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unexpected keyword argument 'net_avg' error when loading cellpose model #481

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ptlzon opened this issue Feb 19, 2024 · 5 comments
Open

unexpected keyword argument 'net_avg' error when loading cellpose model #481

ptlzon opened this issue Feb 19, 2024 · 5 comments
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🐛 Bug Something isn't working

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@ptlzon
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ptlzon commented Feb 19, 2024

Description:

after settings parameters in cellpose parameters window, error appeared.

image

Way to reproduce:

No response

(Optional) Link to data to reproduce error:

No response

Terminal output:

19-02-2024, 17:03:21 - cellacdc-logger-acdc_gui - INFO:
------------------------
Initializing GUI v1.4.20
------------------------

19-02-2024, 17:03:21 - cellacdc-logger-acdc_gui - INFO:
------------------------
Initiliazing profilers...
------------------------

19-02-2024, 17:03:22 - cellacdc-logger-acdc_gui - INFO:
------------------------
GUI ready.
------------------------

19-02-2024, 17:03:24 - cellacdc-logger-acdc_gui - INFO:
------------------------
Asking to select a folder path...
------------------------

19-02-2024, 17:03:26 - cellacdc-logger-acdc_gui - INFO:
------------------------
Loading from D:/tmp/grayscale/train/20240219_161436_acdc/Images
------------------------

19-02-2024, 17:03:26 - cellacdc-logger-acdc_gui - INFO:
------------------------
Using .tif file (D:/tmp/grayscale/train/20240219_161436_acdc/Images\22-696-2_001.tif)...
------------------------

19-02-2024, 17:03:26 - cellacdc-logger-acdc_gui - INFO:
------------------------
Reading  channel metadata...
------------------------

19-02-2024, 17:03:26 - cellacdc-logger-acdc_gui - INFO:
------------------------
Lazy loader paused.
------------------------

19-02-2024, 17:03:26 - cellacdc-logger-acdc_gui - INFO:
------------------------
Closing lazy loader...
------------------------

19-02-2024, 17:03:27 - cellacdc-logger-acdc_gui - INFO:
------------------------
Segmentation filename: D:/tmp/grayscale/train/20240219_161436_acdc/Images\22-696-2_001_segm.npz
------------------------

19-02-2024, 17:03:28 - cellacdc-logger-acdc_gui - INFO:
------------------------
Loading 20240219_161436_acdc\Images\22-696-2_001.tif...
------------------------

19-02-2024, 17:03:28 - cellacdc-logger-acdc_gui - INFO:
------------------------
Loaded paths:
Segmentation file name: 22-696-2_001_segm.npz
ACDC output file name 22-696-2_001_acdc_output.csv
------------------------

19-02-2024, 17:03:28 - cellacdc-logger-acdc_gui - INFO:
------------------------
Full dataset shape = Not Loaded
------------------------

19-02-2024, 17:03:28 - cellacdc-logger-acdc_gui - INFO:
------------------------
Loaded dataset shape = (1, 2304, 3072)
------------------------

19-02-2024, 17:03:28 - cellacdc-logger-acdc_gui - INFO:
------------------------
Number of frames = 1
------------------------

19-02-2024, 17:03:28 - cellacdc-logger-acdc_gui - INFO:
------------------------
Number of z-slices per frame = 1
------------------------

19-02-2024, 17:03:28 - cellacdc-logger-acdc_gui - INFO:
------------------------
Creating graphical items...
------------------------

19-02-2024, 17:03:28 - cellacdc-logger-acdc_gui - INFO:
------------------------
Initializing measurements...
------------------------

19-02-2024, 17:03:28 - cellacdc-logger-acdc_gui - INFO:
------------------------
Setting GUI mode to "Snapshots"...
------------------------

19-02-2024, 17:03:28 - cellacdc-logger-acdc_gui - INFO:
------------------------
20240219_161436_acdc || Basename: 22-696-2_001 || Segmented channel:  || Segmentation file name: _segm.npz
------------------------

