Add .vscode settings

.gitignore

@@ -9,5 +9,4 @@ CMakeLists.txt.user*
 .project
 .cproject
 .*.swp
-.vscode
-.idea
+.idea

.vscode/c_cpp_properties.json

@@ -0,0 +1,17 @@
+{
+    "configurations": [
+        {
+            "name": "Linux",
+            "includePath": [
+                "${workspaceFolder}/**"
+            ],
+            "defines": [],
+            "compilerPath": "/usr/bin/clang",
+            "cStandard": "c11",
+            "cppStandard": "c++17",
+            "intelliSenseMode": "clang-x64",
+            "compileCommands": "/vol/medic01/users/as12312/Projects/MIRTK/Build/compile_commands.json"
+        }
+    ],
+    "version": 4
+}

.vscode/extensions.json

@@ -0,0 +1,14 @@
+{
+    "recommendations": [
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "ms-vscode-remote.remote-ssh",
+        "ms-vscode-remote.remote-ssh-edit",
+        "visualstudioexptteam.vscodeintellicode",
+        "ms-azuretools.vscode-docker",
+        "eamodio.gitlens",
+        "yzhang.markdown-all-in-one",
+        "shd101wyy.markdown-preview-enhanced",
+        "github.vscode-pull-request-github",
+    ]
+}

