Add apodisation, fixed phase and conjugation.

fsl_mrs/scripts/fsl_mrs_proc

@@ -75,6 +75,8 @@ def main():
                                   ' (default=0.2->4.2)')
     align_group.add_argument('--reference', type=str, required=False,
                              help='Align to this reference data.')
+    align_group.add_argument('--apod', type=float, default=10,
+                             help='Apodise data to reduce noise (Hz).')
     alignparser.set_defaults(func=align)
     add_common_args(alignparser)
 
@@ -228,6 +230,21 @@ def main():
     phaseparser.set_defaults(func=phase)
     add_common_args(phaseparser)
 
+    fixphaseparser = sp.add_parser('fixed_phase', add_help=False,
+                                   help='Apply fixed phase to spectrum')
+    fphase_group = fixphaseparser.add_argument_group('Phase arguments')
+    fphase_group.add_argument('--file', type=str, nargs='+', required=True,
+                              help='Data file(s) to shift')
+    fphase_group.add_argument('--p0', type=float,
+                              metavar='<degrees>',
+                              help='Zero order phase (degrees)')
+    fphase_group.add_argument('--p1', type=float,
+                              default=0.0,
+                              metavar='<seconds>',
+                              help='First order phase (seconds)')
+    fixphaseparser.set_defaults(func=fixed_phase)
+    add_common_args(fixphaseparser)
+
     # subtraction - subtraction of FIDs
     subtractparser = sp.add_parser('subtract', add_help=False,
                                    help='Subtract two FIDs')
@@ -246,6 +263,14 @@ def main():
     addparser.set_defaults(func=add)
     add_common_args(addparser)
 
+    # conj - conjugation
+    conjparser = sp.add_parser('conj', add_help=False, help='Conjugate fids')
+    conj_group = conjparser.add_argument_group('Conjugation arguments')
+    conj_group.add_argument('--file', type=str, nargs='+', required=True,
+                            help='Data file(s) to conjugate')
+    conj_group.set_defaults(func=conj)
+    add_common_args(conj_group)
+
     # Parse command-line arguments
     args = p.parse_args()
 
@@ -552,6 +577,7 @@ def align(dataobj, args):
                                                 centralFrequency,
                                                 ppmlim=args['ppm'],
                                                 niter=2,
+                                                apodize=args['apod'],
                                                 verbose=False,
                                                 target=dataobj[0].reference)
 
@@ -881,6 +907,38 @@ def phase(dataobj, args):
     return dataout
 
 
+def fixed_phase(dataobj, args):
+    dataout = []
+    for idx, d in enumerate(dataobj):
+        phased = np.zeros(d.data.shape, dtype=np.complex128)
+        for ijk in np.ndindex(d.data.shape[:3]):
+            phased[ijk] = preproc.applyPhase(d.data[ijk],
+                                             (np.pi/180.0)*args['p0'])
+
+            if args['p1'] != 0.0:
+                phased[ijk], newDT = preproc.timeshift(
+                    phased[ijk],
+                    d.dataheader['dwelltime'],
+                    args['p1'],
+                    args['p1'])
+
+            if args['generateReports'] and \
+               np.prod(d.data.shape[:3]) == 1 and \
+               ((idx in args['reportIndicies']) or args['allreports']):
+                from fsl_mrs.utils.preproc.general import generic_report
+
+                generic_report(d.data[ijk],
+                               phased[ijk],
+                               d.dataheader,
+                               d.dataheader,
+                               ppmlim=(0.2, 4.2),
+                               html=args['output'],
+                               function='fixed phase')
+
+        dataout.append(datacontainer(phased, d.dataheader, d.datafilename))
+    return dataout
+
+
 def subtract(dataobj, args):
     dataout = []
     subtracted = preproc.subtract(dataobj[0].data, dataobj[1].data)
@@ -920,5 +978,29 @@ def add(dataobj, args):
     return dataout
 
