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Merge pull request #60 from Dirack/develop/2.1
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‎.gitignore‎

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*.jp2
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.ipynb_checkpoints/
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*.asc
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*.x
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*.deploy

‎.travis.yml‎

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language: bash
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os: linux
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dist: xenial
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env:
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global:
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- UNIT_TEST=true
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- MODELING_GAUSS=true
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- MODELING_MULTI=true
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- DEPLOY=false
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git:
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depth: 1
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branches:
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only:
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- master
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- /^develop.*$/
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- teste
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- test
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jobs:
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include:
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- stage: modeling
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script: ./test_travis_docker.sh test_gaussianModelBuild
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- script: ./test_travis_docker.sh test_multiLayerModelBuild
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- stage: deploy
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script: echo "TODO deploy"
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- stage: Unit test
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name: Unit test
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if: env(UNIT_TEST)=true
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script: ./TDD/test_travis_docker.sh 'make'
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- stage: Modeling
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name: Gaussian Reflector
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if: env(MODELING_GAUSS)=true
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script: ./TDD/test_travis_docker.sh 'python -m unittest test_gaussianModelBuild'
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- if: env(MODELING_MULTI)=true
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script: ./TDD/test_travis_docker.sh 'python -m unittest test_multiLayerModelBuild'
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name: Multi Layer
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- stage: Deploy
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name: Deploy
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if: env(DEPLOY)=true
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script: echo "Deploy"
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before_deploy:
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- git config --local user.name "dirack"
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- git config --local user.email "[email protected]"
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- export TRAVIS_TAG=$(cat VERSION.md)
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- deploy/build_tag_message.sh
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- git tag -a $TRAVIS_TAG -F tag.deploy
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deploy:
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provider: releases
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token: $GITHUB_TOKEN
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skip_cleanup: true
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draft: true
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script: 'git push --tag'
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on:
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repo: Dirack/creGatherStack
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branch:
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- master
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- test

