Untangle dependencies, fix iter bug

src/cpp/interface/interface.cpp

@@ -4,6 +4,8 @@
 #include <tuple>
 #include "../reader/tsreader.h"
 #include "../reader/sequence.h"
+#include "../reader/utilities.h"
+
 namespace py = pybind11;
 using bfiocpp::Seq;
 
@@ -79,8 +81,7 @@ PYBIND11_MODULE(libbfiocpp, m) {
     .def("get_tile_depth", &bfiocpp::TsReaderCPP::GetTileDepth) 
     .def("get_channel_count", &bfiocpp::TsReaderCPP::GetChannelCount) 
     .def("get_tstep_count", &bfiocpp::TsReaderCPP::GetTstepCount) 
-    .def("get_datatype", &bfiocpp::TsReaderCPP::GetDataType) 
-    .def("get_ome_xml_metadata", &bfiocpp::TsReaderCPP::GetOmeXml)
+    .def("get_datatype", &bfiocpp::TsReaderCPP::GetDataType)
     .def("get_tile_coordinate",
         [](bfiocpp::TsReaderCPP& tl, std::int64_t y_start, std::int64_t x_start, std::int64_t row_stride, std::int64_t col_stride) { 
             auto row_index = static_cast<std::int64_t>(y_start/row_stride);
@@ -113,4 +114,6 @@ PYBIND11_MODULE(libbfiocpp, m) {
         .value("OmeTiff", bfiocpp::FileType::OmeTiff)
         .value("OmeZarr", bfiocpp::FileType::OmeZarr)
         .export_values();
+
+    m.def("get_ome_xml", &bfiocpp::GetOmeXml);
 }

src/cpp/reader/tsreader.cpp

@@ -9,7 +9,6 @@
 #include "tsreader.h"
 #include "utilities.h"
 #include "type_info.h"
-#include <tiffio.h>
 
 
 using ::tensorstore::internal_zarr::ChooseBaseDType;
@@ -185,32 +184,19 @@ std::shared_ptr<image_data> TsReaderCPP::GetImageData(const Seq& rows, const Seq
     }
 } 
 
-std::string TsReaderCPP::GetOmeXml() const{
-    TIFF *tiff_file = TIFFOpen(_filename.c_str(), "r");
-    std::string OmeXmlInfo{""};
-    if (tiff_file != nullptr) {
-        char* infobuf;        
-        TIFFGetField(tiff_file, TIFFTAG_IMAGEDESCRIPTION , &infobuf);
-        if (strlen(infobuf)>0){
-            OmeXmlInfo = std::string(infobuf);
-        }
-    }
-    TIFFClose(tiff_file);
-    return OmeXmlInfo;
-}
 
 void TsReaderCPP::SetIterReadRequests(std::int64_t const tile_width, std::int64_t const tile_height, std::int64_t const row_stride, std::int64_t const col_stride){
     iter_request_list.clear();
     for(std::int64_t t=0; t<_num_tsteps;++t){
         for(std::int64_t c=0; c<_num_channels;++c){
             for(std::int64_t z=0; z<_image_depth;++z){
-                for(std::int64_t y=0; y<=_image_height;y+=row_stride)
+                for(std::int64_t y=0; y<_image_height;y+=row_stride)
                 {
                     auto y_min = y;
                     auto y_max = y_min + row_stride - 1;
                     y_max = y_max < _image_height ? y_max : _image_height-1;
 
-                    for(std::int64_t x=0; x<=_image_width;x+=col_stride){
+                    for(std::int64_t x=0; x<_image_width;x+=col_stride){
                         auto x_min = x;
                         auto x_max = x_min + col_stride - 1;
                         x_max = x_max < _image_width ? x_max : _image_width-1;

src/cpp/reader/tsreader.h

@@ -42,7 +42,6 @@ class TsReaderCPP{
     std::int64_t GetTstepCount () const;
     std::string GetDataType() const;
     std::shared_ptr<image_data> GetImageData(const Seq& rows, const Seq& cols, const Seq& layers, const Seq& channels, const Seq& tsteps);
-    std::string GetOmeXml() const;
     void SetIterReadRequests(std::int64_t const tile_width, std::int64_t const tile_height, std::int64_t const row_stride, std::int64_t const col_stride);
     //tuple of (T,C,Z,Y_min, Y_max, X_min, X_max)
     std::vector<iter_indicies> iter_request_list;

src/cpp/reader/utilities.cpp

@@ -3,6 +3,7 @@
 #include <chrono>
 #include "utilities.h"
 #include <cassert>
+#include <tiffio.h>
 
 namespace bfiocpp {
 tensorstore::Spec GetOmeTiffSpecToRead(const std::string& filename){
@@ -91,4 +92,20 @@ std::tuple<std::optional<int>, std::optional<int>, std::optional<int>>ParseMulti
     }
     return {t_index, c_index, z_index};
 }
+
+
+std::string GetOmeXml(const std::string& file_path){
+    TIFF *tiff_file = TIFFOpen(file_path.c_str(), "r");
+    std::string OmeXmlInfo{""};
+    if (tiff_file != nullptr) {
+        char* infobuf;        
+        TIFFGetField(tiff_file, TIFFTAG_IMAGEDESCRIPTION , &infobuf);
+        if (strlen(infobuf)>0){
+            OmeXmlInfo = std::string(infobuf);
+        }
+        TIFFClose(tiff_file);
+    }
+    return OmeXmlInfo;
+}
+
 } // ns bfiocpp

src/cpp/reader/utilities.h

@@ -16,5 +16,6 @@ tensorstore::Spec GetZarrSpecToRead(const std::string& filename);
 
 uint16_t GetDataTypeCode (std::string_view type_name);
 std::string GetUTCString();
+std::string GetOmeXml(const std::string& file_path);
 std::tuple<std::optional<int>, std::optional<int>, std::optional<int>>ParseMultiscaleMetadata(const std::string& axes_list, int len);
 } // ns bfiocpp

src/python/bfiocpp/__init__.py

@@ -1,4 +1,4 @@
-from .tsreader import TSReader, Seq, FileType  # NOQA: F401
+from .tsreader import TSReader, Seq, FileType, get_ome_xml  # NOQA: F401
 from . import _version
 
 __version__ = _version.get_versions()["version"]

src/python/bfiocpp/tsreader.py

@@ -1,6 +1,6 @@
 import numpy as np
 from typing import Tuple
-from .libbfiocpp import TsReaderCPP, Seq, FileType  # NOQA: F401
+from .libbfiocpp import TsReaderCPP, Seq, FileType, get_ome_xml  # NOQA: F401
 
 
 class TSReader:
@@ -22,12 +22,6 @@ def data(
     ) -> np.ndarray:
         return self._image_reader.get_image_data(rows, cols, layers, channels, tsteps)
 
-    def get_ome_metadata(self) -> str:
-        if self._filetype == FileType.OmeTiff:
-            return self._image_reader.get_ome_xml_metadata()
-        else:
-            return ""
-
     def send_iter_read_request(
         self, tile_size: Tuple[int, int], tile_stride: Tuple[int, int]
     ) -> None: