Feature/corechanges logging

.github/presets/common.json

@@ -6,7 +6,7 @@
       "name": "common",
       "displayName": "Modules GHA",
       "cacheVariables": {
-        "VCPKG_MANIFEST_FEATURES" : "python;qt;graphviz;openmesh;nanovg;vtk;ttk;ezc3d",
+        "VCPKG_MANIFEST_FEATURES" : "python;qt;graphviz;openmesh;nanovg;vtk;ttk;ezc3d;dicom",
         "VCPKG_INSTALL_OPTIONS": "--clean-after-build;--x-abi-tools-use-exact-versions",
 
         "CMAKE_CXX_SCAN_FOR_MODULES": "OFF",

.github/presets/linux.json

@@ -30,7 +30,7 @@
         "IVW_TEST_UNIT_TESTS": { "type": "BOOL", "value": "OFF"},
 
         "$comment": "The vcpkg graphvis package file in static mode",
-        "VCPKG_MANIFEST_FEATURES" : "python;qt;openmesh;nanovg;vtk;ttk;ezc3d",
+        "VCPKG_MANIFEST_FEATURES" : "python;qt;openmesh;nanovg;vtk;ttk;ezc3d;dicom",
         "IVW_MODULE_GRAPHVIZ":      { "type": "BOOL", "value": "OFF"},
         "IVW_MODULE_PYTHONTOOLS":   { "type": "BOOL", "value": "OFF"}
       }

.github/presets/macos.json

@@ -24,7 +24,7 @@
         "IVW_TEST_UNIT_TESTS": { "type": "BOOL", "value": "OFF"},
 
         "$comment1": "The vcpkg graphvis package file in static mode",
-        "VCPKG_MANIFEST_FEATURES" : "python;qt;openmesh;nanovg;vtk;ttk;ezc3d",
+        "VCPKG_MANIFEST_FEATURES" : "python;qt;openmesh;nanovg;vtk;ttk;ezc3d;dicom",
         "IVW_MODULE_GRAPHVIZ":      { "type": "BOOL", "value": "OFF"},
 
         "$comment2": " Assimp and nanovg both implement stb_image in their static libs causing linker issues",

.github/presets/windows.json

@@ -12,7 +12,7 @@
         "IVW_CFG_USE_CCACHE_MSVC": "ON",
         "IVW_MODULE_SGCT": "ON",
         "IVW_APP_INVIWO_DOME": "ON",
-        "VCPKG_MANIFEST_FEATURES": "python;qt;sgct;graphviz;openmesh;nanovg;vtk;ttk;ezc3d"
+        "VCPKG_MANIFEST_FEATURES": "python;qt;sgct;graphviz;openmesh;nanovg;vtk;ttk;ezc3d;dicom"
       }
     },
     {
@@ -27,7 +27,7 @@
         "IVW_TEST_UNIT_TESTS": { "type": "BOOL", "value": "OFF"},
 
         "$comment1": "The vcpkg graphvis package file in static mode",
-        "VCPKG_MANIFEST_FEATURES" : "python;qt;sgct;openmesh;nanovg;vtk;ttk;ezc3d",
+        "VCPKG_MANIFEST_FEATURES" : "python;qt;sgct;openmesh;nanovg;vtk;ttk;ezc3d;dicom",
         "IVW_MODULE_GRAPHVIZ":      { "type": "BOOL", "value": "OFF"},
 
         "$comment": "Linker issues with STB being defined in both nanovgutils and sgct",

.github/workflows/modules.yml

@@ -510,7 +510,7 @@ jobs:
         -DIVW_MODULE_WEBBROWSER=ON
         -DIVW_MODULE_SGCT=ON
         -DIVW_APP_INVIWO_DOME=ON
-        -DVCPKG_MANIFEST_FEATURES="python;qt;sgct;graphviz;openmesh;nanovg;vtk;ttk;ezc3d"
+        -DVCPKG_MANIFEST_FEATURES="python;qt;sgct;graphviz;openmesh;nanovg;vtk;ttk;ezc3d;dicom"
 
     - name: "Run clang-tidy"
       uses: cpp-linter/cpp-linter-action@v2.16.7

medvis/dicom/CMakeLists.txt

@@ -31,7 +31,7 @@ ivw_group("Source Files" ${SOURCE_FILES})
 ivw_create_module(${SOURCE_FILES} ${HEADER_FILES})
 
 find_package(TIFF REQUIRED)
-find_package(gdcm CONFIG REQUIRED)
+find_package(GDCM CONFIG REQUIRED)
 
 target_link_libraries(inviwo-module-dicom 
     PUBLIC 
@@ -48,8 +48,8 @@ target_link_libraries(inviwo-module-dicom
     PRIVATE
     TIFF::TIFF
 )
-target_include_directories(inviwo-module-dicom PUBLIC gdcm)
-ivw_vcpkg_install(gdcm MODULE DICOM)
+target_include_directories(inviwo-module-dicom PUBLIC GDCM)
+ivw_vcpkg_install(GDCM MODULE DICOM)
 
