DOC: doc review and warnings

Documentation/Cookbook/Scripts/otb_warnings.py

@@ -38,8 +38,9 @@ def application_documentation_warnings(app):
     description = app.GetDescription()
     longdescription = app.GetDocLongDescription()
 
-    if not longdescription[-1] == ".":
-        warn("Application Long Description does not end with a period (.)")
+    # disable because there are so many for now
+    #if not longdescription[-1] == ".":
+        #warn("Application Long Description does not end with a period (.)")
 
     if re.search("\\n [a-zA-Z]", longdescription):
         warn("Application Long Description contains '\\n ' pattern (usually not intended)")

Modules/Applications/AppClassification/app/otbComputePolylineFeatureFromImage.cxx

@@ -82,7 +82,7 @@ private:
     SetDescription("This application computes the chosen descriptors for each studied polyline contained in the input VectorData.");
 
     SetDocName("Compute Polyline Feature From Image");
-    SetDocLongDescription("The first step in the classifier fusion based validation is to compute the chosen descriptors for each studied polyline. ");
+    SetDocLongDescription("The first step in the classifier fusion based validation is to compute the chosen descriptors for each studied polyline.");
     SetDocLimitations("Since it does not rely on streaming process, take care of the size of input image before launching application.");
     SetDocAuthors("OTB-Team");
     SetDocSeeAlso(" ");

Modules/Applications/AppDimensionalityReduction/app/otbDimensionalityReduction.cxx

@@ -108,7 +108,7 @@ private:
     AddParameter(ParameterType_OutputImage, "out", "Output Image");
     SetParameterDescription("out", "output image. Components are ordered by decreasing eigenvalues.");
     MandatoryOff("out");
-    AddParameter(ParameterType_Group, "rescale", "Rescale Output.");
+    AddParameter(ParameterType_Group, "rescale", "Rescale Output");
 
     MandatoryOff("rescale");
     //  AddChoice("rescale.no","No rescale");
@@ -132,10 +132,10 @@ private:
     SetParameterDescription("method.pca", "Principal Component Analysis.");
     AddChoice("method.napca", "NA-PCA");
     SetParameterDescription("method.napca", "Noise Adjusted Principal Component Analysis.");
-    AddParameter(ParameterType_Int, "method.napca.radiusx", "Set the x radius of the sliding window.");
+    AddParameter(ParameterType_Int, "method.napca.radiusx", "Set the x radius of the sliding window");
     SetMinimumParameterIntValue("method.napca.radiusx", 1);
     SetDefaultParameterInt("method.napca.radiusx", 1);
-    AddParameter(ParameterType_Int, "method.napca.radiusy", "Set the y radius of the sliding window.");
+    AddParameter(ParameterType_Int, "method.napca.radiusy", "Set the y radius of the sliding window");
     SetMinimumParameterIntValue("method.napca.radiusy", 1);
     SetDefaultParameterInt("method.napca.radiusy", 1);
 
@@ -158,14 +158,14 @@ private:
     //SetParameterDescription("method.vd","Virtual Dimension.");
     //MandatoryOff("method");
 
-    AddParameter(ParameterType_Int, "nbcomp", "Number of Components.");
+    AddParameter(ParameterType_Int, "nbcomp", "Number of Components");
     SetParameterDescription("nbcomp", "Number of relevant components kept. By default all components are kept.");
     SetDefaultParameterInt("nbcomp", 0);
     MandatoryOff("nbcomp");
     SetMinimumParameterIntValue("nbcomp", 0);
 
-    AddParameter(ParameterType_Bool, "normalize", "Normalize.");
-    SetParameterDescription("normalize", "center AND reduce data before Dimensionality reduction.");
+    AddParameter(ParameterType_Bool, "normalize", "Normalize");
+    SetParameterDescription("normalize", "Center and reduce data before Dimensionality reduction.");
 
     AddParameter(ParameterType_OutputFilename, "outmatrix", "Transformation matrix output (text format)");
     SetParameterDescription("outmatrix", "Filename to store the transformation matrix (csv format)");

Modules/Applications/AppDimensionalityReduction/app/otbImageDimensionalityReduction.cxx

@@ -137,7 +137,7 @@ private:
                           "the model. The input pixels"
                           " can be optionally centered and reduced according "
                           "to the statistics file produced by the "
-                          "ComputeImagesStatistics application. ");
+                          "ComputeImagesStatistics application.");
 
