kushalkolar / mesmerize Goto Github PK

Platform for Calcium Imaging analysis. DEPRECATED.

License: GNU General Public License v3.0

Python 99.99% Shell 0.01%

calcium-imaging neuroscience interactive-visualizations plotting signal-processing calcium-imaging-analysis caiman pypi-package

mesmerize's Introduction

New Mesmerize Packages

The Mesmerize desktop application within this repo is no longer supported. Please checkout the new mesmerize packages which have longterm support.

These new packages are much easier to install! They are also much more efficient, versatile, and offer rich visualizations.

The batch management system offered by the new package is conceptually similar to the original Mesmerize desktop application, but it is much more efficient.

mesmerize-core: https://github.com/nel-lab/mesmerize-core
mesmerize-viz: https://github.com/kushalkolar/mesmerize-viz

mesmerize-viz is the new "GUI"

Motion correction visualization using mesmerize-viz

mesviz-mcorr.mp4

Explore CNMF variants

mesviz-variants.mp4

CNMF Componment Evaluation

mesviz-eval-interactive.mp4

gSig_filt viz for 1p mcorr

gsig_filt-2023-03-07_18.39.07.mp4

corr-pnr image viz for 1p CNMFE seeding

corr_pnr.mp4

mesmerize's People

Contributors

Stargazers

Watchers

Forkers

chatzigeorgiougroup tvajtay gitter-badger marrekko kevinj24fr ndominica asaleh33 danieldondorp pr4deepr richardyando ericthomson bpirka zmillan phaedrus2018

mesmerize's Issues

[FEATURE REQUEST] Option to save memmap files for caiman batch items

Some people might find the memmap files useful, should be simple to add a checkbox which prevents memmaps from being deleted if the user checks it.

HOME environment variable is not set on some Windows machines

For whatever reason, some (not all) Windows machines don't have the HOME env variable set by default. Perhaps find a more reliable way to get the user's dir on Windows.

  File "c:\users\nadtochi\anaconda\envs\try_me\lib\site-packages\mesmerize\viewer\main_window.py", line 137, in <lambda>
    self.ui.actionScript_Editor.triggered.connect(lambda: self.run_module(script_editor.ModuleGUI))
  File "c:\users\nadtochi\anaconda\envs\try_me\lib\site-packages\mesmerize\viewer\main_window.py", line 279, in run_module
    m = module_class(self, self._viewer)
  File "c:\users\nadtochi\anaconda\envs\try_me\lib\site-packages\mesmerize\viewer\modules\script_editor.py", line 27, in __init__
    self.open_temp_script()
  File "c:\users\nadtochi\anaconda\envs\try_me\lib\site-packages\mesmerize\viewer\modules\script_editor.py", line 72, in open_temp_script
    home_dir = os.environ['HOME']
  File "c:\users\nadtochi\anaconda\envs\try_me\lib\os.py", line 669, in __getitem__
    raise KeyError(key) from None
KeyError: 'HOME'

Motion correction error: ModuleNotFoundError: No module named 'caiman'

I am trying to run motion correction with my own data. I am following the video tutorial but when I start to run the batch for motion correction, I get the following error:

File "c:\users\panyi\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\viewer\modules\batch_run_modules\caiman_motion_correction.py", line 23, in
import caiman as cm
ModuleNotFoundError: No module named 'caiman'

Is there a way to solve this issue?
I have successfully installed the caiman manager using "caimanmanager.py install", but the caiman_data file is showing under the path "C:\Users\panyi". Is this an issue?

[FEATURE REQUEST] Add Rejected ROIs to the ROI Manager

Is your feature request related to a problem? Please describe.
Sometimes rejected ROI components generated by Caiman have activity of interest and easing the accept/reject threshold doesn't help. I sometimes like to see the rejected components.

Describe the solution or feature you'd like
Would it be possible to add rejected components on the .hdf5 import in the ROI Manager?

Do you think this feature will be useful for a broad range of users or is it very specific to your problem or particular analysis method

Broad range since rejected components can still be of potential interest to other users.

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Add any other context, a diagram or screenshots about the feature request here.

[INSTALLATION HELP]

Operating System & specs (CPU, RAM etc.)
MacOS Monterey, Apple M1 pro, 32GB RAM

Details about your Mesmerize install
Followed installation on the mesmerize document page for MacOS except for caiman installation.
Used "mamba create -n caiman -c conda-forge caiman" after "source activate mesmerize" as the original code gets stuck at solving environment

Describe the issue, please be as explicit and detailed as possible.
I have finished all installation steps, however when opening mesmerize, this is the error i am getting:

(mesmerize) kevin@Kevins-MacBook-Pro ~ % mesmerize
Traceback (most recent call last):
File "/opt/anaconda3/envs/mesmerize/bin/mesmerize", line 5, in
from mesmerize.main import main
File "/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/mesmerize/init.py", line 1, in
from .analysis import *
File "/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/mesmerize/analysis/init.py", line 1, in
from .data_types import Transmission
File "/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/mesmerize/analysis/data_types.py", line 14, in
import pandas as pd
File "/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/pandas/init.py", line 55, in
from pandas.core.api import (
File "/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/pandas/core/api.py", line 5, in
from pandas.core.arrays.integer import (
File "/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/pandas/core/arrays/init.py", line 13, in
from .sparse import SparseArray # noqa: F401
File "/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/pandas/core/arrays/sparse/init.py", line 3, in
from pandas.core.arrays.sparse.accessor import SparseAccessor, SparseFrameAccessor
File "/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/pandas/core/arrays/sparse/accessor.py", line 10, in
from pandas.core.arrays.sparse.array import SparseArray
File "/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/pandas/core/arrays/sparse/array.py", line 44, in
from pandas.core.arrays.sparse.dtype import SparseDtype
File "/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/pandas/core/arrays/sparse/dtype.py", line 9, in
from pandas._typing import Dtype, DtypeObj
ImportError: cannot import name 'DtypeObj'

How should I be able to solve this? Thank you!

ModuleNotFoundError: No module named 'caiman'

Operating System & specs (CPU, RAM etc.)

Windows, Intel Core i7, 16GB RAM

Details about your Mesmerize install

Followed installation on the mesmerize document page for windows.

Describe the issue, please be as explicit and detailed as possible.

I am trying to run motion correction with my own data. I am following the video tutorial but when I start to run the batch for motion correction, I get the following error:

Using mesmerize to select cells by tuning Caiman Quality parameters

With your help, I have successfully installed mesmerize and got caiman working in Windows 10.

I have already used caiman to correct for motion and detect cells from in vivo Calcium imaging datasets. I am trying to select good quality cells using the quality params of caiman. As the data is processed already as mentioned, i have the .mmap files, the corr and pnr files alongwith the cnm_estimates object saved as well.

I'd like to know how to use mesmerize to interactively tuning all quality params simultaneously (using sliders for instance) (rval_thr, use_cnn, min_snr etc) so that i can minimize false positives and also select all good quality cells (that are visually well defined, visible to the eye)

for example, in the above image, some cells are missed, many overlap.

Can you please tell me how to do this using mesmerize with the mmap file and cnm_Estimate obj?

RuntimeError Using CNMF Module

I am running the CNMF module on motion corrected tiff image. I am getting a runtime error. Below is entire traceback, thank you very much!

C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:516: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint8 = np.dtype([("qint8", np.int8, 1)])
C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint8 = np.dtype([("quint8", np.uint8, 1)])
C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint16 = np.dtype([("qint16", np.int16, 1)])
C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint16 = np.dtype([("quint16", np.uint16, 1)])
C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint32 = np.dtype([("qint32", np.int32, 1)])
C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_resource = np.dtype([("resource", np.ubyte, 1)])
C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:541: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint8 = np.dtype([("qint8", np.int8, 1)])
C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:542: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint8 = np.dtype([("quint8", np.uint8, 1)])
C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:543: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint16 = np.dtype([("qint16", np.int16, 1)])
C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:544: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint16 = np.dtype([("quint16", np.uint16, 1)])
C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint32 = np.dtype([("qint32", np.int32, 1)])
C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_resource = np.dtype([("resource", np.ubyte, 1)])
Traceback (most recent call last):
File "", line 1, in
File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 105, in spawn_main
exitcode = _main(fd)
File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 114, in _main
prepare(preparation_data)
File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 225, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 277, in _fixup_main_from_path
run_name="mp_main")
File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\runpy.py", line 263, in run_path
pkg_name=pkg_name, script_name=fname)
File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\runpy.py", line 96, in run_module_code
mod_name, mod_spec, pkg_name, script_name)
File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\runpy.py", line 85, in run_code
exec(code, run_globals)
File "c:\users\panyi\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\viewer\modules\batch_run_modules\CNMF.py", line 34, in
from mesmerize.common.utils import HdfTools
File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\mesmerize_init.py", line 1, in
from .analysis import *
File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\analysis_init.py", line 3, in
from .math import cross_correlation, drfft_dtw, tvregdiff
File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\analysis\math\drfft_dtw.py", line 17, in
raw_curve: np.ndarray = None, rf_curve: np.ndarray = None) -> list:
File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\context.py", line 56, in Manager
m.start()
File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\managers.py", line 513, in start
self._process.start()
File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\process.py", line 105, in start
self._popen = self._Popen(self)
File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\context.py", line 322, in _Popen
return Popen(process_obj)
File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\popen_spawn_win32.py", line 33, in init
prep_data = spawn.get_preparation_data(process_obj._name)
File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 143, in get_preparation_data
_check_not_importing_main()
File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 136, in _check_not_importing_main
is not going to be frozen to produce an executable.''')
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.

    This probably means that you are not using fork to start your
    child processes and you have forgotten to use the proper idiom
    in the main module:

        if __name__ == '__main__':
            freeze_support()
            ...

    The "freeze_support()" line can be omitted if the program
    is not going to be frozen to produce an executable.

===== 2020.12.28 21:12:31 =====

[BUG] ROIs in HDF5 file are not matching with their respective traces correctly

Describe the bug
If you were to create an HDF5 file from caiman commands in a jupyter notebook and load the the hdf5 file ROIs in mesmerize, there is a problem.

The traces load properly, and the ROI map loads properly. However, the traces do not correctly associate with the ROI. Below is an example. In the notebook, the trace is associated with an ROI (may be hard to see but it's a shadow overlay on the middle-left of the Bokeh figure. However, in mesmerize the same trace is associated with a different ROI.

I can share files associated with the photo privately if that works.

Operating System & specs (CPU, RAM etc.). Please complete the following information:

OS: Windows 10, 64 GB RAM, i7, GTX 3070

Details about your Mesmerize install

anaconda prompt installed mesmerize

[BUG] mesmerize sometimes hangs on logfile removal and will not open

Describe the bug
After using mesmerize successfully, when I try to start it again, I get the message that it cannot because some old logfiles are being used by another process.

To Reproduce
Steps to reproduce the behavior, for example:

Run mesmerize (sometimes a few times)
Start another instances of powershell, and the mesmerize environment, and try to start mesmerize.

Expected behavior
Mesmerize should start.

Copy paste message from the error window (if any)

EXCEPTION ENCOUNTERED
Traceback (most recent call last):
File "c:\users\lab_user\miniconda3\envs\mesmerize\lib\runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "c:\users\lab_user\miniconda3\envs\mesmerize\lib\runpy.py", line 85, in run_code
exec(code, run_globals)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\Scripts\mesmerize.exe_main.py", line 7, in
sys.exit(main())
File "c:\users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\click\core.py", line 1134, in call
return self.main(*args, **kwargs)
File "c:\users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\click\core.py", line 1059, in main
rv = self.invoke(ctx)
File "c:\users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\click\core.py", line 1401, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "c:\users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\click\core.py", line 767, in invoke
return callback(*args, **kwargs)
File "c:\users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\mesmerize_main.py", line 132, in main
move_old_logfiles(root_logger, log_file_dir)
File "c:\users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\mesmerize_main.py", line 75, in move_old_logfiles
os.remove(old_logfile)
PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\Users\lab_user\.mesmerize\2021-05-25_13.29.41-279226.log'
EXCEPTION ENCOUNTERED
Traceback (most recent call last):
File "c:\users\lab_user\miniconda3\envs\mesmerize\lib\runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "c:\users\lab_user\miniconda3\envs\mesmerize\lib\runpy.py", line 85, in run_code
exec(code, run_globals)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\Scripts\mesmerize.exe_main.py", line 7, in
sys.exit(main())
File "c:\users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\click\core.py", line 1134, in call
return self.main(*args, **kwargs)
File "c:\users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\click\core.py", line 1059, in main
rv = self.invoke(ctx)
File "c:\users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\click\core.py", line 1401, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "c:\users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\click\core.py", line 767, in invoke
return callback(*args, **kwargs)
File "c:\users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\mesmerize_main.py", line 132, in main
move_old_logfiles(root_logger, log_file_dir)
File "c:\users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\mesmerize_main.py", line 75, in move_old_logfiles
os.remove(old_logfile)
PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\Users\lab_user\.mesmerize\2021-05-25_13.29.41-279226.log'

Copy-paste or take a screenshot of the terminal that Mesmerize is running in

Operating System & specs (CPU, RAM etc.). Please complete the following information:
Windows 10, 128GB Ram

Details about your Mesmerize install
mamba for caiman, pip for mesmerize

Additional context
This has happened a few times. When I manually delete the log files things work fine.

