Brining in changes (#93)

src/RawFile.cpp

@@ -13,9 +13,13 @@ RawFile::RawFile(const std::filesystem::path &fname, const std::string &mode)
     : m_master(fname) {
     m_mode = mode;
     if (mode == "r") {
-        find_number_of_subfiles();
-        n_subfile_parts = m_master.geometry().col * m_master.geometry().row;
+
+        n_subfiles = find_number_of_subfiles(); // f0,f1...fn
+        n_subfile_parts =
+            m_master.geometry().col * m_master.geometry().row; // d0,d1...dn
         find_geometry();
+        update_geometry_with_roi();
+
         open_subfiles();
     } else {
         throw std::runtime_error(LOCATION +
@@ -38,10 +42,20 @@ void RawFile::read_into(std::byte *image_buf, size_t n_frames) {
         image_buf += bytes_per_frame();
     }
 }
+
 void RawFile::read_into(std::byte *image_buf) {
     return get_frame_into(m_current_frame++, image_buf);
 };
 
+
+void RawFile::read_into(std::byte *image_buf, DetectorHeader *header) {
+
+    return get_frame_into(m_current_frame++, image_buf, header);
+};
+
+size_t RawFile::n_mod() const { return n_subfile_parts; }
+
+
 size_t RawFile::bytes_per_frame() {
     return m_rows * m_cols * m_master.bitdepth() / 8;
 }
@@ -71,12 +85,13 @@ xy RawFile::geometry() { return m_master.geometry(); }
 void RawFile::open_subfiles() {
     if (m_mode == "r")
         for (size_t i = 0; i != n_subfiles; ++i) {
-            auto v = std::vector<SubFile *>(n_subfile_parts);
+            auto v = std::vector<RawSubFile *>(n_subfile_parts);
             for (size_t j = 0; j != n_subfile_parts; ++j) {
-                v[j] =
-                    new SubFile(m_master.data_fname(j, i),
-                                m_master.detector_type(), m_master.pixels_y(),
-                                m_master.pixels_x(), m_master.bitdepth());
+                auto pos = m_module_pixel_0[j];
+                v[j] = new RawSubFile(m_master.data_fname(j, i),
+                                      m_master.detector_type(), pos.height,
+                                      pos.width, m_master.bitdepth());
+
             }
             subfiles.push_back(v);
         }
@@ -107,27 +122,36 @@ bool RawFile::is_master_file(const std::filesystem::path &fpath) {
     return stem.find("_master_") != std::string::npos;
 }
 
-void RawFile::find_number_of_subfiles() {
-    int n_mod = 0;
-    while (std::filesystem::exists(m_master.data_fname(0, ++n_mod)))
-        ;
-    n_subfiles = n_mod;
-    #ifdef AARE_VERBOSE
-    fmt::print("Found: {} subfiles\n", n_subfiles);
-    #endif
+int RawFile::find_number_of_subfiles() {
+    int n_files = 0;
+    // f0,f1...fn How many files is the data split into?
+    while (std::filesystem::exists(m_master.data_fname(0, n_files)))
+        n_files++; // increment after test
+
+#ifdef AARE_VERBOSE
+    fmt::print("Found: {} subfiles\n", n_files);
+#endif
+    return n_files;
+
 }
 
 void RawFile::find_geometry() {
     uint16_t r{};
     uint16_t c{};
-    for (size_t i = 0; i < n_subfile_parts; i++) {
-        for (size_t j = 0; j != n_subfiles; ++j) {
-            auto h = this->read_header(m_master.data_fname(i, j));
-            r = std::max(r, h.row);
-            c = std::max(c, h.column);
 
