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kushalkolar / MESmerize

Platform for Calcium Imaging analysis. DEPRECATED.
GNU General Public License v3.0
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Could not find Caiman #29

Closed leironf closed 3 years ago

leironf commented 3 years ago

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

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

leironf commented 3 years ago

(mesmerize) PS C:\Users\ferrares> mesmerize c:\users\ferrares\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\ferrares\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\ferrares\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\ferrares\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\ferrares\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\ferrares\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\ferrares\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\ferrares\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\ferrares\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\ferrares\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\ferrares\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\ferrares\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\ferrares\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\ferrares\anaconda3\envs\mesmerize\lib\site-packages\sklearn\utils\deprecation.py:143: FutureWarning: The sklearn.cluster.kmeans 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... ===== 2020.11.18 21:11:25 ===== Traceback (most recent call last): File "c:\users\ferrares\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\common\system_config_window.py", line 55, in set_ui_from_config n_threads = config['_MESMERIZE_N_THREADS'] TypeError: 'bool' object is not subscriptable Work environment dumped! ===== 2020.11.18 21:11:00 ===== Traceback (most recent call last): File "c:\users\ferrares\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\pyqtgraphCore__init.py", line 312, in cleanup if isinstance(o, QtGui.QGraphicsItem) and isQObjectAlive(o) and o.scene() is None: ReferenceError: weakly-referenced object no longer exists Error in atexit._run_exitfuncs: Traceback (most recent call last): File "c:\users\ferrares\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\pyqtgraphCore\init__.py", line 312, in cleanup if isinstance(o, QtGui.QGraphicsItem) and isQObjectAlive(o) and o.scene() is None: ReferenceError: weakly-referenced object no longer exists (mesmerize) PS C:\Users\ferrares>

kushalkolar commented 3 years ago

Hi, thanks for posting an issue!

  1. Are you sure that caiman is installed in the same environment as mesmerize? Can you import caiman from an ipython session?

  2. I would not recommend installing mesmerize directly from the repo unless you want to modify/develop the code further.

  3. Is there a specific reason you are using this within a VM? You will get better performance if you run it on bare metal.

leironf commented 3 years ago

Hi, thanks for replying.

  1. I don't know: I did conda install -c conda-forge caiman with mesmerize active it did it smoothly and told me done at the end. inside anaconda mesmerize environment I can see the entry caiman. How can I import caiman from an ipython session?
  2. Sorry I actually used this link http://docs.mesmerizelab.org/en/master/user_guides/installation.html#windows so the package not the repo
  3. I have it also on a cluster but it's not interactive, I wanted it on the a VM with dedicated resources (it is powerful) so that I can find parameters interactively and then run the heavy part on the cluster.
leironf commented 3 years ago

I have restarted from scratch and found the problem, it was with pip installing mesmerize: ERROR: After October 2020 you may experience errors when installing or updating packages. This is because pip will change the way that it resolves dependency conflicts.

We recommend you use --use-feature=2020-resolver to test your packages with the new resolver before it becomes the default.

panel 0.10.2 requires bokeh>=2.2.2, but you'll have bokeh 2.1.1 which is incompatible.

Now mesmerize can see caiman

Thanks Best Leiron

kushalkolar commented 3 years ago

Great to hear you got it working!