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when fetched, SNIRFs are read into RAW objects #46

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when fetched, SNIRFs are read into RAW objects #46

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3e8b178
adjusted mislabeled hbm filetypes
P-Oveisi Aug 1, 2022
7eae3fe
Update fetchers.py
P-Oveisi Aug 2, 2022
f1b80e2
Update fetchers.py
P-Oveisi Aug 2, 2022
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18 changes: 10 additions & 8 deletions kftools/data/fetchers.py
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
from curses import raw
import os,sys,glob,shutil,numpy as np, pandas as pd
import requests, zipfile,gdown
from datetime import datetime
#from eegnb import DATA_DIR

from mne.io.snirf import read_raw_snirf
from kftools import data

# dictionary format : kftools -> type -> experiments -> site -> subjects
Expand Down Expand Up @@ -32,10 +32,10 @@ def load_info(info_file=None):


def fetch_file(data_dir=None,info_file=None,site='snic',task='ft',subid='sub001',sesid='ses01',
filetype='kp-nii-evs', download_method='gdown'):
filetype='kp-nii-evs', download_method='gdown', load_raw=True):

"""
Pull selected data files.
Pull selected data files and load into dictionary as mne.raw objects

Usage:
------
Expand All @@ -50,8 +50,8 @@ def fetch_file(data_dir=None,info_file=None,site='snic',task='ft',subid='sub001'

"""



raw_dict = {} # dictionary containing mne raw objects
if 'NoneType' in str(type(data_dir)):
data_dir = os.path.expanduser('~/.kftools')
if not os.path.isdir(data_dir): os.makedirs(data_dir)
Expand All @@ -66,12 +66,14 @@ def fetch_file(data_dir=None,info_file=None,site='snic',task='ft',subid='sub001'
assert eval(k) in df_info[k].values

idxstoget = df_info.query(qstr).index.values
for idx in idxstoget:
for n, idx in enumerate(idxstoget):
dlcode,fname = df_info.loc[idx][['dlcode', 'fname']].values
fname = os.path.join(data_dir, fname)
if not os.path.isfile(fname):
pull_file(dlcode,fname,download_method)

if load_raw and 'snf' in filetype:
raw_dict[n] = read_raw_snirf(fname)
return raw_dict


def pull_file(dlcode,destination,download_method):
Expand Down
6 changes: 3 additions & 3 deletions kftools/data/info.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -21,9 +21,9 @@ snic_sub006_reo_ses02_1116-1655_kp-nii-hbo.nii.gz 1v6sbXiDtELiidKeJlOqtT1L5Rdmyp
snic_sub006_reo_ses02_1116-1655_kp-nii-hbr.nii.gz 1kOI6GiljhcqeeSzbnLmAKFFOT1UHeN-M
snic_sub006_reo_ses03_1117-1740_kp-nii-hbo.nii.gz 1UnXDo19JFth23X7VdDVM04pftMLbFCXy
snic_sub006_reo_ses03_1117-1740_kp-nii-hbr.nii.gz 1MmrtuMry25o7yJEtJ-rFRLA1MCUxUyZM
snic_sub006_reo_ses01_1101-1810_kp-snf-hmb.snirf 11fZdBlJDfAtPNtneSat8b4H3I-BxE14l
snic_sub006_reo_ses01_1101-1810_kp-snf-hbm.snirf 11fZdBlJDfAtPNtneSat8b4H3I-BxE14l
snic_sub006_reo_ses01_1101-1810_kp-snf-mom.snirf 1Av65sSi-PlVdPcfyZ0u37WrsN1pHLORR
snic_sub006_reo_ses02_1116-1655_kp-snf-hmb.snirf 1mk3u81bo676Sk4j1w8Qi36DxHiUF8u4D
snic_sub006_reo_ses02_1116-1655_kp-snf-hbm.snirf 1mk3u81bo676Sk4j1w8Qi36DxHiUF8u4D
snic_sub006_reo_ses02_1116-1655_kp-snf-mom.snirf 1mOsq2wWPgXJFJx-bNpBrTzn5yDF1YYuX
snic_sub006_reo_ses03_1117-1740_kp-snf-hmb.snirf 1TPqZbkqqHHAq68A6GlmrB3NyyY1dNZ2h
snic_sub006_reo_ses03_1117-1740_kp-snf-hbm.snirf 1TPqZbkqqHHAq68A6GlmrB3NyyY1dNZ2h
snic_sub006_reo_ses03_1117-1740_kp-snf-mom.snirf 1ff4pc5WRnqwL9w18vzetl5GHDFZ5DuTu