-            positions.push_back({h.row, h.column});
-        }
+
+    for (size_t i = 0; i < n_subfile_parts; i++) {
+        auto h = this->read_header(m_master.data_fname(i, 0));
+        r = std::max(r, h.row);
+        c = std::max(c, h.column);
+        positions.push_back({h.row, h.column});
+        ModuleGeometry g;
+        g.x = h.column * m_master.pixels_x();
+        g.y = h.row * m_master.pixels_y();
+        g.width = m_master.pixels_x();
+        g.height = m_master.pixels_y();
+        m_module_pixel_0.push_back(g);
+
     }
 
     r++;
@@ -137,6 +161,81 @@ void RawFile::find_geometry() {
     m_cols = (c * m_master.pixels_x());
 
     m_rows += static_cast<size_t>((r - 1) * cfg.module_gap_row);
+
+#ifdef AARE_VERBOSE
+    fmt::print("\nRawFile::find_geometry()\n");
+    for (size_t i = 0; i < m_module_pixel_0.size(); i++) {
+        fmt::print("Module {} at position: (r:{},c:{})\n", i,
+                   m_module_pixel_0[i].y, m_module_pixel_0[i].x);
+    }
+    fmt::print("Image size: {}x{}\n\n", m_rows, m_cols);
+#endif
+}
+
+void RawFile::update_geometry_with_roi() {
+    // TODO! implement this
+    if (m_master.roi()) {
+        auto roi = m_master.roi().value();
+
+        // TODO! can we do this cleaner?
+        int pos_y = 0;
+        int pos_y_increment = 0;
+        for (size_t row = 0; row < m_master.geometry().row; row++) {
+            int pos_x = 0;
+            for (size_t col = 0; col < m_master.geometry().col; col++) {
+                auto &m = m_module_pixel_0[row * m_master.geometry().col + col];
+                auto original_height = m.height;
+                auto original_width = m.width;
+
+                // module is to the left of the roi
+                if (m.x + m.width < roi.xmin) {
+                    m.width = 0;
+
+                    // roi is in module
+                } else {
+                    // here we only arrive when the roi is in or to the left of
+                    // the module
+                    if (roi.xmin > m.x) {
+                        m.width -= roi.xmin - m.x;
+                    }
+                    if (roi.xmax < m.x + m.width) {
+                        m.width -= m.x + original_width - roi.xmax;
+                    }
+                    m.x = pos_x;
+                    pos_x += m.width;
+                }
+
+                if (m.y + m.height < roi.ymin) {
+                    m.height = 0;
+                } else {
+                    if (roi.ymin < m.y + m.height) {
+                        m.height -= roi.ymin;
+                    }
+                    if (roi.ymax < m.y + m.height) {
+                        m.height -= m.y + original_height - roi.ymax;
+                    }
+                    m.y = pos_y;
+                    pos_y_increment = m.height;
+                }
+            }
+            // increment pos_y
+            pos_y += pos_y_increment;
+        }
+
+        m_rows = roi.height();
+        m_cols = roi.width();
+    }
+
+#ifdef AARE_VERBOSE
+    fmt::print("RawFile::update_geometry_with_roi()\n");
+    for (const auto &m : m_module_pixel_0) {
+        fmt::print("Module at position: (r:{}, c:{}, h:{}, w:{})\n", m.y, m.x,
+                   m.height, m.width);
+    }
+    fmt::print("Updated image size: {}x{}\n\n", m_rows, m_cols);
+    fmt::print("\n");
+#endif
+
 }
 
 Frame RawFile::get_frame(size_t frame_index) {
@@ -146,13 +245,22 @@ Frame RawFile::get_frame(size_t frame_index) {
     return f;
 }
 
-void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer) {
+
+size_t RawFile::bytes_per_pixel() const {
+    return m_master.bitdepth() / 8;
+}
+
+void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, DetectorHeader *header) {
+
     if (frame_index > total_frames()) {
         throw std::runtime_error(LOCATION + "Frame number out of range");
     }
     std::vector<size_t> frame_numbers(n_subfile_parts);
     std::vector<size_t> frame_indices(n_subfile_parts, frame_index);
 
+
+    // sync the frame numbers
+
     if (n_subfile_parts != 1) {
         for (size_t part_idx = 0; part_idx != n_subfile_parts; ++part_idx) {
             auto subfile_id = frame_index / m_master.max_frames_per_file();
@@ -189,15 +297,25 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer) {
         for (size_t part_idx = 0; part_idx != n_subfile_parts; ++part_idx) {
             auto corrected_idx = frame_indices[part_idx];
             auto subfile_id = corrected_idx / m_master.max_frames_per_file();
-            auto part_offset = subfiles[subfile_id][part_idx]->bytes_per_part();
-            subfiles[subfile_id][part_idx]->get_part(
-                frame_buffer + part_idx * part_offset,
-                corrected_idx % m_master.max_frames_per_file());
+
+            // This is where we start writing
+            auto offset = (m_module_pixel_0[part_idx].y * m_cols +
+                          m_module_pixel_0[part_idx].x)*m_master.bitdepth()/8;
+
+            if (m_module_pixel_0[part_idx].x!=0)
+                throw std::runtime_error(LOCATION + "Implementation error. x pos not 0.");
+
+            subfiles[subfile_id][part_idx]->seek(corrected_idx % m_master.max_frames_per_file());
+            subfiles[subfile_id][part_idx]->read_into(frame_buffer + offset, header);
+            if (header)
+                ++header;
         }
 
