Add support to NeuroJSON (.jnii and .bnii) files (cleaned)

SuperBuild/SuperBuild.cmake

@@ -40,6 +40,7 @@ option(USE_TURBOJPEG "Use TurboJPEG to decode classic JPEG" OFF)
 option(USE_JASPER "Build with JPEG2000 support using Jasper" OFF)
 option(USE_OPENJPEG "Build with JPEG2000 support using OpenJPEG" OFF)
 option(USE_JPEGLS "Build with JPEG-LS support using CharLS" OFF)
+option(USE_JNIFTI "Build with JNIFTI support" ON)
 
 option(BATCH_VERSION "Build dcm2niibatch for multiple conversions" OFF)
 
@@ -150,6 +151,7 @@ ExternalProject_Add(console
         -DUSE_TURBOJPEG:BOOL=${USE_TURBOJPEG}
         -DUSE_JASPER:BOOL=${USE_JASPER}
         -DUSE_JPEGLS:BOOL=${USE_JPEGLS}
+        -DUSE_JNIFTI:BOOL=${USE_JNIFTI}
         -DZLIB_IMPLEMENTATION:STRING=${ZLIB_IMPLEMENTATION}
         -DZLIB_ROOT:PATH=${ZLIB_ROOT}
          # OpenJPEG

console/CMakeLists.txt

@@ -90,6 +90,13 @@ set(DCM2NIIX_SRCS
     nii_ortho.cpp
     nii_dicom_batch.cpp)
 
+
+option(USE_JNIfTI "Build with JNIfTI support" ON)
+if(USE_JNIFTI)
+    add_definitions(-DmyEnableJNIfTI)
+    set(DCM2NIIX_SRCS ${DCM2NIIX_SRCS} cJSON.cpp base64.cpp)
+endif()
+
 if(BUILD_DCM2NIIXFSLIB)
     set(DCM2NIIXFSLIB dcm2niixfs)
     set(DCM2NIIXFSLIB_SRCS
@@ -189,6 +196,10 @@ if(BATCH_VERSION)
         nii_ortho.cpp
         nii_dicom_batch.cpp)
 
+    if(USE_JNIFTI)
+        set(DCM2NIIBATCH_SRCS ${DCM2NIIBATCH_SRCS} cJSON.cpp base64.cpp)
+    endif()
+
     if(USE_JPEGLS)
         add_executable(dcm2niibatch ${DCM2NIIBATCH_SRCS} ${CHARLS_SRCS})
     else()

