iamdonovan / spymicmac Goto Github PK

As noted by @ogaking, running register_relative without any masks causes an UnboundLocalError in _get_mask() at line 255. This should be fixed so that register_relative can be run without requiring a mask.

I use Malt to compute a relative DEM and orthoimages,But I encountered this problem, how can I solve it

add a T12 (mid-side + corner markers) as an option to spymicmac.matching.match_fairchild

What is the cause of this error? Please help me, thank you!

generate_micmac_measures calls to create id_fiducial.txt, MeasuresCamera.xml, and Tmp-SL-Glob.xml files for KH-9 Hexagon images. 1、1、However, how is measureSIM-DZb1215-500425L002001.tif-s2d.xml generated?
2、Tmp-SL-Glob-MeasuresIm-DZB1215-500425L002001.tif.xml= Tmp-SL-Glob.xml+"-MeasuresIm-DZB1215-500425L002001.tif" ? Can I understand it this way?

Hello,

How to overcome this error for hexagon joining:

Unable to allocate 19.2 GiB for an array with shape (35515, 72718) and data type float 64

Regards,
Hazem

in spymicmac.image.join_hexagon, explicitly choose float32 datatype to reduce memory requirement.

As part of standardizing/updating documentation (#42), add annotations to functions (https://peps.python.org/pep-3107/).

Error encountered running post_process_micmac whilst assigning CRS to DEM.

Spymicmac version:
0.2.1.dev41+g09496fc

(spymicmac) C:\Users\nok25\spymicmac_processing\SantaCruz>post_process_micmac "EPSG:32718" DEM_UTM.tif MEC-Malt
C:\Users\nok25\Software\spymicmac\src\spymicmac\image.py:22: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def nanstd(a):
Input file size is 17423, 19452
0...10...20...30...40...50...60...70...80...90...100 - done.
Input file size is 17423, 19452
0...10...20...30...40...50...60...70...80...90...100 - done.
Input file size is 17423, 19452
0...10...20...30...40...50...60...70...80...90...100 - done.
Traceback (most recent call last):
  File "C:\Users\nok25\AppData\Local\anaconda3\envs\spymicmac\lib\runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "C:\Users\nok25\AppData\Local\anaconda3\envs\spymicmac\lib\runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "C:\Users\nok25\AppData\Local\anaconda3\envs\spymicmac\Scripts\post_process_micmac.exe\__main__.py", line 7, in <module>
  File "C:\Users\nok25\Software\spymicmac\src\spymicmac\tools\post_process_micmac.py", line 27, in main
    post_process(**vars(args))
  File "C:\Users\nok25\Software\spymicmac\src\spymicmac\micmac.py", line 1225, in post_process
    subprocess.Popen(['gdal_calc.py', '--quiet', '-A', 'tmp_mask.tif', '-B', 'tmp_geo.tif',
  File "C:\Users\nok25\AppData\Local\anaconda3\envs\spymicmac\lib\subprocess.py", line 971, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "C:\Users\nok25\AppData\Local\anaconda3\envs\spymicmac\lib\subprocess.py", line 1456, in _execute_child
    hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
OSError: [WinError 193] %1 is not a valid Win32 application

Do the row and column numbers of the reference files Landsat and DEM need to be the same, and do they all need to cover the kh-9 image? Why does this problem always occur

Showing default values in function docstrings is not consistent, even within modules. A single, consistent format should be used.

