Merge pull request #14 from neurolabusc/batch_processing

Batch processing

CMakeLists.txt

@@ -1,10 +1,33 @@
 project(dcm2niix)
+cmake_minimum_required(VERSION 2.6)
+
+# Option1: Choose whether to build the batch version
+option(BATCH_VERSION "Build dcm2niibatch for multiple conversions as well" OFF)
+message(${BATCH_VERSION})
+
+# Option2: Build qt gui
+# TODO
+
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/bin")
 
 cmake_minimum_required(VERSION 2.6)
 #
 # Zlib
 #
-find_package(ZLIB)
+#find_package(ZLIB)
+
+# Resolve system dependency on yaml-cpp, which apparently does not
+# provide a CMake find_package() module.
+find_package(PkgConfig)
+if(PKG_CONFIG_FOUND)
+    pkg_check_modules(YAML_CPP yaml-cpp)
+    find_path(YAML_CPP_INCLUDE_DIR
+            NAMES yaml_cpp.h
+            PATHS ${YAML_CPP_INCLUDE_DIRS})
+    find_library(YAML_CPP_LIBRARY
+            NAMES YAML_CPP
+            PATHS ${YAML_CPP_LIBRARY_DIRS})
+endif()
 
 # Predefined permission set to enforce proper permissions
 # during install even if files in the sources have different

README.md

@@ -1,8 +1,8 @@
-##### About
+## About
 
-dcm2nii is a designed to convert neuroimaging data from the NIfTI format to the DICOM format. For details and compiled versions visit the [NITRC wiki](http://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage)
+dcm2niix is a designed to convert neuroimaging data from the NIfTI format to the DICOM format. For details and compiled versions visit the [NITRC wiki](http://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage)
 
-##### Versions
+## Versions
 
 12-Dec-2015
  - Support PAR/REC FP values when possible(see PMC3998685)
@@ -29,25 +29,89 @@ dcm2nii is a designed to convert neuroimaging data from the NIfTI format to the
 11-Oct-2014
  - Initial public release
 
-Building command line version:
+## Running
 
- This requires a C compiler. With a terminal, change directory to the 'conosle' folder and run the following:
+See help: `dcm2niix -h`
+e.g. `dcm2niix /path/to/dicom/folder`
+
+**Optional batch processing version:**
+
+Perform a batch conversion of multiple dicoms using the configurations specified in a yaml file. 
+```bash
+dcm2niibatch run_configuration.yaml
+```
+
+The configuration file should be in yaml format as shown in example `run_configuration.yaml`
+
+```yaml
+Options:
+  isGz:             false
+  isFlipY:          false
+  isVerbose:        false
+  isCreateBIDS:     false
+  isOnlySingleFile: false
+Files:
+    -
+      in_dir:           /path/to/first/folder
+      out_dir:          /path/to/output/folder
+      filename:         dcemri
+    -
+      in_dir:           /path/to/second/folder
+      out_dir:          /path/to/output/folder
+      filename:         fa3
+```
+
+You can add as many files as you want to convert as long as this structure stays consistent. Note that a dash must separate each file. 
+
+## Build
+ 
+### Build command line version with cmake (Linux, Windows, OSx)
+
+```bash
+mkdir build
+cd build
+cmake ..
+```
+`dcm2niix` will be created in the `bin` folder
+
+**optional batch processing version:**
+
+The batch processing binary `dcm2niibatch` is optional. To build `dcm2niibatch` as well change the cmake command to `cmake -DBATCH_VERSION=ON ..`
+
+This requires the following libraries:
+- pkg-config
+- yaml-cpp
+- a compiler that supports c++11
+
+e.g. the dependencies can be installed on Ubuntu 14.04 by running
+```
+sudo apt-get install pkg-config libyaml-cpp-dev libyaml-cpp0.5 cmake
+```
+
+### Building the command line version without cmake
+
+ This requires a C compiler. With a terminal, change directory to the 'console' folder and run the following:
 
 ##### DEFAULT BUILD
 
-- g++ -O3 -DmyDisableOpenJPEG -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -dead_strip -o dcm2niix
+```
+g++ -O3 -DmyDisableOpenJPEG -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -dead_strip -o dcm2niix
+```
 
 ##### ZLIB BUILD
  If we have zlib, we can use it (-lz) and disable [miniz](https://code.google.com/p/miniz/) (-myDisableMiniZ)
 
- - g++ -O3 -DmyDisableOpenJPEG -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -dead_strip -o dcm2niix -lz -DmyDisableMiniZ
+```
+g++ -O3 -DmyDisableOpenJPEG -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -dead_strip -o dcm2niix -lz -DmyDisableMiniZ
+```
 
 ##### MINGW BUILD
 
-If you use the (osbsolete) compiler MinGW on Windows you will want to include the rare libgcc libraries with your executable so others can use it. Here I also demonstrate the optional "-DmyDisableZLib" to remove zip support.
-
- - g++ -O3 -s -DmyDisableOpenJPEG -DmyDisableZLib -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -o dcm2niix  -static-libgcc
+If you use the (obsolete) compiler MinGW on Windows you will want to include the rare libgcc libraries with your executable so others can use it. Here I also demonstrate the optional "-DmyDisableZLib" to remove zip support.
 
+```
+g++ -O3 -s -DmyDisableOpenJPEG -DmyDisableZLib -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -o dcm2niix  -static-libgcc
+```
 
 ##### JPEG2000 BUILD
 
@@ -58,17 +122,25 @@ If you use the (osbsolete) compiler MinGW on Windows you will want to include th
  sudo make install
 You should then be able to run then run:
 
- - g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp  jpg_0XC3.cpp ujpeg.cpp -o dcm2niix -lopenjp2
+```
+g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp  jpg_0XC3.cpp ujpeg.cpp -o dcm2niix -lopenjp2
+```
 
 But in my experience this works best if you explicitly tell the software how to find the libraries, so your compile will probably look like one of these two options:
 
- - g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -o dcm2niix  -I/usr/local/include /usr/local/lib/libopenjp2.a
+```
+g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -o dcm2niix  -I/usr/local/include /usr/local/lib/libopenjp2.a
+```
 
- - g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -o dcm2niix  -I/usr/local/lib /usr/local/lib/libopenjp2.a
+```
+g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -o dcm2niix  -I/usr/local/lib /usr/local/lib/libopenjp2.a
+```
 
  If you want to build this with JPEG2000 decompression support using Jasper: You will need to have the Jasper (http://www.ece.uvic.ca/~frodo/jasper/) and libjpeg (http://www.ijg.org) libraries installed which for Linux users may be as easy as running 'sudo apt-get install libjasper-dev' (otherwise, see http://www.ece.uvic.ca/~frodo/jasper/#doc). You can then run:
 
- - g++ -O3 -DmyDisableOpenJPEG -DmyEnableJasper -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp  -s -o dcm2niix -ljasper -ljpeg
+```
+g++ -O3 -DmyDisableOpenJPEG -DmyEnableJasper -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp  -s -o dcm2niix -ljasper -ljpeg
+```
 
 ##### VISUAL STUDIO BUILD
 
@@ -79,15 +151,23 @@ You should be able to click on the Visual Studio icons to open and build this co
 Building command line version universal binary from OSX 64 bit system:
  This requires a C compiler. With a terminal, change directory to the 'conosle' folder and run the following:
 
- - g++ -O3 -DmyDisableOpenJPEG -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -dead_strip -arch i386 -o dcm2niix32
+```
+g++ -O3 -DmyDisableOpenJPEG -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -dead_strip -arch i386 -o dcm2niix32
+```
 
- - g++ -O3 -DmyDisableOpenJPEG -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -dead_strip -o dcm2niix64
+```
+g++ -O3 -DmyDisableOpenJPEG -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp -dead_strip -o dcm2niix64
+```
 
- - lipo -create dcm2niix32 dcm2niix64 -o dcm2niix
+```
+lipo -create dcm2niix32 dcm2niix64 -o dcm2niix
+```
 
  To validate that the resulting executable supports both architectures type
 
- - file ./dcm2niix
+```
+file ./dcm2niix
+```
 
 ##### OSX GRAPHICAL INTERFACE BUILD
 

console/CMakeLists.txt

@@ -1,18 +1,9 @@
 project(console)
 set(PROGRAMS dcm2niix)
 
