fix tests

Author: cx1111

devtests.ipynb

@@ -449,50 +449,6 @@
     "    \n",
     "    return fields, t"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 7,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
-   "source": [
-    "import wfdb\n",
-    "\n",
-    "x = wfdb.Record()\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "True"
-      ]
-     },
-     "execution_count": 2,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "type(5.4) == float"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

tests/test_records.py

@@ -18,7 +18,7 @@ def test_1(self):
     def test_2(self):
         record = wfdb.rdsamp('sampledata/100', sampfrom=1,
                              sampto=10800, channels=[1], physical=False)
-        sig = record.signals
+        sig = record.d_signals
         targetsig = np.genfromtxt('tests/targetoutputdata/target2')
         targetsig = targetsig.reshape(len(targetsig), 1)
         assert np.array_equal(sig, targetsig)
@@ -28,7 +28,7 @@ def test_2(self):
     # target3
     def test_3(self):
         record = wfdb.rdsamp('sampledata/test01_00s', physical=False)
-        sig = record.signals
+        sig = record.d_signals
         targetsig = np.genfromtxt('tests/targetoutputdata/target3')
         assert np.array_equal(sig, targetsig)
 
@@ -48,7 +48,7 @@ def test_4(self):
     def test_5(self):
         record = wfdb.rdsamp('sampledata/a103l',
                              sampfrom=20000, channels=[0, 1], physical=False)
-        sig = record.signals
+        sig = record.d_signals
         targetsig = np.genfromtxt('tests/targetoutputdata/target5')
         assert np.array_equal(sig, targetsig)
 
@@ -68,7 +68,7 @@ def test_6(self):
     # target7
     def test_7(self):
         record= wfdb.rdsamp('sampledata/s0010_re', physical=False)
-        sig = record.signals
+        sig = record.d_signals
         targetsig = np.genfromtxt('tests/targetoutputdata/target7')
         assert np.array_equal(sig, targetsig)
 
@@ -87,7 +87,7 @@ def test_8(self):
     # target9
     def test_9(self):
         record = wfdb.rdsamp('sampledata/03700181', physical=False)
-        sig = record.signals
+        sig = record.d_signals
         # The WFDB library rdsamp does not return the final N samples for all
         # channels due to the skew.
         sig = sig[:-4, :]

wfdb/annotations.py

@@ -27,15 +27,15 @@ class Annotation():
     annotations that are not one of the codes go in the 'aux' field rather than the 'anntype'
     field.
     """
-    def __init__(self, recordname, annotator, annsamp, anntype, num = None, subtype = None, chan = None, aux = None, fs = None):
+    def __init__(self, recordname, annotator, annsamp, anntype, subtype = None, chan = None, num = None, aux = None, fs = None):
         self.recordname = recordname
         self.annotator = annotator
 
         self.annsamp = annsamp
         self.anntype = anntype
-        self.num = num
         self.subtype = subtype
         self.chan = chan
+        self.num = num
         self.aux = aux
         self.fs = fs
 
@@ -408,7 +408,8 @@ def rdann(recordname, annotator, sampfrom=0, sampto=None):
 
         AT = filebytes[bpi, 1] >> 2
 
-        while (AT > 59):  # Process any other fields belonging to this annotation
+        # Process any other fields belonging to this annotation
+        while (AT > 59):  
 
             subtype,bpi,num,chan,cpychan,cpynum,aux = proc_extra_fields(AT,
                 subtype,ai,filebytes,bpi,num,chan,cpychan,cpynum,aux)
@@ -435,7 +436,7 @@ def rdann(recordname, annotator, sampfrom=0, sampto=None):
     # 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)
+    # Apply annotation range
     annsamp,anntype,num,subtype,chan,aux = apply_annotation_range(annsamp,
         sampfrom,sampto,anntype,num,subtype,chan,aux)
 

wfdb/plots.py

@@ -1,8 +1,10 @@
 import numpy as np
+import sys
+import matplotlib.pyplot as plt
 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): 
@@ -176,11 +178,11 @@ def checkannplotitems(annotation, title, timeunits):
     if timeunits == 'samples':
         plotvals = annotation.annsamp
     elif timeunits == 'seconds':
-        plotvals = annotation.annsamp
+        plotvals = annotation.annsamp/annotation.fs
     elif timeunits == 'minutes':
-        plotvals = annotation.annsamp
-    else:
-        t = np.linspace(0, siglen-1, siglen)/fs/3600
+        plotvals = annotation.annsamp/(annotation.fs*60)
+    elif timeunits == 'hours':
+        plotvals = annotation.annsamp/(annotation.fs*3600)
 
     # title
     if title is not None and type(title) != str:

wfdb/records.py

@@ -150,7 +150,7 @@ def checkfield(self, field):
             for f in self.segname:
                 if f == '~':
                     continue
-                acceptedstring = re.match('[-\w]+',f).string
+                acceptedstring = re.match('[-\w]+',f)
                 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':

wfdbdemo.ipynb

@@ -51,17 +51,28 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "image/png": 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F67mA7pfW+5K8HriF7vOX9qZbTgfYkwmop6puTvcp2/8tyQX967+c7hfuRf1c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\nAABJRU5ErkJggg==\n",
+      "text/plain": [
+       "<matplotlib.figure.Figure at 0x7fcea07b99b0>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
-    "# Demo 3 - Read a WFDB annotation and plot the samples\n",
+    "# Demo 3 - Read part of a WFDB annotation file and plot the samples\n",
     "import wfdb\n",
-    "annotation = wfdb.rdann('sampledata/12726', 'wabp')\n",
-    "wfdb.plotann(annotation)\n",
-    "annotation.__dict__"
+    "annotation = wfdb.rdann('sampledata/12726', 'wabp', sampfrom = 100000, sampto = 110000)\n",
+    "annotation.fs = 120\n",
+    "wfdb.plotann(annotation, timeunits = 'seconds')"
    ]
   },
   {
@@ -72,7 +83,7 @@
    },
    "outputs": [],
    "source": [
-    "# Demo 4 - Read a WFDB record and annotation and plot them together.\n",
+    "# Demo 4 - Read a WFDB record and annotation, and plot them together.\n",
     "\n",
     "signals, fields=wfdb.srdsamp('sampledata/100')\n",
     "annotation = wfdb.rdann('sampledata/100', 'atr')\n",