enable read custom anntypes

Author: cx1111

README.rst

@@ -80,15 +80,15 @@ the metadata as a dictionary.
 
 ::
 
-    sig, fields = rdsamp(recordname, sampfrom=0, sampto=[], channels=[], physical=1, 
+    wrsamp(recordname, sampfrom=0, sampto=[], channels=[], physical=1, 
         stacksegments=1, pbdl=0, dldir=os.cwd())
 
 Example Usage:
 
 ::
 
     import wfdb
-    sig, fields = wfdb.rdsamp('mitdb/100', sampto=2000, pbdl=1)
+    sig, fields = wfdb.wrsamp('mitdb/100', sampto=2000, pbdl=1)
 
 Input Arguments:
 

wfdb/__init__.py

@@ -2,4 +2,4 @@
 
 from .records import Record, MultiRecord, rdheader, rdsamp, srdsamp, wrsamp
 from .annotations import Annotation, rdann, wrann, showanncodes
-from .plots import plotrec
+from .plots import plotrec, plotann

wfdb/annotations.py

@@ -432,12 +432,15 @@ def rdann(recordname, annotator, sampfrom=0, sampto=None):
     # Snip the unallocated end of the arrays
     annsamp,anntype,num,subtype,chan,aux = snip_arrays(annsamp,anntype,num,subtype,chan,aux,ai)
 
+    # Process the fields if there are custom annotation types
+    allannsyms,annsamp,anntype,num,subtype,chan,aux = proccustomtypes(annsamp,anntype,num,subtype,chan,aux)
+
     # Apply annotation range (from X to Y)
     annsamp,anntype,num,subtype,chan,aux = apply_annotation_range(annsamp,
         sampfrom,sampto,anntype,num,subtype,chan,aux)
 
-    # Set the annotation type to annotation codes
-    anntype = [annsyms[code] for code in anntype]
+    # Set the annotation type to the annotation codes
+    anntype = [allannsyms[code] for code in anntype]
 
     # Store fields in an Annotation object
     annotation = Annotation(recordname, annotator, annsamp, anntype, 
@@ -539,7 +542,7 @@ def snip_arrays(annsamp,anntype,num,subtype,chan,aux,ai):
     aux = aux[0:ai]
     return annsamp,anntype,num,subtype,chan,aux
 
-# Keep only the specified annotations
+# Keep annotations within a sample range
 def apply_annotation_range(annsamp,sampfrom,sampto,anntype,num,subtype,chan,aux):
 
     returnempty = 0
@@ -578,6 +581,43 @@ def apply_annotation_range(annsamp,sampfrom,sampto,anntype,num,subtype,chan,aux)
     return annsamp,anntype,num,subtype,chan,aux
 
 
+# Process the fields if there are custom annotation types
+def proccustomtypes(annsamp,anntype,num,subtype,chan,aux):
+    # Custom anncodes appear as regular annotations in the form: 
+    # sample = 0, anntype = 22 (note annotation '"'), aux = "NUMBER[ \t]CUSTOMANNCODE[ \t]Calibration"
+    s0 = np.where(annsamp == 0)[0]
+    t22 = np.where(anntype == 22)[0]
+    s0t22 = list(set(s0).intersection(t22))
+
+    allannsyms = annsyms.copy()
+    if s0t22 != []:
+        # The custom anncode indices
+        custominds = []
+        # Check aux for custom codes
+        for i in s0t22:
+            acceptedstring = re.match('(\d+)[ \t](\w+)[ \t]Calibration', aux[i])
+            # Found custom annotation code. 
+            if acceptedstring is not None and acceptedstring.string==aux[i]:
+                # Keep track of index
+                custominds.append(i)
+                # Add code to annsym dictionary
+                codenum, codesym = acceptedstring.group(1, 2)
+                allannsyms[int(codenum)] = codesym
+
+        # Remove the attributes with the custom anncode indices
+        if custominds != []:
+            keepinds = [i for i in range(len(annsamp)) if i not in custominds]
+
+            annsamp = annsamp[keepinds]
+            anntype = anntype[keepinds]
+            num = num[keepinds]
+            subtype = subtype[keepinds]
+            chan = chan[keepinds]
+            aux = [aux[i] for i in keepinds]
+
+    return (allannsyms,annsamp,anntype,num,subtype,chan,aux)
+    
+
 ## ------------- /Reading Annotations ------------- ##
 
