Merge pull request #588 from astrorama/develop

Release 0.22

.github/workflows/dependencies.txt

@@ -2,6 +2,7 @@ $PYTHON-devel
 $PYTHON-numpy
 $PYTHON-pytest
 $PYTHON-sphinx
+$PYTHON-setuptools
 CCfits-devel
 blas-devel
 $BOOST-$PYTHON-devel

.github/workflows/run-litmus.sh

@@ -6,6 +6,8 @@ TARGET_BRANCH=${GITHUB_BASE_REF:-$GITHUB_REF}
 # In the case of pull requests, this is the origin branch
 ORIGIN_BRANCH=${GITHUB_HEAD_REF:-$GITHUB_REF}
 
+export GIT_CLONE_PROTECTION_ACTIVE=false
+
 # Platform-specific configuration
 source /etc/os-release
 

CMakeLists.txt

@@ -6,4 +6,4 @@ find_package(ElementsProject)
 #---------------------------------------------------------------
 
 # Declare project name and version
-elements_project(SourceXtractorPlusPlus 0.21 USE Alexandria 2.31.0 DESCRIPTION "SourceXtractor++, the next generation SExtractor")
+elements_project(SourceXtractorPlusPlus 0.22 USE Alexandria 2.31.0 DESCRIPTION "SourceXtractor++, the next generation SExtractor")

README.md

@@ -17,13 +17,13 @@ Documentation: https://astrorama.github.io/SourceXtractorPlusPlus/
 SourceXtractor++ is available on [Anaconda Cloud for Linux and MacOSX](https://anaconda.org/astrorama/sourcextractor)
 
 ```bash
-conda install -c conda-forge -c astrorama sourcextractor==0.19.2
+conda install -c conda-forge -c astrorama sourcextractor==0.21
  ```
 
 We would recommend, however, to install it into its own environment.
 
 ```bash
-conda create -n sourcex -c astrorama -c conda-forge sourcextractor==0.19.2
+conda create -n sourcex -c astrorama -c conda-forge sourcextractor==0.21
 conda activate sourcex
  ```
 

SEFramework/SEFramework/Pipeline/SourceGrouping.h

@@ -27,6 +27,7 @@
 #include <memory>
 #include <set>
 
+#include "SEFramework/Property/PropertyId.h"
 #include "SEFramework/Pipeline/PipelineStage.h"
 #include "SEFramework/Source/SourceGroupFactory.h"
 #include "SEFramework/Source/SourceGroupInterface.h"
@@ -81,14 +82,20 @@ class GroupingCriteria {
   virtual std::set<PropertyId> requiredProperties() const { return {}; }
 };
 
+class SourceGroupingInterface : public PipelineEmitter<SourceGroupInterface>, public PipelineReceiver<SourceInterface> {
+public:
+  /// Returns the set of required properties to compute the grouping
+  virtual std::set<PropertyId> requiredProperties() const = 0;
+};
+
 /**
  * @class SourceGrouping
  * @brief SourceGrouping takes Source, groups them together according to its GroupingCriteria and stores them.
  *  When a ProcessSourcesEvent is received the sources that need to be processed are output together with the
  *  sources they are grouped with as a SourceGroup.
  *
  */
-class SourceGrouping : public PipelineEmitter<SourceGroupInterface>, public PipelineReceiver<SourceInterface> {
+class SourceGrouping : public SourceGroupingInterface {
 public:
 
   /**
@@ -101,7 +108,7 @@ class SourceGrouping : public PipelineEmitter<SourceGroupInterface>, public Pipe
                  unsigned int hard_limit);
 
   /// Returns the set of required properties to compute the grouping
-  std::set<PropertyId> requiredProperties() const;
+  std::set<PropertyId> requiredProperties() const override;
 
   /// Handles a new Source
   void receiveSource(std::unique_ptr<SourceInterface> source) override;

SEImplementation/SEImplementation/Configuration/RngConfig.h

@@ -0,0 +1,38 @@
+/*
+ * RngConfig.h
+ *
+ *  Created on: Mar 21, 2024
+ *      Author: mschefer
+ */
+
+#ifndef _SEIMPLEMENTATION_CONFIGURATION_RNGCONFIG_H_
+#define _SEIMPLEMENTATION_CONFIGURATION_RNGCONFIG_H_
+
+#include "Configuration/Configuration.h"
+#include "AlexandriaKernel/ThreadPool.h"
+
+namespace SourceXtractor {
+
+class RngConfig : public Euclid::Configuration::Configuration {
+public:
+  explicit RngConfig(long manager_id);
+
+  virtual ~RngConfig() = default;
+
+  std::map<std::string, OptionDescriptionList> getProgramOptions() override;
+
+  void initialize(const UserValues& args) override;
+
+  unsigned int getSeed() const {
+    return m_seed;
+  }
+
+private:
+  unsigned int m_seed;
+};
+
+
+}
+
+
+#endif /* _SEIMPLEMENTATION_CONFIGURATION_RNGCONFIG_H_ */

