libvips extract area of NDPI from Ex40 not from map
I am using libvips to get pyramids of .ndpi images.
through this answer and searching the documentation I found this command
vips extract_area myimage.ndpi[level=0] mypyramid.dz 0 0 10000 10000
Which extracts a crop starting at 0 0 and size 10000 10000 to a dzi file.
The level parameter is the magnification, 0 is the highest.
The problem is that the ndpi has the following images inside:
- myimage_macro.tif
- myimage_map.tif
- myimage_x0.15625_z0.tif
- myimage_x0.625_z0.tif
- myimage_x10_z0.tif
- myimage_x2.5_z0.tif
- myimage_x40_z0.tif
And vips is taking myimage_macro.tif while I need myimage_x40_z0.tif
There should be a parameter like level to choose which from the images inside the OpenSlide (ndpi) I want.
Some people ask. Why not extracting the tif and then running vips?
Well, because vips tells me this:
openslide2vips: opening slide: No such value: directory 0, tag 278
Which means that using ndpisplit to extract the tif is somehow not saving the metadata to allow vips to recognize the image
So I am in a bit of a pesky situation. I have enormous images and I need to extract a slightly less enourmous piece and then have its pyramid.
Please help me, right now I am basically coding it all my self and it works but it is EXTREMELY slow.
image image-processing tiff medical vips
asked Nov 21 '18 at 21:40
Zloy SmiertniyZloy Smiertniy
1,56652441
add a comment |
I am using libvips to get pyramids of .ndpi images.
through this answer and searching the documentation I found this command
vips extract_area myimage.ndpi[level=0] mypyramid.dz 0 0 10000 10000
Which extracts a crop starting at 0 0 and size 10000 10000 to a dzi file.
The level parameter is the magnification, 0 is the highest.
The problem is that the ndpi has the following images inside:
- myimage_macro.tif
- myimage_map.tif
- myimage_x0.15625_z0.tif
- myimage_x0.625_z0.tif
- myimage_x10_z0.tif
- myimage_x2.5_z0.tif
- myimage_x40_z0.tif
And vips is taking myimage_macro.tif while I need myimage_x40_z0.tif
There should be a parameter like level to choose which from the images inside the OpenSlide (ndpi) I want.
Some people ask. Why not extracting the tif and then running vips?
Well, because vips tells me this:
openslide2vips: opening slide: No such value: directory 0, tag 278
Which means that using ndpisplit to extract the tif is somehow not saving the metadata to allow vips to recognize the image
So I am in a bit of a pesky situation. I have enormous images and I need to extract a slightly less enourmous piece and then have its pyramid.
Please help me, right now I am basically coding it all my self and it works but it is EXTREMELY slow.
image image-processing tiff medical vips
asked Nov 21 '18 at 21:40
Zloy SmiertniyZloy Smiertniy
1,56652441
add a comment |
I am using libvips to get pyramids of .ndpi images.
through this answer and searching the documentation I found this command
vips extract_area myimage.ndpi[level=0] mypyramid.dz 0 0 10000 10000
Which extracts a crop starting at 0 0 and size 10000 10000 to a dzi file.
The level parameter is the magnification, 0 is the highest.
The problem is that the ndpi has the following images inside:
- myimage_macro.tif
- myimage_map.tif
- myimage_x0.15625_z0.tif
- myimage_x0.625_z0.tif
- myimage_x10_z0.tif
- myimage_x2.5_z0.tif
- myimage_x40_z0.tif
And vips is taking myimage_macro.tif while I need myimage_x40_z0.tif
There should be a parameter like level to choose which from the images inside the OpenSlide (ndpi) I want.
Some people ask. Why not extracting the tif and then running vips?
Well, because vips tells me this:
openslide2vips: opening slide: No such value: directory 0, tag 278
Which means that using ndpisplit to extract the tif is somehow not saving the metadata to allow vips to recognize the image
So I am in a bit of a pesky situation. I have enormous images and I need to extract a slightly less enourmous piece and then have its pyramid.
