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plateflex's Introduction

Software for mapping the effective elastic thickness of the lithosphere

The flexure of elastic plates is a central concept in the theory of plate tectonics, where the Earth's lithosphere (crust and uppermost mantle) reacts to applied loads by bending, a process referred to as flexural isostasy. Estimating the effective elastic thickness (Te) of the lithosphere (thickness of an equivalent ideal elastic plate) gives important clues on the rheology of the lithosphere and its thermal state. Estimating Te can be done by modeling the cross-spectral properties (admittance and coherence) between topography and gravity anomaly data, which are proxies for the distribution of flexurally compensated surface and subsurface loads.

This package contains python and fortran modules to calculate the wavelet spectral and cross-spectral quantities of 2D gridded data of topography and gravity anomalies. Once obtained, the wavelet cross-spectral quantities (admittance and coherence) are used to determine the parameters of the effectively elastic plate, such as the effective elastic thickness (Te), the initial subsurface-to-surface load ratio (F) and optionally the initial phase difference between surface and subsurface loads (alpha). The estimation can be done using non-linear least-squares or probabilistic (i.e., bayesian) inference methods. The analysis can be done using either the Bouguer or Free air gravity anomalies, and over land or ocean areas. Computational workflows are covered in the Jupyter notebooks bundled with this package. The software contains methods to make publication-quality plots using the seaborn package.

DOI build

Installation, Usage, API documentation and Jupyter Notebooks are described at https://paudetseis.github.io/PlateFlex/

Authors: Pascal Audet (Developer and Maintainer) & Zhezhe Lu (Contributor)

Citing

If you use PlateFlex in your work, please cite the Zenodo DOI.

Contributing

All constructive contributions are welcome, e.g. bug reports, discussions or suggestions for new features. You can either open an issue on GitHub or make a pull request with your proposed changes. Before making a pull request, check if there is a corresponding issue opened and reference it in the pull request. If there isn't one, it is recommended to open one with your rationale for the change. New functionality or significant changes to the code that alter its behavior should come with corresponding tests and documentation. If you are new to contributing, you can open a work-in-progress pull request and have it iteratively reviewed.

Examples of straightforward contributions include notebooks that describe published examples of elastic thickness results. Suggestions for improvements (speed, accuracy, etc.) are also welcome.

References

  • Audet, P. (2014). Toward mapping the effective elastic thickness of planetary lithospheres from a spherical wavelet analysis of gravity and topography. Physics of the Earth and Planetary Interiors, 226, 48-82. https://doi.org/10.1016/j.pepi.2013.09.011

  • Kalnins, L.M., and Watts, A.B. (2009). Spatial variations in effective elastic thickness in the Western Pacific Ocean and their implications for Mesozoic volcanism. Earth and Planetary Science Letters, 286, 89-100. https://doi.org/10.1016/j.epsl.2009.06.018

  • Kirby, J.F., and Swain, C.J. (2009). A reassessment of spectral Te estimation in continental interiors: The case of North America. Journal of Geophysical Research, 114, B08401. https://doi.org/10.1029/2009JB006356

  • Kirby, J.F. (2014). Estimation of the effective elastic thickness of the lithosphere using inverse spectral methods: The state of the art. Tectonophysics, 631, 87-116. https://doi.org/10.1016/j.tecto.2014.04.021

Use cases

  • Lu, Z., Li, C.-F., Zhu, S., and Audet, P. (2020). Effective elastic thickness over the Chinese mainland and surroundings estimated from a joint inversion of Bouguer admittance and coherence. Physics of the Earth and Planetary Interiors, 301, 106456, https://doi.org/10.1016/j.pepi.2020.106456

  • Lu, Z., Audet, P., Li, C.-F., Zhu, S., and Wu, Z. (2021). What Controls Effective Elastic Thickness of the Lithosphere in the Pacific Ocean? Journal of Geophysical Research, https://doi.org/10.1029/2020JB021074

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plateflex's Issues

Problem resampling CRUST1.0

Dear users of plateflex:

I am following the example of the documentation to make a grid for crustal thickness using CRUST1.0. I got crsthk.xyz file and created the 1 degree grid file using:

            gmt xyz2grd crsthk.xyz -Gcrust_thickness_1deg.grd -Rd -I1

However, when I try to resample to 2' grid using:

              gmt grdsample crust_thickness_1deg.grd -Gcrust_thickness_2m.grd -nb -Rg -I2m

I got a grdsample warning related to no valid values in grid [crust_thickness_2m.grd] and as a consequence a grid full of nan values.

I am using GMT 5.4.3.

Have someone had this problem? Any advice/recommendation.

Thanks in advance.

How to run Plateflex on Cygwin

Hello Prof. Pascal Audet
Firstly I do greatly apologize for my previous comments, I am deeply sorry sir.

