V0.10.0

.github/workflows/main.yml

@@ -17,15 +17,15 @@ jobs:
         config:
         - { 
             name: "Ubuntu Low (AppImage)",
-            os:   "ubuntu-20.04",
-            cc:   "gcc-10",
-            cxx:  "g++-10"
+            os:   "ubuntu-22.04",
+            cc:   "gcc-11",
+            cxx:  "g++-11"
           }
         - { 
             name: "Ubuntu High",
-            os:   "ubuntu-22.04",
-            cc:   "clang-14",
-            cxx:  "clang++-14"
+            os:   "ubuntu-24.04",
+            cc:   "clang-18",
+            cxx:  "clang++-18"
           }
       fail-fast: false
     env:
@@ -42,13 +42,13 @@ jobs:
       - name: Update apt
         run: sudo apt update
       - name: Install missing packages
-        run: sudo apt install libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libglu1-mesa-dev freeglut3-dev mesa-common-dev
+        run: sudo apt install libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libglu1-mesa-dev freeglut3-dev libfuse2 mesa-common-dev libwayland-bin libwayland-dev libxkbcommon-dev xorg-dev
       - name: Check config
         run: |
           $CC --version
           $CXX --version
       - name: Configure
-        run: cmake -S . -B $bld_dir -DCMAKE_CXX_COMPILER=$CXX -DCMAKE_C_COMPILER=$CC --install-prefix $app_dir/usr -DARB_ARCH=x86-64-v2
+        run: cmake -S . -B $bld_dir -DCMAKE_CXX_COMPILER=$CXX -DCMAKE_C_COMPILER=$CC --install-prefix $app_dir/usr -DARB_ARCH=haswell
       - name: Build
         run: cmake --build $bld_dir -j 2
       - name: Install

.github/workflows/release.yml

@@ -97,7 +97,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: "Get artifacts"
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
       - name: Move and rename appimage
         run: mv */*.AppImage arbor-gui.AppImage
       - name: Move and rename dmg
@@ -122,4 +122,3 @@ jobs:
           generateReleaseNotes: true
           artifacts: '*.dmg,*.AppImage,*.tar.gz'
           token: ${{ secrets.GITHUB_TOKEN }}
-

CMakeLists.txt

@@ -1,11 +1,13 @@
-cmake_minimum_required(VERSION 3.19)
+cmake_minimum_required(VERSION 3.27)
 
 find_package(Git)
 
 project(the-arbor-gui
-  VERSION 0.8.1
+  VERSION 0.11.1
   LANGUAGES C CXX)
 
+set(EXPORT_COMPILE_COMMANDS ON)
+
 set(CMAKE_CXX_STANDARD 20)
 include(GNUInstallDirs)
 
@@ -141,6 +143,7 @@ target_include_directories(imgui PRIVATE 3rd-party/imgui)
 target_include_directories(imgui PUBLIC 3rd-party/implot)
 target_include_directories(imgui PUBLIC 3rd-party/ImGuizmo/)
 target_link_libraries(imgui PRIVATE glfw)
+target_compile_definitions(arbor-gui-deps INTERFACE SPDLOG_FMT_EXTERNAL)
 
 # Get commit hashes from git and inject into config
 execute_process(COMMAND ${GIT_EXECUTABLE} -C ${PROJECT_SOURCE_DIR} describe --always --dirty --abbrev=0

data/ball_and_stick.swc

@@ -1,2 +1,4 @@
-1 1     -3.0     0.0     0.0     3   -1
-2 1      3.0     0.0     0.0     3    1
+# SWC format: ID, Type, X, Y, Z, Radius, Parent
+1 1 0.0 0.0 0.0 10.0 -1  # Soma
+2 3 0.0 0.0 10.0 1.0 1   # Dendrite
+3 3 0.0 0.0 20.0 1.0 2   # Dendrite

data/swc-interpretation/normal-soma-normal-dend.swc

@@ -0,0 +1,8 @@
+# id, tag,    x,      y,      z, radius, parent
+1    1  -3.0     0.0     0.0     3.0     -1
+2    1  -3.0     0.0     3.0     3.0      1
+3    3  -3.0   -6.0     0.0     3.0       1
+4    3  -3.0   -9.0     0.0     3.0       3
+5    2  -3.0    6.0     0.0     3.0       1
+6    2  -3.0   12.0     0.0     3.0       5
+7    2  -3.0   18.0     0.0     3.0       6

data/swc-interpretation/normal-soma-single-dend.swc

@@ -0,0 +1,7 @@
+# id, tag,    x,      y,      z, radius, parent
+1    1  -3.0    0.0     0.0     3.0      -1
+2    1   3.0    0.0     0.0     3.0       1
+3    3  -3.0   -6.0     0.0     3.0       1
+4    2  -3.0    6.0     0.0     3.0       1
+5    2  -3.0   12.0     0.0     3.0       4
+6    2  -3.0   18.0     0.0     3.0       5

