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gimp/plug-ins/common/file-dicom.c

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/* GIMP - The GNU Image Manipulation Program
* Copyright (C) 1995 Spencer Kimball and Peter Mattis
* PNM reading and writing code Copyright (C) 1996 Erik Nygren
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
/*
* The dicom reading and writing code was written from scratch
* by Dov Grobgeld. (dov.grobgeld@gmail.com).
*/
#include "config.h"
#include <errno.h>
#include <string.h>
#include <time.h>
#include <glib/gstdio.h>
#include <libgimp/gimp.h>
#include <libgimp/gimpui.h>
#include "libgimp/stdplugins-intl.h"
#define LOAD_PROC "file-dicom-load"
#define SAVE_PROC "file-dicom-save"
#define PLUG_IN_BINARY "file-dicom"
#define PLUG_IN_ROLE "gimp-file-dicom"
/* A lot of Dicom images are wrongly encoded. By guessing the endian
* we can get around this problem.
*/
#define GUESS_ENDIAN 1
/* Declare local data types */
typedef struct _DicomInfo
{
guint width, height; /* The size of the image */
gint maxval; /* For 16 and 24 bit image files, the max
value which we need to normalize to */
gint samples_per_pixel; /* Number of image planes (0 for pbm) */
gint bpp;
gint bits_stored;
gint high_bit;
gboolean is_signed;
} DicomInfo;
/* Local function prototypes */
static void query (void);
static void run (const gchar *name,
gint nparams,
const GimpParam *param,
gint *nreturn_vals,
GimpParam **return_vals);
static gint32 load_image (const gchar *filename,
GError **error);
static gboolean save_image (const gchar *filename,
gint32 image_ID,
gint32 drawable_ID,
GError **error);
static void dicom_loader (guint8 *pix_buf,
DicomInfo *info,
GeglBuffer *buffer);
static void guess_and_set_endian2 (guint16 *buf16,
gint length);
static void toggle_endian2 (guint16 *buf16,
gint length);
static void add_tag_pointer (GByteArray *group_stream,
gint group,
gint element,
const gchar *value_rep,
const guint8 *data,
gint length);
static GSList * dicom_add_tags (FILE *DICOM,
GByteArray *group_stream,
GSList *elements);
static gboolean write_group_to_file (FILE *DICOM,
gint group,
GByteArray *group_stream);
const GimpPlugInInfo PLUG_IN_INFO =
{
NULL, /* init_proc */
NULL, /* quit_proc */
query, /* query_proc */
run, /* run_proc */
};
MAIN ()
static void
query (void)
{
static const GimpParamDef load_args[] =
{
{ GIMP_PDB_INT32, "run-mode", "The run mode { RUN-INTERACTIVE (0), RUN-NONINTERACTIVE (1) }" },
{ GIMP_PDB_STRING, "filename", "The name of the file to load" },
{ GIMP_PDB_STRING, "raw-filename", "The name of the file to load" }
};
static const GimpParamDef load_return_vals[] =
{
{ GIMP_PDB_IMAGE, "image", "Output image" }
};
static const GimpParamDef save_args[] =
{
{ GIMP_PDB_INT32, "run-mode", "The run mode { RUN-INTERACTIVE (0), RUN-NONINTERACTIVE (1) }" },
{ GIMP_PDB_IMAGE, "image", "Input image" },
{ GIMP_PDB_DRAWABLE, "drawable", "Drawable to save" },
{ GIMP_PDB_STRING, "filename", "The name of the file to save" },
{ GIMP_PDB_STRING, "raw-filename", "The name of the file to save" },
};
gimp_install_procedure (LOAD_PROC,
"loads files of the dicom file format",
"Load a file in the DICOM standard format."
"The standard is defined at "
"http://medical.nema.org/. The plug-in currently "
"only supports reading images with uncompressed "
"pixel sections.",
"Dov Grobgeld",
"Dov Grobgeld <dov@imagic.weizmann.ac.il>",
"2003",
N_("DICOM image"),
NULL,
GIMP_PLUGIN,
G_N_ELEMENTS (load_args),
G_N_ELEMENTS (load_return_vals),
load_args, load_return_vals);
gimp_register_file_handler_mime (LOAD_PROC, "image/x-dcm");
gimp_register_magic_load_handler (LOAD_PROC,
"dcm,dicom",
"",
"128,string,DICM"
);
gimp_install_procedure (SAVE_PROC,
"Save file in the DICOM file format",
"Save an image in the medical standard DICOM image "
"formats. The standard is defined at "
"http://medical.nema.org/. The file format is "
"defined in section 10 of the standard. The files "
"are saved uncompressed and the compulsory DICOM "
"tags are filled with default dummy values.",
"Dov Grobgeld",
"Dov Grobgeld <dov@imagic.weizmann.ac.il>",
"2003",
N_("Digital Imaging and Communications in "
"Medicine image"),
"RGB, GRAY",
GIMP_PLUGIN,
G_N_ELEMENTS (save_args), 0,
save_args, NULL);
gimp_register_file_handler_mime (SAVE_PROC, "image/x-dcm");
gimp_register_save_handler (SAVE_PROC, "dcm,dicom", "");
}
static void
run (const gchar *name,
gint nparams,
const GimpParam *param,
gint *nreturn_vals,
GimpParam **return_vals)
{
static GimpParam values[2];
GimpRunMode run_mode;
GimpPDBStatusType status = GIMP_PDB_SUCCESS;
gint32 image_ID;
gint32 drawable_ID;
GimpExportReturn export = GIMP_EXPORT_CANCEL;
