Merge pull request #192 from ckiefer0/master

pipelines: added for each analysis step a sub category in the config file

pipelines/1_preprocessing.py

@@ -23,17 +23,20 @@
 subjects = config['subjects']
 
 # noise reducer
-refnotch = config['refnotch']
+refnotch = config['noise_reducer']['refnotch']
 
 # filtering
-flow = config['l_freq']
-fhigh = config['h_freq']
-unfiltered = config['unfiltered']
+flow = config['filtering']['l_freq']
+fhigh = config['filtering']['h_freq']
+unfiltered = config['filtering']['unfiltered']
+fi_method = config['filtering']['method']
+fir_design = config['filtering']['fir_design']
+phase = config['filtering']['phase']
 
 # resampling
-rsfreq = config['rsfreq']
+rsfreq = config['resampling']['rsfreq']
 
-# WIP: the state space file saves the parameters for the creation of each file
+# TODO WIP: the state space file saves the parameters for the creation of each file
 state_space_fname = '_state_space_dict.pkl'
 
 ###############################################################################
@@ -80,13 +83,9 @@
 
         if raw_fname.endswith('bcc-raw.fif') or raw_fname.endswith('bcc-empty.fif'):
 
-            method = 'fir'
-            fir_design = 'firwin'
-            phase = 'zero'
-
             raw = mne.io.Raw(op.join(dirname, raw_fname), preload=True)
 
-            raw_filt = raw.filter(flow, fhigh, method=method, n_jobs=1,
+            raw_filt = raw.filter(flow, fhigh, method=fi_method, n_jobs=1,
                                   fir_design=fir_design, phase=phase)
 
             if raw_fname.endswith('-raw.fif'):
@@ -97,7 +96,7 @@
             fi_dict = dict()
             fi_dict['flow'] = flow
             fi_dict['fhigh'] = fhigh
-            fi_dict['method'] = method
+            fi_dict['method'] = fi_method
             fi_dict['fir_design'] = fir_design
             fi_dict['phase'] = phase
             fi_dict['output_file'] = raw_filt_fname

pipelines/2_artifact_rejection.py

@@ -20,20 +20,20 @@
 subjects = config['subjects']
 
 
-ecg_ch = config['ecg_ch']
-eog_hor_ch = config['eog_hor_ch']
-eog_ver_ch = config['eog_ver_ch']
-
-flow_ecg = config['flow_ecg']
-fhigh_ecg = config['fhigh_ecg']
-flow_eog = config['flow_eog']
-fhigh_eog = config['fhigh_eog']
-
-ecg_thresh = config['ecg_thresh']
-eog_thresh = config['eog_thresh']
-use_jumeg = config['use_jumeg']
-random_state = config['random_state']
-unfiltered = config['unfiltered']
+ecg_ch = config['ica']['ecg_ch']
+eog_hor_ch = config['ica']['eog_hor_ch']
+eog_ver_ch = config['ica']['eog_ver_ch']
+
+flow_ecg = config['ica']['flow_ecg']
+fhigh_ecg = config['ica']['fhigh_ecg']
+flow_eog = config['ica']['flow_eog']
+fhigh_eog = config['ica']['fhigh_eog']
+
+ecg_thresh = config['ica']['ecg_thresh']
+eog_thresh = config['ica']['eog_thresh']
+use_jumeg = config['ica']['use_jumeg']
+random_state = config['ica']['random_state']
+unfiltered = config['ica']['unfiltered']
 
 pre_proc_ext = config['pre_proc_ext']
 

pipelines/3_prepare_epochs.py

@@ -31,7 +31,7 @@
 for cond in config['conditions']:
     print(cond)
 
-    # you may want to use glob etc. to avoid having to write down all file names in the config
+    # TODO: may want to use glob etc. to avoid having to write down all file names in the config
     for fname in config[cond]['raw_fnames']:
         subject = fname.split('_')[0]
         raw_fname = op.join(recordings_dir, subject, fname)
@@ -44,7 +44,7 @@
 