Link for downloading data not allowing access

Hello,

I have tried opening the link to download the sample data files from several browsers but I get an error 'The connection was reset'. Please let me know what I'm doing wrong.
Thanks,
-Miranda

Probable multiprocessing issue on Windows 10

Need to confirm on another machine. Can probably be fixed with if __name___ == "__main__"

The term 'export' is not recognized as the name of a cmdlet, function, script f

ile, or operable program. Check the spelling of the name, or if a path was incl
uded, verify that the path is correct and try again.
At D:\NewFolder\PVC-7\fc94d298-5fc4-42ce-a399-3f7db8ac4e45.ps1:8 char:7
+ export <<<< OPENBLAS_NUM_THREADS=3
 + CategoryInfo : ObjectNotFound: (export:String) [], CommandNotFo
 undException
 + FullyQualifiedErrorId : CommandNotFoundException


C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:516: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
 _np_qint8 = np.dtype([("qint8", np.int8, 1)])
C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
 _np_quint8 = np.dtype([("quint8", np.uint8, 1)])
C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
 _np_qint16 = np.dtype([("qint16", np.int16, 1)])
C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
 _np_quint16 = np.dtype([("quint16", np.uint16, 1)])
C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
 _np_qint32 = np.dtype([("qint32", np.int32, 1)])
C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
 np_resource = np.dtype([("resource", np.ubyte, 1)])
C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:541: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
 _np_qint8 = np.dtype([("qint8", np.int8, 1)])
C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:542: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
 _np_quint8 = np.dtype([("quint8", np.uint8, 1)])
C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:543: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
 _np_qint16 = np.dtype([("qint16", np.int16, 1)])
C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:544: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
 _np_quint16 = np.dtype([("quint16", np.uint16, 1)])
C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
 _np_qint32 = np.dtype([("qint32", np.int32, 1)])
C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
 np_resource = np.dtype([("resource", np.ubyte, 1)])
C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\site-packages\sklearn\utils\deprecation.py:143: FutureWarning: The sklearn.cluster.k_means_ module is deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.cluster. Anything that cannot be imported from sklearn.cluster is now part of the private API.
 warnings.warn(message, FutureWarning)
Traceback (most recent call last):
 File "<string>", line 1, in <module>
 File "C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 105, in spawn_main
 exitcode = _main(fd)
 File "C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 114, in _main
 prepare(preparation_data)
 File "C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 225, in prepare
 _fixup_main_from_path(data['init_main_from_path'])
 File "C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 277, in _fixup_main_from_path
 run_name="__mp_main__")
 File "C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\runpy.py", line 263, in run_path
 pkg_name=pkg_name, script_name=fname)
 File "C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\runpy.py", line 96, in _run_module_code
 mod_name, mod_spec, pkg_name, script_name)
 File "C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\runpy.py", line 85, in _run_code
 exec(code, run_globals)
 File "c:\users\maria2\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\viewer\modules\batch_run_modules\CNMF.py", line 34, in <module>
 from mesmerize.common.utils import HdfTools
 File "C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\site-packages\mesmerize\__init__.py", line 1, in <module>
 from .analysis import *
 File "C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\site-packages\mesmerize\analysis\__init__.py", line 3, in <module>
 from .math import cross_correlation, drfft_dtw, tvregdiff
 File "C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\site-packages\mesmerize\analysis\math\drfft_dtw.py", line 17, in <module>
 raw_curve: np.ndarray = None, rf_curve: np.ndarray = None) -> list:
 File "C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\multiprocessing\context.py", line 56, in Manager
 m.start()
 File "C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\multiprocessing\managers.py", line 513, in start
 self._process.start()
 File "C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\multiprocessing\process.py", line 105, in start
 self._popen = self._Popen(self)
 File "C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\multiprocessing\context.py", line 322, in _Popen
 return Popen(process_obj)
 File "C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\multiprocessing\popen_spawn_win32.py", line 33, in __init__
 prep_data = spawn.get_preparation_data(process_obj._name)
 File "C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 143, in get_preparation_data
 _check_not_importing_main()
 File "C:\Users\Maria2\Anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 136, in _check_not_importing_main
 is not going to be frozen to produce an executable.''')
RuntimeError:
 An attempt has been made to start a new process before the
 current process has finished its bootstrapping phase.

 This probably means that you are not using fork to start your
 child processes and you have forgotten to use the proper idiom
 in the main module:

 if __name__ == '__main__':
 freeze_support()
 ...

 The "freeze_support()" line can be omitted if the program
 is not going to be frozen to produce an executable.

===== 2020.12.02 14:12:46 =====

[BUG] Python hangs in jupyter/ipython after mesmerize import when any exception is hit

Describe the bug
In Jupyter/ipython (but not Python command line), after importing a function from mesmerize, if I hit an exception, Python hangs. (Indefinite asterisk in Jupyter. Booted from ipython nb). In python command line I see the standard error message.

To Reproduce
Steps to reproduce the behavior, for example:

from mesmerize.viewer.modules.caiman_dfof import get_CNMF_obj
Raise some exception (either enter raise or enter something like 1+'a'

Expected behavior
A brief exception message, but Python should continue to work.

Copy paste message from the error window (if any)

ERROR:root:Internal Python error in the inspect module.
Below is the traceback from this internal error.

ERROR:root:Internal Python error in the inspect module.
Below is the traceback from this internal error.

ERROR:root:Internal Python error in the inspect module.
Below is the traceback from this internal error.

Traceback (most recent call last):

File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 3343, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "", line 1, in
1+'a'
TypeError: unsupported operand type(s) for +: 'int' and 'str'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 2044, in showtraceback
stb = value.render_traceback()
AttributeError: 'TypeError' object has no attribute 'render_traceback'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 1169, in get_records
return _fixed_getinnerframes(etb, number_of_lines_of_context, tb_offset)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 316, in wrapped
return f(*args, **kwargs)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 350, in fixed_getinnerframes
records = fix_frame_records_filenames(inspect.getinnerframes(etb, context))
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\inspect.py", line 1490, in getinnerframes
frameinfo = (tb.tb_frame,) + getframeinfo(tb, context)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\inspect.py", line 1448, in getframeinfo
filename = getsourcefile(frame) or getfile(frame)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\inspect.py", line 696, in getsourcefile
if getattr(getmodule(object, filename), 'loader', None) is not None:
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\inspect.py", line 733, in getmodule
if ismodule(module) and hasattr(module, 'file'):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\tensorflow_init.py", line 50, in getattr
module = self.load()
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\tensorflow_init.py", line 44, in _load
module = importlib.import_module(self.name)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\importlib_init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 994, in _gcd_import
File "", line 971, in _find_and_load
File "", line 953, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'tensorflow_core.estimator'
Traceback (most recent call last):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 3343, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "", line 1, in
1+'a'
TypeError: unsupported operand type(s) for +: 'int' and 'str'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 2044, in showtraceback
stb = value.render_traceback()
AttributeError: 'TypeError' object has no attribute 'render_traceback'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 3263, in run_ast_nodes
if (await self.run_code(code, result, async_=asy)):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 3360, in run_code
self.showtraceback(running_compiled_code=True)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 2047, in showtraceback
value, tb, tb_offset=tb_offset)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 1436, in structured_traceback
self, etype, value, tb, tb_offset, number_of_lines_of_context)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 1336, in structured_traceback
self, etype, value, tb, tb_offset, number_of_lines_of_context
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 1193, in structured_traceback
tb_offset)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 1150, in format_exception_as_a_whole
last_unique, recursion_repeat = find_recursion(orig_etype, evalue, records)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 451, in find_recursion
return len(records), 0
TypeError: object of type 'NoneType' has no len()

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 2044, in showtraceback
stb = value.render_traceback()
AttributeError: 'TypeError' object has no attribute 'render_traceback'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 1169, in get_records
return _fixed_getinnerframes(etb, number_of_lines_of_context, tb_offset)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 316, in wrapped
return f(*args, **kwargs)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 350, in fixed_getinnerframes
records = fix_frame_records_filenames(inspect.getinnerframes(etb, context))
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\inspect.py", line 1490, in getinnerframes
frameinfo = (tb.tb_frame,) + getframeinfo(tb, context)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\inspect.py", line 1448, in getframeinfo
filename = getsourcefile(frame) or getfile(frame)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\inspect.py", line 696, in getsourcefile
if getattr(getmodule(object, filename), 'loader', None) is not None:
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\inspect.py", line 733, in getmodule
if ismodule(module) and hasattr(module, 'file'):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\tensorflow_init.py", line 50, in getattr
module = self.load()
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\tensorflow_init.py", line 44, in _load
module = importlib.import_module(self.name)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\importlib_init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 994, in _gcd_import
File "", line 971, in _find_and_load
File "", line 953, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'tensorflow_core.estimator'
Traceback (most recent call last):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 3343, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "", line 1, in
1+'a'
TypeError: unsupported operand type(s) for +: 'int' and 'str'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 2044, in showtraceback
stb = value.render_traceback()
AttributeError: 'TypeError' object has no attribute 'render_traceback'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 3263, in run_ast_nodes
if (await self.run_code(code, result, async_=asy)):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 3360, in run_code
self.showtraceback(running_compiled_code=True)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 2047, in showtraceback
value, tb, tb_offset=tb_offset)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 1436, in structured_traceback
self, etype, value, tb, tb_offset, number_of_lines_of_context)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 1336, in structured_traceback
self, etype, value, tb, tb_offset, number_of_lines_of_context
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 1193, in structured_traceback
tb_offset)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 1150, in format_exception_as_a_whole
last_unique, recursion_repeat = find_recursion(orig_etype, evalue, records)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 451, in find_recursion
return len(records), 0
TypeError: object of type 'NoneType' has no len()

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 2044, in showtraceback
stb = value.render_traceback()
AttributeError: 'TypeError' object has no attribute 'render_traceback'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 2895, in _run_cell
return runner(coro)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\async_helpers.py", line 68, in _pseudo_sync_runner
coro.send(None)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 3072, in run_cell_async
interactivity=interactivity, compiler=compiler, result=result)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 3282, in run_ast_nodes
self.showtraceback()
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 2047, in showtraceback
value, tb, tb_offset=tb_offset)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 1436, in structured_traceback
self, etype, value, tb, tb_offset, number_of_lines_of_context)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 1336, in structured_traceback
self, etype, value, tb, tb_offset, number_of_lines_of_context
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 1211, in structured_traceback
chained_exceptions_tb_offset)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 1150, in format_exception_as_a_whole
last_unique, recursion_repeat = find_recursion(orig_etype, evalue, records)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 451, in find_recursion
return len(records), 0
TypeError: object of type 'NoneType' has no len()

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\interactiveshell.py", line 2044, in showtraceback
stb = value.render_traceback()
AttributeError: 'TypeError' object has no attribute 'render_traceback'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 1169, in get_records
return _fixed_getinnerframes(etb, number_of_lines_of_context, tb_offset)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 316, in wrapped
return f(*args, **kwargs)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\IPython\core\ultratb.py", line 350, in fixed_getinnerframes
records = fix_frame_records_filenames(inspect.getinnerframes(etb, context))
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\inspect.py", line 1490, in getinnerframes
frameinfo = (tb.tb_frame,) + getframeinfo(tb, context)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\inspect.py", line 1448, in getframeinfo
filename = getsourcefile(frame) or getfile(frame)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\inspect.py", line 696, in getsourcefile
if getattr(getmodule(object, filename), 'loader', None) is not None:
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\inspect.py", line 733, in getmodule
if ismodule(module) and hasattr(module, 'file'):
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\tensorflow_init.py", line 50, in getattr
module = self.load()
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\tensorflow_init.py", line 44, in _load
module = importlib.import_module(self.name)
File "C:\Users\lab_user\miniconda3\envs\mesmerize\lib\importlib_init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 994, in _gcd_import
File "", line 971, in _find_and_load
File "", line 953, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'tensorflow_core.estimator'

(Note tensorflow 2.x is installed)

Trace from powershell
It is similar so I won't copy/paste it here (but it isn't exactly the same: if you want it I'll drop it in in a comment).

Screenshots

**Operating System & specs (CPU, RAM etc.). **
Windows 10, with caiman installed with mamba/mesmerize witih pip. 128 GB of RAM. Using main branch of mesmerize.

Additional context
If I don't import mesmerize stuff it doesn't do this in the environment. E.g., numpy and matplotlib are fine. This creates very strong motivation to not raise exceptions in my code. 💯

CaImAn Install Issue - Windows/Linux Dual Boot[INSTALLATION HELP]

System information

OS (Windows 10/Ubuntu 20.04 LTS Dual Boot [run on Ubuntu partition])
CPU (Intel(R) Core(TM) i7-9750H)
RAM (32Gb)
Do you have an SSD or magnetic HDD (SSD)

Copy & paste the entire output of the terminal while you were trying to install when the issue came up:

/home/user/.local/lib/python3.8/site-packages/mesmerize/common/configuration.py:37: UserWarning: Caiman package not found. Caiman features will be disabled.
  warn(
2021-10-21 11:14:33.297075: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2021-10-21 11:14:33.297096: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
/home/user/.local/lib/python3.8/site-packages/sklearn/utils/deprecation.py:143: FutureWarning: The sklearn.cluster.k_means_ module is  deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.cluster. Anything that cannot be imported from sklearn.cluster is now part of the private API.
  warnings.warn(message, FutureWarning)
Loading, please wait... 
%(asctime)s %(levelname)s %(pathname)s %(lineno)s 
 %(message)s 
Moving old logfiles...
Moving old logfiles...
QApplication::exec: Please instantiate the QApplication object first
Segmentation fault (core dumped)

Installation method

Are you using anaconda, python virtual environments, or something else?
conda 4.10.3, but installed with mamba
If you're installing mesmerize through pip, what version of pip is installed in the environment?
pip 21.3
Are you trying to install in developer mode from the repo?
No
What is the python version in the environment you're trying to install mesmerize in?
python=3.8
Information if you're using some other installation method.
Installed caiman using mamba in a conda environment. I can see caiman in the environment, but there seems to be issues, even after using caimanmanager.py. I believe it may stem from dependency issues from tensorflow.

ModuleNotFoundError: No module named 'caiman'

There seem to be similar problems, but the solutions do not seem to be working. I am trying to do motion correction and then CNMF. When I do the motion correction and I originally received the "No module name 'cv2'" and I got that fixed by reinstalling the package. But now I am getting the "ModuleNotFoundError: No module named 'caiman'". I tried reloading caiman and it did not change the error even after I restarted the program.

To Reproduce

Go to CaImAn toolbox and choose motion correct
Put in parameters and add it to the batch
Run the batch
See error

Traceback (most recent call last):
File "c:\users\katherine\miniconda3\envs\mesmerize\lib\site-packages\mesmerize\viewer\modules\batch_run_modules\caiman_motion_correction.py", line 23, in

import caiman as cm

ModuleNotFoundError: No module named 'caiman'

Traceback (most recent call last):
File "c:\users\katherine\miniconda3\envs\mesmerize\lib\site-packages\mesmerize\viewer\modules\batch_run_modules\caiman_motion_correction.py", line 23, in

import caiman as cm

ModuleNotFoundError: No module named 'caiman'

Traceback (most recent call last):
File "c:\users\katherine\miniconda3\envs\mesmerize\lib\site-packages\mesmerize\viewer\modules\batch_run_modules\caiman_motion_correction.py", line 23, in

import caiman as cm

ModuleNotFoundError: No module named 'caiman'

Operating System & specs (CPU, RAM etc.). Please complete the following information:

OS: Windows 10

Details about your Mesmerize install

Anaconda

Improve CNMF with evenly lighted recordings?

Many false negative and false positive results of CNMF

Hi,

I have a problem, that even though I tried very different parameters with CMNF some neurons are not found and at some places, there is a very big amount marked, which creates false-positive results. I attached my photo of my CNMF results (I tried different neuron sizes, SNR, neuron numbers per patch).

The boundaries of the miniscope recordings are darker and I was thinking that maybe this is the problem, because I got stuck that so many neurons are not found.

Do I need to make some preprocessing of the videos, are there some methods that I could use? Or should I look for parts that have the same lightning and crop those parts to analyze further?

Here is my screenshot:

Thank you very much in advance

Installation fails on Mac Mojave

Problem

Hello - I am trying to install Mesmerize on a Mac system version 10.14.6, but I am receiving error messages when I reach the launch steps (http://www.mesmerizelab.org/user_guides/installation.html). Reading the gitter messages, it seems like this may be similar to what smsadegh was reporting. I previously had Caiman running successfully, but uninstalled everything prior to starting the Mesmerize install. Full code pasted below of the install process in terminal.

