def cov_estimation(list_of_recarrays, index_name, pair_wise=False):
def get_the_other_name(rec, index_name):
assert len(rec.dtype.names) == 2
name = [nm for nm in rec.dtype.names if nm != index_name]
assert len(name) == 1
return name[0]
for array in list_of_recarrays:
array[get_the_other_name(array, index_name)] = winsorize(array[get_the_other_name(array, index_name)], 99)
nn = len(list_of_recarrays)
if not pair_wise:
new_rec = list_of_recarrays[0]
for ii in range(1, nn):
new_rec = rec_join(index_name, new_rec, list_of_recarrays[ii], jointype='inner', defaults=None, r1postfix='', r2postfix=str(ii+1))
dat_mat = np.c_[[new_rec[nm] for nm in new_rec.dtype.names if nm != index_name]]
covmat = np.cov(dat_mat)
else :
covmat = np.zeros((nn, nn))
for ii in range(0, nn):
covmat[ii,ii] = list_of_recarrays[ii][get_the_other_name(list_of_recarrays[ii], index_name)].var()
for jj in range(ii+1, nn):
new_rec = rec_join(index_name, list_of_recarrays[ii], list_of_recarrays[jj], jointype='inner', defaults=None, r1postfix='1', r2postfix='2')
dat_mat = np.c_[[new_rec[nm] for nm in new_rec.dtype.names if nm != index_name]]
tmp_cov = np.cov(dat_mat)[0,1]
covmat[ii,jj] = tmp_cov
covmat[jj,ii] = tmp_cov
return covmat
def create_species_plot_count_file(self):
p = self.parameter_parser
# Store list of plot IDs into a string if this variable hasn't
# yet been created
if not hasattr(self, 'id_str'):
self.id_str = self._get_id_string()
spp_plot_table = self.plot_db.get_species_plot_counts(self.id_str)
spp_plot_file = p.model_directory + '/' + p.model_type + \
'_spp_plot_counts.csv'
if p.model_type in p.imagery_model_types:
utilities.rec2csv(spp_plot_table, spp_plot_file)
else:
# Create 2 ID strings for non-imagery models, one with inventory
# and Ecoplots and one with inventory plots only
try:
ecoplot_index = p.plot_types.index('ecoplot')
except ValueError:
# If Ecoplots are not already in the list, create another ID
# string with them included
plot_types_w_eco = p.plot_types
plot_types_w_eco.append('ecoplot')
plot_types_w_eco_str = ','.join(plot_types_w_eco)
id_str2 = self._get_id_string(plot_types_w_eco_str)
id_eco = 2
else:
# If Ecoplot are already in the list, create another ID
# string without them included
plot_types_wo_eco = p.plot_types
plot_types_wo_eco.remove('ecoplot')
plot_types_wo_eco_str = ','.join(plot_types_wo_eco)
id_str2 = self._get_id_string(plot_types_wo_eco_str)
id_eco = 1
spp_plot_table2 = self.plot_db.get_species_plot_counts(id_str2)
# Join the plot counts w/ Ecoplots to the plot counts w/o Ecoplots
if id_eco == 1:
joined_spp_plot_table = mlab.rec_join('SPP_LAYER',
spp_plot_table,
spp_plot_table2,
'leftouter')
else:
joined_spp_plot_table = mlab.rec_join('SPP_LAYER',
spp_plot_table2,
spp_plot_table,
'leftouter')
utilities.rec2csv(joined_spp_plot_table, spp_plot_file)
def recs_inner_join(key, recs, postfixes):
new_rec = recs[0]
for ii in range(1, len(recs)):
r1postfix='1'
r2postfix='2'
new_rec = mlab.rec_join(key, new_rec, recs[ii], jointype='inner',
defaults=None, r1postfix=r1postfix, r2postfix=r2postfix)
return new_rec
def create_species_plot_count_file(self):
p = self.parameter_parser
# Store list of plot IDs into a string if this variable hasn't
# yet been created
if not hasattr(self, 'id_str'):
self.id_str = self._get_id_string()
