Use xt::zeros instead of pytensor constructor for 1d-tensors.

To avoid issue where pytensor is initialized with shape (1,) instead of {size,}. Fixes #125.
DerThorsten · Apr 25, 2019 · 5178c66 · 5178c66
1 parent 0aaf7d9
commit 5178c66
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Showing 16 changed files with 32 additions and 32 deletions.
diff --git a/include/nifty/python/graph/agglo/export_agglomerative_clustering.hxx b/include/nifty/python/graph/agglo/export_agglomerative_clustering.hxx
@@ -46,7 +46,7 @@ namespace agglo{
                     const auto & graph = self->graph();
                     typedef typename xt::pytensor<uint64_t, 1>::shape_type ShapeType;
                     ShapeType shape = {graph.edgeIdUpperBound() + 1};
-                    xt::pytensor<uint64_t, 1> mtimes(shape);
+                    xt::pytensor<uint64_t, 1> mtimes = xt::zeros<uint64_t>(shape);
                     {
                         py::gil_scoped_release allowThreads;
                         self->runAndGetMergeTimes(mtimes, verbose);
@@ -63,8 +63,8 @@ namespace agglo{
                     typedef typename xt::pytensor<uint64_t, 1>::shape_type ShapeType;
                     ShapeType shape = {graph.edgeIdUpperBound() + 1};
 
-                    xt::pytensor<double, 1> dheight(shape);
-                    xt::pytensor<uint64_t, 1> mtimes (shape);
+                    xt::pytensor<double, 1> dheight = xt::zeros<double>(shape);
+                    xt::pytensor<uint64_t, 1> mtimes = xt::zeros<uint64_t>(shape);
                     {
                         py::gil_scoped_release allowThreads;
                         self->runAndGetMergeTimesAndDendrogramHeight(mtimes, dheight,verbose);
@@ -81,7 +81,7 @@ namespace agglo{
                     const auto & graph = self->graph();
                     typedef typename xt::pytensor<double, 1>::shape_type ShapeType;
                     ShapeType shape = {graph.edgeIdUpperBound() + 1};
-                    xt::pytensor<double, 1> dheight(shape);
+                    xt::pytensor<double, 1> dheight = xt::zeros<double>(shape);
                     {
                         py::gil_scoped_release allowThreads;
                         self->runAndGetDendrogramHeight(dheight,verbose);
@@ -99,7 +99,7 @@ namespace agglo{
                     const auto & graph = self->graph();
                     typedef typename xt::pytensor<double, 1>::shape_type ShapeType;
                     ShapeType shape = {graph.edgeIdUpperBound() + 1};
-                    xt::pytensor<double, 1> transformed(shape);
+                    xt::pytensor<double, 1> transformed = xt::zeros<double>(shape);
                     {
                         py::gil_scoped_release allowThreads;
                         self->ucmTransform(edgeValues, transformed);

diff --git a/src/python/lib/cgp/bounds.cxx b/src/python/lib/cgp/bounds.cxx
@@ -135,7 +135,7 @@ namespace cgp{
 
                     typedef typename xt::pytensor<uint32_t, 1>::shape_type ShapeType;
                     ShapeType shape = {int64_t(cell1Labels.size())};
-                    xt::pytensor<uint32_t, 1> ret(shape);
+                    xt::pytensor<uint32_t, 1> ret = xt::zeros<uint32_t>(shape);
                     for(auto i=0; i<ret.size(); ++i){
                         ret[i] = cell1Labels[i];
                     }

diff --git a/src/python/lib/distributed/distributed_graph.cxx b/src/python/lib/distributed/distributed_graph.cxx
@@ -86,10 +86,10 @@ namespace distributed {
                 //
                 typedef typename xt::pytensor<EdgeIndexType, 1>::shape_type ShapeType;
                 ShapeType innerShape = {static_cast<int64_t>(innerEdgesVec.size())};
-                xt::pytensor<EdgeIndexType, 1> innerEdges(innerShape);
+                xt::pytensor<EdgeIndexType, 1> innerEdges = xt::zeros<EdgeIndexType>(innerShape);
 
                 ShapeType outerShape = {static_cast<int64_t>(outerEdgesVec.size())};
-                xt::pytensor<EdgeIndexType, 1> outerEdges(outerShape);
+                xt::pytensor<EdgeIndexType, 1> outerEdges = xt::zeros<EdgeIndexType>(outerShape);
 
