VolInfo

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 volumetric 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))
 

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 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.
@@ -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>

volumetric/CMakeLists.txt

@@ -14,6 +14,7 @@ SET(DGTAL_TOOLS_SRC
   volTrValues
   volIntensityScale
   volFillInterior
+  volInfo
   volMask
 )
 

volumetric/volInfo.cpp

@@ -0,0 +1,115 @@
+/**
+ *  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 2022/02/11
+ *
+ *
+ * This file is part of the DGtal library.
+ */
+
+#include <iostream>
+#include <map>
+#include <DGtal/base/Common.h>
+#include <DGtal/io/readers/GenericReader.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 volInfo volInfo
+
+ @brief Get information from a vol file (size and values).
+
+
+ @b Usage: 	./volumetric/volInfo [OPTIONS] 1 [2]
+
+
+ @b Allowed @b options @b are : 
+ @code
+ 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.
+ @endcode
+
+ @b Example: 
+You can retrieve information from the vol file as:
+ @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 = GenericReader<MyImageC>::import(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;
+}