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kushalkolar / mesmerize-viz

Widgets for calcium imaging analysis visualization in notebooks
GNU General Public License v3.0
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WrongAlgorithmExtensionError #35

Closed bashsyr closed 9 months ago

bashsyr commented 10 months ago

I tried to install mesmerize-viz on a win 11 machine and I got all kinds on errors regarding fastplotlib not finding modules and pygfx incompatibility, I tried pulling the latest ones from the links I also tried every version combination possible and it didn't work, the last error I got is in this attached file Error last build.txt Now I saw that you updated some things and I was happy, I pulled the version and tried it and now I'm getting this

WrongAlgorithmExtensionError              Traceback (most recent call last)
File ~\mambaforge\envs\mestest\lib\site-packages\ipywidgets\widgets\interaction.py:240, in interactive.update(self, *args)
    238     value = widget.get_interact_value()
    239     self.kwargs[widget._kwarg] = value
--> 240 self.result = self.f(**self.kwargs)
    241 show_inline_matplotlib_plots()
    242 if self.auto_display and self.result is not None:

Cell In[3], line 10, in start_widget(parent_path, batch_path)
      7 tab = Tab()
      9 mcorr_container = df.mcorr.viz()
---> 10 cnmf_container = df.cnmf.viz(start_index=2)
     12 tab.children = [mcorr_container.show(), cnmf_container.show()]
     13 tab.titles = ["mcorr", "cnmf"]

File c:\users\ba81\mestest\mesmerize-viz\mesmerize_viz\_cnmf.py:1164, in CNMFDataFrameVizExtension.viz(self, start_index, temporal_data_option, image_data_options, temporal_kwargs, reset_timepoint_on_change, input_movie_kwargs, image_widget_kwargs, data_grid_kwargs)
   1088 def viz(
   1089     self,
   1090     start_index: int = None,
   (...)
   1097     data_grid_kwargs: dict = None,
   1098 ):
   1099     """
   1100     Visualize CNMF output and other data columns such as behavior video (optional).
   1101 
   (...)
   1161         Example: `image_widget_kwargs={"cmap": "viridis"}`
   1162     """
-> 1164     container = CNMFVizContainer(
   1165         dataframe=self._dataframe,
   1166         start_index=start_index,
   1167         temporal_data_option=temporal_data_option,
   1168         image_data_options=image_data_options,
   1169         temporal_kwargs=temporal_kwargs,
   1170         reset_timepoint_on_change=reset_timepoint_on_change,
   1171         input_movie_kwargs=input_movie_kwargs,
   1172         image_widget_kwargs=image_widget_kwargs,
   1173         data_grid_kwargs=data_grid_kwargs,
   1174 
   1175     )
   1177     return container

File c:\users\ba81\mestest\mesmerize-viz\mesmerize_viz\_cnmf.py:570, in CNMFVizContainer.__init__(self, dataframe, start_index, temporal_data_option, image_data_options, temporal_kwargs, reset_timepoint_on_change, input_movie_kwargs, image_widget_kwargs, data_grid_kwargs)
    566 self._component_index = 0
    568 self._cnmf_obj: CNMF = None
--> 570 data_arrays = self._get_row_data(index=start_index)
    571 self._set_data(data_arrays)
    573 self._set_params_text_area(index=start_index)

File c:\users\ba81\mestest\mesmerize-viz\mesmerize_viz\_cnmf.py:596, in CNMFVizContainer._get_row_data(self, index)
    589 def _get_row_data(self, index: int) -> Dict[str, np.ndarray]:
    590     data_mapping = get_cnmf_data_mapping(
    591         series=self._dataframe.iloc[index],
    592         input_movie_kwargs=self.input_movie_kwargs,
    593         temporal_kwargs=self.temporal_kwargs
    594     )
--> 596     temporal = data_mapping[self.temporal_data_option]()
    598     rcm = data_mapping["rcm"]()
    600     shape = rcm.shape

File c:\users\ba81\mestest\mesmerize-viz\mesmerize_viz\_cnmf.py:94, in ExtensionCallWrapper.__call__(self, *args, **kwargs)
     93 def __call__(self, *args, **kwargs):
---> 94     rval = self.func(**self.kwargs)
     96     if self.attr is not None:
     97         return getattr(rval, self.attr)