With a candid heart I write to you sir to kindly guide in the installation process of the plateflex on Cygwin terminal, I have read your papers and others that recently use this plateflex to estimate Te, however going through the software and the materials attached I find it difficult to run or start up on my Cygwin. Sir, I will appreciate if I can be guided on this new developed methods on Te estimation.
Am very curious to learn and know much in the use of this software as I see many advantageous features of plateflex over other and also notice it uniqueness on published papers.
Look forward to receiving an answer soon and also send my apologies.
Ijaodola

Problems Installing

Hi,

I'm having trouble installing PlateFlex. I have created the anaconda environment as suggested in the installation instructions but the installation throws a large amount amount of errors. I'm a little stuck at the moment and don't really understand where the error is coming from.

Any help would be great - even if it's to say that you don't know and its something wrong with my system.

Tim

p.s. I've included the terminal output below

(pflex) tg286@circinus:/space/tg286/PlateFlex$ python -m pip install .
Processing /space/tg286/PlateFlex
Requirement already satisfied: numpy>=1.15 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from plateflex==0.1.0) (1.17.5)
Requirement already satisfied: pymc3 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from plateflex==0.1.0) (3.8)
Requirement already satisfied: matplotlib in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from plateflex==0.1.0) (3.1.2)
Requirement already satisfied: seaborn in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from plateflex==0.1.0) (0.9.0)
Requirement already satisfied: arviz>=0.4.1 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (0.6.1)
Requirement already satisfied: theano>=1.0.4 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (1.0.4)
Requirement already satisfied: tqdm>=4.8.4 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (4.41.1)
Requirement already satisfied: h5py>=2.7.0 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (2.10.0)
Requirement already satisfied: pandas>=0.18.0 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (0.25.3)
Requirement already satisfied: patsy>=0.4.0 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (0.5.1)
Requirement already satisfied: scipy>=0.18.1 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (1.4.1)
Requirement already satisfied: kiwisolver>=1.0.1 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from matplotlib->plateflex==0.1.0) (1.1.0)
Requirement already satisfied: cycler>=0.10 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from matplotlib->plateflex==0.1.0) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from matplotlib->plateflex==0.1.0) (2.4.6)
Requirement already satisfied: python-dateutil>=2.1 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from matplotlib->plateflex==0.1.0) (2.8.1)
Requirement already satisfied: packaging in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from arviz>=0.4.1->pymc3->plateflex==0.1.0) (20.0)
Requirement already satisfied: netcdf4 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from arviz>=0.4.1->pymc3->plateflex==0.1.0) (1.5.3)
Requirement already satisfied: xarray>=0.11 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from arviz>=0.4.1->pymc3->plateflex==0.1.0) (0.14.1)
Requirement already satisfied: six>=1.9.0 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from theano>=1.0.4->pymc3->plateflex==0.1.0) (1.14.0)
Requirement already satisfied: pytz>=2017.2 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pandas>=0.18.0->pymc3->plateflex==0.1.0) (2019.3)
Requirement already satisfied: setuptools in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib->plateflex==0.1.0) (45.1.0.post20200119)
Requirement already satisfied: cftime in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from netcdf4->arviz>=0.4.1->pymc3->plateflex==0.1.0) (1.0.4.2)
Building wheels for collected packages: plateflex
Building wheel for plateflex (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /space/tg286/miniconda_alt/envs/pflex/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-4_zm7t8a/setup.py'"'"'; file='"'"'/tmp/pip-req-build-4_zm7t8a/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-bvv4pwnc --python-tag cp37
cwd: /tmp/pip-req-build-4_zm7t8a/
Complete output (114 lines):
running bdist_wheel
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "plateflex.cpwt" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex' to include_dirs.
adding 'build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.f90' to sources.
building extension "plateflex.flex" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex' to include_dirs.
adding 'build/src.linux-x86_64-3.7/plateflex/flex-f2pywrappers2.f90' to sources.
build_src: building npy-pkg config files
running build_py
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/plateflex
copying plateflex/estimate.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/init.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/doc.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/classes.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/plotting.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/conf.py -> build/lib.linux-x86_64-3.7/plateflex
creating build/lib.linux-x86_64-3.7/plateflex/examples
copying plateflex/examples/data.zip -> build/lib.linux-x86_64-3.7/plateflex/examples
creating build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex2_wavelet_analysis.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex7_full_suite_NW_Pacific.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex5_estimate_flex_parameters_grid.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex1_making_grids.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex3_admittance_coherence.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex4_estimate_flex_parameters_cell.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex6_full_suite_North_America.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
running build_ext
customize UnixCCompiler
C compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /space/tg286/miniconda_alt/envs/pflex/include -fPIC