Error message/Exception in spyder console. Any screenshots

Last login: Sat May 16 11:47:55 on ttys000
(base) macbook-pro-4:~ user1$ conda create --name mesmerize python=3.6
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /anaconda3/envs/mesmerize

  added / updated specs:
    - python=3.6


The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/osx-64::ca-certificates-2020.1.1-0
  certifi            pkgs/main/osx-64::certifi-2020.4.5.1-py36_0
  libcxx             pkgs/main/osx-64::libcxx-10.0.0-1
  libedit            pkgs/main/osx-64::libedit-3.1.20181209-hb402a30_0
  libffi             pkgs/main/osx-64::libffi-3.3-h0a44026_1
  ncurses            pkgs/main/osx-64::ncurses-6.2-h0a44026_1
  openssl            pkgs/main/osx-64::openssl-1.1.1g-h1de35cc_0
  pip                pkgs/main/osx-64::pip-20.0.2-py36_3
  python             pkgs/main/osx-64::python-3.6.10-hf48f09d_2
  readline           pkgs/main/osx-64::readline-8.0-h1de35cc_0
  setuptools         pkgs/main/osx-64::setuptools-46.0.0-py36_0
  sqlite             pkgs/main/osx-64::sqlite-3.31.1-h5c1f38d_1
  tk                 pkgs/main/osx-64::tk-8.6.8-ha441bb4_0
  wheel              pkgs/main/osx-64::wheel-0.34.2-py36_0
  xz                 pkgs/main/osx-64::xz-5.2.5-h1de35cc_0
  zlib               pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate mesmerize
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(base) macbook-pro-4:~ user1$ conda activate mesmerize
(mesmerize) macbook-pro-4:~ user1$ conda install cython numpy pandas
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /anaconda3/envs/mesmerize

  added / updated specs:
    - cython
    - numpy
    - pandas


The following NEW packages will be INSTALLED:

  blas               pkgs/main/osx-64::blas-1.0-mkl
  cython             pkgs/main/osx-64::cython-0.29.17-py36h0a44026_0
  intel-openmp       pkgs/main/osx-64::intel-openmp-2019.4-233
  libgfortran        pkgs/main/osx-64::libgfortran-3.0.1-h93005f0_2
  mkl                pkgs/main/osx-64::mkl-2019.4-233
  mkl-service        pkgs/main/osx-64::mkl-service-2.3.0-py36hfbe908c_0
  mkl_fft            pkgs/main/osx-64::mkl_fft-1.0.15-py36h5e564d8_0
  mkl_random         pkgs/main/osx-64::mkl_random-1.1.0-py36ha771720_0
  numpy              pkgs/main/osx-64::numpy-1.18.1-py36h7241aed_0
  numpy-base         pkgs/main/osx-64::numpy-base-1.18.1-py36h6575580_1
  pandas             pkgs/main/osx-64::pandas-1.0.3-py36h6c726b0_0
  python-dateutil    pkgs/main/noarch::python-dateutil-2.8.1-py_0
  pytz               pkgs/main/noarch::pytz-2020.1-py_0
  six                pkgs/main/osx-64::six-1.14.0-py36_0


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(mesmerize) macbook-pro-4:~ user1$ git clond https://github.com/kushalkolar/MESmerize.git
git: 'clond' is not a git command. See 'git --help'.

The most similar command is
	clone
(mesmerize) macbook-pro-4:~ user1$ git clone https://github.com/kushalkolar/MESmerize.git
Cloning into 'MESmerize'...
remote: Enumerating objects: 881, done.
remote: Counting objects: 100% (881/881), done.
remote: Compressing objects: 100% (645/645), done.
remote: Total 11621 (delta 503), reused 513 (delta 211), pack-reused 10740
Receiving objects: 100% (11621/11621), 299.72 MiB | 12.83 MiB/s, done.
Resolving deltas: 100% (7651/7651), done.
Checking out files: 100% (1198/1198), done.
warning: the following paths have collided (e.g. case-sensitive paths
on a case-insensitive filesystem) and only one from the same
colliding group is in the working tree:

  'mesmerize/plotting/colormaps/Spectral.png'
  'mesmerize/plotting/colormaps/spectral.png'
  'mesmerize/plotting/widgets/colormaps/Spectral.png'
  'mesmerize/plotting/widgets/colormaps/spectral.png'
(mesmerize) macbook-pro-4:~ user1$ cd MESmerize
(mesmerize) macbook-pro-4:MESmerize user1$ git checkout snap
M	mesmerize/plotting/colormaps/Spectral.png
M	mesmerize/plotting/widgets/colormaps/Spectral.png
Branch 'snap' set up to track remote branch 'snap' from 'origin'.
Switched to a new branch 'snap'
(mesmerize) macbook-pro-4:MESmerize user1$ pip install -r requirements.txt
Collecting cycler==0.10.0
  Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting dask==1.1.1
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Processing /Users/user1/Library/Caches/pip/wheels/c4/f0/e2/8e4ecc9e1b12a428a7657ba683576d3e79d0a75982f63e8fd2/future-0.17.1-py3-none-any.whl
Collecting h5py==2.9.0
  Using cached h5py-2.9.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (6.3 MB)
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Collecting ipython==7.3.0
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Collecting ipyparallel==6.2.3
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Collecting MarkupSafe==1.1.1
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Collecting opencv-contrib-python==3.4.1.15
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Collecting opencv-python==3.4.1.15
  Using cached opencv_python-3.4.1.15-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (41.9 MB)
Collecting pandas==0.25.3
  Using cached pandas-0.25.3-cp36-cp36m-macosx_10_9_x86_64.whl (10.4 MB)
Collecting Pillow==5.4.1
  Using cached Pillow-5.4.1-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (3.7 MB)
Processing /Users/user1/Library/Caches/pip/wheels/55/d9/6e/753ea9b05c8842e1f8d3d745713226395aaa7090b27a4e6293/psutil-5.5.1-cp36-cp36m-macosx_10_9_x86_64.whl
Collecting PyQt5==5.9.2
  Using cached PyQt5-5.9.2-5.9.3-cp35.cp36.cp37-abi3-macosx_10_6_intel.whl (81.7 MB)
Collecting QtPy==1.6.0
  Using cached QtPy-1.6.0-py2.py3-none-any.whl (43 kB)
Collecting scikit-image==0.14.2
  Using cached scikit_image-0.14.2-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (28.9 MB)
Collecting scikit-learn==0.20.3
  Using cached scikit_learn-0.20.3-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (8.0 MB)
Collecting scipy==1.3.0
  Using cached scipy-1.3.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (27.7 MB)
Collecting seaborn==0.9.0
  Using cached seaborn-0.9.0-py3-none-any.whl (208 kB)
Processing /Users/user1/Library/Caches/pip/wheels/23/9d/42/5ec745cbbb17517000a53cecc49d6a865450d1f5cb16dc8a9c/sklearn-0.0-py2.py3-none-any.whl
Collecting spyder==3.3.3
  Using cached spyder-3.3.3-py3-none-any.whl (2.8 MB)
Collecting tifffile==0.15.1
  Using cached tifffile-0.15.1-cp36-cp36m-macosx_10_7_x86_64.whl (116 kB)
Collecting tqdm==4.37.0
  Using cached tqdm-4.37.0-py2.py3-none-any.whl (53 kB)
Processing /Users/user1/Library/Caches/pip/wheels/f4/16/80/410b5e600f73d21e3cc507ecc5bb970998db55084e3d38fdf4/PeakUtils-1.3.2-py3-none-any.whl
Collecting tables==3.5.2
  Using cached tables-3.5.2-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (4.4 MB)
Collecting joblib==0.13.2
  Using cached joblib-0.13.2-py2.py3-none-any.whl (278 kB)
Collecting graphviz==0.13
  Using cached graphviz-0.13-py2.py3-none-any.whl (17 kB)
Collecting numba==0.42.1
  Using cached numba-0.42.1-cp36-cp36m-macosx_10_9_x86_64.whl (1.6 MB)
Processing /Users/user1/Library/Caches/pip/wheels/66/97/1a/1df12a9b145ec52cfc551ab4ae669c8eb6ed5e18aefc751ec7/Bottleneck-1.2.1-cp36-cp36m-macosx_10_9_x86_64.whl
Requirement already satisfied: six in /anaconda3/envs/mesmerize/lib/python3.6/site-packages (from cycler==0.10.0->-r requirements.txt (line 1)) (1.14.0)
Requirement already satisfied: numpy>=1.7 in /anaconda3/envs/mesmerize/lib/python3.6/site-packages (from h5py==2.9.0->-r requirements.txt (line 4)) (1.18.1)
Collecting pickleshare
  Using cached pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)
Collecting appnope; sys_platform == "darwin"
  Using cached appnope-0.1.0-py2.py3-none-any.whl (4.0 kB)
Collecting jedi>=0.10
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Requirement already satisfied: setuptools>=18.5 in /anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipython==7.3.0->-r requirements.txt (line 6)) (46.0.0.post20200309)
Collecting traitlets>=4.2
  Using cached traitlets-4.3.3-py2.py3-none-any.whl (75 kB)
Processing /Users/user1/Library/Caches/pip/wheels/b4/cb/f1/d142b3bb45d488612cf3943d8a1db090eb95e6687045ba61d1/backcall-0.1.0-py3-none-any.whl
Collecting prompt-toolkit<2.1.0,>=2.0.0
  Using cached prompt_toolkit-2.0.10-py3-none-any.whl (340 kB)
Collecting pygments
  Using cached Pygments-2.6.1-py3-none-any.whl (914 kB)
Collecting decorator
  Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Collecting pexpect; sys_platform != "win32"
  Using cached pexpect-4.8.0-py2.py3-none-any.whl (59 kB)
Processing /Users/user1/Library/Caches/pip/wheels/37/a7/db/2d592e44029ef817f3ef63ea991db34191cebaef087a96f505/tornado-6.0.4-cp36-cp36m-macosx_10_9_x86_64.whl
Collecting ipython-genutils
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Collecting ipykernel>=4.4
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Requirement already satisfied: python-dateutil>=2.1 in /anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipyparallel==6.2.3->-r requirements.txt (line 7)) (2.8.1)
Collecting jupyter-client
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Collecting pyzmq>=13
  Using cached pyzmq-19.0.1-cp36-cp36m-macosx_10_9_intel.whl (1.4 MB)
Requirement already satisfied: pytz in /anaconda3/envs/mesmerize/lib/python3.6/site-packages (from matplotlib==2.1.2->-r requirements.txt (line 9)) (2020.1)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
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Collecting sip<4.20,>=4.19.4
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Collecting PyWavelets>=0.4.0
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Collecting networkx>=1.8
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Collecting qtconsole>=4.2.0
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Processing /Users/user1/Library/Caches/pip/wheels/7a/97/5e/6885d024ee585fe437a65cc815cbdb10b810ceaa65242ccbea/numpydoc-0.9.2-py3-none-any.whl
Processing /Users/user1/Library/Caches/pip/wheels/f1/90/67/ebd231ce083da4fd4ca67684aa2f0b0e45b135d321335f8598/rope-0.17.0-py3-none-any.whl
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Collecting zipp>=0.5
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Processing /Users/user1/Library/Caches/pip/wheels/32/42/7f/23cae9ff6ef66798d00dc5d659088e57dbba01566f6c60db63/wrapt-1.12.1-cp36-cp36m-macosx_10_9_x86_64.whl
Collecting typed-ast<1.5,>=1.4.0; implementation_name == "cpython" and python_version < "3.8"
  Using cached typed_ast-1.4.1-cp36-cp36m-macosx_10_9_x86_64.whl (223 kB)
Processing /Users/user1/Library/Caches/pip/wheels/74/16/66/f3b601fb6040a9bbc1652bf154faa76f51a84e2f6f850cb7bd/lazy_object_proxy-1.4.3-cp36-cp36m-macosx_10_9_x86_64.whl
Processing /Users/user1/Library/Caches/pip/wheels/d1/8a/1c/32ab9017418a2c64e4fbaf503c08648bed2f8eb311b869a464/pyrsistent-0.16.0-cp36-cp36m-macosx_10_9_x86_64.whl
Collecting attrs>=17.4.0
  Using cached attrs-19.3.0-py2.py3-none-any.whl (39 kB)
Installing collected packages: cycler, dask, future, h5py, hickle, pickleshare, appnope, parso, jedi, ipython-genutils, decorator, traitlets, backcall, wcwidth, prompt-toolkit, pygments, ptyprocess, pexpect, ipython, tornado, jupyter-core, pyzmq, jupyter-client, ipykernel, ipyparallel, MarkupSafe, pyparsing, matplotlib, opencv-contrib-python, opencv-python, pandas, Pillow, psutil, sip, PyQt5, QtPy, scipy, PyWavelets, networkx, cloudpickle, scikit-image, scikit-learn, seaborn, sklearn, qtconsole, qtawesome, entrypoints, mistune, pyrsistent, zipp, importlib-metadata, attrs, jsonschema, nbformat, testpath, defusedxml, webencodings, packaging, bleach, pandocfilters, jinja2, nbconvert, pyflakes, sphinxcontrib-applehelp, sphinxcontrib-jsmath, babel, sphinxcontrib-qthelp, urllib3, idna, chardet, requests, alabaster, docutils, imagesize, sphinxcontrib-serializinghtml, sphinxcontrib-devhelp, sphinxcontrib-htmlhelp, snowballstemmer, sphinx, pycodestyle, numpydoc, rope, keyring, mccabe, toml, isort, wrapt, typed-ast, lazy-object-proxy, astroid, pylint, wurlitzer, spyder-kernels, spyder, tifffile, tqdm, PeakUtils, mock, numexpr, tables, joblib, graphviz, llvmlite, numba, bottleneck
  Attempting uninstall: pandas
    Found existing installation: pandas 1.0.3
    Uninstalling pandas-1.0.3:
      Successfully uninstalled pandas-1.0.3
Successfully installed MarkupSafe-1.1.1 PeakUtils-1.3.2 Pillow-5.4.1 PyQt5-5.9.2 PyWavelets-1.1.1 QtPy-1.6.0 alabaster-0.7.12 appnope-0.1.0 astroid-2.4.1 attrs-19.3.0 babel-2.8.0 backcall-0.1.0 bleach-3.1.5 bottleneck-1.2.1 chardet-3.0.4 cloudpickle-1.4.1 cycler-0.10.0 dask-1.1.1 decorator-4.4.2 defusedxml-0.6.0 docutils-0.16 entrypoints-0.3 future-0.17.1 graphviz-0.13 h5py-2.9.0 hickle-3.4.3 idna-2.9 imagesize-1.2.0 importlib-metadata-1.6.0 ipykernel-5.2.1 ipyparallel-6.2.3 ipython-7.3.0 ipython-genutils-0.2.0 isort-4.3.21 jedi-0.17.0 jinja2-2.11.2 joblib-0.13.2 jsonschema-3.2.0 jupyter-client-6.1.3 jupyter-core-4.6.3 keyring-21.2.1 lazy-object-proxy-1.4.3 llvmlite-0.32.1 matplotlib-2.1.2 mccabe-0.6.1 mistune-0.8.4 mock-4.0.2 nbconvert-5.6.1 nbformat-5.0.6 networkx-2.4 numba-0.42.1 numexpr-2.7.1 numpydoc-0.9.2 opencv-contrib-python-3.4.1.15 opencv-python-3.4.1.15 packaging-20.3 pandas-0.25.3 pandocfilters-1.4.2 parso-0.7.0 pexpect-4.8.0 pickleshare-0.7.5 prompt-toolkit-2.0.10 psutil-5.5.1 ptyprocess-0.6.0 pycodestyle-2.6.0 pyflakes-2.2.0 pygments-2.6.1 pylint-2.5.2 pyparsing-2.4.7 pyrsistent-0.16.0 pyzmq-19.0.1 qtawesome-0.7.2 qtconsole-4.7.4 requests-2.23.0 rope-0.17.0 scikit-image-0.14.2 scikit-learn-0.20.3 scipy-1.3.0 seaborn-0.9.0 sip-4.19.8 sklearn-0.0 snowballstemmer-2.0.0 sphinx-3.0.3 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.4 spyder-3.3.3 spyder-kernels-0.5.2 tables-3.5.2 testpath-0.4.4 tifffile-0.15.1 toml-0.10.1 tornado-6.0.4 tqdm-4.37.0 traitlets-4.3.3 typed-ast-1.4.1 urllib3-1.25.9 wcwidth-0.1.9 webencodings-0.5.1 wrapt-1.12.1 wurlitzer-2.0.0 zipp-3.1.0
(mesmerize) macbook-pro-4:MESmerize user1$ CFLAGS='-stdlib=libc++' python setup.py build_ext -i
running build_ext
cythoning tslearn/cygak.pyx to tslearn/cygak.c
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/user1/MESmerize/tslearn/cygak.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning tslearn/cysax.pyx to tslearn/cysax.c
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/user1/MESmerize/tslearn/cysax.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning tslearn/cycc.pyx to tslearn/cycc.c
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/user1/MESmerize/tslearn/cycc.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning tslearn/soft_dtw_fast.pyx to tslearn/soft_dtw_fast.c
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/user1/MESmerize/tslearn/soft_dtw_fast.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
skipping 'caiman/source_extraction/cnmf/oasis.cpp' Cython extension (up-to-date)
building 'tslearn.cygak' extension
creating build
creating build/temp.macosx-10.9-x86_64-3.6
creating build/temp.macosx-10.9-x86_64-3.6/tslearn
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/include/python3.6m -c tslearn/cygak.c -o build/temp.macosx-10.9-x86_64-3.6/tslearn/cygak.o
In file included from tslearn/cygak.c:600:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: 
      "Using deprecated NumPy API, disable it with "          "#define
      NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
1 warning generated.
gcc -bundle -undefined dynamic_lookup -L/anaconda3/envs/mesmerize/lib -arch x86_64 -L/anaconda3/envs/mesmerize/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/tslearn/cygak.o -o /Users/user1/MESmerize/tslearn/cygak.cpython-36m-darwin.so
building 'tslearn.cysax' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/include/python3.6m -c tslearn/cysax.c -o build/temp.macosx-10.9-x86_64-3.6/tslearn/cysax.o
In file included from tslearn/cysax.c:600:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: 
      "Using deprecated NumPy API, disable it with "          "#define
      NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
1 warning generated.
gcc -bundle -undefined dynamic_lookup -L/anaconda3/envs/mesmerize/lib -arch x86_64 -L/anaconda3/envs/mesmerize/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/tslearn/cysax.o -o /Users/user1/MESmerize/tslearn/cysax.cpython-36m-darwin.so
building 'tslearn.cycc' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/include/python3.6m -c tslearn/cycc.c -o build/temp.macosx-10.9-x86_64-3.6/tslearn/cycc.o
In file included from tslearn/cycc.c:600:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: 
      "Using deprecated NumPy API, disable it with "          "#define
      NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
1 warning generated.
gcc -bundle -undefined dynamic_lookup -L/anaconda3/envs/mesmerize/lib -arch x86_64 -L/anaconda3/envs/mesmerize/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/tslearn/cycc.o -o /Users/user1/MESmerize/tslearn/cycc.cpython-36m-darwin.so
building 'tslearn.soft_dtw_fast' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/include/python3.6m -c tslearn/soft_dtw_fast.c -o build/temp.macosx-10.9-x86_64-3.6/tslearn/soft_dtw_fast.o
In file included from tslearn/soft_dtw_fast.c:600:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: 
      "Using deprecated NumPy API, disable it with "          "#define
      NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
1 warning generated.
gcc -bundle -undefined dynamic_lookup -L/anaconda3/envs/mesmerize/lib -arch x86_64 -L/anaconda3/envs/mesmerize/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/tslearn/soft_dtw_fast.o -o /Users/user1/MESmerize/tslearn/soft_dtw_fast.cpython-36m-darwin.so
building 'caiman.source_extraction.cnmf.oasis' extension
creating build/temp.macosx-10.9-x86_64-3.6/caiman
creating build/temp.macosx-10.9-x86_64-3.6/caiman/source_extraction
creating build/temp.macosx-10.9-x86_64-3.6/caiman/source_extraction/cnmf
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/include/python3.6m -c caiman/source_extraction/cnmf/oasis.cpp -o build/temp.macosx-10.9-x86_64-3.6/caiman/source_extraction/cnmf/oasis.o
In file included from caiman/source_extraction/cnmf/oasis.cpp:627:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: 
      "Using deprecated NumPy API, disable it with "          "#define
      NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
1 warning generated.
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/mesmerize/lib -arch x86_64 -L/anaconda3/envs/mesmerize/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/caiman/source_extraction/cnmf/oasis.o -o /Users/user1/MESmerize/caiman/source_extraction/cnmf/oasis.cpython-36m-darwin.so
(mesmerize) macbook-pro-4:MESmerize user1$ export PYTHONPATH=</Users/user1/MESmerize>
-bash: syntax error near unexpected token `newline'
(mesmerize) macbook-pro-4:MESmerize user1$ 

