Index: sodar/branches/raw2proc-dev/plotSodar.py =================================================================== --- sodar/branches/raw2proc-dev/plotSodar.py (revision 162) +++ (revision ) @@ -1,251 +1,0 @@ -#!/usr/bin/python -""" -Module to process sodar data. -""" - -import optparse -from sodar.utils import openAnything, findMissing -from sodar import arrayData as a -import numpy as n -import pylab as p -import os -import shutil -import csv - -_uComponentsPlotName = 'uComponents.png' -_vComponentsPlotName = 'vComponents.png' -_wComponentsPlotName = 'wComponents.png' -_echoStrengthsPlotName = 'echoStrengths.png' -_quiverPlotName = 'quiver.png' -_latestPlotNamePrefix = 'ims_sodar_latest_' -_catalogName = 'sodar-plot-catalog.csv' - -def plotSingle(filein, pathout): - """ - Plot single sodar raw data file. - - plotSingle(filein, pathout) -> rc - - filein - path to raw data file. - pathout - path to plot images directory. - rc - 0 if successful - """ - - if not os.path.exists(pathout): - os.makedirs(pathout, mode=0775) - - rawDataHandle = openAnything.openAnything(filein) - rawDataString = rawDataHandle.read() - rawDataHandle.close() - - rawDataObject = a.rawData.RawData(rawDataString) - formattedDataObject = a.formattedData.FormattedData(rawDataObject) - arrayDataObject = a.ArrayData(formattedDataObject) - - beginStamp = arrayDataObject.beginStamp - endStamp = arrayDataObject.endStamp - numIntervals = arrayDataObject.numIntervals - timeInterval = arrayDataObject.timeInterval - minAltitude = arrayDataObject.minAltitude - numAltitudes = arrayDataObject.numAltitudes - altInterval = arrayDataObject.altInterval - - def makePcolor(vector, title, fileout, cbLabel): - fig = p.figure(1) - axe = fig.add_subplot(1, 1, 1) - pc = axe.pcolor(vector) - - axe.set_xlabel('Time (hh:mm UTC)') - axe.set_ylabel('Altitude (m)') - axe.set_xbound(upper=numIntervals) - - xticks = axe.get_xticks() - xticklabels = [(int(x) * timeInterval) + beginStamp - for x in xticks] - xticklabels = [':'.join(('%02u' % x.hour, '%02u' % x.minute)) - for x in xticklabels] - axe.set_xticklabels(xticklabels) - - yticks = axe.get_yticks() - yticklabels = [str(y * altInterval + minAltitude) - for y in yticks] - axe.set_yticklabels(yticklabels) - - axe.set_title(title) - cb = p.colorbar(pc) - cb.set_label(cbLabel) - - fig.savefig(os.path.join(pathout, fileout)) - fig.clear() - - return 0 - - uComponents = arrayDataObject.uComponents - maskedUComponents = n.ma.masked_where(n.isnan(uComponents), - uComponents) - makePcolor(maskedUComponents.T, - 'U Component of Wind Velocity for %s' % - (str(beginStamp)[:10],), - _uComponentsPlotName, - 'Speed (cm/sec)') - - vComponents = arrayDataObject.vComponents - maskedVComponents = n.ma.masked_where(n.isnan(vComponents), - vComponents) - makePcolor(maskedVComponents.T, - 'V Component of Wind Velocity for %s' % - (str(beginStamp)[:10],), - _vComponentsPlotName, - 'Speed (cm/sec)') - - wComponents = arrayDataObject.wComponents - maskedWComponents = n.ma.masked_where(n.isnan(wComponents), - wComponents) - makePcolor(maskedWComponents.T, - 'W Component of Wind Velocity for %s' % - (str(beginStamp)[:10],), - _wComponentsPlotName, - 'Speed (cm/sec)') - - echoStrengths = arrayDataObject.echoStrengths - maskedEchoStrenths = n.ma.masked_where(n.isnan(echoStrengths), - echoStrengths) - makePcolor(maskedEchoStrenths.T, - 'Echo Strength for %s' % - (str(beginStamp)[:10],), - _echoStrengthsPlotName, - 'Strength (no units)') - - # timeComponent = n.array(range(numIntervals)) - # altComponent = n.array(range(numAltitudes)) - # fig = p.figure(1) - # axe = fig.add_subplot(1, 1, 1) - # qv = axe.quiver(altComponent, - # timeComponent, - # maskedUComponents.T, - # maskedVComponents.T) - - # axe.set_xlabel('Time (min)') - # axe.set_ylabel('Altitude (m)') - # axe.set_xbound(upper=numIntervals) - - # xticks = axe.get_xticks() - # xticklabels = [(int(x) * timeInterval) + beginStamp - # for x in xticks] - # xticklabels = [':'.join(('%02u' % x.hour, '%02u' % x.minute)) - # for