qweasdf1354 commented 1 year ago

Hi author, i have some issues, could you help me to resovle?

the system is window10 and i run the installation protocal from the github page using anaconda.

when i run the mcorr_cnmf.ipynb, i can run the code until the 'Visualize raw & MCorr movie side-by-side' step.

**when i run the following cell**
 'mcorr_iw = fpl.ImageWidget(
    data=[input_movie, mcorr_movie], 
    vmin_vmax_sliders=True, 
    cmap="gnuplot2"
)
mcorr_iw.show()'

**the following error occur**

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[60], line 1
----> 1 mcorr_iw = fpl.ImageWidget(
      2     data=[input_movie, mcorr_movie], 
      3     vmin_vmax_sliders=True, 
      4     cmap="gnuplot2"
      5 )
      6 mcorr_iw.show()

File D:\software\fastplotlib\fastplotlib\widgets\image.py:554, in ImageWidget.__init__(self, data, dims_order, slider_dims, window_funcs, frame_apply, grid_shape, names, grid_plot_kwargs, **kwargs)
    552 frame = self._process_indices(d, slice_indices=self._current_index)
    553 frame = self._process_frame_apply(frame, data_ix)
--> 554 ig = ImageGraphic(frame, name="image_widget_managed", **kwargs)
    555 subplot.add_graphic(ig)
    556 subplot.name = name

File D:\software\fastplotlib\fastplotlib\graphics\image.py:259, in ImageGraphic.__init__(self, data, vmin, vmax, cmap, filter, isolated_buffer, *args, **kwargs)
    201 def __init__(
    202     self,
    203     data: Any,
   (...)
    210     **kwargs,
    211 ):
    212     """
    213     Create an Image Graphic
    214 
   (...)
    256 
    257     """
--> 259     super().__init__(*args, **kwargs)
    261     data = to_gpu_supported_dtype(data)
    263     # TODO: we need to organize and do this better

TypeError: Graphic.__init__() got an unexpected keyword argument 'vmin_vmax_sliders'

I try to search the similar situation, but it seems it is none, so could you help me?

kushalkolar commented 1 year ago

Hi, thanks for posting the traceback! We just did a new release of fastplotlib yesterday, the vmin vmax sliders have been removed in favor of a histogram widget: https://github.com/fastplotlib/fastplotlib/pull/344

You can just remove that argument.

We will update the notebooks soon.

qweasdf1354 commented 1 year ago

thanks a lot

qweasdf1354 commented 1 year ago

Hi author, today i saw you update the notebook. I try it. that is great! but i still meet some problem i can not resolve by myself. so i try to ask for help.

1.when i run the cell below 'Modify the window_funcs at any time.'

''' iw_means.gridplot[0, 0].auto_scale(maintain_aspect=True)

for g in iw_means.managed_graphics: g.cmap.vmax = 200 '''

the following error occur

'''

NameError Traceback (most recent call last) Cell In[62], line 1 ----> 1 mcorr_iw_means.gridplot[0, 0].auto_scale(maintain_aspect=True) 3 for g in iw_means.managed_graphics: 4 g.cmap.vmax = 200

NameError: name 'mcorr_iw_means' is not defined ''' Although the it seems not have impact to the following code, i wanna to let you know

2.When i use the mcorr_viz.show(), there are some problems.

the above is motion correction viz and when i use the cnmf viz the following is

''' C:\Users\zhouys\anaconda3\envs\mescore\lib\site-packages\ipydatagrid\datagrid.py:460: UserWarning: Index name of 'index' is not round-trippable. schema = pd.io.json.build_table_schema(dataframe) C:\Users\zhouys\anaconda3\envs\mescore\lib\site-packages\fastplotlib\graphics_features_base.py:34: UserWarning: converting float64 array to float32 warn(f"converting {array.dtype} array to float32") '''

3.After run 'Run the cnmf batch items' and 'Load outputs', i try to 'Visualize with mesmerize-viz'. However i not like the mcorr that give me 9 subplot pannel, it give me only one user_surface like i first run the viz when i havent to paraSearch. Is it something i lost? how can i see the total parameters? I also wanna to know how to see the all counters when i running the '''viz_cnmf.show()''' and not scrolling the 'cell contours' bar. if i change the scrolling bar i can not find way to go back to see the full image. In the bottom pannel, what is 'contour co...' what is accepted rejected?snr_comps and so on. and what is 'invisible al...' and what is eval params

4.the last question is could I plot the contours of all cells and i sellected cells? using ' get contours' can satisfy my purpose? purpose: I wanna to plot all contours in grey and some selected contours in color.

And could i plot the contours in the tiff of my raw tif or the style in the mcorr i adjuest [viz.image_widget.gridplot["mcorr"]["image_widget_managed"].cmap.vmax = 2000][viz.image_widget.cmap = "viridis"].

I apologize for a lot of basic question and If you can help me I will appreciate. Looking forward your reply and I wanna to say that is great work! by the way i saw the PCA trace of the cell feature among time plot. but i do not see in this notebook. it will release in the future notebook?

kushalkolar commented 1 year ago

See where it says:

Failed to load model class 'DataGridModel' from module 'ipydatagrid' Error: No version of module ipydatagrid is registered

You need to install ipydatagrid.

Please follow the instructions on the mesmerize-viz repo to install it. :)

On Fri, Nov 3, 2023, 12:05 qweasdf1354 @.***> wrote:

Hi author, today i saw you update the notebook. I try it. that is great! but i still meet some problem i can not resolve by myself. so i try to ask for help.

1.when i run the cell below 'Modify the window_funcs at any time.'

