Merge remote-tracking branch 'origin/master' into issue-2155

cmake/macros.cmake

@@ -151,7 +151,7 @@ macro(PDAL_ADD_PLUGIN _name _type _shortname)
         ARCHIVE DESTINATION ${PDAL_LIB_INSTALL_DIR})
     if (APPLE)
         set_target_properties(${${_name}} PROPERTIES
-            INSTALL_NAME_DIR "@loader_path/../lib")
+            INSTALL_NAME_DIR "@rpath")
     endif()
 endmacro(PDAL_ADD_PLUGIN)
 

filters/AssignFilter.cpp

@@ -123,13 +123,21 @@ void AssignFilter::addArgs(ProgramArgs& args)
 {
     args.add("assignment", "Values to assign to dimensions based on range.",
         m_assignments);
+    args.add("condition", "Condition for assignment based on range.",
+        m_condition);
 }
 
 
 void AssignFilter::prepared(PointTableRef table)
 {
     PointLayoutPtr layout(table.layout());
 
+    m_condition.m_id = layout->findDim(m_condition.m_name);
+    if (m_condition.m_id == Dimension::Id::Unknown)
+        m_doCondition = false;
+    else
+        m_doCondition = true;
+
     for (auto& r : m_assignments)
     {
         r.m_id = layout->findDim(r.m_name);
@@ -142,9 +150,20 @@ void AssignFilter::prepared(PointTableRef table)
 
 bool AssignFilter::processOne(PointRef& point)
 {
-    for (AssignRange& r : m_assignments)
-        if (r.valuePasses(point.getFieldAs<double>(r.m_id)))
-            point.setField(r.m_id, r.m_value);
+    if (m_doCondition)
+    {
+        bool condition = m_condition.valuePasses(point.getFieldAs<double>(m_condition.m_id));
+        for (AssignRange& r : m_assignments)
+            if (r.valuePasses(point.getFieldAs<double>(r.m_id)) &&
+                condition)
+                point.setField(r.m_id, r.m_value);
+    } else
+    {
+
+        for (AssignRange& r : m_assignments)
+            if (r.valuePasses(point.getFieldAs<double>(r.m_id)) )
+                point.setField(r.m_id, r.m_value);
+    }
     return true;
 }
 

filters/AssignFilter.hpp

@@ -37,6 +37,8 @@
 #include <pdal/Filter.hpp>
 #include <pdal/Streamable.hpp>
 
+#include "private/DimRange.hpp"
+
 namespace pdal
 {
 
@@ -60,6 +62,8 @@ class PDAL_DLL AssignFilter : public Filter, public Streamable
     AssignFilter(const AssignFilter&) = delete;
 
     std::vector<AssignRange> m_assignments;
+    DimRange m_condition;
+    bool m_doCondition;
 };
 
 } // namespace pdal

pdal/Options.cpp

@@ -99,10 +99,21 @@ void Options::addConditional(const Option& option)
 }
 
 
-void Options::addConditional(const Options& options)
+void Options::addConditional(const Options& other)
 {
-    for (auto& o : options.m_options)
-        addConditional(o.second);
+    for (auto oi = other.m_options.begin(); oi != other.m_options.end();)
+    {
+        const std::string& name = oi->first;
+        if (m_options.find(name) == m_options.end())
+        {
+            do
+            {
+                m_options.insert(*oi++);
+            } while (oi != other.m_options.end() && name == oi->first);
+        }
+        else
+            oi++;
+    }
 }
 
 

pdal/Stage.cpp

@@ -159,13 +159,15 @@ PointViewSet Stage::execute(PointTableRef table)
 
     std::stack<Stage *> stages;
     std::stack<Stage *> pending;
-    std::map<Stage *, Stage *> parents;
+    std::map<Stage *, Stage *> children;
 
     m_log->get(LogLevel::Debug) << "Executing pipeline in standard mode." <<
         std::endl;
 
     pending.push(this);
-    parents[this] = nullptr;
+
+    // There is no child of the terminal stage.
+    children[this] = nullptr;
 
     // Linearize stage execution.
     Stage *s;
@@ -176,7 +178,7 @@ PointViewSet Stage::execute(PointTableRef table)
         stages.push(s);
         for (auto fi = s->m_inputs.begin(); fi != s->m_inputs.end(); ++fi)
         {
-            parents[*fi] = s;
+            children[*fi] = s;
             pending.push(*fi);
         }
     }
@@ -193,9 +195,9 @@ PointViewSet Stage::execute(PointTableRef table)
             inViews.insert(PointViewPtr(new PointView(table)));
         outViews = s->execute(table, inViews);
 
