def shiftToRef(FID, target, bw, cf, ppmlim=(2.8, 3.2), shift=True):
#Find maximum of absolute spectrum in ppm limit
padFID = pad(FID, FID.size * 3)
MRSargs = {'FID': padFID, 'bw': bw, 'cf': cf}
mrs = MRS(**MRSargs)
spec = extract_spectrum(mrs, padFID, ppmlim=ppmlim, shift=shift)
if shift:
extractedAxis = mrs.getAxes(ppmlim=ppmlim)
else:
extractedAxis = mrs.getAxes(ppmlim=ppmlim, axis='ppm')
maxIndex = np.argmax(np.abs(spec))
shiftAmount = extractedAxis[maxIndex] - target
shiftAmountHz = shiftAmount * mrs.centralFrequency / 1E6
return freqshift(FID, 1 / bw, -shiftAmountHz), shiftAmount
def test_shiftToRef():
testFIDs, testHdrs = syn.syntheticFID(amplitude=[1, 0],
chemicalshift=[-2.1, 0],
phase=[0, 0],
points=1024,
noisecovariance=[[1E-3]])
shiftFID, _ = preproc.shiftToRef(testFIDs[0],
-2.0,
testHdrs['bandwidth'],
testHdrs['centralFrequency'],
ppmlim=(-2.2, -2.0),
shift=False)
mrs = MRS(FID=shiftFID, header=testHdrs)
maxindex = np.argmax(mrs.getSpectrum(shift=False))
position = mrs.getAxes(axis='ppm')[maxindex]
assert np.isclose(position, -2.0, atol=1E-1)
def shift_report(inFID,
outFID,
inHdr,
outHdr,
ppmlim=(0.2, 4.2),
html=None,
function='shift'):
"""
Generate report
"""
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='Shift 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. ')
operation, function, description = reportStrings(function)
opName = operation
timestr = datetime.now().strftime("%H:%M:%S")
datestr = datetime.now().strftime("%d/%m/%Y")
headerinfo = f'Report for fsl_mrs.utils.preproc.shifting.{function}.\n'\
+ f'Generated at {timestr} on {datestr}.'
# Figures
div = plot(fig, output_type='div', include_plotlyjs='cdn')
figurelist = [
figgroup(fig=div, name='', foretext=f'{description}', afttext=f'')
]
singleReport(htmlfile, opName, headerinfo, figurelist)
return fig
else:
return fig