#!/usr/bin/env python
# encoding: utf-8
"""
Top-level routines to compare two files.
Created by rayg Apr 2009.
Copyright (c) 2009 University of Wisconsin SSEC. All rights reserved.
"""
import os, sys, logging, re, subprocess, datetime
import imp as imp
from pprint import pprint, pformat
from numpy import *
import pkg_resources
from pycdf import CDFError
from subprocess import check_call as sh
import glance.io as io
import glance.delta as delta
import glance.plot as plot
import glance.plotcreatefns as plotcreate
import glance.report as report
from urllib import quote
LOG = logging.getLogger(__name__)
# these are the built in defaults for the settings
glance_setting_defaults = {'shouldIncludeReport': True,
'shouldIncludeImages': False,
'doFork': False,
'useThreadsToControlMemory': False,
'useSharedRangeForOriginal': False,
'noLonLatVars': False}
# these are the built in longitude/latitude defaults
glance_lon_lat_defaults = {'longitude': 'pixel_longitude',
'latitude': 'pixel_latitude',
'lon_lat_epsilon': 0.0,
'data_filter_function_lon_in_a': None,
'data_filter_function_lat_in_a': None,
'data_filter_function_lon_in_b': None,
'data_filter_function_lat_in_b': None
}
# these are the built in default settings for the variable analysis
glance_analysis_defaults = {'epsilon': 0.0,
'missing_value': None,
'epsilon_failure_tolerance': 0.0,
'nonfinite_data_tolerance': 0.0
}
def _cvt_names(namelist, epsilon, missing):
""""if variable names are of the format name:epsilon, yield name,epsilon, missing
otherwise yield name,default-epsilon,default-missing
"""
for name in namelist:
if ':' not in name:
yield name, epsilon
else:
n,e,m = name.split(':')
if not e: e = epsilon
else: e = float(e)
if not m: m = missing
else: m = float(m)
yield n, e, m
def _clean_path(string_path) :
"""
Return a clean form of the path without any '.', '..', or '~'
"""
if string_path is not None :
clean_path = os.path.abspath(os.path.expanduser(string_path))
else :
clean_path = string_path
return clean_path
def _parse_varnames(names, terms, epsilon=0.0, missing=None):
"""filter variable names and substitute default epsilon and missing settings if none provided
returns name,epsilon,missing triples
>>> _parse_varnames( ['foo','bar', 'baz', 'zoom', 'cat'], ['f..:0.5:-999', 'ba.*:0.001', 'c.t::-9999'], 1e-7 )
set([('foo', 0.5, -999.0), ('cat', 9.9999999999999995e-08, -9999.0), ('bar', 0.001, None), ('baz', 0.001, None)])
"""
terms = [x.split(':') for x in terms]
terms = [(re.compile(x[0]).match,x[1:]) for x in terms]
def _cvt_em(eps=None, mis=None):
eps = float(eps) if eps else epsilon
mis = float(mis) if mis else missing
return eps, mis
sel = [ ((x,)+_cvt_em(*em)) for x in names for (t,em) in terms if t(x) ]
return set(sel)
def _setup_file(fileNameAndPath, prefexText='', allowWrite=False) :
'''
open the provided file name/path and extract information on the md5sum and last modification time
optional prefext text may be passed in for informational output formatting
'''
# some info to return
fileInfo = {'path': fileNameAndPath}
# check to see if the path exists to be opened
if not (os.path.exists(fileNameAndPath)) :
LOG.warn("Requested file " + fileNameAndPath + " could not be opened because it does not exist.")
return None, fileInfo
# open the file
LOG.info(prefexText + " opening " + fileNameAndPath)
fileNameAndPath = os.path.abspath(os.path.expanduser(fileNameAndPath))
LOG.debug("User provided path after normalization and user expansion: " + fileNameAndPath)
fileObject = io.open(fileNameAndPath, allowWrite=allowWrite)
# get the file md5sum
tempSubProcess = subprocess.Popen("md5sum \'" + fileNameAndPath + "\'", shell=True, stdout=subprocess.PIPE)
fileInfo['md5sum'] = tempSubProcess.communicate()[0].split()[0]
LOG.info(prefexText + " file md5sum: " + str(fileInfo['md5sum']))
# get the last modified stamp
statsForFile = os.stat(fileNameAndPath)
fileInfo['lastModifiedTime'] = datetime.datetime.fromtimestamp(statsForFile.st_mtime).ctime() # should time zone be forced?
LOG.info (prefexText + " file was last modified: " + fileInfo['lastModifiedTime'])
return fileObject, fileInfo
def _check_file_names(fileAObject, fileBObject) :
"""
get information about the names in the two files and how they compare to each other
"""
# get information about the variables stored in the files
aNames = set(fileAObject())
bNames = set(fileBObject())
# get the variable names they have in common
commonNames = aNames.intersection(bNames)
# which names are unique to only one of the two files?
uniqueToANames = aNames - commonNames
uniqueToBNames = bNames - commonNames
return {'sharedVars': commonNames, 'uniqueToAVars': uniqueToANames, 'uniqueToBVars': uniqueToBNames}
def _resolve_names(fileAObject, fileBObject, defaultValues,
requestedNames, usingConfigFileFormat=False) :
"""
figure out which names the two files share and which are unique to each file, as well as which names
were requested and are in both sets
usingConfigFileFormat signals whether the requestedNames parameter will be in the form of the inputed
names from the command line or a more complex dictionary holding information about the names read in
from a configuration file
Note: if we ever need a variable with different names in file A and B to be comparable, this logic
will need to be changed.
"""
# look at the names present in the two files and compare them
nameComparison = _check_file_names(fileAObject, fileBObject)
# figure out which set should be selected based on the user requested names
fileCommonNames = nameComparison['sharedVars']
finalNames = {}
if (usingConfigFileFormat) :
# if the user didn't ask for any, try everything
if (len(requestedNames) is 0) :
finalFromCommandLine = _parse_varnames(fileCommonNames, ['.*'],
defaultValues['epsilon'], defaultValues['missing_value'])
for name, epsilon, missing in finalFromCommandLine :
# we'll use the variable's name as the display name for the time being
finalNames[name] = {}
# make sure we pick up any other controlling defaults
finalNames[name].update(defaultValues)
# but override the values that would have been determined by _parse_varnames
finalNames[name]['variable_name'] = name
finalNames[name]['epsilon'] = epsilon
# load the missing value if it was not provided
missing, missing_b = _get_missing_values_if_needed((fileAObject, fileBObject), name,
missing_value_A=missing, missing_value_B=missing)
finalNames[name]['missing_value'] = missing
finalNames[name]['missing_value_alt_in_b'] = missing_b
# otherwise just do the ones the user asked for
else :
# check each of the names the user asked for to see if it is either in the list of common names
# or, if the user asked for an alternate name mapping in file B, if the two mapped names are in
# files A and B respectively
for dispName in requestedNames :
# hang on to info on the current variable
currNameInfo = requestedNames[dispName]
# get the variable name
if 'variable_name' in currNameInfo :
name = currNameInfo['variable_name']
name_b = name
if ('alternate_name_in_B' in currNameInfo) :
name_b = currNameInfo['alternate_name_in_B']
if ( (name in fileCommonNames) and (not currNameInfo.has_key('alternate_name_in_B')) ) or \
( (currNameInfo.has_key('alternate_name_in_B') and
((name in nameComparison['uniqueToAVars']) or (name in fileCommonNames)) and
((name_b in nameComparison['uniqueToBVars']) or (name_b in fileCommonNames))) ) :
finalNames[dispName] = defaultValues.copy()
finalNames[dispName]['display_name'] = dispName
finalNames[dispName].update(currNameInfo)
# load the missing value if it was not provided
missing = finalNames[dispName]['missing_value']
if ('missing_value_alt_in_b' in finalNames[dispName]) :
missing_b = finalNames[dispName]['missing_value_alt_in_b']
else :
missing_b = missing
finalNames[dispName]['missing_value'], finalNames[dispName]['missing_value_alt_in_b'] = \
_get_missing_values_if_needed((fileAObject, fileBObject), name, name_b,
missing, missing_b)
else :
LOG.warn('No technical variable name was given for the entry described as "' + dispName + '". ' +
'Skipping this variable.')
