Append ROI data

[aurquieta]

Not able to append ROI data. Task has 1 animal in a maze spontaneous alternation, and I am trying to calculate ROI directionality but keep getting the following error:

Exception in Tkinter callback
Traceback (most recent call last):
File "C:\ProgramData\miniconda3\envs\simba\lib\tkinter_init_.py", line 1705, in call
return self.func(*args)
File "C:\ProgramData\miniconda3\envs\simba\lib\site-packages\simba\ui\tkinter_functions.py", line 436, in execute_command
cmd(**evaluated_kwargs)
File "C:\ProgramData\miniconda3\envs\simba\lib\site-packages\simba\ui\pop_ups\append_roi_features_bodypart_pop_up.py", line 32, in run
threading.Thread(target=roi_feature_creator.run()).start()
File "C:\ProgramData\miniconda3\envs\simba\lib\site-packages\simba\roi_tools\ROI_feature_analyzer.py", line 198, in run
self.out_df[c].mean().round(4),
AttributeError: 'float' object has no attribute 'round'

I tried as well to change csv data file to have the values as np.float64 values, but still got the same error.
I'll attach my features_extracted as well. Is there anything I am doing wrong? Please let me know, thanks!

Using anaconda and python version is 3.6.13

sa79m7_1_23.csv

[sronilsson]

Thanks for reporting @aurquieta - seems like a bug that we should fix. I tried the code on some test projects I have but couldn't immediately replicate the error. Before I dig, could you let me know which version of SimBA you are running? You can find out by typing pip show simba-uw-tf-dev in the SimBA environment.

[aurquieta]

Thanks for the quick reply!! It's version 2.5.1

[sronilsson]

Thanks, let me insert something that will take care of this.

... I assume its becase self.out_df[c].mean() returns a float, and .round(4) is a pandas DataFrame method which expects.. a dataframe. As I said I can't for some reason replicate the error, but something like round(results[c].mean(), 4) should fix it.

... anyway, I will update the code (it looks a little dated) and get back to you.

[sronilsson]

@aurquieta if you update SimBA with pip install simba-uw-tf-dev --upgrade (to version 2.6.3) - can you let me know how it runs on your end? If there are any errors, please let me know what you see.

thanks!
Simon

[aurquieta]

So I have an error here:

