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Cannot select points layer #314

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rhornb opened this issue Apr 22, 2024 · 4 comments
Closed

Cannot select points layer #314

rhornb opened this issue Apr 22, 2024 · 4 comments

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@rhornb
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rhornb commented Apr 22, 2024

Hey all,

thanks for creating this amazing tool!

I tried to reproduce this example notebook for points layers. However, I cannot select the points layer in the drop-down menu in any of the napari-clusters-plotter functionalities. Any clue what could cause this? Here is a screenshot of the example dataset:

image

For label images everything works as it should.

I am working on a mac M1 in this environment:
`

Name Version Build Channel

alabaster 0.7.16 pyhd8ed1ab_0 conda-forge
annotated-types 0.6.0 pyhd8ed1ab_0 conda-forge
aom 3.8.2 h73e2aa4_0 conda-forge
app-model 0.2.6 pyhd8ed1ab_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
appnope 0.1.4 pyhd8ed1ab_0 conda-forge
asciitree 0.3.3 py_2 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
attrs 23.2.0 pyh71513ae_0 conda-forge
autopep8 2.1.0 pyhd8ed1ab_0 conda-forge
aws-c-auth 0.7.17 hb47d15a_2 conda-forge
aws-c-cal 0.6.11 hbce485b_0 conda-forge
aws-c-common 0.9.15 h10d778d_0 conda-forge
aws-c-compression 0.2.18 h53e3db5_3 conda-forge
aws-c-event-stream 0.4.2 he461af8_8 conda-forge
aws-c-http 0.8.1 h0afc28a_10 conda-forge
aws-c-io 0.14.7 h6254544_6 conda-forge
aws-c-mqtt 0.10.3 hd66502f_4 conda-forge
aws-c-s3 0.5.7 h4907f8a_1 conda-forge
aws-c-sdkutils 0.1.15 h53e3db5_3 conda-forge
aws-checksums 0.1.18 h53e3db5_3 conda-forge
aws-crt-cpp 0.26.6 hfb53d2e_4 conda-forge
aws-sdk-cpp 1.11.267 h01edc24_6 conda-forge
babel 2.14.0 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
blosc 1.21.5 hafa3907_1 conda-forge
bokeh 3.4.1 pyhd8ed1ab_0 conda-forge
brotli 1.1.0 h0dc2134_1 conda-forge
brotli-bin 1.1.0 h0dc2134_1 conda-forge
brotli-python 1.1.0 py39h840bb9f_1 conda-forge
brunsli 0.1 h046ec9c_0 conda-forge
bzip2 1.0.8 h10d778d_5 conda-forge
c-ares 1.28.1 h10d778d_0 conda-forge
c-blosc2 2.14.4 h0ae8482_1 conda-forge
ca-certificates 2024.2.2 h8857fd0_0 conda-forge
cachey 0.2.1 pyh9f0ad1d_0 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
charls 2.4.2 he965462_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.2.2 pyhd8ed1ab_0 conda-forge
contourpy 1.2.1 py39h0ca7971_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
cython 0.29.37 py39hd253f6c_0 conda-forge
cytoolz 0.12.3 py39ha09f3b3_0 conda-forge
dask 2024.4.2 pyhd8ed1ab_0 conda-forge
dask-core 2024.4.2 pyhd8ed1ab_0 conda-forge
dask-expr 1.0.12 pyhd8ed1ab_0 conda-forge
dav1d 1.2.1 h0dc2134_0 conda-forge
debugpy 1.8.1 py39hd253f6c_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
deprecated 1.2.14 pyh1a96a4e_0 conda-forge
distributed 2024.4.2 pyhd8ed1ab_0 conda-forge
docstring_parser 0.16 pyhd8ed1ab_0 conda-forge
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executing 2.0.1 pyhd8ed1ab_0 conda-forge
expat 2.6.2 h73e2aa4_0 conda-forge
fasteners 0.17.3 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_1 conda-forge
fontconfig 2.14.2 h5bb23bf_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.51.0 py39ha09f3b3_0 conda-forge
freetype 2.12.1 h60636b9_2 conda-forge
freetype-py 2.4.0 pyhd8ed1ab_0 conda-forge
fsspec 2024.3.1 pyhca7485f_0 conda-forge
gettext 0.22.5 h5ff76d1_2 conda-forge
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gflags 2.2.2 hb1e8313_1004 conda-forge
giflib 5.2.2 h10d778d_0 conda-forge
glib 2.80.0 h81c1438_6 conda-forge
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gst-plugins-base 1.24.1 h12dd0d4_1 conda-forge
gstreamer 1.24.1 h7c243d7_1 conda-forge
hdbscan 0.8.33 py39h5b4affa_5 conda-forge