x in xticklabels] - # axe.set_xticklabels(xticklabels) - - # yticks = axe.get_yticks() - # yticklabels = [str(y * altInterval + minAltitude) - # for y in yticks] - # axe.set_yticklabels(yticklabels) - - # axe.set_title('Wind Velocty for %s' % - # (str(beginStamp)[:10],)) - # cb = p.colorbar(qv) - # cb.set_label('W Component Speed (cm/sec)') - - # fig.savefig(os.path.join(pathout, _quiverPlotName)) - # fig.clear() - - return 0 - -def copyLatest(pathout, latest, plotName): - """ - Copy the latest plot to the official NCCOOS place. - - copyLatest(pathout, latest, plotName) -> rc - - pathout - path to directory where the latest plot is. - latest - path to directory where the latest plot is to be copied. - plotName - name of the plot file to copy. - rc - 0 if successful - """ - shutil.copy(os.path.join(pathout, plotName), - os.path.join(latest, - _latestPlotNamePrefix + plotName)) - return 0 - -def createCatalog(destination, catalog): - """ - Create catalog of plots. - - createCatalog(destination, catalog) -> rc - - destination - path to plot images directory in NCCOOS format. - catalog - path to plot catalog. - rc - 0 if successful - """ - destinationWalk = findMissing.computeDestinationWalk(destination, False) - catalogData = [destpath.split(os.sep)[-1] - for destpath in destinationWalk] - catalogData = [(catalogDate[:4], catalogDate[4:6], catalogDate[6:]) - for catalogDate in catalogData] - catalogHandle = open(os.path.join(catalog, _catalogName), 'wb') - writer = csv.writer(catalogHandle) - writer.writerows(catalogData) - catalogHandle.close() - - return 0 - -def plotAll(source, destination, latest, catalog, force): - """ - Plot all sodar raw data files. - - plotAll(source, destination, latest, catalog, force) -> rc - - source - path to raw data directory in NCCOOS format. - destination - path to plot images directory in NCCOOS format. - latest - path to latest plots images directory in NCCOOS format. - catalog - path to plot catalog. - force - update all destination plots for which raw data sources exist. - rc - 0 if successful - """ - - if source.endswith(os.path.sep): - source = source.rstrip(os.path.sep) - - if destination.endswith(os.path.sep): - destination = destination.rstrip(os.path.sep) - - walkList = findMissing.findMissing(source, destination, force) - - for filein, pathout in walkList: - plotSingle(filein, pathout) - - if not os.path.exists(latest): - os.makedirs(latest, mode=0775) - - filein, pathout = walkList[-1] - copyLatest(pathout, latest, _uComponentsPlotName) - copyLatest(pathout, latest, _vComponentsPlotName) - copyLatest(pathout, latest, _wComponentsPlotName) - copyLatest(pathout, latest, _echoStrengthsPlotName) - # copyLatest(pathout, latest, _quiverPlotName) - - createCatalog(destination, catalog) - - return 0 - -def _main(): - """bin/python %prog [options] /path/to/raw/files/ /path/to/plots/ /path/to/latest/plot/ /path/to/catalog/""" - - __description__ = 'Plot all sodar raw data files.' - - parser = optparse.OptionParser(usage=_main.__doc__, - version='%prog 1.0', - description=__description__) - parser.set_defaults(force=False) - parser.add_option('-f', '--force-update', - action='store_true', - dest='force', - help='update all plots for which raw data exists') - (values, args) = parser.parse_args() - (source, destination, latest, catalog) = tuple(args) - plotAll(source, destination, latest, catalog, values.force) - - return 0 - -if __name__ == "__main__": - _main() Index: sodar/branches/raw2proc-dev/sodar/CREDITS.txt =================================================================== --- sodar/branches/raw2proc-dev/sodar/CREDITS.txt (revision 119) +++ (revision ) @@ -1,2 +1,0 @@ -Chris Calloway (cbcunc) - lead developer -Harvey E. Seim - chief science officer Index: sodar/branches/raw2proc-dev/sodar/HISTORY.txt =================================================================== --- sodar/branches/raw2proc-dev/sodar/HISTORY.txt (revision 119) +++ (revision ) @@ -1,1 +1,0 @@ -sodar 1.0 - initial release, August 2007 Index: sodar/branches/raw2proc-dev/sodar/LICENSE.GPL2 =================================================================== --- sodar/branches/raw2proc-dev/sodar/LICENSE.GPL2 (revision 119) +++ (revision ) @@ -1,280 +1,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 2, June 1991 - - Copyright (C) 1989, 1991 Free Software Foundation, Inc., - 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The licenses for most software are designed to take away your -freedom to share and change it. 