-add_executable(dcm2niix
-  main_console.cpp
-  nii_dicom.cpp
-  jpg_0XC3.cpp
-  ujpeg.cpp
-  nifti1_io_core.cpp
-  nii_ortho.cpp
-  nii_dicom_batch.cpp)
-
 if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
   # using Clang
-  ADD_DEFINITIONS(-dead_strip)
+  add_definitions(-dead_strip)
 elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
   # using GCC
 elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
@@ -28,7 +19,34 @@ endif()
 #else(ZLIB_FOUND)
 #  ADD_DEFINITIONS(-DmyDisableZlib)
 #endif(ZLIB_FOUND)
-ADD_DEFINITIONS(-DmyDisableJasper)
-ADD_DEFINITIONS(-DmyDisableOpenJPEG)
+add_definitions(-DmyDisableJasper)
+add_definitions(-DmyDisableOpenJPEG)
+
+add_executable(dcm2niix
+        main_console.cpp
+        nii_dicom.cpp
+        jpg_0XC3.cpp
+        ujpeg.cpp
+        nifti1_io_core.cpp
+        nii_ortho.cpp
+        nii_dicom_batch.cpp)
+
+
+if (BATCH_VERSION)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+
+    message("Creating batch version")
+
+    add_executable(dcm2niibatch
+            main_console_batch.cpp
+            nii_dicom.cpp
+            jpg_0XC3.cpp
+            ujpeg.cpp
+            nifti1_io_core.cpp
+            nii_ortho.cpp
+            nii_dicom_batch.cpp)
+
+   target_link_libraries(dcm2niibatch yaml-cpp)
+endif()
 
 install(TARGETS ${PROGRAMS} DESTINATION bin)

console/main_console_batch.cpp

@@ -0,0 +1,80 @@
+//  main.m dcm2niix
+// by Chris Rorden on 3/22/14, released under Gnu General Public License, Version 2.
+//  Copyright (c) 2014 Chris Rorden. All rights reserved.
+
+
+#include <stdlib.h>
+#include <stdbool.h>
+#include <time.h>  // clock_t, clock, CLOCKS_PER_SEC
+#include <stdio.h>
+#include <cmath>
+#include <string>
+#include <iostream>
+
+#include "nii_dicom_batch.h"
+
+#include <fstream>
+#include <yaml-cpp/yaml.h>
+
+const char* removePath(const char* path) { // "/usr/path/filename.exe" -> "filename.exe"
+    const char* pDelimeter = strrchr (path, '\\');
+    if (pDelimeter)
+        path = pDelimeter+1;
+    pDelimeter = strrchr (path, '/');
+    if (pDelimeter)
+        path = pDelimeter+1;
+    return path;
+} //removePath()
+
+
+int rmainbatch(TDCMopts opts)
+{
+    printf("Chris Rorden's dcm2niiX version %s (%lu-bit)\n",kDCMvers, sizeof(size_t)*8);
+
+    clock_t start = clock();
+    nii_loadDir(&opts);
+    printf ("Conversion required %f seconds.\n",((float)(clock()-start))/CLOCKS_PER_SEC);
+    return EXIT_SUCCESS;
+}
+
+int main(int argc, const char * argv[])
+{
+
+    if (argc != 2) {
+        std::cout << "Do not include additional inputs with a config file \n";
+        throw;
+    }
+
+    // Process it all via a yaml file
+    std::string yaml_file = argv[1];
+    std::cout << "yaml_path: " << yaml_file << std::endl;
+    YAML::Node config = YAML::LoadFile(yaml_file);
+
+    struct TDCMopts opts;
+
+    opts.isCreateBIDS = config["Options"]["isCreateBIDS"].as<bool>();
+    opts.isOnlySingleFile = config["Options"]["isOnlySingleFile"].as<bool>();
+    opts.isCreateText = false;
+    opts.isVerbose = false;
+    opts.isGz = config["Options"]["isGz"].as<bool>(); //force use of internal compression instead of pigz
+    if (opts.isGz) {
+        // TODO this is not the same as previous
+        strcpy(opts.pigzname, "");
+    }
+
+    for (auto i: config["Files"]) {
+
+        std::string indir = i["in_dir"].as<std::string>();
+        strcpy(opts.indir, indir.c_str());
+
+        std::string outdir = i["out_dir"].as<std::string>();
+        strcpy(opts.outdir, outdir.c_str());
+
+        std::string filename = i["filename"].as<std::string>();
+        strcpy(opts.filename, filename.c_str());
+
+        rmainbatch(opts);
+
+    }
+    return 1;
+}

run_configuration.yaml

@@ -0,0 +1,16 @@
+Options:
+  isGz:             false
+  isFlipY:          false
+  isVerbose:        false
+  isCreateBIDS:     false
+  isOnlySingleFile: false
+
+Files:
+    -
+      in_dir:           /path/to/first/folder
+      out_dir:          /path/to/output/folder
+      filename:         dcemri
+    -
+      in_dir:           /path/to/second/folder
+      out_dir:          /path/to/output/folder
+      filename:         fa3