
+* CMake ≥ 3.12
+* GCC ≥ 4.8  (with C++11 support)
+* Python ≥ 3.5
+* Cython
+* FFTW 3
+* GDAL
+
+```sh
+git clone https://github.com/isce-framework/isce2
+cd isce2
+mkdir build
+cd build
+cmake .. -DCMAKE_INSTALL_PREFIX=/my/isce/install/location
+make install
+```
+
+#### Additional cmake configuration options
+
+CMake uses `CMAKE_PREFIX_PATH` as a global prefix for finding packages,
+which can come in handy when using e.g. Anaconda:
+
+```sh
+cmake [...] -DCMAKE_PREFIX_PATH=$CONDA_PREFIX
+```
+
+On macOS, cmake will also look for systemwide "frameworks",
+which is usually not what you want when using Conda or Macports.
+
+```sh
+cmake [...] -DCMAKE_FIND_FRAMEWORK=NEVER
+```
+
+For packagers, the `PYTHON_MODULE_DIR` can be used to specify ISCE2's
+package installation location relative to the installation prefix
+
+```sh
+cmake [...] -DPYTHON_MODULE_DIR=lib/python3.8m/site-packages
+```
+
 ### Setup Your Environment
 
 Once everything is installed, you will need to set the following environment

components/isceobj/Sensor/CMakeLists.txt

@@ -2,7 +2,14 @@ add_subdirectory(db)
 add_subdirectory(TOPS)
 add_subdirectory(MultiMode)
 
+add_library(asa_im_decode src/asa_im_decode/asa_im_decode.c)
+set_target_properties(asa_im_decode PROPERTIES
+    PREFIX ""
+    OUTPUT_NAME envisat
+    SUFFIX .so)
+
 set(installfiles
+    asa_im_decode
     alos
     __init__.py
     ALOS.py

components/isceobj/Util/CMakeLists.txt

@@ -81,15 +81,9 @@ add_library(utilLib SHARED
 target_include_directories(utilLib PUBLIC
     include
     )
-target_link_libraries(utilLib PUBLIC
+target_link_libraries(utilLib PRIVATE
     FFTW::Float
     )
-# TODO (fortran module include)
-# This seems to be needed to use this library's modules,
-# but is there a more idiomatic way to do this?
-target_include_directories(utilLib INTERFACE
-    ${CMAKE_CURRENT_BINARY_DIR}
-    )
 
 add_library(combinedLib SHARED
     Library/geometry/src/geometryModule.F
@@ -120,17 +114,24 @@ target_include_directories(combinedlibmodule PUBLIC
 target_link_libraries(combinedlibmodule PUBLIC
     combinedLib
     )
-# TODO (fortran module include)
+
-# This seems to be needed to use this library's modules,
+# Set up fortran module paths
-# but is there a more idiomatic way to do this?
+set(mdir ${CMAKE_CURRENT_BINARY_DIR}/utillib_fortran_modules)
+set_property(TARGET utilLib PROPERTY Fortran_MODULE_DIRECTORY ${mdir})
+target_include_directories(utilLib INTERFACE
+    $<$<COMPILE_LANGUAGE:Fortran>:${mdir}>
+    )
+set(mdir ${CMAKE_CURRENT_BINARY_DIR}/combinelib_fortran_modules)
+set_property(TARGET combinedLib PROPERTY Fortran_MODULE_DIRECTORY ${mdir})
 target_include_directories(combinedLib INTERFACE
-    ${CMAKE_CURRENT_BINARY_DIR}
+    $<$<COMPILE_LANGUAGE:Fortran>:${mdir}>
     )
 
 install(TARGETS
     utilLib
     combinedLib
-    LIBRARY DESTINATION lib)
+    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    )
 