hello
I encountered the following issues while running register_ortho.py

start.
No date information read from filename.
Traceback (most recent call last):
File "/media/rs/5AA23466A23448B11/例子/register_ortho.py", line 55, in
main()
File "/media/rs/5AA23466A23448B11/例子/register_ortho.py", line 41, in main
register_ortho(args.fn_ortho, args.fn_ref, args.fn_reldem, args.fn_dem,
File "/home/rs/anaconda3/envs/spymicmac/lib/python3.10/site-packages/spymicmac/register.py", line 330, in register_ortho
mask_full, _, ref_img = get_mask(footprints, ref_img, imlist, landmask, glacmask)
File "/home/rs/anaconda3/envs/spymicmac/lib/python3.10/site-packages/spymicmac/register.py", line 244, in get_mask
fmask, fprint = get_footprint_mask(footprints, img, imlist, fprint_out=True)
File "/home/rs/anaconda3/envs/spymicmac/lib/python3.10/site-packages/spymicmac/register.py", line 211, in get_footprint_mask
fprint = get_footprint_overlap(fp.to_crs(geoimg.proj4))
File "/home/rs/anaconda3/envs/spymicmac/lib/python3.10/site-packages/geopandas/geodataframe.py", line 1364, in to_crs
geom = df.geometry.to_crs(crs=crs, epsg=epsg)
File "/home/rs/anaconda3/envs/spymicmac/lib/python3.10/site-packages/geopandas/geoseries.py", line 1124, in to_crs
self.values.to_crs(crs=crs, epsg=epsg), index=self.index, name=self.name
File "/home/rs/anaconda3/envs/spymicmac/lib/python3.10/site-packages/geopandas/array.py", line 767, in to_crs
crs = CRS.from_user_input(crs)
File "/home/rs/anaconda3/envs/spymicmac/lib/python3.10/site-packages/pyproj/crs/crs.py", line 501, in from_user_input
return cls(value, **kwargs)
File "/home/rs/anaconda3/envs/spymicmac/lib/python3.10/site-packages/pyproj/crs/crs.py", line 348, in init
self._local.crs = _CRS(self.srs)
File "pyproj/_crs.pyx", line 2366, in pyproj._crs._CRS.init
pyproj.exceptions.CRSError: Invalid projection: : (Internal Proj Error: proj_create: unrecognized format / unknown name)

finish working on the tools for removing frames from panoramic images as part of the pre-processing steps

[EDIT: Solved]
I managed to solve my problem by indicating the correct library to search for qt in the CMAKE command line:

cmake .. -DWITH_QT5=1 -DWERROR=0 -DWITH_CCACHE=OFF -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu/qt5/plugins

Hello,

I have trouble properly installing MicMac. Following the installation guidelines everything works fine until there:
/home/bob/software/micmac/build:~$ cmake .. -DWITH_QT5=1 -DWERROR=0 -DWITH_CCACHE=OFF

The following error is displayed:

CMake Error at /home/avallet/anaconda3/envs/spatial_otb/conda-otb/lib/cmake/Qt5Xml/Qt5XmlConfig.cmake:14 (message):
The imported target "Qt5::Xml" references the file

 "/home/avallet/anaconda3/envs/spatial_otb/conda-otb/lib/libQt5Xml.so.5.15.2"

but this file does not exist. Possible reasons include:

• The file was deleted, renamed, or moved to another location.

• An install or uninstall procedure did not complete successfully.

• The installation package was faulty and contained

  "/home/avallet/anaconda3/envs/spatial_otb/conda-otb/lib/cmake/Qt5Xml/Qt5XmlConfig.cmake"

but not all the files it references.

Call Stack (most recent call first):
/home/avallet/anaconda3/envs/spatial_otb/conda-otb/lib/cmake/Qt5Xml/Qt5XmlConfig.cmake:32 (_qt5_Xml_check_file_exists)
/home/avallet/anaconda3/envs/spatial_otb/conda-otb/lib/cmake/Qt5Xml/Qt5XmlConfig.cmake:202 (_populate_Xml_target_properties)
CMakeLists.txt:210 (find_package)`

I am not very familiar with this, but from what i understand, the following file "libQt5Xml.so.5.15.2" is not found in the directory it searches in (the library of one of my conda environments). However libQt5Xml.so.5.15.3" (a newer version i assume) exists on my computer in the following directory "/usr/lib/x86_64-linux-gnu".

I have tried to modify my environment variables accordingly by adding

• "/usr" to C_MAKE_PREFIX

• /usr/lib/x86_64-linux-gnu to LD_LIBRARY_PATH

However the same arror displays when trying to run the cmake command line.
I am working with the following distribution: Description: Ubuntu 22.04.2 LTS

Jules Michard,
Regards.