19-02-2024, 17:03:28 - cellacdc-logger-acdc_gui - INFO:
------------------------
Autosaving worker started.
------------------------

19-02-2024, 17:03:35 - cellacdc-logger-acdc_gui - INFO:
------------------------
Importing cellpose...
------------------------

19-02-2024, 17:03:48 - cellacdc-logger-acdc_gui - ERROR:
------------------------
Traceback (most recent call last):
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\myutils.py", line 2592, in init_segm_model
    model = acdcSegment.Model(**init_kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\models\cellpose\acdcSegment.py", line 35, in __init__
    self.model = models.CellposeModel(
TypeError: __init__() got an unexpected keyword argument 'net_avg'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\__init__.py", line 368, in inner_function
    result = func(self, *args, **kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\gui.py", line 13719, in repeatSegm
    model = myutils.init_segm_model(acdcSegment, posData, win.init_kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\myutils.py", line 2863, in init_segm_model
    model = acdcSegment.Model(segm_data, **init_kwargs)
TypeError: __init__() got multiple values for argument 'model_type'

------------------------
Traceback (most recent call last):
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\myutils.py", line 2592, in init_segm_model
    model = acdcSegment.Model(**init_kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\models\cellpose\acdcSegment.py", line 35, in __init__
    self.model = models.CellposeModel(
TypeError: __init__() got an unexpected keyword argument 'net_avg'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\__init__.py", line 368, in inner_function
    result = func(self, *args, **kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\gui.py", line 13719, in repeatSegm
    model = myutils.init_segm_model(acdcSegment, posData, win.init_kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\myutils.py", line 2863, in init_segm_model
    model = acdcSegment.Model(segm_data, **init_kwargs)
TypeError: __init__() got multiple values for argument 'model_type'
19-02-2024, 17:03:48 - cellacdc-logger-acdc_gui - INFO:
------------------------
====================================
WARNING: Cell-ACDC is in error state. Please, restart.
====================================
------------------------

19-02-2024, 17:05:05 - cellacdc-logger-acdc_gui - ERROR:
------------------------
Traceback (most recent call last):
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\myutils.py", line 2592, in init_segm_model
    model = acdcSegment.Model(**init_kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\models\cellpose\acdcSegment.py", line 35, in __init__
    self.model = models.CellposeModel(
TypeError: __init__() got an unexpected keyword argument 'net_avg'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\__init__.py", line 368, in inner_function
    result = func(self, *args, **kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\gui.py", line 13719, in repeatSegm
    model = myutils.init_segm_model(acdcSegment, posData, win.init_kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\myutils.py", line 2863, in init_segm_model
    model = acdcSegment.Model(segm_data, **init_kwargs)
TypeError: __init__() got multiple values for argument 'model_type'

------------------------
Traceback (most recent call last):
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\myutils.py", line 2592, in init_segm_model
    model = acdcSegment.Model(**init_kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\models\cellpose\acdcSegment.py", line 35, in __init__
    self.model = models.CellposeModel(
TypeError: __init__() got an unexpected keyword argument 'net_avg'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\__init__.py", line 368, in inner_function
    result = func(self, *args, **kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\gui.py", line 13719, in repeatSegm
    model = myutils.init_segm_model(acdcSegment, posData, win.init_kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\myutils.py", line 2863, in init_segm_model
    model = acdcSegment.Model(segm_data, **init_kwargs)
TypeError: __init__() got multiple values for argument 'model_type'
19-02-2024, 17:05:05 - cellacdc-logger-acdc_gui - INFO:
------------------------
====================================
WARNING: Cell-ACDC is in error state. Please, restart.
====================================
------------------------

Version information:

(acdc) D:\tmp>python -c "import sys; print(sys.version); import platform; print(platform.platform()); import cellacdc; print(f'Cell-ACDC version: {cellacdc.__version__}')"
3.9.18 | packaged by conda-forge | (main, Dec 23 2023, 16:29:04) [MSC v.1929 64 bit (AMD64)]
Windows-10-10.0.19045-SP0
Cell-ACDC version: 1.4.20
@ptlzon ptlzon added the 🐛 Bug Something isn't working label Feb 19, 2024
@ElpadoCan
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ElpadoCan commented Feb 19, 2024 •
edited
Loading

Hi @ptlzon, I see that you have Cell-ACDC version v1.4.20 and Cellpose v3 is not available with that version. Unfortunately, I did not realize that your version would install latest cellpose even if not compatible, sorry about that.