GError *error = NULL;
INIT_I18N ();
gegl_init (NULL, NULL);
run_mode = param[0].data.d_int32;
*nreturn_vals = 1;
*return_vals = values;
values[0].type = GIMP_PDB_STATUS;
values[0].data.d_status = GIMP_PDB_EXECUTION_ERROR;
if (strcmp (name, LOAD_PROC) == 0)
{
image_ID = load_image (param[1].data.d_string, &error);
if (image_ID != -1)
{
*nreturn_vals = 2;
values[1].type = GIMP_PDB_IMAGE;
values[1].data.d_image = image_ID;
}
else
{
status = GIMP_PDB_EXECUTION_ERROR;
if (error)
{
*nreturn_vals = 2;
values[1].type = GIMP_PDB_STRING;
values[1].data.d_string = error->message;
}
}
}
else if (strcmp (name, SAVE_PROC) == 0)
{
image_ID = param[1].data.d_int32;
drawable_ID = param[2].data.d_int32;
switch (run_mode)
{
case GIMP_RUN_INTERACTIVE:
case GIMP_RUN_WITH_LAST_VALS:
gimp_ui_init (PLUG_IN_BINARY, FALSE);
export = gimp_export_image (&image_ID, &drawable_ID, "DICOM",
GIMP_EXPORT_CAN_HANDLE_RGB |
GIMP_EXPORT_CAN_HANDLE_GRAY);
if (export == GIMP_EXPORT_CANCEL)
{
values[0].data.d_status = GIMP_PDB_CANCEL;
return;
}
break;
default:
break;
}
switch (run_mode)
{
case GIMP_RUN_INTERACTIVE:
break;
case GIMP_RUN_NONINTERACTIVE:
/* Make sure all the arguments are there! */
if (nparams != 5)
status = GIMP_PDB_CALLING_ERROR;
break;
case GIMP_RUN_WITH_LAST_VALS:
break;
default:
break;
}
if (status == GIMP_PDB_SUCCESS)
{
if (! save_image (param[3].data.d_string, image_ID, drawable_ID,
&error))
{
status = GIMP_PDB_EXECUTION_ERROR;
if (error)
{
*nreturn_vals = 2;
values[1].type = GIMP_PDB_STRING;
values[1].data.d_string = error->message;
}
}
}
if (export == GIMP_EXPORT_EXPORT)
gimp_image_delete (image_ID);
}
else
{
status = GIMP_PDB_CALLING_ERROR;
}
values[0].data.d_status = status;
}
/**
* add_parasites_to_image:
* @data: pointer to a GimpParasite to be attached to the image
* specified by @user_data.
* @user_data: pointer to the image_ID to which parasite @data should
* be added.
*
* Attaches parasite to image and also frees that parasite
**/
static void
add_parasites_to_image (gpointer data,
gpointer user_data)
{
GimpParasite *parasite = (GimpParasite *) data;
gint32 *image_ID = (gint32 *) user_data;
gimp_image_attach_parasite (*image_ID, parasite);
gimp_parasite_free (parasite);
}
static gint32
load_image (const gchar *filename,
GError **error)
{
gint32 volatile image_ID = -1;
gint32 layer_ID;
GeglBuffer *buffer;
GSList *elements = NULL;
FILE *DICOM;
gchar buf[500]; /* buffer for random things like scanning */
DicomInfo *dicominfo;
guint width = 0;
guint height = 0;
gint samples_per_pixel = 0;
gint bpp = 0;
gint bits_stored = 0;
gint high_bit = 0;
guint8 *pix_buf = NULL;
gboolean is_signed = FALSE;
guint8 in_sequence = 0;
gimp_progress_init_printf (_("Opening '%s'"),
gimp_filename_to_utf8 (filename));
DICOM = g_fopen (filename, "rb");
if (! DICOM)
{
g_set_error (error, G_FILE_ERROR, g_file_error_from_errno (errno),
_("Could not open '%s' for reading: %s"),
gimp_filename_to_utf8 (filename), g_strerror (errno));
return -1;
}
/* allocate the necessary structures */
dicominfo = g_new0 (DicomInfo, 1);
/* Parse the file */
fread (buf, 1, 128, DICOM); /* skip past buffer */
/* Check for unsupported formats */
if (g_ascii_strncasecmp (buf, "PAPYRUS", 7) == 0)
{
g_message ("'%s' is a PAPYRUS DICOM file.\n"
"This plug-in does not support this type yet.",
gimp_filename_to_utf8 (filename));
g_free (dicominfo);
fclose (DICOM);
return -1;
}
fread (buf, 1, 4, DICOM); /* This should be dicom */
if (g_ascii_strncasecmp (buf,"DICM",4) != 0)
{
g_set_error (error, G_FILE_ERROR, G_FILE_ERROR_FAILED,
_("'%s' is not a DICOM file."),
gimp_filename_to_utf8 (filename));
g_free (dicominfo);
fclose (DICOM);
return -1;
}
while (!feof (DICOM))
{
guint16 group_word;
guint16 element_word;
gchar value_rep[3];
guint32 element_length;
guint16 ctx_us;
guint8 *value;
guint32 tag;
gboolean __attribute__((unused))do_toggle_endian = FALSE;
gboolean implicit_encoding = FALSE;
if (fread (&group_word, 1, 2, DICOM) == 0)
break;
group_word = g_ntohs (GUINT16_SWAP_LE_BE (group_word));
fread (&element_word, 1, 2, DICOM);
element_word = g_ntohs (GUINT16_SWAP_LE_BE (element_word));
tag = (group_word << 16) | element_word;
fread(value_rep, 2, 1, DICOM);
value_rep[2] = 0;
/* Check if the value rep looks valid. There probably is a
better way of checking this...
*/
if ((/* Always need lookup for implicit encoding */
tag > 0x0002ffff && implicit_encoding)
/* This heuristics isn't used if we are doing implicit
encoding according to the value representation... */
|| ((value_rep[0] < 'A' || value_rep[0] > 'Z'
|| value_rep[1] < 'A' || value_rep[1] > 'Z')
/* I found this in one of Ednas images. It seems like a
bug...