''' iw_means.gridplot[0, 0].auto_scale(maintain_aspect=True)

for g in iw_means.managed_graphics: g.cmap.vmax = 200 '''

the following error occur '''

NameError Traceback (most recent call last) Cell In[62], line 1 ----> 1 mcorr_iw_means.gridplot[0, 0].auto_scale(maintain_aspect=True) 3 for g in iw_means.managed_graphics: 4 g.cmap.vmax = 200

NameError: name 'mcorr_iw_means' is not defined ''' Although the it seems not have impact to the following code, i wanna to let you know

2.When i use the mcorr_viz.show(), there are some problems.

a. I see the left up panel show error and ask me to 'Click to show javascript error' the following is the error ''' [Open Browser Console for more detailed log - Double click to close this message] Failed to load model class 'DataGridModel' from module 'ipydatagrid' Error: No version of module ipydatagrid is registered at f.loadClass ( @./jupyterlab-manager/static/134.a63a8d293fb35a52dc25.js?v=a63a8d293fb35a52dc25:1:74936 ) at f.loadModelClass ( @./jupyterlab-manager/static/336.ebc7a55ea1768712771f.js?v=ebc7a55ea1768712771f:1:10729 ) at f._make_model ( @./jupyterlab-manager/static/336.ebc7a55ea1768712771f.js?v=ebc7a55ea1768712771f:1:7517 ) at f.new_model ( @./jupyterlab-manager/static/336.ebc7a55ea1768712771f.js?v=ebc7a55ea1768712771f:1:5137 ) at f.handle_comm_open ( @./jupyterlab-manager/static/336.ebc7a55ea1768712771f.js?v=ebc7a55ea1768712771f:1:3894 ) at _handleCommOpen ( @./jupyterlab-manager/static/134.a63a8d293fb35a52dc25.js?v=a63a8d293fb35a52dc25:1:73473 ) at v._handleCommOpen ( http://localhost:8888/static/notebook/3676.bundle.js:1:30809) at async v._handleMessage ( http://localhost:8888/static/notebook/3676.bundle.js:1:32703) '''

the above is motion correction viz and when i use the cnmf viz the following is

''' [Open Browser Console for more detailed log - Double click to close this message] Failed to load model class 'DataGridModel' from module 'ipydatagrid' Error: No version of module ipydatagrid is registered at f.loadClass ( @./jupyterlab-manager/static/134.a63a8d293fb35a52dc25.js?v=a63a8d293fb35a52dc25:1:74936 ) at f.loadModelClass ( @./jupyterlab-manager/static/336.ebc7a55ea1768712771f.js?v=ebc7a55ea1768712771f:1:10729 ) at f._make_model ( @./jupyterlab-manager/static/336.ebc7a55ea1768712771f.js?v=ebc7a55ea1768712771f:1:7517 ) at f.new_model ( @./jupyterlab-manager/static/336.ebc7a55ea1768712771f.js?v=ebc7a55ea1768712771f:1:5137 ) at f.handle_comm_open ( @./jupyterlab-manager/static/336.ebc7a55ea1768712771f.js?v=ebc7a55ea1768712771f:1:3894 ) at _handleCommOpen ( @./jupyterlab-manager/static/134.a63a8d293fb35a52dc25.js?v=a63a8d293fb35a52dc25:1:73473 ) at v._handleCommOpen ( http://localhost:8888/static/notebook/3676.bundle.js:1:30809) at async v._handleMessage ( http://localhost:8888/static/notebook/3676.bundle.js:1:32703) ''' there are also some wanning

''' C:\Users\zhouys\anaconda3\envs\mescore\lib\site-packages\ipydatagrid\datagrid.py:460: UserWarning: Index name of 'index' is not round-trippable. schema = pd.io.json.build_table_schema(dataframe) C:\Users\zhouys\anaconda3\envs\mescore\lib\site-packages\fastplotlib\graphics_features_base.py:34: UserWarning: converting float64 array to float32 warn(f"converting {array.dtype} array to float32") '''

3.After run 'Run the cnmf batch items' and 'Load outputs', i try to 'Visualize with mesmerize-viz'. However i not like the mcorr that give me 9 subplot pannel, it give me only one user_surface like i first run the viz when i havent to paraSearch. Is it something i lost? how can i see the total parameters? I also wanna to know how to see the all counters when i running the '''viz_cnmf.show()''' and not scrolling the 'cell contours' bar. if i change the scrolling bar i can not find way to go back to see the full image. In the bottom pannel, what is 'contour co...' what is accepted rejected?snr_comps and so on. and what is 'invisible al...' and what is eval params

4.the last question is could I plot the contours of all cells and i sellected cells? using ' get contours' can satisfy my purpose? purpose: I wanna to plot all contours in grey and some selected contours in color.

And could i plot the contours in the tiff of my raw tif or the style in the mcorr i adjuest [viz.image_widget.gridplot["mcorr"]["image_widget_managed"].cmap.vmax = 2000][viz.image_widget.cmap = "viridis"].

I apologize for a lot of basic question and If you can help me I will appreciate. Looking forward your reply and I wanna to say that is great work! by the way i saw the PCA trace of the cell feature among time plot. but i do not see in this notebook. it will release in the future notebook?

— Reply to this email directly, view it on GitHub https://github.com/nel-lab/mesmerize-core/issues/240#issuecomment-1792711410, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACHXXREFRPAGLJVCVMQZN63YCUI6DAVCNFSM6AAAAAA6ZC3NGGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOJSG4YTCNBRGA . You are receiving this because you commented.Message ID: @.***>

kushalkolar commented 1 year ago

I forgot to fully get rid of the iw_means stuff, ignore it XD.

The notebooks will be in a better state by mid next week.

qweasdf1354 commented 12 months ago

Hi author, I am follow the instructions on the mesmerize-viz repo to install it. and I check is it already install the 'ipydatagrid' using pip install 'ipydatagrid'. the results is following

