Initial commit

Signed-off-by: Filip Leonarski <filip.leonarski@psi.ch>
2023-04-06 11:06:26 +02:00
commit 1757d42182
493 changed files with 170747 additions and 0 deletions
@@ -0,0 +1,103 @@
+// Copyright (2019-2022) Paul Scherrer Institute
+// SPDX-License-Identifier: GPL-3.0-or-later
+
+#include <cstdio>
+
+#include "HDF5DataFile.h"
+#include "../compression/JFJochCompressor.h"
+
+HDF5DataFile::HDF5DataFile(const std::string &in_filename, int64_t width, int64_t height,
+                           int64_t pixel_depth_byte, bool is_signed, CompressionAlgorithm compression,
+                           size_t in_max_spots) : data_type(pixel_depth_byte, is_signed),
+                           max_spots(in_max_spots) {
+    max_image_number = 0;
+    nimages = 0;
+
+    if (max_spots > 256)
+        throw JFJochException(JFJochExceptionCategory::ArrayOutOfBounds, "Max spot count must be less than 256 for performance reasons");
+
+    filename = in_filename;
+
+    xpixel = width;
+    ypixel = height;
+
+    dcpl.SetCompression(compression, pixel_depth_byte, JFJochBitShuffleCompressor::DefaultBlockSize);
+    dcpl.SetChunking( {1, ypixel, xpixel});
+}
+
+HDF5DataFile::~HDF5DataFile() {
+    data_set.reset();
+
+    if (!spot_count.empty()) {
+        HDF5Group group(*data_file, "/entry/result");
+        group.NXClass("NXcollection");
+        std::vector<hsize_t> dims = {spot_count.size(), max_spots};
+        group.SaveVector("nPeaks", spot_count);
+        group.SaveVector("peakXPosRaw", spot_x, dims, CompressionAlgorithm::BSHUF_LZ4);
+        group.SaveVector("peakYPosRaw", spot_y, dims, CompressionAlgorithm::BSHUF_LZ4);
+        group.SaveVector("peakTotalIntensity", spot_intensity, dims, CompressionAlgorithm::BSHUF_LZ4);
+    }
+
+    data_file.reset();
+}
+
+void HDF5DataFile::CreateFile() {
+    data_file = std::make_unique<HDF5File>(filename, true,false, false);
+    HDF5Group(*data_file, "/entry").NXClass("NXentry");
+    HDF5Group(*data_file, "/entry/data").NXClass("NXdata");
+
+    HDF5DataSpace data_space({1, ypixel, xpixel},{H5S_UNLIMITED, ypixel, xpixel});
+    data_set = std::make_unique<HDF5DataSet>(*data_file, "/entry/data/data", data_type, data_space, dcpl);
+}
+
+void HDF5DataFile::WriteImage(const void *data, size_t data_size, uint64_t image_number) {
+    if (image_number > max_image_number) {
+        max_image_number = image_number;
+        data_set->SetExtent({max_image_number+1, ypixel, xpixel});
+    }
+    nimages++;
+    data_set->WriteDirectChunk(data, data_size, {image_number, 0, 0});
+}
+
+void HDF5DataFile::WriteSpots(const std::vector<SpotToSave> &spots, uint64_t image_number) {
+    std::unique_lock<std::mutex> ul(spot_mutex);
+
+    size_t cnt = std::min(spots.size(), max_spots);
+    if (spot_count.size() < image_number + 1) {
+        spot_count.resize(image_number + 1);
+        spot_x.resize(max_spots * (image_number + 1));
+        spot_y.resize(max_spots * (image_number + 1));
+        spot_intensity.resize(max_spots * (image_number + 1));
+    }
+
+    spot_count[image_number] = cnt;
+
+    for (int i = 0; i < cnt; i++) {
+        spot_x[max_spots * image_number + i] = spots[i].x;
+        spot_y[max_spots * image_number + i] = spots[i].y;
+        spot_intensity[max_spots * image_number + i] = spots[i].intensity;
+    }
+}
+
+void HDF5DataFile::Write(const void *data, size_t data_size, const std::vector<SpotToSave> &spots,
+                         uint64_t image_number) {
+    std::lock_guard<std::mutex> lock(hdf5_mutex);
+    if (!data_file)
+        CreateFile();
+
+    WriteImage(data, data_size, image_number);
+    if (!spots.empty())
+        WriteSpots(spots, image_number);
+}
+
+size_t HDF5DataFile::GetMaxImageNumber() const {
+    return max_image_number;
+}
+
+size_t HDF5DataFile::GetNumImages() const {
+    return nimages;
+}
+
+std::string HDF5DataFile::GetFilename() const {
+    return filename;
+}