File ~\mestest\mesmerize-core\mesmerize_core\caiman_extensions\_utils.py:18, in validate.<locals>.dec.<locals>.wrapper(self, *args, **kwargs)
     16 if algo is not None:
     17     if algo not in self._series["algo"]:
---> 18         raise WrongAlgorithmExtensionError(
     19             f"<{algo}> extension called for a <{self._series.algo}> item"
     20         )
     22 if not self._series["outputs"]["success"]:
     23     tb = self._series["outputs"]["traceback"]

WrongAlgorithmExtensionError: <cnmf> extension called for a <mcorr> item

which doesn't look like a problem with my setup, so I though, instead of spending two days debugging I could ask you for advice. Thank you so much for the help :)

bashsyr commented 10 months ago

Here are the packages in the environment:

name: mestest2 channels: - defaults - pkgs/main - conda-forge dependencies: - _tflow_select=2.3.0 - absl-py=2.0.0 - aiohttp=3.8.6 - aiosignal=1.3.1 - anyio=4.0.0 - aom=3.5.0 - argon2-cffi=23.1.0 - argon2-cffi-bindings=21.2.0 - arrow=1.3.0 - asttokens=2.4.1 - astunparse=1.6.3 - async-lru=2.0.4 - async-timeout=4.0.3 - attrs=23.1.0 - av=10.0.0 - babel=2.13.1 - backports=1.0 - backports.functools_lru_cache=1.6.5 - beautifulsoup4=4.12.2 - bleach=6.1.0 - blinker=1.7.0 - blosc=1.21.5 - bokeh=3.3.0 - brotli=1.1.0 - brotli-bin=1.1.0 - brotli-python=1.1.0 - bzip2=1.0.8 - c-ares=1.20.1 - ca-certificates=2023.7.22 - cached-property=1.5.2 - cached_property=1.5.2 - cachetools=5.3.2 - caiman=1.9.16 - certifi=2023.7.22 - cffi=1.16.0 - charset-normalizer=3.3.2 - click=8.1.7 - cloudpickle=3.0.0 - colorama=0.4.6 - colorcet=3.0.1 - comm=0.1.4 - contourpy=1.1.1 - cryptography=39.0.0 - cycler=0.12.1 - cytoolz=0.12.2 - dask-core=2023.10.1 - dav1d=1.2.0 - debugpy=1.8.0 - decorator=5.1.1 - defusedxml=0.7.1 - eigen=3.4.0 - entrypoints=0.4 - exceptiongroup=1.1.3 - executing=2.0.1 - expat=2.5.0 - ffmpeg=6.0.0 - flatbuffers=23.5.26 - font-ttf-dejavu-sans-mono=2.37 - font-ttf-inconsolata=3.000 - font-ttf-source-code-pro=2.038 - font-ttf-ubuntu=0.83 - fontconfig=2.14.2 - fonts-conda-ecosystem=1 - fonts-conda-forge=1 - fonttools=4.43.1 - fqdn=1.5.1 - freetype=2.12.1 - frozenlist=1.4.0 - fsspec=2023.10.0 - future=0.18.3 - gast=0.4.0 - gettext=0.21.1 - giflib=5.2.1 - glib=2.78.0 - glib-tools=2.78.0 - google-auth=2.23.4 - google-auth-oauthlib=0.4.6 - google-pasta=0.2.0 - grpc-cpp=1.48.1 - grpcio=1.48.1 - gst-plugins-base=1.18.5 - gstreamer=1.18.5 - h5py=3.9.0 - hdf5=1.14.0 - hdmf=3.11.0 - holoviews=1.18.0 - icu=58.2 - idna=3.4 - imagecodecs-lite=2019.12.3 - imageio=2.31.5 - importlib-metadata=6.8.0 - importlib_metadata=6.8.0 - importlib_resources=6.1.0 - iniconfig=2.0.0 - intel-openmp=2023.2.0 - ipykernel=6.26.0 - ipyparallel=8.6.1 - ipython=8.17.2 - ipython_genutils=0.2.0 - ipywidgets=8.1.1 - isoduration=20.11.0 - jedi=0.19.1 - jinja2=3.1.2 - joblib=1.3.2 - jpeg=9e - json5=0.9.14 - jsonpointer=2.4 - jsonschema=4.19.2 - jsonschema-specifications=2023.7.1 - jsonschema-with-format-nongpl=4.19.2 - jupyter=1.0.0 - jupyter-lsp=2.2.0 - jupyter_bokeh=2.0.4 - jupyter_client=8.5.0 - jupyter_console=6.6.3 - jupyter_core=5.5.0 - jupyter_events=0.8.0 - jupyter_server=2.9.1 - jupyter_server_terminals=0.4.4 - jupyterlab=4.0.7 - jupyterlab_pygments=0.2.2 - jupyterlab_server=2.25.0 - jupyterlab_widgets=3.0.9 - keras=2.10.0 - kiwisolver=1.4.5 - krb5=1.20.1 - lazy_loader=0.3 - lcms2=2.15 - lerc=4.0.0 - libabseil=20220623.0 - libaec=1.1.2 - libblas=3.9.0 - libbrotlicommon=1.1.0 - libbrotlidec=1.1.0 - libbrotlienc=1.1.0 - libcblas=3.9.0 - libclang=14.0.6 - libclang13=14.0.6 - libcurl=8.1.2 - libdeflate=1.17 - libexpat=2.5.0 - libffi=3.4.2 - libglib=2.78.0 - libhwloc=2.9.1 - libiconv=1.17 - liblapack=3.9.0 - libogg=1.3.4 - libopus=1.3.1 - libpng=1.6.39 - libpq=12.15 - libprotobuf=3.20.3 - libsodium=1.0.18 - libsqlite=3.44.0 - libssh2=1.10.0 - libtiff=4.5.0 - libvorbis=1.3.7 - libwebp=1.3.2 - libwebp-base=1.3.2 - libxcb=1.13 - libxml2=2.10.4 - libxslt=1.1.37 - libzlib=1.2.13 - linkify-it-py=2.0.0 - locket=1.0.0 - lz4-c=1.9.4 - m2w64-gcc-libgfortran=5.3.0 - m2w64-gcc-libs=5.3.0 - m2w64-gcc-libs-core=5.3.0 - m2w64-gmp=6.1.0 - m2w64-libwinpthread-git=5.0.0.4634.697f757 - markdown=3.5.1 - markdown-it-py=3.0.0 - markupsafe=2.1.3 - matplotlib=3.8.1 - matplotlib-base=3.8.1 - matplotlib-inline=0.1.6 - mdit-py-plugins=0.4.0 - mdurl=0.1.0 - mesmerize-core=0.3.0 - mistune=3.0.1 - mkl=2023.2.0 - msys2-conda-epoch=20160418 - multidict=6.0.4 - munkres=1.1.4 - mypy=1.6.1 - mypy_extensions=1.0.0 - nbconvert=7.10.0 - nbconvert-core=7.10.0 - nbconvert-pandoc=7.10.0 - nbformat=5.9.2 - nest-asyncio=1.5.8 - networkx=3.2.1 - nose=1.3.7 - notebook=7.0.6 - notebook-shim=0.2.3 - numpy=1.26.0 - oauthlib=3.2.2 - opencv=4.6.0 - openh264=2.3.1 - openjpeg=2.5.0 - openssl=1.1.1w - opt_einsum=3.3.0 - overrides=7.4.0 - packaging=23.2 - pandas=2.1.2 - pandoc=3.1.3 - pandocfilters=1.5.0 - panel=1.3.1 - param=2.0.0 - parso=0.8.3 - partd=1.4.1 - pcre2=10.40 - peakutils=1.3.4 - pickleshare=0.7.5 - pillow=9.4.0 - pims=0.6.1 - pip=23.3.1 - pkgutil-resolve-name=1.3.10 - platformdirs=3.11.0 - pluggy=1.3.0 - prometheus_client=0.18.0 - prompt-toolkit=3.0.39 - prompt_toolkit=3.0.39 - protobuf=3.20.3 - psutil=5.9.5 - pthread-stubs=0.4 - pthreads-win32=2.9.1 - pure_eval=0.2.2 - pyasn1=0.5.0 - pyasn1-modules=0.3.0 - pycparser=2.21 - pyct=0.4.6 - pyct-core=0.4.6 - pygments=2.16.1 - pyjwt=2.8.0 - pynwb=2.5.0 - pyopenssl=23.2.0 - pyparsing=3.1.1 - pyqt=5.15.4 - pyqt5-sip=12.9.0 - pyqtgraph=0.13.3 - pysocks=1.7.1 - pytest=7.4.3 - python=3.10.8 - python-dateutil=2.8.2 - python-fastjsonschema=2.18.1 - python-flatbuffers=23.5.26 - python-json-logger=2.0.7 - python-tzdata=2023.3 - python_abi=3.10 - pytz=2023.3.post1 - pyu2f=0.1.5 - pyviz_comms=3.0.0 - pywavelets=1.4.1 - pywin32=306 - pywinpty=2.0.12 - pyyaml=6.0.1 - pyzmq=25.1.1 - qt-main=5.15.2 - qt-webengine=5.15.9 - qtconsole-base=5.4.4 - qtpy=2.4.1 - qtwebkit=5.212 - re2=2022.06.01 - referencing=0.30.2 - requests=2.31.0 - requests-oauthlib=1.3.1 - rfc3339-validator=0.1.4 - rfc3986-validator=0.1.1 - rpds-py=0.10.6 - rsa=4.9 - ruamel.yaml=0.18.4 - ruamel.yaml.clib=0.2.7 - scikit-image=0.20.0 - scikit-learn=1.3.2 - scipy=1.11.3 - send2trash=1.8.2 - setuptools=68.2.2 - sip=6.5.1 - six=1.16.0 - slicerator=1.1.0 - snappy=1.1.10 - sniffio=1.3.0 - soupsieve=2.5 - sqlite=3.44.0 - stack_data=0.6.2 - svt-av1=1.5.0 - tbb=2021.9.0 - tensorboard=2.10.1 - tensorboard-data-server=0.6.1 - tensorboard-plugin-wit=1.8.1 - tensorflow=2.10.0 - tensorflow-base=2.10.0 - tensorflow-estimator=2.10.0 - termcolor=2.3.0 - terminado=0.17.0 - threadpoolctl=3.2.0 - tifffile=2020.6.3 - tinycss2=1.2.1 - tk=8.6.13 - toml=0.10.2 - tomli=2.0.1 - toolz=0.12.0 - tornado=6.3.3 - tqdm=4.66.1 - traitlets=5.13.0 - types-python-dateutil=2.8.19.14 - typing-extensions=4.8.0 - typing_extensions=4.8.0 - typing_utils=0.1.0 - tzdata=2023c - uc-micro-py=1.0.1 - ucrt=10.0.22621.0 - unicodedata2=15.1.0 - uri-template=1.3.0 - urllib3=2.0.7 - vc=14.3 - vc14_runtime=14.36.32532 - vs2015_runtime=14.36.32532 - wcwidth=0.2.9 - webcolors=1.13 - webencodings=0.5.1 - websocket-client=1.6.4 - werkzeug=3.0.1 - wheel=0.41.3 - widgetsnbextension=4.0.9 - win_inet_pton=1.1.0 - winpty=0.4.3 - wrapt=1.15.0 - x264=1!164.3095 - x265=3.5 - xorg-libxau=1.0.11 - xorg-libxdmcp=1.1.3 - xyzservices=2023.10.1 - xz=5.2.6 - yaml=0.2.5 - yarl=1.9.2 - z5py=2.0.17 - zeromq=4.3.5 - zipp=3.17.0 - zlib=1.2.13 - zstd=1.5.5 - pip: - bqplot==0.12.42 - fastplotlib==0.1.0a14 - freetype-py==2.4.0 - ipydatagrid==1.2.0 - jupyter-rfb==0.4.1 - llvmlite==0.41.1 - nbclient==0.7.4 - numba==0.58.1 - py2vega==0.6.1 - pygfx==0.1.15 - pylinalg==0.4.1 - pyqt6==6.6.0 - pyqt6-qt6==6.6.0 - pyqt6-sip==13.6.0 - sidecar==0.7.0 - traittypes==0.2.1 - tslearn==0.6.2 - uharfbuzz==0.37.3 - voila==0.5.5 - websockets==12.0 - wgpu==0.11.0
kushalkolar commented 10 months ago