.vscode/launch.json

@@ -0,0 +1,192 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "merge-surfaces",
+            "type": "cppdbg",
+            "request": "launch",
+            "program": "${workspaceFolder}/Build/lib/tools/merge-surfaces",
+            "args": [
+                "-input", "cerebrum-rh.vtp", "cerebrum-lh.vtp",
+                "-output", "debug_merged_surfaces.vtp",
+                "-labels", "region-labels.nii.gz",
+                "-source-array", "RegionId",
+                "-tolerance", "1",
+                "-largest", "on",
+                "-dividers", "on",
+                "-snap-tolerance", "0.1",
+                "-smoothing-iterations", "10",
+                "-smoothing-lambda", "0.1",
+                "-debug",
+            ],
+            "stopAtEntry": false,
+            "cwd": "/vol/dhcp-derived-data/derived_aug20_recon07_extra_debug_surface_recon/config_antonis/temp-recon/CC00663XX12-195000",
+            "environment": [
+                //{"name": "LD_LIBRARY_PATH", "value": "${workspaceFolder}/Build/lib"},
+            ],
+            "externalConsole": false,
+            "MIMode": "gdb",
+            "setupCommands": [
+                {
+                    "description": "Enable pretty-printing for gdb",
+                    "text": "-enable-pretty-printing",
+                    "ignoreFailures": true
+                }
+            ]
+        },
+        {
+            "name": "clean-surface",
+            "type": "cppdbg",
+            "request": "launch",
+            "program": "${workspaceFolder}/Build/lib/tools/clean-surface",
+            "args": [
+                "CC01084XX13-69330/cerebrum-rh.vtp", "CC01084XX13-69330/cerebrum-rh-clean.vtp",
+                "-remove-intersections",
+                "-remove-spikes",
+                "-threads", "0",
+            ],
+            "stopAtEntry": false,
+            "cwd": "/vol/dhcp-derived-data/derived_aug20_recon07_extra_debug_surface_recon/config_dhcp/temp-recon",
+            "externalConsole": false,
+            "MIMode": "gdb",
+            "setupCommands": [
+                {
+                    "description": "Enable pretty-printing for gdb",
+                    "text": "-enable-pretty-printing",
+                    "ignoreFailures": true
+                }
+            ]
+        },
+        {
+            "name": "evaluate-surface-mesh",
+            "type": "cppdbg",
+            "request": "launch",
+            "program": "${workspaceFolder}/Build/lib/tools/evaluate-surface-mesh",
+            "args": [
+                //"CC00257XX10-84700/cerebrum-rh-2-clean.vtp", "CC00257XX10-84700/cerebrum-rh-2-clean.vtp",
+                //"CC00946XX23-26330/cerebrum-rh-2.vtp", "CC00946XX23-26330/cerebrum-rh-2-collisions.vtp",
+                "CC01084XX13-69330/cerebrum-rh-2.vtp", "CC01084XX13-69330/cerebrum-rh-2-collisions.vtp",
+                "-collisions", "0", "1", "20",
+            ],
+            "stopAtEntry": false,
+            "cwd": "/vol/dhcp-derived-data/derived_aug20_recon07_extra_debug_surface_recon/config_dhcp/temp-recon",
+            "externalConsole": false,
+            "MIMode": "gdb",
+            "setupCommands": [
+                {
+                    "description": "Enable pretty-printing for gdb",
+                    "text": "-enable-pretty-printing",
+                    "ignoreFailures": true
+                }
+            ]
+        },
+        {
+            "name": "subdivide-brain-image (CC00152AN04-65700)",
+            "type": "cppdbg",
+            "request": "launch",
+            "program": "${workspaceFolder}/Build/lib/tools/subdivide-brain-image",
+            "args": [
+                "/vol/dhcp-derived-data/derived_aug20_recon07_extra/derivatives/sub-CC00152AN04/ses-65700/anat/sub-CC00152AN04_ses-65700_drawem_all_labels.nii.gz",
+                "debug_region_labels.nii.gz",
+                "-fg", "/vol/dhcp-derived-data/derived_aug20_recon07_extra/derivatives/sub-CC00152AN04/ses-65700/anat/sub-CC00152AN04_ses-65700_brainmask_bet.nii.gz",
+                "-rh", "2", "4", "6", "8", "10", "12", "14", "16", "18", "20", "22", "24", "26", "28", "30", "32", "34", "36", "38", "40", "42", "44", "46", "50", "52", "54", "56" ,"58", "60", "62", "63", "65", "67", "69", "71", "73", "75", "77", "79", "81", "86",
+                "-lh", "1", "3", "5", "7", "9", "11", "13", "15", "17", "21", "23", "25", "27", "29", "31", "33", "35", "37", "39", "41", "43", "45", "47", "49", "51", "53", "55", "57", "59", "61", "64", "66", "68", "70", "72", "74", "76", "78", "80", "82", "87",
+                "-wm", "51..82", "1..4", "40..47", "48", "49", "50", "85..87",
+                "-gm", "5..16", "20..39",
+                "-sb", "40..47", "48", "85..87",
+                "-bs", "19",
+                "-cb", "17", "18",
+                "-bs+cb", "on",
+                "-subcortical-closing", "5",
+                "-brainstem-closing", "5",
+                "-cerebellum-closing", "5",
+                "-fill-wm-holes",
+                "-debug", "2",
+            ],
+            "stopAtEntry": false,
+            "cwd": "/vol/dhcp-derived-data/derived_aug20_recon07_extra_debug_surface_recon/config_dhcp/temp-recon/CC00152AN04-65700",
+            "externalConsole": false,
+            "MIMode": "gdb",
+            "setupCommands": [
+                {
+                    "description": "Enable pretty-printing for gdb",
+                    "text": "-enable-pretty-printing",
+                    "ignoreFailures": true
+                }
+            ]
+        },
+        {
+            "name": "subdivide-brain-image (CC00605XX11-172700)",
+            "type": "cppdbg",
+            "request": "launch",
+            "program": "${workspaceFolder}/Build/lib/tools/subdivide-brain-image",
+            "args": [
+                "/vol/dhcp-derived-data/derived_aug20_recon07_extra/derivatives/sub-CC00605XX11/ses-172700/anat/sub-CC00605XX11_ses-172700_drawem_all_labels.nii.gz",
