imfuse: ERROR: Error while cutting images about microscopy-tools HOT 14 CLOSED

I've reproduced all steps and could not reproduce the issue, sorry.
Not sure what is going wrong.

You are using option --cache. Maybe something get wrong one time, and now a broken image is stored in cache.
Could you please remove cache.imfuse and try again?

I've made an update that gives some more messages about the progress.
Also it helps to run with --verbose to see in detail at which point the progress stops.

from microscopy-tools.

You are using option --cache. Maybe something get wrong one time, and now a broken image is stored in cache.
Could you please remove cache.imfuse and try again?
Ok, now there is no folder made by imfuse.

I've made an update that gives some more messages about the progress.
Also it helps to run with --verbose to see in detail at which point the progress stops.

1. got the newest version (imfuse v0.6.1-beta)

2. starting imfuse: imfuse -o imfu_diff_pc20.tif --diffstat --verbose pc20-aligned_C_m_c40_order_00??.tif

3. It does'nt work: Error while flattening images
   Error while flattening images.txt

4. I took only 3 files for input, but the result was the same. "magick: insufficient image data in file `/mnt/Daten/holger/Fotos/stacks/20210203_Motte4_Kopf_Mikroskopobj/cache.imfuse/montage-diffstat.8f1e91.tif' @ error/tiff.c/ReadTIFFImage/1774.
   imfuse ERROR: Error while flattening images"

Here are the files:
pc20-aligned_C_m_c40_order_000x.zip

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Likely the error depends on the version of ImageMagick.
I have three versions available:

$ magick --version
Version: ImageMagick 7.0.10-13 Q16 x86_64 2020-05-17 https://imagemagick.org
$ convert --version
Version: ImageMagick 6.9.11-24 Q16 x86_64 20200718 https://imagemagick.org
$ convert --version
Version: ImageMagick 6.9.10-23 Q16 x86_64 20190101 https://imagemagick.org

It runs well with v7.0.10. I got a different error than yours with v6.9.11. (fixed now)
What is your version?

I assume that this command creating a transparent image is failing:

nice convert -size 899x597 xc:blue -transparent blue -type TrueColorAlpha +repage -quality 100% -compress lzw montage.tif

Could you check this command and its resulting image? Maybe the -compress lzw option fails and should be omitted.

Edit:
On the other hand, why does imfuse succeed with non-resized images? Where is the difference?
Just in case, I've added a note containing the command when transparent images are created.
The one with montage in the file name would be the failing image.

from microscopy-tools.

Likely the error depends on the version of ImageMagick.
I have three versions available:

$ magick --version
Version: ImageMagick 7.0.10-13 Q16 x86_64 2020-05-17 https://imagemagick.org
$ convert --version
Version: ImageMagick 6.9.11-24 Q16 x86_64 20200718 https://imagemagick.org
$ convert --version
Version: ImageMagick 6.9.10-23 Q16 x86_64 20190101 https://imagemagick.org

It runs well with v7.0.10. I got a different error than yours with v6.9.11. (fixed now)
What is your version?
I have:
~> magick --version
Version: ImageMagick 7.0.7-34 Q16 x86_64 20180520
~> convert --version
Version: ImageMagick 7.0.7-34 Q16 x86_64 20180520

In an other openSUSE repository I found version 7.0.10.53, but have not installed so far.

from microscopy-tools.

You have a quite recent version, ok. That should make a bug or different syntax in ImageMagick less likely.

I've changed the command to generate the transparent image a bit, and also added some verbose output around the point where the error occurs. Could you please try again?

from microscopy-tools.

nice convert -size 899x597 xc:blue -transparent blue -type TrueColorAlpha +repage -quality 100% -compress lzw montage.tif

Could you check this command and its resulting image? Maybe the `-compress lzw` option fails and should be omitted.

I'm not familiar with convert an it's args, but here is what I done:
nice convert aligned_C_m_c40_order_0001.tif -size 899x597 xc:blue -transparent blue -type TrueColorAlpha +repage -quality 100% -compress lzw montage.tif
It shows the known warnings because of exif data. But it works as far as I can see.

nice convert pc20-aligned_C_m_c40_order_00??.tif -size 899x597 xc:blue -transparent blue -type TrueColorAlpha +repage -quality 100% -compress lzw montage.tif
No exif data = no warnings. It works.

But I don't know what the result (montage.tif) should look like.

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I've changed the command to generate the transparent image a bit, and also added some verbose output around the point where the error occurs. Could you please try again?

1. starting imfuse using the shrunk images
   imfuse -o imfu_morphologyr3_pc20_aligned_C_m_c40_order.tif --verbose --morphology=r3 pc20-aligned_C_m_c40_order_00??.tif

No errors, no warnings. And the result is ok too.

from microscopy-tools.

No errors, no warnings. And the result is ok too.

So this seems to be fixed? Great!
Thanks for your patience. I am grateful to get some feedback to the project.

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So this seems to be fixed? Great!
Yes!

Thanks for your patience.
Patience? You are very fast in bug fixing.

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I got it again:

~>imfuse --verbose --dog --less --close --finalblur=w47,s2 --alpha --threshold=50 --bg=enfuse aligned_C_c60_m_order_00??.tif

imfuse: --bg: enfuse enfuse

...

imfuse: Montage 27/64. Duration: 00:13:03; ETA: 00:17:53
magick: no images for write '-write' 'mpr:lessthanmax' at CLI arg 60 @ error/operation.c/CLINoImageOperator/4882.
imfuse ERROR: Error while cutting images

imfuse: Montage 28/64. Duration: 00:13:09; ETA: 00:16:54

Error while cutting images_20210218.zip

imfuse v0.6.7.0-beta
Version: ImageMagick 7.0.10-53 Q16 x86_64

from microscopy-tools.

Quite odd.
It happend in step 27/64, so the command already succeeded several times before failing.

Do you still have the cache.imfuse folder?
Please check image /mnt/Daten/holger/Fotos/stacks/20210207_Fliege_Kopf_gelb_Mikroskopobj/cache.imfuse/lessthanmax.tif. This is the image loaded for the failed -write mpr:lessthanmax command.

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t happend in step 27/64, so the command already succeeded several times before failing.

Ah, perhaps that's the problem. I started imfuse two times in the same folder.
If there can be only one cache.imfuse folder, ...

Do you still have the cache.imfuse folder?

No.
There is one folder cache.imfuse, but it belongs to an other process of imfuse.

from microscopy-tools.

Ok, yes, that it is.
If you want to run a second instance, you can specify another cache folder, e.g. --cache=cache2.

from microscopy-tools.

you can specify another cache folder, e.g. --cache=cache2.

Ok, I try it.

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