(mesmerize) macbook-pro-4:MESmerize user1$ export PYTHONPATH=</Users/user1/MESmerize>
-bash: syntax error near unexpected token `newline'
(mesmerize) macbook-pro-4:MESmerize user1$ echo "backend: qt5" >> ~/.matplotlib/matplotlibrc
(mesmerize) macbook-pro-4:MESmerize user1$ export PYTHONPATH=</Users/user1/MESmerize>
-bash: syntax error near unexpected token `newline'
(mesmerize) macbook-pro-4:MESmerize user1$ python </Users/user1/MESmerize>/mesmerize
-bash: /mesmerize: Permission denied
(mesmerize) macbook-pro-4:MESmerize user1$

Steps to reproduce the problem

Operating System

Mac system version 10.14.6

Commit ID

[BUG] ROIs are rotated 90degrees using CNMF

Describe the bug
When running CNMF on a 3D image, (in this case 7 Z-planes and 500 Time-frames) the output is rotated 90 degrees relative to the image.

To Reproduce

Download the test files: https://www.dropbox.com/sh/klpfxg9mgcu0iw2/AAAExCvJBX6cyr3DhZvUXLfya?dl=0
Load Warwick_test.tif using asarray and choose json_minimal format. This file should be loaded used a custom Image Axes order of tzyx, although the bug persists using the default order of tzxy so that isn't actually an issue. There should be 7 z-planes in this image.
Make a batch and run default settings CNMF (the specific CNMF settings don't seem to matter)
View the finished CNMF and the ROIs should be rotates 90 degrees relative the image.

Expected behavior
Using a single Z-plane for CNMF the ROIs are lined up correctly and I expected this to occur.

**Operating System & specs (CPU, RAM etc.).

Running 64 bit Windows 10, but using the VM.
-i7 8700
-32gb RAM
-512 gb SSD

Details about your Mesmerize install
-I am using the VirtualBox VM of Mesmerize

Help with VM installation

System information

OS - Windowa 10
CPU - Intel(R) Xeon (R) X 5650 - 12 cores and 24 logical processors
RAM - 96GB
HDD

Hi all,
I am trying to use mesmerize in the VM provided in the repository. I installed Oracle Virtual box, and downloaded the file containing the mesmerize VM. I could import and launch the VM, which has the venv corresponding to mesmerize, as well as the test data (see screenshots).

However, when double clicking in the mesmerize desktop icon, it does not launch. It does not launch either when I try to call it from the terminal. A terminal window pops up, but then it closes and the program does not launch.

I tried installing the VM again, and encountered the same issue.
This is the configuration of the VM I installed:

Please let me know if you'd like to see some more of the settings.
Thank you in advance!

Towards v0.9, conda install, update package versions etc.

not able to get mesmerize to work with caiman?

Hi all, first off thanks for making mesmerize. Looks very promising.

I have installed mesmerize without a hitch but what I really want is to integrate caimen into mesmerize and I am stuck.

After install, the mesmerize gui seems to run fine, except when I run with 'mesmerize' I get a popup telling me ...

Caiman not found ... The caiman package could not be found in your python environment. Caiman features will not work.

Operating System

Ubuntu 20.0.4

Details about your Mesmerize install

Are you using the pip install? If so which version?

yes, using 'pip --version', as follows ('mesmerize-env' is my Python3.6 venv):

pip 20.2.3 from /home/cudmore/Sites/MESmerize/mesmerize-env/lib/python3.6/site-packages/pip (python 3.6)

Are you using a clone of the master branch from the GitHub repo?

No, I was not able to install mesmerize from a cloned source? I installed from PyPi with

pip install mesmerize

I would prefer to install mesmerize from a cloned source, any suggestions?

In the cloned mesmerize source folder the following failed:

pip install -e .

with

    ERROR: Command errored out with exit status 1:
     command: /home/cudmore/Sites/MESmerize/mesmerize-env/bin/python3.6 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/cudmore/Sites/MESmerize/setup.py'"'"'; __file__='"'"'/home/cudmore/Sites/MESmerize/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-ck5wbdq8
         cwd: /home/cudmore/Sites/MESmerize/
    Complete output (5 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/home/cudmore/Sites/MESmerize/setup.py", line 71, in <module>
        with open(Path(__file__).joinpath('mesmerize').joinpath('VERSION'), 'r') as vf:
    NotADirectoryError: [Errno 20] Not a directory: '/home/cudmore/Sites/MESmerize/setup.py/mesmerize/VERSION'
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

are you using anaconda or venv (the python built-in virtual environment management)

I am using Python3.6 venv following your install instructions

Describe the issue, please be as explicit and detailed as possible.

When I follow your install instructions, all goes well except (for my) attempting to use caiman with mesmerize. When I run mesmerize I am warned 'Caiman not found ... The caiman package could not be found in your python environment. Caiman features will not work.'

Steps that can be followed to reproduce the problem. What exactly were you were doing that lead to the issue.

I followed your Ubuntu/Linux install instructions here and all went well.

Once I am in my Python3.6 mesmerize venv (named mesmerize-env), I install caiman from source with

# activate my mesmerize python 3.6 environment
source mesmerize-env/bin/activate
# install caiman (from source, CaimAn is in a different folder)
pip install ../CaImAn/.

Now, still, in my mesmerize-env python 3.6 environment

pip freeze | grep caiman

gives me

caiman==1.8.5

But when I run 'mesmerize' I get the error

Caiman not found ... The caiman package could not be found in your python environment. Caiman features will not work.

Your recipe/pattern for installing caiman is unfamiliar to me?

git clone https://github.com/flatironinstitute/CaImAn
cd CaImAn/
source activate caiman # !!! Is this assuming a conda install of caiman ???
pip install .

I am confused by 'source activate caiman'. Is this assuming caiman has been previously installed with conda? That is actually the case for me, I have a conda environment named 'caimen'.

Am I supposed to activate the conda caiman environment and then install caiman? Wouldn't this deactivate my python 3.6 ven v named 'mesmerized-env'?

Anything else which you think is relevant

Thanks for making mesmerize and I look forward to using it ...

CaImAn instalattion error

Dear all!

I'm trying to install mesmerize on Windows and been stuck with installation. (see attached image) I've been waiting more than 28 hours and still not doing anything and not moving forward. I tried a few commands for caiman install and both ended up here.
Someone has some idea how to solve it?

Thanks in advance,
Szilárd

Import ROI ImageJ error

Describe the bug
When importing ImageJ ROIs into MESmerize, it does not read ROIs created by different drawing tools (oval and rectangle) in ImageJ. It recognises freehand ROIs.

To Reproduce
Go to Viewer -> ROI Manager -> Import ROI Manager (attached)

Expected behavior
Ideally, It should import all ROIs regardless of size/type.

Error

I have fixed it by modifying the function import_from_imagej in managers.py. Not the most elegant code, but it works.

Attached ImageJ ROI file for testing.
roi_test.zip

    def import_from_imagej(self, path: str):
        """
        Uses read-roi package created by Hadrien Mary.
        https://pypi.org/project/read-roi/

        :param path: Full path to the ImageJ ROIs zip file
        """
        ij_roi = read_imagej(path)
        for k in ij_roi.keys():
            if ij_roi[k]['type'] in ('oval', 'rectangle'):
                width=ij_roi[k]['width']
                height=ij_roi[k]['height']
                left=ij_roi[k]['left']
                top=ij_roi[k]['top']
                x_center=left+width/2
                y_center=top+height/2
                if ij_roi[k]['type'] == 'oval':
                    shape=Ellipse((x_center,y_center),width,height)
                    vertices_orig=shape.get_path().vertices #get all vertices  
                    vertices = shape.get_patch_transform().transform(vertices_orig)
                    ps=[tuple(x) for x in vertices]
                else:
                    ps=list(itertools.product((left,left+width),(top,top+height)))
                    ps[2],ps[3]=ps[3],ps[2] #swap coordinates so it draws coordinates in sequence, must be a better way to do this
            else:
                xs = ij_roi[k]['x']
                ys = ij_roi[k]['y']
                ps = list(zip(xs, ys))
            
            roi = ManualROI.from_positions(positions=ps,
                                                curve_plot_item=self.get_plot_item(),
                                                view_box=self.vi.viewer.getView())
            self.roi_list.append(roi)
        self.roi_list.reindex_colormap()

Operating System & specs (CPU, RAM etc.). Please complete the following information:

Windows 10

Details about your Mesmerize install

Anaconda envt

Cheers
Pradeep

Need help using Mesmerize

First of all, im on ubuntu 20.04 LTS FRESH INSTALL only for this.
I tried both installation method but I would prefer to make the github one work (since it has less limitations)

When I open mesmerize from the snap installation. I get [Errno 13] permission denied joblib will operate in serial mode.
I tried to give all the right to /dev/shm but the error persist.

On the other hand. with thee github installation everything looks fine(except for some numpy warning when running python setup.py build_ext -i)

However I cant seem to make the motion correction work. The tif file load perfectly and the batch manager receive it but it always end up red or orange.

