From 41df1f4abbb7a294fa3e1571897043c0d03fa064 Mon Sep 17 00:00:00 2001
From: CesarCaballeroGaudes <c.caballero@bcbl.eu>
Date: Mon, 11 May 2020 13:06:38 +0200
Subject: [PATCH 1/2] implementing retroicor

---
 phys2denoise/metrics/retroicor.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 phys2denoise/metrics/retroicor.py

diff --git a/phys2denoise/metrics/retroicor.py b/phys2denoise/metrics/retroicor.py
new file mode 100644
index 0000000..df9ee3c
--- /dev/null
+++ b/phys2denoise/metrics/retroicor.py
@@ -0,0 +1,12 @@
+"""implementation of retroicor"""
+
+import argparse as ap
+import numpy as np
+import scipy as sp
+import json
+import string
+import random
+import matplotlib as mpl; mpl.use('TkAgg')
+import matplotlib.pyplot as plt
+from scipy.signal import argrelmax
+

From 4ad18ba408801976ec0373ff813252499106b72d Mon Sep 17 00:00:00 2001
From: CesarCaballeroGaudes <c.caballero@bcbl.eu>
Date: Wed, 17 Jun 2020 13:31:14 +0200
Subject: [PATCH 2/2] draft implementation of retroicor

---
 phys2denoise/metrics/retroicor.py | 75 +++++++++++++++++++++++++++++++
 1 file changed, 75 insertions(+)

diff --git a/phys2denoise/metrics/retroicor.py b/phys2denoise/metrics/retroicor.py
index df9ee3c..e63e929 100644
--- a/phys2denoise/metrics/retroicor.py
+++ b/phys2denoise/metrics/retroicor.py
@@ -10,3 +10,78 @@
 import matplotlib.pyplot as plt
 from scipy.signal import argrelmax
 
+"""
+This function computes RETROICOR regressors (Glover et al. 2000) 
+"""
+
+
+def compute_card_phase(card_peaks_timings,slice_timings,nscans,TR):
+    """
+
+    This function creates cardiac phase from cardiac peaks.
+    Assumes that timing of cardiac events are given in same units
+    as slice timings, for example seconds.
+    
+    """
+
+    nscans = np.shape(slice_timings)
+    phase_card = np.zeros(nscans)
+    for ii in range(nscans):
+        # find previous cardiac peaks
+        previous_card_peaks = np.asarray(np.nonzero(card_peaks_timings < slice_timings[ii]))
+        if np.size(previous_card_peaks) == 0:
+            t1 = 0
+        else:
+            last_peak = previous_card_peaks[0][-1]
+            t1 = card_peaks_timings[last_peak]
+        
+        # find posterior cardiac peaks
+        next_card_peaks = np.asarray(np.nonzero(card_peaks_timings > slice_timings[ii]))
+        if np.size(next_card_peaks) == 0:
+            t2 = nscans * TR
+        else:
+            next_peak = next_card_peaks[0][0]
+            t2 = card_peaks_timings[next_peak]
+        
+        # compute cardiac phase
+        phase_card[ii] = (2*np.math.pi*(slice_timings[ii] - t1))/(t2-t1)
+
+    return phase_card
+
+def compute_resp_phase(resp,sampling_time):
+
+    """
+    This function creates respiration phase from resp trace. 
+    """
+
+
+def compute_retroicor_regressors(physio,TR,nscans,slice_timings,n_harmonics,card=FALSE,resp=FALSE):
+    nslices = np.shape(slice_timings) # number of slices
+
+    # if respiration, compute histogram and temporal derivative of respiration signal
+    if resp:
+        resp_hist, resp_hist_bins = plt.hist(physio,bins=100)
+        resp_diff = np.diff(physio,n=1)
+    
+    #initialize output variables
+    retroicor_regressors = []
+    phase = np.empty((nscans,nslices))
+
+    for jj in range(nslices):
+        # Initialize slice timings for current slice
+        crslice_timings = TR * np.arange(nscans)+slice_timings[jj]
+        # Compute physiological phases using the timings of physio events (e.g. peaks) slice sampling times
+        if card:
+            phase[,jj] = compute_phase_card(physio,crslice_timings)
+        if resp:
+            phase[,jj] = compute_phase_resp(resp_diff,resp_hist,resp_hist_bins,crslice_timings)
+        # Compute retroicor regressors
+        for nn in range(n_harmonics):
+            retroicor_regressors[jj][:,2*nn] = np.cos((nn+1)*phase[jj])
+            retricor_regressor[jj][:,2*nn+1] = np.sin((nn+1)*phase[jj])
+
+    return retroicor_regressors,phase
+
+
+        
+