creating /tmp/tmpiylvn2_z/tmp
creating /tmp/tmpiylvn2_z/tmp/tmpiylvn2_z
compile options: '-MMD -MF /tmp/tmpiylvn2_z/file.c.d -c'
x86_64-conda_cos6-linux-gnu-cc: /tmp/tmpiylvn2_z/file.c
customize UnixCCompiler using build_ext
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ld
Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ar
Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ranlib
/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/distutils/fcompiler/init.py:530: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release).
linker_so_flags = self.flag_vars.linker_so
/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/distutils/fcompiler/init.py:540: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release).
linker_exe_flags = self.flag_vars.linker_exe
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'plateflex.cpwt' extension
compiling C sources
C compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /space/tg286/miniconda_alt/envs/pflex/include -fPIC

creating build/temp.linux-x86_64-3.7/build
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex
compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c'
x86_64-conda_cos6-linux-gnu-cc: build/src.linux-x86_64-3.7/plateflex/cpwtmodule.cx86_64-conda_cos6-linux-gnu-cc: build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c

In file included from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830:0,
from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.h:13,
from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c:2:
/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it with "
^~~~~~~
In file included from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830:0,
from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.h:13,
from build/src.linux-x86_64-3.7/plateflex/cpwtmodule.c:16:
/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it with "
^~~~~~~
build/src.linux-x86_64-3.7/plateflex/cpwtmodule.c:148:12: warning: 'f2py_size' defined but not used [-Wunused-function]
static int f2py_size(PyArrayObject* var, ...)
^~~~~~~~~
compiling Fortran 90 module sources
creating build/temp.linux-x86_64-3.7/plateflex
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
creating build/temp.linux-x86_64-3.7/src
creating build/temp.linux-x86_64-3.7/src/cpwt
compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c'
extra options: '-Jbuild/temp.linux-x86_64-3.7/plateflex -Ibuild/temp.linux-x86_64-3.7/plateflex'
gfortran:f90: src/cpwt/cpwt.f90
compiling Fortran sources
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c'
extra options: '-Jbuild/temp.linux-x86_64-3.7/plateflex -Ibuild/temp.linux-x86_64-3.7/plateflex'
gfortran:f90: src/cpwt/cpwt_sub.f90
gfortran:f90: build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.f90
/usr/bin/gfortran -Wall -g -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/space/tg286/miniconda_alt/envs/pflex/lib -Wl,-rpath-link,/space/tg286/miniconda_alt/envs/pflex/lib -L/space/tg286/miniconda_alt/envs/pflex/lib build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwtmodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt_sub.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran -lgfortran -o build/lib.linux-x86_64-3.7/plateflex/cpwt.cpython-37m-x86_64-linux-gnu.so
/usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/Scrt1.o: In function _start': (.text+0x20): undefined reference to main'
collect2: error: ld returned 1 exit status
error: Command "/usr/bin/gfortran -Wall -g -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/space/tg286/miniconda_alt/envs/pflex/lib -Wl,-rpath-link,/space/tg286/miniconda_alt/envs/pflex/lib -L/space/tg286/miniconda_alt/envs/pflex/lib build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwtmodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt_sub.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran -lgfortran -o build/lib.linux-x86_64-3.7/plateflex/cpwt.cpython-37m-x86_64-linux-gnu.so" failed with exit status 1

ERROR: Failed building wheel for plateflex
Running setup.py clean for plateflex
Failed to build plateflex
Installing collected packages: plateflex
Running setup.py install for plateflex ... error
ERROR: Command errored out with exit status 1:
command: /space/tg286/miniconda_alt/envs/pflex/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-4_zm7t8a/setup.py'"'"'; file='"'"'/tmp/pip-req-build-4_zm7t8a/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-ka0tb788/install-record.txt --single-version-externally-managed --compile
cwd: /tmp/pip-req-build-4_zm7t8a/
Complete output (114 lines):
running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "plateflex.cpwt" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex' to include_dirs.
adding 'build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.f90' to sources.
building extension "plateflex.flex" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex' to include_dirs.
adding 'build/src.linux-x86_64-3.7/plateflex/flex-f2pywrappers2.f90' to sources.
build_src: building npy-pkg config files
running build_py
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/plateflex
copying plateflex/estimate.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/init.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/doc.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/classes.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/plotting.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/conf.py -> build/lib.linux-x86_64-3.7/plateflex
creating build/lib.linux-x86_64-3.7/plateflex/examples
copying plateflex/examples/data.zip -> build/lib.linux-x86_64-3.7/plateflex/examples
creating build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex2_wavelet_analysis.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex7_full_suite_NW_Pacific.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex5_estimate_flex_parameters_grid.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex1_making_grids.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex3_admittance_coherence.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex4_estimate_flex_parameters_cell.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex6_full_suite_North_America.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
running build_ext
customize UnixCCompiler
C compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /space/tg286/miniconda_alt/envs/pflex/include -fPIC

