gender → sex

README.rst

@@ -87,7 +87,7 @@ Additionally functionality as anonymizing, dropping or renaming channels can be
     signals = np.random.rand(5, 256*300)*200 # 5 minutes of random signal
     channel_names = ['ch1', 'ch2', 'ch3', 'ch4', 'ch5']
     signal_headers = highlevel.make_signal_headers(channel_names, sample_frequency=256)
-    header = highlevel.make_header(patientname='patient_x', gender='Female')
+    header = highlevel.make_header(patientname='patient_x', sex='Female')
     highlevel.write_edf('edf_file.edf', signals, signal_headers, header)
 
     # read an edf file

demo/readEDFFile.py

@@ -20,7 +20,7 @@
     # print("patient: %s" % f.getP);
     # print("recording: %s" % f.getPatientAdditional())
     print("patientcode: %s" % f.getPatientCode())
-    print("gender: %s" % f.getGender())
+    print("sex: %s" % f.getSex())
     print("birthdate: %s" % f.getBirthdate())
     print("patient_name: %s" % f.getPatientName())
     print("patient_additional: %s" % f.getPatientAdditional())

pyedflib/_extensions/_pyedflib.pyx

@@ -10,7 +10,7 @@ __all__ = ['lib_version', 'CyEdfReader', 'set_patientcode', 'set_starttime_subse
            'read_physical_samples', 'close_file', 'set_physical_maximum', 'open_file_writeonly',
            'set_patient_additional', 'set_digital_maximum', 'set_birthdate', 'set_digital_minimum',
            'write_digital_samples', 'set_equipment', 'set_samples_per_record','set_admincode', 'set_label',
-           'tell', 'rewind', 'set_gender','set_physical_dimension', 'set_transducer', 'set_prefilter',
+           'tell', 'rewind', 'set_sex','set_physical_dimension', 'set_transducer', 'set_prefilter',
            'seek', 'set_startdatetime' ,'set_datarecord_duration', 'set_number_of_annotation_signals',
            'open_errors', 'FILETYPE_EDFPLUS',
            'FILETYPE_EDF','FILETYPE_BDF','FILETYPE_BDFPLUS', 'write_errors', 'get_number_of_open_files',
@@ -270,8 +270,13 @@ cdef class CyEdfReader:
         def __get__(self):
             return self.hdr.patientcode
 
+    property sex:
+        def __get__(self):
+            return self.hdr.gender
+
     property gender:
         def __get__(self):
+            warnings.warn('This property is deprecated.', DeprecationWarning, stacklevel=2)
             return self.hdr.gender
 
     property birthdate:
@@ -615,10 +620,14 @@ def rewind(handle, edfsignal):
     """void edfrewind(int handle, int edfsignal)"""
     c_edf.edfrewind(handle, edfsignal)
 
+def set_sex(handle, sex):
+    """int edf_set_sex(int handle, int sex)"""
+    if sex is None: return 0 #don't set sex at all to prevent default 'F'
+    return c_edf.edf_set_gender(handle, sex)
+
 def set_gender(handle, gender):
-    """int edf_set_gender(int handle, int gender)"""
-    if gender is None: return 0 #don't set gender at all to prevent default 'F'
-    return c_edf.edf_set_gender(handle, gender)
+    warnings.warn('This function is deprecated.', DeprecationWarning, stacklevel=2)
+    set_sex(handle, gender)
 
 def set_physical_dimension(handle, edfsignal, phys_dim):
     """int edf_set_physical_dimension(int handle, int edfsignal, const char *phys_dim)"""

pyedflib/edfreader.py

@@ -139,8 +139,9 @@ def getHeader(self):
         return {"technician": self.getTechnician(), "recording_additional": self.getRecordingAdditional(),
                 "patientname": self.getPatientName(), "patient_additional": self.getPatientAdditional(),
                 "patientcode": self.getPatientCode(), "equipment": self.getEquipment(),
-                "admincode": self.getAdmincode(), "gender": self.getGender(), "startdate": self.getStartdatetime(),
-                "birthdate": self.getBirthdate()}
+                "admincode": self.getAdmincode(), "sex": self.getSex(), "startdate": self.getStartdatetime(),
+                "birthdate": self.getBirthdate(),
+                "gender": self.getSex()}  # backwards compatibility
 
     def getSignalHeader(self, chn):
         """
@@ -307,9 +308,9 @@ def getAdmincode(self):
         """
         return self._convert_string(self.admincode.rstrip())
 
-    def getGender(self):
+    def getSex(self):
         """
-        Returns the Gender of the patient.
+        Returns the Sex of the patient.
 
