Merge pull request #48 from Dirack/develop/2.2.0

Develop/2.2.0

.github/PULL_REQUEST_TEMPLATE.md

@@ -17,16 +17,16 @@ Please delete options that are not relevant.
 - Breaking change (fix or feature that would cause existing functionality to not work as expected)
 - This change requires a documentation update
 
-**Add images bellow and aditional context if needed**
+**Add images bellow and additional context if needed**
 
 Please describe more information and tests that you ran to verify your changes.
 Or add descriptive images.
 
 **For new a version deploy (pull request to main branch)**
 
 Please check out the list of manual tests and checks. Add new tests if needed before deploy of a new version.
-Merge is only allowed for completed checklist. You can detail those itens in pull request comentaries (this
-will suspend merge until all the comentaries are resolved).
+Merge is only allowed for completed checklist. You can detail those items in pull request commentaries (this
+will suspend merge until all the commentaries are resolved).
 
 - [ ] Verify README.md of this version
 - [ ] Verify README.md links

.gitignore

@@ -19,3 +19,6 @@ Fig/
 *.x
 convgraph
 mtconvgraph
+vfsacrsnh_lib.h
+nhcrssurf_lib.h
+dummyfile

Mnhcrssurf.c

@@ -1,7 +1,5 @@
 /* Build Non-Hyperbolic CRS approximation surface (Fomel and Kazinnik, 2013) for RN, RNIP and BETA parameters given.
 
-Package version: 2.0.1
-
 Programmer: Rodolfo A. C. Neves (Dirack) 19/09/2019
 
 Email:  rodolfo_profissional@hotmail.com
@@ -10,6 +8,7 @@ License: GPL-3.0 <https://www.gnu.org/licenses/gpl-3.0.txt>.
 
  */
 
+#include "nhcrssurf_lib.h"
 #include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
@@ -37,6 +36,7 @@ int main(int argc, char* argv[])
 	float h; // half-offset
 	int nc; // number of parameters
 	int ih, im; // loop counters
+	char strerr[100]; // Buffer to show error message
 
 	/* RSF files I/O */  
 	sf_file in; // Traveltime surface with the output dimensions
@@ -68,7 +68,8 @@ int main(int argc, char* argv[])
 	if (!sf_histfloat(in,"d2",&dm)) sf_error("No d2= in input");
 	if (!sf_histfloat(in,"o2",&om)) sf_error("No o2= in input");
 
-	if(!sf_histint(par,"n1",&nc)) sf_error("No n1= in parameters input");
+	if(!checkParametersFileDimensionN1(par,&nc,strerr))
+		sf_error("%s",strerr);
 
 	if(! sf_getbool("verb",&verb)) verb=0;
 	/* 1: active mode; 0: quiet mode */
@@ -92,6 +93,8 @@ int main(int argc, char* argv[])
 	RNIP = c[1];
 	BETA  = c[2];
 
+	if(!checkIfParametersAreTooSmall(v0,RN,RNIP,strerr))
+		sf_error("%s",strerr);
 
 	t = sf_floatalloc2(nh,nm);
 

Mvfsacrsnh.c

@@ -1,6 +1,4 @@
-/* Zero offset CRS parameter inversion of RN, RNIP, BETA with Very Fast Simulated Annealing (VFSA) Global Optimization. This program uses the Non-Hyperbolic CRS approximation (Fomel and Kazinnik, 2013) to fit seismic data cube and get the best parameters using semblance criteria.
-
-Package version: 2.1.1
+/* Zero offset CRS parameters optimization of RN, RNIP, BETA with Very Fast Simulated Annealing (VFSA) Global Optimization. This program uses the Non-Hyperbolic CRS approximation (Fomel and Kazinnik, 2013) to fit seismic data cube and get the best parameters using semblance criteria.
 
