Move Selection to its own header.

CMakeLists.txt

@@ -100,6 +100,7 @@ set(SONATA_SRC
  src/nodes.cpp
  src/population.cpp
  src/report_reader.cpp
+ src/selection.cpp
  src/utils.cpp
  ${CMAKE_CURRENT_BINARY_DIR}/src/version.cpp
  )

include/bbp/sonata/population.h

@@ -19,81 +19,11 @@
 #include <utility> // std::move
 #include <vector>
 
+#include <bbp/sonata/selection.h>
 
 namespace bbp {
 namespace sonata {
 
-//--------------------------------------------------------------------------------------------------
-
-class SONATA_API Selection
-{
- public:
- using Value = uint64_t;
- using Values = std::vector<Value>;
- using Range = std::pair<Value, Value>;
- using Ranges = std::vector<Range>;
-
- Selection(Ranges ranges);
-
- template <typename Iterator>
- static Selection fromValues(Iterator first, Iterator last);
- static Selection fromValues(const Values& values);
-
- /**
- * Get a list of ranges constituting Selection
- */
- const Ranges& ranges() const;
-
- /**
- * Array of IDs constituting Selection
- */
- Values flatten() const;
-
- /**
- * Total number of elements constituting Selection
- */
- size_t flatSize() const;
-
- bool empty() const;
-
- private:
- Ranges ranges_;
-};
-
-bool SONATA_API operator==(const Selection&, const Selection&);
-bool SONATA_API operator!=(const Selection&, const Selection&);
-
-Selection SONATA_API operator&(const Selection&, const Selection&);
-Selection SONATA_API operator|(const Selection&, const Selection&);
-
-template <typename Iterator>
-Selection Selection::fromValues(Iterator first, Iterator last) {
- Selection::Ranges ranges;
-
- Selection::Range range{0, 0};
- while (first != last) {
- const auto v = *first;
- if (v == range.second) {
- ++range.second;
- } else {
- if (range.first < range.second) {
- ranges.push_back(range);
- }
- range.first = v;
- range.second = v + 1;
- }
- ++first;
- }
-
- if (range.first < range.second) {
- ranges.push_back(range);
- }
-
- return Selection(std::move(ranges));
-}
-
-//--------------------------------------------------------------------------------------------------
-
 class SONATA_API Population
 {
  public:

include/bbp/sonata/selection.h

@@ -0,0 +1,80 @@
+#pragma once
+
+#include "common.h"
+
+#include <cstdint>
+#include <utility> // std::move
+#include <vector>
+
+namespace bbp {
+namespace sonata {
+
+class SONATA_API Selection
+{
+ public:
+ using Value = uint64_t;
+ using Values = std::vector<Value>;
+ using Range = std::pair<Value, Value>;
+ using Ranges = std::vector<Range>;
+
+ Selection(Ranges ranges);
+
+ template <typename Iterator>
+ static Selection fromValues(Iterator first, Iterator last);
+ static Selection fromValues(const Values& values);
+
+ /**
+ * Get a list of ranges constituting Selection
+ */
+ const Ranges& ranges() const;
+
+ /**
+ * Array of IDs constituting Selection
+ */
+ Values flatten() const;
+
+ /**
+ * Total number of elements constituting Selection
+ */
+ size_t flatSize() const;
+
+ bool empty() const;
+
+ private:
+ Ranges ranges_;
+};
+
+bool SONATA_API operator==(const Selection&, const Selection&);
+bool SONATA_API operator!=(const Selection&, const Selection&);
+
+Selection SONATA_API operator&(const Selection&, const Selection&);
+Selection SONATA_API operator|(const Selection&, const Selection&);
+
+template <typename Iterator>
+Selection Selection::fromValues(Iterator first, Iterator last) {
+ Selection::Ranges ranges;
+
+ Selection::Range range{0, 0};
+ while (first != last) {
+ const auto v = *first;
+ if (v == range.second) {
+ ++range.second;
+ } else {
+ if (range.first < range.second) {
+ ranges.push_back(range);
+ }
+ range.first = v;
+ range.second = v + 1;
+ }
+ ++first;
+ }
+
+ if (range.first < range.second) {
+ ranges.push_back(range);
+ }
+
+ return Selection(std::move(ranges));
+}
+
+} // namespace sonata
+} // namespace bbp

