void write_tiff_stack_rgb( char *name, rgb* buf, int width, int height, int depth )
{ int iframe;
Tiff_Writer *tiff = Open_Tiff_Writer(name,0);
Tiff_Image *plane = Create_Tiff_Image( width, height );
void *tr,*tb,*tg;
Add_Tiff_Image_Channel( plane, CHAN_RED, 8, CHAN_UNSIGNED );
Add_Tiff_Image_Channel( plane, CHAN_GREEN, 8, CHAN_UNSIGNED );
Add_Tiff_Image_Channel( plane, CHAN_BLUE, 8, CHAN_UNSIGNED );
for( iframe = 0; iframe < depth; iframe++ )
{ uint8 *dest;
rgb *im, *src;
/* Select Plane and copy out to channels of Tiff_Image */
im = buf + iframe * width * height;
/* red */
src = im + width*height ;
dest = (uint8*) ( plane->channels[0]->plane)+ width*height ;
while( --src >= im )
*(--dest) = src->r;
/* green */
src = im + width*height ;
dest = (uint8*) ( plane->channels[1]->plane)+ width*height ;
while( --src >= im )
*(--dest) = src->g;
/* blue */
src = im + width*height ;
dest = (uint8*) ( plane->channels[2]->plane)+ width*height ;
while( --src >= im )
*(--dest) = src->b;
{ Tiff_IFD *ifd = Make_IFD_For_Image( plane, 0 );
Write_Tiff_IFD(tiff, ifd );
Free_Tiff_IFD(ifd);
}
}
Free_Tiff_Image( plane );
Close_Tiff_Writer(tiff);
Free_Tiff_Writer(tiff);
}
int main(int argc, char *argv[])
{ char *in, *out;
Tiff_Reader *reader;
Tiff_Writer *writer;
Tiff_IFD *ifd;
int flag64, first, source, target;
int *colors, nchan;
Process_Arguments(argc,argv,Spec,0);
in = Get_String_Arg("in");
out = Get_String_Arg("out");
reader = Open_Tiff_Reader(in,NULL,&flag64,strcmp(in+(strlen(in)-4),".lsm") == 0);
if (reader == NULL)
{ fprintf(stderr,"Error opening tif %s:\n %s\n",in,Tiff_Error_String());
exit (1);
}
writer = Open_Tiff_Writer(out,flag64,0);
if (writer == NULL)
{ fprintf(stderr,"Error opening tif %s:\n %s\n",out,Tiff_Error_String());
exit (1);
}
nchan = 0;
colors = NULL;
target = 0;
source = 0;
first = 1;
while ( ! End_Of_Tiff(reader))
{ ifd = Read_Tiff_IFD(reader);
if (ifd == NULL)
{ fprintf(stderr,"Error reading IFD:\n %s\n",Tiff_Error_String());
exit (1);
}
if (first)
{ first = 0;
if (Is_Arg_Matched("-m"))
{ source = Get_Int_Arg("-m",1);
target = Get_Int_Arg("-m",2);
if (source < 0 || source > 1)
{ fprintf(stderr,"Source is not 0 or 1\n"); exit (1); }
if (target < 0 || target > 2)
{ fprintf(stderr,"Target is not 0, 1, or 2\n"); exit (1); }
}
else if (Get_Tiff_Tag(ifd,TIFF_CZ_LSM_INFO,NULL,NULL) != NULL)
{ if (nchan == 0)
{ nchan = Count_LSM_Colors(ifd);
colors = (int *) Guarded_Malloc(sizeof(int)*((size_t) nchan),Program_Name());
}
Get_LSM_Colors(ifd,nchan,colors); // Figure out which channel is green
for (source = 0; source < nchan; source++) // and map to green in the RGB
if ((colors[source] & 0xff00) != 0)
break;
if (source >= nchan)
source = 0;
target = 1;
}
else
{ source = 0;
target = 1;
}
}
if (Convert_2_RGB(ifd,source,target) != NULL)
{ if (Write_Tiff_IFD(writer,ifd))
{ fprintf(stderr,"Error writing IFD:\n %s\n",Tiff_Error_String());