spp_plot_table = self.plot_db.get_species_plot_counts(self.id_str)
spp_plot_file = p.model_directory + '/' + p.model_type + \
'_spp_plot_counts.csv'
if p.model_type in p.imagery_model_types:
utilities.rec2csv(spp_plot_table, spp_plot_file)
else:
# Create 2 ID strings for non-imagery models, one with inventory
# and Ecoplots and one with inventory plots only
try:
ecoplot_index = p.plot_types.index('ecoplot')
except ValueError:
# If Ecoplots are not already in the list, create another ID
# string with them included
plot_types_w_eco = p.plot_types
plot_types_w_eco.append('ecoplot')
plot_types_w_eco_str = ','.join(plot_types_w_eco)
id_str2 = self._get_id_string(plot_types_w_eco_str)
id_eco = 2
else:
# If Ecoplot are already in the list, create another ID
# string without them included
plot_types_wo_eco = p.plot_types
plot_types_wo_eco.remove('ecoplot')
plot_types_wo_eco_str = ','.join(plot_types_wo_eco)
id_str2 = self._get_id_string(plot_types_wo_eco_str)
id_eco = 1
spp_plot_table2 = self.plot_db.get_species_plot_counts(id_str2)
# Join the plot counts w/ Ecoplots to the plot counts w/o Ecoplots
if id_eco == 1:
joined_spp_plot_table = mlab.rec_join(
'SPP_LAYER', spp_plot_table, spp_plot_table2, 'leftouter')
else:
joined_spp_plot_table = mlab.rec_join(
'SPP_LAYER', spp_plot_table2, spp_plot_table, 'leftouter')
utilities.rec2csv(joined_spp_plot_table, spp_plot_file)
def get_predicted_estimates(self):
# Read in the predicted raster
ds = gdal.Open(self.predicted_raster, gdalconst.GA_ReadOnly)
rat = ds.GetRasterBand(1).GetDefaultRAT()
# Get the cell area for converting from pixel counts to hectares
gt = ds.GetGeoTransform()
cell_area = gt[1] * gt[1]
# Get the IDs and counts (converted to hectares)
id_recs = []
nf_hectares = 0
for i in range(rat.GetRowCount()):
id = rat.GetValueAsInt(i, 0)
hectares = rat.GetValueAsInt(i, 1) * cell_area / 10000.0
if id <= 0:
nf_hectares += hectares
else:
id_recs.append((id, hectares))
# Release the dataset
ds = None
# Convert this to a recarray
names = (self.id_field, 'HECTARES')
ids = np.rec.fromrecords(id_recs, names=names)
# Read in the attribute file
sad = utilities.csv2rec(self.stand_attribute_file)
# Ensure that all IDs in the id_count_dict are in the attribute data
ids_1 = getattr(ids, self.id_field)
ids_2 = getattr(sad, self.id_field)
if not np.all(np.in1d(ids_1, ids_2)):
err_msg = 'Not all values in the raster are present in the '
err_msg += 'attribute data'
raise ValueError(err_msg)
# Join the two recarrays together
predicted_data = mlab.rec_join(self.id_field, ids, sad)
return (predicted_data, nf_hectares)
def get_predicted_estimates(self):
# Read in the predicted raster
ds = gdal.Open(self.predicted_raster, gdalconst.GA_ReadOnly)
rat = ds.GetRasterBand(1).GetDefaultRAT()
# Get the cell area for converting from pixel counts to hectares
gt = ds.GetGeoTransform()
cell_area = gt[1] * gt[1]
# Get the IDs and counts (converted to hectares)
id_recs = []
nf_hectares = 0
for i in range(rat.GetRowCount()):
id = rat.GetValueAsInt(i, 0)
hectares = rat.GetValueAsInt(i, 1) * cell_area / 10000.0
if id <= 0:
nf_hectares += hectares
else:
id_recs.append((id, hectares))
# Release the dataset
ds = None
# Convert this to a recarray
names = (self.id_field, 'HECTARES')
ids = np.rec.fromrecords(id_recs, names=names)