Please help me, right now I am basically coding it all my self and it works but it is EXTREMELY slow.
image image-processing tiff medical vips
asked Nov 21 '18 at 21:40
Zloy SmiertniyZloy Smiertniy
1,56652441
I am using libvips to get pyramids of .ndpi images.
through this answer and searching the documentation I found this command
vips extract_area myimage.ndpi[level=0] mypyramid.dz 0 0 10000 10000
Which extracts a crop starting at 0 0 and size 10000 10000 to a dzi file.
The level parameter is the magnification, 0 is the highest.
The problem is that the ndpi has the following images inside:
- myimage_macro.tif
- myimage_map.tif
- myimage_x0.15625_z0.tif
- myimage_x0.625_z0.tif
- myimage_x10_z0.tif
- myimage_x2.5_z0.tif
- myimage_x40_z0.tif
And vips is taking myimage_macro.tif while I need myimage_x40_z0.tif
There should be a parameter like level to choose which from the images inside the OpenSlide (ndpi) I want.
Some people ask. Why not extracting the tif and then running vips?
Well, because vips tells me this:
openslide2vips: opening slide: No such value: directory 0, tag 278
Which means that using ndpisplit to extract the tif is somehow not saving the metadata to allow vips to recognize the image
So I am in a bit of a pesky situation. I have enormous images and I need to extract a slightly less enourmous piece and then have its pyramid.
Please help me, right now I am basically coding it all my self and it works but it is EXTREMELY slow.
image image-processing tiff medical vips
image image-processing tiff medical vips
asked Nov 21 '18 at 21:40
Zloy SmiertniyZloy Smiertniy
1,56652441
asked Nov 21 '18 at 21:40
Zloy SmiertniyZloy Smiertniy
1,56652441
asked Nov 21 '18 at 21:40
Zloy SmiertniyZloy Smiertniy
1,56652441
asked Nov 21 '18 at 21:40
Zloy SmiertniyZloy Smiertniy
1,56652441
asked Nov 21 '18 at 21:40
Zloy SmiertniyZloy Smiertniy
1,56652441
1,56652441
add a comment |
add a comment |
1 Answer
1
active
oldest
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I've written this as an answer, though it's not really an answer. It seemed too long as just a comment.
The libvips openslideload operation lets you pick an associated image to load. You can get a list of the associated images from the slide-associated-images metadata tag. For example:
$ vipsheader -f slide-associated-images 2013_09_20_29.ndpi
macro
$ vipsheader -f slide-associated-images CMU-1.svs
label, macro, thumbnail
You then pick out an associated image with perhaps:
$ vips crop CMU-1.svs[associated=label] x.jpg 10 10 100 100
To get a small part of the label.
So ... check what associated images openslide reports for your slide. If you can get the one you need, pick that with the associated parameter. If the image you need is not listed, I would contact the openslide project, since they will need to add support.
You could also check the openslide command-line tools, they might perhaps offer more options.
answered Nov 22 '18 at 9:36
jcupittjcupitt
4,19411421
Oh that looks fantastic, it was the "associated" keyword I was looking for. I will try it. In the meantime I already did a python script to do this for me but my DZI looks a bit weird in the smaller resolutions haha
– Zloy Smiertniy
Nov 22 '18 at 10:34
Oh no, sadly it didn't work. I triedvipsheader myimage.ndpi myimage.ndpi: 226176x90880 uchar, 4 bands, rgb, openslideloadandvipsheader -f slide-associated-images : macrothen I didvips crop myimage.ndpi[associated=macro] macrofromheader.dz 0 0 10000 10000and it says extract_area: bad extract area
– Zloy Smiertniy
Nov 22 '18 at 10:38
Also for crop since crop is an alias of extract_area.
– Zloy Smiertniy
Nov 22 '18 at 10:41
Ok so now something worked and I am at a loss why but it is good. Thank you for helping me out! What I finally ran wasvips extract_area myimage.ndpi[level=0] mypyramid.dz[tile-size=1024] 0 0 20000 20000(which was the same from my question), but now it loads the colors properly. The only difference is the tile-size property for the dzi. I wonder if it is a bug because at first it only gave me a weird greyscale image.
– Zloy Smiertniy
Nov 22 '18 at 10:59
Oh huh how strange.level=0is the default, you shouldn't need that. If you can find a smallish image which shows the problem, please open an issue on the libvips bug tracker github.com/libvips/libvips/issues/new
– jcupitt
Nov 22 '18 at 11:45
add a comment |
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I've written this as an answer, though it's not really an answer. It seemed too long as just a comment.