else:
# format command line input similarly to the stuff from the config file
print (requestedNames)
finalFromCommandLine = _parse_varnames(fileCommonNames, requestedNames,
defaultValues['epsilon'], defaultValues['missing_value'])
for name, epsilon, missing in finalFromCommandLine :
## we'll use the variable's name as the display name for the time being
finalNames[name] = {}
# make sure we pick up any other controlling defaults
finalNames[name].update(defaultValues)
# but override the values that would have been determined by _parse_varnames
finalNames[name]['variable_name'] = name
finalNames[name]['epsilon'] = epsilon
# load the missing value if it was not provided
missing, missing_b = _get_missing_values_if_needed((fileAObject, fileBObject), name,
missing_value_A=missing, missing_value_B=missing)
finalNames[name]['missing_value'] = missing
finalNames[name]['missing_value_alt_in_b'] = missing_b
LOG.debug("Final selected set of variables to analyze:")
LOG.debug(str(finalNames))
return finalNames, nameComparison
def _get_missing_values_if_needed((fileA, fileB),
var_name, alt_var_name=None,
missing_value_A=None, missing_value_B=None) :
"""
get the missing values for two files based on the variable name(s)
if the alternate variable name is passed it will be used for the
second file in place of the primary variable name
"""
# if we don't have an alternate variable name, use the existing one
if alt_var_name is None :
alt_var_name = var_name
if missing_value_A is None :
missing_value_A = fileA.missing_value(var_name)
if missing_value_B is None :
missing_value_B = fileB.missing_value(alt_var_name)
return missing_value_A, missing_value_B
def _load_config_or_options(aPath, bPath, optionsSet, requestedVars = [ ]) :
"""
load information on how the user wants to run the command from a dictionary of options
and info on the files and variables to compare
note: the options may include a configuration file, which will override many of the
settings in the options
"""
# basic defaults for stuff we will need to return
runInfo = {}
runInfo.update(glance_setting_defaults) # get the default settings
if ('noLonLatVars' not in optionsSet) or (not optionsSet['noLonLatVars']):
runInfo.update(glance_lon_lat_defaults) # get the default lon/lat info
# by default, we don't have any particular variables to analyze
desiredVariables = { }
# use the built in default values, to start with
defaultsToUse = glance_analysis_defaults.copy()
requestedNames = None
# set up the paths, they can only come from the command line
paths = {}
paths['a'] = aPath
paths['b'] = bPath
paths['out'] = optionsSet['outputpath']
# the colocation selection can only come from the command line options
# TODO since this is really only coming from the user's selection of the call,
# this is ok for the moment, may want to reconsider later
runInfo['doColocate'] = ('doColocate' in optionsSet) and (optionsSet['doColocate'])
# check to see if the user wants to use a config file and if the path exists
requestedConfigFile = optionsSet['configFile']
usedConfigFile = False
if (not (requestedConfigFile is None)) and os.path.exists(requestedConfigFile):
LOG.info ("Using Config File Settings")
# this will handle relative paths
requestedConfigFile = os.path.abspath(os.path.expanduser(requestedConfigFile))
# split out the file base name and the file path
(filePath, fileName) = os.path.split(requestedConfigFile)
splitFileName = fileName.split('.')
fileBaseName = fileName[:-3] # remove the '.py' from the end
# hang onto info about the config file for later
runInfo['config_file_name'] = fileName
runInfo['config_file_path'] = requestedConfigFile
# load the file
LOG.debug ('loading config file: ' + str(requestedConfigFile))
glanceRunConfig = imp.load_module(fileBaseName, file(requestedConfigFile, 'U'),
filePath, ('.py' , 'U', 1))
# this is an exception, since it is not advertised to the user we don't expect it to be in the file
# (at least not at the moment, it could be added later and if they did happen to put it in the
# config file, it would override this line)
runInfo['shouldIncludeReport'] = not optionsSet['imagesOnly'] if 'imagesOnly' in optionsSet else False
runInfo['noLonLatVars'] = optionsSet['noLonLatVars'] if 'noLonLatVars' in optionsSet else False
# get everything from the config file
runInfo.update(glanceRunConfig.settings)
if ('noLonLatVars' not in runInfo) or (not runInfo['noLonLatVars']) :
runInfo.update(glanceRunConfig.lat_lon_info) # get info on the lat/lon variables
# get any requested names
requestedNames = glanceRunConfig.setOfVariables.copy()
# user selected defaults, if they omit any we'll still be using the program defaults
defaultsToUse.update(glanceRunConfig.defaultValues)
usedConfigFile = True
# if we didn't get the info from the config file for some reason
# (the user didn't want to, we couldn't, etc...) get it from the command line options
if not usedConfigFile:
LOG.info ('Using Command Line Settings')
# so get everything from the options directly
runInfo['shouldIncludeReport'] = not optionsSet['imagesOnly']
runInfo['shouldIncludeImages'] = not optionsSet['htmlOnly']
runInfo['doFork'] = optionsSet['doFork']
# only record these if we are using lon/lat
runInfo['noLonLatVars'] = optionsSet['noLonLatVars']
if not runInfo['noLonLatVars'] :
runInfo['latitude'] = optionsSet['latitudeVar'] or runInfo['latitude']
runInfo['longitude'] = optionsSet['longitudeVar'] or runInfo['longitude']
runInfo['lon_lat_epsilon'] = optionsSet['lonlatepsilon']
# get any requested names from the command line
requestedNames = requestedVars or ['.*']
# user selected defaults
defaultsToUse['epsilon'] = optionsSet['epsilon']
defaultsToUse['missing_value'] = optionsSet['missing']
# note: there is no way to set the tolerances from the command line
return paths, runInfo, defaultsToUse, requestedNames, usedConfigFile
def _get_and_analyze_lon_lat (fileObject,
latitudeVariableName, longitudeVariableName,
latitudeDataFilterFn=None, longitudeDataFilterFn=None) :
"""
get the longitude and latitude data from the given file, assuming they are in the given variable names
and analyze them to identify spacially invalid data (ie. data that would fall off the earth)
"""
# get the data from the file TODO, handle these exits out in the calling method?
LOG.info ('longitude name: ' + longitudeVariableName)
try :
longitudeData = array(fileObject[longitudeVariableName], dtype=float)
except CDFError :
LOG.warn ('Unable to retrieve longitude data. The variable name (' + longitudeVariableName +
') may not exist in this file or an error may have occured while attempting to' +
' access the data.')
LOG.warn ('Unable to continue analysis without longitude data. Aborting analysis.')
sys.exit(1)
LOG.info ('latitude name: ' + latitudeVariableName)
try :
latitudeData = array(fileObject[latitudeVariableName], dtype=float)
except CDFError :
LOG.warn ('Unable to retrieve latitude data. The variable name (' + latitudeVariableName +
') may not exist in this file or an error may have occured while attempting to' +
' access the data.')
LOG.warn ('Unable to continue analysis without latitude data. Aborting analysis.')
sys.exit(1)
# if we have filters, use them
if not (latitudeDataFilterFn is None) :
latitudeData = latitudeDataFilterFn(latitudeData)
LOG.debug ('latitude size after application of filter: ' + str(latitudeData.shape))
if not (longitudeDataFilterFn is None) :
longitudeData = longitudeDataFilterFn(longitudeData)
LOG.debug ('longitude size after application of filter: ' + str(longitudeData.shape))
# we are going to have issues with our comparision if they aren't the same shape
LOG.debug('latitude shape: ' + str(latitudeData.shape))
LOG.debug('longitude shape: ' + str(longitudeData.shape))
assert (latitudeData.shape == longitudeData.shape)
# build a mask of our spacially invalid data TODO, load actual valid range attributes?
invalidLatitude = (latitudeData < -90) | (latitudeData > 90) | ~isfinite(latitudeData)
invalidLongitude = (longitudeData < -180) | (longitudeData > 360) | ~isfinite(longitudeData)
spaciallyInvalidMask = invalidLatitude | invalidLongitude
# analyze our spacially invalid data
percentageOfSpaciallyInvalidPts, numberOfSpaciallyInvalidPts = _get_percentage_from_mask(spaciallyInvalidMask)
return longitudeData, latitudeData, spaciallyInvalidMask, {
'totNumInvPts': numberOfSpaciallyInvalidPts,
'perInvPts': percentageOfSpaciallyInvalidPts
}
def _get_percentage_from_mask(dataMask) :
"""
given a mask that marks the elements we want the percentage of as True (and is the size of our original data),
figure out what percentage of the whole they are
"""
numMarkedDataPts = sum(dataMask)
totalDataPts = dataMask.size
# avoid dividing by 0
if totalDataPts is 0 :
return 0.0, 0
percentage = 100.0 * float(numMarkedDataPts) / float(totalDataPts)
return percentage, numMarkedDataPts
def _check_lon_lat_equality(longitudeA, latitudeA,
longitudeB, latitudeB,
ignoreMaskA, ignoreMaskB,
llepsilon, doMakeImages, outputPath) :
"""
check to make sure the longitude and latitude are equal everywhere that's not in the ignore masks
if they are not and doMakeImages was passed as True, generate appropriate figures to show where
return the number of points where they are not equal (0 would mean they're the same)
"""
# first of all, if the latitude and longitude are not the same shape, then things can't ever be "equal"
if (longitudeA.shape != longitudeB.shape) | (latitudeA.shape != latitudeB.shape) :
return None
lon_lat_not_equal_points_count = 0
lon_lat_not_equal_points_percent = 0.0
# get information about how the latitude and longitude differ
longitudeDiff, finiteLongitudeMask, _, _, lon_not_equal_mask, _, _, _ = delta.diff(longitudeA, longitudeB,
llepsilon,
(None, None),
(ignoreMaskA, ignoreMaskB))
latitudeDiff, finiteLatitudeMask, _, _, lat_not_equal_mask, _, _, _ = delta.diff(latitudeA, latitudeB,
llepsilon,
(None, None),
(ignoreMaskA, ignoreMaskB))
lon_lat_not_equal_mask = lon_not_equal_mask | lat_not_equal_mask
lon_lat_not_equal_points_count = sum(lon_lat_not_equal_mask)
lon_lat_not_equal_points_percent = (float(lon_lat_not_equal_points_count) / float(lon_lat_not_equal_mask.size)) * 100.0
# if we have unequal points, create user legible info about the problem
if (lon_lat_not_equal_points_count > 0) :
LOG.warn("Possible mismatch in values stored in file a and file b longitude and latitude values."