(mescore) PS C:\Windows\system32> pip install ipydatagrid Looking in indexes: https://pypi.mirrors.ustc.edu.cn/simple/ Requirement already satisfied: ipydatagrid in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (1.2.0) Requirement already satisfied: bqplot>=0.11.6 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from ipydatagrid) (0.12.42) Requirement already satisfied: ipywidgets<9,>=7.6 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from ipydatagrid) (8.1.1) Requirement already satisfied: pandas>=1.3.5 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from ipydatagrid) (2.1.2) Requirement already satisfied: py2vega>=0.5 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from ipydatagrid) (0.6.1) Requirement already satisfied: traitlets>=4.3.0 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from bqplot>=0.11.6->ipydatagrid) (5.13.0) Requirement already satisfied: traittypes>=0.0.6 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from bqplot>=0.11.6->ipydatagrid) (0.2.1) Requirement already satisfied: numpy>=1.10.4 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from bqplot>=0.11.6->ipydatagrid) (1.26.0) Requirement already satisfied: comm>=0.1.3 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from ipywidgets<9,>=7.6->ipydatagrid) (0.1.4) Requirement already satisfied: ipython>=6.1.0 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from ipywidgets<9,>=7.6->ipydatagrid) (8.17.2) Requirement already satisfied: widgetsnbextension~=4.0.9 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from ipywidgets<9,>=7.6->ipydatagrid) (4.0.9) Requirement already satisfied: jupyterlab-widgets~=3.0.9 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from ipywidgets<9,>=7.6->ipydatagrid) (3.0.9) Requirement already satisfied: python-dateutil>=2.8.2 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from pandas>=1.3.5->ipydatagrid) (2.8.2) Requirement already satisfied: pytz>=2020.1 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from pandas>=1.3.5->ipydatagrid) (2023.3.post1) Requirement already satisfied: tzdata>=2022.1 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from pandas>=1.3.5->ipydatagrid) (2023.3) Requirement already satisfied: gast<0.5,>=0.4.0 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from py2vega>=0.5->ipydatagrid) (0.4.0) Requirement already satisfied: decorator in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from ipython>=6.1.0->ipywidgets<9,>=7.6->ipydatagrid) (5.1.1) Requirement already satisfied: jedi>=0.16 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from ipython>=6.1.0->ipywidgets<9,>=7.6->ipydatagrid) (0.19.1) Requirement already satisfied: matplotlib-inline in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from ipython>=6.1.0->ipywidgets<9,>=7.6->ipydatagrid) (0.1.6) Requirement already satisfied: prompt-toolkit!=3.0.37,<3.1.0,>=3.0.30 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from ipython>=6.1.0->ipywidgets<9,>=7.6->ipydatagrid) (3.0.39) Requirement already satisfied: pygments>=2.4.0 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from ipython>=6.1.0->ipywidgets<9,>=7.6->ipydatagrid) (2.16.1) Requirement already satisfied: stack-data in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from ipython>=6.1.0->ipywidgets<9,>=7.6->ipydatagrid) (0.6.2) Requirement already satisfied: exceptiongroup in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from ipython>=6.1.0->ipywidgets<9,>=7.6->ipydatagrid) (1.1.3) Requirement already satisfied: colorama in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from ipython>=6.1.0->ipywidgets<9,>=7.6->ipydatagrid) (0.4.6) Requirement already satisfied: six>=1.5 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from python-dateutil>=2.8.2->pandas>=1.3.5->ipydatagrid) (1.16.0) Requirement already satisfied: parso<0.9.0,>=0.8.3 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from jedi>=0.16->ipython>=6.1.0->ipywidgets<9,>=7.6->ipydatagrid) (0.8.3) Requirement already satisfied: wcwidth in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from prompt-toolkit!=3.0.37,<3.1.0,>=3.0.30->ipython>=6.1.0->ipywidgets<9,>=7.6->ipydatagrid) (0.2.9) Requirement already satisfied: executing>=1.2.0 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from stack-data->ipython>=6.1.0->ipywidgets<9,>=7.6->ipydatagrid) (2.0.1) Requirement already satisfied: asttokens>=2.1.0 in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from stack-data->ipython>=6.1.0->ipywidgets<9,>=7.6->ipydatagrid) (2.4.1) Requirement already satisfied: pure-eval in c:\users\zhouys\anaconda3\envs\mescore\lib\site-packages (from stack-data->ipython>=6.1.0->ipywidgets<9,>=7.6->ipydatagrid) (0.2.2)

I am looking forward the next generation of notebooks!

kushalkolar commented 12 months ago

Did you restart the jupyter server, i.e. not just restarting the kernel but fully shutting down jupyter lab and starting it up again from your terminal/conda prompt with jupyter lab.

In general installing/updating/changing any jupyter widget libraries (ipywidgets, ipydatagrid, ipy-anything pretty much) you have to restart the jupyter server, it's not sufficient to just restart the kernel.

qweasdf1354 commented 12 months ago

I restrat the anaconda powershell and there are not change in the error

Failed to load model class 'DataGridModel' from module 'ipydatagrid' Error: No version of module ipydatagrid is registered

by the way is it the mamba activate mescore process may produce this error? when i use mamban activate there is error and i have to use conda to activate this env

**(base) PS C:\Windows\system32> mamba activate mescore

C:\Windows\system32>set MKL_NUM_THREADS=1

C:\Windows\system32>set OPENBLAS_NUM_THREADS=1**

(base) PS C:\Windows\system32> conda activate mescore

qweasdf1354 commented 12 months ago

Hi author I use the record function button, but where can i found the record results?

kushalkolar commented 12 months ago

What if you try to install ipydatagrid from conda instead of pip:

mamba install -c conda-forge ipydatagrid

I restrat the anaconda powershell and there are not change in the error

Failed to load model class 'DataGridModel' from module 'ipydatagrid' Error: No version of module ipydatagrid is registered

by the way is it the mamba activate mescore process may produce this error? when i use mamban activate there is error and i have to use conda to activate this env

**(base) PS C:\Windows\system32> mamba activate mescore

C:\Windows\system32>set MKL_NUM_THREADS=1

C:\Windows\system32>set OPENBLAS_NUM_THREADS=1**

(base) PS C:\Windows\system32> conda activate mescore

If you are using conda, I belive you have to use conda activate. mamba activate in conda produces weirdness as far as I know, @pgunn any thoughts?

Hi author I use the record function button, but where can i found the record results?

It should be in the same dir as the notebook with a timestamp as the filename.

pgunn commented 12 months ago

When mamba says to use mamba activate, use conda activate instead; I believe it's a bug in some of the conda libraries that mamba uses that they get the name of the program they're being called by and use that to build that string to tell the user what to do, not realising that separate tools to build versus activate an environment would eventually be a thing.

qweasdf1354 commented 12 months ago

Hi, kushalkolar I use the cmd to activate mescore using mamba and using cmd to 'mamba install -c conda-forge ipydatagrid' in the mescore environment.

folloing were the process and detail

C:\Users\zhouys>mamba activate mescore

C:\Users\zhouys>set MKL_NUM_THREADS=1

C:\Users\zhouys>set OPENBLAS_NUM_THREADS=1

(mescore) C:\Users\zhouys>mamba install -c conda-forge ipydatagrid

Looking for: ['ipydatagrid']

anaconda/pkgs/main/win-64 No change anaconda/pkgs/r/win-64 No change conda-forge/win-64 No change conda-forge/noarch No change anaconda/pkgs/main/noarch No change anaconda/pkgs/r/noarch No change anaconda/pkgs/msys2/win-64 No change anaconda/pkgs/msys2/noarch No change

