Align the starting_time of the processed fiber photometry data
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…d and align the starting time
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Example 20200205-0001.nwb: |
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I'll first test this for all sessions and then reopen, sorry for pinging too early @alessandratrapani |
weiglszonja
commented
May 24, 2024
src/dombeck_lab_to_nwb/azcorra2023/interfaces/azcorra2023_processedfiberphotometryinterface.py
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…essedfiberphotometryinterface.py
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@alessandratrapani I think this is ready for review (we can discuss in our next meeting if something is unclear), also will add this as a note for the mid-way meeting to double check with them. |
alessandratrapani
approved these changes
May 27, 2024
weiglszonja
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May 27, 2024
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| def get_original_timestamps(self) -> np.ndarray: | ||
| binned_photometry_data = read_mat(filename=str(self.file_path))["#subsystem#"]["MCOS"][2] | ||
| channel_index = self.column_names.index("chMov") | ||
| data = binned_photometry_data[channel_index] | ||
| if len(self.depth_ids) > 1: | ||
| data = data[self.depth_index] | ||
| num_frames = len(data) | ||
| return np.arange(num_frames) / self._sampling_frequency | ||
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| def get_timestamps(self, stub_test: bool = False) -> np.ndarray: | ||
| timestamps = self._timestamps if self._timestamps is not None else self.get_original_timestamps() | ||
| if stub_test: | ||
| return timestamps[:6000] | ||
| return timestamps | ||
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| def set_aligned_timestamps(self, aligned_timestamps: np.ndarray) -> None: | ||
| self._timestamps = np.array(aligned_timestamps) | ||
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After looking at the converted files I noticed that some recordings might be cropped (the picoscope data was longer than the processed data). After digging into their processing code I found out that in some cases they were cropping the beginning of the recording and saving the crop point named "cropStart".
I'm using this variable to align the starting time of the processed interface, so we are saving the processed behavior data and fiber photometry data with the correct starting time.