+ " Depending on the degree of mismatch, some data value comparisons may be "
+ "distorted or spacially nonsensical.")
# if we are making images, make two showing the invalid lons/lats
if (doMakeImages) :
if (len(longitudeA[~ignoreMaskA]) > 0) and (len(latitudeA[~ignoreMaskA]) > 0) :
plot.plot_and_save_spacial_trouble(longitudeA, latitudeA,
lon_lat_not_equal_mask,
ignoreMaskA,
"A", "Lon./Lat. Points Mismatched between A and B\n" +
"(Shown in A)",
"LonLatMismatch",
outputPath, True)
if (len(longitudeB[~ignoreMaskB]) > 0) and (len(latitudeB[~ignoreMaskB]) > 0) :
plot.plot_and_save_spacial_trouble(longitudeB, latitudeB,
lon_lat_not_equal_mask,
ignoreMaskB,
"B", "Lon./Lat. Points Mismatched between A and B\n" +
"(Shown in B)",
"LonLatMismatch",
outputPath, True)
# setup our return data
returnInfo = {}
returnInfo['lon_lat_not_equal_points_count'] = lon_lat_not_equal_points_count
returnInfo['lon_lat_not_equal_points_percent'] = lon_lat_not_equal_points_percent
return returnInfo
def _compare_spatial_invalidity(invalid_in_a_mask, invalid_in_b_mask, spatial_info,
longitude_a, longitude_b, latitude_a, latitude_b,
do_include_images, output_path) :
"""
Given information about where the two files are spatially invalid, figure
out what invalidity they share and save information or plots for later use
also build a shared longitude/latitude based on A but also including valid
points in B
"""
# for convenience,
# make a combined mask
invalid_in_common_mask = invalid_in_a_mask | invalid_in_b_mask
# make a "common" latitude based on A
longitude_common = longitude_a
latitude_common = latitude_a
# compare our spacialy invalid info
spatial_info['perInvPtsInBoth'] = spatial_info['file A']['perInvPts']
# a default that will hold if the two files have the same spatially invalid pts
if not all(invalid_in_a_mask.ravel() == invalid_in_b_mask.ravel()) :
LOG.info("Mismatch in number of spatially invalid points. " +
"Files may not have corresponding data where expected.")
# figure out which points are only valid in one of the two files
valid_only_in_mask_a = (~invalid_in_a_mask) & invalid_in_b_mask
spatial_info['file A']['numInvPts'] = sum(valid_only_in_mask_a.ravel())
valid_only_in_mask_b = (~invalid_in_b_mask) & invalid_in_a_mask
spatial_info['file B']['numInvPts'] = sum(valid_only_in_mask_b.ravel())
# so how many do they have together?
spatial_info['perInvPtsInBoth'] = _get_percentage_from_mask(invalid_in_common_mask)[0]
# make a "clean" version of the lon/lat
longitude_common[valid_only_in_mask_a] = longitude_a[valid_only_in_mask_a]
longitude_common[valid_only_in_mask_b] = longitude_b[valid_only_in_mask_b]
latitude_common [valid_only_in_mask_a] = latitude_a [valid_only_in_mask_a]
latitude_common [valid_only_in_mask_b] = latitude_b [valid_only_in_mask_b]
# plot the points that are only valid one file and not the other
if ((spatial_info['file A']['numInvPts'] > 0) and (do_include_images) and
(len(longitude_a[~invalid_in_a_mask]) > 0) and (len(latitude_a[~invalid_in_a_mask]) > 0)) :
plot.plot_and_save_spacial_trouble(longitude_a, latitude_a,
valid_only_in_mask_a,
invalid_in_a_mask,
"A", "Points only valid in\nFile A\'s longitude & latitude",
"SpatialMismatch",
output_path, True)
if ((spatial_info['file B']['numInvPts'] > 0) and (do_include_images) and
(len(longitude_b[~invalid_in_b_mask]) > 0) and (len(latitude_b[~invalid_in_b_mask]) > 0)
) :
plot.plot_and_save_spacial_trouble(longitude_b, latitude_b,
valid_only_in_mask_b,
invalid_in_b_mask,
"B", "Points only valid in\nFile B\'s longitude & latitude",
"SpatialMismatch",
output_path, True)
return invalid_in_common_mask, spatial_info, longitude_common, latitude_common
def _handle_lon_lat_info (lon_lat_settings, a_file_object, b_file_object, output_path,
should_make_images=False, should_check_equality=True) :
"""
Manage loading and comparing longitude and latitude information for two files
Note: if the error message is returned as anything but None, something uncrecoverable
occured while trying to get the lon/lat info. TODO, replace this with a proper thrown exception
"""
# a place to save some general stats about our lon/lat data
spatialInfo = { }
# a place to put possible error messages TODO remove this in favor of an exception
error_msg = None
# if there is no lon/lat specified, stop now
if ( ('longitude' not in lon_lat_settings) or ('latitude' not in lon_lat_settings)
or (('noLonLatVars' in lon_lat_settings) and lon_lat_settings['noLonLatVars']) ) :
return { }, spatialInfo, error_msg
# if we should not be comparing against the logitude and latitude, stop now
print ('lon_lat_settings: ' + str(lon_lat_settings))
# figure out the names to be used for the longitude and latitude variables
a_longitude_name = lon_lat_settings['longitude']
a_latitude_name = lon_lat_settings['latitude']
b_longitude_name = a_longitude_name
b_latitude_name = a_latitude_name
# if we have alternate b names, use those for b instead
if ('longitude_alt_name_in_b' in lon_lat_settings) :
b_longitude_name = lon_lat_settings['longitude_alt_name_in_b']
if ( 'latitude_alt_name_in_b' in lon_lat_settings):
b_latitude_name = lon_lat_settings['latitude_alt_name_in_b']
# if we need to load our lon/lat from different files, open those files
# for the a file, do we have an alternate?
file_for_a_lon_lat = a_file_object
if ('a_lon_lat_from_alt_file' in lon_lat_settings) :
LOG.info("Loading alternate file (" + lon_lat_settings['a_lon_lat_from_alt_file'] + ") for file a longitude/latitude.")
file_for_a_lon_lat, _ = _setup_file(lon_lat_settings['a_lon_lat_from_alt_file'], "\t")
# for the b file, do we have an alternate?
file_for_b_lon_lat = b_file_object
if ('b_lon_lat_from_alt_file' in lon_lat_settings) :
LOG.info("Loading alternate file (" + lon_lat_settings['b_lon_lat_from_alt_file'] + ") for file b longitude/latitude.")
file_for_b_lon_lat, _ = _setup_file(lon_lat_settings['b_lon_lat_from_alt_file'], "\t")
# load our longitude and latitude and do some analysis on them
longitude_a, latitude_a, spaciallyInvalidMaskA, spatialInfo['file A'] = \
_get_and_analyze_lon_lat (file_for_a_lon_lat, a_latitude_name, a_longitude_name,
lon_lat_settings['data_filter_function_lat_in_a'], lon_lat_settings['data_filter_function_lon_in_a'])
longitude_b, latitude_b, spaciallyInvalidMaskB, spatialInfo['file B'] = \
_get_and_analyze_lon_lat (file_for_b_lon_lat, b_latitude_name, b_longitude_name,
lon_lat_settings['data_filter_function_lat_in_b'], lon_lat_settings['data_filter_function_lon_in_b'])
# if we need to, test the level of equality of the "valid" values in our lon/lat
if should_check_equality :
moreSpatialInfo = _check_lon_lat_equality(longitude_a, latitude_a, longitude_b, latitude_b,
spaciallyInvalidMaskA, spaciallyInvalidMaskB,
lon_lat_settings['lon_lat_epsilon'],
should_make_images, output_path)
# if we got the worst type of error result from the comparison this data is too dissimilar to continue
if moreSpatialInfo is None :
error_msg = ("Unable to reconcile sizes of longitude and latitude for variables "
+ str(lon_lat_settings['longitude']) + str(longitude_a.shape) + "/"
+ str(lon_lat_settings['latitude']) + str(latitude_a.shape) + " in file A and variables "
+ str(b_longitude_name) + str(longitude_b.shape) + "/"
+ str(b_latitude_name) + str(latitude_b.shape) + " in file B. Aborting attempt to compare files.")
