diff --git a/SuperBuild/SuperBuild.cmake b/SuperBuild/SuperBuild.cmake index 7047a4ff..44d28689 100644 --- a/SuperBuild/SuperBuild.cmake +++ b/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 diff --git a/console/CMakeLists.txt b/console/CMakeLists.txt index e98755af..0dcfe303 100644 --- a/console/CMakeLists.txt +++ b/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() diff --git a/console/base64.cpp b/console/base64.cpp new file mode 100644 index 00000000..e7033279 --- /dev/null +++ b/console/base64.cpp @@ -0,0 +1,162 @@ +/* + * Base64 encoding/decoding (RFC1341) + * Copyright (c) 2005-2011, Jouni Malinen + * + * 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 +#include +#include +#include + +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; +} \ No newline at end of file diff --git a/console/base64.h b/console/base64.h new file mode 100644 index 00000000..c05eb158 --- /dev/null +++ b/console/base64.h @@ -0,0 +1,25 @@ +/* + * Base64 encoding/decoding (RFC1341) + * Copyright (c) 2005, Jouni Malinen + * + * This software may be distributed under the terms of the BSD license. + * See README for more details. + */ + +#ifndef BASE64_H +#define BASE64_H + +#include + +#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 */ diff --git a/console/cJSON.cpp b/console/cJSON.cpp new file mode 100644 index 00000000..bc95cde6 --- /dev/null +++ b/console/cJSON.cpp @@ -0,0 +1,2979 @@ +/* + Copyright (c) 2009-2017 Dave Gamble and cJSON contributors + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + THE SOFTWARE. +*/ + +/* cJSON */ +/* JSON parser in C. */ + +/* disable warnings about old C89 functions in MSVC */ +#if !defined(_CRT_SECURE_NO_DEPRECATE) && defined(_MSC_VER) +#define _CRT_SECURE_NO_DEPRECATE +#endif + +#ifdef __GNUC__ +#pragma GCC visibility push(default) +#endif +#if defined(_MSC_VER) +#pragma warning (push) +/* disable warning about single line comments in system headers */ +#pragma warning (disable : 4001) +#endif + +#include +#include +#include +#include +#include +#include + +#ifdef ENABLE_LOCALES +#include +#endif + +#if defined(_MSC_VER) +#pragma warning (pop) +#endif +#ifdef __GNUC__ +#pragma GCC visibility pop +#endif + +#include "cJSON.h" + +/* define our own boolean type */ +#ifdef true +#undef true +#endif +#define true ((cJSON_bool)1) + +#ifdef false +#undef false +#endif +#define false ((cJSON_bool)0) + +typedef struct { + const unsigned char *json; + size_t position; +} error; +static error global_error = { NULL, 0 }; + +CJSON_PUBLIC(const char *) cJSON_GetErrorPtr(void) +{ + return (const char*) (global_error.json + global_error.position); +} + +CJSON_PUBLIC(char *) cJSON_GetStringValue(const cJSON * const item) { + if (!cJSON_IsString(item)) { + return NULL; + } + + return item->valuestring; +} + +/* This is a safeguard to prevent copy-pasters from using incompatible C and header files */ +#if (CJSON_VERSION_MAJOR != 1) || (CJSON_VERSION_MINOR != 7) || (CJSON_VERSION_PATCH != 12) + #error cJSON.h and cJSON.c have different versions. Make sure that both have the same. +#endif + +CJSON_PUBLIC(const char*) cJSON_Version(void) +{ + static char version[15]; + sprintf(version, "%i.%i.%i", CJSON_VERSION_MAJOR, CJSON_VERSION_MINOR, CJSON_VERSION_PATCH); + + return version; +} + +/* Case insensitive string comparison, doesn't consider two NULL pointers equal though */ +static int case_insensitive_strcmp(const unsigned char *string1, const unsigned char *string2) +{ + if ((string1 == NULL) || (string2 == NULL)) + { + return 1; + } + + if (string1 == string2) + { + return 0; + } + + for(; tolower(*string1) == tolower(*string2); (void)string1++, string2++) + { + if (*string1 == '\0') + { + return 0; + } + } + + return tolower(*string1) - tolower(*string2); +} + +typedef struct internal_hooks +{ + void *(CJSON_CDECL *allocate)(size_t size); + void (CJSON_CDECL *deallocate)(void *pointer); + void *(CJSON_CDECL *reallocate)(void *pointer, size_t size); +} internal_hooks; + +#if defined(_MSC_VER) +/* work around MSVC error C2322: '...' address of dllimport '...' is not static */ +static void * CJSON_CDECL internal_malloc(size_t size) +{ + return malloc(size); +} +static void CJSON_CDECL internal_free(void *pointer) +{ + free(pointer); +} +static void * CJSON_CDECL internal_realloc(void *pointer, size_t size) +{ + return realloc(pointer, size); +} +#else +#define internal_malloc malloc +#define internal_free free +#define internal_realloc realloc +#endif + +/* strlen of character literals resolved at compile time */ +#define static_strlen(string_literal) (sizeof(string_literal) - sizeof("")) + +static internal_hooks global_hooks = { internal_malloc, internal_free, internal_realloc }; + +static unsigned char* cJSON_strdup(const unsigned char* string, const internal_hooks * const hooks) +{ + size_t length = 0; + unsigned char *copy = NULL; + + if (string == NULL) + { + return NULL; + } + + length = strlen((const char*)string) + sizeof(""); + copy = (unsigned char*)hooks->allocate(length); + if (copy == NULL) + { + return NULL; + } + memcpy(copy, string, length); + + return copy; +} + +CJSON_PUBLIC(void) cJSON_InitHooks(cJSON_Hooks* hooks) +{ + if (hooks == NULL) + { + /* Reset hooks */ + global_hooks.allocate = malloc; + global_hooks.deallocate = free; + global_hooks.reallocate = realloc; + return; + } + + global_hooks.allocate = malloc; + if (hooks->malloc_fn != NULL) + { + global_hooks.allocate = hooks->malloc_fn; + } + + global_hooks.deallocate = free; + if (hooks->free_fn != NULL) + { + global_hooks.deallocate = hooks->free_fn; + } + + /* use realloc only if both free and malloc are used */ + global_hooks.reallocate = NULL; + if ((global_hooks.allocate == malloc) && (global_hooks.deallocate == free)) + { + global_hooks.reallocate = realloc; + } +} + +/* Internal constructor. */ +static cJSON *cJSON_New_Item(const internal_hooks * const hooks) +{ + cJSON* node = (cJSON*)hooks->allocate(sizeof(cJSON)); + if (node) + { + memset(node, '\0', sizeof(cJSON)); + } + + return node; +} + +/* Delete a cJSON structure. */ +CJSON_PUBLIC(void) cJSON_Delete(cJSON *item) +{ + cJSON *next = NULL; + while (item != NULL) + { + next = item->next; + if (!(item->type & cJSON_IsReference) && (item->child != NULL)) + { + cJSON_Delete(item->child); + } + if (!(item->type & cJSON_IsReference) && (item->valuestring != NULL)) + { + global_hooks.deallocate(item->valuestring); + } + if (!(item->type & cJSON_StringIsConst) && (item->string != NULL)) + { + global_hooks.deallocate(item->string); + } + global_hooks.deallocate(item); + item = next; + } +} + +/* get the decimal point character of the current locale */ +static unsigned char get_decimal_point(void) +{ +#ifdef ENABLE_LOCALES + struct lconv *lconv = localeconv(); + return (unsigned char) lconv->decimal_point[0]; +#else + return '.'; +#endif +} + +typedef struct +{ + const unsigned char *content; + size_t length; + size_t offset; + size_t depth; /* How deeply nested (in arrays/objects) is the input at the current offset. */ + internal_hooks hooks; +} parse_buffer; + +/* check if the given size is left to read in a given parse buffer (starting with 1) */ +#define can_read(buffer, size) ((buffer != NULL) && (((buffer)->offset + size) <= (buffer)->length)) +/* check if the buffer can be accessed at the given index (starting with 0) */ +#define can_access_at_index(buffer, index) ((buffer != NULL) && (((buffer)->offset + index) < (buffer)->length)) +#define cannot_access_at_index(buffer, index) (!can_access_at_index(buffer, index)) +/* get a pointer to the buffer at the position */ +#define buffer_at_offset(buffer) ((buffer)->content + (buffer)->offset) + +/* Parse the input text to generate a number, and populate the result into item. */ +static cJSON_bool parse_number(cJSON * const item, parse_buffer * const input_buffer) +{ + double number = 0; + unsigned char *after_end = NULL; + unsigned char number_c_string[64]; + unsigned char decimal_point = get_decimal_point(); + size_t i = 0; + + if ((input_buffer == NULL) || (input_buffer->content == NULL)) + { + return false; + } + + /* copy the number into a temporary buffer and replace '.' with the decimal point + * of the current locale (for strtod) + * This also takes care of '\0' not necessarily being available for marking the end of the input */ + for (i = 0; (i < (sizeof(number_c_string) - 1)) && can_access_at_index(input_buffer, i); i++) + { + switch (buffer_at_offset(input_buffer)[i]) + { + case '0': + case '1': + case '2': + case '3': + case '4': + case '5': + case '6': + case '7': + case '8': + case '9': + case '+': + case '-': + case 'e': + case 'E': + number_c_string[i] = buffer_at_offset(input_buffer)[i]; + break; + + case '.': + number_c_string[i] = decimal_point; + break; + + default: + goto loop_end; + } + } +loop_end: + number_c_string[i] = '\0'; + + number = strtod((const char*)number_c_string, (char**)&after_end); + if (number_c_string == after_end) + { + return false; /* parse_error */ + } + + item->valuedouble = number; + + /* use saturation in case of overflow */ + if (number >= INT_MAX) + { + item->valueint = INT_MAX; + } + else if (number <= (double)INT_MIN) + { + item->valueint = INT_MIN; + } + else + { + item->valueint = (int)number; + } + + item->type = cJSON_Number; + + input_buffer->offset += (size_t)(after_end - number_c_string); + return true; +} + +/* don't ask me, but the original cJSON_SetNumberValue returns an integer or double */ +CJSON_PUBLIC(double) cJSON_SetNumberHelper(cJSON *object, double number) +{ + if (number >= INT_MAX) + { + object->valueint = INT_MAX; + } + else if (number <= (double)INT_MIN) + { + object->valueint = INT_MIN; + } + else + { + object->valueint = (int)number; + } + + return object->valuedouble = number; +} + +typedef struct +{ + unsigned char *buffer; + size_t length; + size_t offset; + size_t depth; /* current nesting depth (for formatted printing) */ + cJSON_bool noalloc; + cJSON_bool format; /* is this print a formatted print */ + internal_hooks hooks; +} printbuffer; + +/* realloc printbuffer if necessary to have at least "needed" bytes more */ +static unsigned char* ensure(printbuffer * const p, size_t needed) +{ + unsigned char *newbuffer = NULL; + size_t newsize = 0; + + if ((p == NULL) || (p->buffer == NULL)) + { + return NULL; + } + + if ((p->length > 0) && (p->offset >= p->length)) + { + /* make sure that offset is valid */ + return NULL; + } + + if (needed > INT_MAX) + { + /* sizes bigger than INT_MAX are currently not supported */ + return NULL; + } + + needed += p->offset + 1; + if (needed <= p->length) + { + return p->buffer + p->offset; + } + + if (p->noalloc) { + return NULL; + } + + /* calculate new buffer size */ + if (needed > (INT_MAX / 2)) + { + /* overflow of int, use INT_MAX if possible */ + if (needed <= INT_MAX) + { + newsize = INT_MAX; + } + else + { + return NULL; + } + } + else + { + newsize = needed * 2; + } + + if (p->hooks.reallocate != NULL) + { + /* reallocate with realloc if available */ + newbuffer = (unsigned char*)p->hooks.reallocate(p->buffer, newsize); + if (newbuffer == NULL) + { + p->hooks.deallocate(p->buffer); + p->length = 0; + p->buffer = NULL; + + return NULL; + } + } + else + { + /* otherwise reallocate manually */ + newbuffer = (unsigned char*)p->hooks.allocate(newsize); + if (!newbuffer) + { + p->hooks.deallocate(p->buffer); + p->length = 0; + p->buffer = NULL; + + return NULL; + } + if (newbuffer) + { + memcpy(newbuffer, p->buffer, p->offset + 1); + } + p->hooks.deallocate(p->buffer); + } + p->length = newsize; + p->buffer = newbuffer; + + return newbuffer + p->offset; +} + +/* calculate the new length of the string in a printbuffer and update the offset */ +static void update_offset(printbuffer * const buffer) +{ + const unsigned char *buffer_pointer = NULL; + if ((buffer == NULL) || (buffer->buffer == NULL)) + { + return; + } + buffer_pointer = buffer->buffer + buffer->offset; + + buffer->offset += strlen((const char*)buffer_pointer); +} + +/* securely comparison of floating-point variables */ +static cJSON_bool compare_double(double a, double b) +{ + return (fabs(a - b) <= CJSON_DOUBLE_PRECISION); +} + +/* Render the number nicely from the given item into a string. */ +static cJSON_bool print_number(const cJSON * const item, printbuffer * const output_buffer) +{ + unsigned char *output_pointer = NULL; + double d = item->valuedouble; + int length = 0; + size_t i = 0; + unsigned char number_buffer[26] = {0}; /* temporary buffer to print the number into */ + unsigned char decimal_point = get_decimal_point(); + double test = 0.0; + + if (output_buffer == NULL) + { + return false; + } + + /* This checks for NaN and Infinity */ + if ((d * 0) != 0) + { + length = sprintf((char*)number_buffer, "null"); + } + else + { + /* Try 15 decimal places of precision to avoid nonsignificant nonzero digits */ + length = sprintf((char*)number_buffer, "%1.15g", d); + + /* Check