From dc3c5c28d6e26f8b5c47c3f1e54271b5e9679643 Mon Sep 17 00:00:00 2001
From: Stephen Plaza <plazas@janelia.hhmi.org>
Date: Fri, 20 Nov 2015 02:26:31 -0500
Subject: [PATCH] exposes agglomeration routine to python

---
 integration_tests/testpyagglom.py | 25 ++++++++++++++
 python/CMakeLists.txt             | 12 ++++++-
 python/src/Agglomeration.cpp      | 56 +++++++++++++++++++++++++++++--
 3 files changed, 90 insertions(+), 3 deletions(-)
 create mode 100644 integration_tests/testpyagglom.py

diff --git a/integration_tests/testpyagglom.py b/integration_tests/testpyagglom.py
new file mode 100644
index 0000000..f49a2f6
--- /dev/null
+++ b/integration_tests/testpyagglom.py
@@ -0,0 +1,25 @@
+import sys
+import h5py
+import numpy
+
+segh5 = sys.argv[1]
+predh5 = sys.argv[2]
+classifier = sys.argv[3]
+threshold = float(sys.argv[4])
+
+from neuroproof import Agglomeration
+
+# open as uint32 and float respectively
+seg = numpy.array(h5py.File(segh5)['stack'], numpy.uint32)
+pred = numpy.array(h5py.File(predh5)['volume/predictions'], numpy.float32)
+
+pred = pred.transpose((2,1,0,3))
+pred = pred.copy()
+
+res = Agglomeration.agglomerate(seg, pred, classifier, threshold)
+
+# should be 232 unique labels (including 0) in the resulting segmentation
+if len(numpy.unique(res)) != 232:
+    exit(1)
+
+print "SUCCESS"
diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
index 50e048f..660bb86 100644
--- a/python/CMakeLists.txt
+++ b/python/CMakeLists.txt
@@ -166,7 +166,7 @@ add_library( _agglomeration_python SHARED src/Agglomeration.cpp)
 target_link_libraries( _classifier_python Classifier ${NEUROPROOF_EXT_LIBS} ${boostpython_LIB} ${PYTHON_LIBRARIES} )
 set_target_properties( _classifier_python PROPERTIES PREFIX  ""
                                                DEBUG_POSTFIX "" )
-target_link_libraries( _agglomeration_python Stack ${NEUROPROOF_EXT_LIBS} ${boostpython_LIB} ${PYTHON_LIBRARIES} )
+target_link_libraries( _agglomeration_python ${NEUROPROOF_INT_LIBS} ${NEUROPROOF_EXT_LIBS} ${boostpython_LIB} ${PYTHON_LIBRARIES} )
 set_target_properties( _agglomeration_python PROPERTIES PREFIX  "")
 
 if (APPLE)
@@ -194,3 +194,13 @@ install(FILES neuroproof/Agglomeration/__init__.py
     DESTINATION ${LIBDVID_PYTHON_INSTALL_DIR}/neuroproof/Agglomeration)
 
 enable_testing() 
+
+add_test("test_agglom_python"
+    ${PYTHON_EXE}
+    ${CMAKE_SOURCE_DIR}/integration_tests/testpyagglom.py
+    ${CMAKE_SOURCE_DIR}/integration_tests/inputs/samp1_labels.h5 
+    ${CMAKE_SOURCE_DIR}/integration_tests/inputs/samp1_prediction.h5
+    ${CMAKE_SOURCE_DIR}/integration_tests/inputs/250-1_agglo_itr1_trial1_opencv_rf_tr255.xml
+    0.2
+)
+
diff --git a/python/src/Agglomeration.cpp b/python/src/Agglomeration.cpp
index f16b29b..7c074e8 100644
--- a/python/src/Agglomeration.cpp
+++ b/python/src/Agglomeration.cpp
@@ -9,14 +9,66 @@
 
 #include "converters.hpp"
 
+
+#include <boost/algorithm/string/predicate.hpp>
+#include <Utilities/ScopeTime.h>
+#include <Classifier/vigraRFclassifier.h>
+#include <Classifier/opencvRFclassifier.h>
+
+#include <FeatureManager/FeatureMgr.h>
+#include <BioPriors/BioStack.h>
+#include <BioPriors/StackAgglomAlgs.h>
+
 using namespace boost::python;
+using namespace boost::algorithm;
 using std::vector;
+using std::cout; using std::endl;
 
 namespace NeuroProof { namespace python {
 
-VolumeLabelPtr agglomerate(VolumeLabelPtr labels, vector<VolumeProbPtr> prob_array)
+// ?! build classifier in function for now -- use Classifier object in the future
+// Note: always assumes mito is third channel
+// TODO: allow segmentation constraints (e.g., synapses)
+VolumeLabelPtr agglomerate(VolumeLabelPtr labels,
+        vector<VolumeProbPtr> prob_array, std::string fn, double threshold)
 {
-    return labels;
+    ScopeTime timer;
+    // create classifier from file
+    EdgeClassifier* eclfr;
+    if (ends_with(fn, ".h5")) {
+        eclfr = new VigraRFclassifier(fn.c_str());	
+    } else if (ends_with(fn, ".xml")) {	
+        eclfr = new OpencvRFclassifier(fn.c_str());	
+    }
+    
+    // create feature manager and load classifier
+    FeatureMgrPtr feature_manager(new FeatureMgr(prob_array.size()));
+    feature_manager->set_basic_features(); 
+    feature_manager->set_classifier(eclfr);   	 
+
+    // create stack to hold segmentation state
+    BioStack stack(labels); 
+    stack.set_feature_manager(feature_manager);
+    stack.set_prob_list(prob_array);
+
+    // build graph
+    stack.build_rag();
+    cout<< "Initial number of regions: "<< stack.get_num_labels()<< endl;	
+
+    // remove inclusions
+    stack.remove_inclusions();
+    cout<< "Regions after inclusion removal: "<< stack.get_num_labels()<< endl;	
+
+    // perform agglomeration    
+    agglomerate_stack(stack, threshold, true);
+    cout<< "Regions after agglomeration: "<< stack.get_num_labels()<< endl;	
+    stack.remove_inclusions();
+    cout<< "Regions after inclusion removal: "<< stack.get_num_labels()<< endl;	
+   
+    agglomerate_stack_mito(stack);
+    cout<< "Regions after mito agglomeration: "<< stack.get_num_labels()<< endl;	
+
+    return stack.get_labelvol();
 }
 
 BOOST_PYTHON_MODULE(_agglomeration_python)