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IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING -WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR -REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, -INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING -OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED -TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY -YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER -PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE -POSSIBILITY OF SUCH DAMAGES. - - END OF TERMS AND CONDITIONS Index: sodar/branches/raw2proc-dev/sodar/LICENSE.txt =================================================================== --- sodar/branches/raw2proc-dev/sodar/LICENSE.txt (revision 57) +++ (revision ) @@ -1,14 +1,0 @@ -This program is free software; you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation; either version 2 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program; if not, write to the Free Software -Foundation, Inc., 59 Temple Place, Suite 330, Boston, -MA 02111-1307 USA. Index: sodar/branches/raw2proc-dev/sodar/README.txt =================================================================== --- sodar/branches/raw2proc-dev/sodar/README.txt (revision 57) +++ (revision ) @@ -1,4 +1,0 @@ -Sodar is a Python package providing modules which process wind column data files -produced by REMTECH sodar. - -Installation instructions may be found in INSTALL.txt. Index: sodar/branches/raw2proc-dev/sodar/TODO.txt =================================================================== --- sodar/branches/raw2proc-dev/sodar/TODO.txt (revision 57) +++ (revision ) @@ -1,2 +1,0 @@ -- create test framework -- create distutils based setup.py Index: sodar/branches/raw2proc-dev/sodar/VERSION.txt =================================================================== --- sodar/branches/raw2proc-dev/sodar/VERSION.txt (revision 57) +++ (revision ) @@ -1,1 +1,0 @@ -1.0 Index: sodar/branches/raw2proc-dev/sodar/__init__.py =================================================================== --- sodar/branches/raw2proc-dev/sodar/__init__.py (revision 132) +++ (revision ) @@ -1,10 +1,0 @@ -#!/usr/bin/python -""" -Modules for sodar data -""" - -__all__ = ['rawData', - 'formattedData', - 'adjustedData', - 'arrayData', - 'utils'] Index: sodar/branches/raw2proc-dev/sodar/adjustedData.py =================================================================== --- sodar/branches/raw2proc-dev/sodar/adjustedData.py (revision 119) +++ (revision ) @@ -1,26 +1,0 @@ -#!/usr/bin/python -""" -Module to handle adjusting sodar data samples for missing data. - -A list of sample data. - -A sample: formattedDataObject[0] -> dictionary - -A sample header: formattedDataObject[0]['header'] -> dictionary - -A sample body: formattedDataObject[0]['body'] -> list of dictionaries - -Altitude data from a sample: formattedDataObject[0]['body'][0] -> dictionary -""" - -__author__ = 'Chris Calloway' -__email__ = 'cbc@unc.edu' -__copyright__ = 'Copyright 2007 UNC-CH Department of Marine Science' -__license__ = 'GPL2' - -import rawData -import numpy as n -import datetime - -class AdjustedData(list): - pass Index: sodar/branches/raw2proc-dev/sodar/arrayData.py =================================================================== --- sodar/branches/raw2proc-dev/sodar/arrayData.py (revision 138) +++ (revision ) @@ -1,109 +1,0 @@ -#!