whether the original double can be recovered */ + if ((sscanf((char*)number_buffer, "%lg", &test) != 1) || !compare_double((double)test, d)) + { + /* If not, print with 17 decimal places of precision */ + length = sprintf((char*)number_buffer, "%1.17g", d); + } + } + + /* sprintf failed or buffer overrun occurred */ + if ((length < 0) || (length > (int)(sizeof(number_buffer) - 1))) + { + return false; + } + + /* reserve appropriate space in the output */ + output_pointer = ensure(output_buffer, (size_t)length + sizeof("")); + if (output_pointer == NULL) + { + return false; + } + + /* copy the printed number to the output and replace locale + * dependent decimal point with '.' */ + for (i = 0; i < ((size_t)length); i++) + { + if (number_buffer[i] == decimal_point) + { + output_pointer[i] = '.'; + continue; + } + + output_pointer[i] = number_buffer[i]; + } + output_pointer[i] = '\0'; + + output_buffer->offset += (size_t)length; + + return true; +} + +/* parse 4 digit hexadecimal number */ +static unsigned parse_hex4(const unsigned char * const input) +{ + unsigned int h = 0; + size_t i = 0; + + for (i = 0; i < 4; i++) + { + /* parse digit */ + if ((input[i] >= '0') && (input[i] <= '9')) + { + h += (unsigned int) input[i] - '0'; + } + else if ((input[i] >= 'A') && (input[i] <= 'F')) + { + h += (unsigned int) 10 + input[i] - 'A'; + } + else if ((input[i] >= 'a') && (input[i] <= 'f')) + { + h += (unsigned int) 10 + input[i] - 'a'; + } + else /* invalid */ + { + return 0; + } + + if (i < 3) + { + /* shift left to make place for the next nibble */ + h = h << 4; + } + } + + return h; +} + +/* converts a UTF-16 literal to UTF-8 + * A literal can be one or two sequences of the form \uXXXX */ +static unsigned char utf16_literal_to_utf8(const unsigned char * const input_pointer, const unsigned char * const input_end, unsigned char **output_pointer) +{ + long unsigned int codepoint = 0; + unsigned int first_code = 0; + const unsigned char *first_sequence = input_pointer; + unsigned char utf8_length = 0; + unsigned char utf8_position = 0; + unsigned char sequence_length = 0; + unsigned char first_byte_mark = 0; + + if ((input_end - first_sequence) < 6) + { + /* input ends unexpectedly */ + goto fail; + } + + /* get the first utf16 sequence */ + first_code = parse_hex4(first_sequence + 2); + + /* check that the code is valid */ + if (((first_code >= 0xDC00) && (first_code <= 0xDFFF))) + { + goto fail; + } + + /* UTF16 surrogate pair */ + if ((first_code >= 0xD800) && (first_code <= 0xDBFF)) + { + const unsigned char *second_sequence = first_sequence + 6; + unsigned int second_code = 0; + sequence_length = 12; /* \uXXXX\uXXXX */ + + if ((input_end - second_sequence) < 6) + { + /* input ends unexpectedly */ + goto fail; + } + + if ((second_sequence[0] != '\\') || (second_sequence[1] != 'u')) + { + /* missing second half of the surrogate pair */ + goto fail; + } + + /* get the second utf16 sequence */ + second_code = parse_hex4(second_sequence + 2); + /* check that the code is valid */ + if ((second_code < 0xDC00) || (second_code > 0xDFFF)) + { + /* invalid second half of the surrogate pair */ + goto fail; + } + + + /* calculate the unicode codepoint from the surrogate pair */ + codepoint = 0x10000 + (((first_code & 0x3FF) << 10) | (second_code & 0x3FF)); + } + else + { + sequence_length = 6; /* \uXXXX */ + codepoint = first_code; + } + + /* encode as UTF-8 + * takes at maximum 4 bytes to encode: + * 11110xxx 10xxxxxx 10xxxxxx 10xxxxxx */ + if (codepoint < 0x80) + { + /* normal ascii, encoding 0xxxxxxx */ + utf8_length = 1; + } + else if (codepoint < 0x800) + { + /* two bytes, encoding 110xxxxx 10xxxxxx */ + utf8_length = 2; + first_byte_mark = 0xC0; /* 11000000 */ + } + else if (codepoint < 0x10000) + { + /* three bytes, encoding 1110xxxx 10xxxxxx 10xxxxxx */ + utf8_length = 3; + first_byte_mark = 0xE0; /* 11100000 */ + } + else if (codepoint <= 0x10FFFF) + { + /* four bytes, encoding 1110xxxx 10xxxxxx 10xxxxxx 10xxxxxx */ + utf8_length = 4; + first_byte_mark = 0xF0; /* 11110000 */ + } + else + { + /* invalid unicode codepoint */ + goto fail; + } + + /* encode as utf8 */ + for (utf8_position = (unsigned char)(utf8_length - 1); utf8_position > 0; utf8_position--) + { + /* 10xxxxxx */ + (*output_pointer)[utf8_position] = (unsigned char)((codepoint | 0x80) & 0xBF); + codepoint >>= 6; + } + /* encode first byte */ + if (utf8_length > 1) + { + (*output_pointer)[0] = (unsigned char)((codepoint | first_byte_mark) & 0xFF); + } + else + { + (*output_pointer)[0] = (unsigned char)(codepoint & 0x7F); + } + + *output_pointer += utf8_length; + + return sequence_length; + +fail: + return 0; +} + +/* Parse the input text into an unescaped cinput, and populate item. */ +static cJSON_bool parse_string(cJSON * const item, parse_buffer * const input_buffer) +{ + const unsigned char *input_pointer = buffer_at_offset(input_buffer) + 1; + const unsigned char *input_end = buffer_at_offset(input_buffer) + 1; + unsigned char *output_pointer = NULL; + unsigned char *output = NULL; + + /* not a string */ + if (buffer_at_offset(input_buffer)[0] != '\"') + { + goto fail; + } + + { + /* calculate approximate size of the output (overestimate) */ + size_t allocation_length = 0; + size_t skipped_bytes = 0; + while (((size_t)(input_end - input_buffer->content) < input_buffer->length) && (*input_end != '\"')) + { + /* is escape sequence */ + if (input_end[0] == '\\') + { + if ((size_t)(input_end + 1 - input_buffer->content) >= input_buffer->length) + { + /* prevent buffer overflow when last input character is a backslash */ + goto fail; + } + skipped_bytes++; + input_end++; + } + input_end++; + } + if (((size_t)(input_end - input_buffer->content) >= input_buffer->length) || (*input_end != '\"')) + { + goto fail; /* string ended unexpectedly */ + } + + /* This is at most how much we need for the output */ + allocation_length = (size_t) (input_end - buffer_at_offset(input_buffer)) - skipped_bytes; + output = (unsigned char*)input_buffer->hooks.allocate(allocation_length + sizeof("")); + if (output == NULL) + { + goto fail; /* allocation failure */ + } + } + + output_pointer = output; + /* loop through the string literal */ + while (input_pointer < input_end) + { + if (*input_pointer != '\\') + { + *output_pointer++ = *input_pointer++; + } + /* escape sequence */ + else + { + unsigned char sequence_length = 2; + if ((input_end - input_pointer) < 1) + { + goto fail; + } + + switch (input_pointer[1]) + { + case 'b': + *output_pointer++ = '\b'; + break; + case 'f': + *output_pointer++ = '\f'; + break; + case 'n': + *output_pointer++ = '\n'; + break; + case 'r': + *output_pointer++ = '\r'; + break; + case 't': + *output_pointer++ = '\t'; + break; + case '\"': + case '\\': + case '/': + *output_pointer++ = input_pointer[1]; + break; + + /* UTF-16 literal */ + case 'u': + sequence_length = utf16_literal_to_utf8(input_pointer, input_end, &output_pointer); + if (sequence_length == 0) + { + /* failed to convert UTF16-literal to UTF-8 */ + goto fail; + } + break; + + default: + goto fail; + } + input_pointer += sequence_length; + } + } + + /* zero terminate the output */ + *output_pointer = '\0'; + + item->type = cJSON_String; + item->valuestring = (char*)output; + + input_buffer->offset = (size_t) (input_end - input_buffer->content); + input_buffer->offset++; + + return true; + +fail: + if (output != NULL) + { + input_buffer->hooks.deallocate(output); + } + + if (input_pointer != NULL) + { + input_buffer->offset = (size_t)(input_pointer - input_buffer->content); + } + + return false; +} + +/* Render the cstring provided to an escaped version that can be printed. */ +static cJSON_bool print_string_ptr(const unsigned char * const input, printbuffer * const output_buffer) +{ + const unsigned char *input_pointer = NULL; + unsigned char *output = NULL; + unsigned char *output_pointer = NULL; + size_t output_length = 0; + /* numbers of additional characters needed for escaping */ + size_t escape_characters = 0; + + if (output_buffer == NULL) + { + return false; + } + + /* empty string */ + if (input == NULL) + { + output = ensure(output_buffer, sizeof("\"\"")); + if (output == NULL) + { + return false; + } + strcpy((char*)output, "\"\""); + + return true; + } + + /* set "flag" to 1 if something needs to be escaped */ + for (input_pointer = input; *input_pointer; input_pointer++) + { + switch (*input_pointer) + { + case '\"': + case '\\': + case '\b': + case '\f': + case '\n': + case '\r': + case '\t': + /* one character escape sequence */ + escape_characters++; + break; + default: + if (*input_pointer < 32) + { + /* UTF-16 escape sequence uXXXX */ + escape_characters += 5; + } + break; + } + } + output_length = (size_t)(input_pointer - input) + escape_characters; + + output = ensure(output_buffer, output_length + sizeof("\"\"")); + if (output == NULL) + { + return false; + } + + /* no characters have to be escaped */ + if (escape_characters == 0) + { + output[0] = '\"'; + memcpy(output + 1, input, output_length); + output[output_length + 1] = '\"'; + output[output_length + 2] = '\0'; + + return true; + } + + output[0] = '\"'; + output_pointer = output + 1; + /* copy the string */ + for (input_pointer = input; *input_pointer != '\0'; (void)input_pointer++, output_pointer++) + { + if ((*input_pointer > 31) && (*input_pointer != '\"') && (*input_pointer != '\\')) + { + /* normal character, copy */ + *output_pointer = *input_pointer; + } + else + { + /* character needs to be escaped */ + *output_pointer++ = '\\'; + switch (*input_pointer) + { + case '\\': + *output_pointer = '\\'; + break; + case '\"': + *output_pointer = '\"'; + break; + case '\b': + *output_pointer = 'b'; + break; + case '\f': + *output_pointer = 'f'; + break; + case '\n': + *output_pointer = 'n'; + break; + case '\r': + *output_pointer = 'r'; + break; + case '\t': + *output_pointer = 't'; + break; + default: + /* escape and print as unicode codepoint */ + sprintf((char*)output_pointer, "u%04x", *input_pointer); + output_pointer += 4; + break; + } + } + } + output[output_length + 1] = '\"'; + output[output_length + 2] = '\0'; + + return true; +} + +/* Invoke print_string_ptr (which is useful) on an item. */ +static cJSON_bool print_string(const cJSON * const item, printbuffer * const p) +{ + return print_string_ptr((unsigned char*)item->valuestring, p); +} + +/* Predeclare these prototypes. */ +static cJSON_bool parse_value(cJSON * const item, parse_buffer * const input_buffer); +static cJSON_bool print_value(const cJSON * const item, printbuffer * const output_buffer); +static cJSON_bool parse_array(cJSON * const item, parse_buffer * const input_buffer); +static cJSON_bool print_array(const cJSON * const item, printbuffer * const output_buffer); +static cJSON_bool parse_object(cJSON * const item, parse_buffer * const input_buffer); +static cJSON_bool print_object(const cJSON * const item, printbuffer * const output_buffer); + +/* Utility to jump whitespace and cr/lf */ +static parse_buffer *buffer_skip_whitespace(parse_buffer * const buffer) +{ + if ((buffer == NULL) || (buffer->content == NULL)) + { + return NULL; + } + + while (can_access_at_index(buffer, 0) && (buffer_at_offset(buffer)[0] <= 32)) + { + buffer->offset++; + } + + if (buffer->offset == buffer->length) + { + buffer->offset--; + } + + return buffer; +} + +/* skip the UTF-8 BOM (byte order mark) if it is at the beginning of a buffer */ +static parse_buffer *skip_utf8_bom(parse_buffer * const buffer) +{ + if ((buffer == NULL) || (buffer->content == NULL) || (buffer->offset != 0)) + { + return NULL; + } + + if (can_access_at_index(buffer, 4) && (strncmp((const char*)buffer_at_offset(buffer), "\xEF\xBB\xBF", 3) == 0)) + { + buffer->offset += 3; + } + + return buffer; +} + +/* Parse an object - create a new root, and populate. */ +CJSON_PUBLIC(cJSON *) cJSON_ParseWithOpts(const char *value, const char **return_parse_end, cJSON_bool require_null_terminated) +{ + parse_buffer buffer = { 0, 0, 0, 0, { 0, 0, 0 } }; + cJSON *item = NULL; + + /* reset error position */ + global_error.json = NULL; + global_error.position = 0; + + if (value == NULL) + { + goto fail; + } + + buffer.content = (const unsigned char*)value; + buffer.length = strlen((const char*)value) + sizeof(""); + buffer.offset = 0; + buffer.hooks = global_hooks; + + item = cJSON_New_Item(&global_hooks); + if (item == NULL) /* memory fail */ + { + goto fail; + } + + if (!parse_value(item, buffer_skip_whitespace(skip_utf8_bom(&buffer)))) + { + /* parse failure. ep is set. */ + goto fail; + } + + /* if we require null-terminated JSON without appended garbage, skip and then check for a null terminator */ + if (require_null_terminated) + { + buffer_skip_whitespace(&buffer); + if ((buffer.offset >= buffer.length) || buffer_at_offset(&buffer)[0] != '\0') + { + goto fail; + } + } + if (return_parse_end) + { + *return_parse_end = (const