creating /tmp/tmp75p4d3k_/tmp
creating /tmp/tmp75p4d3k_/tmp/tmp75p4d3k_
compile options: '-MMD -MF /tmp/tmp75p4d3k_/file.c.d -c'
x86_64-conda_cos6-linux-gnu-cc: /tmp/tmp75p4d3k_/file.c
customize UnixCCompiler using build_ext
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ld
Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ar
Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ranlib
/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/distutils/fcompiler/__init__.py:530: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release).
  linker_so_flags = self.flag_vars.linker_so
/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/distutils/fcompiler/__init__.py:540: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release).
  linker_exe_flags = self.flag_vars.linker_exe
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'plateflex.cpwt' extension
compiling C sources
C compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /space/tg286/miniconda_alt/envs/pflex/include -fPIC

creating build/temp.linux-x86_64-3.7/build
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex
compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c'
x86_64-conda_cos6-linux-gnu-cc: build/src.linux-x86_64-3.7/plateflex/cpwtmodule.c
x86_64-conda_cos6-linux-gnu-cc: build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c
In file included from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830:0,
                 from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.h:13,
                 from build/src.linux-x86_64-3.7/plateflex/cpwtmodule.c:16:
/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^~~~~~~
In file included from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830:0,
                 from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.h:13,
                 from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c:2:
/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^~~~~~~
build/src.linux-x86_64-3.7/plateflex/cpwtmodule.c:148:12: warning: 'f2py_size' defined but not used [-Wunused-function]
 static int f2py_size(PyArrayObject* var, ...)
            ^~~~~~~~~
compiling Fortran 90 module sources
creating build/temp.linux-x86_64-3.7/plateflex
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
creating build/temp.linux-x86_64-3.7/src
creating build/temp.linux-x86_64-3.7/src/cpwt
compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c'
extra options: '-Jbuild/temp.linux-x86_64-3.7/plateflex -Ibuild/temp.linux-x86_64-3.7/plateflex'
gfortran:f90: src/cpwt/cpwt.f90
compiling Fortran sources
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c'
extra options: '-Jbuild/temp.linux-x86_64-3.7/plateflex -Ibuild/temp.linux-x86_64-3.7/plateflex'
gfortran:f90: src/cpwt/cpwt_sub.f90
gfortran:f90: build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.f90
/usr/bin/gfortran -Wall -g -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/space/tg286/miniconda_alt/envs/pflex/lib -Wl,-rpath-link,/space/tg286/miniconda_alt/envs/pflex/lib -L/space/tg286/miniconda_alt/envs/pflex/lib build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwtmodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt_sub.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran -lgfortran -o build/lib.linux-x86_64-3.7/plateflex/cpwt.cpython-37m-x86_64-linux-gnu.so
/usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/Scrt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: error: ld returned 1 exit status
error: Command "/usr/bin/gfortran -Wall -g -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/space/tg286/miniconda_alt/envs/pflex/lib -Wl,-rpath-link,/space/tg286/miniconda_alt/envs/pflex/lib -L/space/tg286/miniconda_alt/envs/pflex/lib build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwtmodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt_sub.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran -lgfortran -o build/lib.linux-x86_64-3.7/plateflex/cpwt.cpython-37m-x86_64-linux-gnu.so" failed with exit status 1
----------------------------------------

ERROR: Command errored out with exit status 1: /space/tg286/miniconda_alt/envs/pflex/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-4_zm7t8a/setup.py'"'"'; file='"'"'/tmp/pip-req-build-4_zm7t8a/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-ka0tb788/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.

problem reading file

good afternoon everyone!

Guys, next: I managed to install everything just right, but I'm having trouble reading my generated file, I opened the "Topo_NA" file of the examples left, and compared it with mine, and then the following question came to me: where was it extracted from , or how to calculate that part of the top that you have in the example file?

ETOPO1_NA.grd 0 6805.75136468 0 6819.00580269 -8302.53808594 3603.22363281 20.0169157785 19.9970844654 341 342

0 6819.00580269 -31.3442268372

the only difference between my file and the example is: it doesn't have the top, I saw that it has nx,ny and some information passed in the example file, but where does that come from? if anyone can give me a tip i would appreciate it. thanks!

teste

Error while installing plateflex

Hello Prof. Pascal Audet
When i pip install . ,the error is ocurring.
ERROR: Could not build wheels for plateflex, which is required to install pyproject.toml-based projects.
i follow all the steps of installation.
please tell me how can i do next?
thanks!!!

Problems when executing PlateFlex

Hi Dr. Pascal Audet,

I'm tring to use PlateCurie but when installing the envinonment for PlateFlex, some issues occous as the messagem "WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions.

I'm wondering why this and I guess is due to some incompatibilty between Pymc3 3.10 and Theano. What version of Theano is compatible with Pymc3 3.10.