 Programmer: Rodolfo A. C. Neves (Dirack) 13/08/2021
 

debug/Makefile

@@ -37,7 +37,7 @@ else
 endif
 	@echo "...done"
 
-# run optimization test with scons to measure execution time
+# Generate input data for debug session
 generate_data_cube:	test_data_cube/SConstruct
 	@echo "\033[95mGenerate a data cube for tests\033[m"
 	cd test_data_cube && scons -s -Q

debug/README.md

@@ -1,15 +1,6 @@
-#### TESTS DIRECTORY OF VFSA PROGRAMS
+# Debug directory for vfsa debug sessions with GDB
 
-Those tests run in the program make. There are several
-types of tests that can be done:
-
-- Unit tests: Just run the command 'make' to run all unit tests
-in the file 'Test\_vfsacrsnh.c'.
-
-- Optimization tests: Run 'make time' to run the optimization
-tests and to show execution time of the program with scons.
-
-- GDB debug: Run 'make vfsa.x' to generate the executable vfsa.x
+- GDB debug session: Run 'make' or 'make vfsa.x' to generate the executable vfsa.x
 to be used in debugging with GNU Debugger (GDB). The 'gdb\_scripts/gdb\_script'
 file can be used to load all arguments needed to run the program in GDB. Use
 'source gdb\_scripts/gdb\_script' in GDB shell.

debug/gdb_scripts/README.md

@@ -0,0 +1,15 @@
+# GDB scripts for debug
+
+This is a repository of several GNU Debugger (GDB) Scripts for debug sessions using GDB.
+You can load those scripts in GDB console or use it as a template to load parameters in GDB.
+Use the command inside gdb shell to load args for 'Mvfsacrsnh.c':
+
+```
+source gdb_script
+```
+
+Or you could load the GDB script when calling gdb to starting a new debug session:
+
+```
+gdb --command=gdb_script vfsa.x
+```

debug/gdb_scripts/gdb_script

@@ -3,7 +3,7 @@
 # Purpose: Load test parameters in GDB. Use the command
 # 'source gdb_script' inside gdb shell to load args.
 # 
-# Site: https://dirack.github.io
+# Site: https://www.geofisicando.com
 # 
 # Programmer: Rodolfo A C Neves (Dirack) 04/01/2021
 # 

debug/gdb_scripts/gdb_test

@@ -1,8 +1,9 @@
 # gdb_script (GDB Script)
 # 
-# Purpose: Run test in GDB shell.
+# Purpose: Load test parameters in GDB. Use the command
+# 'source gdb_script' inside gdb shell to load args.
 # 
-# Site: https://dirack.github.io
+# Site: https://www.geofisicando.com
 # 
 # Programmer: Rodolfo A C Neves (Dirack) 04/01/2021
 # 

debug/gdb_scripts/gdb_test_mtgraph

@@ -1,8 +1,9 @@
 # gdb_script (GDB Script)
 # 
-# Purpose: Run test in GDB shell.
+# Purpose: Load test parameters in GDB. Use the command
+# 'source gdb_script' inside gdb shell to load args.
 # 
-# Site: https://dirack.github.io
+# Site: https://www.geofisicando.com
 # 
 # Programmer: Rodolfo A C Neves (Dirack) 04/01/2021
 # 

debug/gdb_scripts/gdb_test_varlim

@@ -1,8 +1,9 @@
 # gdb_script (GDB Script)
 # 
-# Purpose: Run test in GDB shell.
+# Purpose: Load test parameters in GDB. Use the command
+# 'source gdb_script' inside gdb shell to load args.
 # 
-# Site: https://dirack.github.io
+# Site: https://www.geofisicando.com
 # 
 # Programmer: Rodolfo A C Neves (Dirack) 04/01/2021
 # 

debug/test_data_cube/README.md

@@ -1,4 +1,3 @@
-#### Optimization test of the programs with scons
+# Generate data for debug vfsa package
 
-Generate a datacube and run vfsa global optimization to
-measure execution time using scons.
+Generate a datacube and parameters files for vfsa debug session using scons.

debug/test_data_cube/SConstruct

@@ -3,11 +3,9 @@
 #
 # SConstruct  (Madagascar Script)
 #
-# Purpose: Optimization test of VFSA process.
+# Purpose: Generate data for debug vfsa package
 #
-# Site: https://dirack.github.io
-# 
-# Version 1.0
+# Site: https://www.geofisicando.com
 #
 # Programer: Rodolfo A. C. Neves (Dirack) 10/11/2020
 #

docs/CONTRIBUTING.md

@@ -1,4 +1,4 @@
-## How to contribute to this project?
+# How to contribute to this project?
 