/usr/bin/python -""" -Module to handle sodar data samples as arrays. -""" - -__author__ = 'Chris Calloway' -__email__ = 'cbc@unc.edu' -__copyright__ = 'Copyright 2007 UNC-CH Department of Marine Science' -__license__ = 'GPL2' - -import rawData -import formattedData -import numpy as n -import datetime - -class ArrayData(object): - - """Class to handle Daily sodar file data as arrays.""" - - def __init__(self, data): - """Create arrays from formatted data.""" - super(ArrayData, self).__init__() - self.beginStamp = data.beginStamp - self.endStamp = data.endStamp - self.numIntervals = data.numIntervals - self.timeInterval = data.timeInterval - self.altInterval = data.altInterval - self.numAltitudes = data.numAltitudes - self.minAltitude = data.minAltitude - self.maxAltitude = data.maxAltitude - self._thetas(data) - self._uComponents(data) - self._vComponents(data) - self._wComponents(data) - self._echoStrengths(data) - - def _thetas(self, data): - """Convert direction to polar azimuth in radians CW from North""" - self.thetas = n.pi * (n.array(data.thetas()) / 180.0) - - def _uComponents(self,data): - """Compute u component array""" - self.uComponents = n.array(data.radials()) * n.sin(self.thetas) - - def _vComponents(self,data): - """Compute v component array""" - self.vComponents = n.array(data.radials()) * n.cos(self.thetas) - - def _wComponents(self,data): - """Create w component array""" - self.wComponents = n.array(data.wComponents()) - - def _echoStrengths(self,data): - """Create an echo strength array""" - self.echoStrengths = n.array(data.echoStrengths()) - - -def _main(): - """Process as script from command line.""" - import urllib2 - try: - rawDataHandle = urllib2.urlopen('http://nemo.isis.unc.edu/'\ - 'data/nccoos/level0/ims/sodar/'\ - '2008_01/20080101.dat') - rawDataString = rawDataHandle.read() - rawDataHandle.close() - except: - raise IOError("Failure to read raw test data") - rawDataObject = rawData.RawData(rawDataString) - formattedDataObject = formattedData.FormattedData(rawDataObject) - arrayDataObject = ArrayData(formattedDataObject) - - import pylab as p - - home = '/var/www/html/sodar/plots/' - - fig = p.figure() - p.pcolor(arrayDataObject.uComponents.T) - p.colorbar() - fig.savefig(home + 'uComponents.png') - - fig = p.figure() - p.pcolor(arrayDataObject.vComponents.T) - p.colorbar() - fig.savefig(home + 'vComponents.png') - - fig = p.figure() - p.pcolor(arrayDataObject.wComponents.T) - p.colorbar() - fig.savefig(home + 'wComponents.png') - - fig = p.figure() - p.pcolor(arrayDataObject.echoStrengths.T) - p.colorbar() - fig.savefig(home + 'echoStrengths.png') - - fig = p.figure() - p.quiver(arrayDataObject.uComponents, - arrayDataObject.vComponents, - arrayDataObject.wComponents) - p.colorbar() - xmin,xmax,ymin,ymax = p.axis() - dx,dy = xmax-xmin, ymax-ymin - p.axis([xmin-0.1*dx, xmax+0.1*dx, ymin-0.1*dy, ymax+0.1*dy]) - p.title('Horizontal wind vectors: time vs. altitude') - fig.savefig(home + 'quiver.png') - -if __name__ == "__main__": - _main() Index: sodar/branches/raw2proc-dev/sodar/formattedData.py =================================================================== --- sodar/branches/raw2proc-dev/sodar/formattedData.py (revision 136) +++ (revision ) @@ -1,163 +1,0 @@ -#!/usr/bin/python -""" -Module to handle formatting sodar data samples. - -A list of sample data. - -A sample: formattedDataObject[0] -> dictionary - -A sample header: formattedDataObject[0]['header'] -> dictionary - -A sample body: formattedDataObject[0]['body'] -> list of dictionaries - -Altitude data from a sample: formattedDataObject[0]['body'][0] -> dictionary -""" - -__author__ = 'Chris Calloway' -__email__ = 'cbc@unc.edu' -__copyright__ = 'Copyright 2007 UNC-CH Department of Marine Science' -__license__ = 'GPL2' - -import rawData -import numpy as n -import datetime - -class FormattedData(list): - - """Class to handle formatted daily sodar file data. - - A list of samples. - """ - - def __init__(self, data): - """Create formatted sodar daily data.""" - super(FormattedData, self).