char*)buffer_at_offset(&buffer); + } + + return item; + +fail: + if (item != NULL) + { + cJSON_Delete(item); + } + + if (value != NULL) + { + error local_error; + local_error.json = (const unsigned char*)value; + local_error.position = 0; + + if (buffer.offset < buffer.length) + { + local_error.position = buffer.offset; + } + else if (buffer.length > 0) + { + local_error.position = buffer.length - 1; + } + + if (return_parse_end != NULL) + { + *return_parse_end = (const char*)local_error.json + local_error.position; + } + + global_error = local_error; + } + + return NULL; +} + +/* Default options for cJSON_Parse */ +CJSON_PUBLIC(cJSON *) cJSON_Parse(const char *value) +{ + return cJSON_ParseWithOpts(value, 0, 0); +} + +#define cjson_min(a, b) ((a < b) ? a : b) + +static unsigned char *print(const cJSON * const item, cJSON_bool format, const internal_hooks * const hooks) +{ + static const size_t default_buffer_size = 256; + printbuffer buffer[1]; + unsigned char *printed = NULL; + + memset(buffer, 0, sizeof(buffer)); + + /* create buffer */ + buffer->buffer = (unsigned char*) hooks->allocate(default_buffer_size); + buffer->length = default_buffer_size; + buffer->format = format; + buffer->hooks = *hooks; + if (buffer->buffer == NULL) + { + goto fail; + } + + /* print the value */ + if (!print_value(item, buffer)) + { + goto fail; + } + update_offset(buffer); + + /* check if reallocate is available */ + if (hooks->reallocate != NULL) + { + printed = (unsigned char*) hooks->reallocate(buffer->buffer, buffer->offset + 1); + if (printed == NULL) { + goto fail; + } + buffer->buffer = NULL; + } + else /* otherwise copy the JSON over to a new buffer */ + { + printed = (unsigned char*) hooks->allocate(buffer->offset + 1); + if (printed == NULL) + { + goto fail; + } + memcpy(printed, buffer->buffer, cjson_min(buffer->length, buffer->offset + 1)); + printed[buffer->offset] = '\0'; /* just to be sure */ + + /* free the buffer */ + hooks->deallocate(buffer->buffer); + } + + return printed; + +fail: + if (buffer->buffer != NULL) + { + hooks->deallocate(buffer->buffer); + } + + if (printed != NULL) + { + hooks->deallocate(printed); + } + + return NULL; +} + +/* Render a cJSON item/entity/structure to text. */ +CJSON_PUBLIC(char *) cJSON_Print(const cJSON *item) +{ + return (char*)print(item, true, &global_hooks); +} + +CJSON_PUBLIC(char *) cJSON_PrintUnformatted(const cJSON *item) +{ + return (char*)print(item, false, &global_hooks); +} + +CJSON_PUBLIC(char *) cJSON_PrintBuffered(const cJSON *item, int prebuffer, cJSON_bool fmt) +{ + printbuffer p = { 0, 0, 0, 0, 0, 0, { 0, 0, 0 } }; + + if (prebuffer < 0) + { + return NULL; + } + + p.buffer = (unsigned char*)global_hooks.allocate((size_t)prebuffer); + if (!p.buffer) + { + return NULL; + } + + p.length = (size_t)prebuffer; + p.offset = 0; + p.noalloc = false; + p.format = fmt; + p.hooks = global_hooks; + + if (!print_value(item, &p)) + { + global_hooks.deallocate(p.buffer); + return NULL; + } + + return (char*)p.buffer; +} + +CJSON_PUBLIC(cJSON_bool) cJSON_PrintPreallocated(cJSON *item, char *buffer, const int length, const cJSON_bool format) +{ + printbuffer p = { 0, 0, 0, 0, 0, 0, { 0, 0, 0 } }; + + if ((length < 0) || (buffer == NULL)) + { + return false; + } + + p.buffer = (unsigned char*)buffer; + p.length = (size_t)length; + p.offset = 0; + p.noalloc = true; + p.format = format; + p.hooks = global_hooks; + + return print_value(item, &p); +} + +/* Parser core - when encountering text, process appropriately. */ +static cJSON_bool parse_value(cJSON * const item, parse_buffer * const input_buffer) +{ + if ((input_buffer == NULL) || (input_buffer->content == NULL)) + { + return false; /* no input */ + } + + /* parse the different types of values */ + /* null */ + if (can_read(input_buffer, 4) && (strncmp((const char*)buffer_at_offset(input_buffer), "null", 4) == 0)) + { + item->type = cJSON_NULL; + input_buffer->offset += 4; + return true; + } + /* false */ + if (can_read(input_buffer, 5) && (strncmp((const char*)buffer_at_offset(input_buffer), "false", 5) == 0)) + { + item->type = cJSON_False; + input_buffer->offset += 5; + return true; + } + /* true */ + if (can_read(input_buffer, 4) && (strncmp((const char*)buffer_at_offset(input_buffer), "true", 4) == 0)) + { + item->type = cJSON_True; + item->valueint = 1; + input_buffer->offset += 4; + return true; + } + /* string */ + if (can_access_at_index(input_buffer, 0) && (buffer_at_offset(input_buffer)[0] == '\"')) + { + return parse_string(item, input_buffer); + } + /* number */ + if (can_access_at_index(input_buffer, 0) && ((buffer_at_offset(input_buffer)[0] == '-') || ((buffer_at_offset(input_buffer)[0] >= '0') && (buffer_at_offset(input_buffer)[0] <= '9')))) + { + return parse_number(item, input_buffer); + } + /* array */ + if (can_access_at_index(input_buffer, 0) && (buffer_at_offset(input_buffer)[0] == '[')) + { + return parse_array(item, input_buffer); + } + /* object */ + if (can_access_at_index(input_buffer, 0) && (buffer_at_offset(input_buffer)[0] == '{')) + { + return parse_object(item, input_buffer); + } + + return false; +} + +/* Render a value to text. */ +static cJSON_bool print_value(const cJSON * const item, printbuffer * const output_buffer) +{ + unsigned char *output = NULL; + + if ((item == NULL) || (output_buffer == NULL)) + { + return false; + } + + switch ((item->type) & 0xFF) + { + case cJSON_NULL: + output = ensure(output_buffer, 5); + if (output == NULL) + { + return false; + } + strcpy((char*)output, "null"); + return true; + + case cJSON_False: + output = ensure(output_buffer, 6); + if (output == NULL) + { + return false; + } + strcpy((char*)output, "false"); + return true; + + case cJSON_True: + output = ensure(output_buffer, 5); + if (output == NULL) + { + return false; + } + strcpy((char*)output, "true"); + return true; + + case cJSON_Number: + return print_number(item, output_buffer); + + case cJSON_Raw: + { + size_t raw_length = 0; + if (item->valuestring == NULL) + { + return false; + } + + raw_length = strlen(item->valuestring) + sizeof(""); + output = ensure(output_buffer, raw_length); + if (output == NULL) + { + return false; + } + memcpy(output, item->valuestring, raw_length); + return true; + } + + case cJSON_String: + return print_string(item, output_buffer); + + case cJSON_Array: + return print_array(item, output_buffer); + + case cJSON_Object: + return print_object(item, output_buffer); + + default: + return false; + } +} + +/* Build an array from input text. */ +static cJSON_bool parse_array(cJSON * const item, parse_buffer * const input_buffer) +{ + cJSON *head = NULL; /* head of the linked list */ + cJSON *current_item = NULL; + + if (input_buffer->depth >= CJSON_NESTING_LIMIT) + { + return false; /* to deeply nested */ + } + input_buffer->depth++; + + if (buffer_at_offset(input_buffer)[0] != '[') + { + /* not an array */ + goto fail; + } + + input_buffer->offset++; + buffer_skip_whitespace(input_buffer); + if (can_access_at_index(input_buffer, 0) && (buffer_at_offset(input_buffer)[0] == ']')) + { + /* empty array */ + goto success; + } + + /* check if we skipped to the end of the buffer */ + if (cannot_access_at_index(input_buffer, 0)) + { + input_buffer->offset--; + goto fail; + } + + /* step back to character in front of the first element */ + input_buffer->offset--; + /* loop through the comma separated array elements */ + do + { + /* allocate next item */ + cJSON *new_item = cJSON_New_Item(&(input_buffer->hooks)); + if (new_item == NULL) + { + goto fail; /* allocation failure */ + } + + /* attach next item to list */ + if (head == NULL) + { + /* start the linked list */ + current_item = head = new_item; + } + else + { + /* add to the end and advance */ + current_item->next = new_item; + new_item->prev = current_item; + current_item = new_item; + } + + /* parse next value */ + input_buffer->offset++; + buffer_skip_whitespace(input_buffer); + if (!parse_value(current_item, input_buffer)) + { + goto fail; /* failed to parse value */ + } + buffer_skip_whitespace(input_buffer); + } + while (can_access_at_index(input_buffer, 0) && (buffer_at_offset(input_buffer)[0] == ',')); + + if (cannot_access_at_index(input_buffer, 0) || buffer_at_offset(input_buffer)[0] != ']') + { + goto fail; /* expected end of array */ + } + +success: + input_buffer->depth--; + + item->type = cJSON_Array; + item->child = head; + + input_buffer->offset++; + + return true; + +fail: + if (head != NULL) + { + cJSON_Delete(head); + } + + return false; +} + +/* Render an array to text */ +static cJSON_bool print_array(const cJSON * const item, printbuffer * const output_buffer) +{ + unsigned char *output_pointer = NULL; + size_t length = 0; + cJSON *current_element = item->child; + + if (output_buffer == NULL) + { + return false; + } + + /* Compose the output array. */ + /* opening square bracket */ + output_pointer = ensure(output_buffer, 1); + if (output_pointer == NULL) + { + return false; + } + + *output_pointer = '['; + output_buffer->offset++; + output_buffer->depth++; + + while (current_element != NULL) + { + if (!print_value(current_element, output_buffer)) + { + return false; + } + update_offset(output_buffer); + if (current_element->next) + { + length = (size_t) (output_buffer->format ? 2 : 1); + output_pointer = ensure(output_buffer, length + 1); + if (output_pointer == NULL) + { + return false; + } + *output_pointer++ = ','; + if(output_buffer->format) + { + *output_pointer++ = ' '; + } + *output_pointer = '\0'; + output_buffer->offset += length; + } + current_element = current_element->next; + } + + output_pointer = ensure(output_buffer, 2); + if (output_pointer == NULL) + { + return false; + } + *output_pointer++ = ']'; + *output_pointer = '\0'; + output_buffer->depth--; + + return true; +} + +/* Build an object from the text. */ +static cJSON_bool parse_object(cJSON * const item, parse_buffer * const input_buffer) +{ + cJSON *head = NULL; /* linked list head */ + cJSON *current_item = NULL; + + if (input_buffer->depth >= CJSON_NESTING_LIMIT) + { + return false; /* to deeply nested */ + } + input_buffer->depth++; + + if (cannot_access_at_index(input_buffer, 0) || (buffer_at_offset(input_buffer)[0] != '{')) + { + goto fail; /* not an object */ + } + + input_buffer->offset++; + buffer_skip_whitespace(input_buffer); + if (can_access_at_index(input_buffer, 0) && (buffer_at_offset(input_buffer)[0] == '}')) + { + goto success; /* empty object */ + } + + /* check if we skipped to the end of the buffer */ + if (cannot_access_at_index(input_buffer, 0)) + { + input_buffer->offset--; + goto fail; + } + + /* step back to character in front of the first element */ + input_buffer->offset--; + /* loop through the comma separated array elements */ + do + { + /* allocate next item */ + cJSON *new_item = cJSON_New_Item(&(input_buffer->hooks)); + if (new_item == NULL) + { + goto fail; /* allocation failure */ + } + + /* attach next item to list */ + if (head == NULL) + { + /* start the linked list */ + current_item = head = new_item; + } + else + { + /* add to the end and advance */ + current_item->next = new_item; + new_item->prev = current_item; + current_item = new_item; + } + + /* parse the name of the child */ + input_buffer->offset++; + buffer_skip_whitespace(input_buffer); + if (!parse_string(current_item, input_buffer)) + { + goto fail; /* failed to parse name */ + } + buffer_skip_whitespace(input_buffer); + + /* swap valuestring and string, because we parsed the name */ + current_item->string = current_item->valuestring; + current_item->valuestring = NULL; + + if (cannot_access_at_index(input_buffer, 0) || (buffer_at_offset(input_buffer)[0] != ':')) + { + goto fail; /* invalid object */ + } + + /* parse the value */ + input_buffer->offset++; + buffer_skip_whitespace(input_buffer); + if (!parse_value(current_item, input_buffer)) + { + goto fail; /* failed to parse value */ + } + buffer_skip_whitespace(input_buffer); + } + while (can_access_at_index(input_buffer, 0) && (buffer_at_offset(input_buffer)[0] == ',')); + + if (cannot_access_at_index(input_buffer, 0) || (buffer_at_offset(input_buffer)[0] != '}')) + { + goto fail; /* expected end of object */ + } + +success: + input_buffer->depth--; + + item->type = cJSON_Object; + item->child = head; + + input_buffer->offset++; + return true; + +fail: + if (head != NULL) + { + cJSON_Delete(head); + } + + return false; +} + +/* Render an object to text. */ +static cJSON_bool print_object(const cJSON * const item, printbuffer * const output_buffer) +{ + unsigned char *output_pointer = NULL; + size_t length = 0; + cJSON *current_item = item->child; + + if (output_buffer == NULL) + { + return false; + } + + /* Compose the output: */ + length = (size_t) (output_buffer->format ? 