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tand826 / wsiprocess

Whole Slide Image (WSI) Processing Library for Histopathological / Cytopathological Machine Learning Tasks
Apache License 2.0
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Parser for SlideRunner annotations #20

Closed tand826 closed 3 years ago

tand826 commented 4 years ago

Now

tand826 commented 4 years ago

Exmperimental implementation at this commit

tand826 commented 4 years ago

I implemented to read all the database and parse them later because I don't know how fast sqlite3 reads. It might be slower than the implementation to read the database every time wsiprcess needs data. Anyway, now you can use the SQLite file of SlideRunner. HOWEVER, there are some restrictions.

tand826 commented 4 years ago

SlideRunner v1.31.0 might be able to make polygon annotations...?

bnapora commented 4 years ago

One of the main differences between v1.31.0 and v1.99 db structure is in "Annotations_coordinates" table. He added a coordinateZ column.

tand826 commented 4 years ago

@bnapora Brian,

Thanks for the information of db. I added if sentence for polygon annotation, but I could not add the process for circle annotation because the parameters of circle annotations are unclear to me. If you know the parameters, can you teach me? Or, can you implement the feature?

bnapora commented 4 years ago

Below is an excerpt of how the circle annotations are extracted. Very similar to Dot (x & y for center) except has a radius

eg. - DB.annotations[4].x1, DB.annotations[4].y1, DB.annotations[4].r

Below is the calculation the SlideRunner folks use: down_factor = slide.level_downsamples[level] d = 2 * annotation.r / down_factor x_min = (annotation.x1 - annotation.r) / down_factor y_min = (annotation.y1 - annotation.r) / down_factor x_max = x_min + d y_max = y_min + d

I'll take a look at implementing, but want to make sure I don't mess up your well structured code.

Brian

tand826 commented 4 years ago

@bnapora

Thanks for the information of coordinates! I think this can parse circle annotations. Can you test with this implementation?

Takumi

bnapora commented 4 years ago

@tand826

Very cool! Parser is extracting Circle annotations now. However when annotation has larger radius then the dot_bbox value, then it seems to generate unexpected output. I'll have to do some more testing to see if I can suggest a solution to that challenge.

Currently I'm trying to get WSIProcess to work with other OpenSlide formats besides TIF. I think it may be an issue with libvips integration with OpenSlide, but haven't been able to figure it out. (Any tips you might have on that beast would be appreciated. =)

Brian

bnapora commented 4 years ago

Can you provide me an example of what command would be to use CLI for extracting patches from SlideRunner db? I'm currently using

wsiprocess detection ./sample/CMU-1.tif ./sample/CMU1_spot.sqlite -dw 80 -dh 80 -pw 448 -ph 448 -co -ra 10:0:0 -st ./projects/

But get an errof indicating it doesn't know what slidename to look up in db: File "/home/bnapora/development/wsiprocess/wsiprocess/annotationparser/SlideRunner_parser.py", line 70, in read_annotations query += f" where slide=='{self.slidename2uid[slidename]}'" KeyError: './sample/CMU-1.tif'

tand826 commented 4 years ago

@bnapora

dot_bbox value works only if the annotation have only one coordinate like [[100, 200]] while the circle annotations always have more than 2 coordinates like [[100, 200], [150, 250]]. Can you tell me the command you used?

Some slides are tested, and listed here. Which scanner vendor's slides are you using?

That KeyError is a bug! Thanks for the bug report. I fixed it here. It was because wsiprocess have slidename as its absolute path although SlideRunner annotations have slidename as its basename.

bnapora commented 4 years ago

Tested the KeyError fix. Was able to export dot annotations from SlideRunner using CLI. I haven't done much more testing. Still haven't figured out why I can't get SVS format images to work. (The only image I've been able to use with WSIPROCESS is CMU-tif.)

My CLI call: !wsiprocess detection /mnt/c/WSI/9374efe6ac06388cc877.svs /mnt/c/WSI/databases/WSILoader_SpotAnno_Small.sqlite -dw 80 -dh 80 -pw 448 -ph 448 -co -ra 10:0:0 -st ./projects/

