added copyright and bits od docstring

fsl_mrs/utils/constants.py

@@ -3,6 +3,7 @@
 # constants.py - Definition of all the constants
 #
 # Author: Saad Jbabdi <saad@fmrib.ox.ac.uk>
+#         William Clarke <william.clarke@ndcn.ox.ac.uk>
 #
 # Copyright (C) 2019 University of Oxford 
 # SHBASECOPYRIGHT

fsl_mrs/utils/preproc/align.py

-""" Module containing alignment functions (align and aligndiff)"""
+#!/usr/bin/env python
+
+# align.py - Module containing alignment functions (align and aligndiff)
+#
+# Author: Saad Jbabdi <saad@fmrib.ox.ac.uk>
+#         William Clarke <william.clarke@ndcn.ox.ac.uk>
+#
+# Copyright (C) 2019 University of Oxford 
+# SHBASECOPYRIGHT
+
 from fsl_mrs.utils.preproc.general import get_target_FID,add,subtract
 from fsl_mrs.core import MRS
 from fsl_mrs.utils.misc import extract_spectrum,shift_FID
@@ -192,6 +201,9 @@ def phase_freq_align_diff(FIDlist0,FIDlist1,bandwidth,centralFrequency,diffType
 # Reporting functions
 
 def phase_freq_align_report(inFIDs,outFIDs,hdr,phi,eps,ppmlim=None,shift=True,html=None):
+    """
+    Generate phase alignment report
+    """
     from fsl_mrs.utils.preproc.combine import combine_FIDs
     import plotly.graph_objects as go    
     from fsl_mrs.utils.preproc.reporting import plotStyles,plotAxesStyle
@@ -527,4 +539,4 @@ def phase_freq_align_diff_report(inFIDs0,inFIDs1,outFIDs0,outFIDs1,hdr,eps,phi,p
 #     styleSpectrumAxes(ax=plt.gca())
 #     plt.legend()
 #     plt.rcParams.update({'font.size': 12})
-#     plt.show()
\ No newline at end of file
+#     plt.show()

fsl_mrs/utils/preproc/combine.py

-'''Module containing functions for combining FIDs, includes coil combination.'''
+#!/usr/bin/env python
+
+# combine.py - Module containing functions for combining FIDs, includes coil combination
+#
+# Author: Saad Jbabdi <saad@fmrib.ox.ac.uk>
+#         William Clarke <william.clarke@ndcn.ox.ac.uk>
+#
+# Copyright (C) 2019 University of Oxford 
+# SHBASECOPYRIGHT
+
+
 
 import numpy as np
 
@@ -287,4 +297,4 @@ def combine_FIDs_report(inFIDs,outFID,hdr,ncha=2,ppmlim = (0.0,6.0),method='not
 #     for fid in toPlotOut:
 #         ax.plot(fid.getAxes(ppmlim=ppmlim),np.real(fid.getSpectrum(ppmlim=ppmlim)),'k-')    
 #     styleSpectrumAxes(ax)
-#     plt.show()
\ No newline at end of file
+#     plt.show()

fsl_mrs/utils/preproc/eddycorrect.py

+#!/usr/bin/env python
+
+# eddycorrect.py - Eddy current correction routines
+#
+# Author: Saad Jbabdi <saad@fmrib.ox.ac.uk>
+#         William Clarke <william.clarke@ndcn.ox.ac.uk>
+#
+# Copyright (C) 2019 University of Oxford 
+# SHBASECOPYRIGHT
+
 import numpy as np
 def eddy_correct(FIDmet,FIDPhsRef):
     """
@@ -17,6 +27,9 @@ def eddy_correct(FIDmet,FIDPhsRef):
     return np.abs(FIDmet) * np.exp(1j*(np.angle(FIDmet)-phsRef))
 
 def eddy_correct_report(inFID,outFID,phsRef,hdr,ppmlim = (0.2,4.2),html=None):
+    """
+    Generate Eddy correction report
+    """
     # from matplotlib import pyplot as plt
     from fsl_mrs.core import MRS
     import plotly.graph_objects as go    
@@ -120,4 +133,4 @@ def eddy_correct_report(inFID,outFID,phsRef,hdr,ppmlim = (0.2,4.2),html=None):
     # styleSpectrumAxes(ax=plt.gca())
     # plt.legend()
     # plt.rcParams.update({'font.size': 12})
-    # plt.show()
\ No newline at end of file
+    # plt.show()