Pinned packages:

python 3.10.*

Transaction

Prefix: C:\Users\zhouys\anaconda3\envs\mescore

All requested packages already installed

(mescore) C:\Users\zhouys>

However there is still a error when i 'viz = df.mcorr.viz() viz.show()'

I restart the cmd and not work too

qweasdf1354 commented 12 months ago

and when i use the record buttom there is not show the saved file. Is it something usage method i havent got? or something i am doing is wrong?

pgunn commented 12 months ago

Please do a conda env list and send us the result

qweasdf1354 commented 12 months ago

Hi pgunn, (mescore) C:\Users\zhouys>conda env list

conda environments:

# base C:\Users\zhouys\anaconda3 analysis C:\Users\zhouys\anaconda3\envs\analysis caiman C:\Users\zhouys\anaconda3\envs\caiman cell C:\Users\zhouys\anaconda3\envs\cell cellpose C:\Users\zhouys\anaconda3\envs\cellpose deepcadrt C:\Users\zhouys\anaconda3\envs\deepcadrt dlc C:\Users\zhouys\anaconda3\envs\dlc mescore * C:\Users\zhouys\anaconda3\envs\mescore simba C:\Users\zhouys\anaconda3\envs\simba sleap C:\Users\zhouys\anaconda3\envs\sleap suite2p C:\Users\zhouys\anaconda3\envs\suite2p trace C:\Users\zhouys\anaconda3\envs\trace

pgunn commented 12 months ago

And in that environment, please do a conda list

and send us the result

qweasdf1354 commented 12 months ago

(mescore) C:\Users\zhouys>conda list

packages in environment at C:\Users\zhouys\anaconda3\envs\mescore:

#

Name Version Build Channel

_tflow_select 2.3.0 mkl defaults absl-py 2.0.0 pyhd8ed1ab_0 conda-forge aiohttp 3.8.6 py310h8d17308_1 conda-forge aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge anyio 4.0.0 pyhd8ed1ab_0 conda-forge aom 3.5.0 h63175ca_0 conda-forge argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py310h8d17308_4 conda-forge arrow 1.3.0 pyhd8ed1ab_0 conda-forge asttokens 2.4.1 pyhd8ed1ab_0 conda-forge astunparse 1.6.3 pyhd8ed1ab_0 conda-forge async-lru 2.0.4 pyhd8ed1ab_0 conda-forge async-timeout 4.0.3 pyhd8ed1ab_0 conda-forge attrs 23.1.0 pyh71513ae_1 conda-forge av 10.0.0 py310hef11e44_4 conda-forge babel 2.13.1 pyhd8ed1ab_0 conda-forge backports 1.0 pyhd8ed1ab_3 conda-forge backports.functools_lru_cache 1.6.5 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.12.2 pyha770c72_0 conda-forge bleach 6.1.0 pyhd8ed1ab_0 conda-forge blinker 1.7.0 pyhd8ed1ab_0 conda-forge blosc 1.21.5 hdccc3a2_0 conda-forge bokeh 3.3.0 pyhd8ed1ab_0 conda-forge bqplot 0.12.42 pypi_0 pypi brotli 1.1.0 hcfcfb64_1 conda-forge brotli-bin 1.1.0 hcfcfb64_1 conda-forge brotli-python 1.1.0 py310h00ffb61_1 conda-forge bzip2 1.0.8 h8ffe710_4 conda-forge c-ares 1.21.0 hcfcfb64_0 conda-forge ca-certificates 2023.7.22 h56e8100_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 5.3.2 pyhd8ed1ab_0 conda-forge caiman 1.9.16 py310h00ffb61_0 conda-forge certifi 2023.7.22 pyhd8ed1ab_0 conda-forge cffi 1.16.0 py310h8d17308_0 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge click 8.1.7 win_pyh7428d3b_0 conda-forge cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge colorcet 3.0.1 pyhd8ed1ab_0 conda-forge comm 0.1.4 pyhd8ed1ab_0 conda-forge contourpy 1.1.1 py310h232114e_1 conda-forge cryptography 39.0.0 py310h52f42fa_0 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge cytoolz 0.12.2 py310h8d17308_1 conda-forge dask-core 2023.10.1 pyhd8ed1ab_0 conda-forge dav1d 1.2.0 hcfcfb64_0 conda-forge debugpy 1.8.0 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qweasdf1354 commented 12 months ago

Hi, author, sorry to bother you i have encounter some new questions. i can got the temperal data using the temporal_good function. however, it is not DeltaF/F in the cnmf. i notice that it is different to the common definition of the DeltaF/F in cnmf. how can i got the DeltaF/F results?

kushalkolar commented 12 months ago

Were you able to get ipydatagrid working? Are you in jupyterlab and not jupyter notebook? I'd try updating to the latest jupyterlab and latest ipywidgets.

For dfof you first need to run it: https://mesmerize-core.readthedocs.io/en/latest/api/cnmf.html#mesmerize_core.CNMFExtensions.run_detrend_dfof

qweasdf1354 commented 12 months ago

sorry i am use the jupyter notebook

kushalkolar commented 12 months ago

That might explain it, install jupyterlab and try it in there :D

qweasdf1354 commented 12 months ago

thanks i will try it soon

qweasdf1354 commented 12 months ago

Hi author, when i using the jupyter lab the original problem is resolved however the record buttum is remain problem

the following is the log

Traceback (most recent call last): File "C:\Users\zhouys\anaconda3\envs\mescore\lib\site-packages\fastplotlib\layouts_frame_ipywidget_toolbar.py", line 179, in record_plot self.plot.record_start( File "C:\Users\zhouys\anaconda3\envs\mescore\lib\site-packages\fastplotlib\layouts_record_mixin.py", line 208, in record_start self._video_writer.start() File "C:\Users\zhouys\anaconda3\envs\mescore\lib\multiprocessing\process.py", line 121, in start self._popen = self._Popen(self) File "C:\Users\zhouys\anaconda3\envs\mescore\lib\multiprocessing\context.py", line 224, in _Popen return _default_context.get_context().Process._Popen(process_obj) File "C:\Users\zhouys\anaconda3\envs\mescore\lib\multiprocessing\context.py", line 336, in _Popen return Popen(process_obj) File "C:\Users\zhouys\anaconda3\envs\mescore\lib\multiprocessing\popen_spawn_win32.py", line 93, in init reduction.dump(process_obj, to_child) File "C:\Users\zhouys\anaconda3\envs\mescore\lib\multiprocessing\reduction.py", line 60, in dump ForkingPickler(file, protocol).dump(obj) File "", line 2, in av.container.output.OutputContainer.__reduce_cython TypeError: no default reduce due to non-trivial cinit__ 10:18:57

