Merge pull request #188 from favreau/master

Version 1.5.0

Author: Cyrille Favreau

CMakeLists.txt

@@ -19,7 +19,7 @@
 cmake_minimum_required(VERSION 3.1 FATAL_ERROR)
 
 set(NAME BIOEXPLORER)
-set(BIOEXPLORER_PACKAGE_VERSION 1.4.0)
+set(BIOEXPLORER_PACKAGE_VERSION 1.5.0)
 project(${NAME} VERSION ${BIOEXPLORER_PACKAGE_VERSION})
 
 list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/CMake)

bioexplorer/core/plugin/connectomics/synapses/SynapseEfficacySimulationHandler.cpp

@@ -89,9 +89,9 @@ void* SynapseEfficacySimulationHandler::getFrameData(const uint32_t frame)
                                                      _currentFrame,
                                                      _details.sqlFilter);
 
-        if( values.size() != _frameData.size())
+        if (values.size() != _frameData.size())
             _frameData.resize(values.size());
-            
+
         uint64_t i = 0;
         for (const auto& value : values)
         {

bioexplorer/core/plugin/io/db/DBConnector.cpp

@@ -1235,21 +1235,23 @@ Vector3ds DBConnector::getSynapseEfficacyPositions(
     return positions;
 }
 
-uint8_ts DBConnector::getSynapseEfficacyReportValues(
+floats DBConnector::getSynapseEfficacyReportValues(
     const std::string& populationName, const uint64_t frame,
     const std::string& sqlCondition) const
 {
     CHECK_DB_INITIALIZATION
-    uint8_ts reportValues;
+    floats reportValues;
     const uint64_t offset = 1;
+    const auto size = sizeof(float);
     pqxx::nontransaction transaction(
         *_connections[omp_get_thread_num() % _dbNbConnections]);
     try
     {
         Timer chrono;
         std::string sql = "SELECT SUBSTRING(values::bytea FROM " +
-                          std::to_string(offset + frame) + " FOR 1) FROM " +
-                          populationName + ".synapse_efficacy";
+                          std::to_string(offset + frame * size) + " FOR " +
+                          std::to_string(size) + ") FROM " + populationName +
+                          ".synapse_efficacy";
         if (!sqlCondition.empty())
             sql += " WHERE " + sqlCondition;
         sql += " ORDER BY synapse_guid";
@@ -1260,9 +1262,9 @@ uint8_ts DBConnector::getSynapseEfficacyReportValues(
         uint64_t i = 0;
         for (auto c = res.begin(); c != res.end(); ++c)
         {
-            uint8_t value;
+            float value;
             const pqxx::binarystring buffer(c[0]);
-            memcpy(&value, buffer.data(), sizeof(uint8_t));
+            memcpy(&value, buffer.data(), size);
             reportValues[i] = value;
             ++i;
         }

bioexplorer/core/plugin/io/db/DBConnector.h

@@ -403,9 +403,9 @@ class DBConnector
      * @param populationName Name of the population
      * @param frame Simulation frame
      * @param sqlCondition SQL condition
-     * @return Positions of synapses for efficacy report
+     * @return Values of synapses efficacy
      */
-    uint8_ts getSynapseEfficacyReportValues(
+    floats getSynapseEfficacyReportValues(
         const std::string& populationName, const uint64_t frame,
         const std::string& sqlCondition = "") const;
 

bioexplorer/pythonsdk/Makefile

@@ -60,7 +60,7 @@ run_tests: $(VENV_INSTALLED)
 
 run_tests_xunit: $(VENV_INSTALLED)
 	@mkdir -p $(ROOT_DIR)/test-reports
-	$(VENV_BIN)/nosetests bioexplorer --with-coverage --cover-min-percentage=$(MIN_COV) --cover-inclusive --cover-erase --cover-package=bioexplorer --with-xunit --xunit-file=test-reports/nosetests_bioexplorer.xml
+	$(VENV_BIN)/nosetests bioexplorer --with-coverage --cover-min-percentage=$(MIN_COV) --cover-inclusive --cover-erase --cover-package=bioexplorer --with-xunit --xunit-file=nosetests_bioexplorer.xml
 
 lint: run_pycodestyle run_pydocstyle run_pylint
 

bioexplorer/pythonsdk/bioexplorer/version.py

@@ -21,4 +21,4 @@
 # You should have received a copy of the GNU General Public License along with
 # this program.  If not, see <https://www.gnu.org/licenses/>.
 
