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vc_render_tifxyz: provide voxel size scale to ome-zarr #804

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2417b6f
vc_render_tifxyz: provide voxel size scale to ome-zarr
jrudolph Apr 1, 2026
c2a2afc
vc_render_tifxyz: resurrect anisotropic scaling
jrudolph Apr 1, 2026
afaebb6
vc_render_tifxyz: fail when merge-tiff step failed
jrudolph Apr 2, 2026
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60 changes: 57 additions & 3 deletions volume-cartographer/apps/src/vc_render_tifxyz.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
#include <chrono>
#include <cstdarg>
#include <thread>
#include <optional>
#include <unordered_set>
#include <tiffio.h>
#include <omp.h>
Expand Down Expand Up @@ -1054,6 +1055,34 @@ static void renderTiles(
}


// ============================================================
// readVolumeVoxelSize – read voxelsize from volume metadata
// ============================================================

static std::optional<double> readVolumeVoxelSize(const std::filesystem::path& volPath)
{
using json = nlohmann::json;
auto tryFile = [](const std::filesystem::path& p, const char* key) -> std::optional<double> {
if (!std::filesystem::exists(p)) return std::nullopt;
try {
auto j = json::parse(std::ifstream(p));
if (key) {
if (j.contains(key) && j[key].is_object())
j = j[key];
else
return std::nullopt;
}
if (j.contains("voxelsize") && j["voxelsize"].is_number())
return j["voxelsize"].get<double>();
} catch (...) {}
return std::nullopt;
};
if (auto v = tryFile(volPath / "meta.json", nullptr)) return v;
if (auto v = tryFile(volPath / "metadata.json", "scan")) return v;
if (auto v = tryFile(volPath / "metadata.json", nullptr)) return v;
return std::nullopt;
}

// ============================================================
// main
// ============================================================
Expand Down Expand Up @@ -1111,7 +1140,9 @@ int main(int argc, char *argv[])
("merge-tiff-parts", po::bool_switch()->default_value(false), "Merge partial TIFFs from multi-VM render")
("pyramid", po::value<bool>()->default_value(true), "Build pyramid levels L1-L5 (default: true)")
("resume", po::bool_switch()->default_value(false), "Skip chunks that already exist on disk")
("pre", po::bool_switch()->default_value(false), "Create zarr + all level datasets");
("pre", po::bool_switch()->default_value(false), "Create zarr + all level datasets")
("voxel-size", po::value<double>(), "Physical voxel size for OME-Zarr scale metadata (reads from volume metadata if omitted)")
("voxel-unit", po::value<std::string>()->default_value("nanometer"), "Physical unit for OME-Zarr axes (e.g. nanometer, micrometer)");
// clang-format on

po::options_description all("Usage");
Expand Down Expand Up @@ -1357,6 +1388,27 @@ int main(int argc, char *argv[])
logPrintf(stdout, "chunk shape [%s]\n", oss.str().c_str());
}

// --- Resolve voxel size for OME-Zarr metadata ---
const std::string voxel_unit = parsed["voxel-unit"].as<std::string>();
double base_voxel_size = 1.0;
if (parsed.count("voxel-size")) {
base_voxel_size = parsed["voxel-size"].as<double>();
if (!std::isfinite(base_voxel_size) || base_voxel_size <= 0.0) {
logPrintf(stderr, "Error: --voxel-size must be a positive finite number\n");
return EXIT_FAILURE;
}
logPrintf(stdout, "Voxel size (from CLI): %g %s\n", base_voxel_size, voxel_unit.c_str());
} else if (auto mv = readVolumeVoxelSize(vol_path); mv.has_value()) {
if (std::isfinite(*mv) && *mv > 0.0) {
base_voxel_size = *mv;
logPrintf(stdout, "Voxel size (from volume metadata): %g %s\n", base_voxel_size, voxel_unit.c_str());
} else {
logPrintf(stderr, "Warning: ignoring invalid metadata voxelsize; using default 1.0\n");
}
} else {
logPrintf(stdout, "Voxel size: 1.0 (no metadata found; override with --voxel-size)\n");
}