Output Traceback (most recent call last): File "/home/bnapora/miniconda3/envs/wsiprocess/bin/wsiprocess", line 11, in load_entry_point('wsiprocess', 'console_scripts', 'wsiprocess')() File "/home/bnapora/development/wsiprocess/wsiprocess/cli.py", line 207, in main annotation = process_annotation(args, slide, rule) File "/home/bnapora/development/wsiprocess/wsiprocess/cli.py", line 194, in process_annotation annotation.make_masks(slide, rule, foreground=True) File "/home/bnapora/development/wsiprocess/wsiprocess/annotation.py", line 156, in makemasks slide, size, method=foreground, min=min, max=max_) File "/home/bnapora/development/wsiprocess/wsiprocess/annotation.py", line 286, in make_foreground_mask buffer=thumb.write_to_memory(), File "/home/bnapora/miniconda3/envs/wsiprocess/lib/python3.6/site-packages/pyvips/vimage.py", line 619, in write_to_memory raise Error('unable to write to memory') pyvips.error.Error: unable to write to memory source input: Compression scheme 33005 tile decoding is not implemented source input: Compression scheme 33005 tile decoding is not implemented

tand826 commented 4 years ago

Can you provide me an example of what command would be to use CLI for extracting patches from SlideRunner db? I'm currently using

I missed this. As you have noticed, set your SlideRunner annotation file in the "annotation" argument.

The only image I've been able to use with WSIPROCESS is CMU-tif.

You might have compiled libvips without OpenSlide support. See the OpenSlide section in the installation notes and type vips --vips-config to see file import with OpenSlide: yes in the output. If you don't find "yes" there, perhaps, you need to install openslide and recompile libvips like

sudo apt install openslide-tools

# download vips tarball

tar xvfz vips-8.10.1.tar.gz
cd vips-8.10.1 && ./configure && make -j && sudo make install
bnapora commented 4 years ago

Takumi,

Thanks for the help. Libvips currently doesn’t see the OpenSlide library installed on the machine. I use openslide-tools in many other projects, so I know it works. But for some reason libvips doesn’t see it when building. I tried building it a couple times. I haven’t been able to find any posts online indicating how to force libvips to find openslide during the make process. Do you know how to force libvips to see openslide?

Brian

From: Takumi Ando notifications@github.com Sent: Monday, November 9, 2020 10:55 PM To: tand826/wsiprocess wsiprocess@noreply.github.com Cc: Brian Napora bnapora@gestaltdiagnostics.com; Mention mention@noreply.github.com Subject: Re: [tand826/wsiprocess] Parser for SlideRunner annotations (#20)

Can you provide me an example of what command would be to use CLI for extracting patches from SlideRunner db? I'm currently using

I missed this. As you have noticed, set your SlideRunner annotation file in the "annotation" argument.

The only image I've been able to use with WSIPROCESS is CMU-tif.

You might have compiled libvips without OpenSlide support. See the OpenSlide section in the installation noteshttps://libvips.github.io/libvips/install.html and type vips --vips-config to see file import with OpenSlide: yes in the output. If you don't find "yes" there, perhaps, you need to install openslide and recompile libvips like

sudo apt install openslide-tools

download vips tarball

tar xvfz vips-8.10.1.tar.gz

cd vips-8.10.1 && ./configure && make -j && sudo make install

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/tand826/wsiprocess/issues/20#issuecomment-724503144, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AH6SIZJOGKCVJROAR5YB6TTSPDPV7ANCNFSM4SUMFQJQ.

tand826 commented 4 years ago

How about this?

pkg-config --list-all | grep openslide
# in the vips directory
./configure --with-openslide
bnapora commented 4 years ago

Takumi,

We really appreciate your assistance on this. If you have any other ideas, we’d love to try them. I’ve tried getting openslide working with vips on two different Ubuntu 18.04 machines. On both machines I can use vips with no Openslide, and Openslide works fine on its own. I’ve posted the output of the recent attempts on one of those machines below.

Openslide is installed: (wsiprocess) bnapora@DESKTOP-MUE6PMA:~/development/wsiprocess/vips-8.10.2$mailto:bnapora@DESKTOP-MUE6PMA:~/development/wsiprocess/vips-8.10.2$ dpkg --list | grep openslide

ii libopenslide0 3.4.1+dfsg-2 amd64 library for reading whole slide image files ii openslide-tools 3.4.1+dfsg-2 amd64 Manipulation and conversion tools for OpenSlide ii python-openslide-examples 1.1.1-2ubuntu4 all Python examples for python-openslide and python3-openslide ii python3-openslide 1.1.1-2ubuntu4 amd64 Python 3 wrapper for reading whole slide image files

I tried reinstalling vips (vips-8.10.2) using the “—with-openslide” directive. When running vips config check, still see openslide integration as no: file import with OpenEXR: no file import with OpenSlide: no

The only resource I’ve been able to find that might address is an issue thread posted on libvips repo from last year: https://github.com/libvips/libvips/issues/1316

However neither of my installations have a folder called “openslide-3.4.1” to even add to the PKG_CONFIG_PATH variable.

