From ca860824d3376ac7cfec182098d54e08ea8383b5 Mon Sep 17 00:00:00 2001
From: David Coeurjolly <david.coeurjolly@liris.cnrs.fr>
Date: Fri, 11 Feb 2022 13:08:48 +0100
Subject: [PATCH 01/14] VolInfo

---
 volumetric/CMakeLists.txt |   1 +
 volumetric/volInfo.cpp    | 125 ++++++++++++++++++++++++++++++++++++++
 2 files changed, 126 insertions(+)
 create mode 100644 volumetric/volInfo.cpp

diff --git a/volumetric/CMakeLists.txt b/volumetric/CMakeLists.txt
index 943970e3..fb027102 100644
--- a/volumetric/CMakeLists.txt
+++ b/volumetric/CMakeLists.txt
@@ -14,6 +14,7 @@ SET(DGTAL_TOOLS_SRC
   volTrValues
   volIntensityScale
   volFillInterior
+  volInfo
   volMask
 )
 
diff --git a/volumetric/volInfo.cpp b/volumetric/volInfo.cpp
new file mode 100644
index 00000000..1d665a40
--- /dev/null
+++ b/volumetric/volInfo.cpp
@@ -0,0 +1,125 @@
+/**
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as
+ *  published by the Free Software Foundation, either version 3 of the
+ *  License, or  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ **/
+
+/**
+ * @file volInfo.cpp
+ * @author David Coeurjolly (\c david.coeurjolly@liris.cnrs.fr )
+ * Laboratoire d'InfoRmatique en Image et Systèmes d'information - LIRIS (CNRS, UMR 5205), CNRS, France
+ *
+ * @date 2021/02/11
+ *
+ *
+ * This file is part of the DGtal library.
+ */
+
+#include <iostream>
+#include <map>
+#include <DGtal/base/Common.h>
+#include <DGtal/io/readers/VolReader.h>
+#include <DGtal/io/writers/VolWriter.h>
+#include <DGtal/helpers/StdDefs.h>
+#include <DGtal/images/Image.h>
+#include <DGtal/images/ImageContainerBySTLVector.h>
+
+#include "CLI11.hpp"
+
+
+using namespace std;
+using namespace DGtal;
+using namespace Z3i;
+
+/**
+ @page volSubSample volSubSample
+ 
+ @brief Get information from a vol file (size and values).
+
+
+ @b Usage: 	./volumetric/volInfo [OPTIONS] 1 [2]
+
+
+ @b Allowed @b options @b are : 
+ @code
+ Positionals:
+   1 TEXT:FILE REQUIRED                  Input vol file.
+  
+ Options:
+   -h,--help                             Print this help message and exit
+   -i,--input TEXT:FILE REQUIRED         Input vol file.
+  
+ Positionals:
+   1 TEXT:FILE REQUIRED                  Input vol file.
+  
+ Options:
+   -h,--help                             Print this help message and exit
+   -i,--input TEXT:FILE REQUIRED         Input vol file.
+ 
+ @endcode
+
+ @b Example: 
+You can apply several sub sampling:
+ @code
+ $ volInfo $DGtal/examples/samples/lobster.vol
+ @endcode
+
+ @see
+ @ref volInfo.cpp
+
+ */
+
+/**
+ * Missing parameter error message.
+ *
+ * @param param
+ */
+void missingParam ( std::string param )
+{
+  trace.error() <<" Parameter: "<<param<<" is required..";
+  trace.info() <<std::endl;
+  exit ( 1 );
+}
+
+
+int main(int argc, char**argv)
+{
+    // parse command line using CLI ----------------------------------------------
+  CLI::App app;
+  std::string inputFileName;
+    
+  app.description("Retreive information from vol file\n Basic usage: \n \tvolInfo  <volFileName>  ");
+  app.add_option("-i,--input,1", inputFileName, "Input vol file." )->required()->check(CLI::ExistingFile);
+  
+  app.get_formatter()->column_width(40);
+  CLI11_PARSE(app, argc, argv);
+  // END parse command line using CLI ----------------------------------------------
+
+  trace.beginBlock("Loading file");
+  typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char>  MyImageC;
+
+  MyImageC  imageC = VolReader< MyImageC >::importVol ( inputFileName );
+  
+  trace.info()<<imageC<<std::endl;
+  trace.info()<<"Scanning the values:"<<std::endl;
+
+  std::map<unsigned char, size_t> values;
+  for(auto v: imageC.range())
+    values[ v ] ++;
+  
+  for(auto val: values)
+    std::cout<<"\tvalue "<< (int)val.first<<": "<< val.second<<" voxels."<<std::endl;
+  
+  trace.endBlock();
+  return 0;
+}