 InstallSameDir(
     combinedlibmodule

components/stdproc/stdproc/CMakeLists.txt

@@ -8,15 +8,14 @@ add_library(formslcLib SHARED
     formslcLib/src/io.c
     )
 set_property(TARGET formslcLib PROPERTY POSITION_INDEPENDENT_CODE ON)
-target_include_directories(formslcLib PRIVATE formslcLib/include)
 target_link_libraries(formslcLib PUBLIC
     utilLib
     )
-# TODO (fortran module include)
+
-# This seems to be needed to use this library's modules,
+set(mdir ${CMAKE_CURRENT_BINARY_DIR}/formslc_fortran_modules)
-# but is there a more idiomatic way to do this?
+set_property(TARGET formslcLib PROPERTY Fortran_MODULE_DIRECTORY ${mdir})
 target_include_directories(formslcLib INTERFACE
-    ${CMAKE_CURRENT_BINARY_DIR}
+    $<$<COMPILE_LANGUAGE:Fortran>:${mdir}>
     )
 
 add_subdirectory(correct)

components/zerodop/CMakeLists.txt

@@ -3,7 +3,13 @@ add_subdirectory(geozero)
 add_subdirectory(topozero)
 
 if(CMAKE_CUDA_COMPILER)
-    # add_subdirectory(GPUampcor) TODO cublas_device removed from CUDA ≥ 10
+
+    # cublas_device removed from CUDA ≥ 10
+    if(CMAKE_CUDA_COMPILER_ID STREQUAL "NVIDIA" AND
+       CMAKE_CUDA_COMPILER_VERSION VERSION_LESS 10)
+        add_subdirectory(GPUampcor)
+    endif()
+
     add_subdirectory(GPUgeo2rdr)
 endif()
 

components/zerodop/GPUampcor/CMakeLists.txt

@@ -1,3 +1,9 @@
+if(NOT TARGET CUDA::cublas)
+    return()
+endif()
+
+return() # TODO get cublas_device working or remove usage of it
+
 cython_add_module(GPUampcor
     GPUampcor.pyx
     cuda/GPUamp.cu
@@ -9,6 +15,11 @@ target_include_directories(GPUampcor PUBLIC
     include
     )
 target_link_libraries(GPUampcor PRIVATE
-    cublas
+    CUDA::cublas
     DataAccessor_static
+    FFTW::Float
+    )
+InstallSameDir(
+    GPUampcor
+    __init__.py
     )

contrib/CMakeLists.txt

@@ -5,7 +5,7 @@ add_subdirectory(frameUtils)
 #add_subdirectory(unwUtils)
 add_subdirectory(downsample_unwrapper)
 
-#add_subdirectory(PyCuAmpcor)
+add_subdirectory(PyCuAmpcor)
 add_subdirectory(splitSpectrum)
 add_subdirectory(alos2filter)
 add_subdirectory(alos2proc)

contrib/PyCuAmpcor/CMakeLists.txt

@@ -0,0 +1,46 @@
+# Early exit if prereqs not available
+if(NOT TARGET GDAL::GDAL
+OR NOT TARGET Python::NumPy
+OR NOT TARGET CUDA::cublas
+OR NOT TARGET CUDA::cufft
+   )
+    return()
+endif()
+
+set(CMAKE_CUDA_STANDARD 11)
+set(CMAKE_CUDA_STANDARD_REQUIRED TRUE)
+
+cython_add_module(PyCuAmpcor
+    src/PyCuAmpcor.pyx
+    src/GDALImage.cu
+    src/SConscript
+    src/SlcImage.cu
+    src/cuAmpcorChunk.cu
+    src/cuAmpcorController.cu
+    src/cuAmpcorParameter.cu
+    src/cuArrays.cu
+    src/cuArraysCopy.cu
+    src/cuArraysPadding.cu
+    src/cuCorrFrequency.cu
+    src/cuCorrNormalization.cu
+    src/cuCorrTimeDomain.cu
+    src/cuDeramp.cu
+    src/cuEstimateStats.cu
+    src/cuOffset.cu
+    src/cuOverSampler.cu
+    src/cuSincOverSampler.cu
+    )
+target_include_directories(PyCuAmpcor PRIVATE
+    src
+    )
+target_link_libraries(PyCuAmpcor PRIVATE
+    CUDA::cufft
+    CUDA::cublas
+    GDAL::GDAL
+    Python::NumPy
+    )
+
+InstallSameDir(
+    __init__.py
+    PyCuAmpcor
+    )

contrib/PyCuAmpcor/examples/cuDenseOffsets.py

@@ -2,108 +2,134 @@
 
 # Author: Minyan Zhong, Lijun Zhu
 
-import argparse
+
 import os
+import argparse
+import numpy as np
+
 import isce
 import isceobj
 from isceobj.Util.decorators import use_api
-
-import numpy as np 
 from contrib.PyCuAmpcor.PyCuAmpcor import PyCuAmpcor
 
