Initial commit, 2018-05-22 dthomas

fixhdr/Makefile

+# Requires sourcing the setup information in setup_passoft
+
+EXEC	=	fixhdr
+PYEXEC	=	fixhdr.py
+
+MODLIB	=	lib/python/$(EXEC)
+
+all:
+
+install:
+		@$(PASSINSTALL) -d -m 0755 $(PASSCAL)/$(MODLIB)
+		@$(PASSCHEXE) $(PYEXEC)
+		@$(PASSCP) $(PYEXEC) $(PASSCAL)/$(MODLIB)
+		@$(PASSCHEXE) $(EXEC)
+		@$(PASSCP) $(EXEC) $(PASSCAL)/bin
+		@$(PASSINSTALL) -d -m 0755 $(PASSCAL)/man/manl
+		@$(PASSCP) $(EXEC).man $(PASSCAL)/man/manl/$(EXEC).l
+
+installl:
+		@$(PASSINSTALL) -d -m 0755 $(PASSOFT)/$(MODLIB)
+		@$(PASSCHEXE) $(PYEXEC)
+		@$(PASSCP) $(PYEXEC) $(PASSOFT)/$(MODLIB)
+		@$(PASSCHEXE) $(EXEC)
+		@$(PASSCP) $(EXEC) $(PASSOFT)/bin/$(EXEC)
+
+tarsrc:
+		@$(PASSINSTALL) -d -m 0755 $(PASSCAL)/tar
+		@$(PASSCP) $(PASSOFT)/src/setup_passoft .
+		@$(PASSTAR) cf $(EXEC)src.tar setup_passoft Makefile \
+			$(EXEC) *.man *.py
+		@$(PASSCP) $(EXEC)src.tar $(PASSCAL)/tar
+
+tarbin:
+		@$(PASSINSTALL) -d -m 0755 $(PASSCAL)/tar
+		@$(PASSCP) $(PASSOFT)/src/setup_passoft .
+		@$(PASSTAR) cf $(EXEC)bin.tar setup_passoft Makefile \
+			$(EXEC) *.man *py
+		@$(PASSCP) $(EXEC)bin.tar $(PASSCAL)/tar
+
+clean:
+		@$(PASSRM) *~
+
+uninstall:
+		@$(PASSRM) $(PASSCAL)/bin/$(EXEC)
+		@$(PASSRM) -r $(PASSCAL)/$(MODLIB)
+		@$(PASSRM) $(PASSCAL)/man/manl/$(EXEC).l

fixhdr/__init__.py

+# -*- coding: utf-8 -*-
+
+"""Top-level package for fixhdr."""
+
+__author__ = """IRIS PASSCAL"""
+__email__ = 'software-support@passcal.nmt.edu'
+__version__ = '2009.175'

fixhdr/fixhdr

+#!/bin/bash
+#    Launch fixhdr.py
+
+if [ ! -z "${PASSCAL}" ]
+then
+   PYTHON=${PASSCAL}/other/bin/picpython
+   export PYTHON
+   PYTHONPATH=${PASSCAL}/lib:${PASSCAL}/lib/python/libtrace
+   export PYTHONPATH
+else
+   echo "PASSCAL environment variable not set! Cannot continue."
+   exit 1
+fi
+
+if [ $# = 0 ]
+then
+   echo "Starting fixhdr..."
+   ${PYTHON} ${PASSCAL}/lib/python/fixhdr/fixhdr.py $* &
+   exit 0
+fi
+if [ $1 = "-#" ]
+then
+   ${PYTHON} ${PASSCAL}/lib/python/fixhdr/fixhdr.py $*
+   exit 0
+fi
+echo "Starting fixhdr..."
+${PYTHON} ${PASSCAL}/lib/python/fixhdr/fixhdr.py $* &
+