-        Stage *parent = parents[s];
-        if (parent)
-            sets[parent].insert(outViews.begin(), outViews.end());
+        Stage *child = children[s];
+        if (child)
+            sets[child].insert(outViews.begin(), outViews.end());
         // Allow previous point views to be freed.
         sets.erase(s);
     }

plugins/python/io/NumpyReader.cpp

@@ -43,10 +43,28 @@
 
 #include "../plang/Environment.hpp"
 
+
+std::string toString(PyObject *pname)
+{
+    std::stringstream mssg;
+    PyObject* r = PyObject_Str(pname);
+    if (!r)
+        throw pdal::pdal_error("couldn't make string representation value");
+#if PY_MAJOR_VERSION >= 3
+    Py_ssize_t size;
+    const char *d = PyUnicode_AsUTF8AndSize(r, &size);
+#else
+    const char *d = PyString_AsString(r);
+#endif
+    mssg << d;
+    return mssg.str();
+}
+
+
 namespace pdal
 {
 
-static PluginInfo const s_info 
+static PluginInfo const s_info
 {
     "readers.numpy",
     "Read data from .npy files.",
@@ -89,6 +107,16 @@ std::istream& operator >> (std::istream& in, NumpyReader::Order& order)
 }
 
 
+void NumpyReader::setArray(PyObject* array)
+{
+    plang::Environment::get();
+    if (!PyArray_Check(array))
+        throw pdal::pdal_error("object provided to setArray is not a python numpy array!");
+
+    m_array = (PyArrayObject*)array;
+    Py_XINCREF(m_array);
+}
+
 PyArrayObject* load_npy(std::string const& filename)
 {
 
@@ -128,17 +156,21 @@ void NumpyReader::initialize()
     m_ndims = 0;
 
     m_iter = NULL;
-    m_array = NULL;
 
     p_data = NULL;
     m_dataptr = NULL;
     m_strideptr = NULL;
     m_innersizeptr = NULL;
+    m_dtype = NULL;
 
-    m_array = load_npy(m_filename);
-    if (!PyArray_Check(m_array))
-        throw pdal::pdal_error("Object in file  '" + m_filename +
-            "' is not a numpy array");
+    if (m_filename.size())
+    {
+        m_array = load_npy(m_filename);
+    }
+    if (m_array)
+        if (!PyArray_Check(m_array))
+            throw pdal::pdal_error("Object in file  '" + m_filename +
+                "' is not a numpy array");
 }
 
 
@@ -242,18 +274,6 @@ Dimension::Id NumpyReader::registerDim(PointLayoutPtr layout,
 namespace
 {
 
-std::string toString(PyObject *pname)
-{
-    if (!pname)
-        return std::string();
-
-#if PY_MAJOR_VERSION >= 3
-    return PyBytes_AsString(PyUnicode_AsUTF8String(pname));
-#else
-    return PyString_AsString(pname);
-#endif
-}
-
 
 Dimension::Type getType(PyArray_Descr *dtype, const std::string& name)
 {
@@ -282,7 +302,7 @@ void NumpyReader::createFields(PointLayoutPtr layout)
     int offset;
 
     m_numFields = 0;
-    if (m_dtype->fields)
+    if (m_dtype->fields != Py_None)
         m_numFields = PyDict_Size(m_dtype->fields);
 
     // Array isn't structured - just a bunch of data.

plugins/python/io/NumpyReader.hpp

@@ -60,9 +60,10 @@ class PDAL_DLL NumpyReader : public Reader, public Streamable
 public:
     NumpyReader& operator=(const NumpyReader&) = delete;
     NumpyReader(const NumpyReader&) = delete;
-    NumpyReader()
+    NumpyReader() : m_array(NULL)
     {}
 