WrongAlgorithmExtensionError means you're calling the wrong algorithm extension on a row, ex: calling a cnmf function in a mcorr row.

Also mesmerize-viz demos are a WIP, trying to get them done by early next week.

On Thu, Nov 2, 2023, 06:50 bashsyr @.***> wrote:

Here are the packages in the environment: name: mestest2 channels: - defaults - pkgs/main - conda-forge dependencies: - _tflow_select=2.3.0 - absl-py=2.0.0 - aiohttp=3.8.6 - aiosignal=1.3.1 - anyio=4.0.0 - aom=3.5.0 - argon2-cffi=23.1.0 - argon2-cffi-bindings=21.2.0 - arrow=1.3.0 - asttokens=2.4.1 - astunparse=1.6.3 - async-lru=2.0.4 - async-timeout=4.0.3 - attrs=23.1.0 - av=10.0.0 - babel=2.13.1 - backports=1.0 - backports.functools_lru_cache=1.6.5 - beautifulsoup4=4.12.2 - bleach=6.1.0

  • blinker=1.7.0 - blosc=1.21.5 - bokeh=3.3.0 - brotli=1.1.0 - brotli-bin=1.1.0 - brotli-python=1.1.0 - bzip2=1.0.8 - c-ares=1.20.1 - ca-certificates=2023.7.22 - cached-property=1.5.2 - cached_property=1.5.2 - cachetools=5.3.2 - caiman=1.9.16 - certifi=2023.7.22 - cffi=1.16.0 - charset-normalizer=3.3.2 - click=8.1.7 - cloudpickle=3.0.0 - colorama=0.4.6
  • colorcet=3.0.1 - comm=0.1.4 - contourpy=1.1.1 - cryptography=39.0.0 - cycler=0.12.1 - cytoolz=0.12.2 - dask-core=2023.10.1 - dav1d=1.2.0 - debugpy=1.8.0 - decorator=5.1.1 - defusedxml=0.7.1 - eigen=3.4.0 - entrypoints=0.4 - exceptiongroup=1.1.3 - executing=2.0.1 - expat=2.5.0 - ffmpeg=6.0.0 - flatbuffers=23.5.26 - font-ttf-dejavu-sans-mono=2.37 - font-ttf-inconsolata=3.000 - font-ttf-source-code-pro=2.038 - font-ttf-ubuntu=0.83 - fontconfig=2.14.2 - fonts-conda-ecosystem=1 - fonts-conda-forge=1 - fonttools=4.43.1 - fqdn=1.5.1 - freetype=2.12.1 - frozenlist=1.4.0 - fsspec=2023.10.0 - future=0.18.3 - gast=0.4.0 - gettext=0.21.1 - giflib=5.2.1 - glib=2.78.0 - glib-tools=2.78.0 - google-auth=2.23.4 - google-auth-oauthlib=0.4.6 - google-pasta=0.2.0 - grpc-cpp=1.48.1 - grpcio=1.48.1 - gst-plugins-base=1.18.5 - gstreamer=1.18.5 - h5py=3.9.0 - hdf5=1.14.0 - hdmf=3.11.0 - holoviews=1.18.0 - icu=58.2 - idna=3.4 - imagecodecs-lite=2019.12.3 - imageio=2.31.5 - importlib-metadata=6.8.0 - importlib_metadata=6.8.0 - importlib_resources=6.1.0 - iniconfig=2.0.0 - intel-openmp=2023.2.0 - ipykernel=6.26.0 - ipyparallel=8.6.1 - ipython=8.17.2 - ipython_genutils=0.2.0 - ipywidgets=8.1.1 - isoduration=20.11.0 - jedi=0.19.1 - jinja2=3.1.2 - joblib=1.3.2 - jpeg=9e - json5=0.9.14 - jsonpointer=2.4 - jsonschema=4.19.2 - jsonschema-specifications=2023.7.1 - jsonschema-with-format-nongpl=4.19.2 - jupyter=1.0.0 - jupyter-lsp=2.2.0 - jupyter_bokeh=2.0.4 - jupyter_client=8.5.0 - jupyter_console=6.6.3 - jupyter_core=5.5.0 - jupyter_events=0.8.0 - jupyter_server=2.9.1 - jupyter_server_terminals=0.4.4 - jupyterlab=4.0.7 - jupyterlab_pygments=0.2.2 - jupyterlab_server=2.25.0 - jupyterlab_widgets=3.0.9 - keras=2.10.0 - kiwisolver=1.4.5 - krb5=1.20.1 - lazy_loader=0.3 - lcms2=2.15 - lerc=4.0.0 - libabseil=20220623.0 - libaec=1.1.2 - libblas=3.9.0 - libbrotlicommon=1.1.0 - libbrotlidec=1.1.0 - libbrotlienc=1.1.0 - libcblas=3.9.0 - libclang=14.0.6 - libclang13=14.0.6 - libcurl=8.1.2 - libdeflate=1.17 - libexpat=2.5.0 - libffi=3.4.2 - libglib=2.78.0 - libhwloc=2.9.1 - libiconv=1.17 - liblapack=3.9.0 - libogg=1.3.4 - libopus=1.3.1 - libpng=1.6.39 - libpq=12.15 - libprotobuf=3.20.3 - libsodium=1.0.18 - libsqlite=3.44.0 - libssh2=1.10.0 - libtiff=4.5.0 - libvorbis=1.3.7 - libwebp=1.3.2 - libwebp-base=1.3.2 - libxcb=1.13 - libxml2=2.10.4 - libxslt=1.1.37 - libzlib=1.2.13 - linkify-it-py=2.0.0 - locket=1.0.0 - lz4-c=1.9.4 - m2w64-gcc-libgfortran=5.3.0 - m2w64-gcc-libs=5.3.0 - m2w64-gcc-libs-core=5.3.0 - m2w64-gmp=6.1.0 - m2w64-libwinpthread-git=5.0.0.4634.697f757 - markdown=3.5.1 - markdown-it-py=3.0.0 - markupsafe=2.1.3 - matplotlib=3.8.1 - matplotlib-base=3.8.1 - matplotlib-inline=0.1.6 - mdit-py-plugins=0.4.0 - mdurl=0.1.0 - mesmerize-core=0.3.0 - mistune=3.0.1 - mkl=2023.2.0 - msys2-conda-epoch=20160418 - multidict=6.0.4 - munkres=1.1.4 - mypy=1.6.1 - mypy_extensions=1.0.0 - nbconvert=7.10.0 - nbconvert-core=7.10.0 - nbconvert-pandoc=7.10.0 - nbformat=5.9.2 - nest-asyncio=1.5.8 - networkx=3.2.1 - nose=1.3.7 - notebook=7.0.6 - notebook-shim=0.2.3 - numpy=1.26.0 - oauthlib=3.2.2 - opencv=4.6.0 - openh264=2.3.1 - openjpeg=2.5.0 - openssl=1.1.1w - opt_einsum=3.3.0 - overrides=7.4.0 - packaging=23.2 - pandas=2.1.2 - pandoc=3.1.3 - pandocfilters=1.5.0 - panel=1.3.1 - param=2.0.0 - parso=0.8.3 - partd=1.4.1 - pcre2=10.40 - peakutils=1.3.4 - pickleshare=0.7.5 - pillow=9.4.0 - pims=0.6.1 - pip=23.3.1 - pkgutil-resolve-name=1.3.10 - platformdirs=3.11.0 - pluggy=1.3.0 - prometheus_client=0.18.0 - prompt-toolkit=3.0.39 - prompt_toolkit=3.0.39 - protobuf=3.20.3 - psutil=5.9.5 - pthread-stubs=0.4