return { }, { }, error_msg # things have gone wrong
# update our existing spatial information
spatialInfo.update(moreSpatialInfo)
# compare our spatially invalid info to see if the two files have invalid longitudes and latitudes in the same places
spaciallyInvalidMask, spatialInfo, longitude_common, latitude_common = \
_compare_spatial_invalidity(spaciallyInvalidMaskA, spaciallyInvalidMaskB, spatialInfo,
longitude_a, longitude_b, latitude_a, latitude_b,
should_make_images, output_path)
else:
spaciallyInvalidMask = None
longitude_common = None
latitude_common = None
return {'a': {"lon": longitude_a, "lat": latitude_a, "inv_mask": spaciallyInvalidMaskA},
'b': {"lon": longitude_b, "lat": latitude_b, "inv_mask": spaciallyInvalidMaskB},
'common': {"lon": longitude_common, "lat": latitude_common, "inv_mask": spaciallyInvalidMask} }, \
spatialInfo, error_msg
def _open_and_process_files (args, numFilesExpected):
"""
open files listed in the args and get information about the variables in them
"""
# get all the file names
fileNames = args[:numFilesExpected]
# open all the files & get their variable names
files = {}
commonNames = None
for fileName in fileNames:
LOG.info("opening %s" % fileName)
files[fileName] = {}
tempFileObject = (io.open(fileName))
files[fileName]['fileObject'] = tempFileObject
tempNames = set(tempFileObject())
LOG.debug ('variable names for ' + fileName + ': ' + str(tempNames))
files[fileName]['varNames'] = tempNames
if commonNames is None :
commonNames = tempNames
else :
commonNames = commonNames.intersection(tempNames)
files['commonVarNames'] = commonNames
return files
def _check_pass_or_fail(varRunInfo, variableStats, defaultValues) :
"""
Check whether the variable passed analysis, failed analysis, or
did not need to be quantitatively tested
also returns information about the fractions of failure
"""
didPass = None
# get our tolerance values
# get the tolerance for failures in comparison compared to epsilon
epsilonTolerance = None
if ('epsilon_failure_tolerance' in varRunInfo) :
epsilonTolerance = varRunInfo['epsilon_failure_tolerance']
else :
epsilonTolerance = defaultValues['epsilon_failure_tolerance']
# get the tolerance for failures in amount of nonfinite data
# found in spatially valid areas
nonfiniteTolerance = None
if ('nonfinite_data_tolerance' in varRunInfo) :
nonfiniteTolerance = varRunInfo['nonfinite_data_tolerance']
else :
nonfiniteTolerance = defaultValues['nonfinite_data_tolerance']
# test to see if we passed or failed
# check for our epsilon tolerance
failed_fraction = 0.0
if not (epsilonTolerance is None) :
failed_fraction = variableStats['Numerical Comparison Statistics']['diff_outside_epsilon_fraction']
didPass = failed_fraction <= epsilonTolerance
# check to see if it failed on nonfinite data
non_finite_diff_fraction = 0.0
if not (nonfiniteTolerance is None) :
non_finite_diff_fraction = variableStats['Finite Data Statistics']['finite_in_only_one_fraction']
passedNonFinite = non_finite_diff_fraction <= nonfiniteTolerance
# combine the two test results
if (didPass is None) :
didPass = passedNonFinite
else :
didPass = didPass and passedNonFinite
return didPass, failed_fraction, non_finite_diff_fraction
def _get_run_identification_info( ) :
"""
get info about what user/machine/version of glance is being used
"""
info_to_return = { }
# get info on who's doing the run and where
info_to_return['machine'] = os.uname()[1] # the name of the machine running the report
info_to_return['user'] = os.getenv("LOGNAME") #os.getlogin() # the name of the user running the report
info_to_return['version'] = _get_glance_version_string()
return info_to_return
def _get_glance_version_string() :
version_num = pkg_resources.require('glance')[0].version
return "glance, version " + str(version_num)
def _get_name_info_for_variable(original_display_name, variable_run_info) :
"""
based on the variable run info, figure out the various names for
the variable and return them
the various names are:
technical_name - the name the variable is listed under in the file
b_variable_technical_name - the name the variable is listed under in the b file (may be the same as technical_name)
explanation_name - the more verbose name that will be shown to the user to identify the variable
original_display_name - the display name given by the user to describe the variable
"""
# figure out the various name related info
technical_name = variable_run_info['variable_name']
explanation_name = technical_name # for now, will add to this later
# if B has an alternate variable name, figure that out
b_variable_technical_name = technical_name
if 'alternate_name_in_B' in variable_run_info :
b_variable_technical_name = variable_run_info['alternate_name_in_B']
# put both names in our explanation
explanation_name = explanation_name + " / " + b_variable_technical_name
# show both the display and current explanation names if they differ
if not (original_display_name == explanation_name) :
explanation_name = original_display_name + ' (' + explanation_name + ')'
return technical_name, b_variable_technical_name, explanation_name
def _load_variable_data(fileObject, variableNameInFile,
dataFilter=None,
variableToFilterOn=None,
variableBasedFilter=None,
fileDescriptionForDisplay="file") :
"""
load data for a variable from a file
optionally filter the variable data based on a data filter or another variable
dataFilter must be in the form of (lambda data: some manipulation returning the new data)
variableBasedFilter must be in the form of (lambda data, filterData: some manipulation returning the new data))
"""
# get the data for the variable
LOG.debug("loading basic data for variable " + variableNameInFile + " from " + fileDescriptionForDisplay)
variableData = fileObject[variableNameInFile]
# apply the basic filter if there is one
if dataFilter is not None :
LOG.debug ("applying filter function to data from " + fileDescriptionForDisplay + " for variable " + variableNameInFile)
variableData = dataFilter(variableData)
# if we've got another variable to filter on, do that
if (variableToFilterOn is not None) and (variableBasedFilter is not None) :
LOG.debug ("filtering data from " + fileDescriptionForDisplay + " for variable " + variableNameInFile
+ " based on additional data from variable " + variableToFilterOn)
dataToFilterOn = fileObject[variableToFilterOn]
variableData = variableBasedFilter(variableData, dataToFilterOn)
return variableData
def _uri_needs_rsync(uri_to_check) :
"""
check if the uri requires an rsync in order to access the data
this will return some false positives if you phrase local uri's with the machine name
for ex. you are on the machine "lotus" and you use the path "rsync:://lotus/data/"
"""
return not os.path.exists(uri_to_check)
def _get_UV_info_from_magnitude_direction_info(fileObject, magnitudeName, directionName, invalidMask=None) :
"""
If there are magnitude and direction names, load that information and calculate the u and v that correspond to it
"""
# if we don't have magnitude and direction, we can't calculate the U and V values
if (magnitudeName is None) or (directionName is None) :
return None, None
# load the magnitude and direction data sets
magnitude = _load_variable_data(fileObject, magnitudeName)
direction = _load_variable_data(fileObject, directionName)
# convert the magnitude and direction data into u and v vectors
uData, vData = delta.convert_mag_dir_to_U_V_vector(magnitude, direction, invalidMask=invalidMask)
return uData, vData
def rsync_or_copy_files (list_of_files, target_directory='.', additionalFileNameSuffix='') :
"""
If the files in the list are remote, rsync them, otherwise, just copy
them to the target directory
"""
newPaths = [ ]
for file_uri in list_of_files :
fileName = os.path.split(file_uri)[1]
baseFile, ext = os.path.splitext(fileName)
newPath = os.path.join(target_directory, baseFile + additionalFileNameSuffix + ext)
newPaths.append(newPath)
if _uri_needs_rsync(file_uri) :
cmd = ['rsync', '-Cuav', file_uri, newPath]
else :
cmd = ['cp', os.path.abspath(file_uri), newPath]
LOG.debug('running ' + ' '.join(cmd))
sh(cmd)
return newPaths
def colocateToFile_library_call(a_path, b_path, var_list=[ ],
options_set={ },
# todo, this doesn't yet do anything
do_document=False,
# todo, the output channel does nothing at the moment
output_channel=sys.stdout) :
"""
this method handles the actual work of the colocateData command line tool
and can be used as a library routine.
TODO, properly document the options
"""
# load the user settings from either the command line or a user defined config file
pathsTemp, runInfo, defaultValues, requestedNames, usedConfigFile = _load_config_or_options(a_path, b_path,
options_set,
requestedVars = var_list)
# deal with the input and output files
if not (os.path.isdir(pathsTemp['out'])) :
LOG.info("Specified output directory (" + pathsTemp['out'] + ") does not exist.")
LOG.info("Creating output directory.")
os.makedirs(pathsTemp['out'])
# make copies of the input files for colocation TODO, fix paths
[pathsTemp['a'], pathsTemp['b']] = rsync_or_copy_files ([pathsTemp['a'], pathsTemp['b']],
target_directory=pathsTemp['out'],
additionalFileNameSuffix='-collocated')
# open the files
LOG.info("Processing File A:")
aFile, _ = _setup_file(pathsTemp['a'], "\t", allowWrite = True)
if aFile is None:
LOG.warn("Unable to continue with comparison because file a (" + pathsTemp['a'] + ") could not be opened.")
sys.exit(1)
LOG.info("Processing File B:")
bFile, _ = _setup_file(pathsTemp['b'], "\t", allowWrite = True)
if bFile is None:
LOG.warn("Unable to continue with comparison because file b (" + pathsTemp['b'] + ") could not be opened.")
