add demos and tests

Author: cx1111

devtests.ipynb

@@ -18,48 +18,6 @@
     "import wfdb"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "import wfdb\n",
-    "# Testing rdsamp multiple samples per frame (and fmt 12)\n",
-    "sig, fields=wfdb.srdsamp('sampledata/03700181')\n",
-    "print(sig[:20,:])\n",
-    "print(\"\\n\\n\", sig.shape, \"\\n\\n\")\n",
-    "print(fields)\n",
-    "\n",
-    "print(\"\\n\\n\\n\")\n",
-    "print(sig[-20:,:])"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "import wfdb\n",
-    "ann = wfdb.rdann('/home/chen/Downloads/chb01_03.edf','seizures')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "ann.__dict__"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -100,51 +58,6 @@
     "# print([sd & 255, sd & 768, (sd & 768) >> 8])"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 18,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "list"
-      ]
-     },
-     "execution_count": 18,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "type(record.initvalue)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 20,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "[1, 2]"
-      ]
-     },
-     "execution_count": 20,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "x = [1,2,3]\n",
-    "x[:-1]"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,

tests/test_annotations.py

@@ -8,7 +8,7 @@ class test_rdann():
     # Target file created with: rdann -r sampledata/100 -a atr > anntarget1
     def test_1(self):
 
-        # Read data from WFDB python package
+        # Read data using WFDB python package
         annotation = wfdb.rdann('sampledata/100', 'atr')
 
 
@@ -52,7 +52,16 @@ def test_1(self):
                 np.array_equal(annotation.num, Tnum), 
                 annotation.aux == Taux]
 
+        # Test file streaming
+        pbannotation = wfdb.rdann('100', 'atr', pbdir = 'mitdb')
+
+        # Test file writing
+        annotation.wrsamp()
+        annotationwrite = wfdb.rdann('100', 'atr')
+
         assert (comp == [True] * 6)
+        assert annotation.__eq__(pbannotation)
+        assert annotation.__eq__(annotationwrite)
 
     # Test 2 - Annotation file 12726.anI with many aux strings.
     # Target file created with: rdann -r sampledata/100 -a atr > anntarget2
@@ -93,5 +102,13 @@ def test_2(self):
                 np.array_equal(annotation.chan, Tchan), 
                 np.array_equal(annotation.num, Tnum), 
                 annotation.aux == Taux]
+        # Test file streaming
+        pbannotation = wfdb.rdann('12726', 'anI', pbdir = 'prcp')
+
+        # Test file writing
+        annotation.wrsamp()
+        annotationwrite = wfdb.rdann('12726', 'anI')
 
         assert (comp == [True] * 6)
+        assert annotation.__eq__(pbannotation)
+        assert annotation.__eq__(annotationwrite)

tests/test_records.py

@@ -129,8 +129,13 @@ def test_7(self):
         # Compare data streaming from physiobank
         pbrecord= wfdb.rdsamp('s0010_re', physical=False, pbdir = 'ptbdb/patient001')
 
+        # Test file writing
+        record.wrsamp()
+        recordwrite = wfdb.rdsamp('s0010_re', physical=False)
+
         assert np.array_equal(sig, targetsig)
         assert record.__eq__(pbrecord)
+        assert record.__eq__(recordwrite)
 
     # Test 8 - Multi-dat/Selected Duration/Selected Channels/Physical
     # Target file created with: rdsamp -r sampledata/s0010_re -f 5 -t 38 -P -s
@@ -164,8 +169,13 @@ def test_9(self):
         # Compare data streaming from physiobank
         pbrecord = wfdb.rdsamp('03700181', physical=False, pbdir = 'mimicdb/037')
 
+        # Test file writing. Multiple Samples per frame. To do...
+        #record.wrsamp()
+        #recordwrite = wfdb.rdsamp('03700181', physical=False)
+
         assert np.array_equal(sig, targetsig)
         assert record.__eq__(pbrecord)
+        #assert record.__eq__(recordwrite)
 
     # Test 10 - Format 12 multi-samples per frame and skew/Selected Duration/Selected Channels/Physical
     # Target file created with: rdsamp -r sampledata/03700181 -f 8 -t 128 -s 0

wfdb/annotations.py

@@ -86,7 +86,7 @@ def wrann(self):
     # Return indices of anntype field which are not encoded, and thus need
     # to be moved to the aux field.
     def checkfields(self):
-        # Enforce mandatory write fields
+        # Enforce the presence of mandatory write fields
         for field in ['recordname', 'annotator', 'annsamp', 'anntype']:
             if getattr(self, field) is None:
                 print('The ', field, ' field is mandatory for writing annotation files')
@@ -127,9 +127,9 @@ def checkfield(self, field):
         else:
             fielditem = getattr(self, field)
 
