Overflow issues in Vol/Longvol readers

.github/workflows/buildAndDocumentation-PR.yml

@@ -9,7 +9,7 @@ on:
 env:
   # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
   BUILD_TYPE:   Release
-  TESTBLACKLIST: "(testCompressedVolWriter|testLongvol|testLinearStructure)"
+  TESTBLACKLIST: "(testLongvol|testCompressedVolWriter|testLinearStructure)"
   CONFIG_GLOBAL: -DBUILD_EXAMPLES=true -DBUILD_TESTING=true -DDGTAL_RANDOMIZED_TESTING_THRESHOLD=25
   CONFIG_LINUX:  -DWITH_MAGICK=true -DWITH_GMP=true -DWITH_FFTW3=true -DWARNING_AS_ERROR=ON -DWITH_HDF5=true -DWITH_QGLVIEWER=true -DWITH_CAIRO=true    -DWITH_EIGEN=true  -DWITH_ITK=true -DDGTAL_ENABLE_FLOATING_POINT_EXCEPTIONS=true
   CONFIG_MAC:  -DWITH_EIGEN=true -DWITH_GMP=true

ChangeLog.md

@@ -47,7 +47,7 @@
 ## Changes
 - *Image*
   - Bugfix in the SpaceND and HyperRectDomain classes to allow very large extent (e.g. >1024^3)
-    (David Coeurjolly, [#16XX](https://github.com/DGtal-team/DGtal/pull/16XX))
+    (David Coeurjolly, [#1636](https://github.com/DGtal-team/DGtal/pull/1636))
   - Improved ITK image selection in ImageSelector and add ITK xx.gz an other
     format support. New option to keep set domain or to compute current bounding
     box of elements of the set in ImageFromSet.
@@ -69,7 +69,6 @@
     all co-cycling sites (Robin Lamy, David Coeurjolly, Isabelle
     Sivignon [#1605](https://github.com/DGtal-team/DGtal/pull/1605))
 
-
 - *Build*
   - Continuous integration does not use Travis anymore but Github
     Actions. (David Coeurjolly, [#1591](https://github.com/DGtal-team/DGtal/pull/1591))
@@ -122,6 +121,8 @@
     (Bertrand Kerautret, [#1610](https://github.com/DGtal-team/DGtal/pull/1610)
   - Fix compilation issue in MeshReader compilation.
     (Bertrand Kerautret, [#1611](https://github.com/DGtal-team/DGtal/pull/1611)
+  - Minor fixes in VolReader and LongVolReader to be able to load large vol files.
+    (David Coeurjolly, [#1637](https://github.com/DGtal-team/DGtal/pull/1637))
 
 - *Geometry package*
   - the following changes have been made to fix a bug in `examplePlaneProbingSurfaceLocalEstimator`:
@@ -131,7 +132,7 @@
       trivial normal vector if it has been set to 'False'.
   - in `PlaneProbingParallelepipedEstimator`: `isValid` does not call the `isValid` method of the
     delegate, but only checks the relevant parts (which have been pushed in to separate methods).
-  (Tristan Roussillon, [#1607](https://github.com/DGtal-team/DGtal/pull/1607))
+    (Tristan Roussillon, [#1607](https://github.com/DGtal-team/DGtal/pull/1607))
   - Fixing issue with the automatic deploy of the "nightly" documentation.
     (Davi Coeurjolly, [#1620](https://github.com/DGtal-team/DGtal/pull/1620)
 

src/DGtal/io/readers/LongvolReader.ih

@@ -176,12 +176,12 @@ DGtal::LongvolReader<T, TFunctor>::importLongvol( const std::string & filename,
     {
       T image( domain);
 
-      long count = 0;
+      size_t count = 0;
       DGtal::uint64_t val=0;
 
       typename T::Domain::ConstIterator it = domain.begin();
-      long int total = sx * sy * sz ;
-      long int totalbytes = total * sizeof(val);
+      size_t total = sx * sy * sz ;
+      size_t totalbytes = total * sizeof(val);
       std::stringstream main;
 
       unsigned char c_temp;
@@ -194,7 +194,7 @@ DGtal::LongvolReader<T, TFunctor>::importLongvol( const std::string & filename,
 
       if ( count != totalbytes )
       {
-        trace.error() << "LongvolReader: can't read file (raw data) !\n";
+        trace.error() << "LongvolReader: can't read file (raw data). I read "<<count<<" bytes instead of "<<total<<".\n";
         throw dgtalexception;
       }
 