sys.exit(1)
# get information about the names the user requested
finalNames, nameStats = _resolve_names(aFile, bFile,
defaultValues,
requestedNames, usedConfigFile)
# return for lon_lat_data variables will be in the form
#{"lon": longitude_data, "lat": latitude_data, "inv_mask": spaciallyInvalidMaskData}
# or { } if there is no lon/lat info
lon_lat_data, _, fatalErrorMsg = _handle_lon_lat_info (runInfo, aFile, bFile, pathsTemp['out'], should_check_equality=False)
if fatalErrorMsg is not None :
LOG.warn(fatalErrorMsg)
sys.exit(1)
# handle the longitude and latitude colocation
LOG.info("Colocating raw longitude and latitude information")
aColocationInfomation, bColocationInformation, totalNumberOfMatchedPoints = \
delta.create_colocation_mapping_within_epsilon((lon_lat_data['a']['lon'], lon_lat_data['a']['lat']),
(lon_lat_data['b']['lon'], lon_lat_data['b']['lat']),
runInfo['lon_lat_epsilon'],
invalidAMask=lon_lat_data['a']['inv_mask'],
invalidBMask=lon_lat_data['b']['inv_mask'])
(colocatedLongitude, colocatedLatitude, (numMultipleMatchesInA, numMultipleMatchesInB)), \
(unmatchedALongitude, unmatchedALatitude), \
(unmatchedBLongitude, unmatchedBLatitude) = \
delta.create_colocated_lonlat_with_lon_lat_colocation(aColocationInfomation, bColocationInformation,
totalNumberOfMatchedPoints,
lon_lat_data['a']['lon'], lon_lat_data['a']['lat'],
lon_lat_data['b']['lon'], lon_lat_data['b']['lat'])
# TODO, based on unmatched, issue warnings and record info in the file?
LOG.debug("colocated shape of the longitude: " + str(colocatedLongitude.shape))
LOG.debug("colocated shape of the latitude: " + str(colocatedLatitude.shape))
LOG.debug(str(numMultipleMatchesInA) + " lon/lat pairs contain A points used for multiple matches.")
LOG.debug(str(numMultipleMatchesInB) + " lon/lat pairs contain B points used for multiple matches.")
LOG.debug(str(len(unmatchedALatitude)) + " A lon/lat points could not be matched.")
LOG.debug(str(len(unmatchedBLatitude)) + " B lon/lat points could not be matched.")
# go through each of the possible variables in our files
# and do our colocation for whichever ones we can
for displayName in finalNames:
# pull out the information for this variable analysis run
varRunInfo = finalNames[displayName].copy()
# get the various names
technical_name, b_variable_technical_name, \
explanationName = _get_name_info_for_variable(displayName, varRunInfo)
print('analyzing: ' + explanationName + ')')
# load the variable data
aData = _load_variable_data(aFile, technical_name,
dataFilter = varRunInfo['data_filter_function_a'] if 'data_filter_function_a' in varRunInfo else None,
variableToFilterOn = varRunInfo['variable_to_filter_on_a'] if 'variable_to_filter_on_a' in varRunInfo else None,
variableBasedFilter = varRunInfo['variable_based_filter_a'] if 'variable_based_filter_a' in varRunInfo else None,
fileDescriptionForDisplay = "file A")
bData = _load_variable_data(bFile, b_variable_technical_name,
dataFilter = varRunInfo['data_filter_function_b'] if 'data_filter_function_b' in varRunInfo else None,
variableToFilterOn = varRunInfo['variable_to_filter_on_b'] if 'variable_to_filter_on_b' in varRunInfo else None,
variableBasedFilter = varRunInfo['variable_based_filter_b'] if 'variable_based_filter_b' in varRunInfo else None,
fileDescriptionForDisplay = "file B")
# colocate the data for this variable if we have longitude/latitude data
if (len(lon_lat_data.keys()) > 0) and runInfo['doColocate'] :
# figure out the invalid masks
invalidA = lon_lat_data['a']['inv_mask'] | (aData == varRunInfo['missing_value'])
invalidB = lon_lat_data['b']['inv_mask'] | (bData == varRunInfo['missing_value_alt_in_b'])
# match up our points in A and B
(aData, bData, (numberOfMultipleMatchesInA, numberOfMultipleMatchesInB)), \
(aUnmatchedData, unmatchedALongitude, unmatchedALatitude), \
(bUnmatchedData, unmatchedBLongitude, unmatchedBLatitude) = \
delta.create_colocated_data_with_lon_lat_colocation(aColocationInfomation, bColocationInformation,
colocatedLongitude, colocatedLatitude,
aData, bData,
missingData=varRunInfo['missing_value'],
altMissingDataInB=varRunInfo['missing_value_alt_in_b'],
# TODO, should missing data be considered?
invalidAMask=invalidA,
invalidBMask=invalidB)
LOG.debug(str(numberOfMultipleMatchesInA) + " data pairs contain A data points used for multiple matches.")
LOG.debug(str(numberOfMultipleMatchesInB) + " data pairs contain B data points used for multiple matches.")
LOG.debug(str(len(aUnmatchedData)) + " A data points could not be matched.")
LOG.debug(str(len(bUnmatchedData)) + " B data points could not be matched.")
# save the colocated data information in the output files
# all the a file information
aFile.create_new_variable(technical_name + '-colocated', # TODO, how should this suffix be handled?
missingvalue = varRunInfo['missing'] if 'missing' in varRunInfo else None,
data = aData,
variabletocopyattributesfrom = technical_name)
aFile.add_attribute_data_to_variable(technical_name + '-colocated', 'number of multiple matches', numberOfMultipleMatchesInA)
aFile.add_attribute_data_to_variable(technical_name + '-colocated', 'number of unmatched points', len(aUnmatchedData))
# all the b file information
bFile.create_new_variable(b_variable_technical_name + '-colocated', # TODO, how should this suffix be handled?
missingvalue = varRunInfo['missing_value_alt_in_b'] if 'missing_value_alt_in_b' in varRunInfo else None,
data = bData,
variabletocopyattributesfrom = b_variable_technical_name)
bFile.add_attribute_data_to_variable(b_variable_technical_name + '-colocated', 'number of multiple matches', numberOfMultipleMatchesInB)
bFile.add_attribute_data_to_variable(b_variable_technical_name + '-colocated', 'number of unmatched points', len(bUnmatchedData))
# TODO, any additional statistics
else :
LOG.debug(explanationName + " was not selected for colocation and will be ignored.")
# the end of the loop to examine all the variables
# we're done with the files, so close them up
aFile.close()
bFile.close()
return
def reportGen_library_call (a_path, b_path, var_list=[ ],
options_set={ },
# todo, this doesn't yet do anything
do_document=False,
# todo, the output channel does nothing at the moment
output_channel=sys.stdout) :
"""
this method handles the actual work of the reportGen command line tool
and can also be used as a library routine, pass in the slightly parsed
command line input, or call it as a library function... be sure to fill
out the options
TODO at the moment the options are very brittle and need to be fully filled
or this method will fail badly (note: the addition of some glance defaults
has minimized the problem, but you still need to be careful when dealing with
optional boolean values. this needs more work.)
"""
# load the user settings from either the command line or a user defined config file
pathsTemp, runInfo, defaultValues, requestedNames, usedConfigFile = _load_config_or_options(a_path, b_path,
options_set,
requestedVars = var_list)
# note some of this information for debugging purposes
LOG.debug('paths: ' + str(pathsTemp))
LOG.debug('defaults: ' + str(defaultValues))
LOG.debug('run information: ' + str(runInfo))
# if we wouldn't generate anything, just stop now
if (not runInfo['shouldIncludeImages']) and (not runInfo['shouldIncludeReport']) :
LOG.warn("User selection of no image generation and no report generation will result in no " +
"content being generated. Aborting generation function.")
return
# hang onto info to identify who/what/when/where/etc. the report is being run by/for
runInfo.update(_get_run_identification_info( ))
# deal with the input and output files
if not (os.path.isdir(pathsTemp['out'])) :
LOG.info("Specified output directory (" + pathsTemp['out'] + ") does not exist.")
LOG.info("Creating output directory.")
os.makedirs(pathsTemp['out'])
# open the files
files = {}
LOG.info("Processing File A:")
aFile, files['file A'] = _setup_file(pathsTemp['a'], "\t")
if aFile is None:
LOG.warn("Unable to continue with comparison because file a (" + pathsTemp['a'] + ") could not be opened.")
sys.exit(1)
LOG.info("Processing File B:")
bFile, files['file B'] = _setup_file(pathsTemp['b'], "\t")
if bFile is None:
LOG.warn("Unable to continue with comparison because file b (" + pathsTemp['b'] + ") could not be opened.")