*/
&& !(value_rep[0] == ' ' && value_rep[1]))
)
{
/* Look up type from the dictionary. At the time we dont
support this option... */
gchar element_length_chars[4];
/* Store the bytes that were read */
element_length_chars[0] = value_rep[0];
element_length_chars[1] = value_rep[1];
/* Unknown value rep. It is not used right now anyhow */
strcpy (value_rep, "??");
/* For implicit value_values the length is always four bytes,
so we need to read another two. */
fread (&element_length_chars[2], 1, 2, DICOM);
/* Now cast to integer and insert into element_length */
element_length =
g_ntohl (GUINT32_SWAP_LE_BE (*((gint *) element_length_chars)));
}
/* Binary value reps are OB, OW, SQ or UN */
else if (strncmp (value_rep, "OB", 2) == 0
|| strncmp (value_rep, "OW", 2) == 0
|| strncmp (value_rep, "SQ", 2) == 0
|| strncmp (value_rep, "UN", 2) == 0)
{
fread (&element_length, 1, 2, DICOM); /* skip two bytes */
fread (&element_length, 1, 4, DICOM);
element_length = g_ntohl (GUINT32_SWAP_LE_BE (element_length));
}
/* Short length */
else
{
guint16 el16;
fread (&el16, 1, 2, DICOM);
element_length = g_ntohs (GUINT16_SWAP_LE_BE (el16));
}
/* Sequence of items - just ignore the delimiters... */
if (element_length == 0xffffffff)
{
in_sequence = 1;
continue;
}
/* End of Sequence tag */
if (tag == 0xFFFEE0DD)
{
in_sequence = 0;
continue;
}
/* Sequence of items item tag... Ignore as well */
if (tag == 0xFFFEE000)
continue;
/* Even for pixel data, we don't handle very large element
lengths */
if (element_length >= (G_MAXUINT - 6))
{
g_message ("'%s' seems to have an incorrect value field length.",
gimp_filename_to_utf8 (filename));
gimp_quit ();
}
/* Read contents. Allocate a bit more to make room for casts to int
below. */
value = g_new0 (guint8, element_length + 4);
fread (value, 1, element_length, DICOM);
/* ignore everything inside of a sequence */
if (in_sequence)
{
g_free (value);
continue;
}
/* Some special casts that are used below */
ctx_us = *(guint16 *) value;
/* Recognize some critical tags */
if (group_word == 0x0002)
{
switch (element_word)
{
case 0x0010: /* transfer syntax id */
if (strcmp("1.2.840.10008.1.2", (char*)value) == 0)
{
do_toggle_endian = FALSE;
implicit_encoding = TRUE;
}
else if (strcmp("1.2.840.10008.1.2.1", (char*)value) == 0)
do_toggle_endian = FALSE;
else if (strcmp("1.2.840.10008.1.2.2", (char*)value) == 0)
do_toggle_endian = TRUE;
break;
}
}
else if (group_word == 0x0028)
{
switch (element_word)
{
case 0x0002: /* samples per pixel */
samples_per_pixel = ctx_us;
break;
case 0x0010: /* rows */
height = ctx_us;
break;
case 0x0011: /* columns */
width = ctx_us;
break;
case 0x0100: /* bits allocated */
bpp = ctx_us;
break;
case 0x0101: /* bits stored */
bits_stored = ctx_us;
break;
case 0x0102: /* high bit */
high_bit = ctx_us;
break;
case 0x0103: /* is pixel representation signed? */
is_signed = (ctx_us == 0) ? FALSE : TRUE;
break;
}
}
/* Pixel data */
if (group_word == 0x7fe0 && element_word == 0x0010)
{
pix_buf = value;
}
else
{
/* save this element to a parasite for later writing */
GimpParasite *parasite;
gchar pname[255];
/* all elements are retrievable using gimp_get_parasite_list() */
g_snprintf (pname, sizeof (pname),
"dcm/%04x-%04x-%s", group_word, element_word, value_rep);
if ((parasite = gimp_parasite_new (pname,
GIMP_PARASITE_PERSISTENT,
element_length, value)))
{
/*
* at this point, the image has not yet been created, so
* image_ID is not valid. keep the parasite around
* until we're able to attach it.
*/
/* add to our list of parasites to be added (prepending
* for speed. we'll reverse it later)
*/
elements = g_slist_prepend (elements, parasite);
}
g_free (value);
}
}
if ((bpp != 8) && (bpp != 16))
{
g_message ("'%s' has a bpp of %d which GIMP cannot handle.",
gimp_filename_to_utf8 (filename), bpp);
gimp_quit ();
}
if ((width > GIMP_MAX_IMAGE_SIZE) || (height > GIMP_MAX_IMAGE_SIZE))
{
g_message ("'%s' has a larger image size (%d x %d) than GIMP can handle.",
gimp_filename_to_utf8 (filename), width, height);
gimp_quit ();
}
if (samples_per_pixel > 3)
{
g_message ("'%s' has samples per pixel of %d which GIMP cannot handle.",
gimp_filename_to_utf8 (filename), samples_per_pixel);
gimp_quit ();
}
dicominfo->width = width;
dicominfo->height = height;
dicominfo->bpp = bpp;
dicominfo->bits_stored = bits_stored;
dicominfo->high_bit = high_bit;
dicominfo->is_signed = is_signed;
dicominfo->samples_per_pixel = samples_per_pixel;
dicominfo->maxval = -1; /* External normalization factor - not used yet */
/* Create a new image of the proper size and associate the filename with it.
*/
image_ID = gimp_image_new (dicominfo->width, dicominfo->height,
(dicominfo->samples_per_pixel >= 3 ?