 
+def conj(dataobj, args):
+    dataout = []
+    for idx, d in enumerate(dataobj):
+        conj = np.zeros(d.data.shape, dtype=np.complex128)
+        for ijk in np.ndindex(d.data.shape[:3]):
+            conj[ijk] = np.conj(d.data[ijk])
+
+            if args['generateReports'] and \
+               np.prod(d.data.shape[:3]) == 1 and \
+               ((idx in args['reportIndicies']) or args['allreports']):
+                from fsl_mrs.utils.preproc.general import generic_report
+
+                generic_report(d.data[ijk],
+                               conj[ijk],
+                               d.dataheader,
+                               d.dataheader,
+                               ppmlim=(0.2, 4.2),
+                               html=args['output'],
+                               function='conj')
+
+        dataout.append(datacontainer(conj, d.dataheader, d.datafilename))
+    return dataout
+
+
 if __name__ == '__main__':
     main()

fsl_mrs/utils/preproc/align.py

@@ -5,17 +5,19 @@
 # Author: Saad Jbabdi <saad@fmrib.ox.ac.uk>
 #         William Clarke <william.clarke@ndcn.ox.ac.uk>
 #
-# Copyright (C) 2019 University of Oxford 
+# Copyright (C) 2019 University of Oxford
 # SHBASECOPYRIGHT
 
-from fsl_mrs.utils.preproc.general import get_target_FID,add,subtract
+from fsl_mrs.utils.preproc.general import get_target_FID, add, subtract
+from fsl_mrs.utils.preproc.filtering import apodize as apod
 from fsl_mrs.core import MRS
-from fsl_mrs.utils.misc import extract_spectrum,shift_FID
+from fsl_mrs.utils.misc import extract_spectrum, shift_FID
 from scipy.optimize import minimize
 import numpy as np
 
+
 # Phase-Freq alignment functions
-def align_FID(mrs,src_FID,tgt_FID,ppmlim=None,shift=True):
+def align_FID(mrs, src_FID, tgt_FID, ppmlim=None, shift=True):
     """
        Phase and frequency alignment
 
@@ -32,24 +34,26 @@ def align_FID(mrs,src_FID,tgt_FID,ppmlim=None,shift=True):
     """
 
     # Internal functions so they can see globals
-    def shift_phase_freq(FID,phi,eps,extract=True):        
-        sFID = np.exp(-1j*phi)*shift_FID(mrs,FID,eps)
+    def shift_phase_freq(FID, phi, eps, extract=True):
+        sFID = np.exp(-1j*phi)*shift_FID(mrs, FID, eps)
         if extract:
-            sFID = extract_spectrum(mrs,sFID,ppmlim=ppmlim,shift=shift)
+            sFID = extract_spectrum(mrs, sFID, ppmlim=ppmlim, shift=shift)
         return sFID
+
     def cf(p):
-        phi    = p[0] #phase shift
-        eps    = p[1] #freq shift
-        FID    = shift_phase_freq(src_FID,phi,eps)
-        target = extract_spectrum(mrs,tgt_FID,ppmlim=ppmlim,shift=shift)
+        phi    = p[0]  # phase shift
+        eps    = p[1]  # freq shift
+        FID    = shift_phase_freq(src_FID, phi, eps)
+        target = extract_spectrum(mrs, tgt_FID, ppmlim=ppmlim, shift=shift)
         xx     = np.linalg.norm(FID-target)
         return xx
-    x0  = np.array([0,0])
+    x0 = np.array([0, 0])
     res = minimize(cf, x0, method='Powell')
     phi = res.x[0]
     eps = res.x[1]
-    
-    return shift_phase_freq(src_FID,phi,eps,extract=False),phi,eps
+
+    return phi, eps
+
 
 def align_FID_diff(mrs,src_FID0,src_FID1,tgt_FID,diffType = 'add',ppmlim=None,shift=True):
     """
@@ -98,9 +102,10 @@ def align_FID_diff(mrs,src_FID0,src_FID1,tgt_FID,diffType = 'add',ppmlim=None,sh
 
     return alignedFID0,phi,eps
 
+
 # The functions to call
 # 1) For normal FIDs
-def phase_freq_align(FIDlist,bandwidth,centralFrequency,ppmlim=None,niter=2,verbose=False,shift=True,target=None):
+def phase_freq_align(FIDlist,bandwidth,centralFrequency,ppmlim=None,niter=2,apodize=10,verbose=False,shift=True,target=None):
     """
     Algorithm:
        Average spectra
@@ -118,6 +123,7 @@ def phase_freq_align(FIDlist,bandwidth,centralFrequency,ppmlim=None,niter=2,verb
     centralFrequency : float (unit=Hz)
     ppmlim           : tuple
     niter            : int
+    apodize          : float (unit=Hz)
     verbose          : bool
     shift            : apply H20 shift to ppm limit
     ref              : reference data to align to
@@ -128,26 +134,41 @@ def phase_freq_align(FIDlist,bandwidth,centralFrequency,ppmlim=None,niter=2,verb
     """
     all_FIDs = FIDlist.copy()
 