 To contribute to this project, please follow the steps below.
 
@@ -34,7 +34,7 @@ The purpose of this nomination rule is to allow the developer to identify the is
 
 The default branch (main or master) and development branch names follow the rules below:
 
-- The development branch is opened by the repository's administrator, and its name is **develop/VERSION** ('VERSION' means the current tag version being developed, example develop/1.1.0 mean this branch is the development branch of the 1.1.0 version)
+- The development branch is opened by the repository's administrator, and its name is **develop/VERSION** ('VERSION' means the current tag version being developed, example develop/1.1.0 means this branch is the development branch of the 1.1.0 version)
 
 - The default branch is _main_ (or _master_) and only the repository's administrator can modify it
 
@@ -46,7 +46,7 @@ The branch merge follows _gitflow_ rules:
 
 - The branch _master_ receives modifications from _develop_ and bug corrections from _hotfix_
 
-- The branch _develop_ receives modifications from any other branch, include bug corrections from _master_
+- The branch _develop_ receives modifications from any other branch, including bug corrections from _master_
 
 ## 4. Do clear _commit_ messages (a title with 50 characters and two paragraphs of text)
 
@@ -75,7 +75,7 @@ If you add a new file, it is important to add descriptive headers in the top of
 # 
 # Purpose: Test vfsa program in multiple interfaces model.
 # 
-# Site: https://dirack.github.io
+# Site: https://www.geofisicando.com
 # 
 # Programmer: Rodolfo A C Neves (Dirack) 26/03/2020
 # 

docs/VERSION.md

@@ -1 +1 @@
-2.1.1
+2.2.0

examples/fullParametersOptimization/README.md

@@ -1,48 +1,58 @@
-#### Usage examples of sfvfsacrsnh for a set of (t0,m0) pairs
+# Usage examples of sfvfsacrsnh for a set of (t0,m0) pairs
 
 In this usage example we use the same gaussian reflector model as input and kirchhoff modeling. We use _sfvfsacrsnh_ to obtain the CRS parameters for a set of (t0,m0) pairs.
 
-### How to run it?
+## How to run it?
 
 * Run 'scons' in this directory (it may take some time):
 
 ```sh
 ~$ scons
 ```
 
-#### Expected outcomes
+## Expected outcomes
 
 Scons will generate a parameters cube in 'crsParameters.rsf' file. The optimized parameters
-are organized in the current order: RN, RNIP, BETA, Semblance, C0, Temp0, t0, m0.
+are organized in the current order: RN, RNIP, BETA, Semblance.
 The RN, RNIP and BETA are the zero offset CRS parameters. Semblance is the semblance measure
 between the non-hyperbolic CRS traveltime approximation and the seismic data cube in a CMP x
-offset window around Central CMP m0. The parameters C0 and Temp0 are the VFSA parameters used
-inside the optimization algorithm. And (t0,m0) pair is a time x CMP coordinate around the 
-zero offset CRS approximation is calculated.
+offset window around Central CMP m0.
 
 The parameters cube in 'crsParameters.rsf' file is organized as follows:
 
 ```sh
 ~$ sfin crsParameters.rsf
-
 crsParameters.rsf:
-    in="/home/dirack/rsfdata/vfsa/usage_examples/fullParametersOptimization/crsParameters.rsf@"
+    in="/home/rodolfo/rsfdata/vfsa/examples/fullParametersOptimization/crsParameters.rsf@"
     esize=4 type=float form=native 
-    n1=8           d1=1           o1=0          label1="parameters" unit1="" 
-    n2=6           d2=1           o2=0          label2="(t0,m0) index" unit2="" 
-    n3=1           d3=1           o3=0          label3="" unit3="" 
-	48 elements 192 bytes
+    n1=2           d1=0.1         o1=1.1        label1="t0" unit1="s" 
+    n2=3           d2=1           o2=3          label2="m0" unit2="km" 
+    n3=4           d3=1           o3=0          label3="parameters" unit3="RN, RNIP, BETA, Semblance"
 ```
 
-For each (t0,m0) pair (n2 coordinate) we get 8 parameters (n1 coordinate) as described above:
+For each (t0,m0) pair (n1 coordinate, n2 coordinate) we get 4 parameters (n3 coordinate) as described above.
 