After installing PlateFelz in a new environment, this message is shown on screen:

(pflex) d:\PlateFlex>python
Python 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 05:59:45) [MSC v.1929 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.

import plateflex
WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions.
Traceback (most recent call last):
File "", line 1, in
File "d:\PlateFlex\plateflex_init_.py", line 157, in
from . import estimate
File "d:\PlateFlex\plateflex\estimate.py", line 57, in
from plateflex.flex import flex
ModuleNotFoundError: No module named 'plateflex.flex'

It looks like plateflex does not exits or is in conflict with some package.
This is the list of all the packages installed on the environment:

(pflex) d:\PlateFlex>pip list
Package Version


anyio 3.5.0
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
arviz 0.11.1
asttokens 2.0.5
attrs 21.4.0
Babel 2.9.1
backcall 0.2.0
beautifulsoup4 4.11.1
bleach 4.1.0
brotlipy 0.7.0
certifi 2022.6.15
cffi 1.15.1
cftime 1.5.0
charset-normalizer 2.0.4
cloudpickle 2.1.0
colorama 0.4.5
cryptography 37.0.1
cycler 0.11.0
cytoolz 0.12.0
dask 2022.8.1
debugpy 1.5.1
decorator 5.1.1
defusedxml 0.7.1
dill 0.3.5.1
entrypoints 0.4
executing 0.8.3
fastjsonschema 2.16.2
fastprogress 1.0.3
fonttools 4.37.1
fsspec 2022.7.1
idna 3.3
imageio 2.21.1
importlib-metadata 4.11.4
importlib-resources 5.2.0
ipykernel 6.9.1
ipython 8.4.0
ipython-genutils 0.2.0
ipywidgets 7.6.5
jedi 0.18.1
Jinja2 3.0.3
json5 0.9.6
jsonschema 4.4.0
jupyter 1.0.0
jupyter-client 7.2.2
jupyter-console 6.4.3
jupyter-core 4.10.0
jupyter-server 1.18.1
jupyterlab 3.4.4
jupyterlab-pygments 0.1.2
jupyterlab-server 2.12.0
jupyterlab-widgets 1.0.0
kiwisolver 1.4.4
locket 1.0.0
Mako 1.2.1
MarkupSafe 2.1.1
matplotlib 3.4.2
matplotlib-inline 0.1.2
mistune 0.8.4
mkl-service 2.4.0
munkres 1.1.4
nbclassic 0.3.5
nbclient 0.5.13
nbconvert 6.4.4
nbformat 5.3.0
nest-asyncio 1.5.5
netCDF4 1.5.7
networkx 2.8.6
notebook 6.4.12
numpy 1.17.5
packaging 21.3
pandas 1.2.4
pandocfilters 1.5.0
parso 0.8.3
partd 1.3.0
patsy 0.5.2
pickleshare 0.7.5
Pillow 9.2.0
pip 22.2.2
plateflex 0.1.0
ply 3.11
prometheus-client 0.14.1
prompt-toolkit 3.0.20
pure-eval 0.2.2
pycparser 2.21
Pygments 2.11.2
pygpu 0.7.6
pymc3 3.10.0
pyOpenSSL 22.0.0
pyparsing 3.0.9
PyQt5 5.15.7
PyQt5-sip 12.11.0
pyrsistent 0.18.0
PySocks 1.7.1
python-dateutil 2.8.2
pytz 2022.2.1
PyWavelets 1.1.1
pywin32 302
pywinpty 2.0.2
PyYAML 6.0
pyzmq 23.2.0
qtconsole 5.3.1
QtPy 2.0.1
requests 2.28.1
scikit-image 0.16.2
scipy 1.7.0
seaborn 0.11.2
Send2Trash 1.8.0
setuptools 58.0.0
sip 6.6.2
six 1.16.0
sniffio 1.2.0
soupsieve 2.3.1
stack-data 0.2.0
statsmodels 0.12.2
terminado 0.13.1
testpath 0.6.0
Theano-PyMC 1.0.11
toml 0.10.2
toolz 0.12.0
tornado 6.2
traitlets 5.1.1
typing-extensions 3.10.0.2
unicodedata2 14.0.0
urllib3 1.26.11
wcwidth 0.2.5
webencodings 0.5.1
websocket-client 0.58.0
wheel 0.37.1
widgetsnbextension 3.5.2
win-inet-pton 1.1.0
xarray 0.19.0
zipp 3.8.1

problem installing and importing plateflex

I have tried many times ,following all the steps of installation,but the error after installation is "no module named plateflex",Again I tried installing by following steps"

