Updates all instances of Physionet

Corrects all instances of Physionet to PhysioNet which corresponds to the correct capitalization of the platform.

Author: Lucas-Mc

demo.ipynb

@@ -10,7 +10,7 @@
 class TestRecord(unittest.TestCase):
     """
     Test read and write of single segment WFDB records, including
-    Physionet streaming.
+    PhysioNet streaming.
 
     Target files created using the original WFDB Software Package
     version 10.5.24
@@ -160,7 +160,7 @@ def test_2a(self):
         # Compare data streaming from Physionet
         sig_pn, fields_pn = wfdb.rdsamp('100', pn_dir = 'mitdb')
         # This comment line was manually added and is not present in the
-        # original Physionet record
+        # original PhysioNet record
         del(fields['comments'][0])
 
         assert np.array_equal(sig_round, sig_target)
@@ -183,7 +183,7 @@ def test_2b(self):
         record_pn = wfdb.rdrecord('100', sampfrom=1, sampto=10800,
                                   channels=[1], physical=False, pn_dir='mitdb')
         # This comment line was manually added and is not present in the
-        # original Physionet record
+        # original PhysioNet record
         del(record.comments[0])
 
         # Option of selecting channels by name
@@ -530,7 +530,7 @@ def tearDownClass(cls):
 class TestMultiRecord(unittest.TestCase):
     """
     Test read and write of multi segment WFDB records, including
-    Physionet streaming.
+    PhysioNet streaming.
 
     Target files created using the original WFDB Software Package
     version 10.5.24

tests/test_record.py

@@ -873,7 +873,7 @@ def _rd_segment(file_name, dir_name, pn_dir, fmt, n_sig, sig_len, byte_offset,
         The full directory where the dat file(s) are located, if the dat
         file(s) are local.
     pn_dir : str
-        The Physionet directory where the dat file(s) are located, if
+        The PhysioNet directory where the dat file(s) are located, if
         the dat file(s) are remote.
     fmt : list
         The formats of the dat files.
@@ -1042,7 +1042,7 @@ def _rd_dat_signals(file_name, dir_name, pn_dir, fmt, n_sig, sig_len,
         The full directory where the dat file(s) are located, if the dat
         file(s) are local.
     pn_dir : str
-        The Physionet directory where the dat file(s) are located, if
+        The PhysioNet directory where the dat file(s) are located, if
         the dat file(s) are remote.
     fmt : list
         The formats of the dat files.
@@ -1359,7 +1359,7 @@ def _rd_dat_file(file_name, dir_name, pn_dir, fmt, start_byte, n_samp):
         The full directory where the dat file(s) are located, if the dat
         file(s) are local.
     pn_dir : str
-        The Physionet directory where the dat file(s) are located, if
+        The PhysioNet directory where the dat file(s) are located, if
         the dat file(s) are remote.
     fmt : list
         The formats of the dat files.
@@ -2069,7 +2069,7 @@ def _infer_sig_len(file_name, fmt, n_sig, dir_name, pn_dir=None):
         The full directory where the dat file(s) are located, if the dat
         file(s) are local.
     pn_dir : str, optional
-        The Physionet directory where the dat file(s) are located, if
+        The PhysioNet directory where the dat file(s) are located, if
         the dat file(s) are remote.
 
     Returns

wfdb/io/_signal.py

@@ -1579,7 +1579,7 @@ def rdann(record_name, extension, sampfrom=0, sampto=None, shift_samps=False,
         Specifies whether to return the sample indices relative to `sampfrom`
         (True), or sample 0 (False).
     pn_dir : str, optional
-        Option used to stream data from Physionet. The Physionet database
+        Option used to stream data from Physionet. The PhysioNet database
         directory from which to find the required annotation file. eg. For
         record '100' in 'http://physionet.org/content/mitdb': pn_dir='mitdb'.
     return_label_elements : list, optional
@@ -1732,7 +1732,7 @@ def load_byte_pairs(record_name, extension, pn_dir):
         The annotatator extension of the annotation file. ie. for  file
         '100.atr', extension='atr'.
     pn_dir : str
-        Option used to stream data from Physionet. The Physionet database
+        Option used to stream data from Physionet. The PhysioNet database
         directory from which to find the required annotation file. eg. For
         record '100' in 'http://physionet.org/content/mitdb': pn_dir='mitdb'.
 