I have the following environment variables if this can be of any help:

declare -x BROWSER="/usr/lib/rstudio-server/bin/postback/rpostback-browser"
declare -x CLICOLOR_FORCE="1"
declare -x CMAKE_PREFIX_PATH="/usr:/home/avallet/anaconda3/envs/spatial_otb/conda-otb:/home/vallet/anaconda3/lib"
declare -x CONDA_BACKUP_ADDR2LINE="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-addr2line"
declare -x CONDA_BACKUP_AR="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-ar"
declare -x CONDA_BACKUP_AS="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-as"
declare -x CONDA_BACKUP_BUILD="x86_64-conda-linux-gnu"
declare -x CONDA_BACKUP_CC="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-cc"
declare -x CONDA_BACKUP_CC_FOR_BUILD="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-cc"
declare -x CONDA_BACKUP_CFLAGS="-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/avallet/anaconda3/envs/test-iota/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/avallet/anaconda3/envs/test-iota/include"
declare -x CONDA_BACKUP_CMAKE_PREFIX_PATH="/home/avallet/anaconda3/envs/test-iota:/home/avallet/anaconda3/envs/test-iota/x86_64-conda-linux-gnu/sysroot/usr"
declare -x CONDA_BACKUP_CONDA_BUILD_SYSROOT="/home/avallet/anaconda3/envs/test-iota/x86_64-conda-linux-gnu/sysroot"
declare -x CONDA_BACKUP_CONDA_TOOLCHAIN_BUILD="x86_64-conda-linux-gnu"
declare -x CONDA_BACKUP_CONDA_TOOLCHAIN_HOST="x86_64-conda-linux-gnu"
declare -x CONDA_BACKUP_CPP="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-cpp"
declare -x CONDA_BACKUP_CPPFLAGS="-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/avallet/anaconda3/envs/test-iota/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/avallet/anaconda3/envs/test-iota/include"
declare -x CONDA_BACKUP_CXX="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-c++"
declare -x CONDA_BACKUP_CXXFILT="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-c++filt"
declare -x CONDA_BACKUP_CXXFLAGS="-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/avallet/anaconda3/envs/test-iota/include -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/avallet/anaconda3/envs/test-iota/include"
declare -x CONDA_BACKUP_CXX_FOR_BUILD="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-c++"
declare -x CONDA_BACKUP_DEBUG_CFLAGS="-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/avallet/anaconda3/envs/test-iota/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/avallet/anaconda3/envs/test-iota/include"
declare -x CONDA_BACKUP_DEBUG_CPPFLAGS="-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /home/avallet/anaconda3/envs/test-iota/include -D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /home/avallet/anaconda3/envs/test-iota/include"
declare -x CONDA_BACKUP_DEBUG_CXXFLAGS="-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/avallet/anaconda3/envs/test-iota/include -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/avallet/anaconda3/envs/test-iota/include"
declare -x CONDA_BACKUP_ELFEDIT="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-elfedit"
declare -x CONDA_BACKUP_GCC="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-gcc"
