Update untwine to match the current hobu/untwine main branch

Added a minor update to the untwine_to_qgis.bash script as it was
getting confused about the "untwine" subfolders and copying sources
one level deeper as supposed to

external/untwine/bu/Processor.cpp

@@ -307,12 +307,21 @@ Processor::writeOctantCompressed(const OctantInfo& o, Index& index, IndexIter po
         }
     }
 flush:
-    flushCompressed(table, view, o);
+    try
+    {
+        flushCompressed(table, view, o);
+    }
+    catch (pdal::pdal_error& err)
+    {
+        fatal(err.what());
+    }
+
     m_manager.logOctant(o.key(), count);
     return pos;
 }
 
 
+// Copy data from the source file to the point view.
 void Processor::appendCompressed(pdal::PointViewPtr view, const DimInfoList& dims,
     const FileInfo& fi, IndexIter begin, IndexIter end)
 {

external/untwine/epf/BufferCache.cpp

@@ -21,9 +21,11 @@ namespace epf
 {
 
 // If we have a buffer in the cache, return it. Otherwise create a new one and return that.
-DataVecPtr BufferCache::fetch()
+// If nonblock is true and there are no available buffers, return null.
+DataVecPtr BufferCache::fetch(std::unique_lock<std::mutex>& lock, bool nonblock)
 {
-    std::unique_lock<std::mutex> lock(m_mutex);
+    if (nonblock && m_buffers.empty() && m_count >= MaxBuffers)
+        return nullptr;
 
     m_cv.wait(lock, [this](){ return m_buffers.size() || m_count < MaxBuffers; });
     if (m_buffers.size())
@@ -42,17 +44,10 @@ DataVecPtr BufferCache::fetch()
 // Put a buffer back in the cache.
 void BufferCache::replace(DataVecPtr&& buf)
 {
-    std::unique_lock<std::mutex> lock(m_mutex);
-
-    //ABELL - Fix this.
-//    buf->resize(BufSize);
     m_buffers.push_back(std::move(buf));
 
     if (m_count == MaxBuffers)
-    {
-        lock.unlock();
         m_cv.notify_one();
-    }
 }
 
 } // namespace epf

external/untwine/epf/BufferCache.hpp

@@ -31,12 +31,11 @@ class BufferCache
     BufferCache() : m_count(0)
     {}
 
-    DataVecPtr fetch();
+    DataVecPtr fetch(std::unique_lock<std::mutex>& lock, bool nonblock);
     void replace(DataVecPtr&& buf);
 
 private:
     std::deque<DataVecPtr> m_buffers;
-    std::mutex m_mutex;
     std::condition_variable m_cv;
     int m_count;
 };

external/untwine/epf/Cell.cpp

@@ -21,21 +21,26 @@ namespace epf
 
 void Cell::initialize()
 {
-    m_buf = m_writer->bufferCache().fetch();
+    m_buf = m_writer->fetchBuffer();
+
+    // If we couldn't fetch a buffer, flush all the the buffers for this processor and
+    // try again, but block.
+    if (!m_buf)
+    {
+        m_flush(this);
+        m_buf = m_writer->fetchBufferBlocking();
+    }
     m_pos = m_buf->data();
 
     m_endPos = m_pos + m_pointSize * (BufSize / m_pointSize);
 }
 
+// NOTE - After write(), the cell is invalid and must be initialized or destroyed.
 void Cell::write()
 {
-    // Resize the buffer so the writer knows how much to write.
     size_t size = m_pos - m_buf->data();
     if (size)
-//    {
-//        m_buf->resize(size);
         m_writer->enqueue(m_key, std::move(m_buf), size);
-//    }
 }
 
 void Cell::advance()
@@ -61,17 +66,35 @@ Cell *CellMgr::get(const VoxelKey& key)
     auto it = m_cells.find(key);
     if (it == m_cells.end())
     {
-        std::unique_ptr<Cell> cell(new Cell(key, m_pointSize, m_writer));
+        Cell::FlushFunc f = [this](Cell *exclude)
+        {
+            flush(exclude);
+        };
+        std::unique_ptr<Cell> cell(new Cell(key, m_pointSize, m_writer, f));
         it = m_cells.insert( {key, std::move(cell)} ).first;
     }
     Cell& c = *(it->second);
     return &c;
 }
 