The libvips openslideload operation lets you pick an associated image to load. You can get a list of the associated images from the slide-associated-images metadata tag. For example:
$ vipsheader -f slide-associated-images 2013_09_20_29.ndpi
macro
$ vipsheader -f slide-associated-images CMU-1.svs
label, macro, thumbnail
You then pick out an associated image with perhaps:
$ vips crop CMU-1.svs[associated=label] x.jpg 10 10 100 100
To get a small part of the label.
So ... check what associated images openslide reports for your slide. If you can get the one you need, pick that with the associated parameter. If the image you need is not listed, I would contact the openslide project, since they will need to add support.
You could also check the openslide command-line tools, they might perhaps offer more options.
answered Nov 22 '18 at 9:36
jcupittjcupitt
4,19411421
Oh that looks fantastic, it was the "associated" keyword I was looking for. I will try it. In the meantime I already did a python script to do this for me but my DZI looks a bit weird in the smaller resolutions haha
– Zloy Smiertniy
Nov 22 '18 at 10:34
Oh no, sadly it didn't work. I triedvipsheader myimage.ndpi myimage.ndpi: 226176x90880 uchar, 4 bands, rgb, openslideloadandvipsheader -f slide-associated-images : macrothen I didvips crop myimage.ndpi[associated=macro] macrofromheader.dz 0 0 10000 10000and it says extract_area: bad extract area
– Zloy Smiertniy
Nov 22 '18 at 10:38
Also for crop since crop is an alias of extract_area.
– Zloy Smiertniy
Nov 22 '18 at 10:41
Ok so now something worked and I am at a loss why but it is good. Thank you for helping me out! What I finally ran wasvips extract_area myimage.ndpi[level=0] mypyramid.dz[tile-size=1024] 0 0 20000 20000(which was the same from my question), but now it loads the colors properly. The only difference is the tile-size property for the dzi. I wonder if it is a bug because at first it only gave me a weird greyscale image.
– Zloy Smiertniy
Nov 22 '18 at 10:59
Oh huh how strange.level=0is the default, you shouldn't need that. If you can find a smallish image which shows the problem, please open an issue on the libvips bug tracker github.com/libvips/libvips/issues/new
– jcupitt
Nov 22 '18 at 11:45
add a comment |
I've written this as an answer, though it's not really an answer. It seemed too long as just a comment.
The libvips openslideload operation lets you pick an associated image to load. You can get a list of the associated images from the slide-associated-images metadata tag. For example:
$ vipsheader -f slide-associated-images 2013_09_20_29.ndpi
macro
$ vipsheader -f slide-associated-images CMU-1.svs
label, macro, thumbnail
You then pick out an associated image with perhaps:
$ vips crop CMU-1.svs[associated=label] x.jpg 10 10 100 100
To get a small part of the label.
So ... check what associated images openslide reports for your slide. If you can get the one you need, pick that with the associated parameter. If the image you need is not listed, I would contact the openslide project, since they will need to add support.
You could also check the openslide command-line tools, they might perhaps offer more options.
answered Nov 22 '18 at 9:36
jcupittjcupitt
4,19411421
Oh that looks fantastic, it was the "associated" keyword I was looking for. I will try it. In the meantime I already did a python script to do this for me but my DZI looks a bit weird in the smaller resolutions haha
– Zloy Smiertniy
Nov 22 '18 at 10:34
Oh no, sadly it didn't work. I triedvipsheader myimage.ndpi myimage.ndpi: 226176x90880 uchar, 4 bands, rgb, openslideloadandvipsheader -f slide-associated-images : macrothen I didvips crop myimage.ndpi[associated=macro] macrofromheader.dz 0 0 10000 10000and it says extract_area: bad extract area
– Zloy Smiertniy
Nov 22 '18 at 10:38
Also for crop since crop is an alias of extract_area.