 #--------------------------------------------------------------------
 ivw_make_package(InviwoDICOMModule inviwo-module-dicom)

medvis/dicom/depends.cmake

@@ -2,3 +2,4 @@
 # Dependencies for current module
 set(dependencies
 )
+set(EnableByDefault ON)

medvis/dicom/src/datastructures/dicomdirtypes.cpp

@@ -185,20 +185,19 @@ void Series::updateImageInformation(const std::filesystem::path& dicompath) {
     auto sanityCheck = [&](const ImageMetaData& ref, const ImageMetaData& img) {
         if (ref.dims != img.dims) {
             throw DataReaderException(
-                fmt::format(
-                    "image sizes differ in DICOM series '{}', expected {} but found {} ('{}')",
-                    desc, toString(ref.dims), toString(img.dims), dicompath),
-                IVW_CONTEXT);
+                SourceContext{},
+                "image sizes differ in DICOM series '{}', expected {} but found {} ('{}')", desc,
+                toString(ref.dims), toString(img.dims), dicompath);
         }
         if (ref.pixelformat != img.pixelformat) {
-            throw DataReaderException(
-                fmt::format("pixel formats differ in DICOM series '{}' ('{}')", desc, dicompath),
-                IVW_CONTEXT);
+            throw DataReaderException(SourceContext{},
+                                      "pixel formats differ in DICOM series '{}' ('{}')", desc,
+                                      dicompath);
         }
         if (!ref.photometric.IsSameColorSpace(img.photometric)) {
-            throw DataReaderException(
-                fmt::format("photometric info differ in DICOM series '{}' ('{}')", desc, dicompath),
-                IVW_CONTEXT);
+            throw DataReaderException(SourceContext{},
+                                      "photometric info differ in DICOM series '{}' ('{}')", desc,
+                                      dicompath);
         }
         const double dicomDelta = 1.0e-4;
         if (std::abs(ref.slope - img.slope) > dicomDelta ||
@@ -232,10 +231,9 @@ void Series::updateImageInformation(const std::filesystem::path& dicompath) {
             continue;
         }
         if (!imageReader.Read()) {
-            throw DataReaderException(
-                fmt::format("could not read image '{}' in DICOM series '{}' ('{}')", imgInfo.path,
-                            desc, dicompath),
-                IVW_CONTEXT);
+            throw DataReaderException(SourceContext{},
+                                      "could not read image '{}' in DICOM series '{}' ('{}')",
+                                      imgInfo.path, desc, dicompath);
         }
 
         imgInfo.updateInfo(imageReader);
@@ -249,19 +247,17 @@ void Series::updateImageInformation(const std::filesystem::path& dicompath) {
     }
 
     if (warnSlopeIntercept) {
-        LogWarn(
-            fmt::format("varying slopes/intercepts in DICOM series '{}' ('{}')", desc, dicompath));
+        log::warn("varying slopes/intercepts in DICOM series '{}' ('{}')", desc, dicompath);
     }
     if (warnPixelSpacing) {
-        LogWarn(fmt::format("pixel spacings differ in DICOM series '{}', expected {} ('{}')", desc,
-                            toString(refImage.pixelSpacing), dicompath));
+        log::warn("pixel spacings differ in DICOM series '{}', expected {} ('{}')", desc,
+                  toString(refImage.pixelSpacing), dicompath);
     }
     if (warnOrientation) {
-        LogWarn(
-            fmt::format("image orientations differ in DICOM series '{}' ('{}')", desc, dicompath));
+        log::warn("image orientations differ in DICOM series '{}' ('{}')", desc, dicompath);
     }
     if (warnOrigin) {
-        LogWarn(fmt::format("origins differ in DICOM series '{}' ('{}')", desc, dicompath));
+        log::warn("origins differ in DICOM series '{}' ('{}')", desc, dicompath);
     }
 
     util::erase_remove_if(images, [](dicomdir::Image& image) { return image.empty(); });

medvis/dicom/src/errorlogging.cpp

@@ -32,7 +32,6 @@
 
 #include <string>
 #include <exception>
-#include <ios>
 #include <streambuf>
 #include <ostream>
 #include <iostream>
@@ -78,21 +77,20 @@ class StreambufLineout : public std::streambuf {
             if (ch == '\n') {
                 if (!buffer.empty()) {
                     // at the end of a line we want to pass the message to Inviwo's logging system
-                    inviwo::LogCentral::getPtr()->log("Gdcm Volume Importer", loglevel,
-                                                      LogAudience::User, "<GDCM library>", "", 0,
-                                                      buffer);
+                    LogCentral::getPtr()->log("Gdcm Volume Importer", loglevel, LogAudience::User,
+                                              "<GDCM library>", "", 0, buffer);
                 }
                 buffer.clear();
             } else if (!Traits::eq_int_type(ch, Traits::eof())) {
                 buffer.push_back(static_cast<CharT>(ch));
             }
-        } catch (std::exception& ex) {
+        } catch (const std::exception& ex) {
             // error while logging, print what we've got so far
-            inviwo::LogCentral::getPtr()->log("Gdcm Volume Importer", loglevel, LogAudience::User,
-                                              "<GDCM library>", "", 0, buffer);
+            LogCentral::getPtr()->log("Gdcm Volume Importer", loglevel, LogAudience::User,
+                                      "<GDCM library>", "", 0, buffer);
             buffer.clear();
-            // and tell the user what hargspened
-            LogError("Exception while logging Gdcm: " << ex.what());
+            // and tell the user what happened
+            log::error("Exception while logging Gdcm: {}", ex.what());
             // return traits::eof on failure
             return Traits::eof();
         }