(wsiprocess) bnapora@DESKTOP-MUE6PMA:~/development/wsiprocess/vips-8.10.2$mailto:bnapora@DESKTOP-MUE6PMA:~/development/wsiprocess/vips-8.10.2$ dpkg --listfiles openslide-tools /. /usr /usr/bin /usr/bin/openslide-quickhash1sum /usr/bin/openslide-show-properties /usr/bin/openslide-write-png /usr/share /usr/share/doc /usr/share/doc/openslide-tools /usr/share/doc/openslide-tools/copyright /usr/share/man /usr/share/man/man1 /usr/share/man/man1/openslide-quickhash1sum.1.gz /usr/share/man/man1/openslide-show-properties.1.gz /usr/share/man/man1/openslide-write-png.1.gz /usr/share/doc/openslide-tools/changelog.Debian.gz

From: Takumi Ando notifications@github.com Sent: Tuesday, November 10, 2020 1:11 AM To: tand826/wsiprocess wsiprocess@noreply.github.com Cc: Brian Napora bnapora@gestaltdiagnostics.com; Mention mention@noreply.github.com Subject: Re: [tand826/wsiprocess] Parser for SlideRunner annotations (#20)

How about this?

pkg-config --list-all | grep openslide

in the vips directory

./configure --with-openslide

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tand826 commented 4 years ago

There are 3 openslide-related packages. libopenslide-dev seems to be the one we need to install to enable openslide support. I'm sorry for the misdirection in the installation section.

I tried like below.

 # file import with OpenSlide:      no
sudo apt remove libopenslide0 libopenslide-dev openslide-tools
sudo apt install openslide-tools && ./configure

# file import with OpenSlide:       no
sudo apt remove libopenslide0 libopenslide-dev openslide-tools
sudo apt install libopenslide0 && ./configure 

# file import with OpenSlide:       yes
sudo apt remove libopenslide0 libopenslide-dev openslide-tools
sudo apt install libopenslide-dev && ./configure
bnapora commented 4 years ago

Takumi,

Yeah! After following removal steps you suggested, and then reinstalling libvips I was successful in getting libvips to indicate “yes” for Openslide file import. Steps I used are:

sudo apt remove libopenslide0 libopenslide-dev openslide-tools

sudo apt install libopenslide-dev && ./configure

cd vips-8.10.2 && ./configure && make -j && sudo make install

in the vips directory

./configure --with-openslide

Unfortunately when attempting to run WSIPROCESS on an SVS image I now encounter this error:

~/development/wsiprocess/wsiprocess/annotation.py in make_foregroundmask(self, slide, size, method, min, max_) 284 thumb = slide.get_thumbnail(size) 285 thumb = np.ndarray( --> 286 buffer=thumb.write_to_memory(), 287 dtype=np.uint8, 288 shape=[thumb.height, thumb.width, thumb.bands])

~/miniconda3/envs/wsiprocess/lib/python3.6/site-packages/pyvips/vimage.py in write_to_memory(self) 617 pointer = vips_lib.vips_image_write_to_memory(self.pointer, psize) 618 if pointer == ffi.NULL: --> 619 raise Error('unable to write to memory') 620 pointer = ffi.gc(pointer, glib_lib.g_free) 621

Error: unable to write to memory source input: Compression scheme 33005 tile decoding is not implemented source input: Compression scheme 33005 tile decoding is not implemented

It looks like an issue with libvips as well.

If your interested, I’m attaching a copy of a Jupyter notebook I’m using to test WSIPROCESS. In this notebook there is a script to download the specific SVS file I’m testing (2efb541724b5c017c503.svs). I’m also attaching the ASAP annotation file (although I’m sure you can create your own if desired.) You will need to change paths in the notebook to meet your specific set-up.

Brian

From: Takumi Ando notifications@github.com Sent: Tuesday, November 10, 2020 5:14 PM To: tand826/wsiprocess wsiprocess@noreply.github.com Cc: Brian Napora bnapora@gestaltdiagnostics.com; Mention mention@noreply.github.com Subject: Re: [tand826/wsiprocess] Parser for SlideRunner annotations (#20)

There are 3 openslide-related packages. libopenslide-dev seems to be the one we need to install to enable openslide support. I'm sorry for the misdirection in the installation section.

