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How to load stim trace in suite2p? #1002

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Yang-xu328 opened this issue Jul 20, 2023 · 2 comments
Closed

How to load stim trace in suite2p? #1002

Yang-xu328 opened this issue Jul 20, 2023 · 2 comments
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@chriski777

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@Yang-xu328
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Hi,

I'm currently unable to load a stim trace in suite2p.
I write an 1D trace (same length as the recorded file in 2-photon microscope) in matlab and use writeNPY function to convert my trace into npy file. However, when I load stim trace in suite2p, it shows the following error:

Traceback (most recent call last):
File "C:\Users\xy\anaconda3\envs\suite2p\lib\site-packages\suite2p\gui\menus.py", line 40, in
parent.loadBeh.triggered.connect(lambda: io.load_behavior(parent))
File "C:\Users\xy\anaconda3\envs\suite2p\lib\site-packages\suite2p\gui\io.py", line 372, in load_behavior
parent.beh_resampled = resample_frames(parent.beh, parent.beh_time, np.arange(0,parent.Fcell.shape[1]))
File "C:\Users\xy\anaconda3\envs\suite2p\lib\site-packages\suite2p\gui\io.py", line 392, in resample_frames
y = gaussian_filter1d(y, np.ceil(ts/2), axis=0)
NameError: name 'gaussian_filter1d' is not defined

I don't code in python so I have no idea what is wrong about this process. I'm wondering is there any requirement for the format of my stim trace? Cause i just wrote the trace in several pulses with different amplitudes. (for each pulse last for 2 points, figure below)
stim-trace

Thanks for your help!
@shclair
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shclair commented Aug 18, 2023 •
edited
Loading

I am having the same issue! my stim trace is just 0s and 1s to show trains of electrical stimulation...

except my first error is this:

numpy.core._exceptions._UFuncOutputCastingError: Cannot cast ufunc 'divide' output from dtype('float64') to dtype('int32') with casting rule 'same_kind'

I don't know anything about python and we are trying to figure out if Suite2P is right for us!

Would be great if they could have included an example of a stim trace in the documentation...

@chriski777 chriski777 self-assigned this Nov 26, 2023
carsen-stringer pushed a commit that referenced this issue Nov 26, 2023
@chriski777 @carsen-stringer
Update gui.rst to have clearer instructions for #1002.
d808681
@chriski777
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Hi @Yang-xu328, this was an import error and has been addressed in the latest commit of the main branch. An example of how to create a 1D arr to use as a stim trace can be found in this link. Please refer to the section titled "Correlations with 1D var". I'll close this issue for now but feel free to re-open if the issue persists!

tbabola added a commit to tbabola/suite2p that referenced this issue Jun 19, 2024
@tbabola @tdincer
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Merge with devleoper branch (#2)
8adfc64 
* add get_nd2_list method

* remove comment

* support pipelining nd2 files

* support pipelining nd2 files

* fix docstring and whitespaces

* bug fix

* final touch

* Modified README to contain updated suite2p installation instructions for mac Ventura OS. Addresses issue MouseLand#897.

* Fixed issue MouseLand#908 regarding badframes for register.py. Detection module was fixed to properly bin movies AFTEr taking into account bad frames.

* Fix blocks issue for nonrigid registration in MouseLand#907

* Update test_and_deploy.yml

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* Update test_and_deploy.yml

* Update tox.ini

* Update test_and_deploy.yml

Remove the up-term step.

* Updated TwophotonSeries initialization for save_nwb in io

* Bump torch from 1.11.0 to 1.13.1

Bumps [torch](https://github.com/pytorch/pytorch) from 1.11.0 to 1.13.1.
- [Release notes](https://github.com/pytorch/pytorch/releases)
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- [Commits](pytorch/pytorch@v1.11.0...v1.13.1)

---
updated-dependencies:
- dependency-name: torch
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* Update issue templates

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* Fixes issue MouseLand#914 for saving news ops parameters

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* Fixes multiplane issue MouseLand#905 with save_nwb

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* remove spaces

* conform to function signature and usage pattern a few lines above

* add nd2 in requirements

* minor revision

* new logic

* refactor dim sorting

* revert to previous code

* Fixes the from_stat_dict bug mentioned in MouseLand#935.