-    phiOut,epsOut = np.zeros(len(FIDlist)),np.zeros(len(FIDlist))
+    phiOut, epsOut = np.zeros(len(FIDlist)), np.zeros(len(FIDlist))
     for iter in range(niter):
         if verbose:
             print(' ---- iteration {} ----\n'.format(iter))
 
         if target is None:
-            target = get_target_FID(FIDlist,target='nearest_to_mean')
+            target = get_target_FID(all_FIDs, target='nearest_to_mean')
 
-        MRSargs = {'FID':target,'bw':bandwidth,'cf':centralFrequency}
+        MRSargs = {'FID': target, 'bw': bandwidth, 'cf': centralFrequency}
         mrs = MRS(**MRSargs)
-        
-        for idx,FID in enumerate(all_FIDs):
+
+        if apodize > 0:
+            target = apod(target, mrs.dwellTime, [apodize])
+
+        for idx, FID in enumerate(all_FIDs):
             if verbose:
-                print('... aligning FID number {}'.format(idx),end='\r')
-            all_FIDs[idx],phi,eps = align_FID(mrs,FID,target,ppmlim=ppmlim,shift=shift)
+                print(f'... aligning FID number {idx}\r')
+
+            if apodize > 0:
+                FID_apod = apod(FID.copy(), mrs.dwellTime, [apodize])
+            else:
+                FID_apod = FID
+
+            phi, eps = align_FID(mrs,
+                                 FID_apod,
+                                 target,
+                                 ppmlim=ppmlim,
+                                 shift=shift)
+
+            all_FIDs[idx] = np.exp(-1j*phi) * shift_FID(mrs, FID, eps)
             phiOut[idx] += phi
             epsOut[idx] += eps
         if verbose:
             print('\n')
-    return all_FIDs,phiOut,epsOut
+    return all_FIDs, phiOut, epsOut
 
 # 2) To align spectra from different groups with optional processing applied.
 def phase_freq_align_diff(FIDlist0,FIDlist1,bandwidth,centralFrequency,diffType = 'add',ppmlim=None,shift=True,target=None):

fsl_mrs/utils/preproc/filtering.py

@@ -16,7 +16,7 @@ def apodize(FID,dwelltime,broadening,filter='exp'):
     Args:
         FID (ndarray): Time domain data
         dwelltime (float): dwelltime in seconds
-        broadening (tuple,float): shift in Hz
+        broadening (tuple,float): apodisation in Hz
         filter (str,optional):'exp','l2g'
 
     Returns:

fsl_mrs/utils/preproc/general.py

@@ -115,3 +115,90 @@ def add_subtract_report(inFID,inFID2,outFID,hdr,ppmlim=(0.2,4.2),function='Not s
         return fig
     else:
         return fig
+
+
+def generic_report(inFID,outFID,inHdr,outHdr,ppmlim = (0.2,4.2),html=None,function=''):
+    """
+    Generate generic report
+    """
+    from fsl_mrs.core import MRS
+    import plotly.graph_objects as go
+    from plotly.subplots import make_subplots
+    from fsl_mrs.utils.preproc.reporting import plotStyles, plotAxesStyle
+
+    plotIn = MRS(FID=inFID, header=inHdr)
+    plotOut = MRS(FID=outFID, header=outHdr)
+
+    # Fetch line styles
+    lines, colors, _ = plotStyles()
+
+    # Make a new figure
+    fig = make_subplots(rows=1, cols=2, subplot_titles=['Spectra', 'FID'])
+
+    # Add lines to figure
+    trace1 = go.Scatter(x=plotIn.getAxes(ppmlim=ppmlim),
+                        y=np.real(plotIn.getSpectrum(ppmlim=ppmlim)),
+                        mode='lines',
+                        name='Original',
+                        line=lines['in'])
+    trace2 = go.Scatter(x=plotOut.getAxes(ppmlim=ppmlim),
+                        y=np.real(plotOut.getSpectrum(ppmlim=ppmlim)),
+                        mode='lines',
+                        name='Shifted',
+                        line=lines['out'])
+    fig.add_trace(trace1, row=1, col=1)
+    fig.add_trace(trace2, row=1, col=1)
+
+    # Add lines to figure
+    trace3 = go.Scatter(x=plotIn.getAxes(axis='time'),
+                        y=np.real(plotIn.FID),
+                        mode='lines',
+                        name='Original',
+                        line=lines['emph'])
+    trace4 = go.Scatter(x=plotOut.getAxes(axis='time'),
+                        y=np.real(plotOut.FID),
+                        mode='lines',
+                        name='Shifted',
+                        line=lines['diff'])
+    fig.add_trace(trace3, row=1, col=2)
+    fig.add_trace(trace4, row=1, col=2)
+
+    # Axes layout
+    plotAxesStyle(fig, ppmlim, title=f'{function} summary')
+    fig.layout.xaxis2.update(title_text='Time (s)')
+    fig.layout.yaxis2.update(zeroline=True,
+                             zerolinewidth=1,
+                             zerolinecolor='Gray',
+                             showgrid=False,
+                             showticklabels=False)
+
+    if html is not None:
+        from plotly.offline import plot
+        from fsl_mrs.utils.preproc.reporting import figgroup, singleReport
+        from datetime import datetime
+        import os.path as op
+
+        if op.isdir(html):
+            filename = 'report_' + datetime.now().strftime("%Y%m%d_%H%M%S%f")[:-3]+'.html'
+            htmlfile = op.join(html, filename)
+        elif op.isdir(op.dirname(html)) and op.splitext(html)[1] == '.html':
+            htmlfile = html
+        else:
+            raise ValueError('Report html path must be file or directory. ')
+
+        opName = function
+        timestr = datetime.now().strftime("%H:%M:%S")
+        datestr = datetime.now().strftime("%d/%m/%Y")
+        headerinfo = f'Report for {function}.\n' + \
+                     f'Generated at {timestr} on {datestr}.'
+        # Figures
+        div = plot(fig, output_type='div', include_plotlyjs='cdn')
+        figurelist = [figgroup(fig=div,
+                               name='',
+                               foretext='',
+                               afttext='')]
+
+        singleReport(htmlfile, opName, headerinfo, figurelist)
+        return fig
+    else:
+        return fig

fsl_mrs/utils/preproc/phasing.py

@@ -5,7 +5,7 @@
 # Author: Saad Jbabdi <saad@fmrib.ox.ac.uk>
 #         William Clarke <william.clarke@ndcn.ox.ac.uk>
 #
-# Copyright (C) 2019 University of Oxford 
+# Copyright (C) 2019 University of Oxford
 # SHBASECOPYRIGHT
 
 import numpy as np
@@ -13,13 +13,16 @@ from fsl_mrs.core import MRS
 from fsl_mrs.utils.misc import extract_spectrum
 from fsl_mrs.utils.preproc.shifting import pad
 from fsl_mrs.utils.preproc.remove import hlsvd
-def applyPhase(FID,phaseAngle):
+
+
+def applyPhase(FID, phaseAngle):
     """
     Multiply FID by constant phase
     """
     return FID * np.exp(1j*phaseAngle)
 
-def phaseCorrect(FID,bw,cf,ppmlim=(2.8,3.2),shift=True):
+
+def phaseCorrect(FID, bw, cf, ppmlim=(2.8, 3.2), shift=True, no_hlsvd=False):
     """ Phase correction based on the phase of a maximum point.
 