fixhdr/fixhdr.man

+.TH fixhdr l 2007.192 "" "PASSCAL MANUAL PAGES"
+.SH NAME
+\fBfixhdr\fR - a GUI for modifying mseed file header fields
+('Station Name', 'Channel', 'Location Code', and 'Network Code'),
+to apply time shifts and to convert header endianess.
+.SH SYNOPSIS
+\fBfixhdr\fR
+.br
+\fBfixhdr -#\fR
+.br
+\fBfixhdr -h\fR
+.br
+\fBfixhdr  [-d DataDirs] [-m batch_file] [-t batch_file] [-e endianess]\fR
+.SH OPTIONS
+\fB-#\fR returns version number
+.br
+\fB-h \fR returns usage
+.br
+\fB-d DataDirs\fR colon separated list of data directories [default: cwd]
+.br
+\fB-m batch_file\fR correct mseed headers in batch mode using batch_file
+.br
+\fB-t batch_file\fR correct trace timing in batch mode using batch_file
+.br
+\fB-e endianess\fR convert trace headers to endianess [big or little]
+.br
+\fB NOTE: -m, -t & -e are mutually exclusive. If you wish to do
+both timing and headers, run time corrections first.\fR
+.SH DESCRIPTION
+\fBfixhdr\fR
+has seven notebooks: [Trace Headers], [Global Modify], [Time Shift],
+[Endianess], [Log], [Help] and [MSEED format]. [Trace Headers] and [Global Modify]
+provide a means to read and modify mseed header fields (station, channel,
+location code, and network code) for files found beneath a specified 
+directory list. [Time Shift] allows the user to apply a bulk time shift to
+traces that fall between a start and end time and to set a header flag
+indicating that the time tag is questionable. [Endianess] converts traces
+between little and big, or big and little endian headers. The [Log] notebook 
+maintains records of key events.
+.LP
+.SH Root Window
+.LP
+.nf
+Buttons:
+  <Load Template>: loads a previously saved or user created mapping
+    of header and timing modification that then can be applied.
+  <Save Template>: saves a map of all header and timing modifications.
+   Example:
+   # Header Changes
+   # stat:chan:loc:net:sps   stat:chan:loc:net
+   hdrlist{
+     01053:1C4::XX:40.0      SITE:BHZ::PI
+     01053:1C5::XX:40.0      SITE:BHN::PI
+     01053:1C6::XX:40.0      SITE:BHE::PI
+   }
+   # Timing Corrections
+   # sta:loc:net Start_Time        End_Time          Shift(s) Time_Tag     Corr_Type
+   # sta:loc:net yyyy:ddd:hh:mm:ss yyyy:ddd:hh:mm:ss float/NA set/unset/NA add/replace/NA
+   timelist{
+     9294::SS    2005:304:00:00:00 2005:305:22:15:10 0.56     set          add
+   }
+
+  <Exit>: Exits \fBfixhdr\fR and will query if not all mappings in
+    Updata_Dictionary have been applied.
+.fi
+.LP
+.SH Trace Headers
+.LP
+.nf
+General:
+  >>specify/load directories for header investigation/modifications
+  >>manipulate/edit individual <sta><chn><loc><net> entries for
+    loaded headers
+  >>modify trace headers as specified in the "New Value" column
+    for _ALL_ loaded headers
+  >>store and recall header modification templates
+Buttons:
+  <Build Trace db>: Searchs the directories listed in the "Data-
+    Directories" entry box (a colon separated list) and builds a
+    list of mseed files found indexing them on unique values of
+    <sta><chn><loc><net><sps>. You can narrow your search by
+    entering stations in the "Find Only Stations" entry box (a
+    colon separated list).
+  <Find>: Launches a file browser allowing the user to add
+    directories to the "Data Directories" entry box. Double
+    clicking selects the new directory.
+  <Clear>: Clears the "Data Directories" entry box.
+  <List Traces>: Lists all traces for the selected Sta:Chan:Loc:Net:Sps.
+  <Modify Headers>: Applies all current values in the 
+    Update_Dictionary (that can be viewed in the [Log] notebook)
+    to the current trace list that was built using <Build Trace db>
+  <Clear Current>: clears all entries in the Update_Dictionary and 
+    display for the currently selected sta:chan:loc:net:sps that 
+    have not been applied.
+  <Clear All>: clears all entries in the Update_Dictionary that
+    have not been applied.
+.fi
+.LP
+.SH Global Modify
+.LP
+.nf
+General:
+  >>specify header values in "For Headers Matching:" column, using
+    drop-down menus. Wildcards are allowed and are the default.
+  >>enter new header values in "Substitute Values:"
+Buttons:
+  <Global Set>: inserts the values in "Subsitute Values" into the "
+    Update_Dictionary using For Headers Matching" entries to
+    determine which <sta><chn><loc><net><sps> to modify. This only
+    creates entries in the dictionary and does NOT apply them to
+    the mseed headers. You must use [Trace Headers]-><Modify Headers>
+     to apply these updates.
+  <Clear All>: clears all current entries. This does not
+    affect the Update_Dictionary.
+.fi
+.LP
+.SH Time Shift
+.LP
+.nf
+General:
+  >> specify header values in "For Traces Matching:" column, 
+     using drop-down menus. Once selected first and last sample 
+     times will be displayed. The start and end time can be changed.
+  >> enter time in seconds to be added to the blockette start times 
+     in then "Time Shift (s):" window.
+  >> "Time Tag is questionable" allows you to flip a bit in the
+     Data Quality flags in the mseed file's Fixed Section of
+     Data Header.
+  >> "Applied" indicators notify a user when corrections have been
+     appied in this instance of \fBfixhdr\fR.
+Buttons:
+  <How to Treat Existing Corrections>: you can choose to either 
+    "Add To" to any correction listed in the Fixed Header or
+    "Replace" any existing correction with the one entered.
+  <Undo Time Corrections>: Allows user to un-apply previously 
+     applied timing corrections. Note: Use with caution. This 
+     will only remove single and cumulative corrections. 
+     Review 'List Time Corrections' to better understand 
+     corrections already applied to trace headers.
+  <List Time Corrections>: Displays time corrections for traces
+     matching the selected Stat:Loc:Net key.
+  <Apply Time Corrections>: to apply corrections.
+  <Time Set>: Allows user to build a dictionary of timing corrections 
+     to be applied with the "Apply Time Corrections" button. i.e. 
+     timing corrections for multiple Stat:Loc:Net selections can
+     be set prior to applying in a single instance.
+  <Recalc Start/End>: resets the start and end times from the trace 
+     headers. The first time a trace is read in the start and end 
+     times are cached for future use. If you change these times, 
+     this button is used to update the cache and display.
+  <Clear All>: clears all current entries.
+.fi
+.LP
+.SH Endianess
+.LP
+.nf
+General:
+  >> displays the number of big and little endian files found. 
+     Allows user to convert between big and little endian headers.
+Buttons:
+  <Convert to Big>: converts headers from little to big endian.
+  <Convert to Little>: converts headers from big to little endian.
+.fi
+.LP
+.SH Log
+.LP
+.nf
+General:
+  >>displays key events (e.g. "Build Trace db", "Modify Headers",
+    etc.). Radio buttons allow you to select all log messages or
+    window only those messages related to Header events, Time events,
+    or changes in endianess.
+Buttons:
+  <Dump UpdateDict>: Dumps the current values in the Update_Dictionary
+    and indicates whether or not they have been applied (i.e.
+    <Modify Headers> has been run).
+  <Save Log File>: Saves text window to an output file.
+  <Clear Log File>: Clears text window and flushes buffer.
+.fi
+.SH KEYWORDS
+mseed; header information; header modification
+.SH SEE ALSO
+SEED manual (pdf), mseedhdr
+.SH AUTHOR
+Bruce Beaudoin (bruce@passcal.nmt.edu)