         # get channel with events
         stim_channel = config[cond]['ch_name']
-        event_id = config['event_id']
+        event_id = config[cond]['event_id']
 
         # get tmin, tmax for epoch creation
         tmin, tmax = config[cond]['tmin'], config[cond]['tmax']

pipelines/4_covariance_matrices.py

@@ -27,10 +27,10 @@
 subjects = config['subjects']
 l_freq, h_freq = config['l_freq'], config['h_freq']
 pre_proc_ext = config['pre_proc_ext']
-unfiltered = config['unfiltered']
 
-compute_empty_cov = True
-compute_epo_cov = True
+compute_empty_cov = config['cov_matrices']['compute_empty_cov']
+compute_epo_cov = config['cov_matrices']['compute_epo_cov']
+unfiltered = config['cov_matrices']['unfiltered']
 
 ###############################################################################
 # Compute noise covariance matrix based on empty room measurements

pipelines/5_setup_source_localization.py

@@ -50,8 +50,8 @@
 mri_dir = '/mri/orig/001.mgz'
 nii_fname = '_1x1x1mm.nii'
 
-mne_bin_path = '/Users/kiefer/mne/MNE-2.7.3-3268-MacOSX-i386/bin/'  # Path to MNE-C binary files
-freesurfer_home = '/Users/kiefer/mne/freesurfer/'
+mne_bin_path = config['mne_bin_path']
+freesurfer_home = config['freesurfer_home']
 freesurfer_bin = freesurfer_home + 'bin/'
 
 # determiny granularity of source space

pipelines/6_do_source_localization.py

@@ -33,18 +33,19 @@
 # subject list
 subjects = config['subjects']
 
-n_jobs = config['n_jobs']
 pre_proc_ext = config['pre_proc_ext']
 
 # inverse solution
-method = config['inv_method']
-snr = config['snr']
+method = config['source_loc']['inv_method']
+n_jobs = config['source_loc']['n_jobs']
+snr = config['source_loc']['snr']
 lambda2 = 1.0 / snr ** 2
-do_inv_epo = False
+
+do_inv_epo = config['source_loc']['do_inv_epo']
 
 # plotting stc
-plot_stc = True
-time_viewer = True
+plot_stc = config['source_loc']['plot_stc']
+time_viewer = config['source_loc']['time_viewer']
 
 ###############################################################################
 # Calculate forward and inverse solution

pipelines/config_file.yaml

@@ -3,28 +3,55 @@
 
 version: 'v0.1'
 
+###############################################################################
+# subject list
+###############################################################################
+
+subjects: ['101611']
+
+###############################################################################
 # directories
+###############################################################################
+
 basedir: '/path/to/jusample'
-subjects: ['101611']
 recordings_dir: 'recordings'
 subjects_dir: 'subjects'
 plot_dir: 'plots'
 
+# Path to MNE-C binary files
+mne_bin_path: '/Users/kiefer/mne/MNE-2.7.3-3268-MacOSX-i386/bin/'
+freesurfer_home: '/Users/kiefer/mne/freesurfer/'
+
 ###############################################################################
 # pre-processing settings
 ###############################################################################
 
 # noise reducer
-refnotch: [50., 100., 150., 200., 250., 300., 350., 400.,
-           60., 120., 180., 240., 360.]
+noise_reducer:
+    # low pass filter for reference channels, default 5.0 Hz
+    reflp: 5.
+    # high pass filter for reference channels, default 0.1 Hz
+    refhp: 0.1
+    # TODO: check if comment is correct -> Eberhard
+    # Names of the reference channels for high pass filter
+    noiseref_hp: ['RFG ...']
+    # frequencies for notch filter (for power line noise, projector, etc.)
+    refnotch: [50., 100., 150., 200., 250., 300., 350., 400.,
+               60., 120., 180., 240., 360.]
 