     SetDocLimitations("The input image must contain the feature bands used for"
                       " the model training. "

Modules/Applications/AppDomainTransform/app/otbDomainTransform.cxx

@@ -106,7 +106,7 @@ private:
 
     // Documentation
     SetDocName("DomainTransform");
-    SetDocLongDescription("Domain Transform application for wavelet and fourier");
+    SetDocLongDescription("Domain Transform application for wavelet and fourier.");
     SetDocLimitations("This application is not streamed, check your system resources when processing large images");
     SetDocAuthors("OTB-Team");
     SetDocSeeAlso("otbWaveletImageFilter, otbWaveletInverseImageFilter, otbWaveletTransform");

Modules/Applications/AppEdge/app/otbEdgeExtraction.cxx

@@ -108,9 +108,9 @@ private:
                             "This filter is more suited for radar images. It has a spatial parameter "
                             "to avoid speckle noise perturbations. The larger the radius is, "
                             "less sensible to the speckle noise the filter is, but micro edge will be missed.");
-    AddParameter(ParameterType_Int, "filter.touzi.xradius", "The X radius of the neighborhood.");
+    AddParameter(ParameterType_Int, "filter.touzi.xradius", "X radius of the neighborhood");
     SetDefaultParameterInt("filter.touzi.xradius", 1);
-    AddParameter(ParameterType_Int, "filter.touzi.yradius", "The Y radius of the neighborhood.");
+    AddParameter(ParameterType_Int, "filter.touzi.yradius", "Y radius of the neighborhood");
     SetDefaultParameterInt("filter.touzi.yradius", 1);
 
     // Canny Section

Modules/Applications/AppImageUtils/app/otbColorMapping.cxx

@@ -304,7 +304,7 @@ private:
 
     // --- OPERATION --- : Label to color / Color to label
     AddParameter(ParameterType_Choice, "op", "Operation");
-    SetParameterDescription("op","Selection of the operation to execute (default is : label to color).");
+    SetParameterDescription("op", "Selection of the operation to execute (default is: label to color).");
 
     AddChoice("op.labeltocolor","Label to color");
 

Modules/Applications/AppImageUtils/app/otbDownloadSRTMTiles.cxx

@@ -230,7 +230,7 @@ private:
       "check which tiles are already downloaded.");
 
     // UserDefined values
-    AddParameter(ParameterType_Choice, "mode", "Download/List corresponding SRTM tiles.");
+    AddParameter(ParameterType_Choice, "mode", "Download/List corresponding SRTM tiles");
 
     AddChoice("mode.download", "Download");
     SetParameterDescription("mode.download","Download corresponding tiles on USGE server.");

Modules/Applications/AppImageUtils/app/otbDynamicConvert.cxx

@@ -107,7 +107,7 @@ private:
 
       "* **All**: keep all bands.\n"
       "* **Grayscale**: to display mono image as standard color image \n"
-      "* **RGB**: select 3 bands in the input image (multi-bands) \n"
+      "* **RGB**: select 3 bands in the input image (multi-bands)\n"
     );
     SetDocLimitations("The application does not support complex pixel types as output.");
     SetDocAuthors("OTB-Team");

Modules/Applications/AppImageUtils/app/otbExtractROI.cxx

@@ -81,7 +81,7 @@ private:
       "allows the user to enter one point (upper left corner of the region to "
       "extract) and a size. The extent mode needs two points (upper left "
       "corner and lower right) and the radius mode need the center of the "
-      "region and the radius : it will extract the rectangle containing the "
+      "region and the radius: it will extract the rectangle containing the "
       "circle defined and limited by the image dimension. The fit mode "
       "needs a reference image or vector and the dimension of the extracted "
       "region will be the same as the extent of the reference. "
@@ -103,14 +103,14 @@ private:
     AddParameter(ParameterType_Choice,"mode","Extraction mode");
     AddChoice("mode.standard","Standard");
     SetParameterDescription("mode.standard",
-      "In standard mode extraction is done with 2 parameters : the "
+      "In standard mode extraction is done with 2 parameters: the "
       "upper left corner and the size of the region, decomposed "
       "in X and Y coordinates.");
 