From 530189effae9d6dd4438c5d067aa1a782fecb34c Mon Sep 17 00:00:00 2001
From: David Coeurjolly <david.coeurjolly@liris.cnrs.fr>
Date: Fri, 11 Feb 2022 13:11:55 +0100
Subject: [PATCH 02/14] VolInfo

---
 ChangeLog.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/ChangeLog.md b/ChangeLog.md
index 9879a869..7946298a 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -11,7 +11,7 @@
   - New cmake option (DGTAL_RANDOMIZED_BUILD_THRESHOLD) to set the
     (approximated) % of tools build
     (Bertrand Kerautret [#416](https://github.com/DGtal-team/DGtal/pull/416))
-       
+
 - *visualisation*
   - 3dImplicitSurfaceExtractorByThickening: adding OBJ export.
     (David Coeurjolly [#413](https://github.com/DGtal-team/DGtalTools/pull/413))
@@ -21,16 +21,16 @@
 - *volumetric*
   - volSegment: adding new option to get long int images as output (for
     longvol exporting). (Bertrand Kerautret [#420](https://github.com/DGtal-team/DGtalTools/pull/420))
-
+  - volInfo: get information from a vol file. (David Coeurjolly, [#430](https://github.com/DGtal-team/DGtalTools/pull/430))
 
 # DGtalTools 1.2
 - *global*
   - Fix itk2vol and fix ITK cmake configuaration that was making issues with the ITK image read.
     (Bertrand Kerautret [#393](https://github.com/DGtal-team/DGtalTools/pull/393))
   - Travis: Fix old default osx_image with xcode12.2 and remove non used boost
-    cmake references. (Bertrand Kerautret [#394](https://github.com/DGtal-team/DGtalTools/pull/394)) 
+    cmake references. (Bertrand Kerautret [#394](https://github.com/DGtal-team/DGtalTools/pull/394))
   - Uniform input/output option with previous use of CLI11 (issue #405).
-    (Bertrand Kerautret [#406](https://github.com/DGtal-team/DGtalTools/pull/406)) 
+    (Bertrand Kerautret [#406](https://github.com/DGtal-team/DGtalTools/pull/406))
   - Comply with cmake Policy CMP0115 "Source file extensions must be
      explicit". (Bertrand Kerautret and David Coeurjolly, [#407](https://github.com/DGtal-team/DGtalTools/pull/407))
 

From 91ff016a2d8e99ba39b6b4003035e0d74c5542fd Mon Sep 17 00:00:00 2001
From: David Coeurjolly <david.coeurjolly@liris.cnrs.fr>
Date: Fri, 11 Feb 2022 13:13:21 +0100
Subject: [PATCH 03/14] odc

---
 doc/volumetric.dox | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/doc/volumetric.dox b/doc/volumetric.dox
index 9644e478..cd8daee0 100644
--- a/doc/volumetric.dox
+++ b/doc/volumetric.dox
@@ -1,6 +1,6 @@
 /**
  * @file volumetric.dox
- * @author Bertrand Kerautret 
+ * @author Bertrand Kerautret
  * LORIA (CNRS, UMR 7503), University of Lorraine, France
  *
  * @date 2016/05/12
@@ -19,7 +19,7 @@
 
 
   - @ref criticalKernelsThinning3D :  applies an criticalKernels thinning algorithm of a 3d image file (vol,longvol,pgm3d...) with 3D viewer.
-  - @ref Doc3dVolMarchingCubes : outputs the isosurface of the input volume  as an OFF file. 
+  - @ref Doc3dVolMarchingCubes : outputs the isosurface of the input volume  as an OFF file.
   - @ref homotopicThinning3D : applies an homotopic thinning of a 3d image file (vol,longvol,pgm3d...) with 3D viewer.
   - @ref volAddBorder : adds a border of one voxel with value 0 around a vol file.
   - @ref volAddNoise : adds Kanungo noise to a binary object with 0 values as background points and values >0 for the foreground ones.
@@ -32,9 +32,10 @@
   - @ref volMask : extracts a new image from the a mask image.
   - @ref volReSample :  re samples a 3D volumetric image (.vol, .longvol, .pgm3d)  with a given grid size.
   - @ref volSegment : segments volumetric file from a simple threshold.
-  - @ref volShapeMetrics : applies shape measures to compare two volumetric images A and B (shape defined from thresholds). 
+  - @ref volShapeMetrics : applies shape measures to compare two volumetric images A and B (shape defined from thresholds).
   - @ref volSubSample : brutally sub samples a vol file (division by 2 in each direction).
   - @ref volTrValues : applies basic vol image transform from the input values to output values.
+  - @ref volInfo : to get information (domain size, value distributions) from a VOL file.
 