Create the Conda environment with Python 3.8

conda create -n pflex python=3.8 -c conda-forge

Activate the environment

conda activate pflex

Install the individual packages with their specified versions

conda install -c conda-forge fortran-compiler=1.2.1
conda install -c conda-forge numpy=1.21.2
conda install -c conda-forge pymc3=3.10.0
conda install -c conda-forge matplotlib=3.4.3
conda install -c conda-forge seaborn=0.11.2
conda install -c conda-forge scikit-image=0.18.3
conda install -c conda-forge pandas=1.3.2
..Now m not able to install pymc3=3.10.0.Please help me for installation and correct importing of modules.I am using ubuntu 22.04.3.I am attaching the screenshot of the packages:
Screenshot from 2023-12-15 17-43-57
Screenshot from 2023-12-15 17-45-28
Screenshot from 2023-12-15 17-45-42
Screenshot from 2023-12-15 17-45-59

Error while activating PlateFlex

I have problem when activating plateflex. It shows the below error:
`C:\Users\LENOVO>SET DISTUTILS_USE_SDK=1

C:\Users\LENOVO>SET MSSdk=1

C:\Users\LENOVO>SET "VS_VERSION=15.0"

C:\Users\LENOVO>SET "VS_MAJOR=15"

C:\Users\LENOVO>SET "VS_YEAR=2017"

C:\Users\LENOVO>set "MSYS2_ARG_CONV_EXCL=/AI;/AL;/OUT;/out"

C:\Users\LENOVO>set "MSYS2_ENV_CONV_EXCL=CL"

C:\Users\LENOVO>set "PY_VCRUNTIME_REDIST=\bin\vcruntime140.dll"

C:\Users\LENOVO>set "CXX=cl.exe"

C:\Users\LENOVO>set "CC=cl.exe"

C:\Users\LENOVO>set "VSINSTALLDIR="

C:\Users\LENOVO>set "NEWER_VS_WITH_OLDER_VC=0"

C:\Users\LENOVO>for /F "usebackq tokens=*" %i in (vswhere.exe -nologo -products * -version [15.0,16.0) -property installationPath) do (set "VSINSTALLDIR=%i" )

C:\Users\LENOVO>(set "VSINSTALLDIR=C:\Program Files (x86)\Microsoft Visual Studio\2017\Community" )

C:\Users\LENOVO>if not exist "C:\Program Files (x86)\Microsoft Visual Studio\2017\Community" (for /F "usebackq tokens=*" %i in (vswhere.exe -nologo -products * -requires Microsoft.VisualStudio.ComponentGroup.VC.Tools.141.x86.x64 -property installationPath) do (
set "VSINSTALLDIR=%i"
set "NEWER_VS_WITH_OLDER_VC=1"
) )

C:\Users\LENOVO>if not exist "C:\Program Files (x86)\Microsoft Visual Studio\2017\Community" (for /F "usebackq tokens=*" %i in (vswhere.exe -nologo -products * -requires Microsoft.VisualStudio.Component.VC.v141.x86.x64 -property installationPath) do (
set "VSINSTALLDIR=%i"
set "NEWER_VS_WITH_OLDER_VC=1"
) )

C:\Users\LENOVO>if not exist "C:\Program Files (x86)\Microsoft Visual Studio\2017\Community" (set "VSINSTALLDIR=C:\Program Files (x86)\Microsoft Visual Studio\2017\Professional" )

C:\Users\LENOVO>if not exist "C:\Program Files (x86)\Microsoft Visual Studio\2017\Community" (set "VSINSTALLDIR=C:\Program Files (x86)\Microsoft Visual Studio\2017\Community" )

C:\Users\LENOVO>if not exist "C:\Program Files (x86)\Microsoft Visual Studio\2017\Community" (set "VSINSTALLDIR=C:\Program Files (x86)\Microsoft Visual Studio\2017\BuildTools" )

C:\Users\LENOVO>if not exist "C:\Program Files (x86)\Microsoft Visual Studio\2017\Community" (set "VSINSTALLDIR=C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise" )

C:\Users\LENOVO>IF NOT "" == "" (
set "INCLUDE=;"
set "LIB=;;C:\Users\LENOVO\miniconda3\envs\pflex\Library\lib"
set "CMAKE_PREFIX_PATH=;"
)

C:\Users\LENOVO>call :GetWin10SdkDir

C:\Users\LENOVO>call :GetWin10SdkDirHelper HKLM\SOFTWARE\Wow6432Node 1>nul 2>&1

C:\Users\LENOVO>if errorlevel 1 call :GetWin10SdkDirHelper HKCU\SOFTWARE\Wow6432Node 1>nul 2>&1

C:\Users\LENOVO>if errorlevel 1 call :GetWin10SdkDirHelper HKLM\SOFTWARE 1>nul 2>&1

C:\Users\LENOVO>if errorlevel 1 call :GetWin10SdkDirHelper HKCU\SOFTWARE 1>nul 2>&1

C:\Users\LENOVO>if errorlevel 1 exit /B 1

C:\Users\LENOVO>exit /B 0

C:\Users\LENOVO>for /F %i in ('dir /ON /B "\include\10.*"') DO (SET WindowsSDKVer=%~i )
The system cannot find the file specified.