fsl_mrs/utils/preproc/filtering.py

+#!/usr/bin/env python
+
+# filtering.py - Routines for FID filtering
+#
+# Author: Saad Jbabdi <saad@fmrib.ox.ac.uk>
+#         William Clarke <william.clarke@ndcn.ox.ac.uk>
+#
+# Copyright (C) 2019 University of Oxford 
+# SHBASECOPYRIGHT
+
 import numpy as np
 
 def apodize(FID,dwelltime,broadening,filter='exp'):
@@ -24,6 +34,9 @@ def apodize(FID,dwelltime,broadening,filter='exp'):
 
 
 def apodize_report(inFID,outFID,hdr,plotlim = (0.2,6),html=None):
+    """
+    Generate report
+    """
     # from matplotlib import pyplot as plt
     from fsl_mrs.core import MRS
     import plotly.graph_objects as go    
@@ -85,4 +98,4 @@ def apodize_report(inFID,outFID,hdr,plotlim = (0.2,6),html=None):
         singleReport(htmlfile,opName,headerinfo,figurelist)
         return fig
     else:
-        return fig
\ No newline at end of file
+        return fig

fsl_mrs/utils/preproc/general.py

-"""General preprocessing functions"""
+#!/usr/bin/env python
+
+# general.py - General preprocessing functions
+#
+# Author: Saad Jbabdi <saad@fmrib.ox.ac.uk>
+#         William Clarke <william.clarke@ndcn.ox.ac.uk>
+#
+# Copyright (C) 2019 University of Oxford 
+# SHBASECOPYRIGHT
+
+
 import numpy as np
 from dataclasses import dataclass
 
@@ -38,6 +48,9 @@ def add(FID1,FID2):
     return (FID1+FID2)/2.0
 
 def add_subtract_report(inFID,inFID2,outFID,hdr,ppmlim=(0.2,4.2),function='Not specified',html=None):
+    """
+    Generate report
+    """
     # from matplotlib import pyplot as plt
     from fsl_mrs.core import MRS
     import plotly.graph_objects as go    
@@ -101,4 +114,4 @@ def add_subtract_report(inFID,inFID2,outFID,hdr,ppmlim=(0.2,4.2),function='Not s
         singleReport(htmlfile,opName,headerinfo,figurelist)
         return fig
     else:
-        return fig
\ No newline at end of file
+        return fig

fsl_mrs/utils/preproc/phasing.py

+#!/usr/bin/env python
+
+# phasing.py - Phase correction routines
+#
+# Author: Saad Jbabdi <saad@fmrib.ox.ac.uk>
+#         William Clarke <william.clarke@ndcn.ox.ac.uk>
+#
+# Copyright (C) 2019 University of Oxford 
+# SHBASECOPYRIGHT
+
 import numpy as np
 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):
+    """
+    Multiply FID by constant phase
+    """
     return FID * np.exp(1j*phaseAngle)
 
 def phaseCorrect(FID,bw,cf,ppmlim=(2.8,3.2),shift=True):
@@ -40,6 +53,9 @@ 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
+    """
     # from matplotlib import pyplot as plt
     from fsl_mrs.core import MRS
     import plotly.graph_objects as go    
@@ -139,4 +155,4 @@ def phaseCorrect_report(inFID,outFID,hdr,position,ppmlim=(2.8,3.2),html=None):
 #     styleSpectrumAxes(ax=plt.gca())
 #     plt.legend()
 #     plt.rcParams.update({'font.size': 12})
-#     plt.show()
\ No newline at end of file
+#     plt.show()

fsl_mrs/utils/preproc/remove.py

+#!/usr/bin/env python
+
+# remove.py - HLSVD-based correction
+#
+# Author: Saad Jbabdi <saad@fmrib.ox.ac.uk>
+#         William Clarke <william.clarke@ndcn.ox.ac.uk>
+#
+# Copyright (C) 2019 University of Oxford 
+# SHBASECOPYRIGHT
+
 import numpy as np
 import hlsvdpro
 from fsl_mrs.utils.misc import checkCFUnits
@@ -48,6 +58,9 @@ def hlsvd(FID,dwelltime,centralFrequency,limits,limitUnits = 'ppm',numSingularVa
     return FID - sumFID
 