2 : 1); /* fmt: {\n */ + output_pointer = ensure(output_buffer, length + 1); + if (output_pointer == NULL) + { + return false; + } + + *output_pointer++ = '{'; + output_buffer->depth++; + if (output_buffer->format) + { + *output_pointer++ = '\n'; + } + output_buffer->offset += length; + + while (current_item) + { + if (output_buffer->format) + { + size_t i; + output_pointer = ensure(output_buffer, output_buffer->depth); + if (output_pointer == NULL) + { + return false; + } + for (i = 0; i < output_buffer->depth; i++) + { + *output_pointer++ = '\t'; + } + output_buffer->offset += output_buffer->depth; + } + + /* print key */ + if (!print_string_ptr((unsigned char*)current_item->string, output_buffer)) + { + return false; + } + update_offset(output_buffer); + + length = (size_t) (output_buffer->format ? 2 : 1); + output_pointer = ensure(output_buffer, length); + if (output_pointer == NULL) + { + return false; + } + *output_pointer++ = ':'; + if (output_buffer->format) + { + *output_pointer++ = '\t'; + } + output_buffer->offset += length; + + /* print value */ + if (!print_value(current_item, output_buffer)) + { + return false; + } + update_offset(output_buffer); + + /* print comma if not last */ + length = ((size_t)(output_buffer->format ? 1 : 0) + (size_t)(current_item->next ? 1 : 0)); + output_pointer = ensure(output_buffer, length + 1); + if (output_pointer == NULL) + { + return false; + } + if (current_item->next) + { + *output_pointer++ = ','; + } + + if (output_buffer->format) + { + *output_pointer++ = '\n'; + } + *output_pointer = '\0'; + output_buffer->offset += length; + + current_item = current_item->next; + } + + output_pointer = ensure(output_buffer, output_buffer->format ? (output_buffer->depth + 1) : 2); + if (output_pointer == NULL) + { + return false; + } + if (output_buffer->format) + { + size_t i; + for (i = 0; i < (output_buffer->depth - 1); i++) + { + *output_pointer++ = '\t'; + } + } + *output_pointer++ = '}'; + *output_pointer = '\0'; + output_buffer->depth--; + + return true; +} + +/* Get Array size/item / object item. */ +CJSON_PUBLIC(int) cJSON_GetArraySize(const cJSON *array) +{ + cJSON *child = NULL; + size_t size = 0; + + if (array == NULL) + { + return 0; + } + + child = array->child; + + while(child != NULL) + { + size++; + child = child->next; + } + + /* FIXME: Can overflow here. Cannot be fixed without breaking the API */ + + return (int)size; +} + +static cJSON* get_array_item(const cJSON *array, size_t index) +{ + cJSON *current_child = NULL; + + if (array == NULL) + { + return NULL; + } + + current_child = array->child; + while ((current_child != NULL) && (index > 0)) + { + index--; + current_child = current_child->next; + } + + return current_child; +} + +CJSON_PUBLIC(cJSON *) cJSON_GetArrayItem(const cJSON *array, int index) +{ + if (index < 0) + { + return NULL; + } + + return get_array_item(array, (size_t)index); +} + +static cJSON *get_object_item(const cJSON * const object, const char * const name, const cJSON_bool case_sensitive) +{ + cJSON *current_element = NULL; + + if ((object == NULL) || (name == NULL)) + { + return NULL; + } + + current_element = object->child; + if (case_sensitive) + { + while ((current_element != NULL) && (current_element->string != NULL) && (strcmp(name, current_element->string) != 0)) + { + current_element = current_element->next; + } + } + else + { + while ((current_element != NULL) && (case_insensitive_strcmp((const unsigned char*)name, (const unsigned char*)(current_element->string)) != 0)) + { + current_element = current_element->next; + } + } + + if ((current_element == NULL) || (current_element->string == NULL)) { + return NULL; + } + + return current_element; +} + +CJSON_PUBLIC(cJSON *) cJSON_GetObjectItem(const cJSON * const object, const char * const string) +{ + return get_object_item(object, string, false); +} + +CJSON_PUBLIC(cJSON *) cJSON_GetObjectItemCaseSensitive(const cJSON * const object, const char * const string) +{ + return get_object_item(object, string, true); +} + +CJSON_PUBLIC(cJSON_bool) cJSON_HasObjectItem(const cJSON *object, const char *string) +{ + return cJSON_GetObjectItem(object, string) ? 1 : 0; +} + +/* Utility for array list handling. */ +static void suffix_object(cJSON *prev, cJSON *item) +{ + prev->next = item; + item->prev = prev; +} + +/* Utility for handling references. */ +static cJSON *create_reference(const cJSON *item, const internal_hooks * const hooks) +{ + cJSON *reference = NULL; + if (item == NULL) + { + return NULL; + } + + reference = cJSON_New_Item(hooks); + if (reference == NULL) + { + return NULL; + } + + memcpy(reference, item, sizeof(cJSON)); + reference->string = NULL; + reference->type |= cJSON_IsReference; + reference->next = reference->prev = NULL; + return reference; +} + +static cJSON_bool add_item_to_array(cJSON *array, cJSON *item) +{ + cJSON *child = NULL; + + if ((item == NULL) || (array == NULL)) + { + return false; + } + + child = array->child; + + if (child == NULL) + { + /* list is empty, start new one */ + array->child = item; + } + else + { + /* append to the end */ + while (child->next) + { + child = child->next; + } + suffix_object(child, item); + } + + return true; +} + +/* Add item to array/object. */ +CJSON_PUBLIC(void) cJSON_AddItemToArray(cJSON *array, cJSON *item) +{ + add_item_to_array(array, item); +} + +#if defined(__clang__) || (defined(__GNUC__) && ((__GNUC__ > 4) || ((__GNUC__ == 4) && (__GNUC_MINOR__ > 5)))) + #pragma GCC diagnostic push +#endif +#ifdef __GNUC__ +#pragma GCC diagnostic ignored "-Wcast-qual" +#endif +/* helper function to cast away const */ +static void* cast_away_const(const void* string) +{ + return (void*)string; +} +#if defined(__clang__) || (defined(__GNUC__) && ((__GNUC__ > 4) || ((__GNUC__ == 4) && (__GNUC_MINOR__ > 5)))) + #pragma GCC diagnostic pop +#endif + + +static cJSON_bool add_item_to_object(cJSON * const object, const char * const string, cJSON * const item, const internal_hooks * const hooks, const cJSON_bool constant_key) +{ + char *new_key = NULL; + int new_type = cJSON_Invalid; + + if ((object == NULL) || (string == NULL) || (item == NULL)) + { + return false; + } + + if (constant_key) + { + new_key = (char*)cast_away_const(string); + new_type = item->type | cJSON_StringIsConst; + } + else + { + new_key = (char*)cJSON_strdup((const unsigned char*)string, hooks); + if (new_key == NULL) + { + return false; + } + + new_type = item->type & ~cJSON_StringIsConst; + } + + if (!(item->type & cJSON_StringIsConst) && (item->string != NULL)) + { + hooks->deallocate(item->string); + } + + item->string = new_key; + item->type = new_type; + + return add_item_to_array(object, item); +} + +CJSON_PUBLIC(void) cJSON_AddItemToObject(cJSON *object, const char *string, cJSON *item) +{ + add_item_to_object(object, string, item, &global_hooks, false); +} + +/* Add an item to an object with constant string as key */ +CJSON_PUBLIC(void) cJSON_AddItemToObjectCS(cJSON *object, const char *string, cJSON *item) +{ + add_item_to_object(object, string, item, &global_hooks, true); +} + +CJSON_PUBLIC(void) cJSON_AddItemReferenceToArray(cJSON *array, cJSON *item) +{ + if (array == NULL) + { + return; + } + + add_item_to_array(array, create_reference(item, &global_hooks)); +} + +CJSON_PUBLIC(void) cJSON_AddItemReferenceToObject(cJSON *object, const char *string, cJSON *item) +{ + if ((object == NULL) || (string == NULL)) + { + return; + } + + add_item_to_object(object, string, create_reference(item, &global_hooks), &global_hooks, false); +} + +CJSON_PUBLIC(cJSON*) cJSON_AddNullToObject(cJSON * const object, const char * const name) +{ + cJSON *null = cJSON_CreateNull(); + if (add_item_to_object(object, name, null, &global_hooks, false)) + { + return null; + } + + cJSON_Delete(null); + return NULL; +} + +CJSON_PUBLIC(cJSON*) cJSON_AddTrueToObject(cJSON * const object, const char * const name) +{ + cJSON *true_item = cJSON_CreateTrue(); + if (add_item_to_object(object, name, true_item, &global_hooks, false)) + { + return true_item; + } + + cJSON_Delete(true_item); + return NULL; +} + +CJSON_PUBLIC(cJSON*) cJSON_AddFalseToObject(cJSON * const object, const char * const name) +{ + cJSON *false_item = cJSON_CreateFalse(); + if (add_item_to_object(object, name, false_item, &global_hooks, false)) + { + return false_item; + } + + cJSON_Delete(false_item); + return NULL; +} + +CJSON_PUBLIC(cJSON*) cJSON_AddBoolToObject(cJSON * const object, const char * const name, const cJSON_bool boolean) +{ + cJSON *bool_item = cJSON_CreateBool(boolean); + if (add_item_to_object(object, name, bool_item, &global_hooks, false)) + { + return bool_item; + } + + cJSON_Delete(bool_item); + return NULL; +} + +CJSON_PUBLIC(cJSON*) cJSON_AddNumberToObject(cJSON * const object, const char * const name, const double number) +{ + cJSON *number_item = cJSON_CreateNumber(number); + if (add_item_to_object(object, name, number_item, &global_hooks, false)) + { + return number_item; + } + + cJSON_Delete(number_item); + return NULL; +} + +CJSON_PUBLIC(cJSON*) cJSON_AddStringToObject(cJSON * const object, const char * const name, const char * const string) +{ + cJSON *string_item = cJSON_CreateString(string); + if (add_item_to_object(object, name, string_item, &global_hooks, false)) + { + return string_item; + } + + cJSON_Delete(string_item); + return NULL; +} + +CJSON_PUBLIC(cJSON*) cJSON_AddRawToObject(cJSON * const object, const char * const name, const char * const raw) +{ + cJSON *raw_item = cJSON_CreateRaw(raw); + if (add_item_to_object(object, name, raw_item, &global_hooks, false)) + { + return raw_item; + } + + cJSON_Delete(raw_item); + return NULL; +} + +CJSON_PUBLIC(cJSON*) cJSON_AddObjectToObject(cJSON * const object, const char * const name) +{ + cJSON *object_item = cJSON_CreateObject(); + if (add_item_to_object(object, name, object_item, &global_hooks, false)) + { + return object_item; + } + + cJSON_Delete(object_item); + return NULL; +} + +CJSON_PUBLIC(cJSON*) cJSON_AddArrayToObject(cJSON * const object, const char * const name) +{ + cJSON *array = cJSON_CreateArray(); + if (add_item_to_object(object, name, array, &global_hooks, false)) + { + return array; + } + + cJSON_Delete(array); + return NULL; +} + +CJSON_PUBLIC(cJSON *) cJSON_DetachItemViaPointer(cJSON *parent, cJSON * const item) +{ + if ((parent == NULL) || (item == NULL)) + { + return NULL; + } + + if (item->prev != NULL) + { + /* not the first element */ + item->prev->next = item->next; + } + if (item->next != NULL) + { + /* not the last element */ + item->next->prev = item->prev; + } + + if (item == parent->child) + { + /* first element */ + parent->child = item->next; + } + /* make sure the detached item doesn't point anywhere anymore */ + item->prev = NULL; + item->next = NULL; + + return item; +} + +CJSON_PUBLIC(cJSON *) cJSON_DetachItemFromArray(cJSON *array, int which) +{ + if (which < 0) + { + return NULL; + } + + return cJSON_DetachItemViaPointer(array, get_array_item(array, (size_t)which)); +} + +CJSON_PUBLIC(void) cJSON_DeleteItemFromArray(cJSON *array, int which) +{ + cJSON_Delete(cJSON_DetachItemFromArray(array, which)); +} + +CJSON_PUBLIC(cJSON *) cJSON_DetachItemFromObject(cJSON *object, const char *string) +{ + cJSON *to_detach = cJSON_GetObjectItem(object, string); + + return cJSON_DetachItemViaPointer(object, to_detach); +} + +CJSON_PUBLIC(cJSON *) cJSON_DetachItemFromObjectCaseSensitive(cJSON *object, const char *string) +{ + cJSON *to_detach = cJSON_GetObjectItemCaseSensitive(object, string); + + return cJSON_DetachItemViaPointer(object, to_detach); +} + +CJSON_PUBLIC(void) cJSON_DeleteItemFromObject(cJSON *object, const char *string) +{ + cJSON_Delete(cJSON_DetachItemFromObject(object, string)); +} + +CJSON_PUBLIC(void) cJSON_DeleteItemFromObjectCaseSensitive(cJSON *object, const char *string) +{ + cJSON_Delete(cJSON_DetachItemFromObjectCaseSensitive(object, string)); +} + +/* Replace array/object items with new ones. */ +CJSON_PUBLIC(void) cJSON_InsertItemInArray(cJSON *array, int which, cJSON *newitem) +{ + cJSON *after_inserted = NULL; + + if (which < 0) + { + return; + } + + after_inserted = get_array_item(array, (size_t)which); + if (after_inserted == NULL) + { + add_item_to_array(array, newitem); + return; + } + + newitem->next = after_inserted; + newitem->prev = after_inserted->prev; + after_inserted->prev = newitem; + if (after_inserted == array->child) + { + array->child = newitem; + } + else + { + newitem->prev->next = newitem; + } +} + +CJSON_PUBLIC(cJSON_bool) cJSON_ReplaceItemViaPointer(cJSON * const parent, cJSON * const item, cJSON * replacement) +{ + if ((parent == NULL) || (replacement == NULL) || (item == NULL)) + { + return false; + } + + if (replacement == item) + { + return true; + } + + replacement->next = item->next; + replacement->prev = item->prev; + + if (replacement->next != NULL) + { + replacement->next->prev = replacement; + } + if (replacement->prev != NULL) + { + replacement->prev->next = replacement; + } + if (parent->child == item) + { + parent->child = replacement; + } + + item->next = NULL; + item->prev = NULL; + cJSON_Delete(item); + + return true; +} + +CJSON_PUBLIC(void) cJSON_ReplaceItemInArray(cJSON *array, int which, cJSON *newitem) +{ + if (which < 0) + { + return; + } + + cJSON_ReplaceItemViaPointer(array, get_array_item(array, (size_t)which), newitem); +} + +static cJSON_bool replace_item_in_object(cJSON *object, const char *string, cJSON *replacement, cJSON_bool case_sensitive) +{ + if ((replacement == NULL) || (string == NULL)) + { + return false; + } + + /* replace the name in the replacement */ + if (!