added a cmake file

CMakeLists.txt

@@ -0,0 +1,123 @@
+#
+# This is a file to be interpreted by cmake (https://cmake.org/)
+# Please note that all dependencies have to be available first.
+#
+
+# To uninstall:
+#
+# sudo xargs --interactive rm < install_manifest.txt
+#
+# Please note that this will remove also the libraries that might be
+# used by other programs.
+
+cmake_minimum_required(VERSION 3.9)
+
+project(nd2tool
+ DESCRIPTION "convert Nikon nd2 files to tif"
+ LANGUAGES C)
+
+set (CMAKE_C_STANDARD 11)
+
+option (ENABLE_NATIVE_OPTIMIZATION "Enable non-portable optimizations" OFF)
+
+#
+# Default build type is RELEASE
+#
+if(NOT CMAKE_BUILD_TYPE)
+ set(CMAKE_BUILD_TYPE Release)
+endif()
+message(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
+
+#
+# Add source files
+#
+add_executable(nd2tool
+ src/main.c
+ src/nd2tool.c
+ src/tiff_util.c
+ src/json_util.c
+ src/srgb_from_lambda.c
+ src/nd2tool_util.c)
+
+#
+# Add headers
+#
+target_include_directories(nd2tool PRIVATE include/)
+
+#
+# Add Nikon's library
+#
+target_link_libraries(nd2tool "${CMAKE_SOURCE_DIR}/lib/liblimfile.so")
+target_link_libraries(nd2tool "${CMAKE_SOURCE_DIR}/lib/libnd2readsdk-shared.so")
+# Copy it to the build dir upon compilation
+add_custom_command(TARGET nd2tool POST_BUILD # Adds a post-build event to MyTest
+ COMMAND ${CMAKE_COMMAND} -E copy_if_different # which executes "cmake - E copy_if_different..."
+ "${PROJECT_SOURCE_DIR}/lib/*.so" # <--this is in-file
+ $<TARGET_FILE_DIR:nd2tool>) # <--this is out-file path
+
+#
+# Link time optimization
+#
+
+# https://cmake.org/cmake/help/latest/module/CheckIPOSupported.html
+include(CheckIPOSupported)
+check_ipo_supported(RESULT result OUTPUT output)
+if(result)
+ message("Enabling IPO")
+ set_property(TARGET nd2tool PROPERTY INTERPROCEDURAL_OPTIMIZATION TRUE)
+ set(CMAKE_INTERPROCEDURAL_OPTIMIZATION_JOBS 8)
+else()
+ message(WARNING "IPO is not supported: ${output}")
+endif()
+
+#
+# Architecture optimizations
+#
+if(ENABLE_NATIVE_OPTIMIZATION)
+include(CheckCCompilerFlag)
+CHECK_C_COMPILER_FLAG("-march=native" COMPILER_SUPPORTS_MARCH_NATIVE)
+if(COMPILER_SUPPORTS_MARCH_NATIVE)
+ set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -march=native")
+endif()
+CHECK_C_COMPILER_FLAG("-mtune=native" COMPILER_SUPPORTS_MTUNE_NATIVE)
+if(COMPILER_SUPPORTS_MTUNE_NATIVE)
+ set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -mtune=native")
+endif()
+endif()
+
+
+#
+# Math library, if needed
+#
+
+find_library(MATH_LIBRARY m)
+if(MATH_LIBRARY)
+ target_link_libraries(nd2tool ${MATH_LIBRARY})
+endif()
+
+#
+# TIFF
+#
+target_link_libraries(nd2tool tiff)
+
+#
+# cJSON
+#
+target_link_libraries(nd2tool cjson)
+
+# Enable -flto (GCC) and similar if available, see
+# https://cmake.org/cmake/help/latest/policy/CMP0069.html
+check_ipo_supported(RESULT result)
+if(result)
+ message("Enabling IPO")
+ set_property(DIRECTORY PROPERTY INTERPROCEDURAL_OPTIMIZATION TRUE)
+endif()
+
+include(GNUInstallDirs)
+install(TARGETS nd2tool)
+install(FILES "${CMAKE_SOURCE_DIR}/doc/nd2tool.1"
+ DESTINATION "${CMAKE_INSTALL_MANDIR}/man1/" )
+install(FILES
+ "${CMAKE_SOURCE_DIR}/lib/liblimfile.so"
+ "${CMAKE_SOURCE_DIR}/lib/libnd2readsdk-shared.so"
+ TYPE LIB )

