[giv] Added support for float and 16-bit color images in tiff plugin.
- From: Dov Grobgeld <dov src gnome org>
- To: commits-list gnome org
- Cc:
- Subject: [giv] Added support for float and 16-bit color images in tiff plugin.
- Date: Wed, 6 Apr 2011 11:41:50 +0000 (UTC)
commit 08fb7aa307756b9429d808e725ce35465a2b7606
Author: Dov Grobgeld <dov grobgeld gmail com>
Date: Wed Apr 6 14:41:29 2011 +0300
Added support for float and 16-bit color images in tiff plugin.
ChangeLog | 12 ++
doc/giv-m51-with-contrast-tool-screenshot.png | Bin 0 -> 121074 bytes
doc/giv.html | 30 +++-
doc/giv.phtml | 27 +++-
src/givimage.c | 73 +++++++--
.../dcmtk/config/include/dcmtk/config/cfunix.h | 2 +-
src/plugins/dcmtk/dcmdata/libsrc/SConscript | 174 ++++++++++----------
src/plugins/tiff.c | 35 ++++-
8 files changed, 230 insertions(+), 123 deletions(-)
---
diff --git a/ChangeLog b/ChangeLog
index 4b087bb..4849c09 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,5 +1,17 @@
+2011-04-06 Dov Grobgeld <dov grobgeld gmail com>
+
+ * plugins/dcmtk/dcmdata/libsrc/SConscript: Turned of autogeneration of dcdictbi.cc.
+
+ * tiff.c, giv_image.c, giv_image.h : Added support for 16 bit tiff images.
+
+ * tiff.c : Added support for float (SAMPLEFORMAT_IEEEFP) images.
+
+ * cfunix.h : Erased definition of size_to to fix Linux64 bit compilatin.
+
2011-04-05 Dov Grobgeld <dov grobgeld gmail com>
+ * Released version 0.9.18
+
* Sconstruct: Created a dist command for generating distributions.
* giv-win.gob : Created ifdef for windows as pango_cairo was severely broken.
diff --git a/doc/giv-m51-with-contrast-tool-screenshot.png b/doc/giv-m51-with-contrast-tool-screenshot.png
new file mode 100644
index 0000000..6d25fcb
Binary files /dev/null and b/doc/giv-m51-with-contrast-tool-screenshot.png differ
diff --git a/doc/giv.html b/doc/giv.html
index 3fa1f4f..9d40562 100644
--- a/doc/giv.html
+++ b/doc/giv.html
@@ -18,11 +18,11 @@
</center>
<h2 align=center>
<img src="giv-logo-150.png"><br>
- <font size=+2>Version 0.9.17</font><br>
+ <font size=+2>Version 0.9.18</font><br>
<font size=-1>Dov Grobgeld</font><br>
<font size=-1>Homepage: <a href="http://giv.sourceforge.net/giv";>http://giv.sourceforge.net/giv</a></font><br>
<font size=-1><a href="mailto:dov grobgeld gmail com">dov grobgeld gmail com</a></font><br>
- <font size=-1>Last modified: 2010-02-25 </font>
+ <font size=-1>Last modified: 2011-04-05 </font>
</h2>
<h2><a name="SEC1">1. Description</a></h2>
@@ -454,20 +454,36 @@ giv. The result is shown in the screenshow below.
<td colspan="2" align="center"><img src="giv-m51-with-contrast-tool-screenshot.png" width=600></td>
</tr>
<tr>
- <td colspan="2" align="center">The Contrast Tool with a 16-bit image</td>
+ <td colspan="2" align="center">The Contrast Tool with a 16-bit image<br></td>
+ </tr>
+
+ <!----->
+ <tr>
+ <td colspan="2" align="center"><img src="giv-calib-and-measure.png" width=600></td>
+ </tr>
+ <tr>
+ <td colspan="2" align="center">The measurement caliper and the calibration tool<br></td>
</tr>
</table>
</blockquote>
-<h2><a name="SEC4">4. Future plans</a></h2>
+<h2><a name="SEC4">4. Plugins</a></h2>
+
+Giv supports plugins for loading 8-bit, 16-bit, 32-bit and floating point images. Currently there are
+loaders for the following formats:
+<ul>
+<li>Dicom
+<li>FITS
+<li>Tiff
+</ul>
+
+<h2><a name="SEC5">5. Future plans</a></h2>
<blockquote>
Here is a list of possible future development. The direction taken
depends on user feedback!