# Read in the attribute file
sad = utilities.csv2rec(self.stand_attribute_file)
# Ensure that all IDs in the id_count_dict are in the attribute data
ids_1 = getattr(ids, self.id_field)
ids_2 = getattr(sad, self.id_field)
if not np.all(np.in1d(ids_1, ids_2)):
err_msg = 'Not all values in the raster are present in the '
err_msg += 'attribute data'
raise ValueError(err_msg)
# Join the two recarrays together
predicted_data = mlab.rec_join(self.id_field, ids, sad)
return (predicted_data, nf_hectares)
import numpy as np
import matplotlib.mlab as mlab
r = mlab.csv2rec('../data/aapl.csv')
r.sort()
r1 = r[-10:]
# Create a new array
r2 = np.empty(12, dtype=[('date', '|O4'), ('high', np.float),
('marker', np.float)])
r2 = r2.view(np.recarray)
r2.date = r.date[-17:-5]
r2.high = r.high[-17:-5]
r2.marker = np.arange(12)
print "r1:"
print mlab.rec2txt(r1)
print "r2:"
print mlab.rec2txt(r2)
defaults = {'marker':-1, 'close':np.NaN, 'low':-4444.}
for s in ('inner', 'outer', 'leftouter'):
rec = mlab.rec_join(['date', 'high'], r1, r2,
jointype=s, defaults=defaults)
print "\n%sjoin :\n%s" % (s, mlab.rec2txt(rec))
# grab the price data off yahoo
u1 = urllib.urlretrieve('http://ichart.finance.yahoo.com/table.csv?s=AAPL&d=9&e=14&f=2008&g=d&a=8&b=7&c=1984&ignore=.csv')
u2 = urllib.urlretrieve('http://ichart.finance.yahoo.com/table.csv?s=GOOG&d=9&e=14&f=2008&g=d&a=8&b=7&c=1984&ignore=.csv')
# load the CSV files into record arrays
r1 = mlab.csv2rec(file(u1[0]))
r2 = mlab.csv2rec(file(u2[0]))
# compute the daily returns and add these columns to the arrays
gains1 = np.zeros_like(r1.adj_close)
gains2 = np.zeros_like(r2.adj_close)
gains1[1:] = np.diff(r1.adj_close)/r1.adj_close[:-1]
gains2[1:] = np.diff(r2.adj_close)/r2.adj_close[:-1]
r1 = mlab.rec_append_fields(r1, 'gains', gains1)
r2 = mlab.rec_append_fields(r2, 'gains', gains2)
# now join them by date; the default postfixes are 1 and 2
r = mlab.rec_join('date', r1, r2)
# long appl, short goog
g = r.gains1-r.gains2
tr = (1+g).cumprod() # the total return
# plot the return
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(r.date, tr)
ax.set_title('total return: long appl, short goog')
ax.grid()
fig.autofmt_xdate()
plt.show()
r1 = mlab.csv2rec(open(u1[0]))
r2 = mlab.csv2rec(open(u2[0]))
# compute the daily returns and add these columns to the arrays
gains1 = np.zeros_like(r1.adj_close)
gains2 = np.zeros_like(r2.adj_close)
gains1[1:] = np.diff(r1.adj_close) / r1.adj_close[:-1]
gains2[1:] = np.diff(r2.adj_close) / r2.adj_close[:-1]
r1 = mlab.rec_append_fields(r1, 'gains', gains1)
r2 = mlab.rec_append_fields(r2, 'gains', gains2)
# now join them by date; the default postfixes are 1 and 2. The
# default jointype is inner so it will do an intersection of dates and
# drop the dates in AAPL which occurred before GOOG started trading in
# 2004. r1 and r2 are reverse ordered by date since Yahoo returns
# most recent first in the CSV files, but rec_join will sort by key so
# r below will be properly sorted
r = mlab.rec_join('date', r1, r2)
# long appl, short goog
g = r.gains1 - r.gains2
tr = (1 + g).cumprod() # the total return
# plot the return
fig, ax = plt.subplots()
ax.plot(r.date, tr)
ax.set_title('total return: long APPL, short GOOG')
ax.grid()
fig.autofmt_xdate()
plt.show()
def bugtrend(milestone):
baseWorkingDirectory = "/tmp/"