‎CHANGELOG.md‎

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# Changelog
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All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## UNRELEASED - Contribute with the next version
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## [v2.2.0](https://github.com/Dirack/creGatherStack/compare/v2.1.0-beta.1...develop/2.2) - 2020-10-11
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## RELEASED
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## [v2.1.0-beta.1](https://github.com/Dirack/creGatherStack/releases/tag/v2.1.0-beta.1) (Beta) - 2020-10-11
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## Added
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- New program rnip2vmrs to estimate VRMS from RNIP values Resolve [#54](https://github.com/Dirack/creGatherStack/issues/54) [25136ea](https://github.com/Dirack/creGatherStack/commit/25136ea) [6a7b0c9](https://github.com/Dirack/creGatherStack/commit/6a7b0c9)
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- Use sfrnip2vrms program in all experiments [#55](https://github.com/Dirack/creGatherStack/issues/55) [e031436](https://github.com/Dirack/creGatherStack/commit/e031436)
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## Modified
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- CRE Gather stack is now a function of creGatherStack.py recipe, and allow CDS option Resolve [#59](https://github.com/Dirack/creGatherStack/issues/59) [af9c8db](https://github.com/Dirack/creGatherStack/commit/af9c8db)
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- Unit test directory: TDD directory [39eace3](https://github.com/Dirack/creGatherStack/commit/39eace3)
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## Changed
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- Update README with references to the changelog and wiki instead of the release history section [475e679](https://github.com/Dirack/creGatherStack/commit/475e679)
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## [v2.0.0](https://github.com/Dirack/creGatherStack/releases/tag/v2.0) (Stable) - 2020-09-21
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### Added
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- Travis CI test [43a01fe](https://github.com/Dirack/creGatherStack/commit/43a01fe)
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- Travis CI automatic test Resolve [#8](https://github.com/Dirack/creGatherStack/issues/8) [43a58c3](https://github.com/Dirack/vfsa/commit/43a58c3)
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- Establish kimodel.py and pefInterpolation.py as dependencies Resolve [#43](https://github.com/Dirack/creGatherStack/issues/43) [44d8eb9](https://github.com/Dirack/vfsa/commit/44d8eb9)
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- Define aperture=20 for sfgetcregather and correct bug Resolve [#49](https://github.com/Dirack/creGatherStack/issues/49) [feb03c1](https://github.com/Dirack/vfsa/commit/feb03c1) [405199d](https://github.com/Dirack/vfsa/commit/405199d)
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- Use explicit dependency to avoid building errors Resolve [#44](https://github.com/Dirack/creGatherStack/issues/44) [35aa3c9](https://github.com/Dirack/vfsa/commit/35aa3c9)
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- Allow experiments SConstructs to receive parameters from the command line [6edd9ef](https://github.com/Dirack/creGatherStack/commit/6edd9ef)
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## [v1.0.0-beta.1](https://github.com/Dirack/creGatherStack/releases/tag/v1.0-beta.1) (Beta) - 2020-09-12
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### Added
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- New usage example: Multi-layer model, in pull request [#42](https://github.com/Dirack/creGatherStack/issues/42) Resolve [#37](https://github.com/Dirack/vfsa/issues/37) [cf1568e](https://github.com/Dirack/vfsa/commit/cf1568e)
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## Removed
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- Remove pefInterpolation example Resolve [#45](https://github.com/Dirack/creGatherStack/issues/45) [c095796](https://github.com/Dirack/vfsa/commit/c095796)
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## Fixed
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- Avoid CMP coordinate to get out of of model bounds correct bug [#38](https://github.com/Dirack/creGatherStack/issues/38) [3f6b469](https://github.com/Dirack/vfsa/commit/3f6b469) [72ed7c1](72ed7c1)
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- Avoid segmentation fault in sfvfsacrsnh, correct bug [#39](https://github.com/Dirack/creGatherStack/issues/39) [ed9043d](https://github.com/Dirack/vfsa/commit/ed9043d)
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## [v0.1.2-alpha.1](https://github.com/Dirack/creGatherStack/releases/tag/v0.1.2-alpha.1) (Development) - 2020-09-12
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- Test CRE stacking with CDS condition applied to the Non-hyperbolic CRS approximation [#26](https://github.com/Dirack/creGatherStack/issues/26) [d20c1c1](https://github.com/Dirack/vfsa/commit/d20c1c1)
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- Test of the CRE stacking using CRE traveltime approximation [#26](https://github.com/Dirack/creGatherStack/issues/26) [1a0e765](https://github.com/Dirack/vfsa/commit/1a0e765)
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## [v0.1.1-alpha.1](https://github.com/Dirack/creGatherStack/releases/tag/v0.1.2-alpha.1) (Development) - 2020-04-21
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## Added
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- CRE stacking with CDS condition (RNIP=RN) in non-hyperbolic traveltime approximation [#3](https://github.com/Dirack/creGatherStack/issues/3) [4ad17bb](https://github.com/Dirack/vfsa/commit/4ad17bb)
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- Define functions in creStack.py to modeling and interpolation steps [#9](https://github.com/Dirack/creGatherStack/issues/9) [73a38c0](https://github.com/Dirack/vfsa/commit/73a38c0)
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## Removed
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- Delete useless usage examples Resolve [#34](https://github.com/Dirack/creGatherStack/issues/34) [0fe314e](https://github.com/Dirack/vfsa/commit/0fe314e)
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- Remove vfsa programs from package, establish them as a dependency Resolve [#22](https://github.com/Dirack/creGatherStack/issues/22) [d2f9ddf](https://github.com/Dirack/vfsa/commit/d2f9ddf)
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## [v0.1.0-alpha.1](https://github.com/Dirack/creGatherStack/releases/tag/v0.1.2-alpha.1) (Development) - 2020-04-21
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## Added
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- Gaussian reflector Kirchoff modeling [aff870d](https://github.com/Dirack/creGatherStack/commit/aff870d)
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- zero offset CRS parameters optimization with VFSA [14fcbdf](https://github.com/Dirack/creGatherStack/commit/14fcbdf)
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- PEF interpolation of the data cube to increase CMP sampling [8d9a44f](https://github.com/Dirack/creGatherStack/commit/8d9a44f)
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- Program _sfcretrajec_ to calculate CRE trajectory for RNIP and BETA [8b54e94](https://github.com/Dirack/creGatherStack/commit/8b54e94)
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- Program _sfgetcregather_ to build the CRE Gather [2872fdd](https://github.com/Dirack/creGatherStack/commit/2872fdd)
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- Program _sfgetcretimecurve_ to build the CRE traveltime curve [da8b919](https://github.com/Dirack/creGatherStack/commit/da8b919)
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- Program _sfcrestack_ to CRE stacking [5c4e633](https://github.com/Dirack/creGatherStack/commit/5c4e633)
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- Jupyter Notebook of the Kirchhoff modeling step [40ac351](https://github.com/Dirack/creGatherStack/commit/40ac351)
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- Scratch of a reproducible paper for modeling step [494faf2](https://github.com/Dirack/creGatherStack/commit/494faf2)
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## Fixed
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- Correct bug in alpha parameter bounds in the program Mcretrajec.c [699f169](https://github.com/Dirack/creGatherStack/commit/699f169)
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‎Mrnip2vrms.c‎