  • pthreads-win32=2.9.1 - pure_eval=0.2.2 - pyasn1=0.5.0 - pyasn1-modules=0.3.0 - pycparser=2.21 - pyct=0.4.6 - pyct-core=0.4.6 - pygments=2.16.1 - pyjwt=2.8.0 - pynwb=2.5.0 - pyopenssl=23.2.0 - pyparsing=3.1.1 - pyqt=5.15.4 - pyqt5-sip=12.9.0 - pyqtgraph=0.13.3 - pysocks=1.7.1 - pytest=7.4.3 - python=3.10.8 - python-dateutil=2.8.2 - python-fastjsonschema=2.18.1 - python-flatbuffers=23.5.26 - python-json-logger=2.0.7 - python-tzdata=2023.3 - python_abi=3.10 - pytz=2023.3.post1 - pyu2f=0.1.5 - pyviz_comms=3.0.0 - pywavelets=1.4.1 - pywin32=306 - pywinpty=2.0.12 - pyyaml=6.0.1 - pyzmq=25.1.1 - qt-main=5.15.2 - qt-webengine=5.15.9 - qtconsole-base=5.4.4 - qtpy=2.4.1 - qtwebkit=5.212 - re2=2022.06.01 - referencing=0.30.2 - requests=2.31.0 - requests-oauthlib=1.3.1 - rfc3339-validator=0.1.4 - rfc3986-validator=0.1.1
  • rpds-py=0.10.6 - rsa=4.9 - ruamel.yaml=0.18.4 - ruamel.yaml.clib=0.2.7 - scikit-image=0.20.0 - scikit-learn=1.3.2 - scipy=1.11.3 - send2trash=1.8.2
  • setuptools=68.2.2 - sip=6.5.1 - six=1.16.0 - slicerator=1.1.0 - snappy=1.1.10 - sniffio=1.3.0 - soupsieve=2.5 - sqlite=3.44.0 - stack_data=0.6.2 - svt-av1=1.5.0 - tbb=2021.9.0 - tensorboard=2.10.1 - tensorboard-data-server=0.6.1 - tensorboard-plugin-wit=1.8.1 - tensorflow=2.10.0 - tensorflow-base=2.10.0 - tensorflow-estimator=2.10.0 - termcolor=2.3.0 - terminado=0.17.0 - threadpoolctl=3.2.0 - tifffile=2020.6.3 - tinycss2=1.2.1 - tk=8.6.13 - toml=0.10.2 - tomli=2.0.1
  • toolz=0.12.0 - tornado=6.3.3 - tqdm=4.66.1 - traitlets=5.13.0 - types-python-dateutil=2.8.19.14 - typing-extensions=4.8.0 - typing_extensions=4.8.0 - typing_utils=0.1.0 - tzdata=2023c - uc-micro-py=1.0.1 - ucrt=10.0.22621.0 - unicodedata2=15.1.0 - uri-template=1.3.0 - urllib3=2.0.7 - vc=14.3 - vc14_runtime=14.36.32532 - vs2015_runtime=14.36.32532 - wcwidth=0.2.9 - webcolors=1.13 - webencodings=0.5.1 - websocket-client=1.6.4 - werkzeug=3.0.1 - wheel=0.41.3
  • widgetsnbextension=4.0.9 - win_inet_pton=1.1.0 - winpty=0.4.3 - wrapt=1.15.0 - x264=1!164.3095 - x265=3.5 - xorg-libxau=1.0.11 - xorg-libxdmcp=1.1.3 - xyzservices=2023.10.1 - xz=5.2.6 - yaml=0.2.5 - yarl=1.9.2 - z5py=2.0.17 - zeromq=4.3.5 - zipp=3.17.0 - zlib=1.2.13 - zstd=1.5.5 - pip: - bqplot==0.12.42 - fastplotlib==0.1.0a14 - freetype-py==2.4.0 - ipydatagrid==1.2.0 - jupyter-rfb==0.4.1 - llvmlite==0.41.1 - nbclient==0.7.4 - numba==0.58.1 - py2vega==0.6.1 - pygfx==0.1.15 - pylinalg==0.4.1 - pyqt6==6.6.0 - pyqt6-qt6==6.6.0 - pyqt6-sip==13.6.0 - sidecar==0.7.0 - traittypes==0.2.1 - tslearn==0.6.2 - uharfbuzz==0.37.3 - voila==0.5.5 - websockets==12.0 - wgpu==0.11.0