__init__() - self.extend([sample.data() for sample in data]) - self._convert() - self._stamp() - self._beginStamp() - self._endStamp() - self._numIntervals() - self._timeInterval() - self._minAltitude() - self._maxAltitude() - self._numAltitudes() - self._altInterval() - - def _convert(self): - """Convert data to numbers and correct for invalid values.""" - INVALID = "-9999" - for sample in self: - # convert header data to integers - for key,value in sample['header'].items(): - try: - if value == INVALID: - raise ValueError - sample['header'][key] = int(value) - except (ValueError, TypeError): - sample['header'][key] = n.NaN - # convert body data to floats - for altitude in sample['body']: - for key,value in altitude.items(): - try: - if value == INVALID: - raise ValueError - altitude[key] = float(value) - except (ValueError, TypeError): - altitude[key] = n.NaN - - def _stamp(self): - """Add a datetime stamp item to each sample.""" - for sample in self: - header = sample['header'] - sample['stamp'] = datetime.datetime(header['YEAR'], - header['MONTH'], - header['DAY'], - header['HOUR'], - header['MIN']) - - def _beginStamp(self): - self.beginStamp = self[0]['stamp'] - - def _endStamp(self): - self.endStamp = self[-1]['stamp'] - - def _numIntervals(self): - self.numIntervals = len(self) - - def _timeInterval(self): - """Add a time interval attribute.""" - intervals = zip([sample['stamp'] for sample in self[:-1]], - [sample['stamp'] for sample in self[1:]]) - intervals = [interval[1] - interval[0] for interval in intervals] - self.timeInterval = min(intervals) - - def _minAltitude(self): - """Add an overall minimum altitude attribute.""" - altitudes = [sample['body'][0]['ALT'] for sample in self] - self.minAltitude = min(altitudes) - - def _maxAltitude(self): - """Add an overall maximum altitude attribute.""" - altitudes = [sample['body'][-1]['ALT'] for sample in self] - self.maxAltitude = max(altitudes) - - def _numAltitudes(self): - """Add an overall maximum number of altitudes attribute""" - self.numAltitudes = max([len(sample['body']) for sample in self]) - - def _altInterval(self): - """Add an overall altitude interval attribute.""" - self.altInterval = (self.maxAltitude - self.minAltitude) / \ - (self.numAltitudes - 1) - - def thetas(self): - """Create a list of lists of horizontal directional data.""" - return [[altitude['DIR'] - for altitude - in sample['body']] - for sample in self] - - def radials(self): - """Create a list of lists of horizontal radial velocity data.""" - return [[altitude['SPEED'] - for altitude - in sample['body']] - for sample in self] - - def wComponents(self): - """Create a list of lists of vertical velocity data.""" - return [[altitude['W'] - for altitude - in sample['body']] - for sample in self] - - def echoStrengths(self): - """Create a list of lists of echo strength data.""" - return [[altitude['CT'] - for altitude - in sample['body']] - for sample in self] - - -def _main(): - """Process as script from command line.""" - import urllib2 - try: - rawDataHandle = urllib2.urlopen('http://nemo.isis.unc.edu/'\ - 'data/nccoos/level0/ims/sodar/'\ - '2008_01/20080101.dat') - rawDataString = rawDataHandle.read() - rawDataHandle.close() - except: - raise IOError("Failure to read raw test data") - rawDataObject = rawData.RawData(rawDataString) - formattedDataObject = FormattedData(rawDataObject) - print "Time Interval =", formattedDataObject.timeInterval - print "Minumum Altitude =", formattedDataObject.minAltitude - print "Maximum Altitude =", formattedDataObject.maxAltitude - print "Number of Altitudes =", formattedDataObject.numAltitudes - print "Altitude Interval =", formattedDataObject.altInterval - -if __name__ == "__main__": - _main() Index: sodar/branches/raw2proc-dev/sodar/rawData.py =================================================================== --- sodar/branches/raw2proc-dev/sodar/rawData.py (revision 187) +++ (revision ) @@ -1,247 +1,0 @@ -#!