From 0744886fb90ab8c7782eb914ea187b8493a022b7 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Tue, 2 Dec 2014 21:42:40 -0600
Subject: [PATCH] Renamed iaga2002.Parser to iaga2002.IAGA2002Parser, added
docs
---
.../iaga2002/{Parser.py => IAGA2002Parser.py} | 136 ++++++++++--------
.../{ParserTest.py => IAGA2002Parser_test.py} | 65 +++++----
2 files changed, 119 insertions(+), 82 deletions(-)
rename src/python/geomag/io/iaga2002/{Parser.py => IAGA2002Parser.py} (55%)
rename src/python/geomag/io/iaga2002/{ParserTest.py => IAGA2002Parser_test.py} (71%)
diff --git a/src/python/geomag/io/iaga2002/Parser.py b/src/python/geomag/io/iaga2002/IAGA2002Parser.py
similarity index 55%
rename from src/python/geomag/io/iaga2002/Parser.py
rename to src/python/geomag/io/iaga2002/IAGA2002Parser.py
index d5c5bb20..30967632 100644
--- a/src/python/geomag/io/iaga2002/Parser.py
+++ b/src/python/geomag/io/iaga2002/IAGA2002Parser.py
@@ -1,10 +1,9 @@
-"""
-Parsing methods for the IAGA2002 Format.
-"""
+"""Parsing methods for the IAGA2002 Format."""
-from obspy.core.utcdatetime import UTCDateTime
import numpy
+from obspy.core.utcdatetime import UTCDateTime
+from geomag.io import Timeseries
# values that represent missing data points in IAGA2002
@@ -12,36 +11,30 @@ EIGHTS = numpy.float64('88888.88')
NINES = numpy.float64('99999.99')
-def merge_comments(comments):
- """
- Combine multi-line, period-delimited comments.
- """
- merged = []
- partial = None
- for comment in comments:
- if partial is None:
- partial = comment
- else:
- partial = partial + ' ' + comment
- # comments end with period
- if partial.endswith('.'):
- merged.append(partial)
- partial = None
- # comment that doesn't end in a period
- if partial is not None:
- merged.append(partial)
- return merged
-
-
-class Parser(object):
- """
- IAGA2002 parser.
+class IAGA2002Parser(object):
+ """IAGA2002 parser.
+
+ Based on documentation at:
+ http://www.ngdc.noaa.gov/IAGA/vdat/iagaformat.html
+
+ Attributes
+ ----------
+ headers : dict
+ parsed IAGA headers.
+ comments : array
+ parsed comments.
+ channels : array
+ parsed channel names.
+ times : array
+ parsed timeseries times.
+ data : dict
+ keys are channel names (order listed in ``self.channels``).
+ values are ``numpy.array`` of timeseries values, array values are
+ ``numpy.nan`` when values are missing.
"""
def __init__(self):
- """
- Create a new IAGA2002 parser.
- """
+ """Create a new IAGA2002 parser."""
# header fields
self.headers = {}
# header comments
@@ -54,8 +47,12 @@ class Parser(object):
self.data = {}
def parse(self, data):
- """
- Parse a string containing IAGA2002 formatted data.
+ """Parse a string containing IAGA2002 formatted data.
+
+ Parameters
+ ----------
+ data : str
+ IAGA 2002 formatted file contents.
"""
parsing_headers = True
lines = data.splitlines()
@@ -73,25 +70,28 @@ class Parser(object):
else:
self._parse_data(line)
self._post_process()
- return self
def _parse_header(self, line):
- """
- Parse a header line.
+ """Parse header line.
+
+ Adds value to ``self.headers``.
"""
key = line[1:24].strip()
value = line[24:69].strip()
self.headers[key] = value
def _parse_comment(self, line):
- """
- Parse a header comment line.
+ """Parse comment line.
+
+ Adds line to ``self.comments``.
"""
self.comments.append(line[2:69].strip())
def _parse_channels(self, line):
- """
- Parse the data header that contains channel names.
+ """Parse data header that contains channel names.
+
+ Adds channel names to ``self.channels``.
+ Creates empty values arrays in ``self.data``.
"""
iaga_code = self.headers['IAGA CODE']
self.channels.append(line[30:40].strip().replace(iaga_code, ''))
@@ -103,8 +103,10 @@ class Parser(object):
self.data[channel] = []
def _parse_data(self, line):
- """
- Parse one data point in the timeseries
+ """Parse one data point in the timeseries.
+
+ Adds time to ``self.times``.
+ Adds channel values to ``self.data``.
"""
channels = self.channels
self.times.append(UTCDateTime(line[0:24]))
@@ -114,10 +116,14 @@ class Parser(object):
self.data[channels[3]].append(line[61:70].strip())
def _post_process(self):
+ """Post processing after data is parsed.
+
+ Merges comment lines.
+ Parses additional comment-based header values.
+ Converts data to numpy arrays.
+ Replaces empty values with ``numpy.nan``.
"""
- Post processing after data is parsed.
- """
- self.comments = merge_comments(self.comments)
+ self.comments = self._merge_comments(self.comments)
self.parse_comments()
for channel in self.data:
data = numpy.array(self.data[channel], dtype=numpy.float64)
@@ -127,24 +133,38 @@ class Parser(object):
self.data[channel] = data
def parse_comments(self):
- """
- Parse header values embedded in comments.