How can I solve this and complete it.

Thanks a lot

No module named 'cv2'

Hello,
I have just started to use Mesmerize. I tried to run the motion correction (Batch Manager window/Start) and it gave me the following error:
Traceback (most recent call last):
File "c:\programdata\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\viewer\modules\batch_run_modules\caiman_motion_correction.py", line 18, in
import cv2
ModuleNotFoundError: No module named 'cv2'
Could you help me with it? Thank you! (Win10)

Compnent registartion across multiple sessions

Component registration across multiple sessions.

Hi,

I need MESmerize to follow neural activity in long-term measurements. Is there a feature for that to annotate the same neurons in multiple recordings with the same number to compare them later on?

Thank you in advance.

Install caiman for Caiman feature failed on Mac

Operating System & specs (CPU, RAM etc.)

MacOS 10.14.6
2.9GHz Intel Core i9
Processor Speed: 2.9 GHz
Number of Processors: 1
Total Number of Cores: 6
Memory 32GB

Details about your Mesmerize install

Are you using the pip install? If so which version?
pip 19.1.1 from /Users/nadine/anaconda3/lib/python3.7/site-packages/pip (python 3.7)
Are you using a clone of the master branch from the GitHub repo?
following the installation.doc for MacOs send via email
Are you using anaconda or venv (the python built-in virtual environment management)
anaconda

Describe the issue, please be as explicit and detailed as possible.

conda activate mesmerise (works)
next step: it freezes dor >1h
see output below:
conda install -c conda-forge caiman
Collecting package metadata (current_repodata.json): done
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Initial quick solve with frozen env failed. Unfreezing env and trying again.
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: -

Steps that can be followed to reproduce the problem. What exactly were you were doing that lead to the issue.

Screenshot or copy-paste from the terminal that Mesmerize is running in

Make sure the entire stack trace is visible, or that all messages relevant to the issue are visible!

Last login: Sat Nov 28 10:51:45 on ttys000
(base) Nadines-MacBook-Pro:~ nadine$ conda activate mesmerize
(mesmerize) Nadines-MacBook-Pro:~ nadine$ conda install -c conda-forge caiman
Collecting package metadata (current_repodata.json): done
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Initial quick solve with frozen env failed. Unfreezing env and trying again.
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: -

Relevant screenshots

If relevant, messages from the batch manager terminal

Anything else which you think is relevant

Windows and unicode encoding

Add to FAQ that utf-8 encoding must be explicitly set in some cases:

File "c:\users\deb\.conda\envs\mesmerize\lib\site-packages\mesmerize\pyqtgraphCore\console\Console.py", line 171, in execSingle
exec(cmd, self.globals(), self.locals())
File "<string>", line 5
SyntaxError: (unicode error) 'unicodeescape' codec can't decode bytes in position 2-3: truncated \UXXXXXXXX escape

[BUG] System configuration setting yields an error

Describe the bug
When I try to set system configuration (clicking apply in the gui) I get an Insufficient Permissions error popup. I'm running from powershell in admin mode in Windows 10.

To Reproduce
Steps to reproduce the behavior, for example:

Go to Configuration --> System Configuration
Click Apply (it doesn't matter what I do, change number of processes, or nothing, just click apply)

Copy paste message from the error window (if any)
INsufficient permissions. You do not have write access to the chosen work directory.

Operating System & specs (CPU, RAM etc.). Please complete the following information:

OS: [e.g. Windows 10, Mac OSX Mojave 10.14, Ubuntu 20.04 LTS]
Windows 10, 128 GB Ram, Intel Xeon CPU

Details about your Mesmerize install
I used mamba to install caiman, pip to install mesmerize.

add some stuff to @present_exceptions

Add 2 buttons to messageboxes using @present_exceptions:

Button to open repo issue tracker page
Button to copy system info, traceback, and stdout
-> write all stdout to a file in the ~/.mesmerize dir, perhaps contain stdout for the 25 most recently open sessions? Use session launch timestamp + a random number for the filenames.

Still struggling with Caiman installation with Windows 10

I have a folder in Users that is CalmAn but the conda install -c conda-forge caiman step starts but then seems to stall half way through. I have increased the maximum size of my pagefile, could the issue be I need to increase it more? There are no errors just failure to complete after running for a very long time...

Thanks,

Ease installation

The installation process is a little tricky; I wonder if it could be made easier with:

PEP-518 build-time dependency specification for minimum versions of numpy, cython, setuptools
CaImAn, tensorflow, tslearn, bottleneck etc as a optional features
Pip installing CaImAn directly from github without having to clone separately (preferably with a tag specifier): pip install git+https://github.com/flatironinstitute/[email protected]

This should reduce 6 steps in the installation (linux, at least) down to 1. If the installation procedure (once a python environment is set up) can be brought down to a single invocation of pip, matters could be simplified even further by recommending the use of pipx, which would manage the virtual environment and linking onto the path as well, although then the python version limitation may be more problematic.

No worries if these options have been considered and discounted in the past, though! It looks like it's even more tricky on different platforms, which may make these changes not possible.

[BUG] <Loading k-shape project plot error>

Describe the bug
I've performed the K-shape analysis and saved the plot within the project as a .ptrn file. If I reopen Mesmerize and try to access the k_shape plot again, I get the error:

Screenshots


Traceback (most recent call last):
  File "D:\Anaconda3\envs\mesmerize\lib\site-packages\mesmerize\common\qdialogs.py", line 52, in fn
    return func(self, *args, **kwargs)
  File "D:\Anaconda3\envs\mesmerize\lib\site-packages\mesmerize\plotting\widgets\base.py", line 229, in open_plot
    self.set_plot_opts(plot_state)
  File "D:\Anaconda3\envs\mesmerize\lib\site-packages\mesmerize\plotting\widgets\kshape\widget.py", line 933, in set_plot_opts
    setattr(self, k, opts[k])
  File "D:\Anaconda3\envs\mesmerize\lib\site-packages\mesmerize\plotting\widgets\kshape\widget.py", line 481, in _ksgrid_json
    self.ksgrid = kga
  File "D:\Anaconda3\envs\mesmerize\lib\site-packages\mesmerize\plotting\widgets\kshape\widget.py", line 394, in ksgrid
    if self.n_clusters_out[ij] < self.ksgrid[ij].n_clusters:
IndexError: too many indices for array

If I click OK, I get the main k-shape clustering window with the clusters in the center, but I do not get the interactive plot on the side with clusters of different inertia.

If I run: this.inertia_sorted.head() now, I get this error as well:

    Traceback (most recent call last):
      File "D:\Anaconda3\envs\mesmerize\lib\site-packages\mesmerize\pyqtgraphCore\console\Console.py", line 167, in execSingle
        output = eval(cmd, self.globals(), self.locals())
      File "<string>", line 1, in <module>
    AttributeError: 'NoneType' object has no attribute 'head'

I will have to re-run the clustering if I'd like to view the interactive plot for choosing clusters.

Operating System & specs (CPU, RAM etc.). Please complete the following information:

OS: Tried on Windows 10 and 11, 32 GB RAM, AMD Ryzen 9 5900X

Details about your Mesmerize install

Anaconda

Thanks

Pradeep

[BUG] Error running full CNMFe

Describe the bug
I can import a .tif file using the tiff importer and json_minimal metadata importer. Further, I can inspect the correlation and PNR after running that preliminary analysis. However, when I go to run the full CNMFe analysis, I get an error and don't get an output .hdf5 file, but get the other output files that I have gotten previously upon successful CNMFe analysis. The only updates to my machine have been regarding the OS (Ubuntu 20.04), so I'm not sure exactly what has changed that has caused this issue as I have run this analysis before without problem.

To Reproduce

open viewer
modules > load images > tiff file
select file and load asarray, select json file and use json_minimal metadata importer
modules > CaImAn Toolbox > CNMF-E
input gSig size, enter name, and click "add to batch"
Go to batch manager, run the task, double click on task to inspect correlation and PNR values
save correlation/PNR image as .png
return to CNMF-E window, adjust min_corr and min_pnr values accordingly, enter name for analysis, and click "add to batch"
go to batch manager, run the task
Upon notification that task has been run, task will be highlighted in red and no .hdf5 file will be output, disallowing visualization of ROIs. Seemingly all other file outputs are present in working directory.

Expected behavior
Upon running full CNMF-E, I expected to get an .hdf5 file along with other file outputs so that I could visualize the ROIs as I have before.

Copy paste message from the error window (if any)

Copy-paste or take a screenshot of the terminal that Mesmerize is running in

(mez) scoob@alphaomega:~$ mesmerize
/home/scoob/Desktop/Calcium_Imaging/mez/lib/python3.6/site-packages/sklearn/utils/deprecation.py:143: FutureWarning: The sklearn.cluster.k_means_ module is  deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.cluster. Anything that cannot be imported from sklearn.cluster is now part of the private API.
  warnings.warn(message, FutureWarning)
Loading, please wait... 
%(asctime)s %(levelname)s %(pathname)s %(lineno)s 
 %(message)s 
Moving old logfiles...
Moving old logfiles...
%(asctime)s %(levelname)s %(pathname)s %(lineno)s 
 %(message)s 
EXCEPTION ENCOUNTERED
Traceback (most recent call last):
  File "/home/scoob/Desktop/Calcium_Imaging/mez/lib/python3.6/site-packages/mesmerize/viewer/modules/tiff_io.py", line 99, in check_meta_path
    bn = os.path.basename(self.tiff_file_path)
  File "/usr/lib/python3.6/posixpath.py", line 146, in basename
    p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not NoneType
EXCEPTION ENCOUNTERED
Traceback (most recent call last):
  File "/home/scoob/Desktop/Calcium_Imaging/mez/lib/python3.6/site-packages/mesmerize/viewer/modules/tiff_io.py", line 99, in check_meta_path
    bn = os.path.basename(self.tiff_file_path)
  File "/usr/lib/python3.6/posixpath.py", line 146, in basename
    p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not NoneType
%(asctime)s %(levelname)s %(pathname)s %(lineno)s 
 %(message)s 
starting batch mananger
starting batch mananger
showing corr pnr
showing corr pnr
showing corr pnr
showing corr pnr
%(asctime)s %(levelname)s %(pathname)s %(lineno)s 
 %(message)s 
EXCEPTION ENCOUNTERED
Traceback (most recent call last):
  File "/home/scoob/Desktop/Calcium_Imaging/mez/lib/python3.6/site-packages/mesmerize/pyqtgraphCore/exporters/Exporter.py", line 77, in fileSaveFinished
    self.export(fileName=fileName, **self.fileDialog.opts)
  File "/home/scoob/Desktop/Calcium_Imaging/mez/lib/python3.6/site-packages/mesmerize/pyqtgraphCore/exporters/ImageExporter.py", line 70, in export
    bg = np.empty((self.params['width'], self.params['height'], 4), dtype=np.ubyte)
TypeError: 'float' object cannot be interpreted as an integer
EXCEPTION ENCOUNTERED
Traceback (most recent call last):
  File "/home/scoob/Desktop/Calcium_Imaging/mez/lib/python3.6/site-packages/mesmerize/pyqtgraphCore/exporters/Exporter.py", line 77, in fileSaveFinished
    self.export(fileName=fileName, **self.fileDialog.opts)
  File "/home/scoob/Desktop/Calcium_Imaging/mez/lib/python3.6/site-packages/mesmerize/pyqtgraphCore/exporters/ImageExporter.py", line 70, in export
    bg = np.empty((self.params['width'], self.params['height'], 4), dtype=np.ubyte)
TypeError: 'float' object cannot be interpreted as an integer
showing corr pnr

Make sure the entire stack trace is visible, and all messages relevant to the issue are visible.

If relevant, messages from the batch manager terminal
status: 0
output_info: Traceback (most recent call last):
File "/home/scoob/Desktop/Calcium_Imaging/mez/lib/python3.6/site-packages/mesmerize/viewer/modules/batch_run_modules/CNMFE.py", line 173, in run
cnm.fit(Y)
File "/home/scoob/Desktop/Calcium_Imaging/CaImAn/caiman/source_extraction/cnmf/cnmf.py", line 606, in fit
indices=indices)
File "/home/scoob/Desktop/Calcium_Imaging/CaImAn/caiman/source_extraction/cnmf/map_reduce.py", line 249, in run_CNMF_patches
file_res = dview.map_async(cnmf_patches, args_in).get(4294967)
File "/usr/lib/python3.6/multiprocessing/pool.py", line 644, in get
raise self._value
multiprocessing.pool.MaybeEncodingError: Error sending result: '<multiprocessing.pool.ExceptionWithTraceback object at 0x7f6763dd4cc0>'. Reason: 'PicklingError("Can't pickle <class '_flapack.error'>: import of module '_flapack' failed",)'

Y.shape: [565, 512, 512]
processing_time: 1.0152677694956462

Screenshots
If applicable, add screenshots to help explain your problem.

Operating System & specs (CPU, RAM etc.). Please complete the following information:

OS: Ubuntu 20.04 LTS
CPU: Intel(R) Core(TM) i7-4710HQ CPU
RAM: 16 Gb

Details about your Mesmerize install

Are you using anaconda or venv (the python built-in virtual environment management) venv
Are you using the pip install, If so which version?**pip 21.3.1
Are you using a clone of the master branch from the GitHub repo installed in development mode? No

Additional context
I did check the corr/PNR for several gSig values before running the CNMF-E. I don't think this caused the error, but I figured it was worth mentioning.

[BUG] correlation_pnr() output has edge artifacts not present when I run same in caiman

Describe the bug
When I run the "inspect correlation and pnr" step of cnmfe and look at the image, there are very large edge artifacts in both the correlation image and pnr image that are not present when I run the same method in caiman.

To Reproduce
Steps to reproduce the behavior, for example:

Go to Caiman toolbox and select CNMF-E and enter gSig value (say, 7) and add to batch.
Run the batch and then inspect the result.
Anomalous image pops up.

Expected behavior
Should look the same in both caiman and mesmerize.

Screenshots
From caiman:

From mesmerize (note the bright artifact band around the outer edge of the image for both corr and pnr):

Operating System & specs (CPU, RAM etc.). Please complete the following information:
Windows 10 128GB RAM Xeon Processor (2.4GHz)

Details about your Mesmerize install
Mesmerize 0.7.1 installed using pip.

Additional comments
I poked around in the source code:

MESmerize/mesmerize/viewer/modules/batch_run_modules/CNMFE.py

Line 117 in 0b884e7

cn_filter, pnr = cm.summary_images.correlation_pnr(

I can't see anything strange going on it is running the exact same method as the caiman code. This is truly a head-scratcher. I have seen since I started using mesmerize though so I know it's not just a one-off thing. I haven't dug very deeply into it would be nice to know if others see the same thing.

