Hello,
I have recently started to use grid/collection stitching to stitch the
light microscopic images.
I know my code problem is something to do with file name and loop and it
seems simple but i cannot figure out how to fix them.
Nine images are taken for one section of histological sample (image name:
001_1, 001_2....001_9 and 002_1,....002_9...and so on).
All the images are saved in the same folder (VK_test).
I have following macro code for stitching:
//////
Odir = getDirectory("Select an Open Directory ");
Sdir = getDirectory("Select or make a Save Directory ");
list = getFileList(Odir);
for (k=0; k<list.length; k++) {
if (endsWith(list[k], ".tif")){
image = Odir + list[k];
print(image);
run("Grid/Collection stitching", "type=[Grid: column-by-column]
order=[Right & Down ] grid_size_x=3 grid_size_y=3
tile_overlap=20 first_file_index_i=1 directory=[D:\\Histology_2013\
\VK_test\\] file_names=[image]_{i}.tif
output_textfile_name=
>
> TileConfiguration.txt fusion_method=[Linear Blending]
> regression_threshold=0.80 max/avg_displacement_threshold=1
> absolute_displacement_threshold=3.50 compute_overlap ignore_z_stage
> subpixel_accuracy downsample_tiles computation_parameters=[Save computation
> time (but use more RAM)] image_output=[Fuse and display]");
> run("Stack to RGB");
> OutName = "fused_" + File.getName(list[k]);
> saveAs("tiff", Sdir + "/" + OutName);
> close();
> close();
> }
> }
> /////////
>
> But there are two problems:
> 1) file names are not recognized in the stitching process and i get the
> messages that "Cannot find file:"D:\Histology_2013\VK\test\"image"-abrot
> stitching.
> How do i fix the code for let imageJ recognize the file name?
> Print function recognize the file name though.
>
> 2) Although this code works if i replace the file name to exact name of the
> file (ex. 001),
> because of loop the stitching happens 9 times.
> How can i have this stitching one time instead of number of files that i
> want to stitch?
>
> If it easy to code if the images are saved in individual folder, i can do
> that too.
> I have tried that too but i also had encountered problem of identifying the
> folder and file names.
>
>
> I really appreciate if somebody can help me out this.
>
> Thanks!!
>
> rui
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html
Locked