 
 
@@ -44,24 +45,24 @@
   <tr>
         <td> <img height=200px src="res3dVolMarchingCubes2.png"> </td>
         <td><img height=200px src="resHomotopicThinning3D.png"></td>
-        <td><img height=200px src="resVolReSample.png"></td>        
+        <td><img height=200px src="resVolReSample.png"></td>
 </tr>
 <tr>
         <td align = center>@ref Doc3dVolMarchingCubes </td>
-        <td align = center>@ref homotopicThinning3D </td>   
+        <td align = center>@ref homotopicThinning3D </td>
         <td align = center>@ref volReSample</td>
 
 </tr>
 
 <tr>
-<td><img height=200px src="resVolTrValues.png"></td>        
+<td><img height=200px src="resVolTrValues.png"></td>
 <td><img height=200px src="resVolSegment.png"></td>
-<td><img height=200px src="resVolSubSample.png"></td>        
+<td><img height=200px src="resVolSubSample.png"></td>
 </tr>
 <tr>
 <td align = center>@ref volTrValues</td>
 <td align = center>@ref volSegment</td>
-<td align = center>@ref volSubSample</td>            
+<td align = center>@ref volSubSample</td>
 </tr>
 </table>
 </center>

From 7b287cdfb2328015e61b213e6d7361e38311a824 Mon Sep 17 00:00:00 2001
From: David Coeurjolly <david.coeurjolly@liris.cnrs.fr>
Date: Fri, 11 Feb 2022 13:15:08 +0100
Subject: [PATCH 04/14] doc again

---
 doc/volumetric.dox | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/volumetric.dox b/doc/volumetric.dox
index cd8daee0..631c8b29 100644
--- a/doc/volumetric.dox
+++ b/doc/volumetric.dox
@@ -19,7 +19,7 @@
 
 
   - @ref criticalKernelsThinning3D :  applies an criticalKernels thinning algorithm of a 3d image file (vol,longvol,pgm3d...) with 3D viewer.
-  - @ref Doc3dVolMarchingCubes : outputs the isosurface of the input volume  as an OFF file.
+  - @ref 3dVolMarchingCubes : outputs the isosurface of the input volume  as an OFF file.
   - @ref homotopicThinning3D : applies an homotopic thinning of a 3d image file (vol,longvol,pgm3d...) with 3D viewer.
   - @ref volAddBorder : adds a border of one voxel with value 0 around a vol file.
   - @ref volAddNoise : adds Kanungo noise to a binary object with 0 values as background points and values >0 for the foreground ones.

From 296f5419d21292f3419da3c5dbebd7da4b1ecc92 Mon Sep 17 00:00:00 2001
From: David Coeurjolly <david.coeurjolly@liris.cnrs.fr>
Date: Fri, 11 Feb 2022 13:28:00 +0100
Subject: [PATCH 05/14] doc again

---
 volumetric/volInfo.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/volumetric/volInfo.cpp b/volumetric/volInfo.cpp
index 1d665a40..b640f471 100644
--- a/volumetric/volInfo.cpp
+++ b/volumetric/volInfo.cpp
@@ -13,7 +13,6 @@
  *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
  *
  **/
-
 /**
  * @file volInfo.cpp
  * @author David Coeurjolly (\c david.coeurjolly@liris.cnrs.fr )

From c737901f79ba67ec5e97aa6d680ea6c393738a16 Mon Sep 17 00:00:00 2001
From: David Coeurjolly <david.coeurjolly@liris.cnrs.fr>
Date: Fri, 11 Mar 2022 16:48:19 +0100
Subject: [PATCH 06/14] Update volumetric/volInfo.cpp

Co-authored-by: Bertrand Kerautret <bertrand.kerautret@univ-lyon2.fr>
---
 volumetric/volInfo.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/volumetric/volInfo.cpp b/volumetric/volInfo.cpp
index b640f471..cd026ee9 100644
--- a/volumetric/volInfo.cpp
+++ b/volumetric/volInfo.cpp
@@ -18,7 +18,7 @@
  * @author David Coeurjolly (\c david.coeurjolly@liris.cnrs.fr )
  * Laboratoire d'InfoRmatique en Image et Systèmes d'information - LIRIS (CNRS, UMR 5205), CNRS, France
  *
- * @date 2021/02/11
+ * @date 2022/02/11
  *
  *
  * This file is part of the DGtal library.