+
+EXAMPLE = '''example
+  cuDenseOffsets.py -m ./merged/SLC/20151120/20151120.slc.full -s ./merged/SLC/20151214/20151214.slc.full
+      --referencexml ./reference/IW1.xml --outprefix ./merged/offsets/20151120_20151214/offset
+      --ww 256 --wh 256 --oo 32 --kw 300 --kh 100 --nwac 100 --nwdc 1 --sw 8 --sh 8 --gpuid 2
+'''
+
+
 def createParser():
     '''
     Command line parser.
     '''
 
-    parser = argparse.ArgumentParser( description='Generate offset field between two Sentinel slc')
+
+    parser = argparse.ArgumentParser(description='Generate offset field between two Sentinel slc',
+                                     formatter_class=argparse.RawTextHelpFormatter,
+                                     epilog=EXAMPLE)
     parser.add_argument('-m','--reference', type=str, dest='reference', required=True,
-            help='Reference image')
+                        help='Reference image')
     parser.add_argument('-s', '--secondary',type=str, dest='secondary', required=True,
-            help='Secondary image')
+                        help='Secondary image')
     parser.add_argument('-l', '--lat',type=str, dest='lat', required=False,
-           help='Latitude')
+                        help='Latitude')
     parser.add_argument('-L', '--lon',type=str, dest='lon', required=False,
-           help='Longitude')
+                        help='Longitude')
     parser.add_argument('--los',type=str, dest='los', required=False,
-           help='Line of Sight')
+                        help='Line of Sight')
-    parser.add_argument('--referencexml',type=str, dest='referencexml', required=False,
+    parser.add_argument('-x', '--referencexml',type=str, dest='referencexml', required=False,
-           help='Reference Image Xml File')
+                        help='Reference Image XML File')
+
+    parser.add_argument('--op','--outprefix','--output-prefix', type=str, dest='outprefix',
+                        default='offset', required=True,
+                        help='Output prefix, default: offset.')
+    parser.add_argument('--os','--outsuffix', type=str, dest='outsuffix', default='',
+                        help='Output suffix, default:.')
     parser.add_argument('--ww', type=int, dest='winwidth', default=64,
-            help='Window Width')
+                        help='Window width (default: %(default)s).')
     parser.add_argument('--wh', type=int, dest='winhgt', default=64,
-            help='Window height')
+                        help='Window height (default: %(default)s).')
-    parser.add_argument('--sw', type=int, dest='srcwidth', default=20,
+
-            help='Search window width')
+    parser.add_argument('--sw', type=int, dest='srcwidth', default=20, choices=range(8, 33),
-    parser.add_argument('--sh', type=int, dest='srchgt', default=20,
+                        help='Search window width (default: %(default)s).')
-            help='Search window height')
+    parser.add_argument('--sh', type=int, dest='srchgt', default=20, choices=range(8, 33),
+                        help='Search window height (default: %(default)s).')
     parser.add_argument('--mm', type=int, dest='margin', default=50,
-            help='Margin')
+                        help='Margin (default: %(default)s).')
+
     parser.add_argument('--kw', type=int, dest='skipwidth', default=64,
-            help='Skip across')
+                        help='Skip across (default: %(default)s).')
     parser.add_argument('--kh', type=int, dest='skiphgt', default=64,
-            help='Skip down')
+                        help='Skip down (default: %(default)s).')
+
+    parser.add_argument('--raw-osf','--raw-over-samp-factor', type=int, dest='raw_oversample',
+                        default=2, choices=range(2,5),
+                        help='raw data oversampling factor (default: %(default)s).')
+
+    gross = parser.add_argument_group('Initial gross offset')
+    gross.add_argument('-g','--gross', type=int, dest='gross', default=0,
+                       help='Use gross offset or not')
+    gross.add_argument('--aa', type=int, dest='azshift', default=0,
+                       help='Gross azimuth offset (default: %(default)s).')
+    gross.add_argument('--rr', type=int, dest='rgshift', default=0,
+                       help='Gross range offset (default: %(default)s).')
+
+    corr = parser.add_argument_group('Correlation surface')
+    corr.add_argument('--corr-win-size', type=int, dest='corr_win_size', default=-1,
+                      help='Zoom-in window size of the correlation surface for oversampling (default: %(default)s).')
+    corr.add_argument('--corr-osf', '--oo', '--corr-over-samp-factor', type=int, dest='corr_oversample', default=32,
+                      help = 'Oversampling factor of the zoom-in correlation surface (default: %(default)s).')
 