@@ -207,7 +207,7 @@ DGtal::LongvolReader<T, TFunctor>::importLongvol( const std::string & filename,
         in.push(main);
         boost::iostreams::copy(in, uncompressed);
         //Apply to the image structure
-        for(auto i=0; i < total; ++i)
+        for(size_t i=0; i < total; ++i)
         {
           read_word(uncompressed , val);
           image.setValue(( *it ), aFunctor(val) );
@@ -217,7 +217,7 @@ DGtal::LongvolReader<T, TFunctor>::importLongvol( const std::string & filename,
       else
       {
         //Apply to the image structure
-        for(auto i=0; i < total; ++i)
+        for(size_t i=0; i < total; ++i)
         {
           read_word(main, val);
           image.setValue(( *it ), aFunctor(val) );

src/DGtal/io/readers/VolReader.ih

@@ -190,10 +190,10 @@ DGtal::VolReader<T, TFunctor>::importVol( const std::string & filename,
     {
       T image( domain );
 
-      long count = 0;
+      size_t count = 0;
       unsigned char val;
       typename T::Domain::ConstIterator it = domain.begin();
-      long int total = sx * sy * sz;
+      size_t total = sx * sy * sz;
       std::stringstream main;
 
       //main read loop
@@ -206,7 +206,7 @@ DGtal::VolReader<T, TFunctor>::importVol( const std::string & filename,
 
       if ( count != total )
       {
-        trace.error() << "VolReader: can't read file (raw data) !\n";
+        trace.error() << "VolReader: can't read file (raw data). I read "<<count<<" bytes instead of "<<total<<".\n";
         throw dgtalexception;
       }
 
@@ -219,7 +219,7 @@ DGtal::VolReader<T, TFunctor>::importVol( const std::string & filename,
         in.push(main);
         boost::iostreams::copy(in, uncompressed);
         //Apply to the image structure
-        for(auto i=0; i < total; ++i)
+        for(size_t i=0; i < total; ++i)
         {
           val = uncompressed.get();
           image.setValue(( *it ), aFunctor(val) );
@@ -229,7 +229,7 @@ DGtal::VolReader<T, TFunctor>::importVol( const std::string & filename,
       else
       {
         //Apply to the image structure
-      for(auto i=0; i < total; ++i)
+      for(size_t i=0; i < total; ++i)
       {
         val = main.get();
         image.setValue(( *it ), aFunctor(val) );

tests/io/testLongvol.cpp

@@ -37,7 +37,6 @@
 #include "DGtal/io/readers/LongvolReader.h"
 
 ///////////////////////////////////////////////////////////////////////////////
-
 using namespace std;
 using namespace DGtal;
 

tests/io/writers/testCompressedVolWriter.cpp

@@ -39,7 +39,6 @@
 #include "DGtal/io/readers/VolReader.h"
 #include "DGtal/images/ImageContainerBySTLVector.h"
 ///////////////////////////////////////////////////////////////////////////////
-
 using namespace std;
 using namespace DGtal;
 using namespace Z3i;

wrap/azure-pipelines.yml

@@ -98,7 +98,7 @@ stages:
         call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
         python -m pip install cmake
         python -m pip install ninja
-        python -m pip install -r requirements-deploy.txt
+        python -m pip install scikit-build
         python setup.py bdist_wheel --build-type Release -G Ninja -- -DCMAKE_C_COMPILER="cl.exe" -DCMAKE_CXX_COMPILER="cl.exe" -DBOOST_ROOT:PATH=$(DEPENDENCIES_BUILD_DIR)/boost-build -DZLIB_ROOT:PATH=$(DEPENDENCIES_BUILD_DIR)/zlib
       workingDirectory: '$(Build.SourcesDirectory)\wrap\deploy'
       displayName: 'Build project'

wrap/deploy/deploy_macos_one_python.sh

@@ -13,7 +13,7 @@ echo "$(python --version)"
 python -m pip install cmake
 python -m pip install ninja
 python -m pip install delocate
-python -m pip install -r $script_dir/requirements-deploy.txt
+python -m pip install scikit-build
 
 
 pushd ${script_dir}

wrap/deploy/manylinux-build-wheels.sh

@@ -51,8 +51,7 @@ for PYBIN in "${PYBINARIES[@]}"; do
 
     # Remove when scikit-build includes cmake_target PR:
     # https://github.com/scikit-build/scikit-build/pull/477
-    ${PYBIN}/python -m pip uninstall scikit-build -y
-    ${PYBIN}/python -m pip install -r requirements-deploy.txt
+    ${PYBIN}/python -m pip install scikit-build -y
 
     # TODO: Switch BOOST_ROOT to these two when CMake is at least 3.15 and remove Boost_ROOT
     # -DCMAKE_FIND_PACKAGE_PREFER_CONFIG:BOOL=ON \