(replacement->type & cJSON_StringIsConst) && (replacement->string != NULL)) + { + cJSON_free(replacement->string); + } + replacement->string = (char*)cJSON_strdup((const unsigned char*)string, &global_hooks); + replacement->type &= ~cJSON_StringIsConst; + + cJSON_ReplaceItemViaPointer(object, get_object_item(object, string, case_sensitive), replacement); + + return true; +} + +CJSON_PUBLIC(void) cJSON_ReplaceItemInObject(cJSON *object, const char *string, cJSON *newitem) +{ + replace_item_in_object(object, string, newitem, false); +} + +CJSON_PUBLIC(void) cJSON_ReplaceItemInObjectCaseSensitive(cJSON *object, const char *string, cJSON *newitem) +{ + replace_item_in_object(object, string, newitem, true); +} + +/* Create basic types: */ +CJSON_PUBLIC(cJSON *) cJSON_CreateNull(void) +{ + cJSON *item = cJSON_New_Item(&global_hooks); + if(item) + { + item->type = cJSON_NULL; + } + + return item; +} + +CJSON_PUBLIC(cJSON *) cJSON_CreateTrue(void) +{ + cJSON *item = cJSON_New_Item(&global_hooks); + if(item) + { + item->type = cJSON_True; + } + + return item; +} + +CJSON_PUBLIC(cJSON *) cJSON_CreateFalse(void) +{ + cJSON *item = cJSON_New_Item(&global_hooks); + if(item) + { + item->type = cJSON_False; + } + + return item; +} + +CJSON_PUBLIC(cJSON *) cJSON_CreateBool(cJSON_bool boolean) +{ + cJSON *item = cJSON_New_Item(&global_hooks); + if(item) + { + item->type = boolean ? cJSON_True : cJSON_False; + } + + return item; +} + +CJSON_PUBLIC(cJSON *) cJSON_CreateNumber(double num) +{ + cJSON *item = cJSON_New_Item(&global_hooks); + if(item) + { + item->type = cJSON_Number; + item->valuedouble = num; + + /* use saturation in case of overflow */ + if (num >= INT_MAX) + { + item->valueint = INT_MAX; + } + else if (num <= (double)INT_MIN) + { + item->valueint = INT_MIN; + } + else + { + item->valueint = (int)num; + } + } + + return item; +} + +CJSON_PUBLIC(cJSON *) cJSON_CreateString(const char *string) +{ + cJSON *item = cJSON_New_Item(&global_hooks); + if(item) + { + item->type = cJSON_String; + item->valuestring = (char*)cJSON_strdup((const unsigned char*)string, &global_hooks); + if(!item->valuestring) + { + cJSON_Delete(item); + return NULL; + } + } + + return item; +} + +CJSON_PUBLIC(cJSON *) cJSON_CreateStringReference(const char *string) +{ + cJSON *item = cJSON_New_Item(&global_hooks); + if (item != NULL) + { + item->type = cJSON_String | cJSON_IsReference; + item->valuestring = (char*)cast_away_const(string); + } + + return item; +} + +CJSON_PUBLIC(cJSON *) cJSON_CreateObjectReference(const cJSON *child) +{ + cJSON *item = cJSON_New_Item(&global_hooks); + if (item != NULL) { + item->type = cJSON_Object | cJSON_IsReference; + item->child = (cJSON*)cast_away_const(child); + } + + return item; +} + +CJSON_PUBLIC(cJSON *) cJSON_CreateArrayReference(const cJSON *child) { + cJSON *item = cJSON_New_Item(&global_hooks); + if (item != NULL) { + item->type = cJSON_Array | cJSON_IsReference; + item->child = (cJSON*)cast_away_const(child); + } + + return item; +} + +CJSON_PUBLIC(cJSON *) cJSON_CreateRaw(const char *raw) +{ + cJSON *item = cJSON_New_Item(&global_hooks); + if(item) + { + item->type = cJSON_Raw; + item->valuestring = (char*)cJSON_strdup((const unsigned char*)raw, &global_hooks); + if(!item->valuestring) + { + cJSON_Delete(item); + return NULL; + } + } + + return item; +} + +CJSON_PUBLIC(cJSON *) cJSON_CreateArray(void) +{ + cJSON *item = cJSON_New_Item(&global_hooks); + if(item) + { + item->type=cJSON_Array; + } + + return item; +} + +CJSON_PUBLIC(cJSON *) cJSON_CreateObject(void) +{ + cJSON *item = cJSON_New_Item(&global_hooks); + if (item) + { + item->type = cJSON_Object; + } + + return item; +} + +/* Create Arrays: */ +CJSON_PUBLIC(cJSON *) cJSON_CreateIntArray(const int *numbers, int count) +{ + size_t i = 0; + cJSON *n = NULL; + cJSON *p = NULL; + cJSON *a = NULL; + + if ((count < 0) || (numbers == NULL)) + { + return NULL; + } + + a = cJSON_CreateArray(); + for(i = 0; a && (i < (size_t)count); i++) + { + n = cJSON_CreateNumber(numbers[i]); + if (!n) + { + cJSON_Delete(a); + return NULL; + } + if(!i) + { + a->child = n; + } + else + { + suffix_object(p, n); + } + p = n; + } + + return a; +} + +CJSON_PUBLIC(cJSON *) cJSON_CreateFloatArray(const float *numbers, int count) +{ + size_t i = 0; + cJSON *n = NULL; + cJSON *p = NULL; + cJSON *a = NULL; + + if ((count < 0) || (numbers == NULL)) + { + return NULL; + } + + a = cJSON_CreateArray(); + + for(i = 0; a && (i < (size_t)count); i++) + { + n = cJSON_CreateNumber((double)numbers[i]); + if(!n) + { + cJSON_Delete(a); + return NULL; + } + if(!i) + { + a->child = n; + } + else + { + suffix_object(p, n); + } + p = n; + } + + return a; +} + +CJSON_PUBLIC(cJSON *) cJSON_CreateDoubleArray(const double *numbers, int count) +{ + size_t i = 0; + cJSON *n = NULL; + cJSON *p = NULL; + cJSON *a = NULL; + + if ((count < 0) || (numbers == NULL)) + { + return NULL; + } + + a = cJSON_CreateArray(); + + for(i = 0;a && (i < (size_t)count); i++) + { + n = cJSON_CreateNumber(numbers[i]); + if(!n) + { + cJSON_Delete(a); + return NULL; + } + if(!i) + { + a->child = n; + } + else + { + suffix_object(p, n); + } + p = n; + } + + return a; +} + +CJSON_PUBLIC(cJSON *) cJSON_CreateStringArray(const char *const *strings, int count) +{ + size_t i = 0; + cJSON *n = NULL; + cJSON *p = NULL; + cJSON *a = NULL; + + if ((count < 0) || (strings == NULL)) + { + return NULL; + } + + a = cJSON_CreateArray(); + + for (i = 0; a && (i < (size_t)count); i++) + { + n = cJSON_CreateString(strings[i]); + if(!n) + { + cJSON_Delete(a); + return NULL; + } + if(!i) + { + a->child = n; + } + else + { + suffix_object(p,n); + } + p = n; + } + + return a; +} + +/* Duplication */ +CJSON_PUBLIC(cJSON *) cJSON_Duplicate(const cJSON *item, cJSON_bool recurse) +{ + cJSON *newitem = NULL; + cJSON *child = NULL; + cJSON *next = NULL; + cJSON *newchild = NULL; + + /* Bail on bad ptr */ + if (!item) + { + goto fail; + } + /* Create new item */ + newitem = cJSON_New_Item(&global_hooks); + if (!newitem) + { + goto fail; + } + /* Copy over all vars */ + newitem->type = item->type & (~cJSON_IsReference); + newitem->valueint = item->valueint; + newitem->valuedouble = item->valuedouble; + if (item->valuestring) + { + newitem->valuestring = (char*)cJSON_strdup((unsigned char*)item->valuestring, &global_hooks); + if (!newitem->valuestring) + { + goto fail; + } + } + if (item->string) + { + newitem->string = (item->type&cJSON_StringIsConst) ? item->string : (char*)cJSON_strdup((unsigned char*)item->string, &global_hooks); + if (!newitem->string) + { + goto fail; + } + } + /* If non-recursive, then we're done! */ + if (!recurse) + { + return newitem; + } + /* Walk the ->next chain for the child. */ + child = item->child; + while (child != NULL) + { + newchild = cJSON_Duplicate(child, true); /* Duplicate (with recurse) each item in the ->next chain */ + if (!newchild) + { + goto fail; + } + if (next != NULL) + { + /* If newitem->child already set, then crosswire ->prev and ->next and move on */ + next->next = newchild; + newchild->prev = next; + next = newchild; + } + else + { + /* Set newitem->child and move to it */ + newitem->child = newchild; + next = newchild; + } + child = child->next; + } + + return newitem; + +fail: + if (newitem != NULL) + { + cJSON_Delete(newitem); + } + + return NULL; +} + +static void skip_oneline_comment(char **input) +{ + *input += static_strlen("//"); + + for (; (*input)[0] != '\0'; ++(*input)) + { + if ((*input)[0] == '\n') { + *input += static_strlen("\n"); + return; + } + } +} + +static void skip_multiline_comment(char **input) +{ + *input += static_strlen("/*"); + + for (; (*input)[0] != '\0'; ++(*input)) + { + if (((*input)[0] == '*') && ((*input)[1] == '/')) + { + *input += static_strlen("*/"); + return; + } + } +} + +static void minify_string(char **input, char **output) { + (*output)[0] = (*input)[0]; + *input += static_strlen("\""); + *output += static_strlen("\""); + + + for (; (*input)[0] != '\0'; (void)++(*input), ++(*output)) { + (*output)[0] = (*input)[0]; + + if ((*input)[0] == '\"') { + (*output)[0] = '\"'; + *input += static_strlen("\""); + *output += static_strlen("\""); + return; + } else if (((*input)[0] == '\\') && ((*input)[1] == '\"')) { + (*output)[1] = (*input)[1]; + *input += static_strlen("\""); + *output += static_strlen("\""); + } + } +} + +CJSON_PUBLIC(void) cJSON_Minify(char *json) +{ + char *into = json; + + if (json == NULL) + { + return; + } + + while (json[0] != '\0') + { + switch (json[0]) + { + case ' ': + case '\t': + case '\r': + case '\n': + json++; + break; + + case '/': + if (json[1] == '/') + { + skip_oneline_comment(&json); + } + else if (json[1] == '*') + { + skip_multiline_comment(&json); + } else { + json++; + } + break; + + case '\"': + minify_string(&json, (char**)&into); + break; + + default: + into[0] = json[0]; + json++; + into++; + } + } + + /* and null-terminate. */ + *into = '\0'; +} + +CJSON_PUBLIC(cJSON_bool) cJSON_IsInvalid(const cJSON * const item) +{ + if (item == NULL) + { + return false; + } + + return (item->type & 0xFF) == cJSON_Invalid; +} + +CJSON_PUBLIC(cJSON_bool) cJSON_IsFalse(const cJSON * const item) +{ + if (item == NULL) + { + return false; + } + + return (item->type & 0xFF) == cJSON_False; +} + +CJSON_PUBLIC(cJSON_bool) cJSON_IsTrue(const cJSON * const item) +{ + if (item == NULL) + { + return false; + } + + return (item->type & 0xff) == cJSON_True; +} + + +CJSON_PUBLIC(cJSON_bool) cJSON_IsBool(const cJSON * const item) +{ + if (item == NULL) + { + return false; + } + + return (item->type & (cJSON_True | cJSON_False)) != 0; +} +CJSON_PUBLIC(cJSON_bool) cJSON_IsNull(const cJSON * const item) +{ + if (item == NULL) + { + return false; + } + + return (item->type & 0xFF) == cJSON_NULL; +} + +CJSON_PUBLIC(cJSON_bool) cJSON_IsNumber(const cJSON * const item) +{ + if (item == NULL) + { + return false; + } + + return (item->type & 0xFF) == cJSON_Number; +} + +CJSON_PUBLIC(cJSON_bool) cJSON_IsString(const cJSON * const item) +{ + if (item == NULL) + { + return false; + } + + return (item->type & 0xFF) == cJSON_String; +} + +CJSON_PUBLIC(cJSON_bool) cJSON_IsArray(const cJSON * const item) +{ + if (item == NULL) + { + return false; + } + + return (item->type & 0xFF) == cJSON_Array; +} + +CJSON_PUBLIC(cJSON_bool) cJSON_IsObject(const cJSON * const item) +{ + if (item == NULL) + { + return false; + } + + return (item->type & 0xFF) == cJSON_Object; +} + +CJSON_PUBLIC(cJSON_bool) cJSON_IsRaw(const cJSON * const item) +{ + if (item == NULL) + { + return false; + } + + return (item->type & 0xFF) == cJSON_Raw; +} + +CJSON_PUBLIC(cJSON_bool) cJSON_Compare(const cJSON * const a, const cJSON * const b, const cJSON_bool case_sensitive) +{ + if ((a == NULL) || (b == NULL) || ((a->type & 0xFF) != (b->type & 0xFF)) || cJSON_IsInvalid(a)) + { + return false; + } + + /* check if type is valid */ + switch (a->type & 0xFF) + { + case cJSON_False: + case cJSON_True: + case cJSON_NULL: + case cJSON_Number: + case cJSON_String: + case cJSON_Raw: + case cJSON_Array: + case cJSON_Object: + break; + + default: + return false; + } + + /* identical objects are equal */ + if (a == b) + { + return true; + } + + switch (a->type & 0xFF) + { + /* in these cases and equal type is enough */ + case cJSON_False: + case cJSON_True: + case cJSON_NULL: + return true; + + case cJSON_Number: + if (compare_double(a->valuedouble, b->valuedouble)) + { + return true; + } + return false; + + case cJSON_String: + case cJSON_Raw: + if ((a->valuestring == NULL) || (b->valuestring == NULL)) + { + return false; + } + if (strcmp(a->valuestring, b->valuestring) == 0) + { + return true; + } + + return false; + + case cJSON_Array: + { + cJSON *a_element = a->child; + cJSON *b_element = b->child; + + for (; (a_element != NULL) && (b_element != NULL);) + { + if (!cJSON_Compare(a_element, b_element, case_sensitive)) + { + return false; + } + + a_element = a_element->next; + b_element = b_element->next; + } + + /* one of the arrays is longer than the other */ + if (a_element != b_element) { + return false; + } + + return true; + } + + case cJSON_Object: + { + cJSON *a_element = NULL; + cJSON *b_element = NULL; + cJSON_ArrayForEach(a_element, a) + { + /* TODO This has O(n^2) runtime, which is horrible! */ + b_element = get_object_item(b, a_element->string, case_sensitive); + if (b_element == NULL) + { + return false; + } + + if (!cJSON_Compare(a_element, b_element, case_sensitive)) + { + return false; + } + } + + /* doing this twice, once on a and b to prevent true comparison if a subset of b + * TODO: Do this the proper way, this is just a fix for now */ + cJSON_ArrayForEach(b_element, b) + { + a_element = get_object_item(a, b_element->string, case_sensitive); + if (a_element == NULL) + { + return false; + } + + if (!cJSON_Compare(b_element, a_element, case_sensitive)) + { + return false; + } + } + + return true; + } + + default: + return false; + } +} + +CJSON_PUBLIC(void *) cJSON_malloc(size_t size) +{ + return global_hooks.allocate(size); +} + +CJSON_PUBLIC(void) cJSON_free(void *object) +{ + global_hooks.deallocate(object); +} diff --git a/console/cJSON.h b/console/cJSON.h new file mode 100644 index 00000000..2c535628 --- /dev/null +++ b/console/cJSON.h @@ -0,0 +1,293 @@ +/* + Copyright (c) 2009-2017 Dave Gamble and cJSON contributors + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + THE SOFTWARE. +*/ + +#ifndef cJSON__h +#define cJSON__h + +#ifdef __cplusplus +extern "C" +{ +#endif + +#if !defined(__WINDOWS__) && (defined(WIN32) || defined(WIN64) || defined(_MSC_VER) || defined(_WIN32)) +#define __WINDOWS__ +#endif + +#ifdef __WINDOWS__ + +/* When compiling for windows, we specify a specific calling convention to avoid issues where we are being called from a project with a different default calling convention. For windows you have 3 define options: + +CJSON_HIDE_SYMBOLS - Define this in the case where you don't want to ever dllexport symbols +CJSON_EXPORT_SYMBOLS - Define this on library build when you want to dllexport symbols (default) +CJSON_IMPORT_SYMBOLS - Define this if you want to dllimport symbol + +For *nix builds that support visibility attribute, you can define similar behavior by + +setting default visibility to hidden by adding +-fvisibility=hidden (for gcc) +or +-xldscope=hidden (for sun cc) +to CFLAGS + +then using the CJSON_API_VISIBILITY flag to "export" the same symbols the way CJSON_EXPORT_SYMBOLS does + +*/ + +#define CJSON_CDECL __cdecl +#define CJSON_STDCALL __stdcall + +/* export symbols by default, this is necessary for copy pasting the C and header file */ +#if !defined(CJSON_HIDE_SYMBOLS) && !defined(CJSON_IMPORT_SYMBOLS) && !defined(CJSON_EXPORT_SYMBOLS) +#define CJSON_EXPORT_SYMBOLS +#endif + +#if defined(CJSON_HIDE_SYMBOLS) +#define CJSON_PUBLIC(type) type CJSON_STDCALL +#elif defined(CJSON_EXPORT_SYMBOLS) +#define CJSON_PUBLIC(type) __declspec(dllexport) type CJSON_STDCALL +#elif defined(CJSON_IMPORT_SYMBOLS) +#define CJSON_PUBLIC(type) __declspec(dllimport) type CJSON_STDCALL +#endif +#else /* !__WINDOWS__ */ +#define CJSON_CDECL +#define CJSON_STDCALL + +#if (defined(__GNUC__) || defined(__SUNPRO_CC) || defined (__SUNPRO_C)) && defined(CJSON_API_VISIBILITY) +#define CJSON_PUBLIC(type) __attribute__((visibility("default"))) type +#else +#define CJSON_PUBLIC(type) type +#endif +#endif + +/* project version */ +#define CJSON_VERSION_MAJOR 1 +#define CJSON_VERSION_MINOR 7 +#define CJSON_VERSION_PATCH 12 + +#include + +/* cJSON Types: */ +#define cJSON_Invalid (0) +#define cJSON_False (1 << 0) +#define cJSON_True (1 << 1) +#define cJSON_NULL (1 << 2) +#define cJSON_Number (1 << 3) +#define cJSON_String (1 << 4) +#define cJSON_Array (1 << 5) +#define cJSON_Object (1 << 6) +#define cJSON_Raw (1 << 7) /* raw json */ + +#define cJSON_IsReference 256 +#define cJSON_StringIsConst 512 + +/* The cJSON structure: */ +typedef struct cJSON +{ + /* next/prev allow you to walk array/object chains. Alternatively, use GetArraySize/GetArrayItem/GetObjectItem */ + struct cJSON *next; + struct cJSON *prev; + /* An array or object item will have a child pointer pointing to a chain of the items in the array/object. */ + struct cJSON *child; + + /* The type of the item, as above. */ + int type; + + /* The item's string, if type==cJSON_String and type == cJSON_Raw */ + char *valuestring; + /* writing to valueint is DEPRECATED, use cJSON_SetNumberValue instead */ + int valueint; + /* The item's number, if type==cJSON_Number */ + double valuedouble; + + /* The item's name string, if this item is the child of, or is in the list of subitems of an object. */ + char *string; +} cJSON; + +typedef struct cJSON_Hooks +{ + /* malloc/free are CDECL on Windows regardless of the default calling convention of the compiler, so ensure the hooks allow passing those functions directly. */ + void *(CJSON_CDECL *malloc_fn)(size_t sz); + void (CJSON_CDECL *free_fn)(void *ptr); +} cJSON_Hooks; + +typedef int cJSON_bool; + +/* Limits how deeply nested arrays/objects can be before cJSON rejects to parse them. + * This is to prevent stack overflows. */ +#ifndef CJSON_NESTING_LIMIT +#define CJSON_NESTING_LIMIT 1000 +#endif + +/* Precision of double variables comparison */ +#ifndef CJSON_DOUBLE_PRECISION +#define CJSON_DOUBLE_PRECISION .0000000000000001 +#endif + +/* returns the version of cJSON as a string */ +CJSON_PUBLIC(const char*) cJSON_Version(void); + +/* Supply malloc, realloc and free functions to cJSON */ +CJSON_PUBLIC(void) cJSON_InitHooks(cJSON_Hooks* hooks); + +/* Memory Management: the caller is always responsible to free the results from all variants of cJSON_Parse (with cJSON_Delete) and cJSON_Print (with stdlib free, cJSON_Hooks.free_fn, or cJSON_free as appropriate). The exception is cJSON_PrintPreallocated, where the caller has full responsibility of the buffer. */ +/* Supply a block of JSON, and this returns a cJSON object you can interrogate. */ +CJSON_PUBLIC(cJSON *) cJSON_Parse(const char *value); +/* ParseWithOpts allows you to require (and check) that the JSON is null terminated, and to retrieve the pointer to the final byte parsed. */ +/* If you supply a ptr in return_parse_end and parsing fails, then return_parse_end will contain a pointer to the error so will match cJSON_GetErrorPtr(). */ +CJSON_PUBLIC(cJSON *) cJSON_ParseWithOpts(const char *value, const char **return_parse_end, cJSON_bool require_null_terminated); + +/* Render a cJSON entity to text for transfer/storage. */ +CJSON_PUBLIC(char *) cJSON_Print(const cJSON *item); +/* Render a cJSON entity to text for transfer/storage without any formatting. */ +CJSON_PUBLIC(char *) cJSON_PrintUnformatted(const cJSON *item); +/* Render a cJSON entity to text using a buffered strategy. prebuffer is a guess at the final size. guessing well reduces reallocation. fmt=0 gives unformatted, =1 gives formatted */ +CJSON_PUBLIC(char *) cJSON_PrintBuffered(const cJSON *item, int prebuffer, cJSON_bool fmt); +/* Render a cJSON entity to text using a buffer already allocated in memory with given length. Returns 1 on success and 0 on failure. */ +/* NOTE: cJSON is not always 100% accurate in estimating how much memory it will use, so to be safe allocate 5 bytes more than you actually need */ +CJSON_PUBLIC(cJSON_bool) cJSON_PrintPreallocated(cJSON *item, char *buffer, const int length, const cJSON_bool format); +/* Delete a cJSON entity and all subentities. */ +CJSON_PUBLIC(void) cJSON_Delete(cJSON *item); + +/* Returns the number of items in an array (or object). */ +CJSON_PUBLIC(int) cJSON_GetArraySize(const cJSON *array); +/* Retrieve item number "index" from array "array". Returns NULL if unsuccessful. */ +CJSON_PUBLIC(cJSON *) cJSON_GetArrayItem(const cJSON *array, int index); +/* Get item "string" from object. Case insensitive. */ +CJSON_PUBLIC(cJSON *) cJSON_GetObjectItem(const cJSON * const object, const char * const string); +CJSON_PUBLIC(cJSON *) cJSON_GetObjectItemCaseSensitive(const cJSON * const object, const char * const string); +CJSON_PUBLIC(cJSON_bool) cJSON_HasObjectItem(const cJSON *object, const char *string); +/* For analysing failed parses. This returns a pointer to the parse error. You'll probably need to look a few chars back to make sense of it. Defined when cJSON_Parse() returns 0. 0 when cJSON_Parse() succeeds. */ +CJSON_PUBLIC(const char *) cJSON_GetErrorPtr(void); + +/* Check if the item is a string and return its valuestring */ +CJSON_PUBLIC(char *) cJSON_GetStringValue(const cJSON * const item); + +/* These functions check the type of an item */ +CJSON_PUBLIC(cJSON_bool) cJSON_IsInvalid(const cJSON * const item); +CJSON_PUBLIC(cJSON_bool) cJSON_IsFalse(const cJSON * const item); +CJSON_PUBLIC(cJSON_bool) cJSON_IsTrue(const cJSON * const item); +CJSON_PUBLIC(cJSON_bool) cJSON_IsBool(const cJSON * const item); +CJSON_PUBLIC(cJSON_bool) cJSON_IsNull(const cJSON * const item); +CJSON_PUBLIC(cJSON_bool) cJSON_IsNumber(const cJSON * const item); +CJSON_PUBLIC(cJSON_bool) cJSON_IsString(const cJSON * const item); +CJSON_PUBLIC(cJSON_bool) cJSON_IsArray(const cJSON * const item); +CJSON_PUBLIC(cJSON_bool) cJSON_IsObject(const cJSON * const item); +CJSON_PUBLIC(cJSON_bool) cJSON_IsRaw(const cJSON * const item); + +/* These calls create a cJSON item of the appropriate type. */ +CJSON_PUBLIC(cJSON *) cJSON_CreateNull(void); +CJSON_PUBLIC(cJSON *) cJSON_CreateTrue(void); +CJSON_PUBLIC(cJSON *) cJSON_CreateFalse(void); +CJSON_PUBLIC(cJSON *) cJSON_CreateBool(cJSON_bool boolean); +CJSON_PUBLIC(cJSON *) cJSON_CreateNumber(double num); +CJSON_PUBLIC(cJSON *) cJSON_CreateString(const char *string); +/* raw json */ +CJSON_PUBLIC(cJSON *) cJSON_CreateRaw(const char *raw); +CJSON_PUBLIC(cJSON *) cJSON_CreateArray(void); +CJSON_PUBLIC(cJSON *) cJSON_CreateObject(void); + +/* Create a string where valuestring references a string so + * it will not be freed by cJSON_Delete */ +CJSON_PUBLIC(cJSON *) cJSON_CreateStringReference(const char *string); +/* Create an object/array that only references it's elements so + * they will not be freed by cJSON_Delete */ +CJSON_PUBLIC(cJSON *) cJSON_CreateObjectReference(const cJSON *child); +CJSON_PUBLIC(cJSON *) cJSON_CreateArrayReference(const cJSON *child); + +/* These utilities create an Array of count items. + * The parameter count cannot be greater than the number of elements in the number array, otherwise array access will be out of bounds.*/ +CJSON_PUBLIC(cJSON *) cJSON_CreateIntArray(const int *numbers, int count); +CJSON_PUBLIC(cJSON *) cJSON_CreateFloatArray(const float *numbers, int count); +CJSON_PUBLIC(cJSON *) cJSON_CreateDoubleArray(const double *numbers, int count); +CJSON_PUBLIC(cJSON *) cJSON_CreateStringArray(const char *const *strings, int count); + +/* Append item to the specified array/object. */ +CJSON_PUBLIC(void) cJSON_AddItemToArray(cJSON *array, cJSON *item); +CJSON_PUBLIC(void) cJSON_AddItemToObject(cJSON *object, const char *string, cJSON *item); +/* Use this when string is definitely const (i.e. a literal, or as good as), and will definitely survive the cJSON object. + * WARNING: When this function was used, make sure to always check that (item->type & cJSON_StringIsConst) is zero before + * writing to `item->string` */ +CJSON_PUBLIC(void) cJSON_AddItemToObjectCS(cJSON *object, const char *string, cJSON *item); +/* Append reference to item to the specified array/object. Use this when you want to add an existing cJSON to a new cJSON, but don't want to corrupt your existing cJSON. */ +CJSON_PUBLIC(void) cJSON_AddItemReferenceToArray(cJSON *array, cJSON *item); +CJSON_PUBLIC(void) cJSON_AddItemReferenceToObject(cJSON *object, const char *string, cJSON *item); + +/* Remove/Detach items from Arrays/Objects. */ +CJSON_PUBLIC(cJSON *) cJSON_DetachItemViaPointer(cJSON *parent, cJSON * const item); +CJSON_PUBLIC(cJSON *) cJSON_DetachItemFromArray(cJSON *array, int which); +CJSON_PUBLIC(void) cJSON_DeleteItemFromArray(cJSON *array, int which); +CJSON_PUBLIC(cJSON *) cJSON_DetachItemFromObject(cJSON *object, const char *string); +CJSON_PUBLIC(cJSON *) cJSON_DetachItemFromObjectCaseSensitive(cJSON *object, const char *string); +CJSON_PUBLIC(void) cJSON_DeleteItemFromObject(cJSON *object, const char *string); +CJSON_PUBLIC(void) cJSON_DeleteItemFromObjectCaseSensitive(cJSON *object, const char *string); + +/* Update array items. */ +CJSON_PUBLIC(void) cJSON_InsertItemInArray(cJSON *array, int which, cJSON *newitem); /* Shifts pre-existing items to the right. */ +CJSON_PUBLIC(cJSON_bool) cJSON_ReplaceItemViaPointer(cJSON * const parent, cJSON * const item, cJSON * replacement); +CJSON_PUBLIC(void) cJSON_ReplaceItemInArray(cJSON *array, int which, cJSON *newitem); +CJSON_PUBLIC(void) cJSON_ReplaceItemInObject(cJSON *object,const char *string,cJSON *newitem); +CJSON_PUBLIC(void) cJSON_ReplaceItemInObjectCaseSensitive(cJSON *object,const char *string,cJSON *newitem); + +/* Duplicate a cJSON item */ +CJSON_PUBLIC(cJSON *) cJSON_Duplicate(const cJSON *item, cJSON_bool recurse); +/* Duplicate will create a new, identical cJSON item to the one you pass, in new memory that will + * need to be released. With recurse!