     parser.add_argument('--nwa', type=int, dest='numWinAcross', default=-1,
-            help='Number of Window Across')
+                        help='Number of window across (default: %(default)s).')
     parser.add_argument('--nwd', type=int, dest='numWinDown', default=-1,
-            help='Number of Window Down')
+                        help='Number of window down (default: %(default)s).')
 
     parser.add_argument('--nwac', type=int, dest='numWinAcrossInChunk', default=1,
-            help='Number of Window Across in Chunk')
+                        help='Number of window across in chunk (default: %(default)s).')
     parser.add_argument('--nwdc', type=int, dest='numWinDownInChunk', default=1,
-            help='Number of Window Down in Chunk')
+                        help='Number of window down in chunk (default: %(default)s).')
+    parser.add_argument('-r', '--redo', dest='redo', action='store_true',
+                        help='To redo by force (ignore the existing offset fields).')
 
-    parser.add_argument('-op','--outprefix', type=str, dest='outprefix', default='dense_ampcor', required=True,
+    parser.add_argument('--drmp', '--deramp', dest='deramp', type=int, default=0,
-            help='Output prefix')
+                        help='deramp method (0: mag, 1: complex) (default: %(default)s).')
 
-    parser.add_argument('-os','--outsuffix', type=str, dest='outsuffix',default='dense_ampcor',
+    parser.add_argument('--gpuid', '--gid', '--gpu-id', dest='gpuid', type=int, default=-1,
-            help='Output suffix')
+                        help='GPU ID (default: %(default)s).')
-
-    parser.add_argument('-g','--gross', type=int, dest='gross', default=0,
-            help='Use gross offset or not')
-
-    parser.add_argument('--aa', type=int, dest='azshift', default=0,
-            help='Gross azimuth offset')
-
-    parser.add_argument('--rr', type=int, dest='rgshift', default=0,
-            help='Gross range offset')
-
-    parser.add_argument('--oo', type=int, dest='oversample', default=32,
-            help = 'Oversampling factor')
-
-    parser.add_argument('-r', '--redo', dest='redo', type=int, default=0
-       , help='To redo or not')
-
-    parser.add_argument('-drmp', '--deramp', dest='deramp', type=int, default=0
-       , help='deramp method (0: mag, 1: complex)')
-
-    parser.add_argument('-gid', '--gpuid', dest='gpuid', type=int, default=-1
-       , help='GPU ID')
 
     return parser
 
+
 def cmdLineParse(iargs = None):
     parser = createParser()
     inps =  parser.parse_args(args=iargs)
 
+    # check oversampled window size
+    if (inps.winwidth + 2 * inps.srcwidth) * inps.raw_oversample > 1024:
+        msg = 'input oversampled window size in the across/range direction '
+        msg += 'exceeds the current implementaion limit of 1024!'
+        raise ValueError(msg)
+
     return inps
 
+
 @use_api
 def estimateOffsetField(reference, secondary, inps=None):
 
-    import pathlib
 
     ###Loading the secondary image object
     sim = isceobj.createSlcImage()
-    sim.load(pathlib.Path(secondary).with_suffix('.xml'))
+    sim.load(secondary+'.xml')
     sim.setAccessMode('READ')
     sim.createImage()
 
-
     ###Loading the reference image object
     sar = isceobj.createSlcImage()
-    sar.load(pathlib.Path(reference).with_suffix('.xml'))
+    sar.load(reference+'.xml')
+
     sar.setAccessMode('READ')
     sar.createImage()
 