-    // Fit mode : the ROI is computed through a ref vector dataset or a ref image 
+    // Fit mode: the ROI is computed through a ref vector dataset or a ref image 
     AddChoice("mode.fit","Fit");
     SetParameterDescription("mode.fit",
-      "In fit mode, extract is made from a reference : image or vector dataset.");
+      "In fit mode, extract is made from a reference: image or vector dataset.");
 
     AddParameter( ParameterType_InputImage , "mode.fit.im" , 
       "Reference image" );
@@ -122,28 +122,25 @@ private:
       "The extent of the input vector file is computed and then "
       "gives a region of interest that will be extracted." );
 
-    // Extent mode : ROI is computed with two point (upper left and lower left corners)
+    // Extent mode: ROI is computed with two point (upper left and lower left corners)
     AddChoice( "mode.extent" , "Extent" );
     SetParameterDescription( "mode.extent" ,
       "In extent mode, the ROI is defined by two points, the upper left corner "
-      "and the lower right corner, decomposed in 2 coordinates : "
+      "and the lower right corner, decomposed in 2 coordinates: "
       "X and Y. The unit for those coordinates can be set." );
-    AddParameter( ParameterType_Float , "mode.extent.ulx" ,
-                  "X coordinate of the Upper left corner" );
-    SetParameterDescription( "mode.extent.ulx" ,
-      "X coordinate of upper left corner point." );
-    AddParameter( ParameterType_Float , "mode.extent.uly" ,
-                  "Y coordinate of Upper Left corner point." );
-    SetParameterDescription( "mode.extent.uly" ,
-      "Y coordinate of upper left corner point." );
-    AddParameter( ParameterType_Float , "mode.extent.lrx" , 
-                  "X coordinate of Lower Right corner point." );
-    SetParameterDescription( "mode.extent.lrx" ,
-      "X coordinate of lower right corner point." );
-    AddParameter( ParameterType_Float , "mode.extent.lry" ,
-                  "Y coordinate of Lower Right corner point." );
-    SetParameterDescription( "mode.extent.lry" ,
-      "Y coordinate of lower right corner point." );
+
+    AddParameter(ParameterType_Float, "mode.extent.ulx", "X coordinate of the Upper left corner");
+    SetParameterDescription("mode.extent.ulx", "X coordinate of upper left corner point.");
+
+    AddParameter(ParameterType_Float, "mode.extent.uly", "Y coordinate of Upper Left corner point");
+    SetParameterDescription("mode.extent.uly", "Y coordinate of upper left corner point.");
+
+    AddParameter(ParameterType_Float, "mode.extent.lrx", "X coordinate of Lower Right corner point");
+    SetParameterDescription("mode.extent.lrx", "X coordinate of lower right corner point.");
+
+    AddParameter(ParameterType_Float, "mode.extent.lry", "Y coordinate of Lower Right corner point");
+    SetParameterDescription("mode.extent.lry", "Y coordinate of lower right corner point.");
+
     // Unit of extent mode
     AddParameter( ParameterType_Choice , "mode.extent.unit" , "Unit" );
     AddChoice( "mode.extent.unit.pxl" , "Pixel" );
@@ -160,7 +157,7 @@ private:
       "the latitude.");
 
 
-    // Radius mode : ROI is computed through a point and a radius
+    // Radius mode: ROI is computed through a point and a radius
     AddChoice( "mode.radius" , "Radius" );
     SetParameterDescription( "mode.radius" ,
       "In radius mode, the ROI is defined by a point and a radius. The "

Modules/Applications/AppMathParser/app/otbBandMath.cxx

@@ -72,7 +72,7 @@ private:
 
       "The formula can be written using:\n\n"
       "* numerical values ( 2.3, -5, 3.1e4, ...)\n"
-      "* variables containing pixel values (e.g. : ``im2b3`` is the pixel value"
+      "* variables containing pixel values (e.g. ``im2b3`` is the pixel value"
       " in 2nd image, 3rd band)\n"
       "* binary operators:\n\n"
 
@@ -87,7 +87,7 @@ private:
       "  * ``or`` logical or, ``and`` logical and\n"
       "* if-then-else operator: ``if(condition;value_true;value_false)``\n"
 #endif
-      "* functions : ``exp()``, ``log()``, ``sin()``, ``cos()``, ``min()``, ``max()``, ...\n\n"
+      "* functions: ``exp()``, ``log()``, ``sin()``, ``cos()``, ``min()``, ``max()``, ...\n\n"
 
       "The full list of features and operators is available on the muParser website [1]."
       );

