Added the pyphotometry preprocessing steps. There is a function calle… #21
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…d 'import_ppd' that is needed to import .ppd data. I included it in the description of the processppdphotometry function. Is this correct?
src/jdb_to_nwb/convert_photometry.py
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| requires the import_ppd function from the data_import.py script | ||
| The code needed is below. | ||
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| def import_ppd(file_path, low_pass=20, high_pass=15.9): |
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the import_ppd function needs to be on its own instead of in a comment - otherwise the processppdphotometry function won't know what import_ppd means and this will break when you run it
src/jdb_to_nwb/convert_photometry.py
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| sampling_rate = ppd_data['sampling_rate'] | ||
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| b,a = butter(2, 10, btype='low', fs=sampling_rate) | ||
| GACh_denoised = filtfilt(b,a, raw_green) |
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I would name these green_denoised and red_denoised instead of ACh and DA specific because this pipeline should work regardless of the identity of the red/green signals
src/jdb_to_nwb/convert_photometry.py
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| ratio_zscored = np.divide(np.subtract(ratio_highpass,ratio_highpass.mean()),ratio_highpass.std()) | ||
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| return {"green_zscored": green_zscored, "red_zscored": red_zscored, "ratio_zscored": ratio_zscored, "zscored_405": zscored_405} | ||
| pass |
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delete pass - doesn't do anything bc you have already returned a dict
src/jdb_to_nwb/convert_photometry.py
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| @@ -336,6 +336,141 @@ def airPLS(data, lambda_=1e8, max_iterations=50): | |||
| weights[-1] = weights[0] | |||
| return baseline | |||
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| def processppdphotometry(ppd_file_path): | |||
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nitpick but I would rename this process_ppd_photometry for readability and to match style with the other function names
src/jdb_to_nwb/convert_photometry.py
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| ratio_zscored = np.divide(np.subtract(ratio_highpass,ratio_highpass.mean()),ratio_highpass.std()) | ||
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| return {"green_zscored": green_zscored, "red_zscored": red_zscored, "ratio_zscored": ratio_zscored, "zscored_405": zscored_405} |
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also return port visit times for alignment
| @@ -395,9 +601,11 @@ def add_photometry(nwbfile: NWBFile, metadata: dict): | |||
| elif "ppd_file_path" in metadata["photometry"]: | |||
| # Process ppd file from pyPhotometry | |||
| print("Processing ppd file from pyPhotometry...") | |||
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| ppd_file_path = metadata["photometry"]["ppd_file_path"] | |||
| signals = process_ppd_photometry(ppd_file_path) | |||
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Change returned values and arguments to match the function definition
| signals = process_ppd_photometry(ppd_file_path) | |
| sampling_rate, visits = process_ppd_photometry(nwbfile, ppd_file_path) |
| # TODO for Jose - add pyPhotometry processing here!! | ||
| # Probably add the processing functions above and just call them here | ||
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| raise NotImplementedError("pyPhotometry processing is not yet implemented.") |
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Remove TODO and NotImplementedError because it is now implemented
| # TODO for Jose - add pyPhotometry processing here!! | |
| # Probably add the processing functions above and just call them here | |
| raise NotImplementedError("pyPhotometry processing is not yet implemented.") |
| # Return port visits in downsampled photometry time (250 Hz) to use for alignment | ||
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I believe pyPhotometry is 86(?) Hz instead of 250
| # Return port visits in downsampled photometry time (250 Hz) to use for alignment | |
| # Return port visits in downsampled photometry time (86 Hz) to use for alignment |
| data_dict.update(header_dict) | ||
| return data_dict | ||
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| def process_ppd_photometry(ppd_file_path, nwbfile: NWBFile, metadata: dict): |
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Remove metadata here bc we don't use it. Also put nwbfile as the first argument for consistency
| def process_ppd_photometry(ppd_file_path, nwbfile: NWBFile, metadata: dict): | |
| def process_ppd_photometry(nwbfile: NWBFile, ppd_file_path): |
| # Add photometry metadata to the NWB | ||
| print("Adding photometry metadata to NWB ...") | ||
| add_photometry_metadata(NWBFile, metadata) | ||
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Remove this because I will reorganize in the next PR to add it separately (outside of either the LabVIEW or pyPhotometry specific processing)
| # Add photometry metadata to the NWB | |
| print("Adding photometry metadata to NWB ...") | |
| add_photometry_metadata(NWBFile, metadata) |
| zscored_405 = np.divide(np.subtract(highpass_405,highpass_405.mean()),highpass_405.std()) | ||
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| ratio_zscored = np.divide(np.subtract(ratio_highpass,ratio_highpass.mean()),ratio_highpass.std()) | ||
| print('Done processing photometry data! Returning z-scored signals...') |
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Minor but changing this bc we don't actually return them and the next comment is "adding to NWB" which is what we actually do next
| print('Done processing photometry data! Returning z-scored signals...') | |
| print('Done processing photometry data!') |
…d 'import_ppd' that is needed to import .ppd data. I included it in the description of the processppdphotometry function. Is this correct?