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/* Version 1.0 - Estimate root mean square velocity (VRMS) from RNIP
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This program is based on multifocus formula that allows to estimate
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VRMS from RNIP: vrms = sqrt(2*RNIP*v0/t0)
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Reference: Diffraction imaging by multifocusing, Berkovitch A.,
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Belfer I., Hassin Y., and Landa E., 2009.
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Programer: Rodolfo A C Neves (Dirack) 21/09/2020
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Email: [email protected]
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License: GPL-3.0 <https://www.gnu.org/licenses/gpl-3.0.txt>.
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*/
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#include "rnip2vrms_lib.h"
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#include <rsf.h>
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/*^*/
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int main(int argc,char* argv[]){
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bool verb; // Verbose parameter
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int nt0; // Number of t0's in stacked section
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float dt0; // Time sampling in stacked section
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float ot0; // Origin of the time axis in stacked section
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int nm0; // Number of CMP's in stacked section
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float dm0; // CMP sampling in stacked section
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float om0; // Origin of the CMP axis in stacked section
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float v0; // Near surface velocity
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float** rnip; // (t0,m0,rnip) section
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float** vrmsSection; // (t0,m0,VRMS) section
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sf_file in,out;
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sf_init(argc,argv);
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in = sf_input("in");
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out = sf_output("out");
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/* Read coordinates of the stacked section file */
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if(!sf_histint(in,"n1",&nt0)) sf_error("No n1= in input");
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if(!sf_histfloat(in,"d1",&dt0)) sf_error("No d1= in input");
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if(!sf_histfloat(in,"o1",&ot0)) sf_error("No o1= in input");
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if(!sf_histint(in,"n2",&nm0)) sf_error("No n2= in input");
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if(!sf_histfloat(in,"d2",&dm0)) sf_error("No d2= in input");
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if(!sf_histfloat(in,"o2",&om0)) sf_error("No o2= in input");
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if(!sf_getbool("verb",&verb)) verb=0;
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/*1: verbose; 0: quiet*/
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if(!sf_getfloat("v0",&v0)) v0=1.5;
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/* Near surface velocity (Km/s) */
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if(verb){
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sf_warning("Input file (Rnip Section)");
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sf_warning("nt0=%f dt0=%f ot0=%f",nt0,dt0,ot0);
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sf_warning("nm0=%f dm0=%f om0=%f",nm0,dm0,om0);
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sf_warning("Command line parameters");
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sf_warning("v0=%f",v0);
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}
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/* Load rnip values */
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rnip = sf_floatalloc2(nt0,nm0);
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sf_floatread(rnip[0],nm0*nt0,in);
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vrmsSection = sf_floatalloc2(nt0,nm0);
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/* Calculate VRMS from RNIP */
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vrmsSection = calculateVrmsSectionForRnipVector(rnip,nt0,ot0,dt0,nm0,v0);
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/* Output the VRMS section */
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sf_floatwrite(vrmsSection[0],nt0*nm0,out);
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}