int rotQuadGlobal = -1;
if (std::abs(rotate_angle) > 1e-6) {
rotQuadGlobal = normalizeQuadrantRotation(rotate_angle);
Expand Down Expand Up @@ -1506,7 +1558,8 @@ int main(int argc, char *argv[])
cv::Size attrXY = tgt_size;
if (rotQuad >= 0 && (rotQuad % 2) == 1) std::swap(attrXY.width, attrXY.height);
writeZarrAttrs(outFilePath, vol_path, group_idx, baseZ, slice_step, accum_step,
accum_type_str, accumOffsets.size(), attrXY, baseZ, CH, CW);
accum_type_str, accumOffsets.size(), attrXY, baseZ, CH, CW,
base_voxel_size, voxel_unit);
return true;
} else if (numParts > 1) {
if (!std::filesystem::exists(std::filesystem::path(zarrOutputArg) / "0" / ".zarray")) {
Expand Down Expand Up @@ -1705,7 +1758,8 @@ int main(int argc, char *argv[])
cv::Size attrXY = tgt_size;
if (rotQuad >= 0 && (rotQuad % 2) == 1) std::swap(attrXY.width, attrXY.height);
writeZarrAttrs(outFilePath, vol_path, group_idx, baseZ, slice_step, accum_step,
accum_type_str, accumOffsets.size(), attrXY, baseZ, CH, CW);
accum_type_str, accumOffsets.size(), attrXY, baseZ, CH, CW,
base_voxel_size, voxel_unit);
}
}
return true;
Expand Down
4 changes: 3 additions & 1 deletion volume-cartographer/core/include/vc/core/util/Zarr.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,9 @@ void writeZarrAttrs(const std::filesystem::path& outFile,
const std::filesystem::path& volPath, int groupIdx,
size_t baseZ, double sliceStep, double accumStep,
const std::string& accumTypeStr, size_t accumSamples,
const cv::Size& canvasSize, size_t CZ, size_t CH, size_t CW);
const cv::Size& canvasSize, size_t CZ, size_t CH, size_t CW,
double baseVoxelSize = 1.0,
const std::string& voxelUnit = "");

// Write a dense uint8 ZYX subregion into a freshly created dataset via
// writeChunk(). Chunks overlapping the region are materialized; untouched
Expand Down
9 changes: 7 additions & 2 deletions volume-cartographer/core/src/Tiff.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -285,10 +285,11 @@ bool mergeTiffParts(const std::string& outputPath, int numParts)
}

std::cout << "Merging " << groups.size() << " TIFF(s) from " << numParts << " parts..." << std::endl;
size_t failures = 0;
for (auto& [finalPath, partFiles] : groups) {
std::sort(partFiles.begin(), partFiles.end());
TIFF* first = TIFFOpen(partFiles[0].c_str(), "r");
if (!first) { std::cerr << "Cannot open " << partFiles[0] << "\n"; continue; }
if (!first) { std::cerr << "Cannot open " << partFiles[0] << "\n"; failures++; continue; }
uint32_t w, h, tw, th; uint16_t bps, spp, sf, comp;
TIFFGetField(first, TIFFTAG_IMAGEWIDTH, &w);
TIFFGetField(first, TIFFTAG_IMAGELENGTH, &h);
Expand All @@ -301,7 +302,7 @@ bool mergeTiffParts(const std::string& outputPath, int numParts)
TIFFClose(first);