@@ -114,13 +140,15 @@ def estimateOffsetField(reference, secondary, inps=None):
 
     objOffset.algorithm = 0
     objOffset.deviceID = inps.gpuid  # -1:let system find the best GPU
-    objOffset.nStreams =   1 #cudaStreams 
+    objOffset.nStreams = 2 #cudaStreams
     objOffset.derampMethod = inps.deramp
+    print('deramp method (0 for magnitude, 1 for complex): ', objOffset.derampMethod)
 
-    objOffset.referenceImageName = reference
+
+    objOffset.referenceImageName = reference+'.vrt'
     objOffset.referenceImageHeight = length
     objOffset.referenceImageWidth = width
-    objOffset.secondaryImageName = secondary
+    objOffset.secondaryImageName = secondary+'.vrt'
     objOffset.secondaryImageHeight = length
     objOffset.secondaryImageWidth = width
 
@@ -132,39 +160,52 @@ def estimateOffsetField(reference, secondary, inps=None):
 
     if (inps.numWinDown != -1):
         objOffset.numberWindowDown = inps.numWinDown
-
     if (inps.numWinAcross != -1):
         objOffset.numberWindowAcross = inps.numWinAcross
-
     print("offset field length: ",objOffset.numberWindowDown)
     print("offset field width: ",objOffset.numberWindowAcross)
 
     # window size
     objOffset.windowSizeHeight = inps.winhgt
     objOffset.windowSizeWidth = inps.winwidth
+    print('cross correlation window size: {} by {}'.format(objOffset.windowSizeHeight, objOffset.windowSizeWidth))
 
     # search range
     objOffset.halfSearchRangeDown = inps.srchgt
     objOffset.halfSearchRangeAcross = inps.srcwidth
+    print('half search range: {} by {}'.format(inps.srchgt, inps.srcwidth))
 
     # starting pixel
+
     objOffset.referenceStartPixelDownStatic = inps.margin
     objOffset.referenceStartPixelAcrossStatic = inps.margin
  
     # skip size
+    
     objOffset.skipSampleDown = inps.skiphgt
     objOffset.skipSampleAcross = inps.skipwidth
+    print('search step: {} by {}'.format(inps.skiphgt, inps.skipwidth))
+
+    # oversample raw data (SLC)
+    objOffset.rawDataOversamplingFactor = inps.raw_oversample
+    print('raw data oversampling factor:', inps.raw_oversample)
+
+    # correlation surface
+    if inps.corr_win_size == -1:
+        corr_win_size_orig = min(inps.srchgt, inps.srcwidth) * inps.raw_oversample + 1
+        inps.corr_win_size = np.power(2, int(np.log2(corr_win_size_orig)))
+        objOffset.corrSurfaceZoomInWindow = inps.corr_win_size
+        print('correlation surface zoom-in window size:', inps.corr_win_size)
 
-    # oversampling
     objOffset.corrSufaceOverSamplingMethod = 0
-    objOffset.corrSurfaceOverSamplingFactor = inps.oversample
+    objOffset.corrSurfaceOverSamplingFactor = inps.corr_oversample
+    print('correlation surface oversampling factor:', inps.corr_oversample)
 
     # output filenames
     objOffset.offsetImageName = str(inps.outprefix) + str(inps.outsuffix) + '.bip'
     objOffset.grossOffsetImageName = str(inps.outprefix) + str(inps.outsuffix) + '_gross.bip'
     objOffset.snrImageName = str(inps.outprefix) + str(inps.outsuffix) + '_snr.bip'
     objOffset.covImageName = str(inps.outprefix) + str(inps.outsuffix) + '_cov.bip'
-
     print("offsetfield: ",objOffset.offsetImageName)
     print("gross offsetfield: ",objOffset.grossOffsetImageName)
     print("snr: ",objOffset.snrImageName)
@@ -175,17 +216,17 @@ def estimateOffsetField(reference, secondary, inps=None):
     snrImageName = objOffset.snrImageName.decode('utf8')
     covImageName = objOffset.covImageName.decode('utf8')
 
-    if os.path.exists(offsetImageName) and inps.redo==0:
+    print(offsetImageName)
-
+    print(inps.redo)
+    if os.path.exists(offsetImageName) and not inps.redo:
         print('offsetfield file exists')
-        exit()
+        return 0
 