heapdict 1.0.1 py_0 conda-forge
hsluv 5.0.4 pyhd8ed1ab_0 conda-forge
icu 73.2 hf5e326d_0 conda-forge
idna 3.7 pyhd8ed1ab_0 conda-forge
imagecodecs 2024.1.1 py39ha20330a_6 conda-forge
imageio 2.34.1 pyh4b66e23_0 conda-forge
imagesize 1.4.1 pyhd8ed1ab_0 conda-forge
importlib-metadata 7.1.0 pyha770c72_0 conda-forge
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importlib_metadata 7.1.0 hd8ed1ab_0 conda-forge
importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge
in-n-out 0.2.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.29.3 pyh3cd1d5f_0 conda-forge
ipython 8.12.0 pyhd1c38e8_0 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
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joblib 1.4.0 pyhd8ed1ab_0 conda-forge
jsonschema 4.21.1 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge
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libarrow 15.0.2 h965e444_3_cpu conda-forge
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libcblas 3.9.0 22_osx64_openblas conda-forge
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libgfortran 5.0.0 13_2_0_h97931a8_3 conda-forge
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libglib 2.80.0 h81c1438_6 conda-forge
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libpq 16.2 ha925e61_1 conda-forge
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libre2-11 2023.09.01 h81f5012_2 conda-forge
libsodium 1.0.18 hbcb3906_1 conda-forge
libsqlite 3.45.3 h92b6c6a_0 conda-forge
libssh2 1.11.0 hd019ec5_0 conda-forge
libthrift 0.19.0 h064b379_1 conda-forge
libtiff 4.6.0 h129831d_3 conda-forge
libutf8proc 2.8.0 hb7f2c08_0 conda-forge
libvorbis 1.3.7 h046ec9c_0 conda-forge
libwebp-base 1.4.0 h10d778d_0 conda-forge
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libxml2 2.12.6 hc0ae0f7_2 conda-forge
libzlib 1.2.13 h8a1eda9_5 conda-forge
libzopfli 1.0.3 h046ec9c_0 conda-forge
llvm-openmp 18.1.3 hb6ac08f_0 conda-forge
llvmlite 0.42.0 py39he5a6977_1 conda-forge
locket 1.0.0 pyhd8ed1ab_0 conda-forge
lz4 4.3.3 py39h91cfb08_0 conda-forge
lz4-c 1.9.4 hf0c8a7f_0 conda-forge
magicgui 0.8.2 pyhd8ed1ab_1 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.5 py39ha09f3b3_0 conda-forge
matplotlib-base 3.8.4 py39h7070ae8_0 conda-forge
matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge
mdurl 0.1.2 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.7 py39h6be1789_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.3.0 hfd7a639_4 conda-forge
mysql-libs 8.3.0 ha9146f8_4 conda-forge
napari 0.4.17 pyh275ddea_0_pyqt conda-forge
napari-clusters-plotter 0.7.3 pyhd8ed1ab_0 conda-forge
napari-console 0.0.9 pyh9208f05_0 conda-forge
napari-plugin-engine 0.2.0 pyhd8ed1ab_2 conda-forge
napari-skimage-regionprops 0.10.1 pyhd8ed1ab_0 conda-forge
napari-svg 0.1.10 pyhd8ed1ab_0 conda-forge
napari-tools-menu 0.1.19 pyhd8ed1ab_0 conda-forge
napari-workflows 0.2.10 pyhd8ed1ab_0 conda-forge
ncurses 6.4.20240210 h73e2aa4_0 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
networkx 3.2.1 pyhd8ed1ab_0 conda-forge
npe2 0.7.5 pyhd8ed1ab_0 conda-forge
nspr 4.35 hea0b92c_0 conda-forge
nss 3.98 ha05da47_0 conda-forge
numba 0.59.1 py39hb7f44fa_0 conda-forge
numcodecs 0.12.1 py39h110ca85_0 conda-forge
numpy 1.23.5 py39hdfa1d0c_0 conda-forge
numpydoc 1.5.0 pyhd8ed1ab_0 conda-forge
openjpeg 2.5.2 h7310d3a_0 conda-forge
openssl 3.2.1 hd75f5a5_1 conda-forge
orc 2.0.0 hf146577_1 conda-forge
packaging 24.0 pyhd8ed1ab_0 conda-forge
pandas 2.2.2 py39haf03413_0 conda-forge
parso 0.8.4 pyhd8ed1ab_0 conda-forge
partd 1.4.1 pyhd8ed1ab_0 conda-forge
pcre2 10.43 h0ad2156_0 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.3.0 py39h9dabb2a_0 conda-forge
pint 0.23 pyhd8ed1ab_0 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.2.0 pyhd8ed1ab_0 conda-forge
ply 3.11 pyhd8ed1ab_2 conda-forge