From ae9bee02888a7b109339f57bd828d842c560c243 Mon Sep 17 00:00:00 2001
From: David Coeurjolly <david.coeurjolly@liris.cnrs.fr>
Date: Fri, 11 Mar 2022 16:48:43 +0100
Subject: [PATCH 07/14] Update volumetric/volInfo.cpp

Co-authored-by: Bertrand Kerautret <bertrand.kerautret@univ-lyon2.fr>
---
 volumetric/volInfo.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/volumetric/volInfo.cpp b/volumetric/volInfo.cpp
index cd026ee9..376a9d19 100644
--- a/volumetric/volInfo.cpp
+++ b/volumetric/volInfo.cpp
@@ -28,7 +28,6 @@
 #include <map>
 #include <DGtal/base/Common.h>
 #include <DGtal/io/readers/VolReader.h>
-#include <DGtal/io/writers/VolWriter.h>
 #include <DGtal/helpers/StdDefs.h>
 #include <DGtal/images/Image.h>
 #include <DGtal/images/ImageContainerBySTLVector.h>

From 7a7bd41ef9ae9a1e1f7dab2c67b56fe59f15888f Mon Sep 17 00:00:00 2001
From: David Coeurjolly <david.coeurjolly@liris.cnrs.fr>
Date: Fri, 11 Mar 2022 16:48:48 +0100
Subject: [PATCH 08/14] Update volumetric/volInfo.cpp

Co-authored-by: Bertrand Kerautret <bertrand.kerautret@univ-lyon2.fr>
---
 volumetric/volInfo.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/volumetric/volInfo.cpp b/volumetric/volInfo.cpp
index 376a9d19..a37dc29f 100644
--- a/volumetric/volInfo.cpp
+++ b/volumetric/volInfo.cpp
@@ -27,7 +27,7 @@
 #include <iostream>
 #include <map>
 #include <DGtal/base/Common.h>
-#include <DGtal/io/readers/VolReader.h>
+#include <DGtal/io/readers/GenericReader.h>
 #include <DGtal/helpers/StdDefs.h>
 #include <DGtal/images/Image.h>
 #include <DGtal/images/ImageContainerBySTLVector.h>

From 848610d8f1c0e60d60c59097561189a9d2aeac16 Mon Sep 17 00:00:00 2001
From: David Coeurjolly <david.coeurjolly@liris.cnrs.fr>
Date: Fri, 11 Mar 2022 16:48:56 +0100
Subject: [PATCH 09/14] Update volumetric/volInfo.cpp

Co-authored-by: Bertrand Kerautret <bertrand.kerautret@univ-lyon2.fr>
---
 volumetric/volInfo.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/volumetric/volInfo.cpp b/volumetric/volInfo.cpp
index a37dc29f..50444e9e 100644
--- a/volumetric/volInfo.cpp
+++ b/volumetric/volInfo.cpp
@@ -106,7 +106,7 @@ int main(int argc, char**argv)
   trace.beginBlock("Loading file");
   typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char>  MyImageC;
 
-  MyImageC  imageC = VolReader< MyImageC >::importVol ( inputFileName );
+  MyImageC  imageC = GenericReader<MyImageC>::import(inputFileName);
   
   trace.info()<<imageC<<std::endl;
   trace.info()<<"Scanning the values:"<<std::endl;

From 1fda16f66bade17f609d4c6d92ec7b368d10b1e6 Mon Sep 17 00:00:00 2001
From: David Coeurjolly <david.coeurjolly@liris.cnrs.fr>
Date: Fri, 11 Mar 2022 16:50:02 +0100
Subject: [PATCH 10/14] Update volInfo.cpp

---
 volumetric/volInfo.cpp | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/volumetric/volInfo.cpp b/volumetric/volInfo.cpp
index 50444e9e..2e2db98b 100644
--- a/volumetric/volInfo.cpp
+++ b/volumetric/volInfo.cpp
@@ -60,14 +60,12 @@ using namespace Z3i;
  Positionals:
    1 TEXT:FILE REQUIRED                  Input vol file.
   