C:\Users\LENOVO>if errorlevel 1 (echo "Didn't find any windows 10 SDK. I'm not sure if things will work, but let's try..." ) else (echo Windows SDK version found as: "" )
Windows SDK version found as: ""

C:\Users\LENOVO>set "CMAKE_PLAT=x64"

C:\Users\LENOVO>set "VCVARSBAT=64"

C:\Users\LENOVO>set "CMAKE_ARGS=-DCMAKE_BUILD_TYPE=Release"

C:\Users\LENOVO>IF "" == "1" (set "CMAKE_ARGS=-DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX= -DCMAKE_PROGRAM_PATH=\bin;\Scripts;\Library\bin;\bin;\Scripts;\Library\bin" )

C:\Users\LENOVO>IF NOT "win-64" == "win-64" (
set "CONDA_BUILD_CROSS_COMPILATION=1"
set "CMAKE_ARGS=-DCMAKE_BUILD_TYPE=Release -DCMAKE_SYSTEM_NAME=Windows -DCMAKE_SYSTEM_PROCESSOR=AMD64"
) else (set "CONDA_BUILD_CROSS_COMPILATION=0" )

C:\Users\LENOVO>IF 2017 GEQ 2019 (
set "CMAKE_GEN=Visual Studio 15 2017"
set "USE_NEW_CMAKE_GEN_SYNTAX=1"
) ELSE (
IF "win-64" == "win-64" (set "CMAKE_GEN=Visual Studio 15 2017 Win64" ) else (set "CMAKE_GEN=Visual Studio 15 2017" )
set "USE_NEW_CMAKE_GEN_SYNTAX=0"
)

C:\Users\LENOVO>echo "NEWER_VS_WITH_OLDER_VC=0"
"NEWER_VS_WITH_OLDER_VC=0"

C:\Users\LENOVO>if "0" == "1" (set /p NEWER_VS= 0<"C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\Microsoft.VCToolsVersion.default.txt" )

C:\Users\LENOVO>type "C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\Microsoft.VCToolsVersion.default.txt"
The system cannot find the path specified.

C:\Users\LENOVO>dir "C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Redist\MSVC"
The system cannot find the path specified.

C:\Users\LENOVO>if "0" == "1" (
echo ""
if "~0,4" == "14.2" (set "CMAKE_GEN=Visual Studio 16 2019" ) else (set "CMAKE_GEN=Visual Studio 17 2022" )
set "USE_NEW_CMAKE_GEN_SYNTAX=1"
)

C:\Users\LENOVO>IF "Visual Studio 15 2017 Win64" == "" SET "CMAKE_GENERATOR=Visual Studio 15 2017 Win64"

C:\Users\LENOVO>IF "0" == "1" (
IF "" == "" SET "CMAKE_GENERATOR_PLATFORM=x64"
IF "" == "" SET "CMAKE_GENERATOR_TOOLSET=v141"
)

C:\Users\LENOVO>pushd C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\

C:\Program Files (x86)\Microsoft Visual Studio\2017\Community>CALL "VC\Auxiliary\Build\vcvars64.bat" -vcvars_ver=14.16
The system cannot find the path specified.

C:\Program Files (x86)\Microsoft Visual Studio\2017\Community>if 1 NEQ 0 (if "" == "" (CALL "VC\Auxiliary\Build\vcvars64.bat" ) )
The system cannot find the path specified.

C:\Program Files (x86)\Microsoft Visual Studio\2017\Community>popd

C:\Users\LENOVO>call :GetWin10SdkDirHelper HKLM\SOFTWARE\Wow6432Node 1>nul 2>&1

C:\Users\LENOVO>if errorlevel 1 call :GetWin10SdkDirHelper HKCU\SOFTWARE\Wow6432Node 1>nul 2>&1

C:\Users\LENOVO>if errorlevel 1 call :GetWin10SdkDirHelper HKLM\SOFTWARE 1>nul 2>&1

C:\Users\LENOVO>if errorlevel 1 call :GetWin10SdkDirHelper HKCU\SOFTWARE 1>nul 2>&1

C:\Users\LENOVO>if errorlevel 1 exit /B 1

C:\Users\LENOVO>exit /B 0`
I've tried installing Visual studio 2017 but it didn't work. Can you help me with it?

Can this software calculate the spherical case?