requirements_dev.txt

+pip==9.0.1
+bumpversion==0.5.3
+wheel==0.30.0
+watchdog==0.8.3
+flake8==3.5.0
+tox==2.9.1
+coverage==4.5.1
+Sphinx==1.7.1
+twine==1.10.0
+
+

setup.cfg

+[bumpversion]
+current_version = 2009.175
+commit = True
+tag = True
+
+[bumpversion:file:setup.py]
+search = version='{current_version}'
+replace = version='{new_version}'
+
+[bumpversion:file:fixhdr/__init__.py]
+search = __version__ = '{current_version}'
+replace = __version__ = '{new_version}'
+
+[bdist_wheel]
+universal = 1
+
+[flake8]
+exclude = docs
+
+[aliases]
+# Define setup.py command aliases here
+

setup.py

+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""The setup script."""
+
+from setuptools import setup, find_packages
+
+with open('README.rst') as readme_file:
+    readme = readme_file.read()
+
+with open('HISTORY.rst') as history_file:
+    history = history_file.read()
+
+
+setup(
+    author="IRIS PASSCAL",
+    author_email='software-support@passcal.nmt.edu',
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Developers',
+        'License :: OSI Approved ::  GNU General Public License v3 (GPLv3)',
+        'Natural Language :: English',
+        'Programming Language :: Python :: 2.7',
+    ],
+    description="Modifies mseed headers.",
+    entry_points={
+        'console_scripts': [
+            'fixhdr=fixhdr.fixhdr:main',
+        ],
+    },
+    install_requires=[],
+    setup_requires = [],
+    license="GNU General Public License v3",
+    long_description=readme + '\n\n' + history,
+    include_package_data=True,
+    keywords='fixhdr',
+    name='fixhdr',
+    packages=find_packages(include=['fixhdr']),
+    test_suite='tests',
+    url='https://git.passcal.nmt.edu/passoft/fixhdr',
+    version='2009.175',
+    zip_safe=False,
+)

tests/__init__.py

+# -*- coding: utf-8 -*-
+
+"""Unit test package for fixhdr."""

tests/test_fixhdr.py

+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""Tests for `fixhdr` package."""
+
+import unittest
+import sys
+
+try:
+    import fixhdr
+except ImportError:
+     pass
+
+class TestFixhdr(unittest.TestCase):
+    """Tests for `fixhdr` package."""
+
+    def setUp(self):
+        """Set up test fixtures, if any."""
+
+    def tearDown(self):
+        """Tear down test fixtures, if any."""
+
+    def test_import(self):
+        if 'fixhdr' in sys.modules:
+            self.assert_(True, "fixhdr loaded")
+        else:
+            self.fail()
+

tox.ini

+[tox]
+envlist = py27, flake8
+
+[travis]
+python =
+    2.7: py27
+
+[testenv:flake8]
+basepython = python
+deps = flake8
+commands = flake8 fixhdr
+
+[testenv]
+setenv =
+    PYTHONPATH = {toxinidir}
+python setup.py test
+
+