Add conversion script for conditioning sessions #11
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alessandratrapani
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refactor_conversion_pipeline
alessandratrapani
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| @@ -37,5 +37,22 @@ NWBFile: | |||
| - Zaki, Yosif | |||
| Subject: | |||
| species: Mus musculus | |||
| age: TBD # in ISO 8601, such as "P1W2D" | |||
| sex: TBD # One of M, F, U, or O | |||
| age: P12W/P15W # in ISO 8601, such as "P1W2D" | |||
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Is this from the paper?
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Yes, but I will confirm it in the upcoming meeting. I need it defined to run the conversion
| optical_channel: | ||
| - name: OpticalChannel | ||
| description: Green channel of the microscope. | ||
| emission_lambda: 513.0 |
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Is this generic for Miniscope?
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Nope, it's related to the indicator they are using. Since there is no specified emission/excitation lambda wrote the FPbase values. I will also confirm this with them in the upcoming meeting
| @@ -50,6 +61,10 @@ def add_to_nwbfile(self, nwbfile: NWBFile, **conversion_options) -> NWBFile: | |||
| edf_reader = read_raw_edf(input_fname=self.file_path, verbose=self.verbose) | |||
| data, times = edf_reader.get_data(picks=list(channels_dict.keys()), return_times=True) | |||
| data = data.astype("float32") | |||
| # TODO select the correct time range | |||
| if stub_test: | |||
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| # Add Imaging | ||
| folder_path = experiment_dir_path / session_id / date_str / time_str | ||
| miniscope_folder_path = get_miniscope_folder_path(folder_path) |
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OK, this might fail if thE meatdata is not correct but is more automatized.
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I advice to nest the print statements within an if verbose.
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I could not run this on my side. I am getting this error: File "/home/heberto/development/cai-lab-to-nwb/.venv/lib/python3.11/site-packages/neuroconv/tools/roiextractors/roiextractors.py", line 1754, in add_segmentation_to_nwbfile
add_background_plane_segmentation_to_nwbfile(
File "/home/heberto/development/cai-lab-to-nwb/.venv/lib/python3.11/site-packages/neuroconv/tools/roiextractors/roiextractors.py", line 1175, in add_background_plane_segmentation_to_nwbfile
background_ids = segmentation_extractor.get_background_ids()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/heberto/development/roiextractors/src/roiextractors/segmentationextractor.py", line 177, in get_background_ids
return list(range(self.get_num_background_components()))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object cannot be interpreted as an integerIt seems that there is a method missing on minian? Any ideas? |
Yeah, unfortunately it's on roiextractor side, I solved this small bug here: catalystneuro/roiextractors#378 |
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OK, this ran well and the file looks reasonable. I would use f-strings instead of "".format() but that's me. Any reason you prefer format? I am merging this so we can focus on the next one. |
Stub NWBfile: https://catalystneuro-processing.s3.us-east-2.amazonaws.com/cai-lab-to-nwb/Ca_EEG3-4_NeutralExposure.nwb
Add conversion script for conditioning sessions
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