‎README.md‎

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[Developed to Madagascar package, version 3.0.](http://www.ahay.org/wiki/Main_Page)
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[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) [![Build Status](https://travis-ci.org/Dirack/creGatherStack.svg?branch=master)](https://travis-ci.org/Dirack/creGatherStack)
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[![Github release](https://img.shields.io/github/v/release/Dirack/creGatherStack)](https://github.com/Dirack/creGatherStack/releases/latest) [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) [![Madagascar](https://img.shields.io/badge/Madagascar-v3.0-blue)](https://github.com/ahay/src/tree/master) [![Build Status](https://travis-ci.org/Dirack/creGatherStack.svg?branch=master)](https://travis-ci.org/Dirack/creGatherStack)
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![Interpolated CRE Gather](https://github.com/Dirack/creGatherInterpolation/blob/master/images/hugeStackedSection.jpeg)
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We also have many SConstruct examples in this repository in the
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[experiments directory](https://github.com/Dirack/creGatherStack/tree/master/experiments)
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## Release History
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## Release History and Versions
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* [v2.0](https://github.com/Dirack/creGatherStack/releases/tag/v2.0) - (Stable)
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* [v1.0-beta.1](https://github.com/Dirack/creGatherStack/releases/tag/v1.0-beta.1) - (Beta)
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* [v0.1.2-alpha.1](https://github.com/Dirack/creGatherStack/releases/tag/v0.1.2-alpha.1) - (Development)
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[See the complete history decription in our wiki](https://github.com/Dirack/creGatherStack/wiki/Release-history)
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This package version is referenced in VERSION.md file, and you can see the [complete release history in our wiki](https://github.com/Dirack/creGatherStack/wiki/Release-history) or in the CHANGELOG.md file.
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## Meta
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[main page](https://github.com/Dirack/creGatherStack)
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Rodolfo Dirack – [@dirack](https://github.com/Dirack) – [email protected]
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Distributed under the GPL3 license. See ``LICENSE`` for more information.
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[creGatherStack main page](https://github.com/Dirack/creGatherStack)
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## Contributing
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1. Fork it (<https://github.com/Dirack/creGatherStack/fork>)
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2. Create your feature branch (`git checkout -b feature/fooBar`)
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3. Commit your changes (`git commit -am 'Add some fooBar'`)
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4. Push to the branch (`git push origin feature/fooBar`)
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5. Create a new Pull Request
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In order to contribute with this project you should follow the list of steps bellow, please check out ["How to contribute with this project?"](https://github.com/Dirack/creGatherStack/wiki/Contribute) in our Wiki for more details.
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1. Create an issue to your request or choose an issue already defined
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2. Fork this project in https://github.com/Dirack/creGatherStack/fork
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3. Create a branch for your contribution (name it using gitflow)
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4. Do clear _commit_ messages (a title with 50 characters and two paragraphs of text)
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5. _Push_ your contribution to this repository
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6. Create a new Pull Request with a clear description of your contribution
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###### Important contribution tip: The commit history should be clear, with commit mesages around one or two paraghraps describing your modifications. Pull Requests with unsatisfactory commit history will be rejected.
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###### Important: The commit history should be clear, with commit mesages around one or two paraghraps describing your modifications. Pull Requests with unsatisfactory commit history will be rejected.

‎SConstruct‎

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# Put your name programs in progs variable
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# without 'M' preffix and '.c' extension
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progs = '''
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crestack cretrajec getcregather getcretimecurve
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crestack cretrajec getcregather getcretimecurve rnip2vrms
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'''
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try: # distributed version

‎TDD/Makefile‎

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# Makefile
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#
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# Purpose: Run c test with Unity Unity.
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#
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# Site: https://dirack.github.io
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#
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# Version 1.0
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#
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# Programer: Rodolfo A C Neves (Dirack) 21/09/2020
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#
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# Email: [email protected]
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#
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# License: GPL-3.0 <https://www.gnu.org/licenses/gpl-3.0.txt>.
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# Uncomment the line below to run on a CENTOS system. Or call make as 'make CENTOS=1'
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#CENTOS=1
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all: Test_rnip2vrms_lib.x
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%.x: %.c
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ifdef CENTOS
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gcc -I$$RSFSRC/include -I/usr/include/openblas -L$$RSFSRC/lib $< ../rnip2vrms_lib.c Unity/unity.c -o $@ -lm -lrsf -lopenblas -g
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./$@
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rm $@
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else
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gcc -I$$RSFSRC/include -L$$RSFSRC/lib $< ../rnip2vrms_lib.c Unity/unity.c -o $@ -lm -lrsf
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./$@
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rm $@
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endif

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