adding sampsperframe framework

cx1111 · cx1111 · commit 5bfe3aa25ba9 · 2017-05-23T09:13:54.000-04:00
diff --git a/devtests.ipynb b/devtests.ipynb
@@ -45,6 +45,32 @@
     "wfdb.plotrec(rec,timeunits='seconds', ecggrids='all', figsize = (10, 4))"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[1, 2, 3]\n"
+     ]
+    }
+   ],
+   "source": [
+    "def stuff(a):\n",
+    "    a[0]=100\n",
+    "\n",
+    "x = [1,2,3]\n",
+    "\n",
+    "stuff(x[:])\n",
+    "\n",
+    "print(x)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
diff --git a/wfdb/_signals.py b/wfdb/_signals.py
@@ -274,7 +274,8 @@ def wrdatfiles(self):
 # Read the samples from a single segment record's associated dat file(s)
 # 'channels', 'sampfrom', and 'sampto' are user desired input fields.
 # All other input arguments are specifications of the segment
-def rdsegment(filename, dirname, pbdir, nsig, fmt, siglen, byteoffset, sampsperframe, skew, sampfrom, sampto, channels):
+def rdsegment(filename, dirname, pbdir, nsig, fmt, siglen, byteoffset,
+              sampsperframe, skew, sampfrom, sampto, channels, smoothframes):
 
     # Avoid changing outer variables
     byteoffset = byteoffset[:]
@@ -290,12 +291,12 @@ def rdsegment(filename, dirname, pbdir, nsig, fmt, siglen, byteoffset, sampsperf
         if skew[i] == None:
             skew[i] = 0
 
-    # Get the set of dat files, and the 
-    # channels that belong to each file. 
+    # Get the set of dat files, and the
+    # channels that belong to each file.
     filename, datchannel = orderedsetlist(filename)
 
-    # Some files will not be read depending on input channels. 
-    # Get the the wanted fields only. 
+    # Some files will not be read depending on input channels.
+    # Get the the wanted fields only.
     w_filename = [] # one scalar per dat file
     w_fmt = {} # one scalar per dat file
     w_byteoffset = {} # one scalar per dat file
@@ -323,14 +324,25 @@ def rdsegment(filename, dirname, pbdir, nsig, fmt, siglen, byteoffset, sampsperf
     for fn in w_channel:
         r_w_channel[fn] = [c - min(datchannel[fn]) for c in w_channel[fn]]
         out_datchannel[fn] = [channels.index(c) for c in w_channel[fn]]
-        
-    # Allocate signal array
-    signals = np.empty([sampto-sampfrom, len(channels)], dtype = 'int64')
+    
+    # Signals with multiple samples/frame are smoothed
+    if smoothframes:
+
+        # Allocate signal array
+        signals = np.empty([sampto-sampfrom, len(channels)], dtype = 'int64')
+
+        # Read each wanted dat file and store signals
+        for fn in w_filename:
+            signals[:, out_datchannel[fn]] = rddat(fn, dirname, pbdir, w_fmt[fn], len(datchannel[fn]), 
+                siglen, w_byteoffset[fn], w_sampsperframe[fn], w_skew[fn], sampfrom, sampto)[:, r_w_channel[fn]]
+    
+    # Return each sample in signals with multiple samples/frame
+    else:
+        signals=[]
+
+        for fn in w_filename:
+            signals.append(rddat())
 
-    # Read each wanted dat file and store signals
-    for fn in w_filename:
-        signals[:, out_datchannel[fn]] = rddat(fn, dirname, pbdir, w_fmt[fn], len(datchannel[fn]), 
-            siglen, w_byteoffset[fn], w_sampsperframe[fn], w_skew[fn], sampfrom, sampto)[:, r_w_channel[fn]]
 
     return signals 
 
diff --git a/wfdb/records.py b/wfdb/records.py
@@ -320,6 +320,7 @@ def __init__(self, p_signals=None, d_signals=None,
     """
     # Constructor
     def __init__(self, p_signals=None, d_signals=None,
+                 e_p_signals=None, e_d_signals=None,
                  recordname=None, nsig=None,
                  fs=None, counterfreq=None, basecounter=None,
                  siglen=None, basetime=None, basedate=None,
@@ -338,6 +339,9 @@ def __init__(self, p_signals=None, d_signals=None,
 
         self.p_signals = p_signals
         self.d_signals = d_signals
+        self.e_p_signals = e_p_signals
+        self.e_d_signals = e_d_signals       
+
 
         self.filename=filename
         self.fmt=fmt
@@ -695,12 +699,14 @@ def multi_to_single(self):
 #------------------- Reading Records -------------------#
 
