Update to new xtensor

DerThorsten · Jun 14, 2019 · b5754b4 · b5754b4
1 parent cd3f7dc
commit b5754b4
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Showing 8 changed files with 21 additions and 21 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -15,9 +15,9 @@ matrix:
         - conda update -q conda;
         - conda info -a;
 
-        - conda create -q -n dev -c conda-forge/label/gcc7 -c defaults python=$CONDA_PYTHON_VERSION cmake gcc_linux-64 gxx_linux-64
+        - conda create -q -n dev -c conda-forge -c defaults python=$CONDA_PYTHON_VERSION cmake gcc_linux-64 gxx_linux-64
         - source activate dev
-        - conda install -c conda-forge/label/gcc7 glpk xtensor-python boost-cpp scikit-image h5py vigra z5py nlohmann_json
+        - conda install -c conda-forge glpk xtensor-python boost-cpp scikit-image h5py vigra z5py nlohmann_json
 
       script:
 

diff --git a/include/nifty/graph/rag/detail_rag/compute_grid_rag.hxx b/include/nifty/graph/rag/detail_rag/compute_grid_rag.hxx
@@ -94,7 +94,7 @@ struct ComputeRag<GridRag<DIM, LABELS>> {
         ){
             const Coord actualBlockShape = blockEnd - blockBegin;
             auto & blockView = perThreadDataVec[tid].blockLabels;
-            xt::slice_vector slice;
+            xt::xstrided_slice_vector slice;
             xtensor::sliceFromRoi(slice, zeroCoord, actualBlockShape);
             auto blockLabels = xt::strided_view(blockView, slice);
 

diff --git a/include/nifty/graph/rag/feature_accumulation/grid_rag_accumulate_filters_stacked.hxx b/include/nifty/graph/rag/feature_accumulation/grid_rag_accumulate_filters_stacked.hxx
@@ -367,7 +367,7 @@ void accumulateEdgeFeaturesFromFiltersWithAccChain(const GridRagStacked2D<LABELS
         parallel::parallel_foreach(threadpool, numberOfChannels, [&](const int tid, const int64_t c){
             auto & histoOpts = histoOptionsVec[c];
             Coord cBegin({c, static_cast<int64_t>(0), static_cast<int64_t>(0)});
-            xt::slice_vector slice;
+            xt::xstrided_slice_vector slice;
             xtensor::sliceFromOffset(slice, cBegin, cShape);
             auto channelView = xt::strided_view(filter0, slice);
             auto minMax = std::minmax_element(channelView.begin(), channelView.end());
@@ -611,7 +611,7 @@ void accumulateEdgeFeaturesFromFilters(const GridRagStacked2D<LABELS_PROXY> & ra
             FeatCoord endAlignedLocal{(int64_t)edgeEndAlignedLocal, (int64_t)nFeats};
 
             // get view to the aligned features
-            xt::slice_vector sliceAligned;
+            xt::xstrided_slice_vector sliceAligned;
             xtensor::sliceFromRoi(sliceAligned, beginAlignedLocal, endAlignedLocal);
             auto featuresAligned = xt::strided_view(featuresTemp, sliceAligned);
 
@@ -622,7 +622,7 @@ void accumulateEdgeFeaturesFromFilters(const GridRagStacked2D<LABELS_PROXY> & ra
             // write the aligned features - if any exist
             if(edgeEndAlignedLocal > 0 && edgeEndAlignedLocal > overhangBegin) {
                 // get view to the aligned features
-                xt::slice_vector sliceAligned;
+                xt::xstrided_slice_vector sliceAligned;
                 xtensor::sliceFromRoi(sliceAligned, beginAlignedLocal, endAlignedLocal);
                 auto featuresAligned = xt::strided_view(featuresTemp, sliceAligned);
 