wikiTableBaseFileName = baseWorkingDirectory + "DefectChurnReport"
wikiImageFileBaseLocation = "http://metrics.arubanetworks.com/metrics/margot_autopages/"
wikiContent = []
Queries = milestone.split(",")
default_column_value = {
"datemaxbabug_when": datetime.date(2030, 12, 1),
"datebcreation_ts": datetime.date(2005, 1, 1),
"cf_customers": "Aruba Internal",
}
for params in Queries:
print "processing : " + params
wikiContent = []
baseFileName = params
bugReportName = baseWorkingDirectory + baseFileName + "_bugs.csv"
fixedReportName = baseWorkingDirectory + baseFileName + "_fixed.csv"
outputReportName = baseWorkingDirectory + baseFileName + "_merged.csv"
r = mlab.csv2rec(bugReportName)
s = mlab.csv2rec(fixedReportName)
k = mlab.rec_join("bug_id", s, r, jointype="outer", defaults=default_column_value, r1postfix="1", r2postfix="2")
t = mlab.csv2rec("/home/automation/bugzilla_tool/Org_Mapping.csv")
# mlab.rec2csv(k,outputReportName,delimiter=',',missing="",missingd=None,withheader=True)
org_mapping = dict(zip(t.login_name, range(len(t))))
# orgList = []
DirectorArray = np.zeros_like(k.login_name)
ComponentArray = np.zeros_like(k.login_name)
ManagerArray = np.zeros_like(k.login_name)
for i in range(len(k)):
if k[i].login_name in org_mapping.keys():
DirectorArray[i] = t[org_mapping[k[i].login_name]].director
ComponentArray[i] = t[org_mapping[k[i].login_name]].functional_group
ManagerArray[i] = t[org_mapping[k[i].login_name]].manager
else:
DirectorArray[i] = t[org_mapping["*****@*****.**"]].director
ComponentArray[i] = t[org_mapping["*****@*****.**"]].functional_group
ManagerArray[i] = t[org_mapping["*****@*****.**"]].manager
k = mlab.rec_append_fields(k, "Director", DirectorArray)
k = mlab.rec_append_fields(k, "Component", ComponentArray)
k = mlab.rec_append_fields(k, "Manager", ManagerArray)
mlab.rec2csv(k, outputReportName, delimiter=",", missing="", missingd=None, withheader=True)
# Start preparing the data for plotting
chartFileName = baseWorkingDirectory + baseFileName + ".png"
plotDefectTrend(k, chartFileName, baseFileName)
s = "= Overall Defect Trend = \n"
wikiContent.append(s)
s = wikiImageFileBaseLocation + baseFileName + ".png \n"
wikiContent.append(s)
# Directors = ('Murali Duvvury','Shankar','Jie Jiang')
Directors = list(np.unique(np.array(k.Director)))
s = "= Director level Defect Trend = \n"
wikiContent.append(s)
wikiTableFileName = wikiTableBaseFileName + "_" + params + ".wiki"
f = open(wikiTableFileName, "w")
hdrList = ("Director", "Open Defects", "Need Info", "Observe", "Resolved-Fixed", "Resolved-Other", "Incoming")
printWikiTableOpen(f, hdrList)
for Dir in Directors:
s = Dir
DirFileName = Dir.replace(" ", "_")
DirRe = re.compile(s)
DirReMatch = np.vectorize(lambda x: bool(DirRe.match(x)))
sel = DirReMatch(np.array(k.Director))
chartFileName = baseWorkingDirectory + baseFileName + "-" + DirFileName + ".png"
plotDefectTrend(k[sel], chartFileName, baseFileName + "-" + DirFileName)
printChurnReport(k[sel], Dir, f)
s = wikiImageFileBaseLocation + baseFileName + "-" + DirFileName + ".png \n"
wikiContent.append(s)
# chartFileName = baseWorkingDirectory + baseFileName + "-" + Dir +".png"
# plotDefectTrend(k[k.Director == Dir],chartFileName, baseFileName + '-' + Dir)
printWikiTableClose(f)
s = "= Component level Defect Trend = \n"