pooch 1.8.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.42 pyha770c72_0 conda-forge
prompt_toolkit 3.0.42 hd8ed1ab_0 conda-forge
psutil 5.9.8 py39ha09f3b3_0 conda-forge
psygnal 0.11.0 pyhd8ed1ab_0 conda-forge
pthread-stubs 0.4 hc929b4f_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pyarrow 15.0.2 py39h8a9fa87_3_cpu conda-forge
pyarrow-hotfix 0.6 pyhd8ed1ab_0 conda-forge
pycodestyle 2.11.1 pyhd8ed1ab_0 conda-forge
pyconify 0.1.6 pyhd8ed1ab_0 conda-forge
pydantic 1.10.14 py39ha09f3b3_0 conda-forge
pydantic-compat 0.1.2 pyhd8ed1ab_0 conda-forge
pydantic-core 2.18.1 py39hcf47035_0 conda-forge
pygments 2.17.2 pyhd8ed1ab_0 conda-forge
pynndescent 0.5.12 pyhca7485f_0 conda-forge
pyopengl 3.1.6 pyhd8ed1ab_1 conda-forge
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge
pyproject_hooks 1.0.0 pyhd8ed1ab_0 conda-forge
pyqt 5.15.9 py39h3dce684_5 conda-forge
pyqt5-sip 12.12.2 py39hb11a7c1_5 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.9.19 h7a9c478_0_cpython conda-forge
python-build 1.2.1 pyhd8ed1ab_0 conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.9 4_cp39 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pywavelets 1.4.1 py39hd01001f_1 conda-forge
pyyaml 6.0.1 py39hdc70f33_1 conda-forge
pyzmq 26.0.2 py39hffc4518_0 conda-forge
qt-main 5.15.8 hecaf5c3_21 conda-forge
qtconsole-base 5.5.1 pyha770c72_0 conda-forge
qtpy 2.4.1 pyhd8ed1ab_0 conda-forge
rav1e 0.6.6 h7205ca4_2 conda-forge
re2 2023.09.01 hb168e87_2 conda-forge
readline 8.2 h9e318b2_1 conda-forge
referencing 0.34.0 pyhd8ed1ab_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rich 13.7.1 pyhd8ed1ab_0 conda-forge
rpds-py 0.18.0 py39hcf47035_0 conda-forge
scikit-image 0.22.0 py39h5d65943_2 conda-forge
scikit-learn 1.4.2 py39hf36d3f6_0 conda-forge
scipy 1.13.0 py39h0ed1e0f_0 conda-forge
setuptools 69.5.1 pyhd8ed1ab_0 conda-forge
shellingham 1.5.4 pyhd8ed1ab_0 conda-forge
sip 6.7.12 py39h110ca85_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.2.0 h6dc393e_1 conda-forge
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
sphinx 3.5.3 pyhd3eb1b0_0
sphinxcontrib-applehelp 1.0.4 pyhd8ed1ab_0 conda-forge
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-htmlhelp 2.0.1 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jsmath 1.0.1 pyhd8ed1ab_0 conda-forge
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
superqt 0.6.3 pyh9208f05_0 conda-forge
svt-av1 2.0.0 h73e2aa4_0 conda-forge
tabulate 0.9.0 pyhd8ed1ab_1 conda-forge
tbb 2021.12.0 h7728843_0 conda-forge
tblib 3.0.0 pyhd8ed1ab_0 conda-forge
threadpoolctl 3.4.0 pyhc1e730c_0 conda-forge
tifffile 2024.4.18 pyhd8ed1ab_0 conda-forge
tk 8.6.13 h1abcd95_1 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tomli-w 1.0.0 pyhd8ed1ab_0 conda-forge
toolz 0.12.1 pyhd8ed1ab_0 conda-forge
tornado 6.4 py39ha09f3b3_0 conda-forge
tqdm 4.66.2 pyhd8ed1ab_0 conda-forge
traitlets 5.14.3 pyhd8ed1ab_0 conda-forge
typer 0.12.3 pyhd8ed1ab_0 conda-forge
typer-slim 0.12.3 pyhd8ed1ab_0 conda-forge
typer-slim-standard 0.12.3 hd8ed1ab_0 conda-forge
typing-extensions 4.11.0 hd8ed1ab_0 conda-forge
typing_extensions 4.11.0 pyha770c72_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
umap-learn 0.5.5 py39h6e9494a_1 conda-forge
unicodedata2 15.1.0 py39hdc70f33_0 conda-forge
urllib3 2.2.1 pyhd8ed1ab_0 conda-forge
vispy 0.11.0 py39h225dfe9_1 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
wrapt 1.16.0 py39ha09f3b3_0 conda-forge
xorg-libxau 1.0.11 h0dc2134_0 conda-forge
xorg-libxdmcp 1.1.3 h35c211d_0 conda-forge
xyzservices 2024.4.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h775f41a_0 conda-forge
yaml 0.2.5 h0d85af4_2 conda-forge
zarr 2.17.2 pyhd8ed1ab_0 conda-forge
zeromq 4.3.5 h93d8f39_0 conda-forge
zfp 1.0.1 h295e98d_0 conda-forge
zict 3.0.0 pyhd8ed1ab_0 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib-ng 2.0.7 hb7f2c08_0 conda-forge
zstd 1.5.5 h829000d_0 conda-forge`