@@ -1746,7 +1746,7 @@ def load_byte_pairs(record_name, extension, pn_dir):
     if pn_dir is None:
         with open(record_name + '.' + extension, 'rb') as f:
             filebytes = np.fromfile(f, '<u1').reshape([-1, 2])
-    # Physionet file
+    # PhysioNet file
     else:
         filebytes = download._stream_annotation(record_name+'.'+extension, pn_dir).reshape([-1, 2])
 
@@ -2218,7 +2218,7 @@ def ann2rr(record_name, extension, pn_dir=None, start_time=None,
         The annotatator extension of the annotation file. ie. for  file
         '100.atr', extension='atr'.
     pn_dir : str
-        Option used to stream data from Physionet. The Physionet database
+        Option used to stream data from Physionet. The PhysioNet database
         directory from which to find the required annotation file. eg. For
         record '100' in 'http://physionet.org/content/mitdb': pn_dir='mitdb'.
     start_time : float

wfdb/io/annotation.py

@@ -10,13 +10,13 @@
 from wfdb.io import record
 
 
-# The Physionet index url
+# The PhysioNet index url
 PN_INDEX_URL = 'https://physionet.org/files/'
 PN_CONTENT_URL = 'https://physionet.org/content/'
 
 class Config(object):
     """
-    General class structure for the Physionet database.
+    General class structure for the PhysioNet database.
 
     Attributes
     ----------
@@ -25,7 +25,7 @@ class Config(object):
     """
     pass
 
-# The configuration database index url. Uses Physionet index by default.
+# The configuration database index url. Uses PhysioNet index by default.
 config = Config()
 config.db_index_url = PN_INDEX_URL
 
@@ -39,7 +39,7 @@ def set_db_index_url(db_index_url=PN_INDEX_URL):
     ----------
     db_index_url : str, optional
         The desired new database index url. Leave as default to reset
-        to the Physionet index url.
+        to the PhysioNet index url.
 
     Returns
     -------
@@ -94,7 +94,7 @@ def _stream_header(file_name, pn_dir):
     file_name : str
         The name of the headerr file to be read.
     pn_dir : str
-        The Physionet database directory from which to find the
+        The PhysioNet database directory from which to find the
         required header file. eg. For file '100.hea' in
         'http://physionet.org/content/mitdb', pn_dir='mitdb'.
 
@@ -148,7 +148,7 @@ def _stream_dat(file_name, pn_dir, byte_count, start_byte, dtype):
     file_name : str
         The name of the dat file to be read.
     pn_dir : str
-        The Physionet directory where the dat file is located.
+        The PhysioNet directory where the dat file is located.
     byte_count : int
         The number of bytes to be read.
     start_byte : int
@@ -196,7 +196,7 @@ def _stream_annotation(file_name, pn_dir):
     file_name : str
         The name of the annotation file to be read.
     pn_dir : str
-        The Physionet directory where the annotation file is located.
+        The PhysioNet directory where the annotation file is located.
 
     Returns
     -------
@@ -220,7 +220,7 @@ def _stream_annotation(file_name, pn_dir):
 
 def get_dbs():
     """
-    Get a list of all the Physionet databases available.
+    Get a list of all the PhysioNet databases available.
 
     Parameters
     ----------
@@ -251,7 +251,7 @@ def get_dbs():
     return dbs
 
 
-# ---- Helper functions for downloading Physionet files ------- #
+# ---- Helper functions for downloading PhysioNet files ------- #
 
 
 def get_record_list(db_dir, records='all'):
@@ -277,7 +277,7 @@ def get_record_list(db_dir, records='all'):
     >>> wfdb.get_record_list('mitdb')
 
     """
-    # Full url Physionet database
+    # Full url PhysioNet database
     if os.sep not in db_dir:
         db_url = posixpath.join(config.db_index_url, db_dir, record.get_version(db_dir))
     else:
@@ -321,7 +321,7 @@ def get_annotators(db_dir, annotators):
     >>> wfdb.get_annotators('mitdb')
 