 def hlsvd_report(inFID,outFID,hdr,limits,limitUnits = 'ppm',plotlim = (0.2,6),html=None):
+    """
+    Generate report
+    """
     # from matplotlib import pyplot as plt
     from fsl_mrs.core import MRS
     import plotly.graph_objects as go    
@@ -151,4 +164,4 @@ def hlsvd_report(inFID,outFID,hdr,limits,limitUnits = 'ppm',plotlim = (0.2,6),ht
 #     styleSpectrumAxes(ax=plt.gca())
 #     plt.legend()
 #     plt.rcParams.update({'font.size': 12})
-#     plt.show()
\ No newline at end of file
+#     plt.show()

fsl_mrs/utils/preproc/reporting.py

+#!/usr/bin/env python
+
+# reporting.py - Routines for generating proc reports
+#
+# Author: William Clarke <william.clarke@ndcn.ox.ac.uk>
+#
+# Copyright (C) 2019 University of Oxford 
+# SHBASECOPYRIGHT
+
 from jinja2 import FileSystemLoader, Environment
 import os.path as op
 from dataclasses import dataclass

fsl_mrs/utils/preproc/shifting.py

+#!/usr/bin/env python
+
+# shifting.py - Shifting routines
+#
+# Author: Saad Jbabdi <saad@fmrib.ox.ac.uk>
+#         William Clarke <william.clarke@ndcn.ox.ac.uk>
+#
+# Copyright (C) 2019 University of Oxford 
+# SHBASECOPYRIGHT
+
 import numpy as np
 from fsl_mrs.core import MRS
 from fsl_mrs.utils.misc import extract_spectrum
@@ -106,7 +116,10 @@ def pad(FID,k,first_or_last='last'):
     else:
         raise(Exception("Last parameter must either be 'first' or 'last'"))
 
-def shift_report(inFID,outFID,inHdr,outHdr,ppmlim = (0.2,4.2),html=None,function='shift'):    
+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
@@ -241,4 +254,4 @@ def reportStrings(funcName):
 #     ax2.autoscale(enable=True, axis='x', tight=False)
 
 #     plt.rcParams.update({'font.size': 12})
-#     plt.show()
\ No newline at end of file
+#     plt.show()

fsl_mrs/utils/preproc/unlike.py

+#!/usr/bin/env python
+
+# unlike.py - Outlier detection routines
+#
+# Author: William Clarke <william.clarke@ndcn.ox.ac.uk>
+#
+# Copyright (C) 2019 University of Oxford 
+# SHBASECOPYRIGHT
+
 from fsl_mrs.core import MRS
 import numpy as np
 from fsl_mrs.utils.preproc.general import get_target_FID
@@ -202,4 +211,4 @@ def identifyUnlikeFIDs_report(goodFIDs,badFIDs,hdr,keepIndicies,rmIndicies,metri
 #     plt.plot(tgtmrs.getAxes(ppmlim=ppmlim),np.real(tgtmrs.getSpectrum(ppmlim=ppmlim)),'k',label='Target')
 #     styleSpectrumAxes(plt.gca())
 #     plt.legend()
-#     plt.show()
\ No newline at end of file
+#     plt.show()

fsl_mrs/utils/qc.py

+#!/usr/bin/env python
+
+# qc.py - Calculate various QC measures
+#
+# Author: William Clarke <william.clarke@ndcn.ox.ac.uk>
+#
+# Copyright (C) 2019 University of Oxford 
+# SHBASECOPYRIGHT
+
 from fsl_mrs.utils import models
 from fsl_mrs.utils.misc import FIDToSpec,SpecToFID
 from fsl_mrs.core import MRS
@@ -9,6 +18,8 @@ import pandas as pd
 
 SNR = namedtuple('SNR',['spectrum','peaks','residual'])
 
+
+
 class NoiseNotFoundError(ValueError):
     pass