 
@@ -599,9 +639,9 @@ def apply_annotation_range(annsamp,sampfrom,sampto,anntype,num,subtype,chan,aux)
     12: '/',  # paced beat */
     13: 'Q',  # unclassifiable beat */
     14: '~',  # signal quality change */
-    #15: '[15]',
+    15: '[15]',
     16: '|',  # isolated QRS-like artifact */
-    #17: '[17]',
+    17: '[17]',
     18: 's',  # ST change */
     19: 'T',  # T-wave change */
     20: '*',  # systole */
@@ -624,18 +664,16 @@ def apply_annotation_range(annsamp,sampfrom,sampto,anntype,num,subtype,chan,aux)
     37: 'x',  # non-conducted P-wave (blocked APB) */
     38: 'f',  # fusion of paced and normal beat */
     39: '(',  # waveform onset */
-    # 39: 'PQ', # PQ junction (beginning of QRS) */
     40: ')',  # waveform end */
-    # 40: 'JPT', # J point (end of QRS) */
     41: 'r',  # R-on-T premature ventricular contraction */
-    #42: '[42]',
-    #43: '[43]',
-    #44: '[44]',
-    #45: '[45]',
-    #46: '[46]',
-    #47: '[47]',
-    #48: '[48]',
-    #49: '[49]',
+    42: '[42]',
+    43: '[43]',
+    44: '[44]',
+    45: '[45]',
+    46: '[46]',
+    47: '[47]',
+    48: '[48]',
+    49: '[49]',
 }
 # Reverse ann symbols for mapping symbols back to numbers
 revannsyms = {v: k for k, v in annsyms.items()}
@@ -658,7 +696,9 @@ def apply_annotation_range(annsamp,sampfrom,sampto,anntype,num,subtype,chan,aux)
     12: 'PACE',  # paced beat */
     13: 'UNKNOWN',  # unclassifiable beat */
     14: 'NOISE',  # signal quality change */
+    15: '',
     16: 'ARFCT',  # isolated QRS-like artifact */
+    17: '',
     18: 'STCH',  # ST change */
     19: 'TCH',  # T-wave change */
     20: 'SYSTOLE',  # systole */
@@ -681,10 +721,16 @@ def apply_annotation_range(annsamp,sampfrom,sampto,anntype,num,subtype,chan,aux)
     37: 'NAPC',  # non-conducted P-wave (blocked APB) */
     38: 'PFUS',  # fusion of paced and normal beat */
     39: 'WFON',  # waveform onset */
-    # 39: 'PQ', # PQ junction (beginning of QRS) */
     40: 'WFOFF',  # waveform end */
-    # 40: 'JPT', # J point (end of QRS) */
-    41: 'RONT'  # R-on-T premature ventricular contraction */
+    41: 'RONT',  # R-on-T premature ventricular contraction */
+    42: '',
+    43: '', 
+    44: '', 
+    45: '', 
+    46: '',
+    47: '',
+    48: '', 
+    49: ''
 }
 
 # Mapping annotation symbols to the annotation codes

wfdb/plots.py

@@ -1,7 +1,10 @@
 import numpy as np
+from . import records
 from . import _headers
+from . import annotations
 import matplotlib.pyplot as plt
 
+# Plot a WFDB record's signals
 def plotrec(record=None, signals = None, fields = None, title = None, timeunits='samples', returnfig = False): 
 
     # Figure out which arguments to use to plot
@@ -19,7 +22,7 @@ def plotrec(record=None, signals = None, fields = None, title = None, timeunits=
     for ch in range(nsig):
         # Plot signal channel
         plt.subplot(100*nsig+11+ch)
-        plt.plot(t, sig[:,ch]) 
+        plt.plot(t, signals[:,ch]) 
 
         if (title is not None) and (ch==0):
             plt.title(title)
@@ -30,7 +33,7 @@ def plotrec(record=None, signals = None, fields = None, title = None, timeunits=
         else:
             plt.xlabel('time/'+timeunits[:-1])
 
-        if fields["signame"][ch] is not none:
+        if fields["signame"][ch] is not None:
             chanlabel=fields["signame"][ch]
         else:
             chanlabel='channel'
@@ -57,7 +60,7 @@ def getplotitems(record, signals, fields):
         # Use the record object
         if signals is None:
             # If it is a MultiRecord, convert it into single
-            if type(record) == MultiRecord:
+            if type(record) == records.MultiRecord:
                 record = record.multi_to_single()
 
             # Need to ensure p_signals is present
@@ -83,23 +86,23 @@ def checkplotitems(signals, fields, title, timeunits):
     siglen, nsig = signals.shape
 