     # generic control
     objOffset.numberWindowDownInChunk = inps.numWinDownInChunk
     objOffset.numberWindowAcrossInChunk = inps.numWinAcrossInChunk
     objOffset.useMmap = 0
     objOffset.mmapSize = 8
-
     objOffset.setupParams()
 
     ## Set Gross Offset ###
@@ -194,11 +235,13 @@ def estimateOffsetField(reference, secondary, inps=None):
         print("By default, the gross offsets are zero")
         print("You can override the default values here")
         objOffset.setConstantGrossOffset(0, 0)
+
     else:
         print("Set varying grossOffset")
         print("By default, the gross offsets are zero")
         print("You can override the default grossDown and grossAcross arrays here")
-        objOffset.setVaryingGrossOffset(np.zeros(shape=grossDown.shape,dtype=np.int32), np.zeros(shape=grossAcross.shape,dtype=np.int32))
+        objOffset.setVaryingGrossOffset(np.zeros(shape=grossDown.shape,dtype=np.int32),
+                                        np.zeros(shape=grossAcross.shape,dtype=np.int32))
 
     # check
     objOffset.checkPixelInImageRange()
@@ -207,7 +250,6 @@ def estimateOffsetField(reference, secondary, inps=None):
     print('Running PyCuAmpcor')
 
     objOffset.runAmpcor()
-
     print('Finished')
 
     sar.finalizeImage()
@@ -257,17 +299,21 @@ def estimateOffsetField(reference, secondary, inps=None):
     covImg.setAccessMode('read')
     covImg.renderHdr()
 
-    return 0
+    return
+
 
 def main(iargs=None):
 
     inps = cmdLineParse(iargs)
     outDir = os.path.dirname(inps.outprefix)
     print(inps.outprefix)
-    if not os.path.exists(outDir):
+
-         os.makedirs(outDir)
+    os.makedirs(outDir, exist_ok=True)
 
     estimateOffsetField(inps.reference, inps.secondary, inps)
+    return
+
+
 
 if __name__ == '__main__':
 

contrib/demUtils/CMakeLists.txt

@@ -17,8 +17,31 @@ Python_add_library(demStitch MODULE
     demstitcher/bindings/demStitch.c
     )
 
+Python_add_library(upsampledem MODULE
+    upsampledem/bindings/upsampledemmodule.cpp
+    upsampledem/src/upsampledem.f
+    upsampledem/src/upsampledemSetState.f
+    upsampledem/src/upsampledemState.f
+    )
+target_include_directories(upsampledem PRIVATE
+    upsampledem/include
+    )
+target_link_libraries(upsampledem PRIVATE
+    utilLib
+    )
+
+Python_add_library(watermask MODULE
+    watermask/bindings/watermaskmodule.cpp
+    watermask/src/watermask.cpp
+    )
+target_include_directories(watermask PRIVATE
+    watermask/include
+    )
+
 InstallSameDir(
     demStitch
+    upsampledem
+    watermask
     correct_geoid_i2_srtm
     __init__.py
     correct_geoid_i2_srtm/Correct_geoid_i2_srtm.py
@@ -27,6 +50,5 @@ InstallSameDir(
     demstitcher/DemStitcherV3.py
     swbdstitcher/SWBDStitcher.py
     upsampledem/UpsampleDem.py
-    watermask/test/mask.py
     watermask/WaterMask.py
     )

contrib/issi/components/ISSI/CMakeLists.txt

@@ -8,12 +8,19 @@ add_library(issi SHARED
     src/polcal.c
     src/tecToPhase.c
     )
+set_target_properties(issi PROPERTIES
+    PREFIX ""
+    OUTPUT_NAME issi
+    SUFFIX .so)
 target_include_directories(issi PUBLIC include)
 