-void CellMgr::flush()
+// Eliminate all the cells and their associated data buffers except the `exclude`
+// cell.
+void CellMgr::flush(Cell *exclude)
 {
-    for (auto& cp : m_cells)
-        cp.second->write();
+    CellMap::iterator it = m_cells.end();
+    if (exclude)
+        it = m_cells.find(exclude->key());
+
+    // If there was no exclude cell or it isn't in our list, just clear the cells.
+    // Otherwise, save the exclude cell, clear the list, and reinsert.
+    if (it == m_cells.end())
+        m_cells.clear();
+    else
+    {
+        std::unique_ptr<Cell> c = std::move(it->second);
+        m_cells.clear();
+        m_cells.insert({c->key(), std::move(c)});
+    }
 }
 
 } // namespace epf

external/untwine/epf/Cell.hpp

@@ -15,7 +15,8 @@
 
 #include <cstdint>
 #include <cstddef>
-#include <map>
+#include <functional>
+#include <unordered_map>
 #include <memory>
 
 #include "EpfTypes.hpp"
@@ -35,12 +36,18 @@ class Writer;
 class Cell
 {
 public:
-    Cell(const VoxelKey& key, int pointSize, Writer *writer) :
-        m_key(key), m_pointSize(pointSize), m_writer(writer)
+    using FlushFunc = std::function<void(Cell *)>;
+
+    Cell(const VoxelKey& key, int pointSize, Writer *writer, FlushFunc flush) :
+        m_key(key), m_pointSize(pointSize), m_writer(writer), m_flush(flush)
     {
         assert(pointSize < BufSize);
         initialize();
     }
+    ~Cell()
+    {
+        write();
+    }
 
     void initialize();
     Point point()
@@ -49,7 +56,6 @@ class Cell
         { return m_key; }
     void copyPoint(Point& b)
         { std::copy(b.data(), b.data() + m_pointSize, m_pos); }
-    void write();
     void advance();
 
 private:
@@ -59,19 +65,24 @@ class Cell
     Writer *m_writer;
     uint8_t *m_pos;
     uint8_t *m_endPos;
+    FlushFunc m_flush;
+
+    void write();
 };
 
 class CellMgr
 {
 public:
     CellMgr(int pointSize, Writer *writer);
+
     Cell *get(const VoxelKey& key);
-    void flush();
+    void flush(Cell *exclude);
 
 private:
+    using CellMap = std::unordered_map<VoxelKey, std::unique_ptr<Cell>>;
     int m_pointSize;
     Writer *m_writer;
-    std::map<VoxelKey, std::unique_ptr<Cell>> m_cells;
+    CellMap m_cells;
 };
 
 

external/untwine/epf/Epf.cpp

@@ -61,7 +61,7 @@ void writeMetadata(const std::string& tempDir, const Grid& grid,
 
 /// Epf
 
-Epf::Epf() : m_pool(8)
+Epf::Epf() : m_pool(NumFileProcessors)
 {}
 
 
@@ -120,8 +120,8 @@ void Epf::run(const Options& options, ProgressWriter& progress)
         }
     }
 
-    // Make a writer with 4 threads.
-    m_writer.reset(new Writer(options.tempDir, 4, layout->pointSize()));
+    // Make a writer with NumWriters threads.
+    m_writer.reset(new Writer(options.tempDir, NumWriters, layout->pointSize()));
 
     // Sort file infos so the largest files come first. This helps to make sure we don't delay
     // processing big files that take the longest (use threads more efficiently).

external/untwine/epf/EpfTypes.hpp

@@ -36,6 +36,8 @@ using Totals = std::unordered_map<VoxelKey, size_t>;
 constexpr int MaxPointsPerNode = 100000;
 constexpr int BufSize = 4096 * 10;
 constexpr int MaxBuffers = 1000;
+constexpr int NumWriters = 4;
+constexpr int NumFileProcessors = 8;
 
 struct FileInfo
 {

external/untwine/epf/FileProcessor.cpp

@@ -85,12 +85,17 @@ void FileProcessor::run()
 
     pdal::FixedPointTable t(1000);
 
