Merge branch 'restructuremods'

Author: tompollard

tests/test_readannot.py

@@ -1,5 +1,5 @@
 import numpy as np
-from wfdb import readannot
+from wfdb import rdann
 import re
 
 class test_rdann():
@@ -9,7 +9,7 @@ class test_rdann():
     def test_1(self):
 
         # Read data from WFDB python package
-        annsamp, anntype, subtype, chan, num, aux, annfs=readannot.rdann('sampledata/100', 'atr')
+        annsamp, anntype, subtype, chan, num, aux, annfs=rdann('sampledata/100', 'atr')
         aux[0]='(N' # This is not the fault of the script. The annotation file specifies a length 3 
         # aux field with a null written after '(N' which the script correctly picks up. I am just 
         # getting rid of the null in this unit test to compare with the regexp output below which has 
@@ -49,7 +49,7 @@ def test_1(self):
     def test_2(self):
 
         # Read data from WFDB python package
-        annsamp, anntype, subtype, chan, num, aux, annfs=readannot.rdann('sampledata/12726', 'anI')
+        annsamp, anntype, subtype, chan, num, aux, annfs=rdann('sampledata/12726', 'anI')
 
         # Target data from WFDB software package
         lines=tuple(open('tests/targetoutputdata/anntarget2', 'r'))

tests/test_readsignal.py

@@ -1,50 +1,50 @@
 import numpy as np
-from wfdb import readsignal
+from wfdb import rdsamp
 
 class test_rdsamp():
 
     # Test 1 - Format 212/Entire signal/Physical 
     # Target file created with: rdsamp -r sampledata/100 -P | cut -f 2- > target1      
     def test_1(self):
-        sig, fields=readsignal.rdsamp('sampledata/100')
+        sig, fields=rdsamp('sampledata/100')
         sig=np.round(sig, decimals=8)
         targetsig=np.genfromtxt('tests/targetoutputdata/target1')
         assert np.array_equal(sig, targetsig)
 
     # Test 2 - Format 212/Selected Duration/Selected Channel/Digital. 
     # Target file created with: rdsamp -r sampledata/100 -f 0.002 -t 30 -s 1 | cut -f 2- > target2
     def test_2(self): 
-        sig, fields=readsignal.rdsamp('sampledata/100', sampfrom=1, sampto=10800, channels=[1], physical=0) 
+        sig, fields=rdsamp('sampledata/100', sampfrom=1, sampto=10800, channels=[1], physical=0) 
         targetsig=np.genfromtxt('tests/targetoutputdata/target2')
         targetsig=targetsig.reshape(len(targetsig), 1)
         assert np.array_equal(sig, targetsig)
 
     # Test 3 - Format 16/Entire signal/Digital
     # Target file created with: rdsamp -r sampledata/test01_00s | cut -f 2- > target3
     def test_3(self):
-        sig, fields=readsignal.rdsamp('sampledata/test01_00s', physical=0)
+        sig, fields=rdsamp('sampledata/test01_00s', physical=0)
         targetsig=np.genfromtxt('tests/targetoutputdata/target3')
         assert np.array_equal(sig, targetsig)
 
     # Test 4 - Format 16 with byte offset/Selected Duration/Selected Channels/Physical
     # Target file created with: rdsamp -r sampledata/a103l -f 50 -t 160 -s 2 0 -P | cut -f 2- > target4
     def test_4(self):
-        sig, fields=readsignal.rdsamp('sampledata/a103l', sampfrom=12500, sampto=40000, channels=[2, 0])
+        sig, fields=rdsamp('sampledata/a103l', sampfrom=12500, sampto=40000, channels=[2, 0])
         sig=np.round(sig, decimals=8)
         targetsig=np.genfromtxt('tests/targetoutputdata/target4')
         assert np.array_equal(sig, targetsig) 
 
     # Test 5 - Format 16 with byte offset/Selected Duration/Selected Channels/Digital
     # Target file created with: rdsamp -r sampledata/a103l -f 80 -s 0 1 | cut -f 2- > target5
     def test_5(self):
-        sig, fields=readsignal.rdsamp('sampledata/a103l', sampfrom=20000, physical=0, channels=[0, 1])
+        sig, fields=rdsamp('sampledata/a103l', sampfrom=20000, physical=0, channels=[0, 1])
         targetsig=np.genfromtxt('tests/targetoutputdata/target5')
         assert np.array_equal(sig, targetsig) 
 
