replace sys.exit with raise errors

cx1111 · cx1111 · commit f58e9422f140 · 2017-04-14T10:00:41.000-04:00
diff --git a/devtests.ipynb b/devtests.ipynb
@@ -24,7 +24,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true
+    "collapsed": false
    },
    "outputs": [],
    "source": []
diff --git a/wfdb/_headers.py b/wfdb/_headers.py
@@ -1,7 +1,6 @@
 import numpy as np
 import re
 import os
-import sys
 from collections import OrderedDict
 from calendar import monthrange
 from . import _signals
@@ -193,7 +192,7 @@ def checkfieldcohesion(self, recwritefields, sigwritefields):
             # even if some of its elements are None. 
             for f in sigwritefields:
                 if len(getattr(self, f)) != self.nsig:
-                    sys.exit('The length of field: '+f+' must match field nsig.')
+                    raise ValueError('The length of field: '+f+' must match field nsig.')
 
             # Each filename must correspond to only one fmt, (and only one byte offset if defined). 
             datfmts = {}
@@ -202,7 +201,7 @@ def checkfieldcohesion(self, recwritefields, sigwritefields):
                     datfmts[self.filename[ch]] = self.fmt[ch]
                 else:
                     if datfmts[self.filename[ch]] != self.fmt[ch]:
-                        sys.exit('Each filename (dat file) specified must have the same fmt')
+                        raise ValueError('Each filename (dat file) specified must have the same fmt')
             
             datoffsets = {}
             if self.byteoffset is not None:
@@ -214,7 +213,7 @@ def checkfieldcohesion(self, recwritefields, sigwritefields):
                         datoffsets[self.filename[ch]] = self.byteoffset[ch]
                     else:
                         if datoffsets[self.filename[ch]] != self.byteoffset[ch]:
-                            sys.exit('Each filename (dat file) specified must have the same byte offset')
+                            raise ValueError('Each filename (dat file) specified must have the same byte offset')
 
 
     # Write a header file using the specified fields
@@ -320,11 +319,11 @@ def checkfieldcohesion(self):
         # The length of segname and seglen must match nseg
         for f in ['segname', 'seglen']:
             if len(getattr(self, f)) != self.nseg:
-                sys.exit('The length of field: '+f+' does not match field nseg.')
+                raise ValueError('The length of field: '+f+' does not match field nseg.')
 
         # Check the sum of the 'seglen' fields against 'siglen'
         if np.sum(self.seglen) != self.siglen:
-            sys.exit("The sum of the 'seglen' fields do not match the 'siglen' field")
+            raise ValueError("The sum of the 'seglen' fields do not match the 'siglen' field")
 
 
     # Write a header file using the specified fields
diff --git a/wfdb/_signals.py b/wfdb/_signals.py
@@ -1,6 +1,5 @@
 import numpy as np
 import os
-import sys
 from . import downloads
 
 # All defined WFDB dat formats
@@ -32,11 +31,10 @@ def checksignalcohesion(self, writefields):
 
         # Match the actual signal shape against stated length and number of channels
         if (self.siglen, self.nsig) != self.d_signals.shape:
-            print('siglen and nsig do not match shape of d_signals')
             print('siglen: ', self.siglen)
             print('nsig: ', self.nsig)
             print('d_signals.shape: ', self.d_signals.shape)
-            sys.exit()
+            raise ValueError('siglen and nsig do not match shape of d_signals')
 
         # For each channel (if any), make sure the digital format has no values out of bounds
         for ch in range(0, self.nsig):
@@ -46,20 +44,20 @@ def checksignalcohesion(self, writefields):
             chmin = min(self.d_signals[:,ch])
             chmax = max(self.d_signals[:,ch])
             if (chmin < dmin) or (chmax > dmax):
-                sys.exit("Channel "+str(ch)+" contain values outside allowed range ["+str(dmin)+", "+str(dmax)+"] for fmt "+str(fmt))
+                raise IndexError("Channel "+str(ch)+" contain values outside allowed range ["+str(dmin)+", "+str(dmax)+"] for fmt "+str(fmt))
                     