– Zloy Smiertniy
Nov 22 '18 at 10:41
Ok so now something worked and I am at a loss why but it is good. Thank you for helping me out! What I finally ran wasvips extract_area myimage.ndpi[level=0] mypyramid.dz[tile-size=1024] 0 0 20000 20000(which was the same from my question), but now it loads the colors properly. The only difference is the tile-size property for the dzi. I wonder if it is a bug because at first it only gave me a weird greyscale image.
– Zloy Smiertniy
Nov 22 '18 at 10:59
Oh huh how strange.level=0is the default, you shouldn't need that. If you can find a smallish image which shows the problem, please open an issue on the libvips bug tracker github.com/libvips/libvips/issues/new
– jcupitt
Nov 22 '18 at 11:45
add a comment |
I've written this as an answer, though it's not really an answer. It seemed too long as just a comment.
The libvips openslideload operation lets you pick an associated image to load. You can get a list of the associated images from the slide-associated-images metadata tag. For example:
$ vipsheader -f slide-associated-images 2013_09_20_29.ndpi
macro
$ vipsheader -f slide-associated-images CMU-1.svs
label, macro, thumbnail
You then pick out an associated image with perhaps:
$ vips crop CMU-1.svs[associated=label] x.jpg 10 10 100 100
To get a small part of the label.
So ... check what associated images openslide reports for your slide. If you can get the one you need, pick that with the associated parameter. If the image you need is not listed, I would contact the openslide project, since they will need to add support.
You could also check the openslide command-line tools, they might perhaps offer more options.
answered Nov 22 '18 at 9:36
jcupittjcupitt
4,19411421
I've written this as an answer, though it's not really an answer. It seemed too long as just a comment.
The libvips openslideload operation lets you pick an associated image to load. You can get a list of the associated images from the slide-associated-images metadata tag. For example:
$ vipsheader -f slide-associated-images 2013_09_20_29.ndpi
macro
$ vipsheader -f slide-associated-images CMU-1.svs
label, macro, thumbnail
You then pick out an associated image with perhaps:
$ vips crop CMU-1.svs[associated=label] x.jpg 10 10 100 100
To get a small part of the label.
So ... check what associated images openslide reports for your slide. If you can get the one you need, pick that with the associated parameter. If the image you need is not listed, I would contact the openslide project, since they will need to add support.
You could also check the openslide command-line tools, they might perhaps offer more options.
answered Nov 22 '18 at 9:36
jcupittjcupitt
4,19411421
answered Nov 22 '18 at 9:36
jcupittjcupitt
4,19411421
answered Nov 22 '18 at 9:36
jcupittjcupitt
4,19411421
answered Nov 22 '18 at 9:36
jcupittjcupitt
4,19411421
4,19411421
Oh that looks fantastic, it was the "associated" keyword I was looking for. I will try it. In the meantime I already did a python script to do this for me but my DZI looks a bit weird in the smaller resolutions haha
– Zloy Smiertniy
Nov 22 '18 at 10:34
Oh no, sadly it didn't work. I triedvipsheader myimage.ndpi myimage.ndpi: 226176x90880 uchar, 4 bands, rgb, openslideloadandvipsheader -f slide-associated-images : macrothen I didvips crop myimage.ndpi[associated=macro] macrofromheader.dz 0 0 10000 10000and it says extract_area: bad extract area
– Zloy Smiertniy
Nov 22 '18 at 10:38
Also for crop since crop is an alias of extract_area.
– Zloy Smiertniy
Nov 22 '18 at 10:41
Ok so now something worked and I am at a loss why but it is good. Thank you for helping me out! What I finally ran wasvips extract_area myimage.ndpi[level=0] mypyramid.dz[tile-size=1024] 0 0 20000 20000(which was the same from my question), but now it loads the colors properly. The only difference is the tile-size property for the dzi. I wonder if it is a bug because at first it only gave me a weird greyscale image.
– Zloy Smiertniy
Nov 22 '18 at 10:59
Oh huh how strange.level=0is the default, you shouldn't need that. If you can find a smallish image which shows the problem, please open an issue on the libvips bug tracker github.com/libvips/libvips/issues/new
– jcupitt
Nov 22 '18 at 11:45
add a comment |
Oh that looks fantastic, it was the "associated" keyword I was looking for. I will try it. In the meantime I already did a python script to do this for me but my DZI looks a bit weird in the smaller resolutions haha
– Zloy Smiertniy
Nov 22 '18 at 10:34
Oh no, sadly it didn't work. I triedvipsheader myimage.ndpi myimage.ndpi: 226176x90880 uchar, 4 bands, rgb, openslideloadandvipsheader -f slide-associated-images : macrothen I didvips crop myimage.ndpi[associated=macro] macrofromheader.dz 0 0 10000 10000and it says extract_area: bad extract area
– Zloy Smiertniy
Nov 22 '18 at 10:38
Also for crop since crop is an alias of extract_area.