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bashsyr commented 10 months ago

Hi, Thank you for your response. I didn't specifically call anything, I just ran the app file with voila I know the whole mesviz is still WIP, but can you maybe guide me to where can I fix this error ?

kushalkolar commented 10 months ago

Set the start_index as an item which was run using the algorithm that you're calling viz on. Ex: if you're calling cnmf.viz(start_index=2), the item at index 2 should be a cnmf item.

If you don't specify the start index it should determine it automatically.

The voila app is currently non functional, but the cnmf and mcorr examples work.

On Thu, Nov 2, 2023, 09:29 bashsyr @.***> wrote:

Hi, Thank you for your response. I didn't specifically call anything, I just ran the app file with voila I know the whole mesviz is still WIP, but can you maybe guide me to where can I fix this error ?

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bashsyr commented 10 months ago

Thank you, I was just looking at this line rn. I ran the whole code in a Notebook and I choose an appropriate start index. the problem I'm facing now is different: it's looking for b,f and it doesn't accept them being None (I have 1p results), is there a way around this, or is this Visualiztion only for 2p for now ? this is the error I'm getting 

File ~\mambaforge\envs\mestest2\lib\site-packages\mesmerize_core\caiman_extensions\cnmf.py:528, in CNMFExtensions.get_rcb(self)
    525 spatial = cnmf_obj.estimates.b
    526 temporal = cnmf_obj.estimates.f
--> 528 return LazyArrayRCB(spatial=spatial, temporal=temporal, frame_dims=dims)

File ~\mambaforge\envs\mestest2\lib\site-packages\mesmerize_core\arrays\_cnmf.py:34, in LazyArrayRCM.__init__(self, spatial, temporal, frame_dims)
     14 def __init__(
     15         self,
     16         spatial: np.ndarray,
     17         temporal: np.ndarray,
     18         frame_dims: Tuple[int, int],
     19 ):
     20     """
     21     Parameters
     22     ----------
   (...)
     31         
     32     """
---> 34     if spatial.shape[1] != temporal.shape[0]:
     35         raise ValueError(
     36             f"Number of temporal components provided: `{temporal.shape[0]}` "
     37             f"does not equal number of spatial components provided: `{spatial.shape[1]}`"
     38         )
     40     self._spatial = spatial

AttributeError: 'NoneType' object has no attribute 'shape'
kushalkolar commented 10 months ago

Lazy rcb (reconstructed background) for 1p is a on my todo list.

You can visualize just the input movie and rcm for now:

viz(image_data_options=["input", "rcm"])

On Thu, Nov 2, 2023, 09:59 bashsyr @.***> wrote:

Thank you, I was just looking at this line rn. I ran the whole code in a Notebook and I choose an appropriate start index. the problem I'm facing now is different: it's looking for b,f and it doesn't accept them being None (I have 1p results), is there a way around this, or is this Visualiztion only for 2p for now ? this is the error I'm getting

File ~\mambaforge\envs\mestest2\lib\site-packages\mesmerize_core\caiman_extensions\cnmf.py:528, in CNMFExtensions.get_rcb(self) 525 spatial = cnmf_obj.estimates.b 526 temporal = cnmf_obj.estimates.f --> 528 return LazyArrayRCB(spatial=spatial, temporal=temporal, frame_dims=dims)

File ~\mambaforge\envs\mestest2\lib\site-packages\mesmerize_core\arrays_cnmf.py:34, in LazyArrayRCM.init(self, spatial, temporal, frame_dims) 14 def init( 15 self, 16 spatial: np.ndarray, 17 temporal: np.ndarray, 18 frame_dims: Tuple[int, int], 19 ): 20 """ 21 Parameters 22 ---------- (...) 31 32 """ ---> 34 if spatial.shape[1] != temporal.shape[0]: 35 raise ValueError( 36 f"Number of temporal components provided: {temporal.shape[0]} " 37 f"does not equal number of spatial components provided: {spatial.shape[1]}" 38 ) 40 self._spatial = spatial

AttributeError: 'NoneType' object has no attribute 'shape'

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kushalkolar commented 9 months ago

closing, rcb does not yet exist for CNMFE, not sure if/when it will be done.