declare -x CONDA_BACKUP_GCC_AR="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-gcc-ar"
declare -x CONDA_BACKUP_GCC_NM="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-gcc-nm"
declare -x CONDA_BACKUP_GCC_RANLIB="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-gcc-ranlib"
declare -x CONDA_BACKUP_GPROF="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-gprof"
declare -x CONDA_BACKUP_GXX="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-g++"
declare -x CONDA_BACKUP_HOST="x86_64-conda-linux-gnu"
declare -x CONDA_BACKUP_LD="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-ld"
declare -x CONDA_BACKUP_LDFLAGS="-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/avallet/anaconda3/envs/test-iota/lib -Wl,-rpath-link,/home/avallet/anaconda3/envs/test-iota/lib -L/home/avallet/anaconda3/envs/test-iota/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/avallet/anaconda3/envs/test-iota/lib -Wl,-rpath-link,/home/avallet/anaconda3/envs/test-iota/lib -L/home/avallet/anaconda3/envs/test-iota/lib"
declare -x CONDA_BACKUP_LD_GOLD="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-ld.gold"
declare -x CONDA_BACKUP_NM="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-nm"
declare -x CONDA_BACKUP_OBJCOPY="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-objcopy"
declare -x CONDA_BACKUP_OBJDUMP="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-objdump"
declare -x CONDA_BACKUP_RANLIB="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-ranlib"
declare -x CONDA_BACKUP_READELF="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-readelf"
declare -x CONDA_BACKUP_SIZE="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-size"
declare -x CONDA_BACKUP_STRINGS="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-strings"
declare -x CONDA_BACKUP_STRIP="/home/avallet/anaconda3/envs/test-iota/bin/x86_64-conda-linux-gnu-strip"
declare -x CONDA_BACKUP_build_alias="x86_64-conda-linux-gnu"
declare -x CONDA_BACKUP_host_alias="x86_64-conda-linux-gnu"
declare -x CONDA_DEFAULT_ENV="spatial_otb"
declare -x CONDA_EXE="/home/avallet/anaconda3/bin/conda"
declare -x CONDA_PREFIX="/home/avallet/anaconda3/envs/spatial_otb"
declare -x CONDA_PREFIX_1="/home/avallet/anaconda3"
declare -x CONDA_PROMPT_MODIFIER="(spatial_otb) "
declare -x CONDA_PYTHON_EXE="/home/avallet/anaconda3/bin/python"
declare -x CONDA_SHLVL="2"
declare -x CPL_ZIP_ENCODING="UTF-8"
declare -x DISPLAY=":0"
declare -x DQt5_ROOT="/usr"
declare -x EDITOR="vi"
declare -x GDAL_DATA="/home/avallet/anaconda3/envs/spatial_otb/conda-otb/share/gdal"
declare -x GDAL_DRIVER_PATH="disable"
declare -x GIT_ASKPASS="rpostback-askpass"
declare -x GSETTINGS_SCHEMA_DIR="/home/avallet/anaconda3/envs/spatial_otb/share/glib-2.0/schemas"
declare -x GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=""
declare -x HISTCONTROL="ignoreboth"
declare -x HOME="/home/avallet"
declare -x LANG="fr_FR.UTF-8"
declare -x LC_NUMERIC="C"
declare -x LD_LIBRARY_PATH="/usr/lib/R/lib:/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/default-java/lib/server"