=0, it will duplicate any children connected to the item. + * The item->next and ->prev pointers are always zero on return from Duplicate. */ +/* Recursively compare two cJSON items for equality. If either a or b is NULL or invalid, they will be considered unequal. + * case_sensitive determines if object keys are treated case sensitive (1) or case insensitive (0) */ +CJSON_PUBLIC(cJSON_bool) cJSON_Compare(const cJSON * const a, const cJSON * const b, const cJSON_bool case_sensitive); + +/* Minify a strings, remove blank characters(such as ' ', '\t', '\r', '\n') from strings. + * The input pointer json cannot point to a read-only address area, such as a string constant, + * but should point to a readable and writable adress area. */ +CJSON_PUBLIC(void) cJSON_Minify(char *json); + +/* Helper functions for creating and adding items to an object at the same time. + * They return the added item or NULL on failure. */ +CJSON_PUBLIC(cJSON*) cJSON_AddNullToObject(cJSON * const object, const char * const name); +CJSON_PUBLIC(cJSON*) cJSON_AddTrueToObject(cJSON * const object, const char * const name); +CJSON_PUBLIC(cJSON*) cJSON_AddFalseToObject(cJSON * const object, const char * const name); +CJSON_PUBLIC(cJSON*) cJSON_AddBoolToObject(cJSON * const object, const char * const name, const cJSON_bool boolean); +CJSON_PUBLIC(cJSON*) cJSON_AddNumberToObject(cJSON * const object, const char * const name, const double number); +CJSON_PUBLIC(cJSON*) cJSON_AddStringToObject(cJSON * const object, const char * const name, const char * const string); +CJSON_PUBLIC(cJSON*) cJSON_AddRawToObject(cJSON * const object, const char * const name, const char * const raw); +CJSON_PUBLIC(cJSON*) cJSON_AddObjectToObject(cJSON * const object, const char * const name); +CJSON_PUBLIC(cJSON*) cJSON_AddArrayToObject(cJSON * const object, const char * const name); + +/* When assigning an integer value, it needs to be propagated to valuedouble too. */ +#define cJSON_SetIntValue(object, number) ((object) ? (object)->valueint = (object)->valuedouble = (number) : (number)) +/* helper for the cJSON_SetNumberValue macro */ +CJSON_PUBLIC(double) cJSON_SetNumberHelper(cJSON *object, double number); +#define cJSON_SetNumberValue(object, number) ((object != NULL) ? cJSON_SetNumberHelper(object, (double)number) : (number)) + +/* Macro for iterating over an array or object */ +#define cJSON_ArrayForEach(element, array) for(element = (array != NULL) ? (array)->child : NULL; element != NULL; element = element->next) + +/* malloc/free objects using the malloc/free functions that have been set with cJSON_InitHooks */ +CJSON_PUBLIC(void *) cJSON_malloc(size_t size); +CJSON_PUBLIC(void) cJSON_free(void *object); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/console/main_console.cpp b/console/main_console.cpp index a5aaf799..48539dbe 100644 --- a/console/main_console.cpp +++ b/console/main_console.cpp @@ -80,7 +80,11 @@ void showHelp(const char *argv[], struct TDCMopts opts) { printf(" -ba : anonymize BIDS (y/n, default %c)\n", bool2Char(opts.isAnonymizeBIDS)); printf(" -c : comment stored in NIfTI aux_file (provide up to 24 characters e.g. '-c first_visit')\n"); printf(" -d : directory search depth. Convert DICOMs in sub-folders of in_folder? (0..9, default %d)\n", opts.dirSearchDepth); - printf(" -e : export as NRRD (y) or MGH (o) instead of NIfTI (y/n/o, default n)\n"); +#ifdef myEnableJNIfTI + printf(" -e : export as NRRD (y) or MGH (o) or JSON/JNIfTI (j) or BJNIfTI (b) instead of NIfTI (y/n/o/j/b, default n)\n"); +#else + printf(" -e : export as NRRD (y) or MGH (o) instead of NIfTI (y/n/o/j/b, default n)\n"); +#endif #ifdef mySegmentByAcq #define kQstr " %%q=sequence number," #else @@ -174,7 +178,7 @@ void showHelp(const char *argv[], struct TDCMopts opts) { } //showHelp() int invalidParam(int i, const char *argv[]) { - if ((argv[i][0] == 'y') || (argv[i][0] == 'Y') || (argv[i][0] == 'n') || (argv[i][0] == 'N') || (argv[i][0] == 'o') || (argv[i][0] == 'O') || (argv[i][0] == 'h') || (argv[i][0] == 'H') || (argv[i][0] == 'i') || (argv[i][0] == 'I') || (argv[i][0] == '0') || (argv[i][0] == '1') || (argv[i][0] == '2') || (argv[i][0] == '3')) + if (strchr("yYnNoOhHiIjJBb01234",argv[i][0])) return 0; //if (argv[i][0] != '-') return 0; @@ -359,6 +363,16 @@ int main(int argc, const char *argv[]) { opts.saveFormat = kSaveFormatNRRD; if ((argv[i][0] == 'o') || (argv[i][0] == 'O') || (argv[i][0] == '2')) opts.saveFormat = kSaveFormatMGH; + if ((argv[i][0] == 'j') || (argv[i][0] == 'J') || (argv[i][0] == '3')) + opts.saveFormat = kSaveFormatJNII; + if ((argv[i][0] == 'b') || (argv[i][0] == 'B') || (argv[i][0] == '4')) + opts.saveFormat = kSaveFormatBNII; + #ifndef myEnableJNIfTI + if ((opts.saveFormat == kSaveFormatJNII) || (opts.saveFormat == kSaveFormatBNII)) { + printf("Recompile for JNIfTI support.\n"); + return EXIT_SUCCESS; + } + #endif } else if ((argv[i][1] == 'g') && ((i + 1) < argc)) { i++; if (invalidParam(i, argv)) diff --git a/console/makefile b/console/makefile index 49084991..3b14bfa9 100644 --- a/console/makefile +++ b/console/makefile @@ -6,14 +6,20 @@ CFLAGS=-s -O3 #Leak tests: # https://clang.llvm.org/docs/AddressSanitizer.html -# clang++ -O1 -g -fsanitize=address -fno-omit-frame-pointer -I. main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -o dcm2niix -DmyDisableOpenJPEG +# clang++ -O1 -g -fsanitize=address -fno-omit-frame-pointer -I. main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp base64.c cJSON.c -o dcm2niix -DmyDisableOpenJPEG #run "make" for default build #run "JPEGLS=1 make" for JPEGLS build JFLAGS= ifeq "$(JPEGLS)" "1" - JFLAGS=-std=c++14 -DmyEnableJPEGLS charls/jpegls.cpp charls/jpegmarkersegment.cpp charls/interface.cpp charls/jpegstreamwriter.cpp charls/jpegstreamreader.cpp + JFLAGS=-std=c++14 -DmyEnableJPEGLS charls/jpegls.cpp charls/jpegmarkersegment.cpp charls/interface.cpp charls/jpegstreamwriter.cpp charls/jpegstreamreader.cpp +endif + +#run "JNIfTI=0 make" to disable JNIFTI build +JSFLAGS= +ifneq "$(JNIfTI)" "0" + JSFLAGS=-DmyEnableJNIfTI base64.cpp cJSON.cpp endif ifneq ($(OS),Windows_NT) @@ -31,4 +37,4 @@ ifneq ($(OS),Windows_NT) endif endif all: - g++ $(CFLAGS) -I. $(JFLAGS) main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -o dcm2niix -DmyDisableOpenJPEG + g++ $(CFLAGS) -I. $(JSFLAGS) $(JFLAGS) main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -o dcm2niix -DmyDisableOpenJPEG diff --git a/console/nii_dicom_batch.cpp b/console/nii_dicom_batch.cpp index 1a9329f4..7b6a6958 100644 --- a/console/nii_dicom_batch.cpp +++ b/console/nii_dicom_batch.cpp @@ -38,6 +38,10 @@ #endif #include "nii_dicom.h" #include "nii_ortho.h" +#ifdef myEnableJNIfTI + #include "base64.h" + #include "cJSON.h" +#endif #include //toupper #include #include @@ -3340,11 +3344,22 @@ void nii_createDummyFilename(char *niiFilename, struct TDCMopts opts) { nii_createFilename(d, niiFilenameBase, opts); strcpy(niiFilename, "Example output filename: '"); strcat(niiFilename, niiFilenameBase); - if (opts.saveFormat != kSaveFormatNIfTI) { + if (opts.saveFormat == kSaveFormatMGH) { + if (opts.isGz) + strcat(niiFilename, ".mgz'"); + else + strcat(niiFilename, ".mgh'"); + } else if (opts.saveFormat == kSaveFormatNRRD) { if (opts.isGz) strcat(niiFilename, ".nhdr'"); else strcat(niiFilename, ".nrrd'"); + #ifdef myEnableJNIfTI + } else if (opts.saveFormat == kSaveFormatJNII) { + strcat(niiFilename, ".jnii'"); + } else if (opts.saveFormat == kSaveFormatBNII) { + strcat(niiFilename, ".bnii'"); + #endif } else { if (opts.isGz) strcat(niiFilename, ".nii.gz'"); @@ -4138,9 +4153,583 @@ int nii_saveNRRD(char *niiFilename, struct nifti_1_header hdr, unsigned char *im return pigz_File(fname, opts, imgsz); } // nii_saveNRRD() +enum TZipMethod {zmZlib, zmGzip, zmBase64}; + +#ifdef myEnableJNIfTI +#ifdef Z_DEFLATED + +int zmat_run(const size_t inputsize, unsigned char *inputstr, size_t *outputsize, unsigned char **outputbuf, const int zipid, int *ret, const int iscompress){ + z_stream zs; + size_t buflen[2]={0}; + *outputbuf=NULL; + + zs.zalloc = Z_NULL; + zs.zfree = Z_NULL; + zs.opaque = Z_NULL; + + if(inputsize==0) + return -1; + + if(iscompress){ + /** perform compression or encoding */ + if(zipid==zmBase64){ + /** base64 encoding */ + *outputbuf=base64_encode((const unsigned char*)inputstr, inputsize, outputsize); + }else if(zipid==zmZlib || zipid==zmGzip){ + /** zlib (.zip) or gzip (.gz) compression */ + if(zipid==zmZlib){ + if(deflateInit(&zs, (iscompress>0) ? Z_DEFAULT_COMPRESSION : (-iscompress)) != Z_OK) + return -2; + }else{ + if(deflateInit2(&zs, (iscompress>0) ? Z_DEFAULT_COMPRESSION : (-iscompress), Z_DEFLATED, 15|16, MAX_MEM_LEVEL, Z_DEFAULT_STRATEGY) != Z_OK) + return -2; + } + buflen[0] =deflateBound(&zs,inputsize); + *outputbuf=(unsigned char *)malloc(buflen[0]); + zs.avail_in = inputsize; /* size of input, string + terminator*/ + zs.next_in = (Bytef *)inputstr; /* input char array*/ + zs.avail_out = buflen[0]; /* size of output*/ + + zs.next_out = (Bytef *)(*outputbuf); /*(Bytef *)(); // output char array*/ + + *ret=deflate(&zs, Z_FINISH); + *outputsize=zs.total_out; + if(*ret!=Z_STREAM_END && *ret!=Z_OK) + return -3; + deflateEnd(&zs); + }else{ + return -7; + } + }else{ + /** perform decompression or decoding */ + if(zipid==zmBase64){ + /** base64 decoding */ + *outputbuf=base64_decode((const unsigned char*)inputstr, inputsize, outputsize); + }else if(zipid==zmZlib || zipid==zmGzip){ + /** zlib (.zip) or gzip (.gz) decompression */ + int count=1; + if(zipid==zmZlib){ + if(inflateInit(&zs) != Z_OK) + return -2; + }else{ + if(inflateInit2(&zs, 15|32) != Z_OK) + return -2; + } + + buflen[0] =inputsize*20; + *outputbuf=(unsigned char *)malloc(buflen[0]); + + zs.avail_in = inputsize; /* size of input, string + terminator*/ + zs.next_in =inputstr; /* input char array*/ + zs.avail_out = buflen[0]; /* size of output*/ + + zs.next_out = (Bytef *)(*outputbuf); /*(Bytef *)(); // output char array*/ + + while((*ret=inflate(&zs, Z_SYNC_FLUSH))!=Z_STREAM_END && count<=10){ + *outputbuf=(unsigned char *)realloc(*outputbuf, (buflen[0]<1) + dim[ndim++]=jdataelemlen; + + for(int i=0;i0 && output[i][0]!='?'){ // take care all name-tags and constant string values + if(!(slen==1 && output[i][0]=='N')) + fwrite(output[i],1,slen,fp); + if(slen==1 && (output[i][0]=='N' || output[i][0]=='S') && i+20){ + int slotid=0; + if(sscanf(output[i],"\?%d",&slotid)==1 && slotid>0){ + unsigned char *compressed=NULL; + size_t compressedbytes; + int ret=0, status=0; + switch(slotid){ // mapping data to the pre-defined slots in the form of "?number" in the template + case 1: {write_ubjsonint(&hdr.sizeof_hdr,sizeof(hdr.sizeof_hdr),1,fp);break;} + case 2: {fputc(ndim,fp);break;} + case 3: {write_ubjsonint(hdr.dim+1, sizeof(hdr.dim[0]), ndim,fp);break;} + case 4: {write_ubjsonint(&hdr.intent_p1,1,sizeof(hdr.intent_p1),fp);break;} + case 5: {write_ubjsonint(&hdr.intent_p2,1,sizeof(hdr.intent_p2),fp);break;} + case 6: {write_ubjsonint(&hdr.intent_p3,1,sizeof(hdr.intent_p3),fp);break;} + case 7: {unsigned char val=strlen(intent);fputc('U',fp);fputc(val,fp); fwrite(intent,1,val,fp);break;} + case 8: {unsigned char val=strlen(dtype); fputc('U',fp);fputc(val,fp); fwrite(dtype,1,val,fp);break;} + case 9: {fputc(hdr.bitpix,fp);break;} + case 10: {write_ubjsonint(&hdr.slice_start, sizeof(hdr.slice_start),1,fp);break;} + case 11: {fputc(ndim,fp);break;} + case 12: {write_ubjsonint(&hdr.pixdim[1],ndim,sizeof(hdr.pixdim[1]),fp);break;} + case 13: {fputc((int)hdr.pixdim[0] ? 