SEImplementation/SEImplementation/Grouping/AssocGrouping.h

@@ -0,0 +1,50 @@
+/** Copyright © 2019 - 2023 Université de Genève, LMU Munich - Faculty of Physics, IAP-CNRS/Sorbonne Université
+ *
+ * This library is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 3.0 of the License, or (at your option)
+ * any later version.
+ *
+ * This library is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this library; if not, write to the Free Software Foundation, Inc.,
+ * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ */
+
+#ifndef _SEIMPLEMENTATION_GROUPING_ASSOCGROUPING_H_
+#define _SEIMPLEMENTATION_GROUPING_ASSOCGROUPING_H_
+
+#include <map>
+
+#include "SEFramework/Pipeline/SourceGrouping.h"
+
+namespace SourceXtractor {
+
+class AssocGrouping : public SourceGroupingInterface {
+public:
+
+  AssocGrouping(std::shared_ptr<SourceGroupFactory> group_factory, unsigned int hard_limit);
+  virtual ~AssocGrouping() = default;
+
+  std::set<PropertyId> requiredProperties() const override;
+
+  /// Handles a new Source
+  void receiveSource(std::unique_ptr<SourceInterface> source) override;
+
+  /// Handles a ProcessSourcesEvent to trigger the processing of some of the Sources stored in SourceGrouping
+  void receiveProcessSignal(const ProcessSourcesEvent& event) override;
+
+private:
+  std::shared_ptr<SourceGroupFactory> m_group_factory;
+  std::map<unsigned int, std::unique_ptr<SourceGroupInterface>> m_source_groups;
+  unsigned int m_hard_limit;
+
+};
+
+}
+
+#endif /* _SEIMPLEMENTATION_GROUPING_ASSOCGROUPING_H_ */

SEImplementation/SEImplementation/Grouping/GroupingFactory.h

@@ -42,48 +42,24 @@ class GroupingFactory : public Configurable {
 
 public:
 
-  explicit GroupingFactory(std::shared_ptr<SourceGroupFactory> source_group_factory)
-    : m_source_group_factory(source_group_factory), m_hard_limit(0) {}
+  explicit GroupingFactory(std::shared_ptr<SourceGroupFactory> source_group_factory);
 
   virtual ~GroupingFactory() = default;
 
-  void reportConfigDependencies(Euclid::Configuration::ConfigManager& manager) const override {
-    manager.registerConfiguration<GroupingConfig>();
-  }
-
-  void configure(Euclid::Configuration::ConfigManager& manager) override {
-    auto grouping_config = manager.getConfiguration<GroupingConfig>();
-    switch (grouping_config.getAlgorithmOption()) {
-    case GroupingConfig::Algorithm::NO_GROUPING:
-      m_grouping_criteria = std::make_shared<NoGroupingCriteria>();
-      break;
-    case GroupingConfig::Algorithm::OVERLAPPING:
-      m_grouping_criteria = std::make_shared<OverlappingBoundariesCriteria>();
-      break;
-    case GroupingConfig::Algorithm::SPLIT_SOURCES:
-      m_grouping_criteria = std::make_shared<SplitSourcesCriteria>();
-      break;
-    case GroupingConfig::Algorithm::MOFFAT:
-      m_grouping_criteria = std::make_shared<MoffatCriteria>(grouping_config.getMoffatThreshold(), grouping_config.getMoffatMaxDistance());
-      break;
-    case GroupingConfig::Algorithm::ASSOC:
-      m_grouping_criteria = std::make_shared<AssocCriteria>();
-      break;
-    }
-    m_hard_limit = grouping_config.getHardLimit();
-  }
-
-  std::shared_ptr<SourceGrouping> createGrouping() const {
-    assert(m_grouping_criteria != nullptr);
-    assert(m_source_group_factory != nullptr);
-
-    return std::make_shared<SourceGrouping>(m_grouping_criteria, m_source_group_factory, m_hard_limit);
-  }
+  void reportConfigDependencies(Euclid::Configuration::ConfigManager& manager) const override;
+
+  void configure(Euclid::Configuration::ConfigManager& manager) override;
+
+  std::shared_ptr<SourceGroupingInterface> createGrouping() const;
 
 private:
+  std::shared_ptr<GroupingCriteria> getCriteria() const;
+
+  GroupingConfig::Algorithm m_algorithm;
   std::shared_ptr<GroupingCriteria> m_grouping_criteria;
   std::shared_ptr<SourceGroupFactory> m_source_group_factory;
   unsigned int m_hard_limit;
+  double m_moffat_max_distance;
 };
 