console/base64.cpp

@@ -0,0 +1,162 @@
+/*
+ * Base64 encoding/decoding (RFC1341)
+ * Copyright (c) 2005-2011, Jouni Malinen <j@w1.fi>
+ *
+ * This software may be distributed under the terms of the BSD license.
+ * See README for more details.
+ */
+
+//#include "includes.h"
+
+//#include "os.h"
+#include "base64.h"
+#include <stdio.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
+
+static const unsigned char base64_table[65] =
+	"ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/";
+
+/**
+ * base64_encode - Base64 encode
+ * @src: Data to be encoded
+ * @len: Length of the data to be encoded
+ * @out_len: Pointer to output length variable, or %NULL if not used
+ * Returns: Allocated buffer of out_len bytes of encoded data,
+ * or %NULL on failure
+ *
+ * Caller is responsible for freeing the returned buffer. Returned buffer is
+ * nul terminated to make it easier to use as a C string. The nul terminator is
+ * not included in out_len.
+ */
+unsigned char * base64_encode(const unsigned char *src, size_t len,
+			      size_t *out_len)
+{
+	unsigned char *out, *pos;
+	const unsigned char *end, *in;
+	size_t olen;
+
+	olen = len * 4 / 3 + 4; /* 3-byte blocks to 4-byte */
+	#ifdef USE_EOLN
+	int line_len 0;
+	olen += olen / 72; /* line feeds */
+	#endif
+	olen++; /* nul termination */
+	if (olen < len)
+		return NULL; /* integer overflow */
+	out = (unsigned char *) malloc(olen); //os_
+	if (out == NULL)
+		return NULL;
+	end = src + len;
+	in = src;
+	pos = out;
+	while (end - in >= 3) {
+		*pos++ = base64_table[in[0] >> 2];
+		*pos++ = base64_table[((in[0] & 0x03) << 4) | (in[1] >> 4)];
+		*pos++ = base64_table[((in[1] & 0x0f) << 2) | (in[2] >> 6)];
+		*pos++ = base64_table[in[2] & 0x3f];
+		in += 3;
+		#ifdef USE_EOLN
+		line_len += 4;
+		if (line_len >= 72) {
+			*pos++ = '\n';
+			line_len = 0;
+		}
+		#endif
+	}
+
+	if (end - in) {
+		*pos++ = base64_table[in[0] >> 2];
+		if (end - in == 1) {
+			*pos++ = base64_table[(in[0] & 0x03) << 4];
+			*pos++ = '=';
+		} else {
+			*pos++ = base64_table[((in[0] & 0x03) << 4) |
+					      (in[1] >> 4)];
+			*pos++ = base64_table[(in[1] & 0x0f) << 2];
+		}
+		*pos++ = '=';
+		#ifdef USE_EOLN
+		line_len += 4;
+		#endif
+	}
+	#ifdef USE_EOLN
+	if (line_len)
+		*pos++ = '\n';
+	#endif
+	*pos = '\0';
+	if (out_len)
+		*out_len = pos - out;
+	return out;
+}
+
+/**
+ * base64_decode - Base64 decode
+ * @src: Data to be decoded
+ * @len: Length of the data to be decoded
+ * @out_len: Pointer to output length variable
+ * Returns: Allocated buffer of out_len bytes of decoded data,
+ * or %NULL on failure
+ *
+ * Caller is responsible for freeing the returned buffer.
+ */
+unsigned char * base64_decode(const unsigned char *src, size_t len,
+			      size_t *out_len)
+{
+	unsigned char dtable[256], *out, *pos, block[4], tmp;
+	size_t i, count, olen;
+	int pad = 0;
+
+	memset(dtable, 0x80, 256); //os_
+	for (i = 0; i < sizeof(base64_table) - 1; i++)
+		dtable[base64_table[i]] = (unsigned char) i;
+	dtable['='] = 0;
+
+	count = 0;
+	for (i = 0; i < len; i++) {
+		if (dtable[src[i]] != 0x80)
+			count++;
+	}
+
+	if (count == 0 || count % 4)
+		return NULL;
+
+	olen = count / 4 * 3;
+	pos = out = (unsigned char *) malloc(olen);  //os_
+	if (out == NULL)
+		return NULL;
+
+	count = 0;
+	for (i = 0; i < len; i++) {
+		tmp = dtable[src[i]];
+		if (tmp == 0x80)
+			continue;
+
+		if (src[i] == '=')
+			pad++;
+		block[count] = tmp;
+		count++;
+		if (count == 4) {
+			*pos++ = (block[0] << 2) | (block[1] >> 4);
+			*pos++ = (block[1] << 4) | (block[2] >> 2);
+			*pos++ = (block[2] << 6) | block[3];
+			count = 0;
+			if (pad) {
+				if (pad == 1)
+					pos--;
+				else if (pad == 2)
+					pos -= 2;
+				else {
+					/* Invalid padding */
+					free(out); //os_
+					return NULL;
+				}
+				break;
+			}
+		}
+	}
+
+	*out_len = pos - out;
+	return out;
+}

console/base64.h

@@ -0,0 +1,25 @@
+/*
+ * Base64 encoding/decoding (RFC1341)
+ * Copyright (c) 2005, Jouni Malinen <j@w1.fi>
+ *
+ * This software may be distributed under the terms of the BSD license.
+ * See README for more details.
+ */
+
+#ifndef BASE64_H
+#define BASE64_H
+
+#include <stdio.h>
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+
+unsigned char * base64_encode(const unsigned char *src, size_t len,size_t *out_len);
+unsigned char * base64_decode(const unsigned char *src, size_t len,size_t *out_len);
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* BASE64_H */