declare -x LESSCLOSE="/usr/bin/lesspipe %s %s"
declare -x LESSOPEN="| /usr/bin/lesspipe %s"
declare -x LN_S="ln -s"
declare -x LOGNAME="avallet"
declare -x LS_COLORS="rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:.tar=01;31:.tgz=01;31:.arc=01;31:.arj=01;31:.taz=01;31:.lha=01;31:.lz4=01;31:.lzh=01;31:.lzma=01;31:.tlz=01;31:.txz=01;31:.tzo=01;31:.t7z=01;31:.zip=01;31:.z=01;31:.dz=01;31:.gz=01;31:.lrz=01;31:.lz=01;31:.lzo=01;31:.xz=01;31:.zst=01;31:.tzst=01;31:.bz2=01;31:.bz=01;31:.tbz=01;31:.tbz2=01;31:.tz=01;31:.deb=01;31:.rpm=01;31:.jar=01;31:.war=01;31:.ear=01;31:.sar=01;31:.rar=01;31:.alz=01;31:.ace=01;31:.zoo=01;31:.cpio=01;31:.7z=01;31:.rz=01;31:.cab=01;31:.wim=01;31:.swm=01;31:.dwm=01;31:.esd=01;31:.jpg=01;35:.jpeg=01;35:.mjpg=01;35:.mjpeg=01;35:.gif=01;35:.bmp=01;35:.pbm=01;35:.pgm=01;35:.ppm=01;35:.tga=01;35:.xbm=01;35:.xpm=01;35:.tif=01;35:.tiff=01;35:.png=01;35:.svg=01;35:.svgz=01;35:.mng=01;35:.pcx=01;35:.mov=01;35:.mpg=01;35:.mpeg=01;35:.m2v=01;35:.mkv=01;35:.webm=01;35:.webp=01;35:.ogm=01;35:.mp4=01;35:.m4v=01;35:.mp4v=01;35:.vob=01;35:.qt=01;35:.nuv=01;35:.wmv=01;35:.asf=01;35:.rm=01;35:.rmvb=01;35:.flc=01;35:.avi=01;35:.fli=01;35:.flv=01;35:.gl=01;35:.dl=01;35:.xcf=01;35:.xwd=01;35:.yuv=01;35:.cgm=01;35:.emf=01;35:.ogv=01;35:.ogx=01;35:.aac=00;36:.au=00;36:.flac=00;36:.m4a=00;36:.mid=00;36:.midi=00;36:.mka=00;36:.mp3=00;36:.mpc=00;36:.ogg=00;36:.ra=00;36:.wav=00;36:.oga=00;36:.opus=00;36:.spx=00;36:.xspf=00;36:"
declare -x MAKE="make"
declare -x MPLENGINE="tkAgg"
declare -x OLDPWD="/usr"
declare -x OTB_APPLICATION_PATH="/home/avallet/anaconda3/envs/spatial_otb/conda-otb/lib/otb/applications:/home/avallet/anaconda3/envs/spatial_otb/conda-otb/lib/otb/applications"
declare -x PAGER="/usr/bin/pager"
declare -x PATH="/home/avallet/anaconda3/envs/spatial_otb/conda-otb/bin:/home/avallet/anaconda3/envs/spatial_otb/bin:/home/avallet/anaconda3/envs/spatial_otb/conda-otb/bin:/home/avallet/anaconda3/envs/spatial_otb/conda-otb/bin:/home/avallet/anaconda3/bin:/home/avallet/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/usr/lib/rstudio-server/bin/quarto/bin:/usr/lib/rstudio-server/bin/postback/postback:/usr/lib/rstudio-server/bin/postback/postback:/usr/lib/rstudio-server/bin/postback/postback:/usr/lib/rstudio-server/bin/postback/postback:/usr/lib/rstudio-server/bin/postback/postback:/usr/lib/rstudio-server/bin/postback/postback:/usr/bin:/usr/bin:/usr/bin:/usr/bin:/usr/bin:/usr/bin:/usr/bin:/usr/bin:/usr/bin:/usr/bin:/usr/bin:/usr/bin"
declare -x PROJ_DATA="/home/avallet/anaconda3/envs/spatial_otb/share/proj"
declare -x PROJ_LIB="/home/avallet/anaconda3/envs/spatial_otb/conda-otb/share/proj:/home/avallet/anaconda3/envs/spatial_otb/share/proj"
declare -x PROJ_NETWORK="ON"
declare -x PROMPT_COMMAND="echo -ne "\033]0;${PWD/#${HOME}/~}\007""
declare -x PWD="/home/avallet/micmac/build"
declare -x PYTHONPATH="/home/avallet/anaconda3/envs/spatial_otb/conda-otb/lib/python:/home/avallet/anaconda3/envs/spatial_otb/conda-otb/lib/python"
declare -x RETICULATE_MINICONDA_ENABLED=""
declare -x RETICULATE_PYTHON_FALLBACK="/home/avallet/anaconda3/bin/python"