GIMP_RGB : GIMP_GRAY));
gimp_image_set_filename (image_ID, filename);
layer_ID = gimp_layer_new (image_ID, _("Background"),
dicominfo->width, dicominfo->height,
(dicominfo->samples_per_pixel >= 3 ?
GIMP_RGB_IMAGE : GIMP_GRAY_IMAGE),
100,
gimp_image_get_default_new_layer_mode (image_ID));
gimp_image_insert_layer (image_ID, layer_ID, -1, 0);
buffer = gimp_drawable_get_buffer (layer_ID);
#if GUESS_ENDIAN
if (bpp == 16)
guess_and_set_endian2 ((guint16 *) pix_buf, width * height);
#endif
dicom_loader (pix_buf, dicominfo, buffer);
if (elements)
{
/* flip the parasites back around into the order they were
* created (read from the file)
*/
elements = g_slist_reverse (elements);
/* and add each one to the image */
g_slist_foreach (elements, add_parasites_to_image, (gpointer) &image_ID);
g_slist_free (elements);
}
g_free (pix_buf);
g_free (dicominfo);
fclose (DICOM);
g_object_unref (buffer);
return image_ID;
}
static void
dicom_loader (guint8 *pix_buffer,
DicomInfo *info,
GeglBuffer *buffer)
{
guchar *data;
gint row_idx;
gint width = info->width;
gint height = info->height;
gint samples_per_pixel = info->samples_per_pixel;
guint16 *buf16 = (guint16 *) pix_buffer;
if (info->bpp == 16)
{
gulong pix_idx;
guint shift = info->high_bit + 1 - info->bits_stored;
/* Reorder the buffer; also shift the data so that the LSB
* of the pixel data is at the LSB of the 16-bit array entries
* (i.e., compensate for high_bit and bits_stored).
*/
for (pix_idx = 0; pix_idx < width * height * samples_per_pixel; pix_idx++)
buf16[pix_idx] = g_htons (buf16[pix_idx]) >> shift;
}
data = g_malloc (gimp_tile_height () * width * samples_per_pixel);
for (row_idx = 0; row_idx < height; )
{
guchar *d = data;
gint start;
gint end;
gint scanlines;
gint i;
start = row_idx;
end = row_idx + gimp_tile_height ();
end = MIN (end, height);
scanlines = end - start;
for (i = 0; i < scanlines; i++)
{
if (info->bpp == 16)
{
guint16 *row_start;
gint col_idx;
row_start = buf16 + (row_idx + i) * width * samples_per_pixel;
for (col_idx = 0; col_idx < width * samples_per_pixel; col_idx++)
{
/* Shift it by 8 bits, or less in case bits_stored
* is less than bpp.
*/
d[col_idx] = (guint8) (row_start[col_idx] >>
(info->bits_stored - 8));
if (info->is_signed)
{
/* If the data is negative, make it 0. Otherwise,
* multiply the positive value by 2, so that the
* positive values span between 0 and 254.
*/
if (d[col_idx] > 127)
d[col_idx] = 0;
else
d[col_idx] <<= 1;
}
}
}
else if (info->bpp == 8)
{
guint8 *row_start;
gint col_idx;
row_start = (pix_buffer +
(row_idx + i) * width * samples_per_pixel);
for (col_idx = 0; col_idx < width * samples_per_pixel; col_idx++)
{
/* Shift it by 0 bits, or more in case bits_stored is
* less than bpp.
*/
d[col_idx] = row_start[col_idx] << (8 - info->bits_stored);
if (info->is_signed)
{
/* If the data is negative, make it 0. Otherwise,
* multiply the positive value by 2, so that the
* positive values span between 0 and 254.
*/
if (d[col_idx] > 127)
d[col_idx] = 0;
else
d[col_idx] <<= 1;
}
}
}
d += width * samples_per_pixel;
}
gegl_buffer_set (buffer, GEGL_RECTANGLE (0, row_idx, width, scanlines), 0,
NULL, data, GEGL_AUTO_ROWSTRIDE);
row_idx += scanlines;
gimp_progress_update ((gdouble) row_idx / (gdouble) height);
}
g_free (data);
gimp_progress_update (1.0);
}
/* Guess and set endian. Guesses the endian of a buffer by
* checking the maximum value of the first and the last byte
* in the words of the buffer. It assumes that the least
* significant byte has a larger maximum than the most
* significant byte.
*/
static void
guess_and_set_endian2 (guint16 *buf16,
int length)
{
guint16 *p = buf16;
gint max_first = -1;
gint max_second = -1;
while (p<buf16+length)
{
if (*(guint8*)p > max_first)
max_first = *(guint8*)p;
if (((guint8*)p)[1] > max_second)
max_second = ((guint8*)p)[1];
p++;
}
if ( ((max_second > max_first) && (G_BYTE_ORDER == G_LITTLE_ENDIAN))
|| ((max_second < max_first) && (G_BYTE_ORDER == G_BIG_ENDIAN)))
toggle_endian2 (buf16, length);
}
/* toggle_endian2 toggles the endian for a 16 bit entity. */
static void
toggle_endian2 (guint16 *buf16,
gint length)
{
guint16 *p = buf16;
while (p < buf16 + length)
{
*p = ((*p & 0xff) << 8) | (*p >> 8);
p++;
}
}
typedef struct
{
guint16 group_word;
guint16 element_word;
gchar value_rep[3];
guint32 element_length;
guint8 *value;
gboolean free;
} DICOMELEMENT;
/**
* dicom_add_element:
* @elements: head of a GSList containing DICOMELEMENT structures.
* @group_word: Dicom Element group number for the tag to be added to
* @elements.
* @element_word: Dicom Element element number for the tag to be added
* to @elements.
* @value_rep: a string representing the Dicom VR for the new element.
* @value: a pointer to an integer containing the value for the
* element to be created.
*
* Creates a DICOMELEMENT object and inserts it into @elements.