- """
+ """Parse header values embedded in comments."""
for comment in self.comments:
if comment.startswith('DECBAS'):
# parse DECBAS
decbas = comment.replace('DECBAS', '').strip()
self.headers['DECBAS'] = decbas[:decbas.find(' ')]
+ def _merge_comments(self, comments):
+ """Combine multi-line, period-delimited comments.
-def main(data):
- """
- Parse and print an IAGA2002 string.
- """
- from pprint import pprint
- pprint(Parser().parse(data))
-
+ Parameters
+ ----------
+ comments : array_like
+ array of comment strings.
-if __name__ == '__main__':
- import sys
- main(sys.stdin.read())
+ Returns
+ -------
+ array_like
+ merged comment strings.
+ """
+ merged = []
+ partial = None
+ for comment in comments:
+ if partial is None:
+ partial = comment
+ else:
+ partial = partial + ' ' + comment
+ # comments end with period
+ if partial.endswith('.'):
+ merged.append(partial)
+ partial = None
+ # comment that doesn't end in a period
+ if partial is not None:
+ merged.append(partial)
+ return merged
diff --git a/src/python/geomag/io/iaga2002/ParserTest.py b/src/python/geomag/io/iaga2002/IAGA2002Parser_test.py
similarity index 71%
rename from src/python/geomag/io/iaga2002/ParserTest.py
rename to src/python/geomag/io/iaga2002/IAGA2002Parser_test.py
index 30d8a26d..9e759ad2 100644
--- a/src/python/geomag/io/iaga2002/ParserTest.py
+++ b/src/python/geomag/io/iaga2002/IAGA2002Parser_test.py
@@ -1,9 +1,7 @@
-"""
-Tests for the IAGA2002 Parser class.
-"""
+"""Tests for the IAGA2002 Parser class."""
from nose.tools import assert_equals
-from . import Parser
+from IAGA2002Parser import IAGA2002Parser
IAGA2002_EXAMPLE = \
@@ -44,31 +42,41 @@ DATE TIME DOY BDTH BDTD BDTZ BDTF |
2013-09-01 00:09:00.000 244 21515.04 -28.86 47809.04 52532.10"""
-def test_merge_comments():
+def test__merge_comments():
"""
- Verify that merge comments merges lines until they end with a period.
+ geomag.io.iaga2002.IAGA2002Parser_test.test_merge_comments()
+
+ Call the _merge_comments method with 3 lines,
+ only the middle line ending in a period.
+ Verify, the first and second line are merged.
"""
comments = ['line 1', 'line 2.', 'line 3']
assert_equals(
- Parser.merge_comments(comments),
+ IAGA2002Parser()._merge_comments(comments),
['line 1 line 2.', 'line 3'])
-def test_parse_header():
+def test__parse_header():
"""
- Verify that header is parsed correctly.
+ geomag.io.iaga2002.IAGA2002Parser_test.test_parse_header()
+
+ Call the _parse_header method with a header.
+ Verify the header name and value are split at the correct column.
"""
- parser = Parser.Parser()
+ parser = IAGA2002Parser()
parser._parse_header(' Format ' +
'IAGA-2002 |')
assert_equals(parser.headers['Format'], 'IAGA-2002')
-def test_parse_comment():
+def test__parse_comment():
"""
- Verify that header comment is parsed correctly.
+ geomag.io.iaga2002.IAGA2002Parser_test.test_parse_header()
+
+ Call the _parse_comment method with a comment.
+ Verify the comment delimiters are removed.
"""
- parser = Parser.Parser()
+ parser = IAGA2002Parser()
parser._parse_comment(' # Go to www.intermagnet.org for details on' +
' obtaining this product. |')
assert_equals(parser.comments[-1],
@@ -76,22 +84,31 @@ def test_parse_comment():
' obtaining this product.')
-def test_parse_decbas():
- """
- Test that DECBAS is being set.
+def test__parse_channels():
"""
- parser = Parser.Parser()
- parser.parse(IAGA2002_EXAMPLE)
- assert_equals(parser.headers['DECBAS'], '5527')
+ geomag.io.iaga2002.IAGA2002Parser_test.test_parse_channels()
-
-def test_parse_channels():
- """
- Test that channel names are parsed correctly.
+ Call the _parse_header method with an IAGA CODE header, then call
+ the _parse_channels method with a channels header line.
+ Verify the IAGA CODE value is removed from parsed channel names.
"""
- parser = Parser.Parser()
+ parser = IAGA2002Parser()
parser._parse_header(' IAGA CODE ' +
'BDT |')
parser._parse_channels('DATE TIME DOY ' +
'BDTH BDTD BDTZ BDTF |')
assert_equals(parser.channels, ['H', 'D', 'Z', 'F'])
+
+
+def test_parse_decbas():
+ """
+ geomag.io.iaga2002.IAGA2002Parser_test.test_parse_decbas()
+
+ Call the parse method with a portion of an IAGA 2002 File,
+ which contains a DECBAS header comment.
+ Verify DECBAS appears in the headers dict, with the expected value.
+ """
+ parser = IAGA2002Parser()
+ parser.parse(IAGA2002_EXAMPLE)
+ assert_equals(parser.headers['DECBAS'], '5527')
+
--
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