     } else {
+        //TODO! should we read row by row?
+
+        // create a buffer large enough to hold a full module
 
-        // create a buffer that will hold a the frame part
         auto bytes_per_part = m_master.pixels_y() * m_master.pixels_x() *
                               m_master.bitdepth() /
                               8; // TODO! replace with image_size_in_bytes
@@ -207,23 +325,27 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer) {
         // level
 
         for (size_t part_idx = 0; part_idx != n_subfile_parts; ++part_idx) {
+            auto pos = m_module_pixel_0[part_idx];
             auto corrected_idx = frame_indices[part_idx];
             auto subfile_id = corrected_idx / m_master.max_frames_per_file();
 
-            subfiles[subfile_id][part_idx]->get_part(
-                part_buffer, corrected_idx % m_master.max_frames_per_file());
-            for (size_t cur_row = 0; cur_row < (m_master.pixels_y());
+            subfiles[subfile_id][part_idx]->seek(corrected_idx % m_master.max_frames_per_file());
+            subfiles[subfile_id][part_idx]->read_into(part_buffer, header);
+            if(header)
+                ++header;
+
+            for (size_t cur_row = 0; cur_row < (pos.height);
                  cur_row++) {
-                auto irow = cur_row + (part_idx / m_master.geometry().col) *
-                                          m_master.pixels_y();
-                auto icol =
-                    (part_idx % m_master.geometry().col) * m_master.pixels_x();
+
+                auto irow = (pos.y + cur_row);
+                auto icol = pos.x;
                 auto dest = (irow * this->m_cols + icol);
                 dest = dest * m_master.bitdepth() / 8;
                 memcpy(frame_buffer + dest,
-                       part_buffer + cur_row * m_master.pixels_x() *
+                       part_buffer + cur_row * pos.width *
                                          m_master.bitdepth() / 8,
-                       m_master.pixels_x() * m_master.bitdepth() / 8);
+                       pos.width * m_master.bitdepth() / 8);
+
             }
         }
         delete[] part_buffer;

src/RawMasterFile.cpp

@@ -143,6 +143,10 @@ ScanParameters RawMasterFile::scan_parameters() const {
     return m_scan_parameters;
 }
 
+
+std::optional<ROI> RawMasterFile::roi() const { return m_roi; }
+
+
 void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
     std::ifstream ifs(fpath);
     json j;
@@ -240,6 +244,40 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
         // not a scan
     }
 
+
+    try{
+        ROI tmp_roi;
+        auto obj = j.at("Receiver Roi");
+        tmp_roi.xmin = obj.at("xmin");
+        tmp_roi.xmax = obj.at("xmax");
+        tmp_roi.ymin = obj.at("ymin");
+        tmp_roi.ymax = obj.at("ymax");
+
+        //if any of the values are set update the roi
+        if (tmp_roi.xmin != 4294967295 || tmp_roi.xmax != 4294967295 ||
+            tmp_roi.ymin != 4294967295 || tmp_roi.ymax != 4294967295) {
+            
+            if(v<7.21){
+                tmp_roi.xmax++;
+                tmp_roi.ymax++;
+            }
+            
+            m_roi = tmp_roi;
+        }
+
+
+    }catch (const json::out_of_range &e) {
+        // leave the optional empty
+    }
+
+    //if we have an roi we need to update the geometry for the subfiles
+    if (m_roi){
+
+    }
+
+
+
+
     // Update detector type for Moench
     // TODO! How does this work with old .raw master files?
     #ifdef AARE_VERBOSE