Modules/Applications/AppMathParserX/app/otbBandMathX.cxx

@@ -102,7 +102,7 @@ private:
       "  * ``==`` equal, ``!=`` not equal\n"
       "  * logical operators: ``or``, ``and``, ``xor``\n"
       "* if-then-else operator: ``(condition ? value_true : value_false)``\n"
-      "* functions : abs(), exp(), log(), sin(), cos(), min(), max(), ...\n\n"
+      "* functions: abs(), exp(), log(), sin(), cos(), min(), max(), ...\n\n"
 
       "Always keep in mind that this application only addresses mathematically "
       "well-defined formulas. For instance, it is not possible to add vectors of"
@@ -188,7 +188,7 @@ private:
       "whereas #M allows the definition of a vector/matrix. In the latter case, "
       "elements of a row must be separated by commas, and rows must be separated"
       " by semicolons. It is also possible to define expressions within the same"
-      " txt file, with #E <expr> (see limitations, below).\n"
+      " txt file, with #E <expr> (see limitations, below)."
     );
 
     SetDocLimitations(
@@ -376,12 +376,12 @@ private:
     std::string expStr = GetParameterString("exp");
     if (useContext)
       {
-      otbAppLogINFO("Using input context : " << expStr );
+      otbAppLogINFO("Using input context: " << expStr );
       m_Filter->ImportContext(GetParameterString("incontext"));
       }
     else
       {
-      otbAppLogINFO("Using expression : " << expStr );
+      otbAppLogINFO("Using expression: " << expStr );
       m_Filter->SetExpression(expStr);
       }
 

Modules/Applications/AppMorphology/app/otbBinaryMorphologicalOperation.cxx

@@ -179,7 +179,7 @@ SetOfficialDocLink();
 
 void DoUpdateParameters() override
 {
-  // Nothing to do here : all parameters are independent
+  // Nothing to do here: all parameters are independent
 }
 
 void DoExecute() override

Modules/Applications/AppSARUtils/app/otbDespeckle.cxx

@@ -70,10 +70,10 @@ private:
      " different mathematical models of the phenomenon. The application includes four"
      " methods: Lee [1], Frost [2], GammaMAP [3] and Kuan [4]. \n\n"
      "We sum up below the basic principle of this four methods:\n\n"
-     "* Lee : Estimate the signal by mean square error minimization (MMSE) on a sliding window.\n"
-     "* Frost : Also derived from the MMSE criteria with a weighted sum of the values within the window. The weighting factors decrease with distance from the pixel of interest.\n"
-     "* GammaMAP  : Derived under the assumption of the image follows a Gamma distribution.\n"
-     "* Kuan : Also derived from the MMSE criteria under the assumption of non stationary mean and variance. It is quite similar to Lee filter in form."
+     "* Lee: Estimate the signal by mean square error minimization (MMSE) on a sliding window.\n"
+     "* Frost: Also derived from the MMSE criteria with a weighted sum of the values within the window. The weighting factors decrease with distance from the pixel of interest.\n"
+     "* GammaMAP: Derived under the assumption of the image follows a Gamma distribution.\n"
+     "* Kuan: Also derived from the MMSE criteria under the assumption of non stationary mean and variance. It is quite similar to Lee filter in form."
       );
 
     SetDocLimitations("The application does not handle complex image as input.");
@@ -169,7 +169,7 @@ private:
 
   void DoUpdateParameters() override
   {
-    // Nothing to do here : all parameters are independent
+    // Nothing to do here: all parameters are independent
   }
 
   void DoExecute() override

Modules/Applications/AppStereo/app/otbBlockMatching.cxx

@@ -149,9 +149,9 @@ private:
       "vertical directions). A winner-take-all approach is used to select the "
       "best match. There are different metrics implemented to evaluate the "
       "match between two local windows:\n\n"
-      "* SSD : Sum of Squared Distances\n"
-      "* NCC : Normalized Cross-Correlation\n"
-      "* Lp  : Lp pseudo norm\n\n"
+      "* SSD: Sum of Squared Distances\n"
+      "* NCC: Normalized Cross-Correlation\n"
+      "* Lp: Lp pseudo norm\n\n"
 