+    void setArray(PyObject* array);
     std::string getName() const;
 
 private:

scripts/ci/script.sh

@@ -37,6 +37,7 @@ make install
 pip install packaging
 git clone https://github.com/PDAL/python.git pdal-python
 cd pdal-python
+git checkout 2.0.0
 python setup.py build
 echo "current path: " `pwd`
 export PDAL_TEST_DIR=/pdal/_build/test

scripts/docker/ubuntu/Dockerfile

@@ -3,7 +3,7 @@ MAINTAINER Howard Butler <howard@hobu.co>
 
 RUN     git clone https://github.com/PDAL/PDAL.git /pdal; \
     cd /pdal; \
-    git checkout 1.7-maintenance; \
+    git checkout master; \
     mkdir -p _build; \
     cd _build; \
     cmake .. \

test/unit/apps/TranslateTest.cpp

@@ -53,7 +53,7 @@ static int runTranslate(std::string const& cmdline, std::string& output)
     return Utils::run_shell_command(cmd + " " + cmdline, output);
 }
 
-TEST(translateTest, t1)
+TEST(TranslateTest, t1)
 {
     std::string output;
 
@@ -72,7 +72,7 @@ TEST(translateTest, t1)
 }
 
 // Tests for processing JSON input.
-TEST(translateTest, t2)
+TEST(TranslateTest, t2)
 {
     std::string output;
 
@@ -190,7 +190,7 @@ TEST(translateTest, t2)
         output), 0);
 }
 
-TEST(translateTest, t3)
+TEST(TranslateTest, t3)
 {
     std::string output;
 
@@ -206,3 +206,32 @@ TEST(translateTest, t3)
     EXPECT_EQ(std::stoi(output), 1);
 #endif
 }
+
+// Make sure that repeated inputs ("groups" in this case), are propagated
+// to stage.
+TEST(TranslateTest, issue_2114)
+{
+    FileUtils::deleteFile(Support::temppath("out1.las"));
+    FileUtils::deleteFile(Support::temppath("out2.las"));
+    FileUtils::deleteFile(Support::temppath("out3.las"));
+    FileUtils::deleteFile(Support::temppath("out4.las"));
+
+    std::string output;
+    std::string in = Support::datapath("las/autzen_trim.las");
+    std::string out = Support::temppath("out#.las");
+
+    EXPECT_FALSE(FileUtils::fileExists(Support::temppath("out1.las")));
+    EXPECT_FALSE(FileUtils::fileExists(Support::temppath("out2.las")));
+    EXPECT_FALSE(FileUtils::fileExists(Support::temppath("out3.las")));
+    EXPECT_FALSE(FileUtils::fileExists(Support::temppath("out4.las")));
+
+    EXPECT_EQ(runTranslate(in + " " + out + " -f returns "
+        "--filters.returns.groups=last --filters.returns.groups=first",
+        output), 0);
+
+    EXPECT_TRUE(FileUtils::fileExists(Support::temppath("out1.las")));
+    EXPECT_TRUE(FileUtils::fileExists(Support::temppath("out2.las")));
+    EXPECT_FALSE(FileUtils::fileExists(Support::temppath("out3.las")));
+    EXPECT_FALSE(FileUtils::fileExists(Support::temppath("out4.las")));
+}
+

test/unit/filters/AssignFilterTest.cpp

@@ -138,3 +138,42 @@ TEST(AssignFilterTest, t2)
     EXPECT_EQ(i6, 3);
     EXPECT_EQ(i8, 5);
 }
+
+TEST(AssignFilterTest, test_condition)
+{
+    StageFactory factory;
+
+    Stage& r = *factory.createStage("readers.las");
+    Stage& f = *factory.createStage("filters.assign");
+
+    // utm17.las contains 5 points with intensity of 280, 3 of 260 and 2 of 240
+    Options ro;
+    ro.add("filename", Support::datapath("las/utm17.las"));
+    r.setOptions(ro);
+
+    Options fo;
+    fo.add("condition", "Intensity[260:260]");
+    fo.add("assignment", "PointSourceId[:]=6");
+
+    f.setInput(r);
+    f.setOptions(fo);
+
+    PointTable t;
+    f.prepare(t);
+    PointViewSet s = f.execute(t);
+    PointViewPtr v = *s.begin();
+
+    int ielse = 0;
+    int i6 = 0;
+    for (PointId i = 0; i < v->size(); ++i)
+    {
+        int ii = v->getFieldAs<int>(Dimension::Id::PointSourceId, i);
+        if (ii == 6)
+            i6++;
+        else
+            ielse++;
+    }
+    EXPECT_EQ(i6, 3);
+    EXPECT_EQ(v->size(), 10u);
+    EXPECT_EQ(ielse, 7);
+}