-```sh
-~$ sfdisfil < crsParameters.rsf col=8
+Use the following commands to dump parameters values from parameters cube (values should change from one iteration to another).
+
+- Get RN values:
+
+```
+<crsParameters.rsf sfwindow n3=1 f3=0 | sfdisfil col=1
+```
 
-   0:         2.677        2.228      -0.2981       0.4372          0.5           10          1.1            3
-   8:         4.815        3.804      -0.2447        0.374          0.5           10          1.2            3
-  16:         4.768        3.813      -0.2614       0.1921          0.5           10          1.1            4
-  24:         3.127        1.081       -0.287       0.1964          0.5           10          1.2            4
-  32:         3.105        1.129    -0.002743       0.9898          0.5           10          1.1            5
-  40:          3.12        1.168     -0.01008       0.9028          0.5           10          1.2            5
+- Get RNIP values:
+
+```
+<crsParameters.rsf sfwindow n3=1 f3=1 | sfdisfil col=1
 ```
+- Get BETA values:
+
+```
+<crsParameters.rsf sfwindow n3=1 f3=2 | sfdisfil col=1
+```
+- Get Semblance values:
+
+```
+<crsParameters.rsf sfwindow n3=1 f3=3 | sfdisfil col=1
+```
+

examples/fullParametersOptimization/SConstruct

@@ -21,7 +21,6 @@ from rsf.proj import *
 import math
 
 __author__="Rodolfo Dirack <rodolfo_profissional@hotmail.com>"
-__version__="1.0"
 __site__="https://www.geofisicando.com"
 
 Help('''
@@ -32,9 +31,8 @@ Help('''
     global optimization
 
     Author: %s
-    Version: %s
     Site: %s
-    ''' % (__author__,__version__,__site__))
+    ''' % (__author__,__site__))
 
 Help('''
 ### Kirchhoff modeling ###

examples/gaussian_reflector_model/README.md

@@ -4,17 +4,17 @@ In this usage example we use a gaussian reflector model as input and kirchhoff m
 seismic data cube (Seismic data organized in CMP x Offset x Time coordinates) from it.
 
 After that we use _sfvfsacrsnh_ to fit the non-hyperbolic CRS traveltime approximation in the reflection traveltime surface
-exatracted from the data cube. Finally, we plot these surfaces and approximation error side by side.
+exatracted from the data cube. Finally, we plot these surfaces and approximation error side by side using the program _sfnhcrssurf_.
 
-### How to run it?
+## How to run it?
 
 * Run 'scons view' in this directory (it may take some time):
 
 ```sh
 ~$ scons view
 ```
 
-#### Expected outcomes
+## Expected outcomes
 
  After the program _scons_ do all the steps in the SConstruct file, you will see the generated surfaces as follow:
 
@@ -25,10 +25,7 @@ exatracted from the data cube. Finally, we plot these surfaces and approximation
 
  ```sh
  ~$ sfdisfil <crsParameters.rsf
-0:          3.23       0.9706    -0.003872       0.7791          0.5
-5:            10          1.1            5
+0:         4.725       0.2558    -0.001232       0.5248
 ```
 
 The first 3 numbers are RN, RNIP and BETA. The fourth one is the semblance (it may change from one running to another).
-The fifth and sixth are C0 and Temp0, arbitrary parameters used in vfsa that may change from problem to problem. Finally
-t0 (Normal ray traveltime) and m0 (Central CMP of the approximation) are the last ones.