         Parameters
         ----------
@@ -319,12 +320,16 @@ def getGender(self):
         --------
         >>> import pyedflib
         >>> f = pyedflib.data.test_generator()
-        >>> f.getGender()==''
+        >>> f.getSex()==''
         True
         >>> f.close()
 
         """
-        return self._convert_string(self.gender.rstrip())
+        return self._convert_string(self.sex.rstrip())
+
+    def getGender(self):
+        warnings.warn('This method is deprecated.', DeprecationWarning, stacklevel=2)
+        return self.getSex()
 
     def getFileDuration(self):
         """

pyedflib/edfwriter.py

@@ -126,17 +126,22 @@ def isbytestr(s):
     return isinstance(s, bytes)
 
 
-def gender2int(gender):
-    if isinstance(gender, int) or gender is None:
-        return gender
-    elif gender.lower() in ['', 'x', 'xx', 'xxx', 'unknown', '?', '??']:
+def sex2int(sex):
+    if isinstance(sex, int) or sex is None:
+        return sex
+    elif sex.lower() in ['', 'x', 'xx', 'xxx', 'unknown', '?', '??']:
         return None
-    elif gender.lower() in ["female", "woman", "f", "w"]:
+    elif sex.lower() in ["female", "woman", "f", "w"]:
         return 0
-    elif gender.lower() in  ["male", "man", "m"]:
+    elif sex.lower() in  ["male", "man", "m"]:
         return 1
     else:
-        raise ValueError(f"Unknown gender: '{gender}'")
+        raise ValueError(f"Unknown sex: '{sex}'")
+
+
+def gender2int(sex):
+    warnings.warn('This function is deprecated.', DeprecationWarning, stacklevel=2)
+    sex2int(sex)
 
 
 class ChannelDoesNotExist(Exception):
@@ -195,7 +200,7 @@ def __init__(self, file_name, n_channels,
         self.recording_additional = ''
         self.patient_additional = ''
         self.admincode = ''
-        self.gender = None
+        self.sex = None
         self.recording_start_time = datetime.now().replace(microsecond=0)
 
         self.birthdate = ''
@@ -228,13 +233,13 @@ def update_header(self):
         """
         # some checks that warn users if header fields exceed 80 chars
         patient_ident = len(self.patient_code) + len(self.patient_name) \
-                        + len(self.patient_additional) + 3 + 1 + 11 # 3 spaces 1 gender 11 birthdate
+                        + len(self.patient_additional) + 3 + 1 + 11 # 3 spaces 1 sex 11 birthdate
         record_ident = len(self.equipment) + len(self.technician) \
                        + len(self.admincode) + len(self.recording_additional) \
                        + len('Startdate') + 3 + 11 # 3 spaces 11 birthdate
 
         if patient_ident>80:
-            warnings.warn('Patient code, name, gender and birthdate combined must not be larger than 80 chars. ' +
+            warnings.warn('Patient code, name, sex and birthdate combined must not be larger than 80 chars. ' +
                           f'Currently has len of {patient_ident}. See https://www.edfplus.info/specs/edfplus.html#additionalspecs')
         if record_ident>80:
             warnings.warn('Equipment, technician, admincode and recording_additional combined must not be larger than 80 chars. ' +
@@ -254,7 +259,7 @@ def update_header(self):
         set_patient_additional(self.handle, du(self.patient_additional))
         set_equipment(self.handle, du(self.equipment))
         set_admincode(self.handle, du(self.admincode))
-        set_gender(self.handle, gender2int(self.gender))
+        set_gender(self.handle, sex2int(self.sex))
 