     # Test 6 - Format 80/Selected Duration/Selected Channels/Physical
     # Target file created with: rdsamp -r sampledata/3000003_0003 -f 1 -t 8 -s 1 -P | cut -f 2- > target6
     def test_6(self):
-        sig, fields=readsignal.rdsamp('sampledata/3000003_0003', sampfrom=125, sampto=1000, channels=[1])
+        sig, fields=rdsamp('sampledata/3000003_0003', sampfrom=125, sampto=1000, channels=[1])
         sig=np.round(sig, decimals=8)
         targetsig=np.genfromtxt('tests/targetoutputdata/target6')
         targetsig=targetsig.reshape(len(targetsig), 1)
@@ -53,22 +53,22 @@ def test_6(self):
     # Test 7 - Multi-dat/Entire signal/Digital
     # Target file created with: rdsamp -r sampledata/s0010_re | cut -f 2- > target7
     def test_7(self):
-        sig, fields=readsignal.rdsamp('sampledata/s0010_re', physical=0)
+        sig, fields=rdsamp('sampledata/s0010_re', physical=0)
         targetsig=np.genfromtxt('tests/targetoutputdata/target7')
         assert np.array_equal(sig, targetsig) 
 
     # Test 8 - Multi-dat/Selected Duration/Selected Channels/Physical
     # Target file created with: rdsamp -r sampledata/s0010_re -f 5 -t 38 -P -s 13 0 4 8 3 | cut -f 2- > target8
     def test_8(self):
-        sig, fields=readsignal.rdsamp('sampledata/s0010_re', sampfrom=5000, sampto=38000, channels=[13, 0, 4, 8, 3])
+        sig, fields=rdsamp('sampledata/s0010_re', sampfrom=5000, sampto=38000, channels=[13, 0, 4, 8, 3])
         sig=np.round(sig, decimals=8)
         targetsig=np.genfromtxt('tests/targetoutputdata/target8')
         assert np.array_equal(sig, targetsig) 
 
     # Test 9 - Format 12 multi-samples per frame and skew/Entire Signal/Digital
     # Target file created with: rdsamp -r sampledata/03700181 | cut -f 2- > target9
     def test_9(self):
-        sig, fields=readsignal.rdsamp('sampledata/03700181', physical=0)
+        sig, fields=rdsamp('sampledata/03700181', physical=0)
         sig=sig[:-4,:] # The WFDB library rdsamp does not return the final N samples for all channels due to the skew. 
         # The WFDB python rdsamp does return the final N samples, filling in NANs for end of skewed channels only. 
         targetsig=np.genfromtxt('tests/targetoutputdata/target9')
@@ -77,7 +77,7 @@ def test_9(self):
     # 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 2 -P | cut -f 2- > target10
     def test_10(self):
-        sig, fields=readsignal.rdsamp('sampledata/03700181', channels=[0,2], sampfrom=1000, sampto=16000)
+        sig, fields=rdsamp('sampledata/03700181', channels=[0,2], sampfrom=1000, sampto=16000)
         sig=np.round(sig, decimals=8)
         targetsig=np.genfromtxt('tests/targetoutputdata/target10')
         assert np.array_equal(sig, targetsig)
@@ -88,15 +88,15 @@ def test_10(self):
     # Test 11 - Multi-segment variable layout/Entire signal/Physical
     # Target file created with: rdsamp -r sampledata/matched/s25047/s25047-2704-05-04-10-44 -P | cut -f 2- > target11
     #def test_11(self):
-        #sig, fields=readsignal.rdsamp('sampledata/matched/s25047/s25047-2704-05-04-10-44')
+        #sig, fields=rdsamp('sampledata/matched/s25047/s25047-2704-05-04-10-44')
         #sig=np.round(sig, decimals=8)
         #targetsig=np.genfromtxt('tests/targetoutputdata/target11')
         #assert np.array_equal(sig, targetsig)
 
     # Test 12 - Multi-segment variable layout/Selected duration/Selected Channels/Physical
     # Target file created with: rdsamp -r sampledata/matched/s00001/s00001-2896-10-10-00-31 -f 70 -t 4000 -s 3 0 -P | cut -f 2- > target12
     #def test_12(self):
-        #sig, fields=readsignal.rdsamp('sampledata/matched/s00001/s00001-2896-10-10-00-31', sampfrom=8750, sampto=500000, channels=[3, 0])
+        #sig, fields=rdsamp('sampledata/matched/s00001/s00001-2896-10-10-00-31', sampfrom=8750, sampto=500000, channels=[3, 0])
         #sig=np.round(sig, decimals=8)
         #targetsig=np.genfromtxt('tests/targetoutputdata/target12')
         #assert np.array_equal(sig, targetsig)
@@ -107,15 +107,15 @@ def test_10(self):
     # Target file created with: rdsamp -r sampledata/3000003_0003 -f 0 -t 8.21 | cut -f 2- | wrsamp -o 310derive -O 310
     # rdsamp -r 310derive -f 0.007 | cut -f 2- > target13
     def test_13(self):
-        sig, fields=readsignal.rdsamp('sampledata/310derive', sampfrom=2, physical=0)
+        sig, fields=rdsamp('sampledata/310derive', sampfrom=2, physical=0)
         targetsig=np.genfromtxt('tests/targetoutputdata/target13')
         assert np.array_equal(sig, targetsig) 
 