-    f.prepare(t);
-    f.execute(t);
-    m_progress.update(count % CountIncrement);
+    try
+    {
+        f.prepare(t);
+        f.execute(t);
+    }
+    catch (const pdal::pdal_error& err)
+    {
+        fatal(err.what());
+    }
 
-    // Flush any data remaining in the cells.
-    m_cellMgr.flush();
+    m_progress.update(count % CountIncrement);
 }
 
 } // namespace epf

external/untwine/epf/Reprocessor.cpp

@@ -66,7 +66,6 @@ void Reprocessor::run()
         cell->advance();
         pos += m_pointSize;
     }
-    m_mgr.flush();
     pdal::FileUtils::unmapFile(ctx);
     pdal::FileUtils::deleteFile(m_filename);
 }

external/untwine/epf/Writer.cpp

@@ -58,6 +58,24 @@ Totals Writer::totals(size_t minSize)
     return t;
 }
 
+DataVecPtr Writer::fetchBuffer()
+{
+    std::unique_lock<std::mutex> lock(m_mutex);
+
+    // If there are fewer items in the queue than we have FileProcessors, we may choose not
+    // to block and return a nullptr, expecting that the caller will flush outstanding cells.
+    return m_bufferCache.fetch(lock, m_queue.size() < NumFileProcessors);
+}
+
+
+DataVecPtr Writer::fetchBufferBlocking()
+{
+    std::unique_lock<std::mutex> lock(m_mutex);
+
+    return m_bufferCache.fetch(lock, false);
+}
+
+
 void Writer::enqueue(const VoxelKey& key, DataVecPtr data, size_t dataSize)
 {
     {
@@ -123,9 +141,9 @@ void Writer::run()
         out.close();
         if (!out)
             fatal("Failure writing to '" + path(wd.key) + "'.");
-        m_bufferCache.replace(std::move(wd.data));
 
         std::lock_guard<std::mutex> lock(m_mutex);
+        m_bufferCache.replace(std::move(wd.data));
         m_active.remove(wd.key);
     }
 }

external/untwine/epf/Writer.hpp

@@ -43,11 +43,11 @@ class Writer
 
     void enqueue(const VoxelKey& key, DataVecPtr data, size_t dataSize);
     void stop();
-    BufferCache& bufferCache()
-        { return m_bufferCache; }
     const Totals& totals()
         { return m_totals; }
     Totals totals(size_t minSize);
+    DataVecPtr fetchBuffer();
+    DataVecPtr fetchBufferBlocking();
 
 private:
     std::string path(const VoxelKey& key);

external/untwine_to_qgis.bash

@@ -1,12 +1,12 @@
 #!/usr/bin/env bash
 
-if [ "$#" -ne 1 ] ; then 
+if [ "$#" -ne 1 ] ; then
   echo "untwine_to_qgis: untwine directory argument required"
   exit 1
-fi 
+fi
 
-UNTWINE_QGIS_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-UNTWINE_QGIS_DIR=$UNTWINE_QGIS_DIR/untwine
+EXTERNAL_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+UNTWINE_QGIS_DIR=$EXTERNAL_DIR/untwine
 
 UNTWINE_DIR=$1
 if [ ! -d "$UNTWINE_DIR/untwine" ] ; then
@@ -20,7 +20,7 @@ echo "untwine_to_qgis: Remove old version"
 rm -rf $UNTWINE_QGIS_DIR/*
 
 echo "untwine_to_qgis: Copy new version"
-rsync -r $UNTWINE_DIR $UNTWINE_QGIS_DIR --exclude="CMakeLists.txt*" --exclude="cmake/" --exclude="README.md" --exclude=".git" --exclude=".gitignore"
+rsync -r $UNTWINE_DIR/ $UNTWINE_QGIS_DIR/ --exclude="CMakeLists.txt*" --exclude="cmake/" --exclude="README.md" --exclude=".git" --exclude=".gitignore"
 
 echo "untwine_to_qgis: Done"
 cd $PWD