I tried like below.

file import with OpenSlide: no

sudo apt remove libopenslide0 libopenslide-dev openslide-tools

sudo apt install openslide-tools && ./configure

file import with OpenSlide: no

sudo apt remove libopenslide0 libopenslide-dev openslide-tools

sudo apt install libopenslide0 && ./configure

file import with OpenSlide: yes

sudo apt remove libopenslide0 libopenslide-dev openslide-tools

sudo apt install libopenslide-dev && ./configure

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tand826 commented 4 years ago

The problem with the 33005 compression might be because of SVS images. Can you share with me the output of ./configure? Are libtiff, libjpeg, and libpng available? It can be another misdirection in the installation section. As for me, it is like

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
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checking for gawk... gawk
checking whether make sets $(MAKE)... yes
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checking pkg-config is at least version 0.9.0... yes
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checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for needs -lstdc++... yes
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checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
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checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for special C compiler options needed for large files... no
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checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
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checking dynamic linker characteristics... GNU/Linux ld.so
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configure: WARNING: librsvg-2.0 >= 2.40.3 or cairo >= 1.2 not found; disabling SVG load via rsvg
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configure: creating ./config.status
config.status: creating vips.pc
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config.status: creating ./libvips/include/vips/version.h
config.status: creating libvips/include/Makefile
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config.status: creating libvips/Makefile
config.status: creating libvips/arithmetic/Makefile
config.status: creating libvips/colour/Makefile
config.status: creating libvips/colour/profiles/Makefile
config.status: creating libvips/conversion/Makefile
config.status: creating libvips/convolution/Makefile
config.status: creating libvips/deprecated/Makefile
config.status: creating libvips/foreign/Makefile
config.status: creating libvips/freqfilt/Makefile
config.status: creating libvips/histogram/Makefile
config.status: creating libvips/draw/Makefile
config.status: creating libvips/iofuncs/Makefile
config.status: creating libvips/morphology/Makefile
config.status: creating libvips/mosaicing/Makefile
config.status: creating libvips/create/Makefile
config.status: creating libvips/resample/Makefile
config.status: creating cplusplus/include/Makefile
config.status: creating cplusplus/include/vips/Makefile
config.status: creating cplusplus/Makefile
config.status: creating tools/Makefile
config.status: creating tools/batch_crop
config.status: creating tools/batch_image_convert
config.status: creating tools/batch_rubber_sheet
config.status: creating tools/light_correct
config.status: creating tools/shrink_width
config.status: creating test/Makefile
config.status: creating test/variables.sh
config.status: creating test/test-suite/Makefile
config.status: creating test/test-suite/helpers/Makefile
config.status: creating man/Makefile
config.status: creating doc/Makefile
config.status: creating doc/libvips-docs.xml
config.status: creating po/Makefile.in
config.status: creating fuzz/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing default-1 commands
* build options
native win32:               no
native OS X:                no
open files in binary mode:      no
enable debug:               no
enable deprecated library components:   yes
enable docs with gtkdoc:        no
gobject introspection:          no
enable radiance support:        yes
enable analyze support:         yes
enable PPM support:             yes

* optional dependencies
use fftw3 for FFT:          no
Magick package:             none
Magick API version:             none
load with libMagick:            no
save with libMagick:            no
accelerate loops with orc:      no
  (requires orc-0.4.11 or later)
ICC profile support with lcms:      no
file import with niftiio:       no
file import with libheif:       no
file import with OpenEXR:       yes
file import with OpenSlide:     yes
  (requires openslide-3.3.0 or later)
file import with matio:         no
PDF import with PDFium:         no
PDF import with poppler-glib:       no
  (requires poppler-glib 0.16.0 or later)
SVG import with librsvg-2.0:        no
  (requires librsvg-2.0 2.34.0 or later)
zlib:                   yes
file import with cfitsio:       no
file import/export with libwebp:    no
  (requires libwebp, libwebpmux, libwebpdemux 0.6.0 or later)
text rendering with pangoft2:       yes
file import/export with libspng:    no
  (requires libspng-0.6 or later)
file import/export with libpng:     yes (pkg-config libpng >= 1.2.9)
  (requires libpng-1.2.9 or later)
support 8bpp PNG quantisation:      no
  (requires libimagequant)
file import/export with libtiff:    yes (pkg-config libtiff-4)
file import/export with giflib:     no
file import/export with libjpeg:    yes (pkg-config)
image pyramid export:           yes
  (requires libgsf-1 1.14.26 or later)
use libexif to load/save JPEG metadata: yes

I'm a bit curious about the notebook, but I think libvips installation should be the reason though...?

tand826 commented 3 years ago

For now, I close this issue because wsiprocess can now parse SlideRunner annotations. If there are any further questions or problems, feel free to reopen this issue.