src/population.cpp

@@ -22,120 +22,6 @@
 namespace bbp {
 namespace sonata {
 
-namespace detail {
-using Range = Selection::Range;
-using Ranges = Selection::Ranges;
-
-void _checkRanges(const Ranges& ranges) {
- for (const auto& range : ranges) {
- if (range.first >= range.second) {
- throw SonataError(fmt::format("Invalid range: {}-{}", range.first, range.second));
- }
- }
-}
-
-Ranges _sortAndMerge(const Ranges& ranges) {
- return bulk_read::sortAndMerge(ranges);
-}
-
-Selection intersection_(const Ranges& lhs, const Ranges& rhs) {
- if (lhs.empty() || rhs.empty()) {
- return Selection({});
- }
- Ranges r0 = detail::_sortAndMerge(lhs);
- Ranges r1 = detail::_sortAndMerge(rhs);
-
- auto it0 = r0.cbegin();
- auto it1 = r1.cbegin();
-
- Ranges ret;
- while (it0 != r0.cend() && it1 != r1.cend()) {
- auto start = std::max(it0->first, it1->first);
- auto end = std::min(it0->second, it1->second);
- if (start < end) {
- ret.emplace_back(start, end);
- }
-
- if (it0->second < it1->second) {
- ++it0;
- } else {
- ++it1;
- }
- }
-
- return Selection(std::move(ret));
-}
-
-Selection union_(const Ranges& lhs, const Ranges& rhs) {
- Ranges ret;
- std::copy(lhs.begin(), lhs.end(), std::back_inserter(ret));
- std::copy(rhs.begin(), rhs.end(), std::back_inserter(ret));
- ret = detail::_sortAndMerge(ret);
- return Selection(std::move(ret));
-}
-} // namespace detail
-
-
-Selection::Selection(Selection::Ranges ranges)
- : ranges_(std::move(ranges)) {
- detail::_checkRanges(ranges_);
-}
-
-
-Selection Selection::fromValues(const Selection::Values& values) {
- return fromValues(values.begin(), values.end());
-}
-
-
-const Selection::Ranges& Selection::ranges() const {
- return ranges_;
-}
-
-
-Selection::Values Selection::flatten() const {
- Selection::Values result;
- result.reserve(flatSize());
- for (const auto& range : ranges_) {
- for (auto v = range.first; v < range.second; ++v) {
- result.emplace_back(v);
- }
- }
- return result;
-}
-
-
-size_t Selection::flatSize() const {
- return bulk_read::detail::flatSize(ranges_);
-}
-
-
-bool Selection::empty() const {
- return ranges().empty();
-}
-
-//--------------------------------------------------------------------------------------------------
-
-
-bool operator==(const Selection& lhs, const Selection& rhs) {
- return lhs.ranges() == rhs.ranges();
-}
-
-
-bool operator!=(const Selection& lhs, const Selection& rhs) {
- return !(lhs == rhs);
-}
-
-
-Selection operator&(const Selection& lhs, const Selection& rhs) {
- return detail::intersection_(lhs.ranges(), rhs.ranges());
-}
-
-
-Selection operator|(const Selection& lhs, const Selection& rhs) {
- return detail::union_(lhs.ranges(), rhs.ranges());
-}
-
-
 namespace {
 
 std::string _getDataType(const HighFive::DataSet& dset, const std::string& name) {

src/read_bulk.hpp

@@ -1,7 +1,10 @@
 #pragma once
 
-#include <bbp/sonata/population.h>
+#include <algorithm>
 #include <cstdint>
+#include <fmt/format.h>
+
+#include <bbp/sonata/population.h>
 
 #define SONATA_PAGESIZE (4 * 1 << 20)