Merge branch 'master' into rel1.2

ChangeLog.md

@@ -4,6 +4,8 @@
     (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)) 
+  - Uniform input/output option with previous use of CLI11 (issue #405).
+    (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/DGtal/pull/407))
 

converters/convertVol.cpp

@@ -60,12 +60,12 @@ using namespace DGtal;
 
 @b Examples:
 @code 
-$ convertVol -i ${DGtal}/examples/samples/lobster.vol -o convertedVol.p3d 
+$ convertVol ${DGtal}/examples/samples/lobster.vol convertedVol.p3d
 @endcode
 
  To upgrade a "Version-2" vol file to a "Version-3" (default Vol writer):
  @code
- $ convertVol -i ${DGtal}/examples/samples/lobster.vol -o ${DGtal}/examples/samples/lobster.vol
+ $ convertVol ${DGtal}/examples/samples/lobster.vol ${DGtal}/examples/samples/lobster.vol
  @endcode
  
 
@@ -102,7 +102,3 @@ int main( int argc, char** argv )
 
   return EXIT_SUCCESS;  
 }
-
-
-
-

converters/dicom2vol.cpp

@@ -55,6 +55,7 @@ using namespace DGtal;
 @code
 Positionals:
   1 TEXT:FILE REQUIRED                  dicom image  (.dcm).
+  2 TEXT:FILE                           volumetric file (.vol, .longvol .pgm3d, .raw).
 
 Options:
   -h,--help                             Print this help message and exit
@@ -86,7 +87,7 @@ int main( int argc, char** argv )
    DGtal::int64_t dicomMin {-1000};
    DGtal::int64_t dicomMax {3000};
 
-   app.description("Convert dicom file into a volumetric file (.vol, .longvol .pgm3d).\n Example:\n dicom2vol -i ${DGtal}/tests/samples/dicomSample/1629.dcm --dicomMin 0 --dicomMax 300 -o sample.vol.");
+   app.description("Convert dicom file into a volumetric file (.vol, .longvol .pgm3d).\n Example:\n dicom2vol  ${DGtal}/tests/samples/dicomSample/1629.dcm sample.vol --dicomMin 0 --dicomMax 300.");
    app.add_option("-i,--input,1", inputFileName, "dicom image  (.dcm)." )
     ->required()
     ->check(CLI::ExistingFile);

converters/freeman2img.cpp

@@ -65,23 +65,20 @@ using namespace DGtal;
 
 Positionals:
   1 TEXT:FILE REQUIRED                  Input freeman chain file name.
+  2 TEXT:FILE                           the output file name.
 
-Options:
-
-Positionals:
-  1 TEXT:FILE REQUIRED                  Input freeman chain file name.
 
 Options:
   -h,--help                             Print this help message and exit
   -i,--input TEXT:FILE REQUIRED         Input freeman chain file name.
   -b,--border UINT                      add a border in the resulting image (used only in the automatic mode i.e when --space is not used.
-  -o,--output TEXT=result.pgm           the output fileName
+  -o,--output TEXT=result.pgm           the output file name
   -s,--space INT x 4                    Define the space from its bounding box (lower and upper coordinates) else the space is automatically defined from the freemanchain bounding boxes.
 @endcode
 
 @b Example:
 @code
-  $freeman2img -i ${DGtal}/tests/samples/contourS.fc -o sample.pgm
+  $freeman2img ${DGtal}/tests/samples/contourS.fc sample.pgm
 @endcode
 You will obtain such image:
 @image html  resFreeman2img.png "Resulting image"
@@ -92,7 +89,7 @@ You will obtain such image:
 The file located in $DGtal/examples/samples/contourS2.fc contains different contours with some ones corresponds to hole.  We can apply the same conversion as the previous example:
 
 @code
-$ freeman2img -i  $DGtal/examples/samples/contourS2.fc  -o sample2.pgm
+$ freeman2img $DGtal/examples/samples/contourS2.fc  sample2.pgm
 @endcode
 