     # fs and timeunits
-    allowedtimes = ['samples, seconds, minutes, hours']
+    allowedtimes = ['samples', 'seconds', 'minutes', 'hours']
     if timeunits not in allowedtimes:
         print("The 'timeunits' field must be one of the following: ", allowedtimes)
         sys.exit()
     # Get x axis values. fs must be valid when plotting time
     if timeunits == 'samples':
-        t = np.linspace(siglen)
+        t = np.linspace(0, siglen-1, siglen)
     else:
         if type(fields['fs']) not in _headers.floattypes:
             sys.exit("The 'fs' field must be a number")
 
         if timeunits == 'seconds':
-            t = np.linspace(siglen)/fs
+            t = np.linspace(0, siglen-1, siglen)/fs
         elif timeunits == 'minutes':
-            t = np.linspace(siglen)/fs/60
+            t = np.linspace(0, siglen-1, siglen)/fs/60
         else:
-            t = np.linspace(siglen)/fs/3600
+            t = np.linspace(0, siglen-1, siglen)/fs/3600
 
     # units
     if fields['units'] is None:
@@ -124,10 +127,66 @@ def checkplotitems(signals, fields, title, timeunits):
     return fields, t
 
 
+# Plot the sample locations of a WFDB annotation
+def plotann(annotation, title = None, timeunits = 'samples', returnfig = False): 
+    
+    # Check the validity of items used to make the plot
+    # Get the x axis annotation values to plot
+    plotvals = checkannplotitems(annotation, title, timeunits)
+    
+    # Create the plot  
+    fig=plt.figure()
+    
+    plt.plot(plotvals, np.zeros(len(plotvals)), 'r+')
+    
+    if title is not None:
+        plt.title(title)
+        
+    # Axis Labels
+    if timeunits == 'samples':
+        plt.xlabel('index/sample')
+    else:
+        plt.xlabel('time/'+timeunits[:-1])
+
+    plt.show(fig)
+    
+    # Return the figure if requested
+    if returnfig:
+        return fig
 
+# Check the validity of items used to make the annotation plot
+def checkannplotitems(annotation, title, timeunits):
+    
+    # signals
+    if type(annotation)!= annotations.Annotation:
+        sys.exit("The 'annotation' field must be a 'wfdb.Annotation' object")
 
+    # fs and timeunits
+    allowedtimes = ['samples', 'seconds', 'minutes', 'hours']
+    if timeunits not in allowedtimes:
+        print("The 'timeunits' field must be one of the following: ", allowedtimes)
+        sys.exit()
 
+    # fs must be valid when plotting time
+    if timeunits != 'samples':
+        if type(annotation.fs) not in _headers.floattypes:
+            sys.exit("In order to plot time units, the Annotation object must have a valid 'fs' attribute")
 
+    # Get x axis values to plot
+    if timeunits == 'samples':
+        plotvals = annotation.annsamp
+    elif timeunits == 'seconds':
+        plotvals = annotation.annsamp
+    elif timeunits == 'minutes':
+        plotvals = annotation.annsamp
+    else:
+        t = np.linspace(0, siglen-1, siglen)/fs/3600
+
+    # title
+    if title is not None and type(title) != str:
+        sys.exit("The 'title' field must be a string")
+    
+    return plotvals
 
 
 
@@ -189,7 +248,4 @@ def plotreco(sig, fields, annsamp=None, annch=[0], title=None, plottime=1):
             unitlabel='NU'
         plt.ylabel(chanlabel+"/"+unitlabel)
 
-    plt.show(f1)
-
-def plotann():
-    print('on it')
+    plt.show(f1)

wfdb/records.py

@@ -150,7 +150,7 @@ def checkfield(self, field):
             for f in self.segname:
                 if f == '~':
                     continue
-                acceptedstring = re.match('[-\w]+',f)
+                acceptedstring = re.match('[-\w]+',f).string
                 if not acceptedstring or acceptedstring.string != f:
                     sys.exit("Non-null segment names may only contain alphanumerics. Null segment names must be equal to '~'")
         elif field == 'seglen':
@@ -225,8 +225,7 @@ class Record(BaseRecord, _headers.HeadersMixin, _signals.SignalsMixin):
     def __init__(self, p_signals=None, d_signals=None,
                  recordname=None, nsig=None, 
                  fs=None, counterfreq=None, basecounter=None, 
-                 siglen=N
-                 one, basetime=None, basedate=None, 
+                 siglen=None, basetime=None, basedate=None, 
                  filename=None, fmt=None, sampsperframe=None, 
                  skew=None, byteoffset=None, adcgain=None, 
                  baseline=None, units=None, adcres=None,