– Zloy Smiertniy
Nov 22 '18 at 10:41
Ok so now something worked and I am at a loss why but it is good. Thank you for helping me out! What I finally ran wasvips extract_area myimage.ndpi[level=0] mypyramid.dz[tile-size=1024] 0 0 20000 20000(which was the same from my question), but now it loads the colors properly. The only difference is the tile-size property for the dzi. I wonder if it is a bug because at first it only gave me a weird greyscale image.
– Zloy Smiertniy
Nov 22 '18 at 10:59
Oh huh how strange.level=0is the default, you shouldn't need that. If you can find a smallish image which shows the problem, please open an issue on the libvips bug tracker github.com/libvips/libvips/issues/new
– jcupitt
Nov 22 '18 at 11:45
Oh that looks fantastic, it was the "associated" keyword I was looking for. I will try it. In the meantime I already did a python script to do this for me but my DZI looks a bit weird in the smaller resolutions haha
– Zloy Smiertniy
Nov 22 '18 at 10:34
Oh that looks fantastic, it was the "associated" keyword I was looking for. I will try it. In the meantime I already did a python script to do this for me but my DZI looks a bit weird in the smaller resolutions haha
– Zloy Smiertniy
Nov 22 '18 at 10:34
Oh no, sadly it didn't work. I tried
vipsheader myimage.ndpi myimage.ndpi: 226176x90880 uchar, 4 bands, rgb, openslideload and vipsheader -f slide-associated-images : macro then I did vips crop myimage.ndpi[associated=macro] macrofromheader.dz 0 0 10000 10000 and it says extract_area: bad extract area– Zloy Smiertniy
Nov 22 '18 at 10:38
Oh no, sadly it didn't work. I tried
vipsheader myimage.ndpi myimage.ndpi: 226176x90880 uchar, 4 bands, rgb, openslideload and vipsheader -f slide-associated-images : macro then I did vips crop myimage.ndpi[associated=macro] macrofromheader.dz 0 0 10000 10000 and it says extract_area: bad extract area– Zloy Smiertniy
Nov 22 '18 at 10:38
Also for crop since crop is an alias of extract_area.
– Zloy Smiertniy
Nov 22 '18 at 10:41
Also for crop since crop is an alias of extract_area.
– Zloy Smiertniy
Nov 22 '18 at 10:41
Ok so now something worked and I am at a loss why but it is good. Thank you for helping me out! What I finally ran was
vips extract_area myimage.ndpi[level=0] mypyramid.dz[tile-size=1024] 0 0 20000 20000 (which was the same from my question), but now it loads the colors properly. The only difference is the tile-size property for the dzi. I wonder if it is a bug because at first it only gave me a weird greyscale image.– Zloy Smiertniy
Nov 22 '18 at 10:59
Ok so now something worked and I am at a loss why but it is good. Thank you for helping me out! What I finally ran was
vips extract_area myimage.ndpi[level=0] mypyramid.dz[tile-size=1024] 0 0 20000 20000 (which was the same from my question), but now it loads the colors properly. The only difference is the tile-size property for the dzi. I wonder if it is a bug because at first it only gave me a weird greyscale image.– Zloy Smiertniy
Nov 22 '18 at 10:59
Oh huh how strange.
level=0 is the default, you shouldn't need that. If you can find a smallish image which shows the problem, please open an issue on the libvips bug tracker github.com/libvips/libvips/issues/new– jcupitt
Nov 22 '18 at 11:45
Oh huh how strange.
level=0 is the default, you shouldn't need that. If you can find a smallish image which shows the problem, please open an issue on the libvips bug tracker github.com/libvips/libvips/issues/new– jcupitt
Nov 22 '18 at 11:45
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