exit (1);
}
}
else
{ fprintf(stderr,"Error adding extra channel:\n %s\n",Tiff_Error_String());
exit (1);
}
Free_Tiff_IFD(ifd);
}
Free_Tiff_Writer(writer);
exit (0);
}
int main(int argc, char* argv[])
{
#if 0
Mc_Stack *mc_stack = Read_Mc_Stack("../data/benchmark/L3_12bit.lsm", -1);
Stack *stack = Mc_Stack_To_Stack(mc_stack, COLOR, NULL);
Write_Stack_U("../data/test.lsm", stack, "../data/benchmark/L3_12bit.lsm");
#endif
#if 0
//Print_Lsm_Info("/Users/zhaot/Data/stitching_12bit/70208_2BcPhR_R1_GR1_B1_L001.lsm");
Mc_Stack *stack = Read_Mc_Stack("../data/benchmark/L3_12bit.lsm", -1);
Print_Mc_Stack_Info(stack);
Mc_Stack_Grey16_To_8(stack, 1);
Write_Mc_Stack("../data/test.lsm", stack, "../data/benchmark/L3_12bit.lsm");
#endif
#if 0
Read_Stack("/Users/zhaot/Data/slice15overlay/L05.tif");
#endif
#if 0
/*
char *filePath = "test";
if( strlen(filePath)>4 )
if( strcmp(filePath+strlen(filePath)-4,".tif")==0 ||
strcmp(filePath+strlen(filePath)-4,".TIF")==0 )
printf("%d\n", 1);
printf("%d\n", 0);
*/
Is_Tiff("test");
//Write_Stack("/Users/zhaot/Work/neurolabi/data/test.tif", Read_Stack("/Users/zhaot/Data/slice15overlay/L03.tif"));
Write_Stack("../data/test.tif", Read_Stack("../data/L05.tif"));
#endif
#if 0
Stack *stack = Read_Stack("../data/fly_neuron.tif");
Write_Stack("../data/test2.tif", stack);
#endif
#if 0
int big_endian;
Tiff_Reader *tif = Open_Tiff_Reader("/Users/zhaot/Data/Stacks for stitching/Set 1 65C07/GL_100708_R1_GR1_B1_L013.lsm", &big_endian, 1);
Tiff_Writer *tif2 = Open_Tiff_Writer("../data/test.tif", 0);
Tiff_IFD *ifd = NULL;
int depth = 0;
while ((ifd = Read_Tiff_IFD(tif)) != NULL) {
if (Convert_LSM_2_RGB(ifd, 0, 0) != NULL) {
Write_Tiff_IFD(tif2, ifd);
depth++;
}
Free_Tiff_IFD(ifd);
}
printf("%d\n", depth);
//Kill_Tiff_IFD(ifd);
Kill_Tiff_Reader(tif);
Close_Tiff_Writer(tif2);
Stack *stack = Read_Stack("../data/test.tif");
Write_Stack("../data/test.tif", stack);
#endif
#if 0
Tiff_Reader *reader;
reader = Open_Tiff_Reader("../data/test.lsm",NULL,1);
Tiff_IFD *ifd = Read_Tiff_IFD(reader);
Print_Tiff_IFD(ifd, stdout);
Kill_Tiff_Reader(reader);
#endif
#if 0
Stack *stack = Read_Lsm_Stack("/Users/zhaot/Data/stitch/Set 3 17F12/GL_100208_R1_GR1_B1_L07.lsm", -1);
//Stack *stack = Read_Lsm_Stack("/Users/zhaot/Data/nathan/2p internal[497-545,565-649nm] 40x 2x12us 900nm 5pct cleared 1.lsm", 0);
Tiff_IFD *ifd;
{ Tiff_Reader *reader;
reader = Open_Tiff_Reader("/Users/zhaot/Data/stitch/Set 3 17F12/GL_100208_R1_GR1_B1_L08.lsm",NULL,1);
while (lsm_thumbnail_flag(ifd = Read_Tiff_IFD(reader)) != 0) {
//Advance_Tiff_Reader(reader);
if (End_Of_Tiff(reader)) {
ifd = NULL;
TZ_ERROR(ERROR_IO_READ);
break;
}
}
}
//Write_Stack("../data/test.tif", stack);
Print_Tiff_IFD(ifd, stdout);
if (stack != NULL) {
Write_Lsm_Stack("../data/test.lsm", stack, ifd);
}
stack = Read_Lsm_Stack("../data/test.lsm", -1);
Write_Stack("../data/test.tif", stack);