TIFF* out = TIFFOpen(finalPath.c_str(), "w");
if (!out) { std::cerr << "Cannot create " << finalPath << "\n"; continue; }
if (!out) { std::cerr << "Cannot create " << finalPath << "\n"; failures++; continue; }
TIFFSetField(out, TIFFTAG_IMAGEWIDTH, w); TIFFSetField(out, TIFFTAG_IMAGELENGTH, h);
TIFFSetField(out, TIFFTAG_TILEWIDTH, tw); TIFFSetField(out, TIFFTAG_TILELENGTH, th);
TIFFSetField(out, TIFFTAG_BITSPERSAMPLE, bps); TIFFSetField(out, TIFFTAG_SAMPLESPERPIXEL, spp);
Expand Down Expand Up @@ -330,6 +331,10 @@ bool mergeTiffParts(const std::string& outputPath, int numParts)
for (auto& pf : partFiles) std::filesystem::remove(pf);
std::cout << " " << finalPath.filename().string() << ": " << merged << " tiles from " << partFiles.size() << " parts\n";
}
if (failures > 0) {
std::cerr << "Merge failed: " << failures << " of " << groups.size() << " TIFF(s) could not be created.\n";
return false;
}
std::cout << "Merge complete.\n";
return true;
}
23 changes: 13 additions & 10 deletions volume-cartographer/core/src/Zarr.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -322,7 +322,8 @@ void createPyramidDatasets(const std::filesystem::path& outDir,

std::vector<size_t> prevShape = shape0;
for (int level = 1; level <= 5; level++) {
std::vector<size_t> shape = {(prevShape[0]+1)/2, (prevShape[1]+1)/2, (prevShape[2]+1)/2};
// Keep Z fixed and halve only Y/X at each level (anisotropic scaling).
std::vector<size_t> shape = {prevShape[0], (prevShape[1]+1)/2, (prevShape[2]+1)/2};
size_t chZ = std::min(shape[0], shape0[0]);
std::vector<size_t> chunks = {chZ, std::min(CH, shape[1]), std::min(CW, shape[2])};
vc::createZarrDataset(outDir, std::to_string(level), shape, chunks, dtype, "blosc");
Expand All @@ -338,7 +339,8 @@ void writeZarrAttrs(const std::filesystem::path& outDir,
const std::filesystem::path& volPath, int groupIdx,
size_t baseZ, double sliceStep, double accumStep,
const std::string& accumTypeStr, size_t accumSamples,
const cv::Size& canvasSize, size_t CZ, size_t CH, size_t CW)
const cv::Size& canvasSize, size_t CZ, size_t CH, size_t CW,
double baseVoxelSize, const std::string& voxelUnit)
{
json attrs;
attrs["source_zarr"] = volPath.string();
Expand All @@ -356,19 +358,20 @@ void writeZarrAttrs(const std::filesystem::path& outDir,

json ms;
ms["version"] = "0.4"; ms["name"] = "render";
ms["axes"] = json::array({
json{{"name","z"},{"type","space"}},
json{{"name","y"},{"type","space"}},
json{{"name","x"},{"type","space"}}
});
auto makeAxis = [&](const char* name) -> json {
json ax = {{"name", name}, {"type", "space"}};
if (!voxelUnit.empty()) ax["unit"] = voxelUnit;
return ax;
};
ms["axes"] = json::array({makeAxis("z"), makeAxis("y"), makeAxis("x")});
ms["datasets"] = json::array();
for (int l = 0; l <= 5; l++) {
double s = std::pow(2.0, l);
const double sz = 1.0;
const double sYX = baseVoxelSize * std::pow(2.0, l);
const double sZ = baseVoxelSize;
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@chatgpt-codex-connector chatgpt-codex-connector bot Apr 7, 2026

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P2 Badge Include slice-step in multiscale Z spacing

writeZarrAttrs now writes physical OME-Zarr scales, but it hardcodes sZ to baseVoxelSize and ignores the actual rendered slice spacing. When vc_render_tifxyz is run with --slice-step > 1, consecutive output slices are farther apart than one source voxel, so this metadata underreports Z spacing and yields incorrect physical distances/aspect ratios in downstream consumers. Because sliceStep is already passed into writeZarrAttrs, the Z scale should incorporate it (while remaining constant across pyramid levels if Z is preserved).

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ms["datasets"].push_back({
{"path", std::to_string(l)},
{"coordinateTransformations", json::array({
json{{"type","scale"},{"scale",json::array({sz,s,s})}},
json{{"type","scale"},{"scale",json::array({sZ, sYX, sYX})}},
json{{"type","translation"},{"translation",json::array({0.0,0.0,0.0})}}
})}
});
Expand Down
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