 You will obtain such image:
@@ -121,7 +118,7 @@ int main( int argc, char** argv )
     ->required()
     ->check(CLI::ExistingFile);
   app.add_option("-b,--border",border, "add a border in the resulting image (used only in the automatic mode i.e when --space is not used.");
-  app.add_option("-o,--output", outputFileName, "the output fileName", true);
+  app.add_option("-o,--output,2", outputFileName, "the output fileName", true);
   app.add_option("-s,--space", space, "Define the space from its bounding box (lower and upper coordinates) else the space is automatically defined from the freemanchain bounding boxes." )
     ->expected(4);
 
@@ -177,7 +174,6 @@ int main( int argc, char** argv )
     Image2D imageResult (Z2i::Domain(Z2i::Point(minx, miny), Z2i::Point(maxx, maxy))); 
     Surfaces<KSpace>::uFillInterior(aKSpace, functors::SurfelSetPredicate<std::set<SCell>,SCell>(boundarySCell), imageResult, 255, false, false );  
     imageResult >> outputFileName;
-
 
 }
 

converters/freeman2sdp.cpp

@@ -108,7 +108,7 @@ int main( int argc, char** argv )
   bool oneline {false};
   bool info {false};
 
-  app.description("Transform freeman chain into a Sequence of Discrete Points. Result is given to std output.\n Example:\n freeman2sdp -i ${DGtal}/tests/samples/contourS.fc > contourS.sdp \n");
+  app.description("Transform freeman chain into a Sequence of Discrete Points. Result is given to std output.\n Example:\n freeman2sdp ${DGtal}/tests/samples/contourS.fc > contourS.sdp \n");
   app.add_option("-i,--input,1", inputFileName, "Input freeman chain file name." )
     ->required()
     ->check(CLI::ExistingFile);

converters/heightfield2vol.cpp

@@ -21,7 +21,6 @@
  *
  * @date 2015/03/18
  *
- * 
  *
  * This file is part of the DGtalTools.
  */
@@ -70,7 +69,7 @@ using namespace DGtal;
 
 @b Example:
 @code
-  $ heightfield2vol -i ${DGtal}/examples/samples/church.pgm -o volResu.vol -s 0.3 -z 50  
+  $ heightfield2vol ${DGtal}/examples/samples/church.pgm volResu.vol -s 0.3 -z 50
 
 @endcode
 You will obtain such image:
@@ -134,8 +133,9 @@ int main( int argc, char** argv )
    unsigned int  maxZ {255};
 
 
-   app.description("Convert a 2D heightfield image into a volumetric file.\n Example: \n heightfield2vol -i ${DGtal}/examples/samples/church.pgm -o volResu.vol -s 0.3 -z 50  \n");
+   app.description("Convert a 2D heightfield image into a volumetric file.\n Example: \n heightfield2vol ${DGtal}/examples/samples/church.pgm volResu.vol -s 0.3 -z 50  \n");
    app.add_option("-i,--input,1", inputFileName, "input heightfield file (2D image).")
+     ->check(CLI::ExistingFile)
      ->required();
    app.add_option("-o,--output,2", outputFileName,"output volumetric file.", true);
    app.add_option("-s,--scale", scale, "set the scale factor on height values (default 1.0)");

converters/img2freeman.cpp

@@ -41,7 +41,7 @@ using namespace DGtal;
 
 @b Example:
 @code
-  $ img2freeman -i ${DGtal}/examples/samples/church.pgm > contours.fc  
+  $ img2freeman ${DGtal}/examples/samples/church.pgm > contours.fc
 
 @endcode
 You will obtain such results:
@@ -74,13 +74,9 @@ more contours.fc
 */
 
 
-
-
-
 typedef ImageSelector < Z2i::Domain, unsigned char>::Type Image;
 
 
-
 std::vector<unsigned int> getHistoFromImage(const Image &image){
   const Image::Domain &imgDom = image.domain();
   std::vector<unsigned int> vectHisto(UCHAR_MAX);
@@ -90,8 +86,6 @@ std::vector<unsigned int> getHistoFromImage(const Image &image){
   return vectHisto;
 }
 