@@ -647,7 +647,7 @@ void accumulateEdgeFeaturesFromFilters(const GridRagStacked2D<LABELS_PROXY> & ra
                 std::array<std::size_t, 2> storageShape{(std::size_t)overhangBegin, (std::size_t)nFeats};
                 storageFeats.resize(storageShape);
 
-                xt::slice_vector slice;
+                xt::xstrided_slice_vector slice;
                 xtensor::sliceFromOffset(slice, storageBegin, storageShape);
                 const auto overhangView = xt::strided_view(featuresTemp, slice);
                 storageFeats = overhangView;
@@ -669,7 +669,7 @@ void accumulateEdgeFeaturesFromFilters(const GridRagStacked2D<LABELS_PROXY> & ra
                 std::array<std::size_t, 2> storageShape{(std::size_t)overhangEnd, (std::size_t)nFeats};
                 storageFeats.resize(storageShape);
 
-                xt::slice_vector slice;
+                xt::xstrided_slice_vector slice;
                 xtensor::sliceFromOffset(slice, storageBegin, storageShape);
                 const auto overhangView = xt::strided_view(featuresTemp, slice);
                 storageFeats = overhangView;
@@ -696,7 +696,7 @@ void accumulateEdgeFeaturesFromFilters(const GridRagStacked2D<LABELS_PROXY> & ra
                 std::array<std::size_t, 2> storageShape{(std::size_t)overhangBegin, (std::size_t)nFeats};
                 storageFeats.resize(storageShape);
 
-                xt::slice_vector slice;
+                xt::xstrided_slice_vector slice;
                 xtensor::sliceFromOffset(slice, storageBegin, storageShape);
                 const auto overhangView = xt::strided_view(featuresTemp, slice);
                 storageFeats = overhangView;
@@ -718,7 +718,7 @@ void accumulateEdgeFeaturesFromFilters(const GridRagStacked2D<LABELS_PROXY> & ra
                 std::array<std::size_t, 2> storageShape{(std::size_t)overhangEnd, (std::size_t)nFeats};
                 storageFeats.resize(storageShape);
 
-                xt::slice_vector slice;
+                xt::xstrided_slice_vector slice;
                 xtensor::sliceFromOffset(slice, storageBegin, storageShape);
                 const auto overhangView = xt::strided_view(featuresTemp, slice);
                 storageFeats = overhangView;

diff --git a/include/nifty/graph/rag/feature_accumulation/grid_rag_accumulate_stacked.hxx b/include/nifty/graph/rag/feature_accumulation/grid_rag_accumulate_stacked.hxx
@@ -590,7 +590,7 @@ namespace graph{
                 // write the aligned features - if any exist
                 if(edgeEndAlignedLocal > 0 && edgeEndAlignedLocal > overhangBegin) {
                     // get view to the aligned features
-                    xt::slice_vector sliceAligned;
+                    xt::xstrided_slice_vector sliceAligned;
                     xtensor::sliceFromRoi(sliceAligned, beginAlignedLocal, endAlignedLocal);
                     auto featuresAligned = xt::strided_view(featuresTemp, sliceAligned);
 
@@ -615,7 +615,7 @@ namespace graph{
                     std::array<std::size_t, 2> storageShape{(std::size_t)overhangBegin, (std::size_t)nFeats};
                     storageFeats.resize(storageShape);
 
-                    xt::slice_vector slice;
+                    xt::xstrided_slice_vector slice;
                     xtensor::sliceFromOffset(slice, storageBegin, storageShape);
                     const auto overhangView = xt::strided_view(featuresTemp, slice);
                     storageFeats = overhangView;
@@ -637,7 +637,7 @@ namespace graph{
                     std::array<std::size_t, 2> storageShape{(std::size_t)overhangEnd, (std::size_t)nFeats};
                     storageFeats.resize(storageShape);
 