@Cryaaa
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Cryaaa commented Apr 23, 2024

Hello!
The Points layer functionality is something that we are currently finalizing, so it will only work if you install the most current cluster plotter version (which currently is not yet on pypi due to some bugs we need to fix beforehand).

If you want to give this possibly unstable release a try though you could install it by downloading the repository, unpacking it in a destination of your choice, navigating to the repository folder in your command line and installing it using pip install .

Thanks for your interest in the plugin and I hope this helps!

@rhornb
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rhornb commented Apr 23, 2024

Hey @Cryaaa ,

thanks for your quick help! I didn't realise from the documentation that this functionality was still part of the unstable release - maybe would be good to add this as a note. :)

Best,
Ruth

@rhornb rhornb closed this as completed Apr 23, 2024
@Cryaaa
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Cryaaa commented Apr 23, 2024

@rhornb,
Completely agree and will do thanks for the input. If you do happen to test the current version though, we are always happy about any feedback!

@zoccoler
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Hi @rhornb ,

Sorry, @Cryaaa is right, the documentation was updated but the new release is still on the way. We are working to release it pretty soon, so I ask for your patience. I will add a note to the Readme for the time being, sorry for the confusion.

Also, the feature to load a table to the points layer from a plugin perspective is being worked out here: haesleinhuepf/napari-skimage-regionprops#87

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