To fix this, I just released a new version v1.4.21 which is compatible with cellpose v3.

To upgrade activate the acdc environment and then run the command python -m pip install --upgrade cellacdc. Let me know if it works and thank you for your patience!

Best,
Francesco

@ptlzon
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ptlzon commented Feb 19, 2024 •
edited
Loading

Hi @ElpadoCan

The cellacdc v1.4.21 fixed the loading of SAM, but the error of Cellpose above still persisted.

Log

20-02-2024, 08:23:58 - cellacdc-logger-acdc_gui - INFO:
------------------------
Initializing GUI v1.4.21
------------------------

20-02-2024, 08:23:58 - cellacdc-logger-acdc_gui - INFO:
------------------------
Initiliazing profilers...
------------------------

20-02-2024, 08:23:58 - cellacdc-logger-acdc_gui - INFO:
------------------------
GUI ready.
------------------------

20-02-2024, 08:24:03 - cellacdc-logger-acdc_gui - INFO:
------------------------
Asking to select a folder path...
------------------------

20-02-2024, 08:24:05 - cellacdc-logger-acdc_gui - INFO:
------------------------
Loading from D:/tmp/grayscale/20240220_082140_acdc/Images
------------------------

20-02-2024, 08:24:05 - cellacdc-logger-acdc_gui - INFO:
------------------------
Using .tif file (D:/tmp/grayscale/20240220_082140_acdc/Images\9Z15003-1_crop.tif)...
------------------------

20-02-2024, 08:24:05 - cellacdc-logger-acdc_gui - INFO:
------------------------
Reading  channel metadata...
------------------------

20-02-2024, 08:24:05 - cellacdc-logger-acdc_gui - INFO:
------------------------
Lazy loader paused.
------------------------

20-02-2024, 08:24:05 - cellacdc-logger-acdc_gui - INFO:
------------------------
Closing lazy loader...
------------------------

20-02-2024, 08:24:06 - cellacdc-logger-acdc_gui - INFO:
------------------------
Segmentation filename: D:/tmp/grayscale/20240220_082140_acdc/Images\9Z15003-1_crop_segm.npz
------------------------

20-02-2024, 08:24:08 - cellacdc-logger-acdc_gui - INFO:
------------------------
Loading 20240220_082140_acdc\Images\9Z15003-1_crop.tif...
------------------------

20-02-2024, 08:24:08 - cellacdc-logger-acdc_gui - INFO:
------------------------
Loaded paths:
Segmentation file name: 9Z15003-1_crop_segm.npz
ACDC output file name 9Z15003-1_crop__acdc_output.csv
------------------------

20-02-2024, 08:24:08 - cellacdc-logger-acdc_gui - INFO:
------------------------
Full dataset shape = Not Loaded
------------------------

20-02-2024, 08:24:08 - cellacdc-logger-acdc_gui - INFO:
------------------------
Loaded dataset shape = (1, 424, 567)
------------------------

20-02-2024, 08:24:08 - cellacdc-logger-acdc_gui - INFO:
------------------------
Number of frames = 1
------------------------

20-02-2024, 08:24:08 - cellacdc-logger-acdc_gui - INFO:
------------------------
Number of z-slices per frame = 1
------------------------

20-02-2024, 08:24:08 - cellacdc-logger-acdc_gui - INFO:
------------------------
Creating graphical items...
------------------------

20-02-2024, 08:24:09 - cellacdc-logger-acdc_gui - INFO:
------------------------
Initializing measurements...
------------------------

20-02-2024, 08:24:09 - cellacdc-logger-acdc_gui - INFO:
------------------------
Setting GUI mode to "Snapshots"...
------------------------