+                "debug_region_labels.nii.gz",
+                "-fg", "/vol/dhcp-derived-data/derived_aug20_recon07_extra/derivatives/sub-CC00605XX11/ses-172700/anat/sub-CC00605XX11_ses-172700_brainmask_bet.nii.gz",
+                "-rh", "2", "4", "6", "8", "10", "12", "14", "16", "18", "20", "22", "24", "26", "28", "30", "32", "34", "36", "38", "40", "42", "44", "46", "50", "52", "54", "56" ,"58", "60", "62", "63", "65", "67", "69", "71", "73", "75", "77", "79", "81", "86",
+                "-lh", "1", "3", "5", "7", "9", "11", "13", "15", "17", "21", "23", "25", "27", "29", "31", "33", "35", "37", "39", "41", "43", "45", "47", "49", "51", "53", "55", "57", "59", "61", "64", "66", "68", "70", "72", "74", "76", "78", "80", "82", "87",
+                "-wm", "51..82", "1..4", "40..47", "48", "49", "50", "85..87",
+                "-gm", "5..16", "20..39",
+                "-sb", "40..47", "48", "85..87",
+                "-bs", "19",
+                "-cb", "17", "18",
+                "-bs+cb", "on",
+                "-subcortical-closing", "5",
+                "-brainstem-closing", "5",
+                "-cerebellum-closing", "5",
+                "-fill-wm-holes",
+                "-debug", "2",
+            ],
+            "stopAtEntry": false,
+            "cwd": "/vol/dhcp-derived-data/derived_aug20_recon07_extra_debug_surface_recon/config_dhcp/temp-recon/CC00605XX11-172700",
+            "externalConsole": false,
+            "MIMode": "gdb",
+            "setupCommands": [
+                {
+                    "description": "Enable pretty-printing for gdb",
+                    "text": "-enable-pretty-printing",
+                    "ignoreFailures": true
+                }
+            ]
+        },
+        {
+            "name": "subdivide-brain-image (CC00936XX21-11431)",
+            "type": "cppdbg",
+            "request": "launch",
+            "program": "${workspaceFolder}/Build/lib/tools/subdivide-brain-image",
+            "args": [
+                "/vol/dhcp-derived-data/derived_aug20_recon07_extra/derivatives/sub-CC00936XX21/ses-11431/anat/sub-CC00936XX21_ses-11431_drawem_all_labels.nii.gz",
+                "debug_region_labels.nii.gz",
+                "-fg", "/vol/dhcp-derived-data/derived_aug20_recon07_extra/derivatives/sub-CC00936XX21/ses-11431/anat/sub-CC00936XX21_ses-11431_brainmask_bet.nii.gz",
+                "-rh", "2", "4", "6", "8", "10", "12", "14", "16", "18", "20", "22", "24", "26", "28", "30", "32", "34", "36", "38", "40", "42", "44", "46", "50", "52", "54", "56" ,"58", "60", "62", "63", "65", "67", "69", "71", "73", "75", "77", "79", "81", "86",
+                "-lh", "1", "3", "5", "7", "9", "11", "13", "15", "17", "21", "23", "25", "27", "29", "31", "33", "35", "37", "39", "41", "43", "45", "47", "49", "51", "53", "55", "57", "59", "61", "64", "66", "68", "70", "72", "74", "76", "78", "80", "82", "87",
+                "-wm", "51..82", "1..4", "40..47", "48", "49", "50", "85..87",
+                "-gm", "5..16", "20..39",
+                "-sb", "40..47", "48", "85..87",
+                "-bs", "19",
+                "-cb", "17", "18",
+                "-bs+cb", "on",
+                "-subcortical-closing", "5",
+                "-brainstem-closing", "5",
+                "-cerebellum-closing", "5",
+                "-fill-wm-holes",
+                "-debug", "2",
+            ],
+            "stopAtEntry": false,
+            "cwd": "/vol/dhcp-derived-data/derived_aug20_recon07_extra_debug_surface_recon/config_dhcp/temp-recon/CC00936XX21-11431",
+            "externalConsole": false,
+            "MIMode": "gdb",
+            "setupCommands": [
+                {
+                    "description": "Enable pretty-printing for gdb",
+                    "text": "-enable-pretty-printing",
+                    "ignoreFailures": true
+                }
+            ]
+        },
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,58 @@
+{
+    "files.exclude": {
+        "**/__pycache__": true,
+        "**/.git": true,
+        "**/.DS_Store": true,
+        "**/.pytest_cache": true,
+        "**/*.egg-info": true,
+        ".venv": true
+    },
+    "editor.formatOnSave": false,
+    "cmake.cmakePath": "cmake",
+    "cmake.buildDirectory": "${workspaceFolder}/Build",
+    "cmake.configureArgs": [
+        "-DCMAKE_INSTALL_PREFIX=/vol/biomedic/users/as12312",
+        "-DCMAKE_BUILD_TYPE=Release",
+        "-DBUILD_SHARED_LIBS=ON",
+        "-DBUILD_APPLICATIONS=ON",
+        "-DBUILD_TESTING=OFF",
+        "-DBUILD_DOCUMENTATION=OFF",
+        "-DBUILD_CHANGELOG=OFF",
+        "-DWITH_CCACHE=ON",
+        "-DWITH_ARPACK=OFF",
+        "-DWITH_FLANN=ON",
+        "-DWITH_MATLAB=OFF",
+        "-DWITH_NiftiCLib=ON",
+        "-DWITH_PNG=ON",
+        "-DWITH_PROFILING=ON",
+        "-DWITH_TBB=ON",
+        "-DWITH_UMFPACK=OFF",
+        "-DWITH_ITK=OFF",
+        "-DWITH_VTK=ON",
+        "-DWITH_ZLIB=ON",
+        // Default modules
+        "-DMODULE_Common=ON",
+        "-DMODULE_Image=ON",
+        "-DMODULE_Numerics=ON",
+        "-DMODULE_PointSet=ON",
+        "-DMODULE_IO=ON",
+        "-DMODULE_Registration=ON",
+        "-DMODULE_Transformation=ON",
+        // External packages
+        "-DMODULE_Deformable=ON",
+        "-DMODULE_DrawEM=OFF",
+        "-DMODULE_Mapping=ON",
+        "-DMODULE_Scripting=ON",
+        "-DMODULE_Viewer=ON",
+        // Third-party libraries - If not found, set environment variables:
+        // - CMAKE_PREFIX_PATH
+        // - CMAKE_INCLUDE_PATH
+        // See also https://cmake.org/cmake/help/latest/variable/CMAKE_PREFIX_PATH.html
+    ],
+    // Add the following to your local user or remote machine settings JSON file at
+    // $HOME/.vscode-server/data/Machine/settings.json. This deprecates the automatic addition of
+    // "python.pythonPath" to this settings file such that it can be checked into version control.
+    "python.experiments.optInto": [
+        "DeprecatePythonPath - experiment",
+    ]
+}