-VERSION = "1.4.0"
+VERSION = "1.5.0"

bioexplorer/pythonsdk/requirements.txt

@@ -20,14 +20,14 @@
 
 rockets~=1.0.3
 requests~=2.22.0
-python-jsonschema-objects~=0.3.5
+python-jsonschema-objects~=0.4.1
 semver~=2.8.1
 stringcase~=1.2.0
 pyquaternion~=0.9.9
 webcolors~=1.8.1
-seaborn~=0.11.1
-ipywidgets~=7.6.3
-jsonschema~=3.2.0
+seaborn~=0.12.2
+ipywidgets~=8.0.4
+jsonschema~=4.17.3
 sqlalchemy~=1.4.31
 psycopg2-binary~=2.9.2
 tqdm~=4.62.0

bioexplorer/pythonsdk/requirements_dev.txt

@@ -20,7 +20,7 @@
 
 rockets~=1.0.3
 requests~=2.22.0
-python-jsonschema-objects~=0.3.5
+python-jsonschema-objects~=0.4.1
 semver~=2.8.1
 setuptools~=46.0.0
 stringcase~=1.2.0
@@ -29,7 +29,7 @@ pylint~=2.6.0
 pycodestyle~=2.7.0
 pydocstyle~=3.0.0
 nose~=1.3.7
-coverage~=4.5.2
+coverage~=7.1.0
 nosexcover~=1.0.11
 tox~=3.6.1
 mock~=2.0.0
@@ -39,7 +39,7 @@ nbsphinx==0.8.3
 m2r~=0.2.1
 pyquaternion~=0.9.9
 webcolors~=1.8.1
-seaborn~=0.11.1
-ipywidgets~=7.6.3
+seaborn~=0.12.2
+ipywidgets~=8.0.4
 psycopg2-binary~=2.9.2
 tqdm~=4.62.0

bioexplorer/pythonsdk/setup.cfg

@@ -1,5 +1,5 @@
 [metadata]
-version = 1.4.0
+version = 1.5.0
 name = bioexplorer
 summary = Blue Brain BioExplorer python API
 long_description = file: README.md