 # Read a WFDB single or multi segment record. Return a Record or MultiRecord object
-def rdsamp(recordname, sampfrom=0, sampto=None, channels = None, physical = True, pbdir = None, m2s = True):
+def rdsamp(recordname, sampfrom=0, sampto=None, channels = None, physical = True, pbdir = None,
+           m2s = True, smoothframes = True):
     """Read a WFDB record and return the signal and record descriptors as attributes in a
     Record or MultiRecord object.
 
     Usage:
-    record = rdsamp(recordname, sampfrom=0, sampto=None, channels=None, physical=True, pbdir = None, m2s=True)
+    record = rdsamp(recordname, sampfrom=0, sampto=None, channels=None, physical=True, pbdir = None,
+             m2s=True, smoothframes = True)
 
     Input arguments:
     - recordname (required): The name of the WFDB record to be read (without any file extensions).
@@ -715,8 +721,13 @@ def rdsamp(recordname, sampfrom=0, sampto=None, channels = None, physical = True
        directory from which to find the required record files.
       eg. For record '100' in 'http://physionet.org/physiobank/database/mitdb', pbdir = 'mitdb'.
     - m2s (default=True): Flag used when reading multi-segment records. Specifies whether to
-      directly return a wfdb MultiRecord object (false), or to convert it into and return a wfdb
+      directly return a wfdb MultiRecord object (False), or to convert it into and return a wfdb
       Record object (True).
+    - smoothframes (default=True): Flag used when reading records with signals having multiple
+      samples per frame. Specifies whether to smooth the samples in signals with more than
+      one sample per frame to return an mxn uniform numpy array as the d_signals or p_signals
+      field (True), or to return a list of 1d numpy arrays containing every expanded sample as
+      the e_d_signals or e_p_signals field (False).
 
     Output argument:
     - record: The wfdb Record or MultiRecord object representing the contents of the record read.
@@ -752,17 +763,25 @@ def rdsamp(recordname, sampfrom=0, sampto=None, channels = None, physical = True
     record.checkreadinputs(sampfrom, sampto, channels)
     # A single segment record
     if type(record) == Record:
-        # Read signals from the associated dat files that contain wanted channels
-        record.d_signals = _signals.rdsegment(record.filename, dirname, pbdir, record.nsig, record.fmt, record.siglen,
-            record.byteoffset, record.sampsperframe, record.skew,
-            sampfrom, sampto, channels)
-        # Arrange/edit the object fields to reflect user channel and/or signal range input
-        record.arrangefields(channels, sampto - sampfrom)
-        if physical == 1:
-            # Perform dac to get physical signal
-            record.p_signals = record.dac()
-            # Clear memory
-            record.d_signals = None
+
+        # Multi-sample frames are smoothed to make a uniform numpy array
+        if smoothframes or :
+            # Read signals from the associated dat files that contain wanted channels
+            record.d_signals = _signals.rdsegment(record.filename, dirname, pbdir, record.nsig, record.fmt, record.siglen,
+                record.byteoffset, record.sampsperframe, record.skew,
+                sampfrom, sampto, channels)
+            # Arrange/edit the object fields to reflect user channel and/or signal range input
+            record.arrangefields(channels, sampto - sampfrom)
+            if physical == 1:
+                # Perform dac to get physical signal
+                record.p_signals = record.dac()
+                # Clear memory
+                record.d_signals = None
+
+        # Return each sample of the signals with multiple samples per frame
+        else:
+            record.e_d_signals = _signals.rdsegment()
+
     # A multi segment record
 
     # We can make another rdsamp function (called rdsamp_segment) to call