 } /* namespace SourceXtractor */

SEImplementation/SEImplementation/Grouping/MoffatGrouping.h

@@ -0,0 +1,67 @@
+/** Copyright © 2019-2024 Université de Genève, LMU Munich - Faculty of Physics, IAP-CNRS/Sorbonne Université
+ *
+ * This library is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 3.0 of the License, or (at your option)
+ * any later version.
+ *
+ * This library is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this library; if not, write to the Free Software Foundation, Inc.,
+ * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ */
+
+#ifndef _SEIMPLEMENTATION_GROUPING_MOFFATGROUPING_H_
+#define _SEIMPLEMENTATION_GROUPING_MOFFATGROUPING_H_
+
+#include "SEFramework/Pipeline/SourceGrouping.h"
+#include "SEUtils/QuadTree.h"
+
+#include <map>
+#include <vector>
+#include <functional>
+
+namespace SourceXtractor {
+
+class MoffatGrouping : public SourceGroupingInterface {
+public:
+  struct SourceInfo {
+    std::unique_ptr<SourceInterface> m_source;
+    double m_x, m_y;
+    size_t m_group_id;
+  };
+
+  using Group = std::vector<std::shared_ptr<SourceInfo>>;
+
+  MoffatGrouping(std::shared_ptr<GroupingCriteria> grouping_criteria,
+      std::shared_ptr<SourceGroupFactory> group_factory, unsigned int hard_limit, float max_range);
+  virtual ~MoffatGrouping() = default;
+
+  std::set<PropertyId> requiredProperties() const override;
+
+  /// Handles a new Source
+  void receiveSource(std::unique_ptr<SourceInterface> source) override;
+
+  /// Handles a ProcessSourcesEvent to trigger the processing of some of the Sources stored in SourceGrouping
+  void receiveProcessSignal(const ProcessSourcesEvent& event) override;
+
+private:
+  void processGroup(unsigned int group_id);
+
+  std::shared_ptr<GroupingCriteria> m_grouping_criteria;
+  std::shared_ptr<SourceGroupFactory> m_group_factory;
+  unsigned int m_hard_limit;
+  float m_max_range;
+
+  size_t m_group_counter;
+  std::map<unsigned int, std::shared_ptr<Group>> m_groups;
+  QuadTree<std::shared_ptr<SourceInfo>> m_tree;
+};
+
+}
+
+#endif /* _SEIMPLEMENTATION_GROUPING_MOFFATGROUPING_H_ */

SEImplementation/SEImplementation/Grouping/SplitSourcesGrouping.h

@@ -0,0 +1,50 @@
+/** Copyright © 2019 - 2023 Université de Genève, LMU Munich - Faculty of Physics, IAP-CNRS/Sorbonne Université
+ *
+ * This library is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 3.0 of the License, or (at your option)
+ * any later version.
+ *
+ * This library is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this library; if not, write to the Free Software Foundation, Inc.,
+ * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ */
+
+#ifndef _SEIMPLEMENTATION_GROUPING_SPLITSOURCESGROUPING_H_
+#define _SEIMPLEMENTATION_GROUPING_SPLITSOURCESGROUPING_H_
+
+#include "SEFramework/Pipeline/SourceGrouping.h"
+
+#include <map>
+
+namespace SourceXtractor {
+
+class SplitSourcesGrouping : public SourceGroupingInterface {
+public:
+
+  SplitSourcesGrouping(std::shared_ptr<SourceGroupFactory> group_factory, unsigned int hard_limit);
+  virtual ~SplitSourcesGrouping() = default;
+
+  std::set<PropertyId> requiredProperties() const override;
+
+  /// Handles a new Source
+  void receiveSource(std::unique_ptr<SourceInterface> source) override;
+
+  /// Handles a ProcessSourcesEvent to trigger the processing of some of the Sources stored in SourceGrouping
+  void receiveProcessSignal(const ProcessSourcesEvent& event) override;
+
+private:
+  std::shared_ptr<SourceGroupFactory> m_group_factory;
+  std::map<unsigned int, std::unique_ptr<SourceGroupInterface>> m_source_groups;
+  unsigned int m_hard_limit;
+
+};
+
+}
+
+#endif /* _SEIMPLEMENTATION_GROUPING_SPLITSOURCESGROUPING_H_ */

SEImplementation/SEImplementation/Partition/MultiThresholdPartitionStep.h

@@ -24,6 +24,8 @@
 #ifndef _SEIMPLEMENTATION_PARTITION_MULTITHRESHOLDPARTITIONSTEP_H_
 #define _SEIMPLEMENTATION_PARTITION_MULTITHRESHOLDPARTITIONSTEP_H_
 
+#include <boost/random.hpp>
+
 #include "SEUtils/Types.h"
 
 #include "SEImplementation/Property/PixelCoordinateList.h"
@@ -48,7 +50,7 @@ class MultiThresholdPartitionStep : public PartitionStep {
 public:
 
   MultiThresholdPartitionStep(std::shared_ptr<SourceFactory> source_factory, SeFloat contrast,
-      unsigned int thresholds_nb, unsigned int min_deblend_area);
+      unsigned int thresholds_nb, unsigned int min_deblend_area, unsigned int seed);
 
   virtual ~MultiThresholdPartitionStep() = default;
 
@@ -67,6 +69,8 @@ class MultiThresholdPartitionStep : public PartitionStep {
   SeFloat m_contrast;
   unsigned int m_thresholds_nb;
   unsigned int m_min_deblend_area;
+  unsigned int m_seed;
+  boost::random::mt19937 m_rng;
 };