TypeError Traceback (most recent call last) File ~\anaconda3\envs\mescore\lib\site-packages\fastplotlib\layouts_frame_ipywidget_toolbar.py:179, in IpywidgetToolBar.record_plot(self, obj) 178 try: --> 179 self.plot.recordstart( 180 f"./{datetime.now().isoformat(timespec='seconds').replace(':', '')}.mp4" 181 ) 182 except Exception:

File ~\anaconda3\envs\mescore\lib\site-packages\fastplotlib\layouts_record_mixin.py:208, in RecordMixin.record_start(self, path, fps, codec, pixel_format, options) 207 # start writer process --> 208 self._video_writer.start() 210 # 1.3 seems to work well to reduce that difference between playback time and recording time 211 # will properly investigate later

File ~\anaconda3\envs\mescore\lib\multiprocessing\process.py:121, in BaseProcess.start(self) 120 _cleanup() --> 121 self._popen = self._Popen(self) 122 self._sentinel = self._popen.sentinel

File ~\anaconda3\envs\mescore\lib\multiprocessing\context.py:224, in Process._Popen(process_obj) 222 @staticmethod 223 def _Popen(process_obj): --> 224 return _default_context.get_context().Process._Popen(process_obj)

File ~\anaconda3\envs\mescore\lib\multiprocessing\context.py:336, in SpawnProcess._Popen(process_obj) 335 from .popen_spawn_win32 import Popen --> 336 return Popen(process_obj)

File ~\anaconda3\envs\mescore\lib\multiprocessing\popen_spawn_win32.py:93, in Popen.init(self, process_obj) 92 reduction.dump(prep_data, to_child) ---> 93 reduction.dump(process_obj, to_child) 94 finally:

File ~\anaconda3\envs\mescore\lib\multiprocessing\reduction.py:60, in dump(obj, file, protocol) 59 '''Replacement for pickle.dump() using ForkingPickler.''' ---> 60 ForkingPickler(file, protocol).dump(obj)

File :2, in av.container.output.OutputContainer.__reduce_cython__()

TypeError: no default reduce due to non-trivial cinit

During handling of the above exception, another exception occurred:

AssertionError Traceback (most recent call last) File ~\anaconda3\envs\mescore\lib\site-packages\ipywidgets\widgets\widget.py:773, in Widget._handle_msg(self, msg) 771 if 'buffer_paths' in data: 772 _put_buffers(state, data['buffer_paths'], msg['buffers']) --> 773 self.set_state(state) 775 # Handle a state request. 776 elif method == 'request_state':

File ~\anaconda3\envs\mescore\lib\site-packages\ipywidgets\widgets\widget.py:650, in Widget.set_state(self, sync_data) 645 self._send(msg, buffers=echo_buffers) 647 # The order of these context managers is important. Properties must 648 # be locked when the hold_trait_notification context manager is 649 # released and notifications are fired. --> 650 with self._lock_property(**sync_data), self.hold_trait_notifications(): 651 for name in sync_data: 652 if name in self.keys:

File ~\anaconda3\envs\mescore\lib\contextlib.py:142, in _GeneratorContextManager.exit(self, typ, value, traceback) 140 if typ is None: 141 try: --> 142 next(self.gen) 143 except StopIteration: 144 return False

File ~\anaconda3\envs\mescore\lib\site-packages\traitlets\traitlets.py:1512, in HasTraits.hold_trait_notifications(self) 1510 for changes in cache.values(): 1511 for change in changes: -> 1512 self.notify_change(change)

File ~\anaconda3\envs\mescore\lib\site-packages\ipywidgets\widgets\widget.py:701, in Widget.notify_change(self, change) 698 if name in self.keys and self._should_send_property(name, getattr(self, name)): 699 # Send new state to front-end 700 self.send_state(key=name) --> 701 super().notify_change(change)

File ~\anaconda3\envs\mescore\lib\site-packages\traitlets\traitlets.py:1527, in HasTraits.notify_change(self, change) 1525 def notify_change(self, change: Bunch) -> None: 1526 """Notify observers of a change event""" -> 1527 return self._notify_observers(change)

File ~\anaconda3\envs\mescore\lib\site-packages\traitlets\traitlets.py:1570, in HasTraits._notify_observers(self, event) 1567 elif isinstance(c, EventHandler) and c.name is not None: 1568 c = getattr(self, c.name) -> 1570 c(event)

File ~\anaconda3\envs\mescore\lib\site-packages\fastplotlib\layouts_frame_ipywidget_toolbar.py:184, in IpywidgetToolBar.record_plot(self, obj) 182 except Exception: 183 traceback.print_exc() --> 184 self._record_button.value = False 185 else: 186 self.plot.record_stop()

File ~\anaconda3\envs\mescore\lib\site-packages\traitlets\traitlets.py:718, in TraitType.set(self, obj, value) 716 raise TraitError('The "%s" trait is read-only.' % self.name) 717 else: --> 718 self.set(obj, value)

File ~\anaconda3\envs\mescore\lib\site-packages\traitlets\traitlets.py:707, in TraitType.set(self, obj, value) 703 silent = False 704 if silent is not True: 705 # we explicitly compare silent to True just in case the equality 706 # comparison above returns something other than True/False --> 707 obj._notify_trait(self.name, old_value, new_value)

File ~\anaconda3\envs\mescore\lib\site-packages\traitlets\traitlets.py:1515, in HasTraits._notify_trait(self, name, old_value, new_value) 1514 def _notify_trait(self, name: str, old_value: t.Any, new_value: t.Any) -> None: -> 1515 self.notify_change( 1516 Bunch( 1517 name=name, 1518 old=old_value, 1519 new=new_value, 1520 owner=self, 1521 type="change", 1522 ) 1523 )