20-02-2024, 08:24:09 - cellacdc-logger-acdc_gui - INFO:
------------------------
20240220_082140_acdc || Basename: 9Z15003-1_crop || Segmented channel:  || Segmentation file name: _segm.npz
------------------------

20-02-2024, 08:24:09 - cellacdc-logger-acdc_gui - INFO:
------------------------
Autosaving worker started.
------------------------

20-02-2024, 08:24:15 - cellacdc-logger-acdc_gui - INFO:
------------------------
Importing cellpose...
------------------------

20-02-2024, 08:24:32 - cellacdc-logger-acdc_gui - ERROR:
------------------------
Traceback (most recent call last):
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\myutils.py", line 2593, in init_segm_model
    model = acdcSegment.Model(**init_kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\models\cellpose\acdcSegment.py", line 35, in __init__
    self.model = models.CellposeModel(
TypeError: __init__() got an unexpected keyword argument 'net_avg'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\__init__.py", line 372, in inner_function
    result = func(self, *args, **kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\gui.py", line 13807, in repeatSegm
    model = myutils.init_segm_model(acdcSegment, posData, win.init_kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\myutils.py", line 2595, in init_segm_model
    model = acdcSegment.Model(segm_data, **init_kwargs)
TypeError: __init__() got multiple values for argument 'model_type'

------------------------
Traceback (most recent call last):
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\myutils.py", line 2593, in init_segm_model
    model = acdcSegment.Model(**init_kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\models\cellpose\acdcSegment.py", line 35, in __init__
    self.model = models.CellposeModel(
TypeError: __init__() got an unexpected keyword argument 'net_avg'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\__init__.py", line 372, in inner_function
    result = func(self, *args, **kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\gui.py", line 13807, in repeatSegm
    model = myutils.init_segm_model(acdcSegment, posData, win.init_kwargs)
  File "D:\miniconda3_windows\envs\acdc\lib\site-packages\cellacdc\myutils.py", line 2595, in init_segm_model
    model = acdcSegment.Model(segm_data, **init_kwargs)
TypeError: __init__() got multiple values for argument 'model_type'
20-02-2024, 08:24:32 - cellacdc-logger-acdc_gui - INFO:
------------------------
====================================
WARNING: Cell-ACDC is in error state. Please, restart.
====================================
------------------------

20-02-2024, 08:25:01 - cellacdc-logger-acdc_gui - INFO:
------------------------
Closing autosaving worker...
------------------------

20-02-2024, 08:25:01 - cellacdc-logger-acdc_gui - INFO:
------------------------
Autosaving worker closed.
------------------------

20-02-2024, 08:25:01 - cellacdc-logger-acdc_gui - INFO:
------------------------
Clearing memory...
------------------------

20-02-2024, 08:25:01 - cellacdc-logger-acdc_gui - INFO:
------------------------
Closing GUI logger...
------------------------

Version info

(acdc) C:\Users\Z036650>python -c "import sys; print(sys.version); import platform; print(platform.platform()); import cellacdc; print(f'Cell-ACDC version: {cellacdc.__version__}')"
3.9.18 | packaged by conda-forge | (main, Dec 23 2023, 16:29:04) [MSC v.1929 64 bit (AMD64)]
Windows-10-10.0.19045-SP0
Cell-ACDC version: 1.4.21

@ElpadoCan
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Hi @ptlzon, something went wrong with the release of v1.4.21 .

I fixed it now and I released v1.4.23. To upgrade activate the acdc environment and run python -m pip install --upgrade cellacdc.

As explained in #482 you can now run SAM with input points. Let me know if it works, thanks!

@ptlzon
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ptlzon commented Feb 21, 2024

Hi @ElpadoCan

Thanks for the amazingly quick fix.
Both cellpose v2 and cellpose v3 work as my expectation now.
Thanks a lot.

I will reply about SAM input points in that thread.

@ElpadoCan
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Nice, good to hear!

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@ElpadoCan @ptlzon