[BUG] CNMF-E correlation and PNR batch process not working

Describe the bug
When trying to get correlation/pnr inspection plot in cnmf-e pipeline, it doesn't work (I get an error)

To Reproduce
Steps to reproduce the behavior, for example:

caiman toolbox -> cnmfe -> inspect correlation and pnr --> add to batch
within the batch manager window try to run the item (start at selection).
It runs and then turns red and I get the following stack trace:

status: 0
output_info: Traceback (most recent call last):
  File "c:\users\lab_user\miniconda3\envs\mesmerize\lib\site-packages\mesmerize\viewer\modules\batch_run_modules\CNMFE.py", line 143, in run
    os.remove(mf)
PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'F:/mesmerize_projects/mesmerize_testing/batches/motion_correction_testing\\memmap-2f70cc3a-a35f-4338-a240-b531f3b1d23d_d1_600_d2_537_d3_1_order_C_frames_999_.mmap'

output: 2f70cc3a-a35f-4338-a240-b531f3b1d23d
output_files: ['2f70cc3a-a35f-4338-a240-b531f3b1d23d_pnr.pikl', '2f70cc3a-a35f-4338-a240-b531f3b1d23d_cn_filter.pikl']
Y.shape: [999, 600, 537]
processing_time: 1.0310599684715271

Expected behavior
corr/pnr plot to come up like in caiman jupyter and mesmerize docs.

Copy-paste or take a screenshot of the terminal that Mesmerize is running in

Operating System & specs (CPU, RAM etc.). Please complete the following information:
Windows 10

Details about your Mesmerize install
caiman installed with mamba, mesmerize with pip.

Issue with cnmf-e on HPC

Below is the error that I receive when I try to run cnmf-e on the high performance computing system called Rivanna at UVA. The program runs fine with the exact same arguments on a pc laptop. Any ideas?

4 cores requested
128gb of RAM
CentOS operating system

status: 0
output_info: multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/ksm4dk/anaconda3/envs/mesmerize/lib/python3.6/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/home/ksm4dk/anaconda3/envs/mesmerize/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/home/ksm4dk/anaconda3/envs/mesmerize/lib/python3.6/site-packages/caiman/source_extraction/cnmf/map_reduce.py", line 137, in cnmf_patches
cnm = cnm.fit(images)
File "/home/ksm4dk/anaconda3/envs/mesmerize/lib/python3.6/site-packages/caiman/source_extraction/cnmf/cnmf.py", line 506, in fit
self.initialize(Y)
File "/home/ksm4dk/anaconda3/envs/mesmerize/lib/python3.6/site-packages/caiman/source_extraction/cnmf/cnmf.py", line 966, in initialize
**self.params.get_group('init'))
File "/home/ksm4dk/anaconda3/envs/mesmerize/lib/python3.6/site-packages/caiman/source_extraction/cnmf/initialization.py", line 354, in initialize_components
sn=sn, nb=nb, ssub=ssub, ssub_B=ssub_B, init_iter=init_iter, seed_method=seed_method)
File "/home/ksm4dk/anaconda3/envs/mesmerize/lib/python3.6/site-packages/caiman/source_extraction/cnmf/initialization.py", line 1264, in greedyROI_corr
dview=None, dims=(d1, d2), **options['spatial_params'])
File "/home/ksm4dk/anaconda3/envs/mesmerize/lib/python3.6/site-packages/caiman/source_extraction/cnmf/spatial.py", line 218, in update_spatial_components
C_name, Y_name, folder = creatememmap(Y, np.vstack((C, f)), dview)
File "/home/ksm4dk/anaconda3/envs/mesmerize/lib/python3.6/site-packages/caiman/source_extraction/cnmf/spatial.py", line 1125, in creatememmap
folder = tempfile.mkdtemp(dir=tmpf)
File "/home/ksm4dk/anaconda3/envs/mesmerize/lib/python3.6/tempfile.py", line 370, in mkdtemp
_os.mkdir(file, 0o700)
FileNotFoundError: [Errno 2] No such file or directory: '/var/www/ood/apps/sys/dashboard/tmprbl6zye1'
"""

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

Traceback (most recent call last):
File "/home/ksm4dk/anaconda3/envs/mesmerize/lib/python3.6/site-packages/mesmerize/viewer/modules/batch_run_modules/CNMFE.py", line 173, in run
cnm.fit(Y)
File "/home/ksm4dk/anaconda3/envs/mesmerize/lib/python3.6/site-packages/caiman/source_extraction/cnmf/cnmf.py", line 606, in fit
indices=indices)
File "/home/ksm4dk/anaconda3/envs/mesmerize/lib/python3.6/site-packages/caiman/source_extraction/cnmf/map_reduce.py", line 249, in run_CNMF_patches
file_res = dview.map_async(cnmf_patches, args_in).get(4294967)
File "/home/ksm4dk/anaconda3/envs/mesmerize/lib/python3.6/multiprocessing/pool.py", line 644, in get
raise self._value
FileNotFoundError: [Errno 2] No such file or directory: '/var/www/ood/apps/sys/dashboard/tmprbl6zye1'

Y.shape: [1000, 612, 762]
processing_time: 3.812335666020711

Problem Exporting Video

Describe the bug

When I attempt to export my video I get the pop up form, but when I press the second export I get the following error:

AssertionError: Unknown encoder extension

To Reproduce

Go to viewer
Click on image then load image
Press on export button above histogram
With the form, press export again
Then the error occurs

Expected behavior
I expected it to export

Copy paste message from the error window (if any)

This is the error from the 'Show Details':

Traceback (most recent call last):
File "c:\users\katherine\miniconda3\envs\mesmerize\lib\site-packages\mesmerize\common\qdialogs.py", line 52, in fn
return func(self, *args, **kwargs)
File "c:\users\katherine\miniconda3\envs\mesmerize\lib\site-packages\mesmerize\viewer\modules\exporter.py", line 111, in export
writer = skvideo.io.FFmpegWriter(f'{path}.{extn}', outputdict=output_params)
File "c:\users\katherine\miniconda3\envs\mesmerize\lib\site-packages\skvideo\io\ffmpeg.py", line 336, in init
assert str.encode(self.extension).lower() in _FFMPEG_SUPPORTED_ENCODERS, "Unknown encoder extension: " + self.extension.lower()
AssertionError: Unknown encoder extension:

Copy-paste or take a screenshot of the terminal that Mesmerize is running in

![image](<img width="960" alt="terminalfromerror" src="https://user-images.githubusercontent.com/77304549/123695196-430aba00-d828-11eb-8577-a0fd82625234.png">

Make sure the entire stack trace is visible, and all messages relevant to the issue are visible.

If relevant, messages from the batch manager terminal

Screenshots

Operating System & specs (CPU, RAM etc.). Please complete the following information:

OS: Windows 10

Details about your Mesmerize install

anaconda
pip 21.1.2

CNMFE goes to orange

Hello,
Still trying to figure out how to make mesmerize work.
Now when I run the CNMFE it always end up orange. From the logs, it look like it finished but its still not green.
I checked your documentation and orange means that the user aborted it but I didn't

Segmentation fault on macos when trying to start mesmerize

Operating System

macOS catalina 10.15.7

Details about your Mesmerize install

Are you using the pip install? If so which version?
Are you using a clone of the master branch from the GitHub repo?
are you using anaconda or venv (the python built-in virtual environment management)

used pip install with anaconda env. followed the mac anaconda instruction directly: http://docs.mesmerizelab.org/en/master/user_guides/installation.html

Describe the issue, please be as explicit and detailed as possible.

I have followed all the instructions for install, but when I start mesmerize it begins to open, then crashes and has a segmentation fault.

Steps that can be followed to reproduce the problem. What exactly were you were doing that lead to the issue.

I created a new anaconda env and followed the install instructions. started mesmerize then it crashes.

Screenshot or copy-paste from the terminal that Mesmerize is running in

Make sure the entire stack trace is visible, or that all messages relevant to the issue are visible!

(base) kitchlm1@C02CX47SMD6T-ML ~ % conda activate mesmerize
(mesmerize) kitchlm1@C02CX47SMD6T-ML ~ % mesmerize
/Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:516: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint8 = np.dtype([("qint8", np.int8, 1)])
/Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint16 = np.dtype([("qint16", np.int16, 1)])
/Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint32 = np.dtype([("qint32", np.int32, 1)])
/Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_resource = np.dtype([("resource", np.ubyte, 1)])
/Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:541: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint8 = np.dtype([("qint8", np.int8, 1)])
/Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:542: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:543: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint16 = np.dtype([("qint16", np.int16, 1)])
/Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:544: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_qint32 = np.dtype([("qint32", np.int32, 1)])
/Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_resource = np.dtype([("resource", np.ubyte, 1)])
objc[2335]: Class QMacAutoReleasePoolTracker is implemented in both /Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/cv2/.dylibs/QtCore (0x123213700) and /Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/PyQt5/Qt/lib/QtCore.framework/Versions/5/QtCore (0x145ef11d0). One of the two will be used. Which one is undefined.
objc[2335]: Class QT_ROOT_LEVEL_POOL__THESE_OBJECTS_WILL_BE_RELEASED_WHEN_QAPP_GOES_OUT_OF_SCOPE is implemented in both /Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/cv2/.dylibs/QtCore (0x123213778) and /Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/PyQt5/Qt/lib/QtCore.framework/Versions/5/QtCore (0x145ef1248). One of the two will be used. Which one is undefined.
objc[2335]: Class RunLoopModeTracker is implemented in both /Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/cv2/.dylibs/QtCore (0x1232137f0) and /Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/PyQt5/Qt/lib/QtCore.framework/Versions/5/QtCore (0x145ef1270). One of the two will be used. Which one is undefined.
/Users/kitchlm1/opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/sklearn/utils/deprecation.py:143: FutureWarning: The sklearn.cluster.k_means module is deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.cluster. Anything that cannot be imported from sklearn.cluster is now part of the private API.
warnings.warn(message, FutureWarning)
Loading, please wait...
zsh: segmentation fault mesmerize

Relevant screenshots

If relevant, messages from the batch manager terminal

Anything else which you think is relevant

I have previously had mesmerize working on my laptop (though I remember having issues the first time installing, but different issues from the current one), but I recently tried to update caiman and mesmerize in the env. It worked, I thought ( I was able to open and use mesmerize), but a few days later when I tried to open it again, it would not work. I dont remember that error, but I removed the env and started from scratch. Now i cannot get mesmerize to open at all.

[BUG Daemonic processes are not allowed to have children

Hi all,

Describe the bug
I'm trying to run "extractstim" from flowchart and I always get the program bolcked and the error: Daemonic processes are not allowed to have children.

To Reproduce
Steps to reproduce the behavior, for example:

Expected behavior
Extract portions of curves according to stimulus mpas

Copy paste message from the error window (if any)

Operating System & specs (CPU, RAM etc.). Please complete the following information:

OS: Windows 10, 12 cores, 98 GB RAM

Details about your Mesmerize install
using anaconda pip install 21.0.1

Additional context
Add any other context about the problem here.

Thanks in advance!!

Caimen installation issue on Windows 10

Windows 10 i7

Details about your Mesmerize install

Mesmerize installed and will open but not with Caimen features

Unsatisfiable error - incompatible with existing version of python in your environment
Seems to be problem with the version of python (3.8) I am using.

unexpected issues to a new man

Describe the bug
the following error occurred

KeyError: ('No framerate for current image sequence!', 'You must set a framerate for the current image sequence. You can set it manually in the console like this:\nget_meta()["fps"] = ')

To Reproduce
Steps to reproduce the behavior, for example:

Go to 'set CNMF parameters'
Click on 'Add to batch'
See error above

Indeed I run ''' get_meta()["fps"] = 1 ''' in the Console at Mesmerize- Welcome Window-
Expected behavior

Traceback (most recent call last):
File "/home/user/venvs/mesmerize/lib/python3.6/site-packages/mesmerize/pyqtgraphCore/console/Console.py", line 167, in execSingle
output = eval(cmd, self.globals(), self.locals())
File "", line 1
get_meta()["fps"] = 1
^
SyntaxError: invalid syntax

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/user/venvs/mesmerize/lib/python3.6/site-packages/mesmerize/pyqtgraphCore/console/Console.py", line 171, in execSingle
    exec(cmd, self.globals(), self.locals())
  File "<string>", line 1, in <module>
NameError: name 'get_meta' is not defined

Operating System & specs (CPU, RAM etc.). Please complete the following information:
OS: the xubantu posted online, containing mesmerize

Details about your Mesmerize install

Are you using anaconda or venv (the python built-in virtual environment management)
Are you using the pip install, If so which version?**
Are you using a clone of the master branch from the GitHub repo installed in development mode?

Additional context
Add any other context about the problem here.

OSX install failure, psutil

I'm following the installation instructions given here (completed steps 1-3): http://docs.mesmerizelab.org/en/master/user_guides/installation.html
When I try to download mesmerize via pip, it fails at Building wheels for collected packages: psutil

System information

OS (ex. Windows 10, Mac OSX Mojave, Ubuntu 20.04 LTS) -- MacOS Big Sur
CPU (ex. Intel i7 9700k, AMD Ryzen 3950x) -- 2.4 GHz Quad-Core Intel Core i5
RAM -- 8 GB 2133 MHz LPDDR3
Do you have an SSD or magnetic HDD -- SSD