Requirement already satisfied: simba-uw-tf-dev in c:\programdata\miniconda3\envs\simba\lib\site-packages (2.5.1)
Collecting simba-uw-tf-dev
Downloading simba_uw_tf_dev-2.6.3-py3-none-any.whl (7.1 MB)
|████████████████████████████████| 7.1 MB 3.2 MB/s
Requirement already satisfied: plotly==4.9.0 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (4.9.0)
Requirement already satisfied: tabulate==0.8.3 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.8.3)
Requirement already satisfied: shapely==1.8.0 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (1.8.0)
Collecting xlrd==1.2.0
Using cached xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
Requirement already satisfied: cefpython3==66.0 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (66.0)
Requirement already satisfied: imgaug==0.4.0 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.4.0)
Collecting statsmodels==0.12.0
Using cached statsmodels-0.12.0-cp36-none-win_amd64.whl (9.1 MB)
Requirement already satisfied: geos==0.2.3 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.2.3)
Requirement already satisfied: pandas==0.25.3 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.25.3)
Collecting seaborn==0.11.0
Using cached seaborn-0.11.0-py3-none-any.whl (283 kB)
Requirement already satisfied: tables==3.6.1 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (3.6.1)
Requirement already satisfied: numexpr==2.6.9 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (2.6.9)
Requirement already satisfied: matplotlib==3.3.4 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (3.3.4)
Requirement already satisfied: psutil==5.9.8 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (5.9.8)
Requirement already satisfied: scikit-image==0.17.2 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.17.2)
Requirement already satisfied: dtreeviz==0.8.1 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.8.1)
Requirement already satisfied: numpy==1.19.1 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (1.19.1)
Collecting numba==0.52.0
Using cached numba-0.52.0-cp36-cp36m-win_amd64.whl (2.3 MB)
Requirement already satisfied: dash-color-picker==0.0.1 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.0.1)
Requirement already satisfied: openpyxl==3.1.2 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (3.1.2)
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Requirement already satisfied: xgboost==0.90 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.90)
Requirement already satisfied: shap==0.35.0 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.35.0)
Requirement already satisfied: scipy==1.5.4 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (1.5.4)
Requirement already satisfied: yellowbrick==0.9.1 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.9.1)
Requirement already satisfied: Pillow==8.3.2 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (8.3.2)
Requirement already satisfied: ffmpeg-python==0.2.0 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.2.0)
Requirement already satisfied: imbalanced-learn==0.6.2 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.6.2)
Requirement already satisfied: kaleido==0.1.0 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.1.0)
Requirement already satisfied: dash-html-components==1.0.3 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (1.0.3)
Requirement already satisfied: eli5==0.10.1 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.10.1)
Requirement already satisfied: pyarrow==6.0.1 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (6.0.1)
Requirement already satisfied: dash==1.14.0 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (1.14.0)
Collecting pyyaml==5.3.1
Using cached PyYAML-5.3.1-cp36-cp36m-win_amd64.whl (215 kB)
Collecting h5py==2.9.0
Using cached h5py-2.9.0-cp36-cp36m-win_amd64.whl (2.4 MB)
Requirement already satisfied: pyvis==0.3.2 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.3.2)
Requirement already satisfied: imutils==0.5.2 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.5.2)
Requirement already satisfied: tqdm==4.30.0 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (4.30.0)
Requirement already satisfied: joblib==1.1.1 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (1.1.1)
Requirement already satisfied: pyglet==1.5.27 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (1.5.27)
Requirement already satisfied: scikit-learn==0.22.2 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.22.2)
Requirement already satisfied: opencv-python==3.4.5.20 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (3.4.5.20)
Requirement already satisfied: dash-colorscales==0.0.4 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.0.4)
Requirement already satisfied: dash-core-components==1.10.2 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (1.10.2)
Requirement already satisfied: graphviz==0.11 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from simba-uw-tf-dev) (0.11)
Requirement already satisfied: Flask>=1.0.2 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from dash==1.14.0->simba-uw-tf-dev) (2.0.3)
Requirement already satisfied: dash-renderer==1.6.0 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from dash==1.14.0->simba-uw-tf-dev) (1.6.0)
Requirement already satisfied: flask-compress in c:\programdata\miniconda3\envs\simba\lib\site-packages (from dash==1.14.0->simba-uw-tf-dev) (1.15)
Requirement already satisfied: dash-table==4.9.0 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from dash==1.14.0->simba-uw-tf-dev) (4.9.0)
Requirement already satisfied: future in c:\programdata\miniconda3\envs\simba\lib\site-packages (from dash==1.14.0->simba-uw-tf-dev) (1.0.0)