File ~\anaconda3\envs\mescore\lib\site-packages\ipywidgets\widgets\widget.py:701, in Widget.notify_change(self, change) 698 if name in self.keys and self._should_send_property(name, getattr(self, name)): 699 # Send new state to front-end 700 self.send_state(key=name) --> 701 super().notify_change(change)

File ~\anaconda3\envs\mescore\lib\site-packages\traitlets\traitlets.py:1527, in HasTraits.notify_change(self, change) 1525 def notify_change(self, change: Bunch) -> None: 1526 """Notify observers of a change event""" -> 1527 return self._notify_observers(change)

File ~\anaconda3\envs\mescore\lib\site-packages\traitlets\traitlets.py:1570, in HasTraits._notify_observers(self, event) 1567 elif isinstance(c, EventHandler) and c.name is not None: 1568 c = getattr(self, c.name) -> 1570 c(event)

File ~\anaconda3\envs\mescore\lib\site-packages\fastplotlib\layouts_frame_ipywidget_toolbar.py:186, in IpywidgetToolBar.record_plot(self, obj) 184 self._record_button.value = False 185 else: --> 186 self.plot.record_stop()

File ~\anaconda3\envs\mescore\lib\site-packages\fastplotlib\layouts_record_mixin.py:234, in RecordMixin.record_stop(self) 231 self._video_writer_queue.put(None) 233 # wait for writer to finish --> 234 self._video_writer.join(timeout=5) 236 self._video_writer = None 238 # so self._record() is no longer called on every render cycle

File ~\anaconda3\envs\mescore\lib\multiprocessing\process.py:148, in BaseProcess.join(self, timeout) 146 self._check_closed() 147 assert self._parent_pid == os.getpid(), 'can only join a child process' --> 148 assert self._popen is not None, 'can only join a started process' 149 res = self._popen.wait(timeout) 150 if res is not None:

AssertionError: can only join a started process

kushalkolar commented 12 months ago

Do you have pyav and ffmpeg installed?

qweasdf1354 commented 12 months ago

i install the ffmpeg early. although i can use ffmpeg to clip the video by cmd ffmpeg command, i am not sure i install the ffmpeg correctly and i never use pyav before

qweasdf1354 commented 12 months ago

I have got the df/f. thanks a lot kushalkolar! the software is a great work!

qweasdf1354 commented 12 months ago

the packgage in my mescore env have ffmpeg but pyav not find

kushalkolar commented 12 months ago

The fastplotlib record tool is in a primitive state and hasn't been tested on windows (which can be weird with ffmpeg and video stuff) so I would just use a screen recorder for now. This is generally a good screen recorder for windows: https://obsproject.com/

qweasdf1354 commented 12 months ago

I know OBS. This is a great tool and i use it to record animal behaviour previously. Are you mean recording the full screan instead of the user_interface? If that's what you mean, then I know what to do

kushalkolar commented 12 months ago

Yup you could record the full screen of the visualization or draw a box and record.

Right now we have several other priorities with fastplotlib, the recording is a "bonus" feature for now and it will be a few months before that feature gets ironed out.

qweasdf1354 commented 12 months ago

Hi, kushalkolar I appreciate to encounter the elegent tools for calcium extraction.

I would like to acknowledge your support in the acknowledgements section of my project which maybe accomplish recently. I believe that your assistance was instrumental in the progress and completion of our work.

Would you be comfortable with being mentioned in this context?

Thank you for considering this request, and please let me know your thoughts.

Best regards,

kushalkolar commented 12 months ago

That's nice to hear! For now you can cite our older mesmerize paper, I wonder if we'll do a preprint for the new stuff sometime: https://www.nature.com/articles/s41467-021-26550-y

Let us know if you need more help!

qweasdf1354 commented 12 months ago

Thanks a lot! I will cite the paper you mentioned and if preprint online please let me know. i will cite it all

kushalkolar commented 12 months ago

You should also cite the main algorithm papers (depending on which ones you're using) and the caiman paper:

caiman: https://elifesciences.org/articles/38173 motion correction: https://pubmed.ncbi.nlm.nih.gov/28782629/ CNMF (2p): https://pubmed.ncbi.nlm.nih.gov/26774160/ CNMFE (if you're using 1p): https://pubmed.ncbi.nlm.nih.gov/29469809/

kushalkolar commented 12 months ago

I just noticed you had more questions, answer below:

3.After run 'Run the cnmf batch items' and 'Load outputs', i try to 'Visualize with mesmerize-viz'. However i not like the mcorr that give me 9 subplot pannel, it give me only one user_surface like i first run the viz when i havent to paraSearch. Is it something i lost? how can i see the total parameters?

Not sure what you mean here?

I also wanna to know how to see the all counters when i running the '''viz_cnmf.show()''' and not scrolling the 'cell contours' bar. if i change the scrolling bar i can not find way to go back to see the full image.

The toolbar has buttons to auto scale, center the scene, etc. You can uncheck the auto-zoom or change the scale. See https://github.com/kushalkolar/mesmerize-viz#explore-components

In the bottom pannel, what is 'contour co...' what is accepted rejected?snr_comps and so on. and what is 'invisible al...' and what is eval params

You can color the contours based on evaluation metrics or display the accepted/rejected components. The components are accepted or rejeted based on the eval metrics (this is from caiman). See: https://github.com/kushalkolar/mesmerize-viz#visualize-component-evaluation-metrics

4.the last question is could I plot the contours of all cells and i sellected cells? using ' get contours' can satisfy my purpose? purpose: I wanna to plot all contours in grey and some selected contours in color.

Yes, you can index a fastplotlib line collection like this:

contours_coordinates, centers_of_mass = df.iloc[index].cnmf.get_contours()

plot.add_line_collection(contours_coordinates, name="contours")

gray_ixs = np.array([1, 3, 5, 7])
red_ixs = np.array([2, 4, 6, 8])

plot["contours"][gray_ixs].colors = "gray"
plot["contours"][red_ixs].colors = "red"

And could i plot the contours in the tiff of my raw tif or the style in the mcorr i adjuest [viz.image_widget.gridplot["mcorr"]["image_widget_managed"].cmap.vmax = 2000][viz.image_widget.cmap = "viridis"].

I don't understand what you mean here sorry.