#endif
#if 0
Mc_Stack *mc_stack = Read_Mc_Stack("../data/test.tif", 1);
Print_Mc_Stack_Info(mc_stack);
Write_Mc_Stack("../data/test2.tif", mc_stack, NULL);
Free_Mc_Stack(mc_stack);
mc_stack = Read_Mc_Stack("../data/test2.tif", -1);
Print_Mc_Stack_Info(mc_stack);
printf("%d\n", Mc_Stack_Usage());
#endif
#if 0
Stack *stack = Read_Lsm_Stack("../data/test.lsm", -1);
Print_Stack_Info(stack);
Write_Stack("../data/test.tif", stack);
#endif
#if 0
Fix_Lsm_File("../data/test/result1.lsm");
Print_Lsm_Info("../data/test/result1.lsm");
#endif
#if 0
Stack *stack = Make_Stack(1, 5, 5, 5);
int nvoxel = Stack_Voxel_Number(stack);
int i;
for (i = 0; i < nvoxel; i++) {
stack->array[i] = i;
}
Write_Stack("../data/test.tif", stack);
stack = Read_Stack("../data/test.tif");
Write_Stack("../data/test2.tif", stack);
#endif
#if 0
Stack *stack = Read_Stack(fullpath("../data/fly_neuron_n11/", "mask2.tif",
NULL));
Print_Stack_Info(stack);
#endif
#if 0
//Print_Lsm_Info("/Users/zhaot/Data/stitch/Set 3 17F12/GL_100208_R1_GR1_B1_L07.lsm");
//FILE *fp = fopen("/Users/zhaot/Data/stitch/set1/GL_100708_R1_GR1_B1_L015.lsm", "r");
FILE *fp = fopen("../data/test.lsm", "r");
char endian[3];
endian[2] = '\0';
fread(endian, 1, 2, fp);
printf("Endian: %s\n", endian);
uint16_t magic;
fread(&magic, 2, 1, fp);
printf("Magic number: %u\n", magic);
uint32_t ifd_offset;
fread(&ifd_offset, 4, 1, fp);
printf("1st IFD offset: %u\n", ifd_offset);
fseek(fp, ifd_offset, SEEK_SET);
uint16_t nifd;
fread(&nifd, 2, 1, fp);
printf("Number of IFD: %u\n", nifd);
uint16_t ifd_label;
fread(&ifd_label, 2, 1, fp);
uint16_t i;
for (i = 1; i < nifd; i++) {
if (ifd_label == TIF_CZ_LSMINFO) {
break;
}
fseek(fp, 10, SEEK_CUR);
fread(&ifd_label, 2, 1, fp);
}
printf("IFD label: %u\n", ifd_label);
uint16_t ifd_type;
fread(&ifd_type, 2, 1, fp);
printf("IFD type: %u\n", ifd_type);
uint32_t ifd_length;
fread(&ifd_length, 4, 1, fp);
printf("IFD length: %u\n", ifd_length);
fread(&ifd_offset, 4, 1, fp);
printf("Lsm info offset: %u\n", ifd_offset);
/*
fseek(fp, ifd_offset + CZ_LSMINFO_DIMZ_OFFSET, SEEK_SET);
int32_t dimz = 80;
fwrite(&dimz, 4, 1, fp);
printf("Number of slices: %d\n", dimz);
*/
int offset = 88;
fseek(fp, ifd_offset, SEEK_SET);
/*
uint32_t value = 0;
fwrite(&value, 4, 1, fp);
fseek(fp, ifd_offset + offset, SEEK_SET);
*/
/*
Fprint_File_Binary(fp, 24, stdout);
fclose(fp);
return 1;
*/
Cz_Lsminfo lsminfo;
fread(&lsminfo, sizeof(Cz_Lsminfo), 1, fp);
printf("%lu\n", sizeof(Cz_Lsminfo));
if (lsminfo.u32MagicNumber == 67127628) {
printf("Version 1.5, 1.6 and 2.0\n");
} else if (lsminfo.u32MagicNumber == 50350412) {
printf("Version 1.3\n");
} else {
printf("Unknown version\n");
return 1;
}
printf("Structure size: %d\n", lsminfo.s32StructureSize);
printf("Stack size: %d x %d x %d\n", lsminfo.s32DimensionX,
lsminfo.s32DimensionY, lsminfo.s32DimensionZ);