-
-
 unsigned int 
 getOtsuThreshold(const Image &image){
   std::vector<unsigned int> histo = getHistoFromImage(image);
@@ -272,10 +266,10 @@ int main( int argc, char** argv )
   }else{
     for(int i=0; minThreshold+i*increment< maxThreshold; i++){
       if(vectRangeMin.size()==3){
-	min = (int)(minThreshold+(i)*increment);
+        min = (int)(minThreshold+(i)*increment);
       }
       if(vectRangeMax.size()==3){
-	max = (int)(maxThreshold-(i)*increment);
+        max = (int)(maxThreshold-(i)*increment);
       }
       Binarizer b(min, max); 
       functors::PointFunctorPredicate<Image,Binarizer> predicate(image, b); 
@@ -286,15 +280,14 @@ int main( int argc, char** argv )
       Surfaces<Z2i::KSpace>::extractAllPointContours4C( vectContoursBdryPointels,
 							ks, predicate, sAdj );  
       if(select){
-	saveSelContoursAsFC(vectContoursBdryPointels,  minSize, selectCenter,  selectDistanceMax, sortCnt);
+          saveSelContoursAsFC(vectContoursBdryPointels,  minSize,
+                              selectCenter,  selectDistanceMax, sortCnt);
       }else{
-	saveAllContoursAsFc(vectContoursBdryPointels,  minSize, sortCnt); 
+          saveAllContoursAsFc(vectContoursBdryPointels,
+                              minSize, sortCnt);
       }
       trace.info() << " [done]" << std::endl;
     }
   }
-
-
-
 }
 

converters/imgAddNoise.cpp

@@ -67,7 +67,7 @@ using namespace DGtal;
 
 @b Example:
 @code
-  $ imgAddNoise -i ${DGtal}/examples/samples/klokan.pgm -o noise.pgm 
+  $ imgAddNoise  ${DGtal}/examples/samples/klokan.pgm  noise.pgm
 
 @endcode
 You will obtain such image:
@@ -100,7 +100,7 @@ int main( int argc, char** argv )
   std::string outputFileName {"result.png"};
   double noise {0.5};
 
-  app.description("Add Kanungo noise to a binary object with 0 values as background points and values >0 for the foreground ones.\n Example: \n imgAddNoise -i ${DGtal}/examples/samples/klokan.pgm -o noise.pgm ");
+  app.description("Add Kanungo noise to a binary object with 0 values as background points and values >0 for the foreground ones.\n Example: \n imgAddNoise ${DGtal}/examples/samples/klokan.pgm noise.pgm ");
   app.add_option("-i,--input,1", inputFileName, "input image file name (any 2D image format accepted by DGtal::GenericReader)." )
     ->required()
     ->check(CLI::ExistingFile);

converters/itk2vol.cpp

@@ -66,7 +66,7 @@ using namespace DGtal;
 
 @b Example:
 @code
-$itk2vol -i image.mhd --dicomMin -500 --dicomMax -100 -o sample.vol 
+$itk2vol image.mhd sample.vol  --dicomMin -500 --dicomMax -100
 @endcode
 
 @see itk2vol.cpp
@@ -121,7 +121,7 @@ int main( int argc, char** argv )
    string inputMask {""};
    string inputType {""};
 
-   app.description("Converts itk file into a volumetric file (.vol, .pgm3d). \n Example:\n itk2vol -i image.mhd --inputMin -500 --inputMax -100 -o sample.vol \n");
+   app.description("Converts itk file into a volumetric file (.vol, .pgm3d). \n Example:\n itk2vol  image.mhd sample.vol --inputMin -500 --inputMax -100 \n");
    app.add_option("-i,--input,1", inputFileName, "Any file format in the ITK library (mhd, mha, ...)." )
     ->required()
     ->check(CLI::ExistingFile);

converters/longvol2vol.cpp

@@ -65,7 +65,7 @@ using namespace Z3i;
 
 @b Example:
 @code
-  $ longvol2vol -i ${DGtal}/tests/samples/test.longvol -o out.vol 
+  $ longvol2vol ${DGtal}/tests/samples/test.longvol out.vol 
 @endcode
 