       "Once the best integer disparity is found, an optional step of sub-pixel "
       "disparity estimation can be performed, with various algorithms "
@@ -165,7 +165,7 @@ private:
       " by avoiding to investigate disparities that will not be reliable anyway"
       ". For efficiency reasons, if the image of optimal metric values is "
       "desired, it will be concatenated to the output image (which will then "
-      "have three bands : horizontal disparity, vertical disparity and metric "
+      "have three bands: horizontal disparity, vertical disparity and metric "
       "value). One can split these images afterward.");
     SetDocLimitations("None");
     SetDocAuthors("OTB-Team");

Modules/Applications/AppStereo/app/otbDisparityMapToElevationMap.cxx

@@ -83,7 +83,7 @@ private:
       "* skip if position is discarded by the disparity mask\n"
       "* compute left ray: transform the current position from epipolar "
       "geometry to left sensor geometry (left rectification grid)\n"
-      "* compute right ray : shift the current position with current "
+      "* compute right ray: shift the current position with current "
       "disparity and transform from epipolar geometry to right sensor (right "
       "rectification grid)\n"
       "* estimate best 3D intersection between left and right rays\n"
@@ -202,8 +202,8 @@ private:
     m_DispToElev->UpdateOutputInformation();
     FloatVectorImageType::RegionType outputRegion = m_DispToElev->GetOutput()->GetLargestPossibleRegion();
 
-    otbAppLogINFO(<<"Elevation map origin : [" << m_DispToElev->GetOutput()->GetOrigin()[0] << "," << m_DispToElev->GetOutput()->GetOrigin()[1] <<  "]" << std::endl);
-    otbAppLogINFO(<<"Elevation map size : [" << outputRegion.GetSize()[0] << "," << outputRegion.GetSize()[1] << "]" << std::endl);
+    otbAppLogINFO(<<"Elevation map origin: [" << m_DispToElev->GetOutput()->GetOrigin()[0] << "," << m_DispToElev->GetOutput()->GetOrigin()[1] <<  "]" << std::endl);
+    otbAppLogINFO(<<"Elevation map size: [" << outputRegion.GetSize()[0] << "," << outputRegion.GetSize()[1] << "]" << std::endl);
 
     this->SetParameterOutputImage("io.out",m_DispToElev->GetOutput());
   }

Modules/Applications/AppTextures/app/otbHaralickTextureExtraction.cxx

@@ -74,21 +74,24 @@ SetDescription("Computes Haralick textural features on the selected channel of t
 
 // Documentation
 SetDocName("Haralick Texture Extraction");
-SetDocLongDescription("This application computes three sets of Haralick features [1][2].\n"
-    "  * simple: a set of 8 local Haralick features: Energy (texture uniformity) , "
+SetDocLongDescription(
+    "This application computes three sets of Haralick features [1][2].\n\n"
+
+    "* simple: a set of 8 local Haralick features: Energy (texture uniformity) , "
     "Entropy (measure of randomness of intensity image), Correlation (how "
     "correlated a pixel is to its neighborhood), Inverse Difference Moment (measures "
     "the texture homogeneity), Inertia (intensity contrast between a pixel and its "
     "neighborhood), Cluster Shade, Cluster Prominence, Haralick Correlation;\n"
-    "  * advanced: a set of 10 advanced Haralick features : Mean, Variance (measures the "
+    "* advanced: a set of 10 advanced Haralick features: Mean, Variance (measures the "
     "texture heterogeneity), Dissimilarity, Sum Average, Sum Variance, Sum Entropy, "
     "Difference of Entropies, Difference of Variances, IC1, IC2;\n"
-    "  * higher: a set of 11 higher Haralick features : Short Run Emphasis (measures the "
+    "* higher: a set of 11 higher Haralick features: Short Run Emphasis (measures the "
     "texture sharpness), Long Run Emphasis (measures the texture roughness), Grey-Level "
     "Nonuniformity, Run Length Nonuniformity, Run Percentage (measures the texture "
     "sharpness homogeneity), Low Grey-Level Run Emphasis, High Grey-Level Run Emphasis, "
     "Short Run Low Grey-Level Emphasis, Short Run High Grey-Level Emphasis, Long Run Low "
     "Grey-Level Emphasis and Long Run High Grey-Level Emphasis.");
+
 SetDocLimitations("The computation of the features is based on a Gray Level Co-occurrence "
     "matrix (GLCM) from the quantized input image. Consequently the quantization "
     "parameters (min, max, nbbin) must be appropriate to the range of the pixel values.");