printf("Number of channels: %d\n", lsminfo.s32DimensionChannels);
switch (lsminfo.s32DataType) {
case 1:
printf("8-bit unsigned integer.\n");
break;
case 2:
printf("12-bit unsigned integer.\n");
break;
case 5:
printf("32-bit float.\n");
break;
case 0:
printf("Different channels have different types.\n");
break;
}
printf("Thumbnail size: %d x %d\n", lsminfo.s32ThumbnailX,
lsminfo.s32ThumbnailY);
printf("Voxel size: %g x %g x %g um\n", lsminfo.f64VoxelSizeX * 1000000,
lsminfo.f64VoxelSizeY * 1000000, lsminfo.f64VoxelSizeZ * 1000000);
printf("Scan type: ");
switch (lsminfo.u16ScanType) {
case 0:
printf("normal x-y-z-scan\n");
break;
case 1:
printf("Z-Scan\n");
break;
case 2:
printf("Line Scan\n");
break;
case 3:
printf("Time series x-y\n");
break;
case 4:
printf("Time series x-z\n");
break;
case 5:
printf("Time series - Mean of ROIS\n");
break;
}
if (lsminfo.u32OffsetVectorOverlay == 0) {
printf("There is no vector overlay\n");
} else {
printf("Vector overlay found\n");
}
if (lsminfo.u32OffsetInputLut == 0) {
printf("There is no input LUT\n");
} else {
printf("Input LUT found\n");
}
if (lsminfo.u32OffsetOutputLut == 0) {
printf("There is no color palette\n");
} else {
printf("Color palette found\n");
}
if (lsminfo.u32OffsetChannelColors == 0) {
printf("There is no channel color or channel name\n");
} else {
printf("Channel colors and channel names fournd\n");
}
if (lsminfo.f64TimeInterval == 0) {
printf("There is no time interval\n");
} else {
printf("Time interval: %lg sec\n", lsminfo.f64TimeInterval);
}
if (lsminfo.u32OffsetScanInformation == 0) {
printf("There is no information about devide settings\n");
} else {
printf("Scan information found. Offset: %u\n",
lsminfo.u32OffsetScanInformation);
/*
Lsm_Scan_Info *info =
(Lsm_Scan_Info*) (data + lsminfo.u32OffsetScanInformation + 20);
printf("Information type: %u\n", info->u32Entry);
printf("Data type: %u\n", info->u32Type);
printf("Data size: %u\n", info->u32Size);
*/
/*
uint8_t *byte = (uint8_t*) (data + lsminfo.u32OffsetScanInformation);
printf("%u\n", byte[8]);
*/
}
if (lsminfo.u32OffsetKsData == 0) {
printf("There is no Zeiss Vision KS-3d data\n");
} else {
printf("Zeiss Vision KS-3d data found. Offset: %u\n",
lsminfo.u32OffsetKsData);
}
if (lsminfo.u32OffsetRoi == 0) {
printf("There is no ROI\n");
} else {
printf("ROI found\n");
}
if (lsminfo.u32OffsetNextRecording == 0) {
printf("There is no second image\n");
} else {
printf("Second image found\n");
}
fclose(fp);
#endif
#if 0
FILE *fp = fopen("/Users/zhaot/Data/stitch/set1/GL_100708_R1_GR1_B1_L014.lsm", "r+");
char endian[3];
endian[2] = '\0';
fread(endian, 1, 2, fp);
printf("Endian: %s\n", endian);
fpos_t pos;
fgetpos(fp, &pos);
printf("%d\n", pos);
fseek(fp, 0, SEEK_SET);
uint32_t x = 254;
printf("%lu bytes written\n", fwrite(&x, sizeof(uint32_t), 1, fp));
fgetpos(fp, &pos);
printf("%d\n", pos);
Fprint_File_Binary(fp, 8, stdout);