sys.exit(1)
# get information about the names the user requested
finalNames, nameStats = _resolve_names(aFile, bFile,
defaultValues,
requestedNames, usedConfigFile)
LOG.debug("output dir: " + str(pathsTemp['out']))
# return for lon_lat_data variables will be in the form
#{"lon": longitude_data, "lat": latitude_data, "inv_mask": spaciallyInvalidMaskData}
# or { } if there is no lon/lat info
lon_lat_data, spatialInfo, fatalErrorMsg = _handle_lon_lat_info (runInfo,
aFile, bFile,
pathsTemp['out'],
should_make_images = runInfo["shouldIncludeImages"])
if fatalErrorMsg is not None :
LOG.warn(fatalErrorMsg)
sys.exit(1)
# if there is an approved lon/lat shape, hang on to that for future checks
good_shape_from_lon_lat = None
if len(lon_lat_data.keys()) > 0:
good_shape_from_lon_lat = lon_lat_data['common']['lon'].shape
# this will hold information for the summary report
# it will be in the form
# [displayName] = {"passEpsilonPercent": percent ok with epsilon,
# "finite_similar_percent": percent with the same finiteness,
# "epsilon": epsilon value used}
variableComparisons = {}
# go through each of the possible variables in our files
# and make a report section with images for whichever ones we can
for displayName in finalNames:
# pull out the information for this variable analysis run
varRunInfo = finalNames[displayName].copy()
# get the various names
technical_name, b_variable_technical_name, \
explanationName = _get_name_info_for_variable(displayName, varRunInfo)
print('analyzing: ' + explanationName + ')')
# load the variable data
aData = _load_variable_data(aFile, technical_name,
dataFilter = varRunInfo['data_filter_function_a'] if 'data_filter_function_a' in varRunInfo else None,
variableToFilterOn = varRunInfo['variable_to_filter_on_a'] if 'variable_to_filter_on_a' in varRunInfo else None,
variableBasedFilter = varRunInfo['variable_based_filter_a'] if 'variable_based_filter_a' in varRunInfo else None,
fileDescriptionForDisplay = "file A")
bData = _load_variable_data(bFile, b_variable_technical_name,
dataFilter = varRunInfo['data_filter_function_b'] if 'data_filter_function_b' in varRunInfo else None,
variableToFilterOn = varRunInfo['variable_to_filter_on_b'] if 'variable_to_filter_on_b' in varRunInfo else None,
variableBasedFilter = varRunInfo['variable_based_filter_b'] if 'variable_based_filter_b' in varRunInfo else None,
fileDescriptionForDisplay = "file B")
# pre-check if this data should be plotted and if it should be compared to the longitude and latitude
include_images_for_this_variable = ((not('shouldIncludeImages' in runInfo)) or (runInfo['shouldIncludeImages']))
if 'shouldIncludeImages' in varRunInfo :
include_images_for_this_variable = varRunInfo['shouldIncludeImages']
do_not_test_with_lon_lat = (not include_images_for_this_variable) or (len(lon_lat_data.keys()) <= 0)
# handle vector data
isVectorData = ( ('magnitudeName' in varRunInfo) and ('directionName' in varRunInfo) and
('magnitudeBName' in varRunInfo) and ('directionBName' in varRunInfo) )
# check if this data can be displayed but
# don't compare lon/lat sizes if we won't be plotting
if ( (aData.shape == bData.shape)
and
( do_not_test_with_lon_lat
or
((aData.shape == good_shape_from_lon_lat) and (bData.shape == good_shape_from_lon_lat)) ) ) :
# check to see if there is a directory to put information about this variable in,
# if not then create it
variableDir = os.path.join(pathsTemp['out'], './' + displayName)
varRunInfo['variable_dir'] = variableDir
varRunInfo['variable_report_path_escaped'] = quote(os.path.join(displayName, 'index.html'))
LOG.debug ("Directory selected for variable information: " + varRunInfo['variable_report_path_escaped'])
if not (os.path.isdir(variableDir)) :
LOG.debug("Variable directory (" + variableDir + ") does not exist.")
LOG.debug("Creating variable directory.")
os.makedirs(variableDir)
# figure out the masks we want, and then do our statistical analysis
mask_a_to_use = None
mask_b_to_use = None
if not do_not_test_with_lon_lat :
mask_a_to_use = lon_lat_data['a']['inv_mask']
mask_b_to_use = lon_lat_data['b']['inv_mask']
variable_stats = delta.summarize(aData, bData,
varRunInfo['epsilon'],
(varRunInfo['missing_value'],
varRunInfo['missing_value_alt_in_b']),
mask_a_to_use, mask_b_to_use)
# add a little additional info to our variable run info before we squirrel it away
varRunInfo['time'] = datetime.datetime.ctime(datetime.datetime.now()) # todo is this needed?
didPass, epsilon_failed_fraction, non_finite_fail_fraction = _check_pass_or_fail(varRunInfo,
variable_stats,
defaultValues)
varRunInfo['did_pass'] = didPass
# based on the settings and whether the variable passsed or failed,
# should we include images for this variable?
if ('only_plot_on_fail' in varRunInfo) and varRunInfo['only_plot_on_fail'] :
include_images_for_this_variable = include_images_for_this_variable and (not didPass)
varRunInfo['shouldIncludeImages'] = include_images_for_this_variable
# to hold the names of any images created
image_names = {
'original': [ ],
'compared': [ ]
}
# create the images for this variable
# TODO, will need to handle averaged/sliced 3D data at some point
if (include_images_for_this_variable) :
plotFunctionGenerationObjects = [ ]
# if the bin and tuple are defined, try to analyze the data as complex
# multidimentional information requiring careful sampling
if ('binIndex' in varRunInfo) and ('tupleIndex' in varRunInfo) :
plotFunctionGenerationObjects.append(plotcreate.BinTupleAnalysisFunctionFactory())
else :
# if the data is the same size, we can always make our basic statistical comparison plots
if (aData.shape == bData.shape) :
plotFunctionGenerationObjects.append(plotcreate.BasicComparisonPlotsFunctionFactory())
# if it's vector data with longitude and latitude, quiver plot it on the Earth
if isVectorData and (not do_not_test_with_lon_lat) :
plotFunctionGenerationObjects.append(plotcreate.MappedQuiverPlotFunctionFactory())
# if the data is one dimensional we can plot it as lines
elif (len(aData.shape) is 1) :
plotFunctionGenerationObjects.append(plotcreate.LinePlotsFunctionFactory())
# if the data is 2D we have some options based on the type of data
elif (len(aData.shape) is 2) :
# if the data is not mapped to a longitude and latitude, just show it as an image
if (do_not_test_with_lon_lat) :
plotFunctionGenerationObjects.append(plotcreate.IMShowPlotFunctionFactory())
# if it's 2D and mapped to the Earth, contour plot it on the earth
else :
plotFunctionGenerationObjects.append(plotcreate.MappedContourPlotFunctionFactory())
# if there's magnitude and direction data, figure out the u and v, otherwise these will be None
aUData, aVData = _get_UV_info_from_magnitude_direction_info (aFile,
varRunInfo['magnitudeName'] if ('magnitudeName') in varRunInfo else None,
varRunInfo['directionName'] if ('directionName') in varRunInfo else None,
lon_lat_data['a']['inv_mask']
if ('a' in lon_lat_data) and ('inv_mask' in lon_lat_data['a']) else None)
bUData, bVData = _get_UV_info_from_magnitude_direction_info (bFile,
varRunInfo['magnitudeBName'] if ('magnitudeBName') in varRunInfo else None,
varRunInfo['directionBName'] if ('directionBName') in varRunInfo else None,
lon_lat_data['b']['inv_mask']
if ('b' in lon_lat_data) and ('inv_mask' in lon_lat_data['b']) else None)
# plot our lon/lat related info
image_names['original'], image_names['compared'] = \
plot.plot_and_save_comparison_figures \
(aData, bData,
plotFunctionGenerationObjects,
varRunInfo['variable_dir'],
displayName,
varRunInfo['epsilon'],
varRunInfo['missing_value'],
missingValueAltInB = varRunInfo['missingValueAltInB'] if 'missingValueAltInB' in varRunInfo else None,
lonLatDataDict=lon_lat_data,
dataRanges = varRunInfo['display_ranges'] if 'display_ranges' in varRunInfo else None,
dataRangeNames = varRunInfo['display_range_names'] if 'display_range_names' in varRunInfo else None,
dataColors = varRunInfo['display_colors'] if 'display_colors' in varRunInfo else None,
makeSmall=True,
doFork=runInfo['doFork'],
shouldClearMemoryWithThreads=runInfo['useThreadsToControlMemory'],
shouldUseSharedRangeForOriginal=runInfo['useSharedRangeForOriginal'],
doPlotSettingsDict = varRunInfo,
aUData=aUData, aVData=aVData,
bUData=bUData, bVData=bVData,
binIndex= varRunInfo['binIndex'] if 'binIndex' in varRunInfo else None,
tupleIndex=varRunInfo['tupleIndex'] if 'tupleIndex' in varRunInfo else None,
binName= varRunInfo['binName'] if 'binName' in varRunInfo else 'bin',
tupleName= varRunInfo['tupleName'] if 'tupleName' in varRunInfo else 'tuple')
print("\tfinished creating figures for: " + explanationName)
# create the report page for this variable
if (runInfo['shouldIncludeReport']) :
# hang on to our good % and other info to describe our comparison
epsilonPassedPercent = (1.0 - epsilon_failed_fraction) * 100.0
finitePassedPercent = (1.0 - non_finite_fail_fraction) * 100.0
variableComparisons[displayName] = {'pass_epsilon_percent': epsilonPassedPercent,
'finite_similar_percent': finitePassedPercent,
'variable_run_info': varRunInfo
}
print ('\tgenerating report for: ' + explanationName)
report.generate_and_save_variable_report(files,
varRunInfo, runInfo,
variable_stats,
spatialInfo,
image_names,
varRunInfo['variable_dir'], "index.html")
# if we can't compare the variable, we should tell the user
else :
message = (explanationName + ' ' +
'could not be compared. This may be because the data for this variable does not match in shape ' +
'between the two files (file A data shape: ' + str(aData.shape) + '; file B data shape: '
+ str(bData.shape) + ')')
if do_not_test_with_lon_lat :
message = message + '.'
else :
message = (message + ' or the data may not match the shape of the selected '
+ 'longitude ' + str(good_shape_from_lon_lat) + ' and '
+ 'latitude ' + str(good_shape_from_lon_lat) + ' variables.')