-            # Ensure the field item is a list.
-            if type(fielditem) != list:
-                print('The ', field, ' field must be a list')
+            # Ensure the field item is a list or array.
+            if type(fielditem) not in [list, np.ndarray]:
+                print('The ', field, ' field must be a list or numpy array')
                 sys.exit()          
 
             # Check the data types of the elements
@@ -164,20 +164,20 @@ def checkfield(self, field):
                 if set(self.anntype) - set(annsyms.values()) != set():
                     print("The 'anntype' field contains items not encoded in the WFDB annotation library.")
                     print('To see the valid annotation codes call: showanncodes()')
-                    print('To transfer non-encoded anntype items into the aux field call: self.type2aux')
+                    print('To transfer non-encoded anntype items into the aux field call: self.type2aux()')
                     sys.exit()
-            elif field == 'num':
-                # signed character
-                if min(self.num) < 0 or max(self.num) >255:
-                    sys.exit("The 'num' field must only contain non-negative integers up to 255")
             elif field == 'subtype':
                 # signed character
                 if min(self.subtype) < 0 or max(self.subtype) >127:
                     sys.exit("The 'subtype' field must only contain non-negative integers up to 127")
             elif field == 'chan':
                 # unsigned character
-                if min(self.chan) < 0 or max(self.chan) >127:
-                    sys.exit("The 'chan' field must only contain non-negative integers up to 127")
+                if min(self.chan) < 0 or max(self.chan) >255:
+                    sys.exit("The 'chan' field must only contain non-negative integers up to 255")
+            elif field == 'num':
+                # signed character
+                if min(self.num) < 0 or max(self.num) >127:
+                    sys.exit("The 'num' field must only contain non-negative integers up to 127")
             #elif field == 'aux': # No further conditions for aux field.
 
 
@@ -769,7 +769,7 @@ def proccustomtypes(annsamp,anntype,num,subtype,chan,aux):
 
 # Mapping annotation symbols to the annotation codes
 # For printing/user guidance
-symcodes = pd.DataFrame({'Ann Symbol': list(annsyms.values()), 'Ann Code/Meaning': list(anncodes.values())})
+symcodes = pd.DataFrame({'Ann Symbol': list(annsyms.values()), 'Ann Code Meaning': list(anncodes.values())})
 symcodes = symcodes.set_index('Ann Symbol', list(annsyms.values()))
 
 annfields = ['recordname', 'annotator', 'annsamp', 'anntype', 'num', 'subtype', 'chan', 'aux', 'fs']

wfdb/records.py

@@ -88,7 +88,7 @@ def checkfield(self, field, ch=None):
         elif field == 'basetime':
             _ = parsetimestring(self.basetime)
         elif field == 'basedate':
-            _ = parsetimestring(self.basedate)
+            _ = parsedatestring(self.basedate)
 
         # Signal specification fields. Lists of elements. 
         elif field == 'filename':
@@ -114,15 +114,10 @@ def checkfield(self, field, ch=None):
             f = self.skew[ch]
             if f < 0:
                 sys.exit('skew values must be non-negative integers')
-            # Writing a signal with skew shouldn't require anything different
-            #if f > 0:
-            #    sys.exit('Sorry, I have not implemented skew into wrsamp yet')
         elif field == 'byteoffset':
             f = self.byteoffset[ch]
             if f < 0:
                 sys.exit('byteoffset values must be non-negative integers')
-            #if f > 0:
-            #    sys.exit('Sorry, I have not implemented byte offset into wrsamp yet')
         elif field == 'adcgain':
             f = self.adcgain[ch]
             if f <= 0:
@@ -1027,7 +1022,7 @@ def orderednoconseclist(fulllist):
 
 # *This downloading files gateway function relies on the Record/MultiRecord objects.
 # It is placed here rather than in downloads.py in order to avoid circular imports
-
+# These download function only targets databases with WFDB records (EDF and MIT format). If the database doesn't have a 'RECORDS" file, 
 
 # Download WFDB files from a physiobank database
 def dldatabase(pbdb, dlbasedir, records = 'all', annotators = 'all' , keepsubdirs = True, overwrite = False):