(base) andrews-mbp-2:~ andrewsiliciano$ source activate mesmerize
(mesmerize) andrews-mbp-2:~ andrewsiliciano$ pip install mesmerize
Collecting mesmerize
  Using cached mesmerize-0.4.1-py3-none-any.whl (1.2 MB)
Requirement already satisfied: QtPy>=1.6.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (1.9.0)
Requirement already satisfied: holoviews in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (1.14.1)
Requirement already satisfied: Pillow>=5.4.1 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (8.0.1)
Requirement already satisfied: python-dateutil>=2.8.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (2.8.1)
Requirement already satisfied: ipykernel>=4.10 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (5.4.2)
Requirement already satisfied: MarkupSafe>=1.1.1 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (1.1.1)
Requirement already satisfied: ipython>=7.15.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (7.16.1)
Requirement already satisfied: future>=0.18.2 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (0.18.2)
Requirement already satisfied: PyQt5<=5.12,>=5.9.2 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (5.12)
Requirement already satisfied: scipy>=1.2.1 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (1.5.3)
Requirement already satisfied: joblib>=0.15.1 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (1.0.0)
Requirement already satisfied: tqdm>=4.37.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (4.55.0)
Requirement already satisfied: PeakUtils in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (1.3.3)
Requirement already satisfied: cycler==0.10.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (0.10.0)
Requirement already satisfied: tifffile in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (0.15.1)
Requirement already satisfied: pandas~=0.25.3 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (0.25.3)
Requirement already satisfied: dask>=1.1.1 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (2020.12.0)
Requirement already satisfied: pyqtgraph in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (0.11.1)
Requirement already satisfied: pynwb in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (1.4.0)
Requirement already satisfied: scikit-image~=0.15.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (0.15.0)
Requirement already satisfied: h5py~=2.10.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (2.10.0)
Requirement already satisfied: scikit-learn>=0.20.2 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (0.24.0)
Requirement already satisfied: bokeh>=2.2.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (2.2.3)
Requirement already satisfied: ipyparallel>=6.3 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (6.3.0)
Requirement already satisfied: matplotlib<=3.2.1 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from mesmerize) (3.2.1)
Requirement already satisfied: six in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from cycler==0.10.0->mesmerize) (1.15.0)
Collecting seaborn==0.9.0
  Using cached seaborn-0.9.0-py3-none-any.whl (208 kB)
Requirement already satisfied: numpy>=1.9.3 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from seaborn==0.9.0->mesmerize) (1.19.4)
Collecting spyder==3.3.3
  Using cached spyder-3.3.3-py3-none-any.whl (2.8 MB)
Requirement already satisfied: numpydoc in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder==3.3.3->mesmerize) (1.1.0)
Requirement already satisfied: spyder-kernels<1.0,>=0.4.2 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder==3.3.3->mesmerize) (0.5.2)
Requirement already satisfied: qtconsole>=4.2.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder==3.3.3->mesmerize) (5.0.1)
Requirement already satisfied: pyzmq in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder==3.3.3->mesmerize) (20.0.0)
Requirement already satisfied: rope>=0.10.5 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder==3.3.3->mesmerize) (0.18.0)
Requirement already satisfied: pylint in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder==3.3.3->mesmerize) (2.6.0)
Requirement already satisfied: qtawesome>=0.4.1 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder==3.3.3->mesmerize) (1.0.2)
Requirement already satisfied: pyflakes in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder==3.3.3->mesmerize) (2.2.0)
Requirement already satisfied: pycodestyle in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder==3.3.3->mesmerize) (2.6.0)
Requirement already satisfied: sphinx in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder==3.3.3->mesmerize) (3.4.1)
Requirement already satisfied: pickleshare in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder==3.3.3->mesmerize) (0.7.5)
Requirement already satisfied: pygments>=2.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder==3.3.3->mesmerize) (2.7.3)
Requirement already satisfied: nbconvert in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder==3.3.3->mesmerize) (6.0.7)
Requirement already satisfied: keyring in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder==3.3.3->mesmerize) (21.8.0)
Requirement already satisfied: jedi>=0.9.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder==3.3.3->mesmerize) (0.17.2)
Requirement already satisfied: cloudpickle in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder==3.3.3->mesmerize) (1.6.0)
Requirement already satisfied: chardet>=2.0.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder==3.3.3->mesmerize) (4.0.0)
Requirement already satisfied: packaging>=16.8 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from bokeh>=2.2.0->mesmerize) (20.8)
Requirement already satisfied: tornado>=5.1 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from bokeh>=2.2.0->mesmerize) (6.1)
Requirement already satisfied: PyYAML>=3.10 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from bokeh>=2.2.0->mesmerize) (5.3.1)
Requirement already satisfied: typing-extensions>=3.7.4 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from bokeh>=2.2.0->mesmerize) (3.7.4.3)
Requirement already satisfied: Jinja2>=2.7 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from bokeh>=2.2.0->mesmerize) (2.11.2)
Collecting graphviz>=0.13
  Using cached graphviz-0.16-py2.py3-none-any.whl (19 kB)
Requirement already satisfied: jupyter-client in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipykernel>=4.10->mesmerize) (6.1.7)
Requirement already satisfied: traitlets>=4.1.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipykernel>=4.10->mesmerize) (4.3.3)
Requirement already satisfied: appnope in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipykernel>=4.10->mesmerize) (0.1.2)
Requirement already satisfied: decorator in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipyparallel>=6.3->mesmerize) (4.4.2)
Requirement already satisfied: ipython-genutils in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipyparallel>=6.3->mesmerize) (0.2.0)
Requirement already satisfied: setuptools>=18.5 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipython>=7.15.0->mesmerize) (51.0.0.post20201207)
Requirement already satisfied: pexpect in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipython>=7.15.0->mesmerize) (4.8.0)
Requirement already satisfied: backcall in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipython>=7.15.0->mesmerize) (0.2.0)
Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipython>=7.15.0->mesmerize) (3.0.8)
Requirement already satisfied: parso<0.8.0,>=0.7.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from jedi>=0.9.0->spyder==3.3.3->mesmerize) (0.7.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from matplotlib<=3.2.1->mesmerize) (1.3.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from matplotlib<=3.2.1->mesmerize) (2.4.7)
Collecting numba>=0.50.0
  Using cached numba-0.52.0-cp36-cp36m-macosx_10_14_x86_64.whl (2.2 MB)
Collecting llvmlite<0.36,>=0.35.0
  Using cached llvmlite-0.35.0-cp36-cp36m-macosx_10_9_x86_64.whl (18.5 MB)
Collecting opencv-contrib-python>=4.2
  Downloading opencv_contrib_python-4.5.1.48-cp36-cp36m-macosx_10_13_x86_64.whl (51.3 MB)
     |████████████████████████████████| 51.3 MB 6.0 MB/s 
Collecting opencv-python>=4.2
  Downloading opencv_python-4.5.1.48-cp36-cp36m-macosx_10_13_x86_64.whl (40.3 MB)
     |████████████████████████████████| 40.3 MB 7.0 MB/s 
Requirement already satisfied: pytz>=2017.2 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from pandas~=0.25.3->mesmerize) (2020.5)
Requirement already satisfied: wcwidth in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython>=7.15.0->mesmerize) (0.2.5)
Collecting psutil~=5.7.0
  Using cached psutil-5.7.3.tar.gz (465 kB)
Requirement already satisfied: PyQt5_sip<4.20,>=4.19.14 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from PyQt5<=5.12,>=5.9.2->mesmerize) (4.19.18)
Requirement already satisfied: jupyter-core in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from qtconsole>=4.2.0->spyder==3.3.3->mesmerize) (4.7.0)
Requirement already satisfied: imageio>=2.0.1 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from scikit-image~=0.15.0->mesmerize) (2.9.0)
Requirement already satisfied: PyWavelets>=0.4.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from scikit-image~=0.15.0->mesmerize) (1.1.1)
Requirement already satisfied: networkx>=2.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from scikit-image~=0.15.0->mesmerize) (2.5)
Requirement already satisfied: threadpoolctl>=2.0.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from scikit-learn>=0.20.2->mesmerize) (2.1.0)
Requirement already satisfied: wurlitzer in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from spyder-kernels<1.0,>=0.4.2->spyder==3.3.3->mesmerize) (2.0.1)
Collecting tables>=3.6.1
  Using cached tables-3.6.1-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (4.4 MB)
Collecting numexpr>=2.6.2
  Using cached numexpr-2.7.2-cp36-cp36m-macosx_10_9_x86_64.whl (101 kB)
Requirement already satisfied: pyviz-comms>=0.7.3 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from holoviews->mesmerize) (2.0.1)
Requirement already satisfied: panel>=0.8.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from holoviews->mesmerize) (0.10.2)
Requirement already satisfied: param<2.0,>=1.9.3 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from holoviews->mesmerize) (1.10.0)
Requirement already satisfied: colorcet in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from holoviews->mesmerize) (2.0.2)
Requirement already satisfied: pyct>=0.4.4 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from panel>=0.8.0->holoviews->mesmerize) (0.4.8)
Requirement already satisfied: markdown in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from panel>=0.8.0->holoviews->mesmerize) (3.3.3)
Requirement already satisfied: requests in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from panel>=0.8.0->holoviews->mesmerize) (2.25.1)
Collecting jupyter
  Using cached jupyter-1.0.0-py2.py3-none-any.whl (2.7 kB)
Requirement already satisfied: ipywidgets in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from jupyter->mesmerize) (7.6.2)
Requirement already satisfied: jupyter-console in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from jupyter->mesmerize) (6.2.0)
Requirement already satisfied: notebook in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from jupyter->mesmerize) (6.1.6)
Requirement already satisfied: nbformat>=4.2.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipywidgets->jupyter->mesmerize) (5.0.8)
Requirement already satisfied: widgetsnbextension~=3.5.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipywidgets->jupyter->mesmerize) (3.5.1)
Requirement already satisfied: jupyterlab-widgets>=1.0.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipywidgets->jupyter->mesmerize) (1.0.0)
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from nbformat>=4.2.0->ipywidgets->jupyter->mesmerize) (3.2.0)
Requirement already satisfied: attrs>=17.4.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets->jupyter->mesmerize) (20.3.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets->jupyter->mesmerize) (0.17.3)
Requirement already satisfied: importlib-metadata in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets->jupyter->mesmerize) (3.3.0)
Requirement already satisfied: prometheus-client in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from notebook->jupyter->mesmerize) (0.9.0)
Requirement already satisfied: Send2Trash in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from notebook->jupyter->mesmerize) (1.5.0)
Requirement already satisfied: argon2-cffi in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from notebook->jupyter->mesmerize) (20.1.0)
Requirement already satisfied: terminado>=0.8.3 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from notebook->jupyter->mesmerize) (0.9.1)
Requirement already satisfied: ptyprocess in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from terminado>=0.8.3->notebook->jupyter->mesmerize) (0.7.0)
Requirement already satisfied: cffi>=1.0.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from argon2-cffi->notebook->jupyter->mesmerize) (1.14.4)
Requirement already satisfied: pycparser in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from cffi>=1.0.0->argon2-cffi->notebook->jupyter->mesmerize) (2.20)
Requirement already satisfied: zipp>=0.5 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from importlib-metadata->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets->jupyter->mesmerize) (3.4.0)
Requirement already satisfied: mistune<2,>=0.8.1 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from nbconvert->spyder==3.3.3->mesmerize) (0.8.4)
Requirement already satisfied: bleach in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from nbconvert->spyder==3.3.3->mesmerize) (3.2.1)
Requirement already satisfied: pandocfilters>=1.4.1 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from nbconvert->spyder==3.3.3->mesmerize) (1.4.3)
Requirement already satisfied: nbclient<0.6.0,>=0.5.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from nbconvert->spyder==3.3.3->mesmerize) (0.5.1)
Requirement already satisfied: jupyterlab-pygments in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from nbconvert->spyder==3.3.3->mesmerize) (0.1.2)
Requirement already satisfied: defusedxml in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from nbconvert->spyder==3.3.3->mesmerize) (0.6.0)
Requirement already satisfied: entrypoints>=0.2.2 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from nbconvert->spyder==3.3.3->mesmerize) (0.3)
Requirement already satisfied: testpath in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from nbconvert->spyder==3.3.3->mesmerize) (0.4.4)
Requirement already satisfied: nest-asyncio in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from nbclient<0.6.0,>=0.5.0->nbconvert->spyder==3.3.3->mesmerize) (1.4.3)
Requirement already satisfied: async-generator in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from nbclient<0.6.0,>=0.5.0->nbconvert->spyder==3.3.3->mesmerize) (1.10)
Requirement already satisfied: webencodings in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from bleach->nbconvert->spyder==3.3.3->mesmerize) (0.5.1)
Requirement already satisfied: imagesize in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from sphinx->spyder==3.3.3->mesmerize) (1.2.0)
Requirement already satisfied: docutils>=0.12 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from sphinx->spyder==3.3.3->mesmerize) (0.16)
Requirement already satisfied: babel>=1.3 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from sphinx->spyder==3.3.3->mesmerize) (2.9.0)
Requirement already satisfied: sphinxcontrib-jsmath in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from sphinx->spyder==3.3.3->mesmerize) (1.0.1)
Requirement already satisfied: sphinxcontrib-htmlhelp in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from sphinx->spyder==3.3.3->mesmerize) (1.0.3)
Requirement already satisfied: snowballstemmer>=1.1 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from sphinx->spyder==3.3.3->mesmerize) (2.0.0)
Requirement already satisfied: sphinxcontrib-serializinghtml in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from sphinx->spyder==3.3.3->mesmerize) (1.1.4)
Requirement already satisfied: alabaster<0.8,>=0.7 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from sphinx->spyder==3.3.3->mesmerize) (0.7.12)
Requirement already satisfied: sphinxcontrib-qthelp in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from sphinx->spyder==3.3.3->mesmerize) (1.0.3)
Requirement already satisfied: sphinxcontrib-devhelp in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from sphinx->spyder==3.3.3->mesmerize) (1.0.2)
Requirement already satisfied: sphinxcontrib-applehelp in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from sphinx->spyder==3.3.3->mesmerize) (1.0.2)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from requests->panel>=0.8.0->holoviews->mesmerize) (1.26.2)
Requirement already satisfied: certifi>=2017.4.17 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from requests->panel>=0.8.0->holoviews->mesmerize) (2020.12.5)
Requirement already satisfied: idna<3,>=2.5 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from requests->panel>=0.8.0->holoviews->mesmerize) (2.10)
Collecting nuset-lib
  Using cached nuset_lib-0.1.1-py3-none-any.whl (196 kB)
Requirement already satisfied: mccabe<0.7,>=0.6 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from pylint->spyder==3.3.3->mesmerize) (0.6.1)
Requirement already satisfied: isort<6,>=4.2.5 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from pylint->spyder==3.3.3->mesmerize) (5.7.0)
Requirement already satisfied: toml>=0.7.1 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from pylint->spyder==3.3.3->mesmerize) (0.10.2)
Requirement already satisfied: astroid<=2.5,>=2.4.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from pylint->spyder==3.3.3->mesmerize) (2.4.2)
Requirement already satisfied: wrapt~=1.11 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from astroid<=2.5,>=2.4.0->pylint->spyder==3.3.3->mesmerize) (1.11.2)
Requirement already satisfied: typed-ast<1.5,>=1.4.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from astroid<=2.5,>=2.4.0->pylint->spyder==3.3.3->mesmerize) (1.4.1)
Requirement already satisfied: lazy-object-proxy==1.4.* in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from astroid<=2.5,>=2.4.0->pylint->spyder==3.3.3->mesmerize) (1.4.3)
Requirement already satisfied: hdmf<3,>=2.1.0 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from pynwb->mesmerize) (2.2.0)
Requirement already satisfied: ruamel.yaml>=0.15 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from hdmf<3,>=2.1.0->pynwb->mesmerize) (0.16.12)
Requirement already satisfied: ruamel.yaml.clib>=0.1.2 in /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ruamel.yaml>=0.15->hdmf<3,>=2.1.0->pynwb->mesmerize) (0.2.2)
Collecting qtap
  Using cached qtap-0.1.2-py3-none-any.whl (19 kB)
Collecting sk-video
  Using cached sk_video-1.1.10-py2.py3-none-any.whl (2.3 MB)
Collecting tcl
  Using cached Tcl-0.2-py3-none-any.whl (2.4 kB)
Collecting tk
  Using cached tk-0.1.0-py3-none-any.whl (3.9 kB)
Building wheels for collected packages: psutil
  Building wheel for psutil (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /opt/anaconda3/envs/mesmerize/bin/python3.6 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/97/gwt2yy_s4t7927qwbpd95hkc0000gn/T/pip-install-m92bn54t/psutil_576054bc669247aa998ed22374c67e1c/setup.py'"'"'; __file__='"'"'/private/var/folders/97/gwt2yy_s4t7927qwbpd95hkc0000gn/T/pip-install-m92bn54t/psutil_576054bc669247aa998ed22374c67e1c/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/97/gwt2yy_s4t7927qwbpd95hkc0000gn/T/pip-wheel-rnfp8_qo
       cwd: /private/var/folders/97/gwt2yy_s4t7927qwbpd95hkc0000gn/T/pip-install-m92bn54t/psutil_576054bc669247aa998ed22374c67e1c/
  Complete output (44 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.7-x86_64-3.6
  creating build/lib.macosx-10.7-x86_64-3.6/psutil
  copying psutil/_pswindows.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
  copying psutil/_common.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
  copying psutil/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
  copying psutil/_psosx.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
  copying psutil/_psbsd.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
  copying psutil/_psaix.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
  copying psutil/_pslinux.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
  copying psutil/_compat.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
  copying psutil/_psposix.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
  copying psutil/_pssunos.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
  creating build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/test_contracts.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/test_connections.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/runner.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/test_unicode.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/test_misc.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/test_posix.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/test_linux.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/test_sunos.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/test_aix.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/test_process.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/test_bsd.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/test_system.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/test_osx.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/test_memleaks.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/test_windows.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/__main__.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  copying psutil/tests/test_testutils.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
  running build_ext
  building 'psutil._psutil_osx' extension
  creating build/temp.macosx-10.7-x86_64-3.6
  creating build/temp.macosx-10.7-x86_64-3.6/psutil
  creating build/temp.macosx-10.7-x86_64-3.6/psutil/arch
  creating build/temp.macosx-10.7-x86_64-3.6/psutil/arch/osx
  gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/anaconda3/envs/mesmerize/include -arch x86_64 -I/opt/anaconda3/envs/mesmerize/include -arch x86_64 -DPSUTIL_POSIX=1 -DPSUTIL_SIZEOF_PID_T=4 -DPSUTIL_VERSION=573 -DPSUTIL_OSX=1 -I/opt/anaconda3/envs/mesmerize/include/python3.6m -c psutil/_psutil_common.c -o build/temp.macosx-10.7-x86_64-3.6/psutil/_psutil_common.o
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for psutil
  Running setup.py clean for psutil
Failed to build psutil
Installing collected packages: psutil, numexpr, llvmlite, tk, tcl, tables, spyder, sk-video, seaborn, qtap, opencv-python, opencv-contrib-python, nuset-lib, numba, jupyter, graphviz, mesmerize
  Attempting uninstall: psutil
    Found existing installation: psutil 5.8.0
    Uninstalling psutil-5.8.0:
      Successfully uninstalled psutil-5.8.0
    Running setup.py install for psutil ... error
    ERROR: Command errored out with exit status 1:
     command: /opt/anaconda3/envs/mesmerize/bin/python3.6 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/97/gwt2yy_s4t7927qwbpd95hkc0000gn/T/pip-install-m92bn54t/psutil_576054bc669247aa998ed22374c67e1c/setup.py'"'"'; __file__='"'"'/private/var/folders/97/gwt2yy_s4t7927qwbpd95hkc0000gn/T/pip-install-m92bn54t/psutil_576054bc669247aa998ed22374c67e1c/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/97/gwt2yy_s4t7927qwbpd95hkc0000gn/T/pip-record-9c9z1nkv/install-record.txt --single-version-externally-managed --compile --install-headers /opt/anaconda3/envs/mesmerize/include/python3.6m/psutil
         cwd: /private/var/folders/97/gwt2yy_s4t7927qwbpd95hkc0000gn/T/pip-install-m92bn54t/psutil_576054bc669247aa998ed22374c67e1c/
    Complete output (44 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.7-x86_64-3.6
    creating build/lib.macosx-10.7-x86_64-3.6/psutil
    copying psutil/_pswindows.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
    copying psutil/_common.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
    copying psutil/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
    copying psutil/_psosx.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
    copying psutil/_psbsd.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
    copying psutil/_psaix.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
    copying psutil/_pslinux.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
    copying psutil/_compat.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
    copying psutil/_psposix.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
    copying psutil/_pssunos.py -> build/lib.macosx-10.7-x86_64-3.6/psutil
    creating build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/test_contracts.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/test_connections.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/runner.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/test_unicode.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/test_misc.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/test_posix.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/test_linux.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/test_sunos.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/test_aix.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/test_process.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/test_bsd.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/test_system.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/test_osx.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/test_memleaks.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/test_windows.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/__main__.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    copying psutil/tests/test_testutils.py -> build/lib.macosx-10.7-x86_64-3.6/psutil/tests
    running build_ext
    building 'psutil._psutil_osx' extension
    creating build/temp.macosx-10.7-x86_64-3.6
    creating build/temp.macosx-10.7-x86_64-3.6/psutil
    creating build/temp.macosx-10.7-x86_64-3.6/psutil/arch
    creating build/temp.macosx-10.7-x86_64-3.6/psutil/arch/osx
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/anaconda3/envs/mesmerize/include -arch x86_64 -I/opt/anaconda3/envs/mesmerize/include -arch x86_64 -DPSUTIL_POSIX=1 -DPSUTIL_SIZEOF_PID_T=4 -DPSUTIL_VERSION=573 -DPSUTIL_OSX=1 -I/opt/anaconda3/envs/mesmerize/include/python3.6m -c psutil/_psutil_common.c -o build/temp.macosx-10.7-x86_64-3.6/psutil/_psutil_common.o
    xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
  Rolling back uninstall of psutil
  Moving to /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/psutil-5.8.0.dist-info/
   from /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/~sutil-5.8.0.dist-info
  Moving to /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/psutil/
   from /opt/anaconda3/envs/mesmerize/lib/python3.6/site-packages/~sutil
ERROR: Command errored out with exit status 1: /opt/anaconda3/envs/mesmerize/bin/python3.6 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/97/gwt2yy_s4t7927qwbpd95hkc0000gn/T/pip-install-m92bn54t/psutil_576054bc669247aa998ed22374c67e1c/setup.py'"'"'; __file__='"'"'/private/var/folders/97/gwt2yy_s4t7927qwbpd95hkc0000gn/T/pip-install-m92bn54t/psutil_576054bc669247aa998ed22374c67e1c/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/97/gwt2yy_s4t7927qwbpd95hkc0000gn/T/pip-record-9c9z1nkv/install-record.txt --single-version-externally-managed --compile --install-headers /opt/anaconda3/envs/mesmerize/include/python3.6m/psutil Check the logs for full command output.