<UL>
- <LI> Support 16-bit, 32-bit, float, and double images. </LI>
- <LI> Create a framework for external image loader DLL's. </LI>
- <LI> Create loaders for HDF5 and Dicom. </LI>
+ <LI> Create loaders for HDF5. </LI>
<LI> Create a property window to show meta data. E.g. data from a dicom file. </LI>
<LI> Speed up dealing with huge datasets. </LI>
<LI> Create a measuring tool for measuring areas, histograms, etc. </LI>
diff --git a/doc/giv.phtml b/doc/giv.phtml
index e333eaa..d820689 100644
--- a/doc/giv.phtml
+++ b/doc/giv.phtml
@@ -94,11 +94,11 @@ sub code_snippet { # usage: code_snippet($filename, title)
</center>
<h2 align=center>
<img src="giv-logo-150.png"><br>
- <font size=+2>Version 0.9.17</font><br>
+ <font size=+2>Version 0.9.18</font><br>
<font size=-1>Dov Grobgeld</font><br>
<font size=-1>Homepage: <a href="http://giv.sourceforge.net/giv";>http://giv.sourceforge.net/giv</a></font><br>
<font size=-1><a href="mailto:dov grobgeld gmail com">dov grobgeld gmail com</a></font><br>
- <font size=-1>Last modified: 2010-02-25 </font>
+ <font size=-1>Last modified: 2011-04-05 </font>
</h2>
<: section("Description") :>
@@ -374,19 +374,34 @@ giv. The result is shown in the screenshow below.
<td colspan="2" align="center"><img src="giv-m51-with-contrast-tool-screenshot.png" width=600></td>
</tr>
<tr>
- <td colspan="2" align="center">The Contrast Tool with a 16-bit image</td>
+ <td colspan="2" align="center">The Contrast Tool with a 16-bit image<br></td>
+ </tr>
+
+ <!----->
+ <tr>
+ <td colspan="2" align="center"><img src="giv-calib-and-measure.png" width=600></td>
+ </tr>
+ <tr>
+ <td colspan="2" align="center">The measurement caliper and the calibration tool<br></td>
</tr>
</table>
</blockquote>
+<: section("Plugins") :>
+Giv supports plugins for loading 8-bit, 16-bit, 32-bit and floating point images. Currently there are
+loaders for the following formats:
+<ul>
+<li>Dicom
+<li>FITS
+<li>Tiff
+</ul>
+
<: section("Future plans") :>
<blockquote>
Here is a list of possible future development. The direction taken
depends on user feedback!
<UL>
- <LI> Support 16-bit, 32-bit, float, and double images. </LI>
- <LI> Create a framework for external image loader DLL's. </LI>
- <LI> Create loaders for HDF5 and Dicom. </LI>
+ <LI> Create loaders for HDF5. </LI>
<LI> Create a property window to show meta data. E.g. data from a dicom file. </LI>
<LI> Speed up dealing with huge datasets. </LI>
<LI> Create a measuring tool for measuring areas, histograms, etc. </LI>
diff --git a/src/givimage.c b/src/givimage.c
index c35075e..98f185c 100644
--- a/src/givimage.c
+++ b/src/givimage.c
@@ -13,6 +13,16 @@
#include "givregex.h"
#define GIV_IMAGE_ERROR g_spawn_error_quark ()
+
+static guint8 clip_u8(double f)
+{
+ if (f < 0)
+ return 0;
+ if (f > 255)
+ return 255;
+ return (int)f;
+}
+
GQuark
giv_image_error_quark (void)
{
@@ -414,7 +424,15 @@ double giv_image_get_value(GivImage *img,