fclose(fp);
#endif
#if 0
Stack *stack = Read_Lsm_Stack("../data/GL_100208_R1_GR1_B1_L07.lsm", -1);
Write_Stack_U("../data/test.lsm", stack,
"../data/GL_100208_R1_GR1_B1_L07.lsm");
#endif
#if 0
//Stack *stack = Read_Lsm_Stack("/Users/zhaot/Data/neurolineage/lsm/Twin-Spot_Gal4-GH146_nc_11-2.lsm", 0);
Stack *stack = Read_Stack_U("../data/test2.tif");
Write_Stack_U("../data/test.tif", stack, NULL);
#endif
#if 0
Stack *stack = Read_Stack("../data/mouse_single_org/traced.tif");
Write_Stack("../data/test.tif", stack);
#endif
#if 0 /* test writing large stack */
Mc_Stack *stack = Make_Mc_Stack(GREY, 1024, 1024, 1024, 3);
size_t n = (size_t) 1024 * 1024 * 1024 * 3;
size_t i;
for (i = 0; i < n; i++) {
stack->array[i] = i % 255;
}
Write_Mc_Stack("../data/test.tif", stack, NULL);
#endif
#if 0 /* test reading large stack */
Mc_Stack *stack = Read_Mc_Stack("../data/test.tif", -1);
Print_Mc_Stack_Info(stack);
#endif
#if 0 /* test writing a raw stack */
Mc_Stack *stack = Read_Mc_Stack("/Users/zhaot/Data/SynapseSpotted2_S124-3_1to59NF1Crop1_enhanced_Sample.tif", -1);
//Print_Stack_Info(stack);
Write_Mc_Stack("../data/test.raw", stack, NULL);
#endif
#if 0 /* test reading a raw stack */
/*
Stack *stack = Read_Raw_Stack("/Users/zhaot/Data/jinny/slice15_overplaped.raw");
Print_Stack_Info(stack);
Write_Stack("../data/test.tif", stack);
*/
Stack *stack = Read_Sc_Stack("/Users/zhaot/Data/jinny/proofread_slice15_3to11/detectedresults/slice15_3to11_crop01_detected_test.raw", 1);
Print_Stack_Info(stack);
Write_Stack("../data/test.tif", stack);
#endif
#if 0
Stack *stack = Read_Sc_Stack("/Users/zhaot/Data/jinny/drawMask/slice15_3to33_4_30_result.raw", 2);
stack = Read_Stack_U("/Users/zhaot/Data/jinny/drawMask/slice15_3to33.raw");
#endif
#if 0
Stack *stack =
Read_Stack_U("/Users/zhaot/Work/neurolabi/data/diadem_d1_095.xml");
Print_Stack_Info(stack);
#endif
#if 0
Stack *stack =
Read_Stack_U("/Users/zhaot/Work/neurolabi/data/diadem_d1_001.xml");
Print_Stack_Info(stack);
Mc_Stack *mc_stack = Mc_Stack_Rewrap_Stack(stack);
printf("%d\n", Stack_Usage());
printf("%d\n", Mc_Stack_Usage());
Print_Mc_Stack_Info(mc_stack);
Write_Mc_Stack("../data/test.tif", mc_stack, NULL);
Free_Mc_Stack(mc_stack);
mc_stack = Read_Mc_Stack("/Users/zhaot/Work/neurolabi/data/diadem_d1_001.xml", -1);
printf("%d\n", Mc_Stack_Usage());
#endif
#if 0
int size[3];
Stack_Size_F("../data/benchmark/L3_12bit.lsm", size);
iarray_print2(size, 3, 1);
#endif
#if 0
Mc_Stack *stack =
Read_Mc_Stack("/Users/zhaot/Data/Julie/All_tiled_nsyb5_Sum.lsm", -1);
Print_Mc_Stack_Info(stack);
Write_Mc_Stack("../data/test.lsm", stack,
"/Users/zhaot/Data/Julie/All_tiled_nsyb5_Sum.lsm");
#endif
#if 0
Mc_Stack *stack =
Read_Mc_Stack("../data/test.lsm", -1);
Print_Mc_Stack_Info(stack);
#endif
#if 0
Mc_Stack *stack = NULL;
stack = Read_Mc_Stack("/Users/zhaot/Data/colorsep/16D01.1-14.lsm", 0);