/usr/bin/python -""" -Module to handle raw sodar data samples. - -Raw sodar data samples are collected into daily files. Each sample consists of a -header followed by an observation for each height. - -The daily file is split into a list (modeled by the class RawData) of samples -(modeled by the class Sample) in chronological order. A RawData object is -initialized with a string representing the daily file data: - - rawDataHandle = open('20070601.dat') - rawDataString = rawDataHandle.read() - rawDataObject = RawData(rawDataString) - -Each Sample object has attributes for a Header and Body object. The Samples -within a RawData object may also be accessed by time using a string of the -format YYYY-MM-DD-HH-MM as in index on the RawData object to return the first -matching Sample in the RawData object: - - rawDataObject[0] # the first Sample object of the day - rawDataObject['2007-06-01-09-15'] # the Sample object for 9:15am - rawDataObject[15].header # the Header object of the 16th Sample - rawDataObject['2007-06-01-09-15'].body # the Body object for 9:15am - -Header objects act as dictionaries. Access each sample-wide parameter of -interest using the header parameter name as a keyword on the Header object: - - rawDataObject[15].header['VAL2'] # the number of validations for beam 2 - rawDataObject['2007-06-01-09-15'].header['SPU3'] # normalized false signal - # probability on beam 3 - rawDataObject[0].header['SNR1'] # signal to noise on beam 1 - -Consult your Sodar documentation for a complete list of header parameters. -Different sodar models have different sets of header parameters. This model -seeks to be model agnostic, and parses the header parameter names from the -raw data itself. - -Body objects act as lists of dictionaries. The dictionaries access -altitude-specific parameters by name as keywords. The dictionaries are in -altitude-ascending order. Each dictionary may also by accessed by indexing with -an altitude string: - - rawDataObject[15].body[0] # the data for the lowest altitude, 16th sample - rawDataObject['2007-06-01-09-15'].body['70'] # the data for 70 meters - rawDataObject[15].body[0]['SPEED'] # wind speed at lowest altitude - rawDataObject['2007-06-01-09-15'].body['70']['DIR'] # wind direction - # at 70 meters - -The body attribute of a Sample object may also be indexed directly on a Sample -object for the most convenient semantics: - - rawDataObject[15][0]['SPEED'] # wind speed at lowest altitude, 16th sample - rawDataObject['2007-06-01-09-15']['70']['DIR'] # wind direction, - # 70 meters, 9:15am -""" - -__author__ = 'Chris Calloway' -__email__ = 'cbc@unc.edu' -__copyright__ = 'Copyright 2007 UNC-CH Department of Marine Science' -__license__ = 'GPL2' - -import re - -class RawData(list): - - """Class to handle raw daily sodar file data. - - A chronologically ordered list of samples. - """ - - def __init__(self, data): - """Parse raw daily sodar file data.""" - super(RawData, self).__init__() - # Divide daily string into list of Samples separated by $. - self.extend([Sample(sample) - for sample in - [sample.strip() for sample in data.split('$')] - if sample.strip()]) - - def __getitem__(self, index): - """Allow sample retrieval by Sample time in header.""" - try: - return super(RawData,self).__getitem__(index) - except TypeError: - return self._find(index) - - def _find(self, index): - """Find Sample in RawData. - - Where sample time of form YYYY-MM-DD-HH-MM. - """ - - try: - year,month,day,hour,minute = index.split('-') - except ValueError: - raise ValueError('RawData index by date must be '\ - '"YYYY-MM-DD-HH-MM"') - except AttributeError: - raise AttributeError('RawData index by date must be '\ - '"YYYY-MM-DD-HH-MM"') - for sample in self: - try: - if sample.header['YEAR'].rjust(4,'0') != year: continue - if sample.header['MONTH'].rjust(2,'0') != month: continue - if sample.header['DAY'].rjust(2,'0') != day: continue - if sample.header['HOUR'].rjust(2,'0') != hour: continue - if sample.header['MIN'].rjust(2,'0') != minute: continue - return sample - except TypeError: # sample.header may not exist - continue - raise IndexError('RawData index out of range') - - -class Sample(object): - - """A single sample from raw daily sodar file data. - - (A header and a body attribute.) - """ - - def __init__(self,sample): - """Separate Sample into Header and Body objects.""" - super(Sample, self).__init__() - # first three groups of lines are the header; rest is body - samplePattern = re.compile(r'''(?P