case GIVIMAGE_RGBA_U8:
return (((GivImageRgbAlpha8*)row_start)[x_idx]).red;
case GIVIMAGE_RGB_U16:
- return (((GivImageRgb16*)row_start)[x_idx]).red;
+ {
+ GivImageRgb16 rgb = (((GivImageRgb16*)row_start)[x_idx]);
+ int max = rgb.red;
+ if (rgb.green > max)
+ max = rgb.green;
+ if (rgb.blue > max)
+ max = rgb.blue;
+ return max;
+ }
case GIVIMAGE_RGBA_U16:
return (((GivImageRgbAlpha16*)row_start)[x_idx]).red;
default:
@@ -446,6 +464,16 @@ GivImageRgb16 giv_image_get_rgb_value(GivImage *img,
rgb.green = img->buf.rgba8_buf[idx].green;
rgb.blue = img->buf.rgba8_buf[idx].blue;
break;
+ case GIVIMAGE_RGB_U16:
+ rgb.red = img->buf.rgb16_buf[idx].red;
+ rgb.green = img->buf.rgb16_buf[idx].green;
+ rgb.blue = img->buf.rgb16_buf[idx].blue;
+ break;
+ case GIVIMAGE_RGBA_U16:
+ rgb.red = img->buf.rgba16_buf[idx].red;
+ rgb.green = img->buf.rgba16_buf[idx].green;
+ rgb.blue = img->buf.rgba16_buf[idx].blue;
+ break;
default:
;
}
@@ -588,16 +616,33 @@ GdkPixbuf *giv_image_get_pixbuf(GivImage *img,
int row_stride = img->row_stride;
// Silently ignore 16 bit images at the moment
- for (row_idx=0; row_idx<height; row_idx++) {
- for (col_idx=0; col_idx<width; col_idx++) {
- int ch_idx;
- for (ch_idx=0; ch_idx<num_ch_per_pixel; ch_idx++) {
- pbuf[row_idx * pb_rowstride
- + col_idx * num_ch_per_pixel
- + ch_idx]
- = buf[row_idx * row_stride
- +col_idx * num_ch_per_pixel
- + ch_idx];
+ if (img->img_type == GIVIMAGE_RGB_U16) {
+ for (row_idx=0; row_idx<height; row_idx++) {
+ gchar *row = pbuf + row_idx * pb_rowstride;
+ for (col_idx=0; col_idx<width; col_idx++) {
+ GivImageRgb16 rgb16
+ = giv_image_get_rgb_value(img,
+ col_idx,
+ row_idx,
+ slice_idx);
+ row[col_idx * 3] = clip_u8((rgb16.red-min)*255/(max-min));
+ row[col_idx * 3+1] = clip_u8((rgb16.green-min)*255/(max-min));
+ row[col_idx * 3+2] = clip_u8((rgb16.blue-min)*255/(max-min));
+ }
+ }
+ }
+ else {
+ for (row_idx=0; row_idx<height; row_idx++) {
+ for (col_idx=0; col_idx<width; col_idx++) {
+ int ch_idx;
+ for (ch_idx=0; ch_idx<num_ch_per_pixel; ch_idx++) {
+ pbuf[row_idx * pb_rowstride
+ + col_idx * num_ch_per_pixel
+ + ch_idx]
+ = buf[row_idx * row_stride
+ +col_idx * num_ch_per_pixel
+ + ch_idx];
+ }
}
}
}
@@ -613,11 +658,7 @@ GdkPixbuf *giv_image_get_pixbuf(GivImage *img,
if (max == min)
val = 128;
else
- val = 255.0 * (val-min)/(max-min);
- if (val<=0)
- val = 0;
- if (val >= 255)
- val = 255;
+ val = clip_u8(255.0 * (val-min)/(max-min));
for (ch_idx=0; ch_idx<3; ch_idx++)
pbuf[row_idx * pb_rowstride
+ col_idx * 3
diff --git a/src/plugins/dcmtk/config/include/dcmtk/config/cfunix.h b/src/plugins/dcmtk/config/include/dcmtk/config/cfunix.h
index 32dbcbb..b0017fd 100644
--- a/src/plugins/dcmtk/config/include/dcmtk/config/cfunix.h
+++ b/src/plugins/dcmtk/config/include/dcmtk/config/cfunix.h
@@ -332,7 +332,7 @@ typedef int pid_t;
#endif
/* Define `size_t' to `unsigned' if <sys/types.h> does not define. */