*
* Return value: the new head of @elements
**/
static GSList *
dicom_add_element (GSList *elements,
guint16 group_word,
guint16 element_word,
const gchar *value_rep,
guint32 element_length,
guint8 *value)
{
DICOMELEMENT *element = g_slice_new0 (DICOMELEMENT);
element->group_word = group_word;
element->element_word = element_word;
strncpy (element->value_rep, value_rep, sizeof (element->value_rep));
element->element_length = element_length;
element->value = value;
return g_slist_prepend (elements, element);
}
static GSList *
dicom_add_element_copy (GSList *elements,
guint16 group_word,
guint16 element_word,
gchar *value_rep,
guint32 element_length,
const guint8 *value)
{
elements = dicom_add_element (elements,
group_word, element_word, value_rep,
element_length,
g_memdup (value, element_length));
((DICOMELEMENT *) elements->data)->free = TRUE;
return elements;
}
/**
* dicom_add_element_int:
* @elements: head of a GSList containing DICOMELEMENT structures.
* @group_word: Dicom Element group number for the tag to be added to
* @elements.
* @element_word: Dicom Element element number for the tag to be added to
* @elements.
* @value_rep: a string representing the Dicom VR for the new element.
* @value: a pointer to an integer containing the value for the
* element to be created.
*
* Creates a DICOMELEMENT object from the passed integer pointer and
* adds it to @elements. Note: value should be the address of a
* guint16 for @value_rep == %US or guint32 for other values of
* @value_rep
*
* Return value: the new head of @elements
*/
static GSList *
dicom_add_element_int (GSList *elements,
guint16 group_word,
guint16 element_word,
gchar *value_rep,
guint8 *value)
{
guint32 len;
if (strcmp (value_rep, "US") == 0)
len = 2;
else
len = 4;
return dicom_add_element (elements,
group_word, element_word, value_rep,
len, value);
}
/**
* dicom_element_done:
* @data: pointer to a DICOMELEMENT structure which is to be destroyed.
*
* Destroys the DICOMELEMENT passed as @data
**/
static void
dicom_element_done (gpointer data)
{
if (data)
{
DICOMELEMENT *e = data;
if (e->free)
g_free (e->value);
g_slice_free (DICOMELEMENT, data);
}
}
/**
* dicom_elements_destroy:
* @elements: head of a GSList containing DICOMELEMENT structures.
*
* Destroys the list of DICOMELEMENTs
**/
static void
dicom_elements_destroy (GSList *elements)
{
if (elements)
g_slist_free_full (elements, dicom_element_done);
}
/**
* dicom_destroy_element:
* @elements: head of a GSList containing DICOMELEMENT structures.
* @ele: a DICOMELEMENT structure to be removed from @elements
*
* Removes the specified DICOMELEMENT from @elements and Destroys it
*
* Return value: the new head of @elements
**/
static GSList *
dicom_destroy_element (GSList *elements,
DICOMELEMENT *ele)
{
if (ele)
{
elements = g_slist_remove_all (elements, ele);
if (ele->free)
g_free (ele->value);
g_slice_free (DICOMELEMENT, ele);
}
return elements;
}
/**
* dicom_elements_compare:
* @a: pointer to a DICOMELEMENT structure.
* @b: pointer to a DICOMELEMENT structure.
*
* Determines the equality of @a and @b as strcmp
*
* Return value: an integer indicating the equality of @a and @b.
**/
static gint
dicom_elements_compare (gconstpointer a,
gconstpointer b)
{
DICOMELEMENT *e1 = (DICOMELEMENT *)a;
DICOMELEMENT *e2 = (DICOMELEMENT *)b;
if (e1->group_word == e2->group_word)
{
if (e1->element_word == e2->element_word)
{
return 0;
}
else if (e1->element_word > e2->element_word)
{
return 1;
}
else
{
return -1;
}
}
else if (e1->group_word < e2->group_word)
{
return -1;
}
return 1;
}
/**
* dicom_element_find_by_num:
* @head: head of a GSList containing DICOMELEMENT structures.
* @group_word: Dicom Element group number for the tag to be found.
* @element_word: Dicom Element element number for the tag to be found.
*
* Retrieves the specified DICOMELEMENT from @head, if available.
*
* Return value: a DICOMELEMENT matching the specified group,element,
* or NULL if the specified element was not found.
**/
static DICOMELEMENT *
dicom_element_find_by_num (GSList *head,
guint16 group_word,
guint16 element_word)
{
DICOMELEMENT data = { group_word,element_word, "", 0, NULL};
GSList *ele = g_slist_find_custom (head,&data,dicom_elements_compare);
return (ele ? ele->data : NULL);
}
/**
* dicom_get_elements_list:
* @image_ID: the image_ID from which to read parasites in order to
* retrieve the dicom elements
*
* Reads all DICOMELEMENTs from the specified image's parasites.