                 {
                     py::gil_scoped_release allowThreads;

diff --git a/src/python/lib/distributed/graph_extraction.cxx b/src/python/lib/distributed/graph_extraction.cxx
@@ -152,10 +152,10 @@ namespace distributed {
             //
             typedef typename xt::pytensor<EdgeIndexType, 1>::shape_type ShapeType;
             ShapeType innerShape = {static_cast<int64_t>(innerEdgesVec.size())};
-            xt::pytensor<EdgeIndexType, 1> innerEdges(innerShape);
+            xt::pytensor<EdgeIndexType, 1> innerEdges = xt::zeros<EdgeIndexType>(innerShape);
 
             ShapeType outerShape = {static_cast<int64_t>(outerEdgesVec.size())};
-            xt::pytensor<EdgeIndexType, 1> outerEdges(outerShape);
+            xt::pytensor<EdgeIndexType, 1> outerEdges = xt::zeros<EdgeIndexType>(outerShape);
 
             typedef typename xt::pytensor<NodeType, 2>::shape_type UvShapeType;
             UvShapeType uvShape = {static_cast<int64_t>(uvIdsVec.size()), 2L};

diff --git a/src/python/lib/filters/gaussian_curvature.cxx b/src/python/lib/filters/gaussian_curvature.cxx
@@ -35,7 +35,7 @@ namespace filters{
         ){
             typedef typename xt::pytensor<float, 1>::shape_type ShapeType;
             ShapeType shape = {coords.shape()[0]};
-            xt::pytensor<float, 1> out(shape);
+            xt::pytensor<float, 1> out = xt::zeros<float>(shape);
             self(coords, out, loop);
             return out;
         })

diff --git a/src/python/lib/graph/connected_components.cxx b/src/python/lib/graph/connected_components.cxx
@@ -130,7 +130,7 @@ namespace graph{
         ){
             const auto & g = self.graph();
             const std::size_t size = g.nodeIdUpperBound()+1;
-            xt::pytensor<uint64_t, 1> ccLabels({size});
+            xt::pytensor<uint64_t, 1> ccLabels = xt::zeros<uint64_t>({size});
             for(const auto node : g.nodes()){
                 ccLabels[node] = self.componentLabel(node);
             }

diff --git a/src/python/lib/graph/opt/common/export_solver_base.hxx b/src/python/lib/graph/opt/common/export_solver_base.hxx
@@ -59,7 +59,7 @@ namespace common{
                         self->optimize(nodeLabels, nullptr);
                     }
                     ShapeType shape = {graph.nodeIdUpperBound() + 1};
-                    xt::pytensor<uint64_t, 1> array(shape);
+                    xt::pytensor<uint64_t, 1> array = xt::zeros<uint64_t>(shape);
                     for(auto node : graph.nodes()){
                         array(node) = nodeLabels[node];
                     }
@@ -80,7 +80,7 @@ namespace common{
                         self->optimize(nodeLabels, visitor);
                     }
                     ShapeType shape = {graph.nodeIdUpperBound() + 1};
-                    xt::pytensor<uint64_t, 1> array(shape);
+                    xt::pytensor<uint64_t, 1> array = xt::zeros<uint64_t>(shape);
                     for(auto node : graph.nodes()){
                         array(node) = nodeLabels[node];
                     }

diff --git a/src/python/lib/graph/opt/lifted_multicut/lifted_multicut_base.cxx b/src/python/lib/graph/opt/lifted_multicut/lifted_multicut_base.cxx
@@ -55,7 +55,7 @@ namespace lifted_multicut{
                         self->optimize(nodeLabels, nullptr);
                     }
                     ShapeType shape = {graph.nodeIdUpperBound() + 1};
-                    xt::pytensor<uint64_t, 1> array(shape);
+                    xt::pytensor<uint64_t, 1> array = xt::zeros<uint64_t>(shape);
                     for(auto node : graph.nodes()){
                         array(node) = nodeLabels[node];
                     }
@@ -76,7 +76,7 @@ namespace lifted_multicut{
                         self->optimize(nodeLabels, visitor);
                     }
                     ShapeType shape = {graph.nodeIdUpperBound() + 1};
-                    xt::pytensor<uint64_t, 1> array(shape);
+                    xt::pytensor<uint64_t, 1> array = xt::zeros<uint64_t>(shape);
                     for(auto node : graph.nodes()){
                         array(node) = nodeLabels[node];
                     }