-#define HAVE_NO_TYPEDEF_SIZE_T 1
+#undef HAVE_NO_TYPEDEF_SIZE_T
#ifdef HAVE_NO_TYPEDEF_SIZE_T
typedef unsigned size_t;
#endif
diff --git a/src/plugins/dcmtk/dcmdata/libsrc/SConscript b/src/plugins/dcmtk/dcmdata/libsrc/SConscript
index d899c54..cccd69e 100644
--- a/src/plugins/dcmtk/dcmdata/libsrc/SConscript
+++ b/src/plugins/dcmtk/dcmdata/libsrc/SConscript
@@ -7,90 +7,90 @@ lib = env.Library('dcmdata',
env.Install('${OUTLIBDIR}',
lib)
-if not ARGUMENTS.get('mingw', 0):
- env.Command("dcdictbi.cc",
- ["dicom.dic",
- "private.dic",
- "mkdictbi"
- ],
- ["${TARGET.dir}/mkdictbi ${TARGET.dir}/*.dic > ${TARGET}"],
- )
-
- env.Program('mkdictbi',
- ['mkdictbi.cc',
- 'cmdlnarg.cc',
- 'dcbytstr.cc',
- 'dcchrstr.cc',
- 'dccodec.cc',
- 'dcdatset.cc',
- 'dcddirif.cc',
- 'dcdebug.cc',
- 'dcdicdir.cc',
- 'dcdicent.cc',
- 'dcdict.cc',
- 'dcdictzz.cc',
- 'dcdirrec.cc',
- 'dcelem.cc',
- 'dcerror.cc',
- 'dcfilefo.cc',
- 'dchashdi.cc',
- 'dcistrma.cc',
- 'dcistrmb.cc',
- 'dcistrmf.cc',
- 'dcistrmz.cc',
- 'dcitem.cc',
- 'dclist.cc',
- 'dcmetinf.cc',
- 'dcobject.cc',
- 'dcostrma.cc',
- 'dcostrmb.cc',
- 'dcostrmf.cc',
- 'dcostrmz.cc',
- 'dcpcache.cc',
- 'dcpixel.cc',
- 'dcpixseq.cc',
- 'dcpxitem.cc',
- 'dcrleccd.cc',
- 'dcrlecce.cc',
- 'dcrlecp.cc',
- 'dcrledrg.cc',
- 'dcrleerg.cc',
- 'dcrlerp.cc',
- 'dcsequen.cc',
- 'dcstack.cc',
- 'dcswap.cc',
- 'dctag.cc',
- 'dctagkey.cc',
- 'dctypes.cc',
- 'dcuid.cc',
- 'dcvm.cc',
- 'dcvrae.cc',
- 'dcvras.cc',
- 'dcvrat.cc',
- 'dcvr.cc',
- 'dcvrcs.cc',
- 'dcvrda.cc',
- 'dcvrds.cc',
- 'dcvrdt.cc',
- 'dcvrfd.cc',
- 'dcvrfl.cc',
- 'dcvris.cc',
- 'dcvrlo.cc',
- 'dcvrlt.cc',
- 'dcvrobow.cc',
- 'dcvrof.cc',
- 'dcvrpn.cc',
- 'dcvrpobw.cc',
- 'dcvrsh.cc',
- 'dcvrsl.cc',
- 'dcvrss.cc',
- 'dcvrst.cc',
- 'dcvrtm.cc',
- 'dcvrui.cc',
- 'dcvrul.cc',
- 'dcvrulup.cc',
- 'dcvrus.cc',
- 'dcvrut.cc',
- 'dcxfer.cc'
- ],
- LIBS=['ofstd'])
+#if not ARGUMENTS.get('mingw', 0):
+# env.Command("dcdictbi.cc",
+# ["dicom.dic",
+# "private.dic",
+# "mkdictbi"
+# ],
+# ["${TARGET.dir}/mkdictbi ${TARGET.dir}/*.dic > ${TARGET}"],
+# )
+#
+# env.Program('mkdictbi',
+# ['mkdictbi.cc',
+# 'cmdlnarg.cc',
+# 'dcbytstr.cc',
+# 'dcchrstr.cc',
+# 'dccodec.cc',
+# 'dcdatset.cc',
+# 'dcddirif.cc',
+# 'dcdebug.cc',
+# 'dcdicdir.cc',
+# 'dcdicent.cc',
+# 'dcdict.cc',
+# 'dcdictzz.cc',
+# 'dcdirrec.cc',
+# 'dcelem.cc',
+# 'dcerror.cc',
+# 'dcfilefo.cc',
+# 'dchashdi.cc',
+# 'dcistrma.cc',
+# 'dcistrmb.cc',
+# 'dcistrmf.cc',
+# 'dcistrmz.cc',
+# 'dcitem.cc',
+# 'dclist.cc',
+# 'dcmetinf.cc',
+# 'dcobject.cc',
+# 'dcostrma.cc',
+# 'dcostrmb.cc',
+# 'dcostrmf.cc',
+# 'dcostrmz.cc',
+# 'dcpcache.cc',
+# 'dcpixel.cc',
+# 'dcpixseq.cc',
+# 'dcpxitem.cc',
+# 'dcrleccd.cc',
+# 'dcrlecce.cc',
+# 'dcrlecp.cc',
+# 'dcrledrg.cc',
+# 'dcrleerg.cc',
+# 'dcrlerp.cc',
+# 'dcsequen.cc',
+# 'dcstack.cc',
+# 'dcswap.cc',
+# 'dctag.cc',
+# 'dctagkey.cc',
+# 'dctypes.cc',
+# 'dcuid.cc',
+# 'dcvm.cc',
+# 'dcvrae.cc',
+# 'dcvras.cc',