Are you using anaconda, python virtual environments, or something else?
conda 4.9.2
If you're installing mesmerize through pip, what version of pip is installed in the environment?
pip 20.3.3
What is the python version in the environment you're trying to install mesmerize in?
python 3.6

Download data link not allowing access

Hello,

I have tried opening the link to download the sample data files from several browsers but I get an error 'The connection was reset'. Please let me know what I'm doing wrong.
Thanks,
-Miranda

Could not find Caiman

Operating System Windows 10 in VM

Details about your Mesmerize install

Are you using the pip install? If so which version? conda install -c conda-forge caiman
Are you using a clone of the master branch from the GitHub repo?
are you using anaconda or venv (the python built-in virtual environment management)
I followed exactly what's here: http://docs.mesmerizelab.org/en/master/user_guides/installation.html#from-github-development

Describe the issue, please be as explicit and detailed as possible. Mesemerize starts but promts that caiman could not work since it is not in the environment but I can see is there

Also caimanmanager.py install didn't work: instead of running the command it prompted a how to open the .py

Steps that can be followed to reproduce the problem. What exactly were you were doing that lead to the issue.

Screenshot or copy-paste from the terminal that Mesmerize is running in

Make sure the entire stack trace is visible, or that all messages relevant to the issue are visible!

Relevant screenshots

If relevant, messages from the batch manager terminal

Anything else which you think is relevant

KShape bug

Describe the bug
I am using k-Shape Clustering to determine if I can find clusters in my traces based on the shapes of the peak. I get the following error when I click Start.

D:\Anaconda3\envs\mesmerize\lib\site-packages\sklearn\utils\deprecation.py:143: FutureWarning: The sklearn.cluster.k_means_ module is  deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.cluster. Anything that cannot be imported from sklearn.cluster is now part of the private API.
  warnings.warn(message, FutureWarning)
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "D:\Anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 105, in spawn_main
    exitcode = _main(fd)
  File "D:\Anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 114, in _main
    prepare(preparation_data)
  File "D:\Anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 225, in prepare
    _fixup_main_from_path(data['init_main_from_path'])
  File "D:\Anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 277, in _fixup_main_from_path
    run_name="__mp_main__")
  File "D:\Anaconda3\envs\mesmerize\lib\runpy.py", line 263, in run_path
    pkg_name=pkg_name, script_name=fname)
  File "D:\Anaconda3\envs\mesmerize\lib\runpy.py", line 96, in _run_module_code
    mod_name, mod_spec, pkg_name, script_name)
  File "D:\Anaconda3\envs\mesmerize\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "d:\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\plotting\widgets\kshape\kshape_process.py", line 16, in <module>
    from mesmerize.common.configuration import HAS_TSLEARN, get_sys_config
  File "D:\Anaconda3\envs\mesmerize\lib\site-packages\mesmerize\__init__.py", line 1, in <module>
    from .analysis import *
  File "D:\Anaconda3\envs\mesmerize\lib\site-packages\mesmerize\analysis\__init__.py", line 3, in <module>
    from .math import cross_correlation, drfft_dtw, tvregdiff
  File "D:\Anaconda3\envs\mesmerize\lib\site-packages\mesmerize\analysis\math\drfft_dtw.py", line 17, in <module>
    raw_curve: np.ndarray = None, rf_curve: np.ndarray = None) -> list:
  File "D:\Anaconda3\envs\mesmerize\lib\multiprocessing\context.py", line 56, in Manager
    m.start()
  File "D:\Anaconda3\envs\mesmerize\lib\multiprocessing\managers.py", line 513, in start
    self._process.start()
  File "D:\Anaconda3\envs\mesmerize\lib\multiprocessing\process.py", line 105, in start
    self._popen = self._Popen(self)
  File "D:\Anaconda3\envs\mesmerize\lib\multiprocessing\context.py", line 322, in _Popen
    return Popen(process_obj)
  File "D:\Anaconda3\envs\mesmerize\lib\multiprocessing\popen_spawn_win32.py", line 33, in __init__
    prep_data = spawn.get_preparation_data(process_obj._name)
  File "D:\Anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 143, in get_preparation_data
    _check_not_importing_main()
  File "D:\Anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 136, in _check_not_importing_main
    is not going to be frozen to produce an executable.''')
RuntimeError: 
        An attempt has been made to start a new process before the
        current process has finished its bootstrapping phase.

        This probably means that you are not using fork to start your
        child processes and you have forgotten to use the proper idiom
        in the main module:

            if __name__ == '__main__':
                freeze_support()
                ...

        The "freeze_support()" line can be omitted if the program
        is not going to be frozen to produce an executable.

===== 2021.07.21 10:07:11 =====

I followed your video to perform Peak detection and got to the point where I got peak features. I can successfully view different peak parameters using the BeeSwarm Plot. When I go back to the flowchart and connect K-shape to the Peak Detect node, and try the clustering with default options I get the error above. This happens for any peak parameter I select in the data column.

On a related note for K-shape, when I try _pf_peak_curve in the data column, I get this error:

Traceback (most recent call last):
  File "d:\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\common\qdialogs.py", line 52, in fn
    return func(self, *args, **kwargs)
  File "d:\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\plotting\widgets\kshape\widget.py", line 713, in start_process
    padded = self.pad_input_data(self.input_arrays, method='fill-size')
  File "d:\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\plotting\widgets\kshape\widget.py", line 664, in pad_input_data
    s = c.size
AttributeError: 'float' object has no attribute 'size'

Operating System & specs (CPU, RAM etc.). Please complete the following information:

Windows 10, 32 GB RAM, AMD Ryzen 9 5900X 12-Core

Details about your Mesmerize install

Anaconda navigator
Python 3.6
I had a lot of trouble with Windows installation esp with pandas version conflicts and caiman taking too long to install, and eventually settled on this:
- Use this first: conda create -n mesmerize -c conda-forge caiman pandas~=0.25.3 python=3.6
- Follow the rest of instructions on mesmerize doc website, except for caiman and pandas installation...

Thanks for developing and supporting Mesmerize.

Cheers
Pradeep

CalmAn features not enabled and working

Hi,
I am on windows 10 with caiman installed as per instructions here: https://caiman.readthedocs.io/en/master/Installation.html#installation-on-macos-and-linux

I have followed instructions for installing mesmerize on windows. But while running mesmerize, the UI opens but CalmAn is not working.

I checked ../mesmerize/lib/site-packages/ and caiman is installed correctly. Any pointers to resolve this will be helpful.

caiman package not found

Please try these things before posting an installation issue:

Create a fresh new anaconda or virtual environment.
If you're having difficulties with caiman installation try installing a specific version, for example:
conda install -c conda-forge caiman==1.8.5
If you want to use caiman features, caiman must but installed in the same environment as mesmerize.
If you want to use certain features like kshape clustering or cross-correlation, tslearn must be installed in the same environment as mesmerize.

Otherwise use this template:

System information

OS (ex. Windows 10, Mac OSX Mojave, Ubuntu 20.04 LTS)
Windows 10
CPU (ex. Intel i7 9700k, AMD Ryzen 3950x)
Intel i7
RAM
32
Do you have an SSD or magnetic HDD
SSD
Copy & paste the entire output of the terminal while you were trying to install when the issue came up:
(base) PS C:\Users\kates> conda activate mesmerize
(mesmerize) PS C:\Users\kates> mesmerize
C:\Users\kates\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\common\configuration.py:38: UserWarning: Caiman package not found. Caiman features will be disabled.
"Caiman package not found. "
C:\Users\kates\anaconda3\envs\mesmerize\lib\site-packages\sklearn\utils\deprecation.py:143: FutureWarning: The sklearn.cluster.k_means_ module is deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.cluster. Anything that cannot be imported from sklearn.cluster is now part of the private API.
warnings.warn(message, FutureWarning)
Loading, please wait...


**Installation method**
1. Are you using anaconda, python virtual environments, or something else?
  -> if using conda, what is the conda version
4.11.0
2. If you're installing mesmerize through pip, what version of pip is installed in the environment?
pip 21.2.2
3. Are you trying to install in developer mode from the repo?
no
5. What is the python version in the environment you're trying to install `mesmerize` in?
3.6.13
8. Information if you're using some other installation method.

Cross-correlation plot fails when stimulus mapping are absent

Tracking issue to enable exploratory cross-correlation plots between cells if stimulus data are absent

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Windows 10 i7

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Operating System Windows 10 in VM

Details about your Mesmerize install

Describe the issue, please be as explicit and detailed as possible. Mesemerize starts but promts that caiman could not work since it is not in the environment but I can see is there

Steps that can be followed to reproduce the problem. What exactly were you were doing that lead to the issue.

Screenshot or copy-paste from the terminal that Mesmerize is running in

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If relevant, messages from the batch manager terminal

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