     HLSVD is used to remove peaks outside the limits to flatten baseline first.
@@ -30,18 +33,22 @@ def phaseCorrect(FID,bw,cf,ppmlim=(2.8,3.2),shift=True):
         cf (float): central frequency in Hz
         ppmlim (tuple,optional)  : Limit to this ppm range
         shift (bool,optional)    : Apply H20 shft
+        no_hlsvd (bool,optional) : Disable hlsvd step
 
     Returns:
         FID (ndarray): Phase corrected FID
     """
     # Run HLSVD to remove peaks outside limits
-    try:
-        fid_hlsvd = hlsvd(FID,1/bw,cf,(ppmlim[1]+0.5,ppmlim[1]+3.0),limitUnits='ppm+shift')
-        fid_hlsvd = hlsvd(fid_hlsvd,1/bw,cf,(ppmlim[0]-3.0,ppmlim[0]-0.5),limitUnits='ppm+shift')
-    except:
+    if no_hlsvd:
         fid_hlsvd = FID
-        print('Phasing HLSVD failed, proceeding to phaseing.')
-    #Find maximum of absolute spectrum in ppm limit
+    else:
+        try:
+            fid_hlsvd = hlsvd(FID,1/bw,cf,(ppmlim[1]+0.5,ppmlim[1]+3.0),limitUnits='ppm+shift')
+            fid_hlsvd = hlsvd(fid_hlsvd,1/bw,cf,(ppmlim[0]-3.0,ppmlim[0]-0.5),limitUnits='ppm+shift')
+        except:
+            fid_hlsvd = FID
+            print('HLSVD in phaseCorrect failed, proceeding to phasing.')
+    # Find maximum of absolute spectrum in ppm limit
     padFID = pad(fid_hlsvd,FID.size*3)
     MRSargs = {'FID':padFID,'bw':bw,'cf':cf}
     mrs = MRS(**MRSargs)
@@ -52,9 +59,10 @@ def phaseCorrect(FID,bw,cf,ppmlim=(2.8,3.2),shift=True):
     
     return applyPhase(FID,phaseAngle),phaseAngle,int(np.round(maxIndex/4))
 
+
 def phaseCorrect_report(inFID,outFID,hdr,position,ppmlim=(2.8,3.2),html=None):
     """
-    Generate report
+    Generate report for phaseCorrect
     """
     # from matplotlib import pyplot as plt
     from fsl_mrs.core import MRS
@@ -103,7 +111,7 @@ def phaseCorrect_report(inFID,outFID,hdr,position,ppmlim=(2.8,3.2),html=None):
     # Axes layout
     plotAxesStyle(fig,widelimit,title = 'Phase correction summary')
    
-    # Axea 
+    # Axes 
     if html is not None:
         from plotly.offline import plot
         from fsl_mrs.utils.preproc.reporting import figgroup, singleReport
@@ -134,25 +142,3 @@ def phaseCorrect_report(inFID,outFID,hdr,position,ppmlim=(2.8,3.2),html=None):
         return fig
     else:
         return fig
-
-# matplotlib version of report
-# def phaseCorrect_report(inFID,outFID,hdr,position,ppmlim=(2.8,3.2)):
-#     from matplotlib import pyplot as plt
-#     from fsl_mrs.core import MRS
-#     from fsl_mrs.utils.plotting import styleSpectrumAxes
-
-#     toMRSobj = lambda fid : MRS(FID=fid,header=hdr)
-#     plotIn = toMRSobj(inFID)
-#     plotOut = toMRSobj(outFID)
-
-#     widelimit = (0,6)
-
-#     fig = plt.figure(figsize=(10,10))
-#     plt.plot(plotIn.getAxes(ppmlim=widelimit),np.real(plotIn.getSpectrum(ppmlim=widelimit)),'k',label='Unphased', linewidth=2)
-#     plt.plot(plotIn.getAxes(ppmlim=ppmlim),np.real(plotIn.getSpectrum(ppmlim=ppmlim)),'r',label='search region', linewidth=2)
-#     plt.plot(plotIn.getAxes(ppmlim=ppmlim)[position],np.real(plotIn.getSpectrum(ppmlim=ppmlim))[position],'rx',label='max point', linewidth=2)
-#     plt.plot(plotOut.getAxes(ppmlim=widelimit),np.real(plotOut.getSpectrum(ppmlim=widelimit)),'b--',label='Phased', linewidth=2)
-#     styleSpectrumAxes(ax=plt.gca())
-#     plt.legend()
-#     plt.rcParams.update({'font.size': 12})
-#     plt.show()