-add_subdirectory(src)
-
 InstallSameDir(
     issi
     __init__.py
     FR.py
     )
+
+file(RELATIVE_PATH relpath ${isce2_BINARY_DIR} ${CMAKE_CURRENT_BINARY_DIR})
+install(DIRECTORY src/igrf_data
+        DESTINATION ${ISCE2_PKG}/${relpath}
+        )

contrib/issi/components/ISSI/src/CMakeLists.txt

@@ -1 +0,0 @@
-add_subdirectory(igrf_data)

contrib/issi/components/ISSI/src/igrf_data/CMakeLists.txt

@@ -1,18 +0,0 @@
-InstallSameDir(
-    dgrf00.dat
-    dgrf45.dat
-    dgrf50.dat
-    dgrf55.dat
-    dgrf60.dat
-    dgrf65.dat
-    dgrf70.dat
-    dgrf75.dat
-    dgrf80.dat
-    dgrf85.dat
-    dgrf90.dat
-    dgrf95.dat
-    igrf05.dat
-    igrf05full.dat
-    igrf05s.dat
-    igrf10.dat
-    )

contrib/stack/stripmapStack/MaskAndFilter.py

@@ -35,6 +35,13 @@ GDAL2NUMPY_DATATYPE = {
 }
 
 
+EXAMPLE = '''example:
+  MaskAndFilter.py -d offset.bip -s offset_snr.bip
+  MaskAndFilter.py -d offset.bip -s offset_snr.bip --plot
+'''
+
+
+
 EXAMPLE = '''example:
   MaskAndFilter.py -d offset.bip -s offset_snr.bip
   MaskAndFilter.py -d offset.bip -s offset_snr.bip --plot
@@ -184,17 +191,21 @@ def mask_filter(inps, band, outName):
     offset1 = np.array(offset)
     offset1[snr < inps.snrThreshold] = np.nan
 
+    # percentage of masked out pixels among all non-zero SNR pixels
+    perc = np.sum(snr >= inps.snrThreshold) / np.sum(snr > 0)
+    print('percentage of pixels with SNR >= {} among pixels with SNR > 0: {:.0%}'.format(inps.snrThreshold, perc))
+
     # fill the hole in offset with nearest data
     print('fill the masked out region with nearest data')
     offset2 = fill(offset1)
 
     # median filtering
-    print('filtering with median filter with size : ', inps.filterSize)
+    print('filtering with median filter with size: {}'.format(inps.filterSize))
     offset3 = ndimage.median_filter(offset2, size=inps.filterSize)
     length, width = offset3.shape
 
     # write data to file
-    print('writing masked and filtered offsets to: ', outName)
+    print('writing masked and filtered offsets to: {}'.format(outName))
     write(offset3, outName, 1, 6)
 
     # write the xml/vrt/hdr file
@@ -216,33 +227,55 @@ def mask_filter(inps, band, outName):
 
 def plot_mask_and_filtering(az_list, rg_list, inps=None):
 
+    print('-'*30)
+    print('plotting mask and filtering result ...')
+    print('mask pixels with SNR == 0 (for plotting ONLY; data files are untouched)')
+    snr = az_list[0]
+    for i in range(1, len(az_list)):
+        az_list[i][snr == 0] = np.nan
+        rg_list[i][snr == 0] = np.nan
+
+    # percentage of masked out pixels among all non-zero SNR pixels
+    perc = np.sum(snr >= inps.snrThreshold) / np.sum(snr > 0)
+    print('percentage of pixels with SNR >= {} among pixels with SNR > 0: {:.0%}'.format(inps.snrThreshold, perc))
+
     fig, axs = plt.subplots(nrows=2, ncols=5, figsize=inps.figsize, sharex=True, sharey=True)
-    titles = ['SNR', 'offset', 'offset (mask)', 'offset (mask/fill)', 'offset (mask/fill/filter)']
+    titles = ['SNR',
+              'offset',
+              'offset (mask {} - {:.0%} remain)'.format(inps.snrThreshold, perc),
+              'offset (mask {} / fill)'.format(inps.snrThreshold),
+              'offset (mask {} / fill / filter {})'.format(inps.snrThreshold, inps.filterSize)]
 
     # plot SNR
-    im0 = axs[0,0].imshow(az_list[0], vmin=inps.vlim_snr[0], vmax=inps.vlim_snr[1], cmap='RdBu')
+    kwargs = dict(vmin=inps.vlim_snr[0], vmax=inps.vlim_snr[1], cmap='RdBu', interpolation='nearest')
-    im0 = axs[1,0].imshow(rg_list[0], vmin=inps.vlim_snr[0], vmax=inps.vlim_snr[1], cmap='RdBu')
+    im0 = axs[0,0].imshow(snr, **kwargs)
+    im0 = axs[1,0].imshow(snr, **kwargs)
     axs[0,0].set_title('SNR', fontsize=12)
+    print('SNR data range: [{}, {}]'.format(np.nanmin(snr), np.nanmax(snr)))
 