Our scipy talk is a good way to get familiar with fastplotlib: https://www.youtube.com/watch?v=Q-UJpAqljsU

Demo nbs from the talk: https://github.com/fastplotlib/fastplotlib-scipy2023

Note that the demo nbs are slightly out of date, the sidecar stuff is not necessary anymore (you can use show(sidecar=True) to display in sidecar).

qweasdf1354 commented 12 months ago

Thanks kushalkolar! almost everything is done and the previous unclear thing is clear right now. Thank you once again, and I'm amazed at having such a great tool. Looking forward your future work!

qweasdf1354 commented 12 months ago

Hi kushalkolar, i got a problem when i deal with my data. I have 4 tif file (5000,5000,5000,1000 frames) which is the same visual field and I wanna to detect cell across the 4 tif file. I mean the same cell will appear in the all tif. if there any method to identify the same cells? or use one contours to detect all 4 tif deltaF/F?

qweasdf1354 commented 12 months ago

and could i got the [Deconvolution and demixing of calcium imaging data]?

qweasdf1354 commented 12 months ago

it is support big tif format?

kushalkolar commented 12 months ago

Concatenating the tiff files is the easiest way to go as long as these aren't different sessions where the plane is slightly different or some cells that are in one file are not in the other. If that's the case you'll have to do multi-session registration with caiman.

If you want deconvolution, the spike estimates are in cnmf_obj.estimates.S. However I'd recommend looking at CASCADE which is better for deconvolution: https://github.com/HelmchenLabSoftware/Cascade

Yes caiman works with bigtiff.

qweasdf1354 commented 12 months ago

that is great! concatenating the tiff files is sufficient! Thanks a lot!

qweasdf1354 commented 12 months ago

Thank you. I've heard of CASCADE before, and I'll try CASCADE.

qweasdf1354 commented 12 months ago

Hi kushalkolar, sorry to bother you again. i use the folloing code to concate 4 tif file, but when i use mescore, the error occur

import tifffile as tf
import numpy as np

def concatenate_tiffs(tiff_paths, output_path):
    tiffs = [tf.imread(tiff_path) for tiff_path in tiff_paths]
    concatenated = np.vstack(tiffs)
    tf.imwrite(output_path, concatenated)

# Paths to your tiff files and desired output
input_files = [
    'CellVideo_0_E_20_Iter_6030_output.tif',
    'CellVideo_1_E_20_Iter_6030_output.tif',
    'CellVideo_2_E_20_Iter_6030_output.tif',
    'CellVideo_3_E_20_Iter_6030_output.tif'
]
output_file = 'Concatenated_output.tif'

# Concatenate and save
concatenate_tiffs(input_files, output_file)

# Inspect the resulting TIFF
def inspect_tiff(file_path):
    with tf.TiffFile(file_path) as tiff:
        image = tiff.asarray()
        print(f"File: {file_path}")
        print(f"Shape: {image.shape}")
        print(f"Data type: {image.dtype}\n")

inspect_tiff(output_file)

when i run df.iloc[0].caiman.run() in mocrr

the following error occur

Running 2b1d769e-a57d-4412-b5ab-628bfacbfbfa with local backend
starting mc
mc failed, stored traceback in output
<mesmerize_core.caiman_extensions.common.DummyProcess at 0x271a6cf69b0>

i check using the original tif is work.

kushalkolar commented 12 months ago

mc failed, stored traceback in output

The output will print the traceback, df.iloc[index].mcorr.get_output()

qweasdf1354 commented 12 months ago

Hi kushalkolar! the following is the error it seems the RAM is not enough. when i run the bigtif the total 32GB RAM is used and maybe the transition step have not enough RAM to go ahead. it maybe ok, i will try it in the more powerful workstation which have 512GB RAM.

`--------------------------------------------------------------------------- BatchItemUnsuccessfulError Traceback (most recent call last) Cell In[23], line 1 ----> 1 df.iloc[0].mcorr.get_output()

File ~\anaconda3\envs\mescore\lib\site-packages\mesmerize_core\caiman_extensions_utils.py:24, in validate..dec..wrapper(self, *args, *kwargs) 22 if not self._series["outputs"]["success"]: 23 tb = self._series["outputs"]["traceback"] ---> 24 raise BatchItemUnsuccessfulError(f"Batch item was unsuccessful, traceback from subprocess:\n{tb}") 25 return func(self, args, **kwargs)

BatchItemUnsuccessfulError: Batch item was unsuccessful, traceback from subprocess: multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "C:\Users\zhouys\anaconda3\envs\mescore\lib\multiprocessing\pool.py", line 125, in worker result = (True, func(*args, kwds)) File "C:\Users\zhouys\anaconda3\envs\mescore\lib\multiprocessing\pool.py", line 48, in mapstar return list(map(args)) File "C:\Users\zhouys\anaconda3\envs\mescore\lib\site-packages\caiman\motion_correction.py", line 3116, in tile_and_correct_wrapper outv[:, idxs] = np.reshape( File "C:\Users\zhouys\anaconda3\envs\mescore\lib\site-packages\numpy\core\fromnumeric.py", line 285, in reshape return _wrapfunc(a, 'reshape', newshape, order=order) File "C:\Users\zhouys\anaconda3\envs\mescore\lib\site-packages\numpy\core\fromnumeric.py", line 59, in _wrapfunc return bound(args, kwds) numpy.core._exceptions._ArrayMemoryError: Unable to allocate 1.31 GiB for an array with shape (1143, 512, 600) and data type float32 """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "C:\Users\zhouys\anaconda3\envs\mescore\lib\site-packages\mesmerize_core\algorithms\mcorr.py", line 67, in run_algo mc.motion_correct(save_movie=True) File "C:\Users\zhouys\anaconda3\envs\mescore\lib\site-packages\caiman\motion_correction.py", line 252, in motion_correct self.motion_correct_pwrigid(template=template, save_movie=save_movie) File "C:\Users\zhouys\anaconda3\envs\mescore\lib\site-packages\caiman\motion_correction.py", line 366, in motion_correct_pwrigid _x_shifts_els, _y_shifts_els, _z_shifts_els, _coord_shifts_els = motion_correct_batch_pwrigid( File "C:\Users\zhouys\anaconda3\envs\mescore\lib\site-packages\caiman\motion_correction.py", line 3004, in motion_correct_batch_pwrigid fname_tot_els, res_el = motion_correction_piecewise(fname, splits, strides, overlaps, File "C:\Users\zhouys\anaconda3\envs\mescore\lib\site-packages\caiman\motion_correction.py", line 3194, in motion_correction_piecewise res = dview.map_async(tile_and_correct_wrapper, pars).get(4294967) File "C:\Users\zhouys\anaconda3\envs\mescore\lib\multiprocessing\pool.py", line 774, in get raise self._value numpy.core._exceptions._ArrayMemoryError: Unable to allocate 1.31 GiB for an array with shape (1143, 512, 600) and data type float32`

qweasdf1354 commented 12 months ago

Hi kushalkolar! I use the workstation using ubuntu18.04 to run the code and i found the cpu utilization is high(almost 100%) however, after 2-3 min, the cpu utility is low is that normal?