Write_Mc_Stack("/Users/zhaot/Data/colorsep/channel1.tif", stack, NULL);
stack = Read_Mc_Stack("/Users/zhaot/Data/colorsep/16D01.1-14.lsm", 1);
Write_Mc_Stack("/Users/zhaot/Data/colorsep/channel2.tif", stack, NULL);
stack = Read_Mc_Stack("/Users/zhaot/Data/colorsep/16D01.1-14.lsm", 2);
Write_Mc_Stack("/Users/zhaot/Data/colorsep/channel3.tif", stack, NULL);
stack = Read_Mc_Stack("/Users/zhaot/Data/colorsep/16D01.1-14.lsm", 3);
Write_Mc_Stack("/Users/zhaot/Data/colorsep/channel4.tif", stack, NULL);
/*
Write_Mc_Stack("../data/test.lsm", stack,
"/Users/zhaot/Data/Julie/All_tiled_nsyb5_Sum.lsm");
*/
#endif
#if 0
Mc_Stack *stack = Read_Mc_Stack("/Users/zhaot/Data/colorsep/16D01.1-14.lsm",
-1);
Print_Mc_Stack_Info(stack);
Stack grey_stack = Mc_Stack_Channel(stack, 3);
grey_stack.text = "\0";
Write_Stack("../data/test.tif", &grey_stack);
#endif
#if 0
printf("Channel number: %d\n", Lsm_Channel_Number("../data/12bit/70208_2BcPhR_R1_GR1_B1_L003.lsm"));
printf("Image type:");
switch (Lsm_Pixel_Type("../data/12bit/70208_2BcPhR_R1_GR1_B1_L003.lsm")) {
case GREY8:
printf(" uint8\n");
break;
case GREY16:
printf(" uint16\n");
break;
case FLOAT32:
printf(" float32\n");
break;
default:
printf(" unknown\n");
}
#endif
#if 0
Mc_Stack *stack = Read_Mc_Stack("../data/brainbow/CA3.lsm", 0);
Print_Mc_Stack_Info(stack);
Write_Mc_Stack("../data/test.tif", stack, NULL);
#endif
#if 0
Stack *stack = Read_Stack_U("../data/test.xml");
Write_Stack("../data/test.tif", stack);
#endif
#if 0
int width, height, depth, kind;
Tiff_Attribute("../data/stack8.tif", 0, &kind, &width, &height, &depth);
printf("%d %d %d %d\n", width, height, depth, kind);
#endif
#if 0
Mc_Stack *stack = Read_Mc_Stack("../data/neuronsep/Lee_Lab/13C01_BLM00090_D2.v3dpdb", 1);
Print_Mc_Stack_Info(stack);
Write_Mc_Stack("../data/test.tif", stack, NULL);
#endif
#if 0
//Mc_Stack *stack = Read_Mc_Stack("../data/benchmark/bfork_2d.tif", -1);
//Mc_Stack *stack = Read_Mc_Stack("../data/neuronsep/Lee_Lab/13C01_BLM00090_D2.v3dpdb", 0);
Mc_Stack *stack = Read_Mc_Stack("../data/neuronsep/stitched-1.v3dpdb", 0);
//stack->depth = 1;
Stack ch = Mc_Stack_Channel(stack, 0);
printf("%g\n", Stack_Sum(&ch));
int *hist = Stack_Hist(&ch);
Print_Int_Histogram(hist);
Print_Mc_Stack_Info(stack);
Write_Mc_Stack("../data/test.tif", stack, NULL);
#endif
#if 0
Mc_Stack *stack = Read_Mc_Stack("../data/neurosep/aljosha/stitched-1858872924438528098.v3draw", -1);
Print_Mc_Stack_Info(stack);
#endif
#if 1
IMatrix *mat = IMatrix_Read("../data/test/session2/body_map/body_map00161.imat");
printf("%d: %d x %d x %d\n", (int) mat->ndim, mat->dim[0], mat->dim[1],
mat->dim[2]);
Stack *stack = Make_Stack(GREY, mat->dim[0], mat->dim[1], mat->dim[2]);
size_t nvoxel = Stack_Voxel_Number(stack);
for (size_t i = 0; i < nvoxel; ++i) {
stack->array[i] = (mat->array[i]) >> 24;
}
Write_Stack("../data/test.tif", stack);
#endif
return 0;
}