     # label
     axs[0,0].set_ylabel('azimuth', fontsize=12)
     axs[1,0].set_ylabel('range', fontsize=12)
 
     # plot offset
+    kwargs = dict(vmin=inps.vlim[0], vmax=inps.vlim[1], cmap='jet', interpolation='nearest')
     for i in range(1,len(az_list)):
-        im1 = axs[0,i].imshow(az_list[i], vmin=inps.vlim[0], vmax=inps.vlim[1], cmap='jet')
+        im1 = axs[0,i].imshow(az_list[i], **kwargs)
-        im1 = axs[1,i].imshow(rg_list[i], vmin=inps.vlim[0], vmax=inps.vlim[1], cmap='jet')
+        im1 = axs[1,i].imshow(rg_list[i], **kwargs)
         axs[0,i].set_title(titles[i], fontsize=12)
+        print('{} data range'.format(titles[i]))
+        print('azimuth offset: [{:.3f}, {:.3f}]'.format(np.nanmin(az_list[i]), np.nanmax(az_list[i])))
+        print('range   offset: [{:.3f}, {:.3f}]'.format(np.nanmin(rg_list[i]), np.nanmax(rg_list[i])))
     fig.tight_layout()
 
     # colorbar
     fig.subplots_adjust(bottom=0.15)
-    cax0 = fig.add_axes([0.09, 0.1, 0.08, 0.015])
+    cax0 = fig.add_axes([0.08, 0.1, 0.08, 0.015])
     cbar0 = plt.colorbar(im0, cax=cax0, orientation='horizontal')
     cax0.yaxis.set_ticks_position('left')
 
     #fig.subplots_adjust(right=0.93)
-    cax1 = fig.add_axes([0.57, 0.1, 0.08, 0.015])
+    cax1 = fig.add_axes([0.60, 0.1, 0.15, 0.015])
     cbar1 = plt.colorbar(im1, cax=cax1,  orientation='horizontal')
     cbar1.set_label('pixel', fontsize=12)
 
@@ -259,7 +292,7 @@ def main(iargs=None):
 
     inps = cmdLineParse(iargs)
 
-    os.makedirs(inps.outD, exist_ok=True)
+    os.makedirs(inps.outDir, exist_ok=True)
 
     #######################
     # masking the dense offsets based on SNR and median filter the masked offs
@@ -283,4 +316,3 @@ if __name__ == '__main__':
     Main driver.
     '''
     main()
-

contrib/stack/topsStack/grossOffsets.py

@@ -11,13 +11,13 @@ import isceobj
 from iscesys.Component.ProductManager import ProductManager as PM
 import numpy as np
 from netCDF4 import Dataset
-from mpl_toolkits.basemap import Basemap
 import gdal
 
 from scipy.interpolate import interp2d, griddata
 
 import matplotlib.pyplot as plt
 
+
 class grossOffsets:
 
     def __init__(self):
@@ -116,6 +116,7 @@ class grossOffsets:
 
         #x,y = np.meshgrid(self.x0,self.y0)
 
+        #from mpl_toolkits.basemap import Basemap
         #self.AntVeloDataMap = Basemap(width=5600000,height=5600000,\
         #                        resolution='l',projection='stere',\
         #                        lat_ts=-71,lat_0=-90,lon_0=0)

defaults/logging/logging.conf

@@ -21,8 +21,7 @@ propagate=0
 class=handlers.RotatingFileHandler
 formatter=simpleFormatter
 # Filename, file mode, maximum file size in bytes,number of backups to keep
-# encoding, delay
+args=('isce.log','a',1000048576,5)
-args=('isce.log','a',1048576,5,None,True)
 
 [handler_consoleHandler]
 class=StreamHandler

library/isceLib/CMakeLists.txt

@@ -1,4 +1,5 @@
-Python_add_library(isceLib MODULE
+cython_add_module(isceLib
+    pyx/isceLib.pyx
     src/Ellipsoid.cpp
     src/LinAlg.cpp
     src/Orbit.cpp