- Options:
-   -h,--help                             Print this help message and exit
-   -i,--input TEXT:FILE REQUIRED         Input vol file.
+
  
  @endcode
 
  @b Example: 
-You can apply several sub sampling:
+You can retrieve information from the vol file as:
  @code
  $ volInfo $DGtal/examples/samples/lobster.vol
  @endcode

From cf22b4e5cb54ff924c4cadc34128a0b4b71ad06e Mon Sep 17 00:00:00 2001
From: David Coeurjolly <david.coeurjolly@liris.cnrs.fr>
Date: Fri, 11 Mar 2022 16:50:22 +0100
Subject: [PATCH 11/14] Update volInfo.cpp

---
 volumetric/volInfo.cpp | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/volumetric/volInfo.cpp b/volumetric/volInfo.cpp
index 2e2db98b..3b93f244 100644
--- a/volumetric/volInfo.cpp
+++ b/volumetric/volInfo.cpp
@@ -59,9 +59,6 @@ using namespace Z3i;
   
  Positionals:
    1 TEXT:FILE REQUIRED                  Input vol file.
-  
-
- 
  @endcode
 
  @b Example: 

From f5e60e8b48caac70f28a81fd23e4215a7fb4ed46 Mon Sep 17 00:00:00 2001
From: David Coeurjolly <david.coeurjolly@liris.cnrs.fr>
Date: Fri, 11 Mar 2022 16:51:18 +0100
Subject: [PATCH 12/14] Update ChangeLog.md

---
 ChangeLog.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ChangeLog.md b/ChangeLog.md
index 7946298a..06453c4f 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -21,7 +21,7 @@
 - *volumetric*
   - volSegment: adding new option to get long int images as output (for
     longvol exporting). (Bertrand Kerautret [#420](https://github.com/DGtal-team/DGtalTools/pull/420))
-  - volInfo: get information from a vol file. (David Coeurjolly, [#430](https://github.com/DGtal-team/DGtalTools/pull/430))
+  - volInfo: get information from a volumetric file. (David Coeurjolly, [#430](https://github.com/DGtal-team/DGtalTools/pull/430))
 
 # DGtalTools 1.2
 - *global*

From 1c6f739ac42b139a56c4e745d33f6430b632bdf6 Mon Sep 17 00:00:00 2001
From: David Coeurjolly <david.coeurjolly@liris.cnrs.fr>
Date: Fri, 11 Mar 2022 17:17:18 +0100
Subject: [PATCH 13/14] Update volumetric/volInfo.cpp

Co-authored-by: Bertrand Kerautret <bertrand.kerautret@univ-lyon2.fr>
---
 volumetric/volInfo.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/volumetric/volInfo.cpp b/volumetric/volInfo.cpp
index 3b93f244..523cd7db 100644
--- a/volumetric/volInfo.cpp
+++ b/volumetric/volInfo.cpp
@@ -40,7 +40,7 @@ using namespace DGtal;
 using namespace Z3i;
 
 /**
- @page volSubSample volSubSample
+ @page volInfo volInfo
  
  @brief Get information from a vol file (size and values).
 

From 0a6f47018cdeee231f83ee42a2bec5b3a3d037ef Mon Sep 17 00:00:00 2001
From: David Coeurjolly <david.coeurjolly@liris.cnrs.fr>
Date: Fri, 11 Mar 2022 17:18:21 +0100
Subject: [PATCH 14/14] Update volumetric/volInfo.cpp

Co-authored-by: Bertrand Kerautret <bertrand.kerautret@univ-lyon2.fr>
---
 volumetric/volInfo.cpp | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/volumetric/volInfo.cpp b/volumetric/volInfo.cpp
index 523cd7db..95e94285 100644
--- a/volumetric/volInfo.cpp
+++ b/volumetric/volInfo.cpp
@@ -50,9 +50,6 @@ using namespace Z3i;
 
  @b Allowed @b options @b are : 
  @code
- Positionals:
-   1 TEXT:FILE REQUIRED                  Input vol file.
-  
  Options:
    -h,--help                             Print this help message and exit
    -i,--input TEXT:FILE REQUIRED         Input vol file.