Merge branch 'main' into dev/reduce

RELEASE.md

@@ -6,6 +6,7 @@
 Features:
 
 - Cluster finder now works with 5x5, 7x7 and 9x9 clusters
+- Added ClusterVector::empty() member
 
 
 ### 2025.05.22
@@ -17,6 +18,7 @@ Features:
 Bugfixes:
 
 - Fixed crash when opening raw files with large number of data files
+- Fixed reading RawFiles with ROI fully excluding some sub files. 
 
 
 

docs/CMakeLists.txt

@@ -45,12 +45,3 @@ add_custom_target(
     COMMENT "Generating documentation with Sphinx"
 )
 
-add_custom_target(
-    rst
-    COMMAND ${SPHINX_EXECUTABLE} -a -b html
-    -Dbreathe_projects.aare=${CMAKE_CURRENT_BINARY_DIR}/xml
-    -c "${SPHINX_BUILD}"
-    ${SPHINX_BUILD}/src 
-    ${SPHINX_BUILD}/html
-    COMMENT "Generating documentation with Sphinx"
-)

docs/Doxyfile.in

@@ -886,7 +886,7 @@ EXCLUDE_SYMLINKS       = NO
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       = */docs/* */tests/* */python/* */manual */slsDetectorServers/* */libs/* */integrationTests *README* */slsDetectorGui/* */ctbGui/* */slsDetectorCalibration/* *TobiSchluter*
+EXCLUDE_PATTERNS       = *build* */docs/* */tests/* *.test.cpp* */python/* */manual */slsDetectorServers/* */libs/* */integrationTests *README* *_deps* *TobiSchluter*
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the

docs/src/ClusterVector.rst

@@ -3,4 +3,13 @@ ClusterVector
 
 .. doxygenclass:: aare::ClusterVector
    :members:
-   :undoc-members:
+   :undoc-members:
+   :private-members:
+
+
+
+.. doxygenclass:: aare::ClusterVector< Cluster< T, ClusterSizeX, ClusterSizeY, CoordType > > 
+   :members:
+   :undoc-members:
+   :private-members:
+   

docs/src/Workflow.rst

@@ -37,7 +37,7 @@ unfamiliar steps.
 
 
 Checklists for deployment
-~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 **Feature:**
 

include/aare/ClusterFile.hpp

@@ -14,7 +14,7 @@
 namespace aare {
 
 /*
-Binary cluster file. Expects data to be layed out as:
+Binary cluster file. Expects data to be laid out as:
 int32_t frame_number
 uint32_t number_of_clusters
 int16_t x, int16_t y, int32_t data[9] x number_of_clusters

include/aare/ClusterVector.hpp

@@ -32,7 +32,8 @@ class ClusterVector; // Forward declaration
  */
 template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
           typename CoordType>
-class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
+class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> 
+{
 
     std::vector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> m_data{};
     int32_t m_frame_number{0}; // TODO! Check frame number size and type
@@ -122,6 +123,11 @@ class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
      */
     size_t size() const { return m_data.size(); }
 
+    /**
+     * @brief Check if the vector is empty
+     */
+    bool empty() const { return m_data.empty(); }
+
     uint8_t cluster_size_x() const { return ClusterSizeX; }
 
     uint8_t cluster_size_y() const { return ClusterSizeY; }

src/ClusterVector.test.cpp

@@ -7,9 +7,21 @@
 
 using aare::Cluster;
 using aare::ClusterVector;
+using C1 = Cluster<int32_t, 2, 2>;
+
+
+TEST_CASE("A newly created ClusterVector is empty") {
+    ClusterVector<C1> cv(4);
+    REQUIRE(cv.empty());
+}
+
+TEST_CASE("After pushing back one element the ClusterVector is not empty") {
+    ClusterVector<C1> cv(4);
+    cv.push_back(C1{1, 2, {3, 4}});
+    REQUIRE(!cv.empty());
+}
 
 TEST_CASE("item_size return the size of the cluster stored") {
-    using C1 = Cluster<int32_t, 2, 2>;
     ClusterVector<C1> cv(4);
     CHECK(cv.item_size() == sizeof(C1));
 
@@ -43,8 +55,7 @@ TEST_CASE("item_size return the size of the cluster stored") {
     CHECK(cv7.item_size() == sizeof(C7));
 }
 
-TEST_CASE("ClusterVector 2x2 int32_t capacity 4, push back then read",
-          "[.ClusterVector]") {
+TEST_CASE("ClusterVector 2x2 int32_t capacity 4, push back then read") {
 
     ClusterVector<Cluster<int32_t, 2, 2>> cv(4);
     REQUIRE(cv.capacity() == 4);
@@ -70,7 +81,7 @@ TEST_CASE("ClusterVector 2x2 int32_t capacity 4, push back then read",
     }
 }
 
-TEST_CASE("Summing 3x1 clusters of int64", "[.ClusterVector]") {
+TEST_CASE("Summing 3x1 clusters of int64") {
     ClusterVector<Cluster<int32_t, 3, 1>> cv(2);
     REQUIRE(cv.capacity() == 2);
     REQUIRE(cv.size() == 0);
@@ -102,7 +113,7 @@ TEST_CASE("Summing 3x1 clusters of int64", "[.ClusterVector]") {
     */
 }
 
-TEST_CASE("Storing floats", "[.ClusterVector]") {
+TEST_CASE("Storing floats") {
     ClusterVector<Cluster<float, 2, 4>> cv(10);
     REQUIRE(cv.capacity() == 10);
     REQUIRE(cv.size() == 0);
@@ -129,7 +140,7 @@ TEST_CASE("Storing floats", "[.ClusterVector]") {
     */
 }
 
-TEST_CASE("Push back more than initial capacity", "[.ClusterVector]") {
+TEST_CASE("Push back more than initial capacity") {
 
     ClusterVector<Cluster<int32_t, 2, 2>> cv(2);
     auto initial_data = cv.data();
@@ -162,8 +173,7 @@ TEST_CASE("Push back more than initial capacity", "[.ClusterVector]") {
     REQUIRE(initial_data != cv.data());
 }
 
-TEST_CASE("Concatenate two cluster vectors where the first has enough capacity",
-          "[.ClusterVector]") {
+TEST_CASE("Concatenate two cluster vectors where the first has enough capacity") {
     ClusterVector<Cluster<int32_t, 2, 2>> cv1(12);
     Cluster<int32_t, 2, 2> c1 = {1, 2, {3, 4, 5, 6}};
     cv1.push_back(c1);
@@ -192,8 +202,7 @@ TEST_CASE("Concatenate two cluster vectors where the first has enough capacity",
     REQUIRE(ptr[3].y == 17);
 }
 
-TEST_CASE("Concatenate two cluster vectors where we need to allocate",
-          "[.ClusterVector]") {
+TEST_CASE("Concatenate two cluster vectors where we need to allocate") {
     ClusterVector<Cluster<int32_t, 2, 2>> cv1(2);
     Cluster<int32_t, 2, 2> c1 = {1, 2, {3, 4, 5, 6}};
     cv1.push_back(c1);
@@ -229,7 +238,7 @@ struct ClusterTestData {
     std::vector<int64_t> index_map_y;
 };
 
-TEST_CASE("Gain Map Calculation Index Map", "[.ClusterVector][.gain_map]") {
+TEST_CASE("Gain Map Calculation Index Map") {
 
     auto clustertestdata = GENERATE(
         ClusterTestData{3,