 @see longvol2vol.cpp

converters/mesh2heightfield.cpp

@@ -171,7 +171,7 @@ int main( int argc, char** argv )
   double nz{1};
 
 
-  app.description("Convert a mesh file into a projected 2D image given from a normal direction N and from a starting point P. The 3D mesh discretized and scanned in the normal direction N, starting from P with a step 1.\n   Example:\n mesh2heightfield -i ${DGtal}/examples/samples/tref.off --orientAutoFrontZ --width 25 --height 25 -o heighMap.pgm -s 10  \n");  
+  app.description("Convert a mesh file into a projected 2D image given from a normal direction N and from a starting point P. The 3D mesh discretized and scanned in the normal direction N, starting from P with a step 1.\n   Example:\n mesh2heightfield ${DGtal}/examples/samples/tref.off heighMap.pgm --orientAutoFrontZ --width 25 --height 25  -s 10  \n");  
   app.add_option("-i,--input,1", inputFileName, "mesh file (.off)" )
     ->required()
     ->check(CLI::ExistingFile);

converters/mesh2vol.cpp

@@ -138,7 +138,7 @@ int main( int argc, char** argv )
    unsigned int separation {6};
    unsigned int resolution {128};
 
-   app.description("Convert a mesh file into a 26-separated or 6-separated volumetric voxelization in a given resolution grid. \n Example:\n mesh2vol -i ${DGtal}/examples/samples/tref.off -o output.vol --separation 26 --resolution 256 ");
+   app.description("Convert a mesh file into a 26-separated or 6-separated volumetric voxelization in a given resolution grid. \n Example:\n mesh2vol ${DGtal}/examples/samples/tref.off output.vol --separation 26 --resolution 256 ");
 
    app.add_option("-i,--input,1", inputFileName, "mesh file (.off)." )
      ->required()

converters/ofs2off.cpp

@@ -52,6 +52,7 @@ using namespace DGtal;
 @code
 Positionals:
   1 TEXT:FILE REQUIRED                  ofs file (.ofs).
+  2 TEXT:FILE                           ofs file (.ofs).
 
 Options:
   -h,--help                             Print this help message and exit
@@ -61,7 +62,7 @@ using namespace DGtal;
 
 @b Example:
 @code
-  $ ofs2off -i input.ofs -o output.off 
+  $ ofs2off input.ofs output.off 
 @endcode
 
 @see ofs2off.cpp

converters/raw2vol.cpp

@@ -56,6 +56,7 @@ Allowed options are: :
 
 Positionals:
   1 TEXT:FILE REQUIRED                  Input raw file.
+  2 TEXT:FILE REQUIRED                  Input raw file.
 
 Options:
   -h,--help                             Print this help message and exit
@@ -99,7 +100,7 @@ int main(int argc, char**argv)
    std::string inputFileName;
    std::string outputFileName {"result.vol"};
    unsigned int x, y, z;
-   app.description("Converts a  8-bit raw file to  vol.\n Basic example:\n \t raw2vol -x 128 -y 128 -z 128 --input <RawFileName> --output <VolOutputFileName>");
+   app.description("Converts a  8-bit raw file to  vol.\n Basic example:\n \t raw2vol <RawFileName>  <VolOutputFileName> -x 128 -y 128 -z 128");
    app.add_option("-i,--input,1", inputFileName, "Input raw file." )
     ->required()
     ->check(CLI::ExistingFile);

converters/sdp2vol.cpp

@@ -65,7 +65,7 @@ using namespace DGtal;
 
 @b Example:
 @code
-  $ sdp2vol -i volumePoints.sdp -o volume.vol -d 0 0 0 10 10 10
+  $ sdp2vol volumePoints.sdp volume.vol -d 0 0 0 10 10 10
 @endcode
 
 @see sdp2vol.cpp
@@ -92,7 +92,7 @@ int main( int argc, char** argv )
    bool invertY {false};
    std::vector<int> domainCoords;
 