'l' : 'r',fp);break;} + case 14: {write_ubjsonint(&hdr.scl_slope,1,sizeof(hdr.scl_slope),fp);break;} + case 15: {write_ubjsonint(&hdr.scl_inter,1,sizeof(hdr.scl_inter),fp);break;} + case 16: {write_ubjsonint(&hdr.slice_end,sizeof(hdr.slice_end),1,fp);break;} + case 17: {unsigned char val=strlen(slicetype);fputc('U',fp);fputc(val,fp); fwrite(slicetype,1,val,fp);break;} + case 18: {unsigned char val=strlen(lunit);fputc('U',fp);fputc(val,fp); fwrite(lunit,1,val,fp);break;} + case 19: {unsigned char val=strlen(tunit);fputc('U',fp);fputc(val,fp); fwrite(tunit,1,val,fp);break;} + case 20: {write_ubjsonint(&hdr.cal_max,1,sizeof(hdr.cal_max),fp);break;} + case 21: {write_ubjsonint(&hdr.cal_min,1,sizeof(hdr.cal_min),fp);break;} + case 22: {write_ubjsonint(&hdr.slice_duration,1,sizeof(hdr.slice_duration),fp);break;} + case 23: {write_ubjsonint(&hdr.toffset,1,sizeof(hdr.toffset),fp);break;} + case 24: {unsigned char val=strlen(hdr.descrip);fputc('U',fp);fputc(val,fp); fwrite(hdr.descrip,1,val,fp);break;} + case 25: {unsigned char val=strlen(hdr.aux_file);fputc('U',fp);fputc(val,fp); fwrite(hdr.aux_file,1,val,fp);break;} + case 26: {write_ubjsonint(&hdr.qform_code,sizeof(hdr.qform_code),1,fp);break;} + case 27: {write_ubjsonint(&hdr.sform_code,sizeof(hdr.sform_code),1,fp);break;} + case 28: {write_ubjsonint(&hdr.quatern_b,1,sizeof(hdr.quatern_b),fp);break;} + case 29: {write_ubjsonint(&hdr.quatern_c,1,sizeof(hdr.quatern_c),fp);break;} + case 30: {write_ubjsonint(&hdr.quatern_d,1,sizeof(hdr.quatern_d),fp);break;} + case 31: {write_ubjsonint(&hdr.qoffset_x,1,sizeof(hdr.qoffset_x),fp);break;} + case 32: {write_ubjsonint(&hdr.qoffset_y,1,sizeof(hdr.qoffset_y),fp);break;} + case 33: {write_ubjsonint(&hdr.qoffset_z,1,sizeof(hdr.qoffset_z),fp);break;} + case 34: { + write_ubjsonint(&hdr.srow_x[0],4,sizeof(hdr.srow_x[0]),fp); + write_ubjsonint(&hdr.srow_y[0],4,sizeof(hdr.srow_y[0]),fp); + write_ubjsonint(&hdr.srow_z[0],4,sizeof(hdr.srow_z[0]),fp); + break; + } + case 35: {unsigned char val=strlen(hdr.intent_name);fputc('U',fp);fputc(val,fp); fwrite(hdr.intent_name,1,val,fp);break;} + case 36: {unsigned char val=strlen(hdr.magic);fputc('U',fp);fputc(val,fp); fwrite(hdr.magic,1,val,fp);break;} + case 37: {int val=hdr.vox_offset;write_ubjsonint(&val, sizeof(val), 1,fp);break;} + case 38: {unsigned char val=strlen(jdtype);fputc('U',fp);fputc(val,fp); fwrite(jdtype,1,val,fp);break;} + case 39: {fputc(ndim,fp);break;} + case 40: { + write_ubjsonint(dim, sizeof(dim[0]), ndim, fp); + if(!opts.isGz){ + const char *datastub="U\x0b_ArrayData_[$"; + fwrite(datastub,1,strlen(datastub),fp); + fputc(jdatamarker,fp); + fputc('#',fp); + + size_t totalelem=(totalbytes/(hdr.bitpix>>3)); + unsigned int clen=totalelem; + if((size_t)clen==totalelem){ + fputc('l',fp); + write_ubjsonint(&clen, sizeof(clen), 1,fp); + }else{ + fputc('L',fp); + write_ubjsonint(&totalelem, sizeof(totalelem), 1,fp); + } + fwrite(im,1,totalbytes,fp); + fputc('}',fp); // end of NIFTIData + fputc('}',fp); // end of the root object + } + break; + } +#ifdef Z_DEFLATED + case 41: {fputc('U',fp);fputc(4,fp);fwrite("zlib",1,4,fp);break;} + case 42: {unsigned int val=(totalbytes/(hdr.bitpix>>3));write_ubjsonint(&val,sizeof(val), 1,fp);break;} + case 43: + ret=zmat_run(totalbytes, im, &compressedbytes, (unsigned char **)&compressed, zmZlib, &status, -opts.gzLevel); + if(!ret){ + unsigned int clen=compressedbytes; + if((size_t)clen==compressedbytes){ + fputc('l',fp); + write_ubjsonint(&clen, sizeof(clen), 1,fp); + }else{ + fputc('L',fp); + write_ubjsonint(&compressedbytes, sizeof(compressedbytes), 1,fp); + } + fwrite(compressed,1,compressedbytes,fp); + }else{ + printError("Failed to compress data stream, error code=%d, status code=%d\n", ret, status); + return EXIT_FAILURE; + } + if(compressed) + free(compressed); + break; +#endif + } + if(!opts.isGz && slotid==40) + break; + } + } + } + fclose(fp); + return EXIT_SUCCESS; +} + +int nii_savejnii(char *niiFilename, struct nifti_1_header hdr, unsigned char *im, struct TDCMopts opts, struct TDICOMdata d, struct TDTI4D *dti4D, int numDTI) { +// JNIfTI is a JSON wrapper to the NIfTI-1/2 format, supports both plain-text (.jnii) and binary (.bnii) formats +// Specification: https://github.com/NeuroJSON/jnifti/blob/master/JNIfTI_specification.md +// jnii is a plain JSON file and can be parsed in nearly all JSON parsers; to decode the +// embedded binary data as strings, the NIFTIData section can be be parsed in MATLAB using +// jnifty (https://github.com/NeuroJSON/jnifty) and Python using jdata (https://github.com/NeuroJSON/pyjdata) + + FILE *fp; + int dim[8]={0}, ndim=0; /* extra dimension in dim to hold the split data from complex voxel types, such as complex64 */ + + cJSON *root=NULL, *info=NULL, *jhdr=NULL, *dat=NULL, *sub=NULL; + char *jsonstr=NULL; + size_t compressedbytes, totalbytes; + unsigned char *compressed=NULL, *buf=NULL; + + /*jnifti convers code-based header fields to human-readable/standardized strings*/ + int datatypeidx; + const char *datatypestr[]={"uint8","int16","int32","single","complex64","double", + "rgb24" ,"int8","uint16","uint32","int64","uint64", + "double128","complex128","complex256","rgba32",""}; + const char *jdatatypestr[]={"uint8","int16","int32","single","double","double", + "uint8" ,"int8","uint16","uint32","int64","uint64", + "uint8","double","uint8","uint8","uint8"}; + const char jdatamarker[]={'U','I','l','d','D','D','U','i','u','m','L','M', + 'U','D','U','U','U'}; + unsigned char jdataelemlen[]={1,1,1,1,2,1,3,1,1,1,1,1,16,2,32,4,1}; + int datatypeid[]={NIFTI_TYPE_UINT8,NIFTI_TYPE_INT16,NIFTI_TYPE_INT32, + NIFTI_TYPE_FLOAT32,NIFTI_TYPE_COMPLEX64,NIFTI_TYPE_FLOAT64, + NIFTI_TYPE_RGB24,NIFTI_TYPE_INT8,NIFTI_TYPE_UINT16, + NIFTI_TYPE_UINT32,NIFTI_TYPE_INT64,NIFTI_TYPE_UINT64, + NIFTI_TYPE_FLOAT128,NIFTI_TYPE_COMPLEX128, + NIFTI_TYPE_COMPLEX256,NIFTI_TYPE_RGBA32}; + + int lunitidx, tunitidx; + const char *unitstr[]={"m","mm","um","s","ms","us","hz","ppm","rad",""}; + int unitid[]={NIFTI_UNITS_METER,NIFTI_UNITS_MM,NIFTI_UNITS_MICRON, + NIFTI_UNITS_SEC,NIFTI_UNITS_MSEC,NIFTI_UNITS_USEC, + NIFTI_UNITS_HZ,NIFTI_UNITS_PPM,NIFTI_UNITS_RADS}; + + int slicetypeidx; + const char *slicetypestr[]={"","seq+","seq-","alt+","alt-","alt2+","alt2-",""}; + int slicetypeid[]={NIFTI_SLICE_UNKNOWN,NIFTI_SLICE_SEQ_INC, + NIFTI_SLICE_SEQ_DEC,NIFTI_SLICE_ALT_INC,NIFTI_SLICE_ALT_DEC, + NIFTI_SLICE_ALT_INC2,NIFTI_SLICE_ALT_DEC2}; + + int intentidx; + const char *intentstr[]={"","corr","ttest","ftest","zscore","chi2","beta","binomial", + "gamma","poisson","normal","ncftest","ncchi2","logistic","laplace", + "uniform","ncttest","weibull","chi","invgauss","extval","pvalue", + "logpvalue","log10pvalue","estimate","label","neuronames","matrix", + "symmatrix","dispvec","vector","point","triangle","quaternion", + "unitless","tseries","elem","rgb","rgba","shape",""}; + int intentid[]={NIFTI_INTENT_NONE,NIFTI_INTENT_CORREL,NIFTI_INTENT_TTEST, + NIFTI_INTENT_FTEST,NIFTI_INTENT_ZSCORE,NIFTI_INTENT_CHISQ, + NIFTI_INTENT_BETA,NIFTI_INTENT_BINOM,NIFTI_INTENT_GAMMA, + NIFTI_INTENT_POISSON,NIFTI_INTENT_NORMAL,NIFTI_INTENT_FTEST_NONC, + NIFTI_INTENT_CHISQ_NONC,NIFTI_INTENT_LOGISTIC,NIFTI_INTENT_LAPLACE, + NIFTI_INTENT_UNIFORM,NIFTI_INTENT_TTEST_NONC,NIFTI_INTENT_WEIBULL, + NIFTI_INTENT_CHI,NIFTI_INTENT_INVGAUSS,NIFTI_INTENT_EXTVAL, + NIFTI_INTENT_PVAL,NIFTI_INTENT_LOGPVAL,NIFTI_INTENT_LOG10PVAL, + NIFTI_INTENT_ESTIMATE,NIFTI_INTENT_LABEL,NIFTI_INTENT_NEURONAME, + NIFTI_INTENT_GENMATRIX,NIFTI_INTENT_SYMMATRIX,NIFTI_INTENT_DISPVECT, + NIFTI_INTENT_VECTOR,NIFTI_INTENT_POINTSET,NIFTI_INTENT_TRIANGLE, + NIFTI_INTENT_QUATERNION,NIFTI_INTENT_DIMLESS,NIFTI_INTENT_TIME_SERIES, + NIFTI_INTENT_NODE_INDEX,NIFTI_INTENT_RGB_VECTOR,NIFTI_INTENT_RGBA_VECTOR, + NIFTI_INTENT_SHAPE}; + char fname[2048] = {""}; + strcpy(fname, niiFilename); + if (opts.saveFormat == kSaveFormatBNII) + strcat(fname, ".bnii"); + else + strcat(fname, ".jnii"); + + /* preprocess nifti header to convert to human-readable jnifti fields */ + totalbytes=nii_ImgBytes(hdr); + ndim=hdr.dim[0]; + for(int i=1;i<8;i++) + dim[i-1]=hdr.dim[i]; + + datatypeidx=jnifti_lookup(datatypeid, sizeof(datatypeid)/sizeof(int), hdr.datatype); + slicetypeidx=jnifti_lookup(slicetypeid, sizeof(slicetypeid)/sizeof(int), hdr.slice_code); + intentidx=jnifti_lookup(intentid, sizeof(intentid)/sizeof(int), hdr.intent_code); + lunitidx=sizeof(unitid)/sizeof(unitid[0]); + tunitidx=sizeof(unitid)/sizeof(unitid[0]); + for(int i=0;i=NIFTI_UNITS_HZ && hdr.xyzt_units==unitid[i]) + cJSON_AddStringToObject(sub, "Special", unitstr[i]); + } + cJSON_AddNumberToObject(jhdr, "MaxIntensity", hdr.cal_max); + cJSON_AddNumberToObject(jhdr, "MinIntensity", hdr.cal_min); + cJSON_AddNumberToObject(jhdr, "SliceTime", hdr.slice_duration); + cJSON_AddNumberToObject(jhdr, "TimeOffset", hdr.toffset); + cJSON_AddStringToObject(jhdr, "Description", hdr.descrip); + cJSON_AddStringToObject(jhdr, "AuxFile", hdr.aux_file); + cJSON_AddNumberToObject(jhdr, "QForm", hdr.qform_code); + cJSON_AddNumberToObject(jhdr, "SForm", hdr.sform_code); + cJSON_AddItemToObject(jhdr, "Quatern", sub=cJSON_CreateObject()); + cJSON_AddNumberToObject(sub, "b", hdr.quatern_b); + cJSON_AddNumberToObject(sub, "c", hdr.quatern_c); + cJSON_AddNumberToObject(sub, "d", hdr.quatern_d); + cJSON_AddItemToObject(jhdr, "QuaternOffset", sub=cJSON_CreateObject()); + cJSON_AddNumberToObject(sub, "x", hdr.qoffset_x); + cJSON_AddNumberToObject(sub, "y", hdr.qoffset_y); + cJSON_AddNumberToObject(sub, "z", hdr.qoffset_z); + cJSON_AddItemToObject(jhdr, "Affine", sub=cJSON_CreateArray()); + cJSON_AddItemToArray(sub, cJSON_CreateFloatArray(hdr.srow_x,4)); + cJSON_AddItemToArray(sub, cJSON_CreateFloatArray(hdr.srow_y,4)); + cJSON_AddItemToArray(sub, cJSON_CreateFloatArray(hdr.srow_z,4)); + cJSON_AddStringToObject(jhdr, "Name", hdr.intent_name); + cJSON_AddStringToObject(jhdr, "NIIFormat", hdr.magic); + + /* save depreciated header flags if non-trival values are provided */ + if(hdr.vox_offset) + cJSON_AddNumberToObject(jhdr, "NIIByteOffset", hdr.vox_offset); + if(strlen(hdr.data_type)) + cJSON_AddStringToObject(jhdr, "A75DataTypeName", hdr.data_type); + if(strlen(hdr.db_name)) + cJSON_AddStringToObject(jhdr, "A75DBName", hdr.db_name); + if(hdr.extents) + cJSON_AddNumberToObject(jhdr, "A75Extends", hdr.extents); + if(hdr.session_error) + cJSON_AddNumberToObject(jhdr, "A75SessionError", hdr.session_error); + if(hdr.regular) + cJSON_AddNumberToObject(jhdr, "A75DataTypeName", hdr.regular); + if(hdr.glmax) + cJSON_AddNumberToObject(jhdr, "A75GlobalMax", hdr.glmax); + if(hdr.glmin) + cJSON_AddNumberToObject(jhdr, "A75GlobalMin", hdr.glmin); + + /* the "NIFTIData" section stores volumetric data */ + cJSON_AddItemToObject(root, "NIFTIData",dat = cJSON_CreateObject()); + cJSON_AddStringToObject(dat,"_ArrayType_",jdatatypestr[datatypeidx]); + if(jdataelemlen[datatypeidx]>1) + dim[ndim++]=jdataelemlen[datatypeidx]; + cJSON_AddItemToObject(dat, "_ArraySize_",cJSON_CreateIntArray(dim,ndim)); + cJSON_AddStringToObject(dat,"_ArrayOrder_","c"); // NIfTI array is column-major + +#ifdef Z_DEFLATED + if(opts.isGz){ + int ret=0, status=0; + cJSON_AddStringToObject(dat, "_ArrayZipType_", "zlib"); + cJSON_AddNumberToObject(dat, "_ArrayZipSize_",totalbytes/(hdr.bitpix>>3)); + + ret=zmat_run(totalbytes, im, &compressedbytes, (unsigned char **)&compressed, zmZlib, &status, -opts.gzLevel); + + if(!ret){ + ret=zmat_run(compressedbytes, compressed, &totalbytes, (unsigned char **)&buf, zmBase64, &status,1); + cJSON_AddStringToObject(dat, "_ArrayZipData_",(const char *)buf); + }else{ + printError("Failed to compress data stream, error code=%d, status code=%d\n", ret, status); + return EXIT_FAILURE; + } + if(compressed) + free(compressed); + }else{ + cJSON_AddStringToObject(dat, "_ArrayZipType_", "base64"); + cJSON_AddNumberToObject(dat, "_ArrayZipSize_",totalbytes/(hdr.bitpix>>3)); + buf=base64_encode(im, totalbytes, &compressedbytes); + cJSON_AddStringToObject(dat,"_ArrayZipData_", (const char*)buf); + } +#else + cJSON_AddStringToObject(dat, "_ArrayZipType_", "base64"); + cJSON_AddNumberToObject(dat, "_ArrayZipSize_",totalbytes/(hdr.bitpix>>3)); + buf=base64_encode(im, totalbytes, &compressedbytes); + cJSON_AddStringToObject(dat,"_ArrayZipData_", (const char*)buf); +#endif + if(buf) + free(buf); + + /* now save JSON to file */ + jsonstr=cJSON_Print(root); + if(jsonstr==NULL){ + printMessage("Error: error when converting to JNIfTI\n"); + return EXIT_FAILURE; + } + + fp=fopen(fname,"wt"); + if(fp==NULL){ + printMessage("Error: error when writing to JNIfTI file\n"); + return EXIT_FAILURE; + } + fprintf(fp,"%s\n",jsonstr); + fclose(fp); + + if(jsonstr) + free(jsonstr); + if(root) + cJSON_Delete(root); + return EXIT_SUCCESS; +} // nii_savejnii() +#endif //#ifdef myEnableJNIfTI + int nii_saveForeign(char *niiFilename, struct nifti_1_header hdr, unsigned char *im, struct TDCMopts opts, struct TDICOMdata d, struct TDTI4D *dti4D, int numDTI) { if (opts.saveFormat == kSaveFormatMGH) return nii_saveMGH(niiFilename, hdr, im, opts, d, dti4D, numDTI); + #ifdef myEnableJNIfTI + else if (opts.saveFormat == kSaveFormatJNII || opts.saveFormat == kSaveFormatBNII) + return nii_savejnii(niiFilename, hdr, im, opts, d, dti4D, numDTI); + #endif return nii_saveNRRD(niiFilename, hdr, im, opts, d, dti4D, numDTI); }// nii_saveForeign() diff --git a/console/nii_dicom_batch.h b/console/nii_dicom_batch.h index c5f453a5..80902c0d 100644 --- a/console/nii_dicom_batch.h +++ b/console/nii_dicom_batch.h @@ -50,6 +50,8 @@ void nii_clrMrifsStruct(); #define kSaveFormatNIfTI 0 #define kSaveFormatNRRD 1 #define kSaveFormatMGH 2 +#define kSaveFormatJNII 3 +#define kSaveFormatBNII 4 #define MAX_NUM_SERIES 16 diff --git a/dcm_qa b/dcm_qa index 2f59a065..bb457d98 160000 --- a/dcm_qa +++ b/dcm_qa @@ -1 +1 @@ -Subproject commit 2f59a065686f1bdab52f8c4c529e1e2e7e4c133f +Subproject commit bb457d98bdb320af3b9f29fad1c706788490dab8 diff --git a/dcm_qa_nih b/dcm_qa_nih index 0a0aa943..aa82e560 160000 --- a/dcm_qa_nih +++ b/dcm_qa_nih @@ -1 +1 @@ -Subproject commit 0a0aa943b5e5263645a33359e52dedf147c6a5a7 +Subproject commit aa82e560d5471b53f0d0332c4de33d88bf179157 diff --git a/dcm_qa_uih b/dcm_qa_uih index 78f21294..4c0e2b37 160000 --- a/dcm_qa_uih +++ b/dcm_qa_uih @@ -1 +1 @@ -Subproject commit 78f212941ca7adc13bd3810667084b48a0047484 +Subproject commit 4c0e2b37430fa566a501bb65f35a9ad4089e71a9