diff --git a/src/python/lib/graph/opt/lifted_multicut/lifted_multicut_objective.cxx b/src/python/lib/graph/opt/lifted_multicut/lifted_multicut_objective.cxx
@@ -120,7 +120,7 @@ namespace lifted_multicut{
 
                     typedef typename xt::pytensor<uint64_t, 1>::shape_type ShapeType;
                     ShapeType shape = {int64_t(dist.size())};
-                    xt::pytensor<uint64_t, 1> array(shape);
+                    xt::pytensor<uint64_t, 1> array = xt::zeros<uint64_t>(shape);
 
                     for(std::size_t i=0; i<dist.size(); ++i){
                         array(i) = dist[i];

diff --git a/src/python/lib/graph/opt/minstcut/minstcut_base.cxx b/src/python/lib/graph/opt/minstcut/minstcut_base.cxx
@@ -53,7 +53,7 @@ namespace minstcut{
                         self->optimize(nodeLabels, nullptr);
                     }
                     ShapeType shape = {graph.nodeIdUpperBound() + 1};
-                    xt::pytensor<uint64_t, 1> array(shape);
+                    xt::pytensor<uint64_t, 1> array = xt::zeros<uint64_t>(shape);
                     for(auto node : graph.nodes()){
                         array(node) = nodeLabels[node];
                     }
@@ -74,7 +74,7 @@ namespace minstcut{
                         self->optimize(nodeLabels, visitor);
                     }
                     ShapeType shape = {graph.nodeIdUpperBound() + 1};
-                    xt::pytensor<uint64_t, 1> array(shape);
+                    xt::pytensor<uint64_t, 1> array = xt::zeros<uint64_t>(shape);
                     for(auto node : graph.nodes()){
                         array(node) = nodeLabels[node];
                     }

diff --git a/src/python/lib/graph/opt/multicut/multicut_base.cxx b/src/python/lib/graph/opt/multicut/multicut_base.cxx
@@ -54,7 +54,7 @@ namespace multicut{
                     const auto & graph = self->objective().graph();
                     typename McBase::NodeLabelsType nodeLabels(graph,0);
                     ShapeType shape = {graph.nodeIdUpperBound() + 1};
-                    xt::pytensor<uint64_t, 1> array(shape);
+                    xt::pytensor<uint64_t, 1> array = xt::zeros<uint64_t>(shape);
                     {
                         py::gil_scoped_release allowThreads;
                         self->optimize(nodeLabels, nullptr);
@@ -74,7 +74,7 @@ namespace multicut{
                     const auto & graph = self->objective().graph();
                     typename McBase::NodeLabelsType nodeLabels(graph,0);
                     ShapeType shape = {graph.nodeIdUpperBound() + 1};
-                    xt::pytensor<uint64_t, 1> array(shape);
+                    xt::pytensor<uint64_t, 1> array = xt::zeros<uint64_t>(shape);
                     {
                         py::gil_scoped_release allowThreads;
                         self->optimize(nodeLabels, visitor);

diff --git a/src/python/lib/graph/opt/multicut/multicut_visitor_base.cxx b/src/python/lib/graph/opt/multicut/multicut_visitor_base.cxx
@@ -85,7 +85,7 @@ namespace multicut{
                     const auto vec = visitor.iterations();
                     typedef typename xt::pytensor<uint32_t, 1>::shape_type ShapeType;
                     ShapeType shape = {static_cast<int64_t>(vec.size())};
-                    xt::pytensor<uint32_t, 1> ret(shape);
+                    xt::pytensor<uint32_t, 1> ret = xt::zeros<uint32_t>(shape);
                     for(auto i=0; i<vec.size(); ++i)
                         ret[i] = vec[i];
                     return ret;
@@ -94,7 +94,7 @@ namespace multicut{
                     const auto vec = visitor.energies();
                     typedef typename xt::pytensor<double, 1>::shape_type ShapeType;
                     ShapeType shape = {static_cast<int64_t>(vec.size())};
-                    xt::pytensor<double, 1> ret(shape);
+                    xt::pytensor<double, 1> ret = xt::zeros<double>(shape);
                     for(auto i=0; i<vec.size(); ++i)
                         ret[i] = vec[i];
                     return ret;
@@ -103,7 +103,7 @@ namespace multicut{
                     const auto vec = visitor.runtimes();
                     typedef typename xt::pytensor<double, 1>::shape_type ShapeType;
                     ShapeType shape = {static_cast<int64_t>(vec.size())};
-                    xt::pytensor<double, 1> ret(shape);
+                    xt::pytensor<double, 1> ret = xt::zeros<double>(shape);
                     for(auto i=0; i<vec.size(); ++i)
                         ret[i] = vec[i];
                     return ret;