*
* Return value: a GSList of all known dicom elements
**/
static GSList *
dicom_get_elements_list (gint32 image_ID)
{
GSList *elements = NULL;
GimpParasite *parasite;
gchar **parasites = NULL;
gint count = 0;
parasites = gimp_image_get_parasite_list (image_ID, &count);
if (parasites && count > 0)
{
gint i;
for (i = 0; i < count; i++)
{
if (strncmp (parasites[i], "dcm", 3) == 0)
{
parasite = gimp_image_get_parasite (image_ID, parasites[i]);
if (parasite)
{
gchar buf[1024];
gchar *ptr1;
gchar *ptr2;
gchar value_rep[3] = "";
guint16 group_word = 0;
guint16 element_word = 0;
/* sacrificial buffer */
strncpy (buf, parasites[i], sizeof (buf));
/* buf should now hold a string of the form
* dcm/XXXX-XXXX-AA where XXXX are Hex values for
* group and element respectively AA is the Value
* Representation of the element
*
* start off by jumping over the dcm/ to the first Hex blob
*/
ptr1 = strchr (buf, '/');
if (ptr1)
{
gchar t[15];
ptr1++;
ptr2 = strchr (ptr1,'-');
if (ptr2)
*ptr2 = '\0';
g_snprintf (t, sizeof (t), "0x%s", ptr1);
group_word = (guint16) g_ascii_strtoull (t, NULL, 16);
ptr1 = ptr2 + 1;
}
/* now get the second Hex blob */
if (ptr1)
{
gchar t[15];
ptr2 = strchr (ptr1, '-');
if (ptr2)
*ptr2 = '\0';
g_snprintf (t, sizeof (t), "0x%s", ptr1);
element_word = (guint16) g_ascii_strtoull (t, NULL, 16);
ptr1 = ptr2 + 1;
}
/* and lastly, the VR */
if (ptr1)
strncpy (value_rep, ptr1, sizeof (value_rep));
/*
* If all went according to plan, we should be able
* to add this element
*/
if (group_word > 0 && element_word > 0)
{
const guint8 *val = gimp_parasite_data (parasite);
const guint len = gimp_parasite_data_size (parasite);
/* and add the dicom element, asking to have
it's value copied for later garbage collection */
elements = dicom_add_element_copy (elements,
group_word,
element_word,
value_rep, len, val);
}
gimp_parasite_free (parasite);
}
}
}
}
/* cleanup the array of names */
g_strfreev (parasites);
return elements;
}
/**
* dicom_remove_gimp_specified_elements:
* @elements: GSList to remove elements from
* @samples_per_pixel: samples per pixel of the image to be written.
* if set to %3 the planar configuration for color images
* will also be removed from @elements
*
* Removes certain DICOMELEMENTs from the elements list which are specific to the output of this plugin.
*
* Return value: the new head of @elements
**/
static GSList *
dicom_remove_gimp_specified_elements (GSList *elements,
gint samples_per_pixel)
{
DICOMELEMENT remove[] = {
/* Image presentation group */
/* Samples per pixel */
{0x0028, 0x0002, "", 0, NULL},
/* Photometric interpretation */
{0x0028, 0x0004, "", 0, NULL},
/* rows */
{0x0028, 0x0010, "", 0, NULL},
/* columns */
{0x0028, 0x0011, "", 0, NULL},
/* Bits allocated */
{0x0028, 0x0100, "", 0, NULL},
/* Bits Stored */
{0x0028, 0x0101, "", 0, NULL},
/* High bit */
{0x0028, 0x0102, "", 0, NULL},
/* Pixel representation */
{0x0028, 0x0103, "", 0, NULL},
{0,0,"",0,NULL}
};
DICOMELEMENT *ele;
gint i;
/*
* Remove all Dicom elements which will be set as part of the writing of the new file
*/
for (i=0; remove[i].group_word > 0;i++)
{
if ((ele = dicom_element_find_by_num (elements,remove[i].group_word,remove[i].element_word)))
{
elements = dicom_destroy_element (elements,ele);
}
}
/* special case - allow this to be overwritten if necessary */
if (samples_per_pixel == 3)
{
/* Planar configuration for color images */
if ((ele = dicom_element_find_by_num (elements,0x0028,0x0006)))
{
elements = dicom_destroy_element (elements,ele);
}
}
return elements;
}
/**
* dicom_ensure_required_elements_present:
* @elements: GSList to remove elements from
* @today_string: string containing today's date in DICOM format. This
* is used to default any required Dicom elements of date
* type to today's date.
*
* Defaults DICOMELEMENTs to the values set by previous version of
* this plugin, but only if they do not already exist.
*
* Return value: the new head of @elements
**/
static GSList *
dicom_ensure_required_elements_present (GSList *elements,
gchar *today_string)
{
const DICOMELEMENT defaults[] = {
/* Meta element group */
/* 0002, 0001 - File Meta Information Version */
{ 0x0002, 0x0001, "OB", 2, (guint8 *) "\0\1" },
/* 0002, 0010 - Transfer syntax uid */
{ 0x0002, 0x0010, "UI",
strlen ("1.2.840.10008.1.2.1"), (guint8 *) "1.2.840.10008.1.2.1"},
/* 0002, 0013 - Implementation version name */
{ 0x0002, 0x0013, "SH",
strlen ("GIMP Dicom Plugin 1.0"), (guint8 *) "GIMP Dicom Plugin 1.0" },
/* Identifying group */
/* ImageType */
{ 0x0008, 0x0008, "CS",
strlen ("ORIGINAL\\PRIMARY"), (guint8 *) "ORIGINAL\\PRIMARY" },
{ 0x0008, 0x0016, "UI",
strlen ("1.2.840.10008.5.1.4.1.1.7"), (guint8 *) "1.2.840.10008.5.1.4.1.1.7" },
/* Study date */
{ 0x0008, 0x0020, "DA",
strlen (today_string), (guint8 *) today_string },
/* Series date */
{ 0x0008, 0x0021, "DA",
strlen (today_string), (guint8 *) today_string },
/* Acquisition date */
{ 0x0008, 0x0022, "DA",
strlen (today_string), (guint8 *) today_string },
/* Content Date */
{ 0x0008, 0x0023, "DA",
strlen (today_string), (guint8 *) today_string},
/* Content Time */
{ 0x0008, 0x0030, "TM",
strlen ("000000.000000"), (guint8 *) "000000.000000"},
/* AccessionNumber */
{ 0x0008, 0x0050, "SH", strlen (""), (guint8 *) "" },
/* Modality */
{ 0x0008, 0x0060, "CS", strlen ("MR"), (guint8 *) "MR" },
/* ConversionType */
{ 0x0008, 0x0064, "CS", strlen ("WSD"), (guint8 *) "WSD" },
/* ReferringPhysiciansName */