+# 'dcvrat.cc',
+# 'dcvr.cc',
+# 'dcvrcs.cc',
+# 'dcvrda.cc',
+# 'dcvrds.cc',
+# 'dcvrdt.cc',
+# 'dcvrfd.cc',
+# 'dcvrfl.cc',
+# 'dcvris.cc',
+# 'dcvrlo.cc',
+# 'dcvrlt.cc',
+# 'dcvrobow.cc',
+# 'dcvrof.cc',
+# 'dcvrpn.cc',
+# 'dcvrpobw.cc',
+# 'dcvrsh.cc',
+# 'dcvrsl.cc',
+# 'dcvrss.cc',
+# 'dcvrst.cc',
+# 'dcvrtm.cc',
+# 'dcvrui.cc',
+# 'dcvrul.cc',
+# 'dcvrulup.cc',
+# 'dcvrus.cc',
+# 'dcvrut.cc',
+# 'dcxfer.cc'
+# ],
+# LIBS=['ofstd'])
diff --git a/src/plugins/tiff.c b/src/plugins/tiff.c
index 76a07a2..e018b50 100644
--- a/src/plugins/tiff.c
+++ b/src/plugins/tiff.c
@@ -54,7 +54,7 @@ GivImage *giv_plugin_load_file(const char *filename,
GivImageType image_type;
if (tif) {
- uint32 w, h, config=9999, bps=9999, spp=9999;
+ uint32 w, h, config=9999, bps=9999, spp=9999, sample_format=9999;
size_t npixels;
uint8* raster;
gboolean has_colormap = FALSE;
@@ -65,11 +65,15 @@ GivImage *giv_plugin_load_file(const char *filename,
TIFFGetField(tif, TIFFTAG_PLANARCONFIG, &config);
TIFFGetField(tif, TIFFTAG_BITSPERSAMPLE, &bps);
TIFFGetField(tif, TIFFTAG_SAMPLESPERPIXEL, &spp);
+ TIFFGetField(tif, TIFFTAG_SAMPLEFORMAT, &sample_format);
+
if (TIFFGetField(tif, TIFFTAG_COLORMAP, &rmap, &gmap, &bmap))
has_colormap = TRUE;
+#if 0
printf("has_colormap= %d\n", has_colormap);
printf("bps spp=%d %d\n", bps, spp);
+#endif
raster = (uint8*) _TIFFmalloc(TIFFScanlineSize(tif));
if (config == PLANARCONFIG_CONTIG) {
@@ -88,20 +92,39 @@ GivImage *giv_plugin_load_file(const char *filename,
// TBD - Support more types.
if (spp == 3 || has_colormap) {
- image_type = GIVIMAGE_RGB_U8;
+ if (bps == 8)
+ image_type = GIVIMAGE_RGB_U8;
+ else if (bps == 16)
+ image_type = GIVIMAGE_RGB_U16;
dst_spp = 3;
}
- else
+ else if(spp == 1
+ && bps == 32
+ && sample_format == SAMPLEFORMAT_IEEEFP) {
+ image_type = GIVIMAGE_FLOAT;
+ }
+ else if (bps == 8)
image_type = GIVIMAGE_U8;
+ else if (bps == 16)
+ image_type = GIVIMAGE_U16;
+ else if (bps == 32)
+ image_type = GIVIMAGE_I32;
+ else {
+ printf("Unknown Tiff type!\n");
+ return NULL;
+ }
+
img = giv_image_new(image_type, w, h);
guchar *dst = img->buf.buf;
-
+ int dst_bpp = giv_image_type_get_size(image_type);
+ int dst_row_stride = giv_image_get_row_stride(img);
+
// Copy the tiff data to the img structure. This can
// be made more memory conservative by using scanlines.
for (row_idx=0; row_idx<h; row_idx++) {
TIFFReadScanline(tif, raster, row_idx, 0);
guchar *src_ptr = raster;
- guchar *dst_ptr = dst + row_idx * w * dst_spp;
+ guchar *dst_ptr = dst + row_idx * dst_row_stride;
// Split between colormap and not colormap per row which
// is sufficiently fast.
@@ -115,7 +138,7 @@ GivImage *giv_plugin_load_file(const char *filename,
}
else {
for (col_idx=0; col_idx<w; col_idx++) {
- for (clr_idx=0; clr_idx<spp; clr_idx++) {
+ for (clr_idx=0; clr_idx<spp*bps/8; clr_idx++) {
*dst_ptr++ = *src_ptr++;
}
}
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