-   app.description("Convert digital set of points into a volumic file.\n Example:\n sdp2vol -i volumePoints.sdp -o volume.vol -d 0 0 0 10 10 10 \n");
+   app.description("Convert digital set of points into a volumic file.\n Example:\n sdp2vol volumePoints.sdp volume.vol -d 0 0 0 10 10 10 \n");
    app.add_option("-i,--input,1", inputSDP, "Sequence of 3d Discrete points (.sdp)." )
     ->required()
     ->check(CLI::ExistingFile);

converters/vol2heightfield.cpp

@@ -59,11 +59,13 @@ using namespace DGtal;
 
 Positionals:
   1 TEXT:FILE REQUIRED                  vol file (.vol, .longvol .p3d, .pgm3d and if WITH_ITK is selected: dicom, dcm, mha, mhd). For longvol, dicom, dcm, mha or mhd formats, the input values are linearly scaled between 0 and 255.
+  2 TEXT=result.pgm                     resulting image filename (in pgm or other).
 
+ 
 Options:
   -h,--help                             Print this help message and exit
   -i,--input TEXT:FILE REQUIRED         vol file (.vol, .longvol .p3d, .pgm3d and if WITH_ITK is selected: dicom, dcm, mha, mhd). For longvol, dicom, dcm, mha or mhd formats, the input values are linearly scaled between 0 and 255.
-  -o,--output TEXT                      sequence of discrete point file (.sdp)
+  -o,--output TEXT                      resulting image filename (in pgm or other)
   -m,--thresholdMin INT=128             threshold min (excluded) to define binary shape.
   -M,--thresholdMax INT=255             threshold max (included) to define binary shape.
   --rescaleInputMin INT=0               min value used to rescale the input intensity (to avoid basic cast into 8  bits image).
@@ -83,7 +85,7 @@ using namespace DGtal;
 
 @b Example:
 @code 
-$ vol2heightfield -i ${DGtal}/examples/samples/lobster.vol -m 60 -M 500  --nx 0 --ny 0.7 --nz -1 -x 150 -y 0 -z 150 --width 300 --height 300 --heightFieldMaxScan 350  -o resultingHeightMap.pgm 
+$ vol2heightfield ${DGtal}/examples/samples/lobster.vol resultingHeightMap.pgm -m 60 -M 500  --nx 0 --ny 0.7 --nz -1 -x 150 -y 0 -z 150 --width 300 --height 300 --heightFieldMaxScan 350  resultingHeightMap.pgm
 @endcode
 
 You should obtain such a resulting image:
@@ -104,7 +106,7 @@ int main( int argc, char** argv )
 // parse command line using CLI ----------------------------------------------
    CLI::App app;
    std::string inputFileName;
-   std::string outputFileName {"result.raw"};
+   std::string outputFileName {"result.pgm"};
    int thresholdMin {128};
    int thresholdMax {255};
    DGtal::int64_t rescaleInputMin {0};
@@ -125,7 +127,7 @@ int main( int argc, char** argv )
    app.add_option("-i,--input,1", inputFileName, "vol file (.vol, .longvol .p3d, .pgm3d and if WITH_ITK is selected: dicom, dcm, mha, mhd). For longvol, dicom, dcm, mha or mhd formats, the input values are linearly scaled between 0 and 255." )
     ->required()
     ->check(CLI::ExistingFile);
-  app.add_option("-o,--output", outputFileName, "sequence of discrete point file (.sdp)");
+  app.add_option("-o,--output,2", outputFileName, "resulting image filename (in pgm or other).");
   app.add_option("--thresholdMin,-m", thresholdMin, "threshold min (excluded) to define binary shape.", true);
   app.add_option("--thresholdMax,-M", thresholdMax, "threshold max (included) to define binary shape.", true);
   app.add_option("--rescaleInputMin", rescaleInputMin, "min value used to rescale the input intensity (to avoid basic cast into 8  bits image).", true);
@@ -208,7 +210,3 @@ int main( int argc, char** argv )
   trace.info() << " [done] " << std::endl ;   
   return EXIT_SUCCESS;
 }
-
-
-
-