README.md

@@ -1,4 +1,4 @@
-# nd2tool
+# nd2tool v0.1.6
 
 ## Introduction
 Provides the command line tool, [**nd2tool**](doc/nd2tool.txt), that
@@ -23,7 +23,16 @@ moment it only supports loops over XY, Color and Z, i.e., not over
 time. It is furthermore limited to nd2 files where the image data is
 stored as 16-bit unsigned int.
 
-## Example usage
+## Usage
+
+See the [man page](doc/nd2tool.txt) for the full documentation
+(i.e. `man nd2tool`) or use `nd2tool --help` for a quick recap.
+
+### Basic usage -- conversion
+This will convert an nd2 file to a set of tif files. The output will
+be a folder named after the nd2 file, but without the `.nd2`
+extension.
+
 ```
 $ nd2tool iiQV015_20220630_001.nd2
 3 FOV in 4 channels:
@@ -44,8 +53,57 @@ Writing to iiQV015_20220630_001/SpGold_001.tif
 Writing to iiQV015_20220630_001/dapi_003.tif
 ```
 
-See the [man page](doc/nd2tool.txt) for the full documentation
-(i.e. `man nd2tool`) or use `nd2tool --help` for a quick recap.
+### Export the coordinates from multi-FOV images
+
+Coordinates are useful for stitching, detection of overlapping
+regions, detection of mechanical instabilities etc. The example
+command below gives output in a comma separated format (CSV).
+
+
+``` shell
+$ nd2tool --coord iMS441_20191016_001.nd2
+FOV, Channel, Z, X_um, Y_um, Z_um
+1, 1, 1, -3523.100000, 4802.500000, 2120.857777
+1, 1, 2, -3523.100000, 4802.500000, 2121.457777
+1, 1, 3, -3523.100000, 4802.500000, 2122.057777
+...
+```
+
+### Generation of deconvolution script
+nd2tool can generate scripts to use with
+[deconwolf](https://www.github.com/elgw/deconwolf/). Either it creates
+a script that has to be edited manually **--deconwolf** or it asks for
+the key parameters interactively with **--deconwolfx** as in the
+example below:
+
+``` shell
+$ nd2tool --deconwolfx iMS441_20191016_001.nd2
+Writing to deconwolf_iMS441_20191016_001.nd2.sh
+Enter the number of iterations to use
+dapi (default=50)
+> 50
+A647 (default=50)
+> 75
+Enter any extra arguments to deconwolf
+> --gpu
+```
+
+For this file the generated file was:
+
+``` shell
+cat deconwolf_iMS441_20191016_001.nd2.sh
+#!/bin/env bash
+set -e # abort on errors
+
+# PSF Generation
+dw_bw --lambda 385.000000 --resxy 108.333333 --resz 600.000000 --NA 1.400000 --ni 1.515000 'iMS441_20191016_001/PSF_dapi.tif'
+dw_bw --lambda 710.000000 --resxy 108.333333 --resz 600.000000 --NA 1.400000 --ni 1.515000 'iMS441_20191016_001/PSF_A647.tif'
+iter_dapi=50
+iter_A647=75
+xargs="--gpu"
+dw "$xargs" --iter $iter_dapi 'iMS441_20191016_001/dapi_001.tif' 'iMS441_20191016_001/PSF_dapi.tif'
+dw "$xargs" --iter $iter_A647 'iMS441_20191016_001/A647_001.tif' 'iMS441_20191016_001/PSF_A647.tif'
+```
 
 ## Installation
 
@@ -114,3 +172,5 @@ data](https://jsonformatter.org/json-viewer) Copy and paste the
 JSON output from nd2tool (**--meta-file**, **--meta-frame**,
 **--meta-exp**) here for a quick overview. See also [JSON
 specification](https://www.json.org/) if you are new to this.
+- [deconwolf](https://www.github.com/elgw/deconwolf/) for deconvolution of wide
+ field images (and possibly also other modalities).