diff --git a/src/python/lib/graph/opt/multicut/perturb_and_map.cxx b/src/python/lib/graph/opt/multicut/perturb_and_map.cxx
@@ -66,7 +66,7 @@ namespace multicut{
 
                 typedef xt::pytensor<double, 1>::shape_type ShapeType;
                 ShapeType shape = {static_cast<int64_t>(nEdges)};
-                xt::pytensor<double, 1> rarray(shape);
+                xt::pytensor<double, 1> rarray = xt::zeros<double>(shape);
                 for(auto edge: graph.edges())
                     rarray(edge) = edgeState[edge];
                 return rarray;

diff --git a/src/python/lib/graph/undirected_grid_graph.cxx b/src/python/lib/graph/undirected_grid_graph.cxx
@@ -118,7 +118,7 @@ namespace graph{
                 ){
                     typedef typename xt::pytensor<float, 1>::shape_type ShapeType;
                     ShapeType shape = {g.edgeIdUpperBound() + 1};
-                    xt::pytensor<float, 1> out(shape);
+                    xt::pytensor<float, 1> out = xt::zeros<float>(shape);
                     g.affinitiesToEdgeMap(affinities, out);
                     return out;
                 },
@@ -182,8 +182,8 @@ namespace graph{
                     typedef typename xt::pytensor<uint64_t, 2>::shape_type UvShape;
                     UvShape uvShape = {nLiftedTot, 2};
 
-                    xt::pytensor<float, 1> localFeatures(localShape);
-                    xt::pytensor<float, 1> liftedFeatures(liftedShape);
+                    xt::pytensor<float, 1> localFeatures = xt::zeros<float>(localShape);
+                    xt::pytensor<float, 1> liftedFeatures = xt::zeros<float>(liftedShape);
                     xt::pytensor<uint64_t, 2> liftedUvs(uvShape);
                     int64_t nLifted;
                     {

diff --git a/src/python/lib/graph/undirected_list_graph.cxx b/src/python/lib/graph/undirected_list_graph.cxx
@@ -39,7 +39,7 @@ namespace graph{
             .def("serialize",
                 [](const GraphType & g) {
                     typename xt::pytensor<uint64_t, 1>::shape_type shape = {static_cast<int64_t>(g.serializationSize())};
-                    xt::pytensor<uint64_t, 1> out(shape);
+                    xt::pytensor<uint64_t, 1> out = xt::zeros<uint64_t>(shape);
                     auto ptr = &out(0);
                     g.serialize(ptr);
                     return out;
@@ -129,8 +129,8 @@ namespace graph{
 
                 typedef typename xt::pytensor<uint32_t, 1>::shape_type TensorShapeType;
                 TensorShapeType tensorShape = {static_cast<int64_t>(g.numberOfEdges())};
-                xt::pytensor<uint32_t, 1>   offsetsIndex(tensorShape);
-                xt::pytensor<float, 1>      aff({tensorShape});
+                xt::pytensor<uint32_t, 1>   offsetsIndex = xt::zeros<uint32_t>(tensorShape);
+                xt::pytensor<float, 1>      aff = xt::zeros<float>(tensorShape);
 
                 u=0;
                 for(int p0=0; p0<shape[0]; ++p0)

diff --git a/src/python/lib/tools/edge_mapping.cxx b/src/python/lib/tools/edge_mapping.cxx
@@ -106,7 +106,7 @@ namespace tools{
                                    const int numberOfThreads) {
                     typedef typename xt::pytensor<EdgeType, 1>::shape_type ShapeType;
                     ShapeType shape = {static_cast<int64_t>(self.numberOfEdges())};
-                    xt::pytensor<EdgeType, 1> edgeMapping(shape);
+                    xt::pytensor<EdgeType, 1> edgeMapping = xt::zeros<EdgeType>(shape);
 
                     {
                         py::gil_scoped_release allowThreads;