declare -x RMARKDOWN_MATHJAX_PATH="/usr/lib/rstudio-server/resources/mathjax-27"
declare -x RSTUDIO="1"
declare -x RSTUDIO_CHILD_PROCESS_PANE="terminal"
declare -x RSTUDIO_CLI_HYPERLINKS="true"
declare -x RSTUDIO_CONSOLE_COLOR="256"
declare -x RSTUDIO_CONSOLE_WIDTH="135"
declare -x RSTUDIO_HTTP_REFERER="http://157.136.249.10:8080/"
declare -x RSTUDIO_PANDOC="/usr/lib/rstudio-server/bin/quarto/bin/tools"
declare -x RSTUDIO_PROGRAM_MODE="server"
declare -x RSTUDIO_PROJ_NAME=""
declare -x RSTUDIO_R_MODULE=""
declare -x RSTUDIO_R_PRELAUNCH_SCRIPT=""
declare -x RSTUDIO_R_REPO=""
declare -x RSTUDIO_R_VERSION_LABEL=""
declare -x RSTUDIO_SESSION_ID="5deb81d4"
declare -x RSTUDIO_SESSION_PID="1643411"
declare -x RSTUDIO_SESSION_STREAM="avallet-d"
declare -x RSTUDIO_TERM="9E76B53C"
declare -x RSTUDIO_TERMINAL_HOOKS="/usr/lib/rstudio-server/resources/terminal/hooks"
declare -x RSTUDIO_USER_IDENTITY="avallet"
declare -x RSTUDIO_USER_IDENTITY_DISPLAY="avallet"
declare -x RSTUDIO_VERSION="2022.12.0+353"
declare -x RSTUDIO_WINUTILS="bin/winutils"
declare -x RS_PORT_TOKEN="61e1dc358d8e"
declare -x RS_RPOSTBACK_PATH="/usr/lib/rstudio-server/bin/rpostback"
declare -x RS_SERVER_RPC_SOCKET_PATH="/var/run/rstudio-server/rstudio-rserver/session-server-rpc.socket"
declare -x RS_SERVER_URL="http://157.136.249.10:8080/"
declare -x RS_SESSION_TMP_DIR="/var/run/rstudio-server/rstudio-rsession"
declare -x RS_SESSION_URL=""
declare -x R_BROWSER="xdg-open"
declare -x R_BZIPCMD="/bin/bzip2"
declare -x R_CLI_HAS_HYPERLINK_IDE_HELP="true"
declare -x R_CLI_HAS_HYPERLINK_IDE_RUN="true"
declare -x R_CLI_HAS_HYPERLINK_IDE_VIGNETTE="true"
declare -x R_DOC_DIR="/usr/share/R/doc"
declare -x R_GZIPCMD="/bin/gzip -n"
declare -x R_HOME="/usr/lib/R"
declare -x R_INCLUDE_DIR="/usr/share/R/include"
declare -x R_LIBS_SITE="/usr/local/lib/R/site-library/:/usr/lib/R/site-library:/usr/lib/R/library"
declare -x R_LIBS_USER="/home/avallet/R/x86_64-pc-linux-gnu-library/4.2"
declare -x R_PAPERSIZE="letter"
declare -x R_PAPERSIZE_USER="letter"
declare -x R_PDFVIEWER="/usr/bin/xdg-open"
declare -x R_PLATFORM="x86_64-pc-linux-gnu"
declare -x R_PRINTCMD="/usr/bin/lpr"
declare -x R_RD4PDF="times,inconsolata,hyper"
declare -x R_SESSION_TMPDIR="/mnt/disk/temp/Rtmpf3otVI"
declare -x R_SHARE_DIR="/usr/share/R/share"
declare -x R_STRIP_SHARED_LIB="strip --strip-unneeded"
declare -x R_STRIP_STATIC_LIB="strip --strip-debug"
declare -x R_SYSTEM_ABI="linux,gcc,gxx,gfortran,gfortran"
declare -x R_TEXI2DVICMD="/usr/bin/texi2dvi"
declare -x R_UNZIPCMD="/usr/bin/unzip"
declare -x R_ZIPCMD="/usr/bin/zip"
declare -x SED="/bin/sed"
declare -x SHLVL="12"
declare -x SSH_ASKPASS="rpostback-askpass"
declare -x TAR="/bin/tar"
declare -x TEMP="/mnt/disk/temp"
declare -x TERM="xterm-256color"
declare -x TMP="/mnt/disk/temp"
declare -x TMPDIR="/mnt/disk/temp"
declare -x USER="avallet"
declare -x XDG_DATA_DIRS="/usr/local/share:/usr/share:/var/lib/snapd/desktop"
declare -x _CE_CONDA=""
declare -x _CE_M=""
declare -x _REALHOME="/home/avallet"
declare -x R_CHECK_COMPILATION_FLAGS_KNOWN="-Wformat -Werror=format-security -Wdate-time"