         # Ensure that the checksums and initial value fields match the digital signal (if the fields are present)
         if self.nsig>0:
             if 'checksum' in writefields:
                 realchecksum = self.calc_checksum()
                 if self.checksum != realchecksum:
-                    print("checksum field does not match actual checksum of d_signals: ", realchecksum)
-                    sys.exit()
+                    print("The actual checksum of d_signals is: ", realchecksum)
+                    raise ValueError("checksum field does not match actual checksum of d_signals")
             if 'initvalue' in writefields:
                 realinitvalue = list(self.d_signals[0,:])
                 if self.initvalue != realinitvalue:
-                    print("initvalue field does not match actual initvalue of d_signals: ", realinitvalue)
-                    sys.exit()
+                    print("The actual initvalue of d_signals is: ", realinitvalue)
+                    raise ValueError("initvalue field does not match actual initvalue of d_signals")
 
     
     def set_p_features(self, do_dac = False):
@@ -116,7 +114,7 @@ def set_d_features(self, do_adc = False, singlefmt = 1):
             if self.fmt is None:
                 # Make sure that neither adcgain nor baseline are set
                 if self.adcgain is not None or self.baseline is not None:
-                    sys.exit('If fmt is not set, gain and baseline may not be set either.')
+                    raise Exception('If fmt is not set, gain and baseline may not be set either.')
                 # Choose appropriate fmts based on estimated signal resolutions. 
                 res = estres(self.p_signals)
                 self.fmt = wfdbfmt(res, singlefmt)
@@ -130,7 +128,7 @@ def set_d_features(self, do_adc = False, singlefmt = 1):
                     self.adcgain, self.baseline = self.calculate_adcparams()
                 # Exactly one field set
                 elif (self.adcgain is None) ^ (self.baseline is None):
-                    sys.exit('If fmt is set, gain and baseline should both be set or not set.')
+                    raise Exception('If fmt is set, gain and baseline should both be set or not set.')
             
             self.checkfield('adcgain', 'all')
             self.checkfield('baseline', 'all')
@@ -230,7 +228,7 @@ def calculate_adcparams(self):
             
             # WFDB library limits...     
             if abs(gain)>214748364 or abs(baseline)>2147483648:
-                sys.exit('Chen, please fix this')
+                raise Exception('cx1111, please fix this!')
                     
             gains.append(gain)
             baselines.append(baseline)     
@@ -853,7 +851,7 @@ def wfdbfmtres(fmt):
     elif fmt == '32':
         return 32
     else:
-        sys.exit('Invalid WFDB format.')
+        raise ValueError('Invalid WFDB format.')
 
 # Write a dat file.
 # All bytes are written one at a time
@@ -956,7 +954,7 @@ def wrdatfile(filename, fmt, d_signals, byteoffset):
         # Convert to unsigned 8 bit dtype to write
         bwrite = bwrite.astype('uint8')
     else:
-        sys.exit('This library currently only supports the following formats: 80, 16, 24, 32')
+        raise ValueError('This library currently only supports writing the following formats: 80, 16, 24, 32')
         
     # Byte offset in the file
     if byteoffset is not None and byteoffset>0:
diff --git a/wfdb/annotations.py b/wfdb/annotations.py
@@ -1,6 +1,5 @@
 import numpy as np
 import pandas as pd
-import sys
 import re
 import os
 from . import _headers
@@ -99,7 +98,7 @@ def checkfields(self):
         for field in ['recordname', 'annotator', 'annsamp', 'anntype']:
             if getattr(self, field) is None:
                 print('The ', field, ' field is mandatory for writing annotation files')
-                sys.exit()
+                raise Exception('Missing required annotation field')
 
         # Check all set fields
         for field in annfields:
@@ -114,32 +113,30 @@ def checkfield(self, field):
         if field in ['recordname', 'annotator', 'fs']:
             # Check the field type
             if type(getattr(self, field)) not in annfieldtypes[field]:
-                print('The '+field+' field must be one of the following types:')
                 print(annfieldtypes[field])
-                sys.exit()
+                raise TypeError('The '+field+' field must be one of the above types.')
             
             # Field specific checks
             if field == 'recordname':
                 # Allow letters, digits, hyphens, and underscores.
                 acceptedstring = re.match('[-\w]+', self.recordname)
                 if not acceptedstring or acceptedstring.string != self.recordname:
-                    sys.exit('recordname must only comprise of letters, digits, hyphens, and underscores.')
+                    raise ValueError('recordname must only comprise of letters, digits, hyphens, and underscores.')
             elif field == 'annotator':
                 # Allow letters only
                 acceptedstring = re.match('[a-zA-Z]+', self.annotator)
                 if not acceptedstring or acceptedstring.string != self.annotator:
-                    sys.exit('annotator must only comprise of letters')
+                    raise ValueError('annotator must only comprise of letters')
             elif field == 'fs':
                 if self.fs <=0:
-                    sys.exit('The fs field must be a non-negative number')
+                    raise ValueError('The fs field must be a non-negative number')
 
         else:
             fielditem = getattr(self, field)
 
             # 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()          
+                raise TypeError('The '+field+' field must be a list or numpy array')        
 