 # filtering
-l_freq: 1.0
-h_freq: 45.
-unfiltered: True
+filtering:
+    l_freq: 1.0
+    h_freq: 45.
+    method: 'fir'
+    fir_design: 'firwin'
+    phase: 'zero'
+    # create files for unfiltered data as well
+    unfiltered: True
 
 # resampling
-rsfreq: 250
+resampling:
+    rsfreq: 250
 
 # file name extension with the pre-processing steps
 pre_proc_ext: ',nr,bcc,fibp,rs'
@@ -33,39 +60,32 @@ pre_proc_ext: ',nr,bcc,fibp,rs'
 # ica settings
 ###############################################################################
 
-ecg_ch: 'ECG 001'
-eog_hor_ch: 'EOG 001'
-eog_ver_ch: 'EOG 002'
+ica:
+    ecg_ch: 'ECG 001'
+    eog_hor_ch: 'EOG 001'
+    eog_ver_ch: 'EOG 002'
 
-flow_ecg: 8
-fhigh_ecg: 20
-flow_eog: 1
-fhigh_eog: 20
+    flow_ecg: 8
+    fhigh_ecg: 20
+    flow_eog: 1
+    fhigh_eog: 20
 
-ecg_thresh: 0.3
-eog_thresh: 0.3
-use_jumeg: True
-random_state: 42
+    ecg_thresh: 0.3
+    eog_thresh: 0.3
+    use_jumeg: True
+    random_state: 42
 
 ###############################################################################
-#
+# conditions
 ###############################################################################
 
 conditions: ['stim']
 
-n_jobs: 1
-event_id: 1
-
-snr: 1
-inv_method: 'MNE'
-
-snr_list: 3
-inv_methods: ['MNE', 'dSPM']
-
 stim:
     ch_name: 'STI 014'
     tmin: -0.4
     tmax: 0.6
+    event_id: 1
     raw_fnames: [
     '101611_CAU01A_100706_1430_1_c,rfDC,t1,n,meeg,nr,bcc,fibp,rs,ar-raw.fif',
     '101611_CAU01A_100706_1430_1_c,rfDC,t1,n,meeg,nr,bcc,rs,ar-raw.fif'
@@ -74,17 +94,49 @@ paced:
     ch_name: 'STI 013'
     tmin: -0.4
     tmax: 0.6
+    event_id: 1
     raw_fnames: [
     '101611_CAU01A_100706_1429_1_c,rfDC,t1,n_bcc,nr,ar-raw.fif'
     ]
 both:
     ch_name: 'STI 014'
     tmin: -0.4
     tmax: 0.6
+    event_id: 1
     raw_fnames: [
     '101611_CAU01A_100706_1430_2_c,rfDC,t1,n_bcc,nr,ar-raw.fif'
     ]
 
+###############################################################################
+# covariance matrices
+###############################################################################
+
+cov_matrices:
+    # compute covariance matrix based on empty room measurement
+    compute_empty_cov: True
+    # compute covariance matrix based on epochs
+    compute_epo_cov: True
+    # compute covariance matrix for filtered (False) or unfiltered (True) data
+    unfiltered: False
+
+###############################################################################
+# source localization
+###############################################################################
+
+source_loc:
+    n_jobs: 1
+    snr: 1
+    inv_method: 'MNE'
+
+    do_inv_epo: False
+
+    plot_stc: True
+    time_viewer: True
+
+###############################################################################
+# other (unused atm)
+###############################################################################
+
 label_names:
     ['bankssts-lh', 'bankssts-rh', 'caudalanteriorcingulate-lh',
      'caudalanteriorcingulate-rh', 'caudalmiddlefrontal-lh',

pipelines/utils.py

@@ -115,7 +115,6 @@ def noise_reduction(dirname, raw_fname, denoised_fname, refnotch, state_space_fn
 
     # plot final plotting
     plot_name = denoised_fname.rsplit('-raw.fif')[0] + '-plot'
-    # TODO: fix plot_denoising
     plot_denoising([op.join(dirname, raw_fname), op.join(dirname, denoised_fname)],
                    n_jobs=1, fnout=op.join(dirname, plot_name), show=False)