`top - 23:18:34 up 3:26, 1 user, load average: 0.59, 0.34, 0.38 Tasks: 1594 total, 1 running, 884 sleeping, 0 stopped, 127 zombie %Cpu(s): 0.1 us, 0.0 sy, 0.0 ni, 99.9 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st KiB Mem : 52798528+total, 43617897+free, 5901760 used, 85904544 buff/cache KiB Swap: 2097148 total, 2097148 free, 0 used. 51861302+avail Mem

PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
3220 ps 20 0 12.874g 565596 131612 S 4.9 0.1 12:38.48 gnome-she+ 3075 root 20 0 26.619g 134668 102500 S 4.6 0.0 6:23.61 Xorg
4510 ps 20 0 823732 47432 31012 S 3.0 0.0 4:41.79 gnome-ter+ 22444 ps 20 0 47616 6036 3628 R 1.6 0.0 0:44.35 top
21449 ps 20 0 591372 156076 27164 S 1.3 0.0 0:32.52 jupyter-l+ 2534 root -51 0 0 0 0 S 1.0 0.0 2:02.04 irq/435-n+ 3242 ps 9 -11 2572872 17544 13872 S 1.0 0.0 0:51.22 pulseaudio 3676 ps 20 0 4868900 776820 291272 S 1.0 0.1 29:36.83 firefox
16029 ps 20 0 993340 175588 107888 S 1.0 0.0 1:05.60 software-+ 21182 ps 20 0 2844032 243596 102096 S 1.0 0.0 1:22.36 Isolated + 3551 ps 20 0 1137800 74176 59836 S 0.7 0.0 0:03.08 nautilus-+ 1 root 20 0 225768 9516 6740 S 0.3 0.0 0:15.60 systemd
11 root 20 0 0 0 0 I 0.3 0.0 0:04.67 rcu_sched
1223 root 20 0 0 0 0 S 0.3 0.0 0:01.49 jbd2/nvme+ 2170 avahi 20 0 47288 3836 3304 S 0.3 0.0 0:01.69 avahi-dae`

kushalkolar commented 12 months ago

What are you running?

qweasdf1354 commented 11 months ago

I run the mcorr using the caimam.run function and i found in windows it prompt the max threding in windows is 63 and there are 129 . so i using the ubuntu to run the code and there is normal and not error prompt. however after 1 or 2 minutes the utilitys of python processes disappear which the utility is almost 100%. and i stuck in starting mc near 1 hour and can not go to the next step and i shutt down the process. i notice there may be something unexpected. i use miniforege3 to using mamba.

qweasdf1354 commented 11 months ago

Hi kushalkolar! i am looking forward for your help. thanks a lot

I run the mcorr using the caimam.run function and i found in windows it prompt the max threding in windows is 63 and there are 129 . so i using the ubuntu to run the code and there is normal and not error prompt. however after 1 or 2 minutes the utilitys of python processes disappear which the utility is almost 100%. and i stuck in starting mc near 1 hour and can not go to the next step and i shutt down the process. i notice there may be something unexpected. i use miniforege3 to using mamba.

qweasdf1354 commented 11 months ago

i have not intall viz on ubuntu and i install this them. however i meet error i can not install pyqt6 in the mescore env. the following error occur

`pip install PyQt6 --index-url https://pypi.org/simple/ Looking in indexes: https://pypi.org/simple/ Collecting PyQt6 Using cached PyQt6-6.6.0.tar.gz (1.0 MB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... error error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [20 lines of output] Querying qmake about your Qt installation... Traceback (most recent call last): File "/home/ps/miniforge3/envs/mescore/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in main() File "/home/ps/miniforge3/envs/mescore/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main json_out['return_val'] = hook(**hook_input['kwargs']) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/ps/miniforge3/envs/mescore/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 152, in prepare_metadata_for_build_wheel whl_basename = backend.build_wheel(metadata_directory, config_settings) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/pip-build-env-xeavatqa/overlay/lib/python3.11/site-packages/sipbuild/api.py", line 46, in build_wheel project = AbstractProject.bootstrap('wheel', ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/pip-build-env-xeavatqa/overlay/lib/python3.11/site-packages/sipbuild/abstract_project.py", line 87, in bootstrap project.setup(pyproject, tool, tool_description) File "/tmp/pip-build-env-xeavatqa/overlay/lib/python3.11/site-packages/sipbuild/project.py", line 602, in setup self.update(tool) File "/tmp/pip-install-t4a9rybh/pyqt6_085b72a7bd0d446a80c2ab8321c31d1d/project.py", line 163, in update raise UserException( sipbuild.exceptions.UserException [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed

× Encountered error while generating package metadata. ╰─> See above for output.

note: This is an issue with the package mentioned above, not pip. hint: See above for details. `

nel-lab / mesmerize-core

TypeError: Graphic.init() got an unexpected keyword argument 'vmin_vmax_sliders' #240

Hi author, i have some issues, could you help me to resovle?

'''

conda environments:

packages in environment at C:\Users\zhouys\anaconda3\envs\mescore:

Name Version Build Channel

nel-lab / mesmerize-core

TypeError: Graphic.__init__() got an unexpected keyword argument 'vmin_vmax_sliders' #240

Hi author, i have some issues, could you help me to resovle?

'''

conda environments:

packages in environment at C:\Users\zhouys\anaconda3\envs\mescore:

Name Version Build Channel

TypeError: Graphic.init() got an unexpected keyword argument 'vmin_vmax_sliders' #240