Requirement already satisfied: colour in c:\programdata\miniconda3\envs\simba\lib\site-packages (from dtreeviz==0.8.1->simba-uw-tf-dev) (0.1.5)
Requirement already satisfied: attrs>16.0.0 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from eli5==0.10.1->simba-uw-tf-dev) (22.2.0)
Requirement already satisfied: six in c:\programdata\miniconda3\envs\simba\lib\site-packages (from eli5==0.10.1->simba-uw-tf-dev) (1.17.0)
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Requirement already satisfied: imageio in c:\programdata\miniconda3\envs\simba\lib\site-packages (from imgaug==0.4.0->simba-uw-tf-dev) (2.15.0)
Requirement already satisfied: cycler>=0.10 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from matplotlib==3.3.4->simba-uw-tf-dev) (0.11.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from matplotlib==3.3.4->simba-uw-tf-dev) (3.1.4)
Requirement already satisfied: kiwisolver>=1.0.1 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from matplotlib==3.3.4->simba-uw-tf-dev) (1.3.1)
Requirement already satisfied: python-dateutil>=2.1 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from matplotlib==3.3.4->simba-uw-tf-dev) (2.9.0.post0)
Requirement already satisfied: setuptools in c:\programdata\miniconda3\envs\simba\lib\site-packages (from numba==0.52.0->simba-uw-tf-dev) (59.6.0)
Collecting llvmlite<0.36,>=0.35.0
Using cached llvmlite-0.35.0-cp36-cp36m-win_amd64.whl (16.0 MB)
Requirement already satisfied: et-xmlfile in c:\programdata\miniconda3\envs\simba\lib\site-packages (from openpyxl==3.1.2->simba-uw-tf-dev) (1.1.0)
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Requirement already satisfied: ipython>=5.3.0 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from pyvis==0.3.2->simba-uw-tf-dev) (7.16.3)
Requirement already satisfied: jsonpickle>=1.4.1 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from pyvis==0.3.2->simba-uw-tf-dev) (2.2.0)
Requirement already satisfied: tifffile>=2019.7.26 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from scikit-image==0.17.2->simba-uw-tf-dev) (2020.10.1)
Requirement already satisfied: PyWavelets>=1.1.1 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from scikit-image==0.17.2->simba-uw-tf-dev) (1.1.1)
Requirement already satisfied: patsy>=0.5 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from statsmodels==0.12.0->simba-uw-tf-dev) (1.0.1)
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Requirement already satisfied: click>=7.1.2 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from Flask>=1.0.2->dash==1.14.0->simba-uw-tf-dev) (8.0.4)
Requirement already satisfied: itsdangerous>=2.0 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from Flask>=1.0.2->dash==1.14.0->simba-uw-tf-dev) (2.0.1)
Requirement already satisfied: colorama in c:\programdata\miniconda3\envs\simba\lib\site-packages (from click>=7.1.2->Flask>=1.0.2->dash==1.14.0->simba-uw-tf-dev) (0.4.5)
Requirement already satisfied: importlib-metadata in c:\programdata\miniconda3\envs\simba\lib\site-packages (from click>=7.1.2->Flask>=1.0.2->dash==1.14.0->simba-uw-tf-dev) (4.8.3)
Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from ipython>=5.3.0->pyvis==0.3.2->simba-uw-tf-dev) (3.0.36)
Requirement already satisfied: jedi<=0.17.2,>=0.10 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from ipython>=5.3.0->pyvis==0.3.2->simba-uw-tf-dev) (0.17.2)
Requirement already satisfied: pygments in c:\programdata\miniconda3\envs\simba\lib\site-packages (from ipython>=5.3.0->pyvis==0.3.2->simba-uw-tf-dev) (2.14.0)
Requirement already satisfied: pickleshare in c:\programdata\miniconda3\envs\simba\lib\site-packages (from ipython>=5.3.0->pyvis==0.3.2->simba-uw-tf-dev) (0.7.5)
Requirement already satisfied: decorator in c:\programdata\miniconda3\envs\simba\lib\site-packages (from ipython>=5.3.0->pyvis==0.3.2->simba-uw-tf-dev) (4.4.2)
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Requirement already satisfied: MarkupSafe>=2.0 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from jinja2->eli5==0.10.1->simba-uw-tf-dev) (2.0.1)
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Requirement already satisfied: ipython-genutils in c:\programdata\miniconda3\envs\simba\lib\site-packages (from traitlets>=4.2->ipython>=5.3.0->pyvis==0.3.2->simba-uw-tf-dev) (0.2.0)
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Requirement already satisfied: typing-extensions>=3.6.4 in c:\programdata\miniconda3\envs\simba\lib\site-packages (from importlib-metadata->click>=7.1.2->Flask>=1.0.2->dash==1.14.0->simba-uw-tf-dev) (4.1.1)
Installing collected packages: llvmlite, xlrd, statsmodels, seaborn, pyyaml, numba, h5py, simba-uw-tf-dev
Attempting uninstall: llvmlite
Found existing installation: llvmlite 0.36.0
ERROR: Cannot uninstall 'llvmlite'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.

What should I do, could this llvmlite be the issue?

[sronilsson]

It seems like something python related may be running, potentially, or something permission related?

None of the requirements have changed though from the SImBA version you have installed. If you flag that you don't want to change any dependencies with the command below, how does it run?

pip install simba-uw-tf-dev --upgrade --no-deps

[aurquieta]

Okay it updated well:
Requirement already satisfied: simba-uw-tf-dev in c:\programdata\miniconda3\envs\simba\lib\site-packages (2.5.1)
Collecting simba-uw-tf-dev
Using cached simba_uw_tf_dev-2.6.3-py3-none-any.whl (7.1 MB)
Installing collected packages: simba-uw-tf-dev
Attempting uninstall: simba-uw-tf-dev
Found existing installation: simba-uw-tf-dev 2.5.1
Uninstalling simba-uw-tf-dev-2.5.1:
Successfully uninstalled simba-uw-tf-dev-2.5.1
Successfully installed simba-uw-tf-dev-2.6.3

I'll check if directionality is working now, thanks!