* Update run suite2p jupyter notebook to fix issue MouseLand#935

* Addresses MouseLand#930 in which bin_data has trouble dealing with cases in which the current batch has fewer frames than the bin_size

* removed ops assignment

* removed deprecated np.bool

* Update the version of the dependencies for suite2p

* Update np.bool to 'bool' to account for numpy deprecation with latest version

* Add Sparse detection to gui as a setting for running suite2p

* Addresses MouseLand#951 and adds nd2 as an input to gui

* Fix issue with np.asanyarray being changed in numpy 1.24.4

* addressed IndexError

* Update README.md

* Update README.md

* fixing skip torch if version 2.0

* adding pep8 style to repo

* fixing dictionary splitting

* modifying imports

* converting to "" from ''

* converting binaryfile to memmap

* rewriting binarycombined

* removing scanimage-tiff-reader for now

* fixing dragging in gui and linewidth=88

* removing old testing yml

* adding py39, updating readme

* adding option for MouseLand#955

* fixing bug in docstring  (MouseLand#902)

* adding iplane to saved manual ROIs (MouseLand#789)

* fixing MouseLand#747 saving to mat

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* Update README.md

* Update README.md

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* Add method for writing tiff for binaryFile class

* Update write_tiff for binary.py to crop frames, x, and y too

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* fixing import error with h5py and paramiko MouseLand#987

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* Addresses MouseLand#944  leading zero issue with tiff filename.

* Addresses MouseLand#944  leading zero issue with tiff filename.

* Update save_path0 to close MouseLand#991.

* Update save_path0 to close MouseLand#991.

* update visualize.py to import rastermap properly

* Re-add connected to GUI options

* Update README.md

Remove note about scanimage-tiff-reader mac incompatibility

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* Update setup.py

Update rastermap requirement based on issue ticket suggestions

* Update setup.py

* Updated jupyter notebook to work with new binaryFile class in suite2p.io

* Updated jupyter notebook name

* Update colab 2023 to fully fix MouseLand#1011 and update some comments on notebook

* Updated jupyter notebook to work with new binaryFile class in suite2p.io

* Updated jupyter notebook name

* Update colab 2023 to fully fix MouseLand#1011 and update some comments on notebook

* adding pyqt6 and switching to qtpy

* updating readme and fixing spelling error in copyright

* adding license notice

* adding check in setup.py for installation of a pyqt version

* adding tutorial

* Update tutorial.md with additional comments

* Update suite2p gui to work with QFileDialog.Options() not working with pyqt6

* Update binary.py write_tiff to add all frames to a single series

* Updated tiff.py to use contiguous parameter

* Update README.md

* checking h5py key to open binaries before data_path

* fixing bug in code

* adding new data type

* adding support for binary and mp4/avi files

* enabling ops.json loading in reggui and binary-only processing

* increase tolerance on classification regression test

* add more tolerance

* increasing tolerance again

* increasing tolerance again

* Update README.md

* Add explanation for how to apply classifiers

* CheckState Fix

* Fix conda environment creation for developers

* Update utils.py

* Update README.md to fix MouseLand#1060.

Updates badge links for tests and docs

* Update merge.py of gui subpackage to not use deprecated np.bool

* Update merge.py of gui subpackage to not use deprecated np.bool

* Add import to gui/io.py

* Update gui.rst to have clearer instructions for MouseLand#1002.

* bug in h5py key option

* adding support for multipage bruker ome tiffs

* Update inputs.rst to include multipage bruker instructions

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* Added support for Thorlabs RAW files (io.raw)

* Added xmltodict

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* fixing bug with multiplane registration

* allowing reg_file input to compute_zpos

* fixing bug with multi-plane nonrigid ops

* add support for Hamamatsu DCIMG format

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* Addresses MouseLand#1093 with cellpose method having too many arguments

* Addresses MouseLand#1093 with cellpose method having too many arguments

* remove cellpose<3.0 restriction

* Fixes issue MouseLand#1101 with older version of cellpose

* Update zalign.py

Made sure that if a reg_file is given to the zalign function it uses it, rather than the ops reg_file

* Update setup.py

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* removing dcimg extra

---------

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Co-authored-by: tdincer <tolgadincer@gmail.com>
Co-authored-by: Chris Ki <chriski777@berkeley.edu>
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