.*?\n\n.*?\n\n.*?\n\n) - (?P.*$) - ''',re.DOTALL | re.VERBOSE) - self.__dict__.update(samplePattern.match(sample.strip()).groupdict()) - # getattr with default covers parsing invalid Samples - self.header = getattr(self, 'header', None) - if self.header is not None: - self.header = Header(self.header) - self.body = getattr(self, 'body', None) - if self.body is not None: - self.body = Body(self.body) - - def __getitem__(self, index): - """Index Sample by body or header attribute.""" - try: - return self.body[index] - except TypeError: # sample.body may not exist - raise IndexError('Sample index out of range') - except IndexError: # sample.body out of range - try: - return self.header[index] - except KeyError: # sample.header may not exist - raise IndexError('Sample index out of range') - - def data(self): - """Create a deep copy as a dictionary of header and body data.""" - return {'header':self.header.data(), - 'body':self.body.data()} - - -class Header(dict): - - """A raw sodar data sample header. - - (A dictionary of sample-wide parameters.) - """ - - def __init__(self, header): - - """Identify discreet header parameter names and values. - - Every other line contains parameter keys; - every other line contains parameter values. - """ - - super(Header, self).__init__() - headerLines = [headerLine.strip() - for headerLine in header.split('\n') - if headerLine.strip()] - #fix for bad match between names and values - self.update(dict(zip(" ".join(headerLines[::2]).split(), - " ".join(headerLines[1::2]).split()))) - - def data(self): - """Create a deep/shallow copy of the data as a dictionary.""" - return self.copy() - - -class Body(list): - - """A raw sodar data sample body. - - (A list of dictionariess at each altitude.) - """ - - def __init__(self, body): - - """Identify discreet body parameter names and values. - - The first line contains parameter keys; - the remaining lines contains parameter values, - one set of parameters for a single altitude per line. - """ - - super(Body, self).__init__() - bodyLines = [bodyLine.strip() - for bodyLine in body.split('\n') - if bodyLine.strip()] - bodyKeys = bodyLines[0].split() - #fix for bad match between names and values - self.extend([dict(zip(bodyKeys, bodyLine.split())) - for bodyLine in bodyLines[1:]]) - self.reverse() - - def __getitem__(self, index): - """Return raw altitude data by altitude string.""" - try: - return super(Body, self).__getitem__(index) - except TypeError: - return self._find(index) - - def _find(self, index): - """Find raw altitude data in Body.""" - for altitude in self: - try: - if altitude['ALT'] != index: continue - except KeyError: - continue - return altitude - raise IndexError('Body index out of range') - - def data(self): - """Create a deep copy of the data as a list of dictionaries.""" - return [altitude.copy() for altitude in self] - - -def _main(): - """Process as script from command line.""" - import urllib2 - try: - rawDataHandle = urllib2.urlopen('http://nemo.isis.unc.edu/'\ - 'data/nccoos/level0/ims/sodar/'\ - '2008_01/20080101.dat') - rawDataString = rawDataHandle.read() - rawDataHandle.close() - except: - raise IOError("Failure to read raw test data") - rawDataObject = RawData(rawDataString) - print rawDataObject['2008-01-01-09-15']['70']['SPEED'] - -if __name__ == "__main__": - _main() Index: sodar/branches/raw2proc-dev/sodar/utils/__init__.py =================================================================== --- sodar/trunk/sodar/utils/__init__.py (revision 132) +++ sodar/branches/raw2proc-dev/sodar/utils/__init__.py (revision 290) @@ -4,4 +4,4 @@ """ -__all__ = ['openAnything' - 'findMissing'] +__all__ = ['openAnything', + 'findMissing',]