LOG.warn(message)
# the end of the loop to examine all the variables
# generate our general report pages once we've analyzed all the variables
if (runInfo['shouldIncludeReport']) :
# get the current time
runInfo['time'] = datetime.datetime.ctime(datetime.datetime.now())
# make the main summary report
print ('generating summary report')
report.generate_and_save_summary_report(files,
pathsTemp['out'], 'index.html',
runInfo,
variableComparisons,
spatialInfo,
nameStats)
# make the glossary
print ('generating glossary')
report.generate_and_save_doc_page(delta.STATISTICS_DOC, pathsTemp['out'])
return
def stats_library_call(afn, bfn, var_list=[ ],
options_set={ },
do_document=False,
output_channel=sys.stdout):
"""
this method handles the actual work of the stats command line tool and
can also be used as a library routine, simply pass in an output channel
and/or use the returned dictionary of statistics for your own form of
display.
TODO, should this move to a different file?
"""
# unpack some options
epsilon_val = options_set['epsilon']
missing_val = options_set['missing']
LOG.debug ("file a: " + afn)
LOG.debug ("file b: " + bfn)
# open the files
filesInfo = _open_and_process_files([afn, bfn], 2)
aFile = filesInfo[afn]['fileObject']
bFile = filesInfo[bfn]['fileObject']
# figure out the variable names and their individual settings
if len(var_list) <= 0 :
var_list = ['.*']
names = _parse_varnames( filesInfo['commonVarNames'], var_list, epsilon_val, missing_val )
LOG.debug(str(names))
doc_each = do_document and len(names)==1
doc_atend = do_document and len(names)!=1
for name,epsilon,missing in names:
aData = aFile[name]
bData = bFile[name]
if missing is None:
amiss = aFile.missing_value(name)
bmiss = bFile.missing_value(name)
else:
amiss,bmiss = missing,missing
LOG.debug('comparing %s with epsilon %s and missing %s,%s' % (name,epsilon,amiss,bmiss))
aval = aData
bval = bData
print >> output_channel, '-'*32
print >> output_channel, name
print >> output_channel, ''
lal = list(delta.summarize(aval,bval,epsilon,(amiss,bmiss)).items())
lal.sort()
for dictionary_title, dict_data in lal:
print >> output_channel, '%s' % dictionary_title
dict_data
for each_stat in sorted(list(dict_data)):
print >> output_channel, ' %s: %s' % (each_stat, dict_data[each_stat])
if doc_each: print >> output_channel, (' ' + delta.STATISTICS_DOC[each_stat])
print >> output_channel, ''
if doc_atend:
print >> output_channel, ('\n\n' + delta.STATISTICS_DOC_STR)
def main():
import optparse
usage = """
%prog [options]
run "%prog help" to list commands
examples:
python -m glance.compare info A.hdf
python -m glance.compare stats A.hdf B.hdf '.*_prof_retr_.*:1e-4' 'nwp_._index:0'
python -m glance.compare plotDiffs A.hdf B.hdf
python -m glance compare reportGen A.hdf B.hdf
python -m glance
"""
parser = optparse.OptionParser(usage)
parser.add_option('-t', '--test', dest="self_test",
action="store_true", default=False, help="run internal unit tests")
parser.add_option('-q', '--quiet', dest="quiet",
action="store_true", default=False, help="only error output")
parser.add_option('-v', '--verbose', dest="verbose",
action="store_true", default=False, help="enable more informational output")
parser.add_option('-w', '--debug', dest="debug",
action="store_true", default=False, help="enable debug output")
parser.add_option('-e', '--epsilon', dest="epsilon", type='float', default=0.0,
help="set default epsilon value for comparison threshold")
parser.add_option('-m', '--missing', dest="missing", type='float', default=None,
help="set default missing-value")
#report generation related options
parser.add_option('-p', '--outputpath', dest="outputpath", type='string', default='./',
help="set path to output directory")
parser.add_option('-o', '--longitude', dest="longitudeVar", type='string',
help="set name of longitude variable")
parser.add_option('-a', '--latitude', dest="latitudeVar", type='string',
help="set name of latitude variable")
parser.add_option('-i', '--imagesonly', dest="imagesOnly",
action="store_true", default=False,
help="generate only image files (no html report)")
parser.add_option('-r', '--reportonly', dest="htmlOnly",
action="store_true", default=False,
help="generate only html report files (no images)")
parser.add_option('-c', '--configfile', dest="configFile", type='string', default=None,
help="set optional configuration file")
parser.add_option('-l', '--llepsilon', dest='lonlatepsilon', type='float', default=0.0,
help="set default epsilon for longitude and latitude comparsion")
parser.add_option('-n', '--version', dest='version',
action="store_true", default=False, help="view the glance version")
parser.add_option('-f', '--fork', dest='doFork',
action="store_true", default=False, help="start multiple processes to create images in parallel")
parser.add_option('-d', '--nolonlat', dest='noLonLatVars',
action="store_true", default=False, help="do not try to find or analyze logitude and latitude")
options, args = parser.parse_args()
if options.self_test:
import doctest
doctest.testmod()
sys.exit(2)
lvl = logging.WARNING
if options.debug: lvl = logging.DEBUG
elif options.verbose: lvl = logging.INFO
elif options.quiet: lvl = logging.ERROR
logging.basicConfig(level = lvl)
# display the version
if options.version :
print (_get_glance_version_string() + '\n')
commands = {}
prior = None
prior = dict(locals())
def info(*args):
"""list information about a list of files
List available variables for comparison.
"""
for fn in args:
try :
lal = list(io.open(fn)())
lal.sort()
print fn + ': ' + ('\n ' + ' '*len(fn)).join(lal)
except KeyError :
LOG.warn('Unable to open / process file selection: ' + fn)
def sdr_cris(*args):
"""compare sdr_cris output
parameters are variable name followed by detector number
sdr_cris desired.h5 actual.h5 ESRealLW 0
""" # TODO ******* standardize with method?
afn,bfn = args[:2]
LOG.info("opening %s" % afn)
a = io.open(afn)
LOG.info("opening %s" % bfn)
b = io.open(bfn)
# shape is [scanline, field, detector, wnum]
vname = '/All_Data/CrIS-SDR_All/' + args[2]
det_idx = int(args[3])
def get(f):
spc = f[vname][:,:,det_idx,:]
nsl,nfor,nwn = spc.shape
return spc.reshape( (nsl*nfor,nwn) )
aspc = get(a)
bspc = get(b)
plot.compare_spectra(bspc,aspc)
plot.show()
def noisecheck(*args):
"""gives statistics for dataset comparisons against truth with and without noise
usage: noisecheck truth-file noise-file actual-file variable1{:epsilon{:missing}} {variable2...}
glance noisecheck /Volumes/snaapy/data/justins/abi_graffir/coreg/pure/l2_data/geocatL2.GOES-R.2005155.220000.hdf.gz /Volumes/snaapy/data/justins/abi_graffir/noise/noise1x/l2_data/geocatL2.GOES-R.2005155.220000.hdf
""" # TODO ******* standardize with method?
afn,noizfn,bfn = args[:3]
LOG.info("opening truth file %s" % afn)
a = io.open(afn)
LOG.info("opening actual file %s" % noizfn)
noiz = io.open(noizfn)
LOG.info("opening noise file %s" % bfn)
b = io.open(bfn)
anames = set(a())
bnames = set(b())
cnames = anames.intersection(bnames) # common names
pats = args[3:] or ['.*']
names = _parse_varnames( cnames, pats, options.epsilon, options.missing )
for name,epsilon,missing in names:
aData = a[name]
bData = b[name]
nData = noiz[name]
if missing is None:
amiss = a.missing_value(name)
bmiss = b.missing_value(name)
else:
amiss,bmiss = missing,missing
x = aData
y = bData
z = nData
def scat(x,xn,y):
from pylab import plot,show,scatter
scatter(x,y)
show()
nfo = delta.rms_corr_withnoise(x,y,z,epsilon,(amiss,bmiss),plot=scat)
print '-'*32
print name
for kv in sorted(nfo.items()):
print ' %s: %s' % kv
def stats(*args):
"""create statistics summary of variables
Summarize difference statistics between listed variables.
If no variable names are given, summarize all common variables.
Variable names can be of the form varname:epsilon:missing to use non-default epsilon or missing value.
Variable names can be regular expressions, e.g. 'image.*' or '.*prof_retr.*::-999'
Either epsilon or missing can be empty to stay with default.
If _FillValue is an attribute of a variable, that will be used to find missing values where no value is given.
Run with -v to get more detailed information on statistics.