     # Test 14 - Format 311/Selected Duration/Physical
     # Target file created with: rdsamp -r sampledata/3000003_0003 -f 0 -t 8.21 -s 1 | cut -f 2- | wrsamp -o 311derive -O 311
     # rdsamp -r 311derive -f 0.005 -t 3.91 -P | cut -f 2- > target14
     def test_14(self):
-        sig, fields=readsignal.rdsamp('sampledata/311derive', sampfrom=1, sampto=978)
+        sig, fields=rdsamp('sampledata/311derive', sampfrom=1, sampto=978)
         sig=np.round(sig, decimals=8)
         targetsig=np.genfromtxt('tests/targetoutputdata/target14')
         targetsig=targetsig.reshape([977,1])

wfdb/__init__.py

@@ -1,4 +1,2 @@
-import pbdownload
-import plotwfdb
-import readannot
-import readsignal
+from ._rdsamp import rdsamp
+from ._rdann import rdann

wfdb/readannot.py wfdb/_rdann.pywfdb/readannot.py renamed to wfdb/_rdann.py

@@ -31,29 +31,25 @@ def rdann(recordname, annot, sampfrom=0, sampto=[], anndisp=1):
     *NOTE: Every annotation contains the 'annsamp' and 'anntype' field. All other fields default to 0 or empty if not present. 
     """
 
-    if sampto:
-        if sampto<sampfrom:
-            sys.exit("sampto must be greater than sampfrom")
+    if sampto and sampto<=sampfrom:
+        raise ValueError("sampto must be greater than sampfrom")
 
-    #fields=readheader(recordname) # Get the info from the header file
+    # Get the info from the header file
+    #fields=readheader(recordname) 
     dirname, baserecordname=os.path.split(recordname)
 
-    if dirname:
-        dirname=dirname+"/"
-
-    f=open(recordname+'.'+annot, 'rb')
-    filebytes=np.fromfile(f, '<u1').reshape([-1, 2]) # Read the file's byte pairs.
-    f.close()
+    # Read the file's byte pairs.
+    with open(recordname+'.'+annot, 'rb') as f:
+        filebytes=np.fromfile(f, '<u1').reshape([-1, 2])
 
     # Allocate for the maximum possible number of annotations contained in the file. 
-    annsamp=np.zeros(filebytes.shape[0])
-    anntype=np.zeros(filebytes.shape[0])
-    subtype=np.zeros(filebytes.shape[0])
-    chan=np.zeros(filebytes.shape[0])
-    num=np.zeros(filebytes.shape[0])
+    annsamp=np.empty(filebytes.shape[0])
+    anntype=np.empty(filebytes.shape[0])
+    subtype=np.empty(filebytes.shape[0])
+    chan=np.empty(filebytes.shape[0])
+    num=np.empty(filebytes.shape[0])
     aux=['']*filebytes.shape[0] 
-    
-    annfs=[] # Stores the fs written in the annotation file if it exists. 
+    annfs=[] # Stores the frequencies written in the annotation file if it exists. 
     ai=0 # Annotation index, the number of annotations processed. Not to be comfused with the 'num' field of an annotation.
     bpi=0 # Byte pair index, for searching through bytes of the annotation file. 
 
@@ -169,7 +165,6 @@ def rdann(recordname, annot, sampfrom=0, sampto=[], anndisp=1):
         elif anndisp==2:
             anntype=[anncodes[code] for code in anntype]
 
-        
     return (annsamp, anntype, subtype, chan, num, aux, annfs)
 
 
@@ -275,4 +270,7 @@ def rdann(recordname, annot, sampfrom=0, sampto=[], anndisp=1):
     #40: 'JPT', # J point (end of QRS) */
     41: 'RONT' # R-on-T premature ventricular contraction */
     }
+
+if __name__ == '__main__':
+    rdann(sys.argv)