docs/annotated.html

@@ -113,7 +113,9 @@
 <tr id="row_0_1_18_" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="d2/d4a/classbioexplorer_1_1common_1_1ThreadSafeContainer.html" target="_self">ThreadSafeContainer</a></td><td class="desc">Used to load large datasets in parallel. Every individual element is loaded in a separate thread and eventualy merged into a single Brayns model </td></tr>
 <tr id="row_0_1_19_" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="d0/dbd/classbioexplorer_1_1common_1_1UniqueId.html" target="_self">UniqueId</a></td><td class="desc">The UniqueID class provides a way to get a unique identifier accross the application </td></tr>
 <tr id="row_0_2_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_2_" class="arrow" onclick="toggleFolder('0_2_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><b>connectomics</b></td><td class="desc"></td></tr>
-<tr id="row_0_2_0_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="d6/dcd/classbioexplorer_1_1connectomics_1_1WhiteMatter.html" target="_self">WhiteMatter</a></td><td class="desc"></td></tr>
+<tr id="row_0_2_0_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="da/daf/classbioexplorer_1_1connectomics_1_1SynapseEfficacy.html" target="_self">SynapseEfficacy</a></td><td class="desc"></td></tr>
+<tr id="row_0_2_1_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="de/da5/classbioexplorer_1_1connectomics_1_1SynapseEfficacySimulationHandler.html" target="_self">SynapseEfficacySimulationHandler</a></td><td class="desc">The <a class="el" href="de/da5/classbioexplorer_1_1connectomics_1_1SynapseEfficacySimulationHandler.html" title="The SynapseEfficacySimulationHandler handles the reading of simulation information from the database ...">SynapseEfficacySimulationHandler</a> handles the reading of simulation information from the database at a soma level. When attached to a model, the simulation data is communicated to the renderer by Brayns, and mapped to the geometry by the BioExplorer advanced renderer </td></tr>
+<tr id="row_0_2_2_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="d6/dcd/classbioexplorer_1_1connectomics_1_1WhiteMatter.html" target="_self">WhiteMatter</a></td><td class="desc"></td></tr>
 <tr id="row_0_3_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_3_" class="arrow" onclick="toggleFolder('0_3_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><b>details</b></td><td class="desc"></td></tr>
 <tr id="row_0_3_0_" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="dc/d45/structbioexplorer_1_1details_1_1AddBoundingBoxDetails.html" target="_self">AddBoundingBoxDetails</a></td><td class="desc">Defines the parameters needed when adding bounding box to the scene </td></tr>
 <tr id="row_0_3_1_" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="d8/d5c/structbioexplorer_1_1details_1_1AddBoxDetails.html" target="_self">AddBoxDetails</a></td><td class="desc">Defines the parameters needed when adding box to the scene </td></tr>
@@ -163,10 +165,11 @@
 <tr id="row_0_3_45_" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="d1/d00/structbioexplorer_1_1details_1_1RNASequenceDetails.html" target="_self">RNASequenceDetails</a></td><td class="desc">RNA sequence descriptor </td></tr>
 <tr id="row_0_3_46_" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="d2/d03/structbioexplorer_1_1details_1_1SceneInformationDetails.html" target="_self">SceneInformationDetails</a></td><td class="desc">List of metrics for the current scene </td></tr>
 <tr id="row_0_3_47_" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="d6/d93/structbioexplorer_1_1details_1_1SugarDetails.html" target="_self">SugarDetails</a></td><td class="desc">Data structure describing the sugar </td></tr>
-<tr id="row_0_3_48_" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="dd/d98/structbioexplorer_1_1details_1_1VasculatureDetails.html" target="_self">VasculatureDetails</a></td><td class="desc"></td></tr>
-<tr id="row_0_3_49_" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="de/da6/structbioexplorer_1_1details_1_1VasculatureRadiusReportDetails.html" target="_self">VasculatureRadiusReportDetails</a></td><td class="desc"></td></tr>
-<tr id="row_0_3_50_" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="d1/d4e/structbioexplorer_1_1details_1_1VasculatureReportDetails.html" target="_self">VasculatureReportDetails</a></td><td class="desc"></td></tr>
-<tr id="row_0_3_51_" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="da/d1a/structbioexplorer_1_1details_1_1WhiteMatterDetails.html" target="_self">WhiteMatterDetails</a></td><td class="desc"></td></tr>
+<tr id="row_0_3_48_" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="d4/d3d/structbioexplorer_1_1details_1_1SynapseEfficacyDetails.html" target="_self">SynapseEfficacyDetails</a></td><td class="desc"></td></tr>
+<tr id="row_0_3_49_" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="dd/d98/structbioexplorer_1_1details_1_1VasculatureDetails.html" target="_self">VasculatureDetails</a></td><td class="desc"></td></tr>
+<tr id="row_0_3_50_" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="de/da6/structbioexplorer_1_1details_1_1VasculatureRadiusReportDetails.html" target="_self">VasculatureRadiusReportDetails</a></td><td class="desc"></td></tr>
+<tr id="row_0_3_51_" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="d1/d4e/structbioexplorer_1_1details_1_1VasculatureReportDetails.html" target="_self">VasculatureReportDetails</a></td><td class="desc"></td></tr>
+<tr id="row_0_3_52_" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="da/d1a/structbioexplorer_1_1details_1_1WhiteMatterDetails.html" target="_self">WhiteMatterDetails</a></td><td class="desc"></td></tr>
 <tr id="row_0_4_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_4_" class="arrow" onclick="toggleFolder('0_4_')">&#9658;</span><span class="icona"><span class="icon">N</span></span><b>fields</b></td><td class="desc"></td></tr>
 <tr id="row_0_4_0_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="d9/d6e/classbioexplorer_1_1fields_1_1FieldsHandler.html" target="_self">FieldsHandler</a></td><td class="desc">Handles electro-magnetic fields data structures </td></tr>
 <tr id="row_0_4_1_" class="even" style="display:none;"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="dc/d5a/classbioexplorer_1_1fields_1_1Octree.html" target="_self">Octree</a></td><td class="desc">Implements the <a class="el" href="dc/d5a/classbioexplorer_1_1fields_1_1Octree.html" title="The Octree class implements the Octree acceleration structure used by the FieldsRenderer class to ren...">Octree</a> acceleration structure used by the FieldsRenderer class to render magnetic fields </td></tr>