Examples:
python -m glance.compare stats hdffile1 hdffile2
python -m glance.compare stats --epsilon=0.00001 A.hdf B.hdf baseline_cmask_seviri_cloud_mask:0.002:
python -m glance.compare -w stats --epsilon=0.00001 A.hdf A.hdf imager_prof_retr_abi_total_precipitable_water_low::-999
"""
afn, bfn = args[:2]
do_doc = (options.verbose or options.debug)
tempOptions = { }
tempOptions['epsilon'] = options.epsilon
tempOptions['missing'] = options.missing
# add more if needed for stats
_ = stats_library_call(_clean_path(afn), _clean_path(bfn),
var_list=args[2:],
options_set=tempOptions,
do_document=do_doc)
def plotDiffs(*args) :
"""generate a set of images comparing two files
This option creates a set of graphical comparisons of variables in the two given hdf files.
The images detailing the differences between variables in the two hdf files will be
generated and saved to disk.
Variables to be compared may be specified after the names of the two input files. If no variables
are specified, all variables that match the shape of the longitude and latitude will be compared.
Specified variables that do not exist, do not match the correct data shape, or are the longitude/latitude
variables will be ignored.
The user may also use the notation variable_name:epsilon:missing_value to specify the acceptible epsilon
for comparison and the missing_value which indicates missing data. If one or both of these values is absent
(in the case of variable_name:epsilon: variable_name::missing_value or just variable_name) the default value
of 0.0 will be used for epsilon and no missing values will be analyzed.
The created images will be stored in the provided path, or if no path is provided, they will be stored in
the current directory.
The longitude and latitude variables may be specified with --longitude and --latitude
If no longitude or latitude are specified the pixel_latitude and pixel_longitude variables will be used.
Examples:
python -m glance.compare plotDiffs A.hdf B.hdf variable_name_1:epsilon1: variable_name_2 variable_name_3:epsilon3:missing3 variable_name_4::missing4
python -m glance.compare --outputpath=/path/where/output/will/be/placed/ plotDiffs A.hdf B.hdf
python -m glance.compare plotDiffs --longitude=lon_variable_name --latitude=lat_variable_name A.hdf B.hdf variable_name
"""
# set the options so that a report will not be generated
options.imagesOnly = True
# make the images
reportGen(*args)
return
def reportGen(*args) :
"""generate a report comparing two files
This option creates a report comparing variables in the two given hdf files.
An html report and images detailing the differences between variables in the two hdf files will be
generated and saved to disk. The images will be embedded in the report or visible as separate .png files.
Variables to be compared may be specified after the names of the two input files. If no variables
are specified, all variables that match the shape of the longitude and latitude will be compared.
Specified variables that do not exist, do not match the correct data shape, or are the longitude/latitude
variables will be ignored.
The user may also use the notation variable_name:epsilon:missing_value to specify the acceptible epsilon
for comparison and the missing_value which indicates missing data. If one or both of these values is absent
(in the case of variable_name:epsilon: variable_name::missing_value or just variable_name) the default value
of 0.0 will be used for epsilon and no missing values will be analyzed.
The html report page(s) and any created images will be stored in the provided path, or if no path is provided,
they will be stored in the current directory.
If for some reason you would prefer to generate the report without images, use the --reportonly option. This
option will generate the html report but omit the images. This may be significantly faster, depending on
your system, but the differences between the files may be quite a bit more difficult to interpret.
The longitude and latitude variables may be specified with --longitude and --latitude
If no longitude or latitude are specified the pixel_latitude and pixel_longitude variables will be used.
Examples:
python -m glance.compare reportGen A.hdf B.hdf variable_name_1:epsilon1: variable_name_2 variable_name_3:epsilon3:missing3 variable_name_4::missing4
python -m glance.compare --outputpath=/path/where/output/will/be/placed/ reportGen A.hdf B.hdf
python -m glance.compare reportGen --longitude=lon_variable_name --latitude=lat_variable_name A.hdf B.hdf variable_name
python -m glance.compare reportGen --imagesonly A.hdf B.hdf
"""
tempOptions = { }
tempOptions['outputpath'] = _clean_path(options.outputpath)
tempOptions['configFile'] = _clean_path(options.configFile)
tempOptions['imagesOnly'] = options.imagesOnly
tempOptions['htmlOnly'] = options.htmlOnly
tempOptions['doFork'] = options.doFork
tempOptions['noLonLatVars'] = options.noLonLatVars
tempOptions['latitudeVar'] = options.latitudeVar
tempOptions['longitudeVar'] = options.longitudeVar
tempOptions['lonlatepsilon'] = options.lonlatepsilon
tempOptions['epsilon'] = options.epsilon
tempOptions['missing'] = options.missing
a_path = _clean_path(args[0])
b_path = _clean_path(args[1])
reportGen_library_call(a_path, b_path, args[2:], tempOptions)
def colocateData(*args) :
"""colocate data in two files
This option colocates data in the two given input files and saves it to separate output files.
Data will be colocated based on its corresponding longitude and latitude. Multiple matches may be
made between a data point in file A and those in file B if they are within the longitude/latitude epsilon.
Points from each file that could not be matched and the number of duplicate matches will also be
recorded in the output file.
The user may also use the notation variable_name::missing_value to specify the missing_value which indicates
missing data. If no missing value is given, glance will attempt to load a missing value from the input file.
If there is no missing value defined for that variable in the file, no missing value will be analyzed.
Missing value data points will not be considered for colocation.
Data which corresponds to longitude or latitude values which fall outside the earth (outside the normally
accepted valid ranges) will also be considered invalid and will not be considered for colocation.
The longitude and latitude variables may be specified with --longitude and --latitude
If no longitude or latitude are specified the pixel_latitude and pixel_longitude variables will be used.
The longitude and latitude epsilon may be specified with --llepsilon
If no longitude/latitude epsilon is given the value of 0.0 (degrees) will be used
The output data files generated by this option will appear in the selected output directory, or the current
directory if no out put directory is selected. The output files will be named originalFileName-colocation.nc
(replacing "originalFileName" with the names of your input files).
Examples:
python -m glance.compare colocateData A.hdf B.hdf variable_name_1 variable_name_2 variable_name_3::missing3
python -m glance.compare colocateData --outputpath=/path/where/output/will/be/placed/ A.nc B.nc
python -m glance.compare colocateData --longitude=lon_variable_name --latitude=lat_variable_name A.hdf B.hdf variable_name
python -m glance.compare colocateData --llepsilon=0.0001 A.nc B.hdf
"""
tempOptions = { }
tempOptions['outputpath'] = _clean_path(options.outputpath)
tempOptions['configFile'] = _clean_path(options.configFile)
tempOptions['noLonLatVars'] = options.noLonLatVars
tempOptions['latitudeVar'] = options.latitudeVar
tempOptions['longitudeVar'] = options.longitudeVar
tempOptions['lonlatepsilon'] = options.lonlatepsilon
tempOptions['epsilon'] = options.epsilon
tempOptions['missing'] = options.missing
# TODO, remove these eventually
tempOptions['htmlOnly'] = False
tempOptions['imagesOnly'] = False
tempOptions['doFork'] = False
tempOptions['doColocate'] = True
a_path = _clean_path(args[0])
b_path = _clean_path(args[1])
colocateToFile_library_call(a_path, b_path, args[2:], tempOptions)
"""
# This was used to modify files for testing and should not be uncommented
# unless you intend to use it only temporarily for testing purposes
# at the moment it is not written very generally (only works with hdf4),
# requires you to use 'from pyhdf.SD import SD, SDS' and change io to load
# files in write mode rather than read only
def make_renamed_variable_copy(*args) :
'''
make a copy of a variable in a file using the new name given by the user
'''
file_path = args[0]
old_var_name = args[1]
new_var_name = args[2]
print ("Copying variable \'" + old_var_name + "\' to \'" + new_var_name
+ "\' in file " + file_path)
# open the file and get the old variable
LOG.info("\topening " + file_path)
file_object = io.open(file_path)
LOG.info("\tgetting " + old_var_name)
variable_object_old = file_object.get_variable_object(old_var_name)
temp, old_rank, old_shape, old_type, old_num_attributes = SDS.info(variable_object_old)
old_attributes = SDS.attributes(variable_object_old)
# make a copy of the variable with the new name
LOG.info("\tsaving " + new_var_name)
variable_object_new = SD.create(file_object, new_var_name, old_type, old_shape)
SDS.set(variable_object_new, variable_object_old[:])
''' TODO, attribute copying is not working yet
for attribute_name in old_attributes :
variable_object_new[attribute_name] = variable_object_old[attribute_name]
'''
# close up all our access objects
SDS.endaccess(variable_object_old)
SDS.endaccess(variable_object_new)
SD.end(file_object)
return
"""
# def build(*args):
# """build summary
# build extended info
# """
# LOG.info("building database tables")
#
# def grant(*args):
# """grant summary
# grant extended info
# """
# LOG.info("granting permissions for tables")
#
# def index(*args):
# """index summary
# index extended info
# """
# LOG.info("creating indices for tables")
def help(command=None):
"""print help for a specific command or list of commands
e.g. help stats
"""
if command is None:
# print first line of docstring
for cmd in commands:
ds = commands[cmd].__doc__.split('\n')[0]
print "%-16s %s" % (cmd,ds)
else:
print commands[command].__doc__
# def test():
# "run tests"
# test1()
#
commands.update(dict(x for x in locals().items() if x[0] not in prior))
if (not args) or (args[0] not in commands):
parser.print_help()
help()
return 9
else:
locals()[args[0]](*args[1:])
return 0
if __name__=='__main__':
sys.exit(main())