         set_datarecord_duration(self.handle, self.record_duration)
         set_number_of_annotation_signals(self.handle, self.number_of_annotations)
@@ -294,7 +299,7 @@ def setHeader(self, fileHeader):
         self.patient_code = fileHeader["patientcode"]
         self.equipment = fileHeader["equipment"]
         self.admincode = fileHeader["admincode"]
-        self.gender = fileHeader["gender"]
+        self.sex = fileHeader["sex"]
         self.recording_start_time = fileHeader["startdate"]
         self.birthdate = fileHeader["birthdate"]
         self.update_header()
@@ -440,17 +445,17 @@ def setAdmincode(self, admincode):
         self.admincode = admincode
         self.update_header()
 
-    def setGender(self, gender):
+    def setSex(self, sex):
         """
-        Sets the gender.
+        Sets the sex.
         This function is optional and can be called only after opening a file in writemode and before the first sample write action.
 
         Parameters
         ----------
-        gender : int
+        sex : int
             1 is male, 0 is female
         """
-        self.gender = gender2int(gender)
+        self.sex = sex2int(sex)
         self.update_header()
 
     def setDatarecordDuration(self, record_duration):

pyedflib/highlevel.py

@@ -147,7 +147,8 @@ def phys2dig(signal, dmin, dmax, pmin, pmax):
 
 def make_header(technician='', recording_additional='', patientname='',
                 patient_additional='', patientcode= '', equipment= '',
-                admincode= '', gender= '', startdate=None, birthdate= ''):
+                admincode= '', sex= '', startdate=None, birthdate= '',
+                gender=None):
     """
     A convenience function to create an EDF header (a dictionary) that
     can be used by pyedflib to update the main header of the EDF
@@ -168,8 +169,8 @@ def make_header(technician='', recording_additional='', patientname='',
         which system was used. The default is ''.
     admincode : str, optional
         code of the admin. The default is ''.
-    gender : str, optional
-        gender of patient. The default is ''.
+    sex : str, optional
+        sex of patient. The default is ''.
     startdate : datetime.datetime, optional
         startdate of recording. The default is None.
     birthdate : str/datetime.datetime, optional
@@ -191,13 +192,23 @@ def make_header(technician='', recording_additional='', patientname='',
         del now
     if isinstance(birthdate, datetime):
         birthdate = birthdate.strftime('%d %b %Y').lower()
+
+    # backwards compatibility
+    if gender is not None:
+        if sex == '':
+            sex = gender
+        elif gender != sex:
+            raise ValueError(f'Passed both sex and gender, with different values: "{sex}" != "{gender}"')
+    del gender
+
     local = locals()
+
     header = {}
-    for var in local:
-        if isinstance(local[var], datetime):
-            header[var] = local[var]
+    for var, value in local.items():
+        if isinstance(value, datetime):
+            header[var] = value
         else:
-            header[var] = str(local[var])
+            header[var] = str(value)
     return header
 
 

pyedflib/tests/test_edfreader.py

@@ -178,6 +178,7 @@ def test_EdfReader_headerInfos(self):
         np.testing.assert_equal(f.getStartdatetime(),datetimeSoll)
         np.testing.assert_equal(f.getPatientCode(), 'abcxyz99')
         np.testing.assert_equal(f.getPatientName(), 'Hans Muller')
+        np.testing.assert_equal(f.getSex(), 'Male')
         np.testing.assert_equal(f.getGender(), 'Male')
         np.testing.assert_equal(f.getBirthdate(), '30 jun 1969')
         np.testing.assert_equal(f.getPatientAdditional(), 'patient')
@@ -381,7 +382,7 @@ def test_EdfReader_Legacy_Header_Info(self):
             'patientcode': b'',
             'equipment': b'',
             'admincode': b'',
-            'gender': b'',
+            'sex': b'',
             'birthdate': b''
         }