Hi Dr. Audet

I have read your paper "Toward mapping the effective elastic thickness of planetary lithospheres from a spherical wavelet analysis of gravity and topography". Can this package run the spherical wavelet analysis?

project.plot_bayes_stats()

Hi Dr. Audet,

I am using PlatFlex to estimate the effective elastic thickness over southern Africa and I have this error during the Plot stats for estimate

TypeError Traceback (most recent call last)
~/anaconda3/envs/pflex/lib/python3.7/site-packages/pandas/core/indexes/base.py in get_value(self, series, key)
4410 try:
-> 4411 return libindex.get_value_at(s, key)
4412 except IndexError:

pandas/_libs/index.pyx in pandas._libs.index.get_value_at()

pandas/_libs/index.pyx in pandas._libs.index.get_value_at()

pandas/_libs/util.pxd in pandas._libs.util.get_value_at()

pandas/_libs/util.pxd in pandas._libs.util.validate_indexer()

TypeError: 'str' object cannot be interpreted as an integer

During handling of the above exception, another exception occurred:

KeyError Traceback (most recent call last)
~/anaconda3/envs/pflex/lib/python3.7/site-packages/plateflex/classes.py in plot_bayes_stats(self, title, save)
1350 self.map_estimate, title=title,
-> 1351 save=save)
1352 except:

~/anaconda3/envs/pflex/lib/python3.7/site-packages/plateflex/plotting.py in plot_bayes_stats(trace, summary, map_estimate, title, save)
128 # Extract results from summary and map_estimate
--> 129 results = estimate.get_bayes_estimates(summary, map_estimate)
130

~/anaconda3/envs/pflex/lib/python3.7/site-packages/plateflex/estimate.py in get_bayes_estimates(summary, map_estimate)
201 std_te = row['sd']
--> 202 C2_5_te = row['hpd_2.5']
203 C97_5_te = row['hpd_97.5']

~/anaconda3/envs/pflex/lib/python3.7/site-packages/pandas/core/series.py in getitem(self, key)
870 try:
--> 871 result = self.index.get_value(self, key)
872

~/anaconda3/envs/pflex/lib/python3.7/site-packages/pandas/core/indexes/base.py in get_value(self, series, key)
4418 else:
-> 4419 raise e1
4420 except Exception:

~/anaconda3/envs/pflex/lib/python3.7/site-packages/pandas/core/indexes/base.py in get_value(self, series, key)
4404 try:
-> 4405 return self._engine.get_value(s, k, tz=getattr(series.dtype, "tz", None))
4406 except KeyError as e1:

pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_value()

pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_value()

pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()

pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()

KeyError: 'hpd_2.5'

During handling of the above exception, another exception occurred:

Exception Traceback (most recent call last)
in
12
13 # Plot stats for estimate
---> 14 project.plot_bayes_stats()

~/anaconda3/envs/pflex/lib/python3.7/site-packages/plateflex/classes.py in plot_bayes_stats(self, title, save)
1351 save=save)
1352 except:
-> 1353 raise(Exception("No 'cell' estimate available"))
1354
1355 def plot_functions(self, est='mean', title=None, save=None):

Exception: No 'cell' estimate available

Problem while importing plateflex

After successful installation of PlateFlex when I tried importing plateflex by command import plateflex, it showed an error saying arviz has no module geweke. After searching on google related to this issue, I got to know that downgrading arviz version may be a solution but had no luck with that. A new error came saying "no module name plateflex.flex". At this point I am confused what to do.
I am currently using:
Ubuntu 18.04.6 LTS
python: 3.8.15
gcc: 10.0.4
For your reference, I have attached screenshots
Screenshot from 2022-12-10 18-56-11

Issue while cretaing environment

conda create -n pflex python=3.8 fortran-compiler=1.2.1 numpy=1.21.2 pymc3=3.10.0 matplotlib=3.4.3 seaborn=0.11.2 scikit-image=0.18.3 pandas=1.3.2 -c conda-forge
Collecting package metadata (current_repodata.json): done
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed

Plz help

To do list for PlateFlex

Additional features to be expected in the near future:

  • Use the rock-equivalent topography over wet areas in Bouguer analysis - remove water load in this case

  • Zero padding on all sides of the initial rectangular window, as opposed to East and North sides only. This will minimize edge effects on all sides

  • Remove module conf.py

  • Improve documentation for different data sets - try to include PyGMT examples

  • Add tests and package

Error running Ex1_making_grids

When I run the first cell in the first example notebook, I get the following error output:

ImportError Traceback (most recent call last)
Cell In[1], line 3
1 import numpy as np
2 import pandas as pd
----> 3 from plateflex import Grid

File ~\Anaconda3\envs\pflex\lib\site-packages\plateflex_init_.py:157
155 # -- coding: utf-8 --
156 from . import conf as cf
--> 157 from . import estimate
158 from . import plotting
159 from .classes import Grid, TopoGrid, GravGrid, BougGrid, FairGrid

File ~\Anaconda3\envs\pflex\lib\site-packages\plateflex\estimate.py:57
55 import numpy as np
56 import pymc3 as pm
---> 57 from plateflex.flex import flex
58 from plateflex import conf as cf
59 from theano.compile.ops import as_op

ImportError: DLL load failed while importing flex: The specified module could not be found.

Can you help me with this? Thank you!

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