Merge pull request #323 from MIT-LCP/infer-length

Correctly infer length of record when unspecified

Author: tompollard

sample-data/a103l-no-len.hea

@@ -0,0 +1,6 @@
+a103l-no-len 3 250
+a103l.mat 16+24 7247/mV 16 0 -171 -27403 0 II
+a103l.mat 16+24 1.052e+04/mV 16 0 9127 -301 0 V
+a103l.mat 16+24 1.253e+04/NU 16 0 6042 -17391 0 PLETH
+#Asystole
+#False alarm

sample-data/drive02-no-len.hea

@@ -0,0 +1,6 @@
+drive02-no-len 5 15.5
+drive02.dat 16x32 1000 16 0 -1236 14736 0 ECG
+drive02.dat 16x2 1000 16 0 1802 13501 0 foot GSR
+drive02.dat 16 1.0001/bpm 16 0 75 -19070 0 HR
+drive02.dat 16 100 16 0 0 -9226 0 marker
+drive02.dat 16x2 500 16 0 5804 -14191 0 RESP

tests/test_record.py

@@ -703,9 +703,15 @@ def test_infer_sig_len(self):
         Read two headers. The records should be the same.
         """
 
-        record = wfdb.rdrecord('sample-data/100')
-        record_2 = wfdb.rdrecord('sample-data/100-no-len')
-        record_2.record_name = '100'
+        record = wfdb.rdrecord('sample-data/drive02')
+        record_2 = wfdb.rdrecord('sample-data/drive02-no-len')
+        record_2.record_name = record.record_name
+
+        assert record_2.__eq__(record)
+
+        record = wfdb.rdrecord('sample-data/a103l')
+        record_2 = wfdb.rdrecord('sample-data/a103l-no-len')
+        record_2.record_name = record.record_name
 
         assert record_2.__eq__(record)
 

wfdb/io/_signal.py

@@ -2071,7 +2071,8 @@ def describe_list_indices(full_list):
     return unique_elements, element_indices
 
 
-def _infer_sig_len(file_name, fmt, n_sig, dir_name, pn_dir=None):
+def _infer_sig_len(file_name, fmt, tsamps_per_frame, byte_offset,
+                   dir_name, pn_dir=None):
     """
     Infer the length of a signal from a dat file.
 
@@ -2081,8 +2082,10 @@ def _infer_sig_len(file_name, fmt, n_sig, dir_name, pn_dir=None):
         Name of the dat file.
     fmt : str
         WFDB fmt of the dat file.
-    n_sig : int
-        Number of signals contained in the dat file.
+    tsamps_per_frame : int
+        Total number of samples per frame contained in the dat file.
+    byte_offset : int or None
+        The byte offset of the dat file.  None is equivalent to zero.
     dir_name : str
         The full directory where the dat file(s) are located, if the dat
         file(s) are local.
@@ -2093,11 +2096,11 @@ def _infer_sig_len(file_name, fmt, n_sig, dir_name, pn_dir=None):
     Returns
     -------
     sig_len : int
-        The length of the signal.
+        The length of the signal file in frames.
 
     Notes
     -----
-    sig_len * n_sig * bytes_per_sample == file_size
+    sig_len * tsamps_per_frame * bytes_per_sample == file_size
 
     """
     if pn_dir is None:
@@ -2106,7 +2109,10 @@ def _infer_sig_len(file_name, fmt, n_sig, dir_name, pn_dir=None):
         file_size = download._remote_file_size(file_name=file_name,
                                                pn_dir=pn_dir)
 
-    sig_len = int(file_size / (BYTES_PER_SAMPLE[fmt] * n_sig))
+    if byte_offset is None:
+        byte_offset = 0
+    data_size = file_size - byte_offset
+    sig_len = int(data_size / (BYTES_PER_SAMPLE[fmt] * tsamps_per_frame))
 
     return sig_len
 

wfdb/io/record.py

@@ -3441,9 +3441,19 @@ def rdrecord(record_name, sampfrom=0, sampto=None, channels=None,
             if record.n_sig == 0:
                 record.sig_len = 0
             else:
+                # Calculate total number of samples per frame in the
+                # first dat file.
+                tsamps_per_frame = 0
+                for fname, spf in zip(record.file_name,
+                                      record.samps_per_frame):
+                    if fname == record.file_name[0]:
+                        tsamps_per_frame += spf
+
+                # Calculate length from size of the dat file.
                 record.sig_len = _signal._infer_sig_len(
                     file_name=record.file_name[0], fmt=record.fmt[0],
-                    n_sig=record.file_name.count(record.file_name[0]),
+                    tsamps_per_frame=tsamps_per_frame,
+                    byte_offset=record.byte_offset[0],
                     dir_name=dir_name, pn_dir=pn_dir)
         sampto = record.sig_len