data/swc-interpretation/single-soma-normal-dend.swc

@@ -0,0 +1,7 @@
+# id, tag,    x,      y,      z, radius, parent
+1    1  -3.0     0.0     0.0     3.0     -1
+2    3  -3.0   -6.0     0.0     3.0       1
+3    3  -3.0   -9.0     0.0     3.0       2
+4    2  -3.0    6.0     0.0     3.0       1
+5    2  -3.0   12.0     0.0     3.0       4
+6    2  -3.0   18.0     0.0     3.0       5

data/swc-interpretation/single-soma-single-dend.swc

@@ -0,0 +1,6 @@
+# id, tag,    x,      y,      z, radius, parent
+1    1  -3.0    0.0     0.0     3.0     -1
+2    3  -3.0   -6.0     0.0     3.0       1
+3    2  -3.0    6.0     0.0     3.0       1
+4    2  -3.0   12.0     0.0     3.0       3
+5    2  -3.0   18.0     0.0     3.0       4

default.ini

@@ -10,43 +10,43 @@ Collapsed=0
 
 [Window][ Locations]
 Pos=0,24
-Size=339,696
+Size=338,696
 Collapsed=0
 DockId=0x00000001,0
 
 [Window][Cell]
-Pos=341,24
-Size=939,559
+Pos=340,24
+Size=940,559
 Collapsed=0
-DockId=0x00000003,0
+DockId=0x00000002,0
 
 [Window][Traces]
-Pos=341,24
-Size=939,559
+Pos=340,24
+Size=940,559
 Collapsed=0
-DockId=0x00000003,1
+DockId=0x00000002,1
 
 [Window][ Morphology##info]
-Pos=341,585
-Size=480,135
+Pos=340,585
+Size=603,135
 Collapsed=0
-DockId=0x00000005,0
+DockId=0x00000004,0
 
 [Window][ Locations##info]
-Pos=823,585
-Size=457,135
+Pos=945,585
+Size=335,135
 Collapsed=0
-DockId=0x00000006,0
+DockId=0x00000005,0
 
 [Window][ Parameters]
 Pos=0,24
-Size=339,696
+Size=338,696
 Collapsed=0
 DockId=0x00000001,1
 
 [Window][ Simulation]
 Pos=0,24
-Size=339,696
+Size=338,696
 Collapsed=0
 DockId=0x00000001,2
 
@@ -66,11 +66,12 @@ Size=758,446
 Collapsed=0
 
 [Docking][Data]
-DockSpace       ID=0x3BC79352 Window=0x4647B76E Pos=0,24 Size=1280,696 Split=X Selected=0xBF700C0A
-  DockNode      ID=0x00000001 Parent=0x3BC79352 SizeRef=339,696 CentralNode=1 Selected=0xBF700C0A
-  DockNode      ID=0x00000002 Parent=0x3BC79352 SizeRef=939,696 Split=Y Selected=0x90C8F40C
-    DockNode    ID=0x00000003 Parent=0x00000002 SizeRef=939,559 Selected=0x65F68FF8
-    DockNode    ID=0x00000004 Parent=0x00000002 SizeRef=939,135 Split=X Selected=0xAB9526FD
-      DockNode  ID=0x00000005 Parent=0x00000004 SizeRef=480,135 Selected=0x93CAA630
-      DockNode  ID=0x00000006 Parent=0x00000004 SizeRef=457,135 Selected=0xAB9526FD
+DockSpace       ID=0x3BC79352 Pos=0,24 Size=1280,696 CentralNode=1 Selected=0xBF700C0A
+DockSpace       ID=0xC0DFADC4 Window=0xD0388BC8 Pos=0,24 Size=1280,696 Split=X Selected=0x9FA67BE9
+  DockNode      ID=0x00000001 Parent=0xC0DFADC4 SizeRef=338,696 Selected=0xBB245857
+  DockNode      ID=0x00000006 Parent=0xC0DFADC4 SizeRef=940,696 Split=Y
+    DockNode    ID=0x00000002 Parent=0x00000006 SizeRef=1280,559 CentralNode=1 Selected=0x47506C1A
+    DockNode    ID=0x00000003 Parent=0x00000006 SizeRef=1280,135 Split=X Selected=0x29E5A105
+      DockNode  ID=0x00000004 Parent=0x00000003 SizeRef=821,135 Selected=0x29E5A105
+      DockNode  ID=0x00000005 Parent=0x00000003 SizeRef=457,135 Selected=0x655FAFBA
 

src/geometry.cpp

@@ -699,12 +699,14 @@ void geometry::load_geometry(const arb::morphology& morph, bool reset) {
             branch_to_ids[branch].emplace_back(lo, hi);
         }
     }
+    log_info("Loaded {} segments and {} branches", segments.size(), morph.num_branches());
 
     log_info("Making geometry");
     if (segments.empty()) {
         log_info("Empty geometry");
         return;
     }
+
     root = {(float) segments[0].prox.x, (float) segments[0].prox.y, (float) segments[0].prox.z};
     log_debug("New root x={} y={} z={}", root.x, root.y, root.z);
     {
@@ -724,6 +726,7 @@ void geometry::load_geometry(const arb::morphology& morph, bool reset) {
     }
     log_debug("Frustra generated: {} ({} points)", indices.size()/n_indices, vertices.size());
 
+
     {
         // Re-scale into [-1, 1]^3 box
         rescale = ax.scale;