{ 0x0008, 0x0090, "PN", strlen (""), (guint8 *) "" },
/* Patient group */
/* Patient name */
{ 0x0010, 0x0010, "PN",
strlen ("DOE^WILBER"), (guint8 *) "DOE^WILBER" },
/* Patient ID */
{ 0x0010, 0x0020, "LO",
strlen ("314159265"), (guint8 *) "314159265" },
/* Patient Birth date */
{ 0x0010, 0x0030, "DA",
strlen (today_string), (guint8 *) today_string },
/* Patient sex */
{ 0x0010, 0x0040, "CS", strlen (""), (guint8 *) "" /* unknown */ },
/* Relationship group */
/* StudyId */
{ 0x0020, 0x0010, "IS", strlen ("1"), (guint8 *) "1" },
/* SeriesNumber */
{ 0x0020, 0x0011, "IS", strlen ("1"), (guint8 *) "1" },
/* AcquisitionNumber */
{ 0x0020, 0x0012, "IS", strlen ("1"), (guint8 *) "1" },
/* Instance number */
{ 0x0020, 0x0013, "IS", strlen ("1"), (guint8 *) "1" },
{ 0, 0, "", 0, NULL }
};
gint i;
/*
* Make sure that all of the default elements have a value
*/
for (i=0; defaults[i].group_word > 0; i++)
{
if (dicom_element_find_by_num (elements,
defaults[i].group_word,
defaults[i].element_word) == NULL)
{
elements = dicom_add_element (elements,
defaults[i].group_word,
defaults[i].element_word,
defaults[i].value_rep,
defaults[i].element_length,
defaults[i].value);
}
}
return elements;
}
/* save_image() saves an image in the dicom format. The DICOM format
* requires a lot of tags to be set. Some of them have real uses, others
* must just be filled with dummy values.
*/
static gboolean
save_image (const gchar *filename,
gint32 image_ID,
gint32 drawable_ID,
GError **error)
{
FILE *DICOM;
GimpImageType drawable_type;
GeglBuffer *buffer;
const Babl *format;
gint width;
gint height;
GByteArray *group_stream;
GSList *elements = NULL;
gint group;
GDate *date;
gchar today_string[16];
gchar *photometric_interp;
gint samples_per_pixel;
gboolean retval = TRUE;
guint16 zero = 0;
guint16 seven = 7;
guint16 eight = 8;
guchar *src = NULL;
drawable_type = gimp_drawable_type (drawable_ID);
/* Make sure we're not saving an image with an alpha channel */
if (gimp_drawable_has_alpha (drawable_ID))
{
g_message (_("Cannot save images with alpha channel."));
return FALSE;
}
switch (drawable_type)
{
case GIMP_GRAY_IMAGE:
format = babl_format ("Y' u8");
samples_per_pixel = 1;
photometric_interp = "MONOCHROME2";
break;
case GIMP_RGB_IMAGE:
format = babl_format ("R'G'B' u8");
samples_per_pixel = 3;
photometric_interp = "RGB";
break;
default:
g_message (_("Cannot operate on unknown image types."));
return FALSE;
}
date = g_date_new ();
g_date_set_time_t (date, time (NULL));
g_snprintf (today_string, sizeof (today_string),
"%04d%02d%02d", date->year, date->month, date->day);
g_date_free (date);
/* Open the output file. */
DICOM = g_fopen (filename, "wb");
if (!DICOM)
{
g_set_error (error, G_FILE_ERROR, g_file_error_from_errno (errno),
_("Could not open '%s' for writing: %s"),
gimp_filename_to_utf8 (filename), g_strerror (errno));
return FALSE;
}
buffer = gimp_drawable_get_buffer (drawable_ID);
width = gegl_buffer_get_width (buffer);
height = gegl_buffer_get_height (buffer);
/* Print dicom header */
{
guint8 val = 0;
gint i;
for (i = 0; i < 0x80; i++)
fwrite (&val, 1, 1, DICOM);
}
fprintf (DICOM, "DICM");
group_stream = g_byte_array_new ();
elements = dicom_get_elements_list (image_ID);
if (0/*replaceElementsList*/)
{
/* to do */
}
else if (1/*insist_on_basic_elements*/)
{
elements = dicom_ensure_required_elements_present (elements,today_string);
}
/*
* Set value of custom elements
*/
elements = dicom_remove_gimp_specified_elements (elements,samples_per_pixel);
/* Image presentation group */
group = 0x0028;
/* Samples per pixel */
elements = dicom_add_element_int (elements, group, 0x0002, "US",
(guint8 *) &samples_per_pixel);
/* Photometric interpretation */
elements = dicom_add_element (elements, group, 0x0004, "CS",
strlen (photometric_interp),
(guint8 *) photometric_interp);
/* Planar configuration for color images */
if (samples_per_pixel == 3)
elements = dicom_add_element_int (elements, group, 0x0006, "US",
(guint8 *) &zero);
/* rows */
elements = dicom_add_element_int (elements, group, 0x0010, "US",
(guint8 *) &height);
/* columns */
elements = dicom_add_element_int (elements, group, 0x0011, "US",
(guint8 *) &width);
/* Bits allocated */
elements = dicom_add_element_int (elements, group, 0x0100, "US",
(guint8 *) &eight);
/* Bits Stored */
elements = dicom_add_element_int (elements, group, 0x0101, "US",
(guint8 *) &eight);
/* High bit */
elements = dicom_add_element_int (elements, group, 0x0102, "US",
(guint8 *) &seven);
/* Pixel representation */
elements = dicom_add_element_int (elements, group, 0x0103, "US",
(guint8 *) &zero);
/* Pixel data */
group = 0x7fe0;
src = g_new (guchar, height * width * samples_per_pixel);
if (src)
{
gegl_buffer_get (buffer, GEGL_RECTANGLE (0, 0, width, height), 1.0,
format, src,
GEGL_AUTO_ROWSTRIDE, GEGL_ABYSS_NONE);
elements = dicom_add_element (elements, group, 0x0010, "OW",
width * height * samples_per_pixel,
(guint8 *) src);
elements = dicom_add_tags (DICOM, group_stream, elements);
g_free (src);
}
else
{
retval = FALSE;
}
fclose (DICOM);
dicom_elements_destroy (elements);
g_byte_array_free (group_stream, TRUE);
g_object_unref (buffer);
return retval;
}
/**
* dicom_print_tags:
* @data: pointer to a DICOMELEMENT structure which is to be written to file
* @user_data: structure containing state information and output parameters
*
* Writes the specified DICOMELEMENT to @user_data's group_stream member.
