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- import numpy as np
- import os
- import pandas as pd
- ################################################################
- ######## Analysis pipeline for concatenated recordings #########
- ################################################################
- path = "/media/andrey/My Passport/GIN/backup_Anesthesia_CA1/calcium imaging transition state/concatenated/8235/20201103_GCaMP6f_8235_isoflurane/suite2p/plane0"
- Traces = np.load(path + '/F.npy', allow_pickle=True)
- Npil = np.load(path + '/Fneu.npy', allow_pickle=True)
- iscell = np.load(path + '/iscell.npy', allow_pickle=True)
- print(Traces.shape, type(Traces))
- print(Npil.shape, type(Npil))
- print(iscell.shape, type(iscell))
- #path_excel_rec = str(meta_data['Folder'][recording] + meta_data['Subfolder'][recording] + 'suite2p/plane0')
- if not os.path.exists('#8235_iso_minidataset'):
- os.mkdir("./#8235_iso_minidataset")
- if not os.path.exists('#8235_iso_minidataset/suite2p'):
- os.mkdir("./#8235_iso_minidataset/suite2p")
- if not os.path.exists('#8235_iso_minidataset/suite2p/plane0'):
- os.mkdir("./#8235_iso_minidataset/suite2p/plane0")
- np.save('#8235_iso_minidataset/suite2p/plane0/F.npy',Traces[:50,:])
- np.save('#8235_iso_minidataset/suite2p/plane0/Fneu.npy',Npil[:50,:])
- np.save('#8235_iso_minidataset/suite2p/plane0/iscell.npy',iscell[:50,:])
- meta_data = pd.read_excel("../meta_data/meta_recordings_transition_state.xlsx")
- meta_data = meta_data[meta_data.Mouse_all == 8235]
- meta_data.index = np.arange(meta_data.shape[0])
- meta_data["Number"] = meta_data.index
- print(np.arange(meta_data.shape[0]))
- meta_data.Folder = "/media/andrey/My Passport/GIN/Anesthesia_CA1/data_colab/"
- meta_data.Subfolder = "#8235_iso_minidataset/"
- meta_data.to_excel("./#8235_iso_minidataset/meta_recordings_8235.xlsx")
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