Two issues to fix/address here:

• preprocess_pan needs to be updated to allow for additional arguments to join_hexagon, such as (-r)
• the final tmp.tif files need to be deleted once the program finishes

When using find_reseau_grid command, sometimes it will report an error of: numpy.linalg.LinAlgError: Singular matrix. Is it a bug? Or just because of the low image quality?

Also, in some cases, the calculated distortion fields were obvious wrong or contained a few distortion vectors (as the picture show).

Here is the error information:

Finding grid points in DZB1211-500125L006001_b.tif...
Traceback (most recent call last):
  File "/usr/local/miniconda3/bin/find_reseau_grid", line 33, in <module>
    sys.exit(load_entry_point('spymicmac', 'console_scripts', 'find_reseau_grid')())
  File "/usr/local/sPyMicMac/spymicmac/tools/find_reseau_grid.py", line 25, in main
    find_reseau_grid(args.fn_img,
  File "/usr/local/sPyMicMac/spymicmac/image.py", line 964, in find_reseau_grid
    ux = lsq_fit(gcps_df.search_j.values, gcps_df.search_i.values, gcps_df.match_j.values)
  File "/usr/local/sPyMicMac/spymicmac/image.py", line 719, in lsq_fit
    fit = (A.T * A).I * A.T * b.T
  File "/usr/local/miniconda3/lib/python3.8/site-packages/numpy/matrixlib/defmatrix.py", line 835, in I
    return asmatrix(func(self))
  File "<__array_function__ internals>", line 5, in inv
  File "/usr/local/miniconda3/lib/python3.8/site-packages/numpy/linalg/linalg.py", line 545, in inv
    ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
  File "/usr/local/miniconda3/lib/python3.8/site-packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular
    raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
``
![DZB1211-500142L008001_b_matches](https://user-images.githubusercontent.com/37327637/157366425-8be59eac-dc2c-4cfe-92ab-f1b953b538b1.png)

Thanks for providing the code. I completed the KH-9 pre-processing steps in f0b43a0. However, I tried to change the order of the steps. “image joining” was performed first. Next, “reseau field” and “cross removal”. The results look great. Unfortunately, there was a problem in “re-sampling the images”, as shown in the figure. Can you give me some advice on how to make this step work? Thanks a lot.

An error occurred while running the last step Aperi in preprocess_kh9.py

I am trying to import the images but I cant find inside the python scripts any address for the 2 tiff files to start

Regards,
Hazem

Do the row and column numbers of the reference files Landsat and DEM need to be the same, and do they all need to cover the kh-9 image? Why does this problem always occur

scikit-image v0.20.0 has deprecated the greycomatrix and greycoprops functions in skimage.feature, which means that pybob will not import in an environment with scikit-image > 0.19.

Dear Prof. Bob McNabb,

Hope you have a pleasant day.

I am a graduate student of Yunnan University in China. My research is focus on surge-type glacier. I have tried to run your source program for a long time, but no progress. I am wondering if you could kindly provide me some guide. My question is as follows:

1. The generate_micmac_measures() command can only generate id_fiducial.txt, MeasuresCamera.xml, and Tmp-SL-Glob.xml, but before running the find_reseau_grid() command, How is the MeasuresIm-DZB1215-500425L002001.tif.xml. generated? In other words, how do I get the MeasuresIm-DZB1215-500425L002001.tif-S2D.xml file before I run the find_reseau_grid() command?
   
2. When I run find_reseau_grid(), there are no errors. However, as shown in the figure below, this result obviously looks wrong. How can I interpret the results or modify them to make reasonable? Is this result related to the file (such as id_fiducial.txt, MeasuresCamera.xml, Tmp-SL-Glob.xml) generated in the previous step? Or is it related to MeasuresIm-DZB1215-500425L002001.tif.xml?
   
   Thank you very much for your kind consideration and I am looking forward to your early reply.
   Thanks & Regards,
   Miaomiao Qi

update installation to use setup.cfg/pyproject.toml

spymicmac currently ships with two bash scripts:

• bin/get_autogcp_locations.sh
• bin/post_process_micmac.sh

post_process_micmac.sh is not needed for processing, but get_autogcp_locations.sh is (which means that register_ortho will fail in windows). The functionality of both scripts should be converted into functions in one or more modules.