src/RawSubFile.cpp

@@ -0,0 +1,97 @@
+#include "aare/RawSubFile.hpp"
+#include "aare/PixelMap.hpp"
+#include <cstring> // memcpy
+#include <fmt/core.h>
+#include <iostream>
+
+namespace aare {
+
+RawSubFile::RawSubFile(const std::filesystem::path &fname,
+                       DetectorType detector, size_t rows, size_t cols,
+                       size_t bitdepth)
+    : m_bitdepth(bitdepth), m_fname(fname), m_rows(rows), m_cols(cols),
+      m_detector_type(detector),
+      m_bytes_per_frame((m_bitdepth / 8) * m_rows * m_cols) {
+    if (m_detector_type == DetectorType::Moench03_old) {
+        pixel_map = GenerateMoench03PixelMap();
+    }
+
+    if (std::filesystem::exists(fname)) {
+        n_frames = std::filesystem::file_size(fname) /
+                   (sizeof(DetectorHeader) + rows * cols * bitdepth / 8);
+    } else {
+        throw std::runtime_error(
+            LOCATION + fmt::format("File {} does not exist", m_fname.string()));
+    }
+
+    // fp = fopen(m_fname.string().c_str(), "rb");
+    m_file.open(m_fname, std::ios::binary);
+    if (!m_file.is_open()) {
+        throw std::runtime_error(
+            LOCATION + fmt::format("Could not open file {}", m_fname.string()));
+    }
+
+#ifdef AARE_VERBOSE
+    fmt::print("Opened file: {} with {} frames\n", m_fname.string(), n_frames);
+    fmt::print("m_rows: {}, m_cols: {}, m_bitdepth: {}\n", m_rows, m_cols,
+               m_bitdepth);
+    fmt::print("file size: {}\n", std::filesystem::file_size(fname));
+#endif
+}
+
+void RawSubFile::seek(size_t frame_index) {
+    if (frame_index >= n_frames) {
+        throw std::runtime_error("Frame number out of range");
+    }
+    m_file.seekg((sizeof(DetectorHeader) + bytes_per_frame()) * frame_index);
+}
+
+size_t RawSubFile::tell() {
+    return m_file.tellg() / (sizeof(DetectorHeader) + bytes_per_frame());
+}
+
+
+void RawSubFile::read_into(std::byte *image_buf, DetectorHeader *header) {
+    if(header){
+         m_file.read(reinterpret_cast<char *>(header), sizeof(DetectorHeader));
+    } else {
+        m_file.seekg(sizeof(DetectorHeader), std::ios::cur);
+    }
+
+    //TODO! expand support for different bitdepths
+    if(pixel_map){
+        // read into a temporary buffer and then copy the data to the buffer
+        // in the correct order
+        // currently this only supports 16 bit data!
+        auto part_buffer = new std::byte[bytes_per_frame()];
+        m_file.read(reinterpret_cast<char *>(part_buffer), bytes_per_frame());
+        auto *data = reinterpret_cast<uint16_t *>(image_buf);
+        auto *part_data = reinterpret_cast<uint16_t *>(part_buffer);
+        for (size_t i = 0; i < pixels_per_frame(); i++) {
+            data[i] = part_data[(*pixel_map)(i)];
+        }
+        delete[] part_buffer;
+    } else {
+        // read directly into the buffer
+        m_file.read(reinterpret_cast<char *>(image_buf), bytes_per_frame());
+    }
+}
+
+size_t RawSubFile::rows() const { return m_rows; }
+size_t RawSubFile::cols() const { return m_cols; }
+
+
+void RawSubFile::get_part(std::byte *buffer, size_t frame_index) {
+    seek(frame_index);
+    read_into(buffer, nullptr);
+}
+
+size_t RawSubFile::frame_number(size_t frame_index) {
+    seek(frame_index);
+    DetectorHeader h{};
+    m_file.read(reinterpret_cast<char *>(&h), sizeof(DetectorHeader));
+    return h.frameNumber;
+}
+
+
+} // namespace aare

src/defs.cpp

@@ -2,8 +2,18 @@
 #include <stdexcept>
 #include <string>
 
+#include <fmt/core.h>
 namespace aare {
 
+
+void assert_failed(const std::string &msg)
+ {
+    fmt::print(msg);
+    exit(1);
+}
+
+
+
 /**
  * @brief Convert a DetectorType to a string
  * @param type DetectorType