             # Check the data types of the elements
             # annsamp and anntype may NOT have nones. Others may. 
@@ -149,44 +146,44 @@ def checkfield(self, field):
                         print("All elements of the '", field, "' field must be one of the following types:")
                         print(annfieldtypes[field])
                         print("All elements must be present")
-                        sys.exit()
+                        raise Exception()
             else:
                 for item in fielditem:
                     if item is not None and type(item) not in annfieldtypes[field]:
                         print("All elements of the '", field, "' field must be one of the following types:")
                         print(annfieldtypes[field])
                         print("Elements may also be set to 'None'")
-                        sys.exit()
+                        raise Exception()
         
             # Field specific checks
             # The C WFDB library stores num/sub/chan as chars. 
             if field == 'annsamp':
                 sampdiffs = np.concatenate(([self.annsamp[0]], np.diff(self.annsamp)))
                 if min(self.annsamp) < 0 :
-                    sys.exit("The 'annsamp' field must only contain non-negative integers")
+                    raise ValueError("The 'annsamp' field must only contain non-negative integers")
                 if min(sampdiffs) < 0 :
-                    sys.exit("The 'annsamp' field must contain monotonically increasing sample numbers")
+                    raise ValueError("The 'annsamp' field must contain monotonically increasing sample numbers")
                 if max(sampdiffs) > 2147483648:
-                    sys.exit('WFDB annotation files cannot store sample differences greater than 2**31')
+                    raise ValueError('WFDB annotation files cannot store sample differences greater than 2**31')
             elif field == 'anntype':
                 # Ensure all fields lie in standard WFDB annotation codes
                 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()')
-                    sys.exit()
+                    raise Exception()
             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")
+                    raise ValueError("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) >255:
-                    sys.exit("The 'chan' field must only contain non-negative integers up to 255")
+                    raise ValueErrort("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")
+                    raise ValueError("The 'num' field must only contain non-negative integers up to 127")
             #elif field == 'aux': # No further conditions for aux field.
                 
 
@@ -198,7 +195,7 @@ def checkfieldcohesion(self):
         for field in ['annsamp', 'anntype', 'num', 'subtype', 'chan', 'aux']:
             if getattr(self, field) is not None:
                 if len(getattr(self, field)) != nannots:
-                    sys.exit("All written annotation fields: ['annsamp', 'anntype', 'num', 'subtype', 'chan', 'aux'] must have the same length")
+                    raise ValueError("All written annotation fields: ['annsamp', 'anntype', 'num', 'subtype', 'chan', 'aux'] must have the same length")
 
     # Write an annotation file
     def wrannfile(self):
@@ -260,10 +257,10 @@ def type2aux(self):
 
         # Ensure that anntype is a list of strings
         if type(self.anntype)!= list:
-            sys.exit('anntype must be a list')
+            raise TypeError('anntype must be a list')
         for at in self.anntype:
             if type(at) != str:
-                sys.exit('anntype elements must all be strings')
+                raise TypeError('anntype elements must all be strings')
 
         external_anntypes = set(self.anntype) - set(annsyms.values())
 
diff --git a/wfdb/downloads.py b/wfdb/downloads.py
@@ -1,7 +1,6 @@
 import numpy as np
 import re
 import os
-import sys
 import requests
         
 # Read a header file from physiobank
@@ -110,7 +109,7 @@ def getrecordlist(dburl, records):
     if records == 'all':
         r = requests.get(os.path.join(dburl, 'RECORDS'))
         if r.status_code == 404:
-            sys.exit('The database '+dburl+' has no WFDB files to download')
+            raise ValueError('The database '+dburl+' has no WFDB files to download')
 
         # Get each line as a string
         recordlist = r.content.decode('ascii').splitlines()
@@ -129,7 +128,7 @@ def getannotators(dburl, annotators):
             if annotators == 'all':
                 return
             else:
-                sys.exit('The database '+dburl+' has no annotation files to download')
+                raise ValueError('The database '+dburl+' has no annotation files to download')
         # Make sure the input annotators are present in the database
         annlist = r.content.decode('ascii').splitlines()
         annlist = [a.split('\t')[0] for a in annlist]
@@ -145,7 +144,7 @@ def getannotators(dburl, annotators):
             # user input ones. Check validity. 
             for a in annotators:
                 if a not in annlist:
-                    sys.exit('The database contains no annotators with extension: ', a)
+                    raise ValueError('The database contains no annotators with extension: '+a)
 
     return annotators
 
diff --git a/wfdb/plots.py b/wfdb/plots.py
diff --git a/wfdb/records.py b/wfdb/records.py