     """
-    # Full url Physionet database
+    # Full url PhysioNet database
     db_url = posixpath.join(config.db_index_url, db_dir)
 
     if annotators is not None:
@@ -364,7 +364,7 @@ def make_local_dirs(dl_dir, dl_inputs, keep_subdirs):
         The desired input names for creating the directories.
     keep_subdirs : bool
         Whether to keep the relative subdirectories of downloaded files as they
-        are organized in Physionet (True), or to download all files into the
+        are organized in PhysioNet (True), or to download all files into the
         same base directory (False).
 
     Returns
@@ -475,12 +475,12 @@ def dl_full_file(url, save_file_name):
 
 def dl_files(db, dl_dir, files, keep_subdirs=True, overwrite=False):
     """
-    Download specified files from a Physionet database.
+    Download specified files from a PhysioNet database.
 
     Parameters
     ----------
     db : str
-        The Physionet database directory to download. eg. For database:
+        The PhysioNet database directory to download. eg. For database:
         'http://physionet.org/content/mitdb', db='mitdb'.
     dl_dir : str
         The full local directory path in which to download the files.
@@ -489,7 +489,7 @@ def dl_files(db, dl_dir, files, keep_subdirs=True, overwrite=False):
         database base directory.
     keep_subdirs : bool, optional
         Whether to keep the relative subdirectories of downloaded files as they
-        are organized in Physionet (True), or to download all files into the
+        are organized in PhysioNet (True), or to download all files into the
         same base directory (False).
     overwrite : bool, optional
         If True, all files will be redownloaded regardless. If False, existing
@@ -511,7 +511,7 @@ def dl_files(db, dl_dir, files, keep_subdirs=True, overwrite=False):
                       'data/001a.dat'])
 
     """
-    # Full url Physionet database
+    # Full url PhysioNet database
     db_dir = posixpath.join(db, record.get_version(db))
     db_url = posixpath.join(PN_CONTENT_URL, db_dir) + os.sep
 

wfdb/io/download.py

@@ -1232,7 +1232,7 @@ def get_version(pn_dir):
     Parameters
     ----------
     pn_dir : str
-        The Physionet database directory from which to find the
+        The PhysioNet database directory from which to find the
         required version number. eg. For the project 'mitdb' in
         'http://physionet.org/content/mitdb', pn_dir='mitdb'.
 
@@ -2509,13 +2509,13 @@ def dl_database(db_dir, dl_dir, records='all', annotators='all',
                 keep_subdirs=True, overwrite=False):
     """
     Download WFDB record (and optionally annotation) files from a
-    Physionet database. The database must contain a 'RECORDS' file in
+    PhysioNet database. The database must contain a 'RECORDS' file in
     its base directory which lists its WFDB records.
 
     Parameters
     ----------
     db_dir : str
-        The Physionet database directory to download. eg. For database:
+        The PhysioNet database directory to download. eg. For database:
         'http://physionet.org/content/mitdb/', db_dir='mitdb'.
     dl_dir : str
         The full local directory path in which to download the files.
@@ -2535,7 +2535,7 @@ def dl_database(db_dir, dl_dir, records='all', annotators='all',
         https://physionet.org/content/prcp/
     keep_subdirs : bool, optional
         Whether to keep the relative subdirectories of downloaded files
-        as they are organized in Physionet (True), or to download all
+        as they are organized in PhysioNet (True), or to download all
         files into the same base directory (False).
     overwrite : bool, optional
         If True, all files will be redownloaded regardless. If False,
@@ -2556,7 +2556,7 @@ def dl_database(db_dir, dl_dir, records='all', annotators='all',
     >>> wfdb.dl_database('ahadb', os.getcwd())
 
     """
-    # Full url Physionet database
+    # Full url PhysioNet database
     if os.sep in db_dir:
         dir_list = db_dir.split(os.sep)
         db_dir = posixpath.join(dir_list[0], get_version(dir_list[0]), *dir_list[1:])