TIFFIO: Fix memmap endianness issues (#110)

.github/workflows/unit_tests.yml

@@ -96,6 +96,10 @@ jobs:
         run: |
           sudo xcode-select -s /Library/Developer/CommandLineTools
 
+      - name: Remove problematic SDKs
+        run: |
+          sudo rm -rf /Library/Developer/CommandLineTools/SDKs/MacOSX15*.sdk
+
       - name: Install dependencies
         run: |
           brew bundle

apps/src/Packager.cpp

@@ -47,6 +47,7 @@ struct VolumeInfo {
     Flip flipOption{Flip::None};
     vc::Metadata meta;
     bool compress{false};
+    bool forceWrite{false};
 };
 
 static bool DoAnalyze{true};
@@ -99,7 +100,8 @@ auto main(int argc, char* argv[]) -> int
 
     po::options_description all("Usage");
     all.add(helpOpts).add_options()(
-        "analyze", po::value<bool>()->default_value(true), "Analyze volume");
+        "analyze", po::value<bool>()->default_value(true), "Analyze volume")
+        ("force-write", "Force writing new TIFF files even if they could be copied");
     // clang-format on
 
     // Parse the command line and separate out flags for volumes
@@ -194,6 +196,7 @@ auto main(int argc, char* argv[]) -> int
     ///// Add Volumes /////
     for (const auto& v : vargs) {
         VolumeInfo info = GetVolumeInfo(v);
+        info.forceWrite = args.count("force-write") > 0;
         AddVolume(volpkg, info);
     }
 }
@@ -475,7 +478,7 @@ void AddVolume(vc::VolumePkg::Pointer& volpkg, const VolumeInfo& info)
         auto& slice = pair.second;
         // Convert or flip
         if (slice.needsConvert() || slice.needsScale() || needsFlip ||
-            info.compress) {
+            info.compress || info.forceWrite) {
             // Override slice min/max with volume min/max
             if (slice.needsScale()) {
                 slice.setScale(volMax, volMin);

core/include/vc/core/util/MemMap.hpp

@@ -9,6 +9,15 @@
 namespace volcart
 {
 
+namespace endian
+{
+/** Returns whether the system is little endian */
+auto little() -> bool;
+
+/** Returns whether the system is big endian */
+auto big() -> bool;
+}  // namespace endian
+
 /** @brief Memmap record */
 struct mmap_info {
     /** Whether this is a valid mapping */

core/src/MemMap.cpp

@@ -5,6 +5,14 @@
 namespace vc = volcart;
 namespace fs = vc::filesystem;
 
+auto vc::endian::little() -> bool
+{
+    constexpr int i{1};
+    return *reinterpret_cast<const char*>(&i) == 1;
+}
+
+auto vc::endian::big() -> bool { return not little(); }
+
 vc::mmap_info::operator bool() const { return addr and size > 0; }
 
 vc::auto_mmap_info::auto_mmap_info(const mmap_info& rhs) : mmap_info(rhs) {}

core/src/TIFFIO.cpp

@@ -80,6 +80,7 @@ struct TIFFHeader {
     std::uint16_t config = 0;
     std::uint64_t* stripOffsets{nullptr};
     tio::Compression compression{tio::Compression::NONE};
+    bool bigEndian{false};
 };
 
 auto ReadHeader(lt::TIFF* tif)
@@ -95,6 +96,7 @@ auto ReadHeader(lt::TIFF* tif)
     TIFFGetField(tif, TIFFTAG_COMPRESSION, &hdr.compression);
     TIFFGetField(tif, TIFFTAG_ROWSPERSTRIP, &hdr.rowsPerStrip);
     TIFFGetField(tif, TIFFTAG_STRIPOFFSETS, &hdr.stripOffsets);
+    hdr.bigEndian = lt::TIFFIsBigEndian(tif) != 0;
     return hdr;
 }
 
@@ -144,13 +146,15 @@ auto ReadImage(lt::TIFF* tif, const TIFFHeader& hdr) -> cv::Mat
 // Returns whether this TIFF file is encoded for memory mapping
 auto CanMMap(const TIFFHeader& hdr) -> bool
 {
-    auto res = hdr.config == PLANARCONFIG_CONTIG;
-    res &= hdr.type == SAMPLEFORMAT_UINT;
-    res &= hdr.depth == 16 and hdr.channels == 1;
-    res &= hdr.compression == tio::Compression::NONE;
-    // important: full image is in a single strip
-    res &= hdr.rowsPerStrip == hdr.height;
-    return res;
+    const auto isContig = hdr.config == PLANARCONFIG_CONTIG;
+    const auto isUint = hdr.type == SAMPLEFORMAT_UINT;
+    const auto is16bpc = hdr.depth == 16;
+    const auto isMono = hdr.channels == 1;
+    const auto uncompressed = hdr.compression == tio::Compression::NONE;
+    const auto singleStrip = hdr.rowsPerStrip == hdr.height;
+    const auto endianMatch = hdr.bigEndian == vc::endian::big();
+    return isContig and isUint and is16bpc and isMono and uncompressed and
+           singleStrip and endianMatch;
 }
 
 // Memory mapp the tiff