-                    xt::slice_vector slice;
+                    xt::xstrided_slice_vector slice;
                     xtensor::sliceFromOffset(slice, storageBegin, storageShape);
                     const auto overhangView = xt::strided_view(featuresTemp, slice);
                     storageFeats = overhangView;

diff --git a/include/nifty/tools/block_access.hxx b/include/nifty/tools/block_access.hxx
@@ -41,7 +41,7 @@ public:
     template<class SHAPE>
     inline auto getView(const SHAPE & shape, const std::size_t blockIndex) {
         auto & array = arrayVec_[blockIndex];
-        xt::slice_vector slice;
+        xt::xstrided_slice_vector slice;
         xtensor::sliceFromRoi(slice, zeroCoord_, shape);
         return xt::strided_view(array, slice);
     }

diff --git a/include/nifty/tools/nodes_to_blocks.hxx b/include/nifty/tools/nodes_to_blocks.hxx
@@ -76,7 +76,7 @@ namespace tools{
                     blockShape[d] = blockShape3d[d+1];
                 }
 
-                xt::slice_vector slice;
+                xt::xstrided_slice_vector slice;
                 xtensor::sliceFromOffset(slice, blockBegin, blockShape);
                 auto blockView = xt::strided_view(subsegSqueezed, slice);
                 uniques(blockView, blockUniques);

diff --git a/include/nifty/xtensor/xtensor.hxx b/include/nifty/xtensor/xtensor.hxx
@@ -9,7 +9,7 @@ namespace xtensor {
     // helper function to convert a ROI given by (begin, end) into
     // a proper xtensor sliceing
     template<typename COORD1, typename COORD2>
-    inline void sliceFromRoi(xt::slice_vector & roiSlice,
+    inline void sliceFromRoi(xt::xstrided_slice_vector & roiSlice,
                              const COORD1 & begin,
                              const COORD2 & end) {
         for(int d = 0; d < begin.size(); ++d) {
@@ -21,7 +21,7 @@ namespace xtensor {
     // helper function to convert a ROI given by (offset, shape) into
     // a proper xtensor sliceing
     template<typename COORD1, typename COORD2>
-    inline void sliceFromOffset(xt::slice_vector & roiSlice,
+    inline void sliceFromOffset(xt::xstrided_slice_vector & roiSlice,
                                 const COORD1 & offset,
                                 const COORD2 & shape) {
         for(int d = 0; d < offset.size(); ++d) {
@@ -35,7 +35,7 @@ namespace xtensor {
     inline auto squeezedView(xt::xexpression<ARRAY> & arrayExp) {
         auto & array = arrayExp.derived_cast();
         auto & shape = array.shape();
-        xt::slice_vector squeeze;
+        xt::xstrided_slice_vector squeeze;
         for(const auto s : shape) {
             if(s == 1) {
                 squeeze.push_back(1);
@@ -99,7 +99,7 @@ namespace tools {
         auto & subarray = subarrayExpression.derived_cast();
 
         // get the view in the array
-        xt::slice_vector slice;
+        xt::xstrided_slice_vector slice;
         xtensor::sliceFromRoi(slice, beginCoord, endCoord);
         const auto view = xt::strided_view(array, slice);
 
@@ -121,7 +121,7 @@ namespace tools {
         auto & data = dataExpression.derived_cast();
 
         // get the view in the array
-        xt::slice_vector slice;
+        xt::xstrided_slice_vector slice;
         xtensor::sliceFromRoi(slice, beginCoord, endCoord);
         auto view = xt::strided_view(array, slice);
 

diff --git a/include/nifty/z5/upsampling.hxx b/include/nifty/z5/upsampling.hxx
@@ -106,7 +106,7 @@ namespace nz5 {
                 // std::cout << "C2" << std::endl;
                 auto & chunkArray = chunkIt->second;
                 // std::cout << "C3" << std::endl;
-                xt::slice_vector offsetSlice;
+                xt::xstrided_slice_vector offsetSlice;
                 // std::cout << "C4" << std::endl;
                 xtensor::sliceFromOffset(offsetSlice, offsetInChunk, shapeInRequest);
                 // std::cout << "C5" << std::endl;