* Between groups, flushes the group_stream to @user_data's DICOM member.
*/
static void
dicom_print_tags(gpointer data,
gpointer user_data)
{
struct {
FILE *DICOM;
GByteArray *group_stream;
gint last_group;
} *d = user_data;
DICOMELEMENT *e = (DICOMELEMENT *) data;
if (d->last_group >= 0 && e->group_word != d->last_group)
{
write_group_to_file (d->DICOM, d->last_group, d->group_stream);
}
add_tag_pointer (d->group_stream,
e->group_word, e->element_word,
e->value_rep,e->value, e->element_length);
d->last_group = e->group_word;
}
/**
* dicom_add_tags:
* @DICOM: File pointer to which @elements should be written.
* @group_stream: byte array used for staging Dicom Element groups
* before flushing them to disk.
* @elements: GSList container the Dicom Element elements from
*
* Writes all Dicom tags in @elements to the file @DICOM
*
* Return value: the new head of @elements
**/
static GSList *
dicom_add_tags (FILE *DICOM,
GByteArray *group_stream,
GSList *elements)
{
struct {
FILE *DICOM;
GByteArray *group_stream;
gint last_group;
} data = { DICOM, group_stream, -1 };
elements = g_slist_sort (elements, dicom_elements_compare);
g_slist_foreach (elements, dicom_print_tags, &data);
/* make sure that the final group is written to the file */
write_group_to_file (data.DICOM, data.last_group, data.group_stream);
return elements;
}
/* add_tag_pointer () adds to the group_stream one single value with its
* corresponding value_rep. Note that we use "explicit VR".
*/
static void
add_tag_pointer (GByteArray *group_stream,
gint group,
gint element,
const gchar *value_rep,
const guint8 *data,
gint length)
{
gboolean is_long;
guint16 swapped16;
guint32 swapped32;
guint pad = 0;
is_long = (strstr ("OB|OW|SQ|UN", value_rep) != NULL) || length > 65535;
swapped16 = g_ntohs (GUINT16_SWAP_LE_BE (group));
g_byte_array_append (group_stream, (guint8 *) &swapped16, 2);
swapped16 = g_ntohs (GUINT16_SWAP_LE_BE (element));
g_byte_array_append (group_stream, (guint8 *) &swapped16, 2);
g_byte_array_append (group_stream, (const guchar *) value_rep, 2);
if (length % 2 != 0)
{
/* the dicom standard requires all elements to be of even byte
* length. this element would be odd, so we must pad it before
* adding it
*/
pad = 1;
}
if (is_long)
{
g_byte_array_append (group_stream, (const guchar *) "\0\0", 2);
swapped32 = g_ntohl (GUINT32_SWAP_LE_BE (length + pad));
g_byte_array_append (group_stream, (guint8 *) &swapped32, 4);
}
else
{
swapped16 = g_ntohs (GUINT16_SWAP_LE_BE (length + pad));
g_byte_array_append (group_stream, (guint8 *) &swapped16, 2);
}
g_byte_array_append (group_stream, data, length);
if (pad)
{
/* add a padding byte to the stream
*
* From ftp://medical.nema.org/medical/dicom/2009/09_05pu3.pdf:
*
* Values with VRs constructed of character strings, except in
* the case of the VR UI, shall be padded with SPACE characters
* (20H, in the Default Character Repertoire) when necessary to
* achieve even length. Values with a VR of UI shall be padded
* with a single trailing NULL (00H) character when necessary
* to achieve even length. Values with a VR of OB shall be
* padded with a single trailing NULL byte value (00H) when
* necessary to achieve even length.
*/
if (strstr ("UI|OB", value_rep) != NULL)
{
g_byte_array_append (group_stream, (guint8 *) "\0", 1);
}
else
{
g_byte_array_append (group_stream, (guint8 *) " ", 1);
}
}
}
/* Once a group has been built it has to be wrapped with a meta-group
* tag before it is written to the DICOM file. This is done by
* write_group_to_file.
*/
static gboolean
write_group_to_file (FILE *DICOM,
gint group,
GByteArray *group_stream)
{
gboolean retval = TRUE;
guint16 swapped16;
guint32 swapped32;
/* Add header to the group and output it */
swapped16 = g_ntohs (GUINT16_SWAP_LE_BE (group));
fwrite ((gchar *) &swapped16, 1, 2, DICOM);
fputc (0, DICOM);
fputc (0, DICOM);
fputc ('U', DICOM);
fputc ('L', DICOM);
swapped16 = g_ntohs (GUINT16_SWAP_LE_BE (4));
fwrite ((gchar *) &swapped16, 1, 2, DICOM);
swapped32 = g_ntohl (GUINT32_SWAP_LE_BE (group_stream->len));
fwrite ((gchar *) &swapped32, 1, 4, DICOM);
if (fwrite (group_stream->data,
1, group_stream->len, DICOM) != group_stream->len)
retval = FALSE;
g_byte_array_set_size (group_stream, 0);
return retval;
}
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