wikiContent.append(s)
ComponentList = [
["GSM", "GSM"],
["UI-Configuration", "UI"],
["AP-Platform", "11ac"],
["Switch-Datapath", "Datapath"],
["HA-Lite", "HA-Lite"],
["Switch-Platform", "CIMU"],
["Feature-Bugs", "\w+]"],
]
for c in ComponentList:
s = "^\[*" + c[1]
componentRe = re.compile(s)
componentReMatch = np.vectorize(lambda x: bool(componentRe.match(x)))
sel = np.logical_or(componentReMatch(np.array(k.short_desc)), k.name == c[0])
chartFileName = baseWorkingDirectory + baseFileName + "-" + c[0] + ".png"
plotDefectTrend(k[sel], chartFileName, baseFileName + "-" + c[0])
s = "= Keyword level Defect Trend = \n"
wikiContent.append(s)
KeywordList = [
["TC-Blocker", "TC\-blocker"],
["SystemTest", "ST"],
["Smoke", "Smoke\-Failure"],
["CFT", "CFT"],
["MustFix", "MustFix"],
]
for keyword in KeywordList:
s = keyword[1]
keywordRe = re.compile(s)
keywordReMatch = np.vectorize(lambda x: bool(keywordRe.match(x)))
sel = keywordReMatch(np.array(k.keywords))
chartFileName = baseWorkingDirectory + baseFileName + "-" + keyword[0] + ".png"
plotDefectTrend(k[sel], chartFileName, baseFileName + "-" + keyword[0])
# wikiTableFileName = wikiTableBaseFileName + '_' + params + '.wiki'
# f = open(wikiTableFileName , 'w')
hdrList = ("Manager", "Open Defects", "Need Info", "Observe", "Resolved-Fixed", "Resolved-Other", "Incoming")
printWikiTableOpen(f, hdrList)
ManagerList = list(np.unique(np.array(k.Manager)))
today = datetime.date.today()
resolvedDateRange = today + datetime.timedelta(days=-14)
s = "= Manager Defect Trend = \n"
wikiContent.append(s)
for mgr in ManagerList:
s = mgr
mgrFileName = mgr.replace(" ", "_")
mgrRe = re.compile(s)
mgrReMatch = np.vectorize(lambda x: bool(mgrRe.match(x)))
sel = mgrReMatch(np.array(k.Manager))
chartFileName = baseWorkingDirectory + baseFileName + "-" + mgrFileName + ".png"
plotDefectTrend(k[sel], chartFileName, baseFileName + "-" + mgrFileName)
printChurnReport(k[sel], mgr, f)
s = wikiImageFileBaseLocation + baseFileName + "-" + mgrFileName + ".png \n"
wikiContent.append(s)
printWikiTableClose(f)
f.write("".join(wikiContent))
f.close()
plt.close("all")
def customDefectTrend(chartFileName, title):
default_column_value = {
"datemaxbabug_when": datetime.date(2030, 12, 1),
"datebcreation_ts": datetime.date(2005, 1, 1),
"cf_customers": "Aruba Internal",
}
cfdtuple, cfdclose = cfdbug()
k = mlab.rec_join(
"bug_id", cfdtuple, cfdclose, jointype="outer", defaults=default_column_value, r1postfix="1", r2postfix="2"
)
incomingRateList = []
fixRateList = []
fixWeekList = []
resolvedFixedRateList = []
outstandingList = []
today = datetime.date.today()
toRangeDate = today + datetime.timedelta(days=-today.weekday() - 1, weeks=1)
fromRangeDate = toRangeDate + relativedelta.relativedelta(weeks=-13)
iterDate = fromRangeDate
while iterDate <= toRangeDate:
curDate = iterDate
iterDate = iterDate + relativedelta.relativedelta(weeks=1)
fixWeekList.append(iterDate.strftime("%m/%d"))
fixRate = np.logical_and(
np.logical_and(k.datemaxbabug_when > curDate, k.datemaxbabug_when <= iterDate), k.resolution <> ""
).sum()
incomingRate = (np.logical_and(k.datebcreation_ts > curDate, k.datebcreation_ts <= iterDate)).sum()
resolvedFixedRate = np.logical_and(
np.logical_and(k.datemaxbabug_when > curDate, k.datemaxbabug_when <= iterDate), k.resolution == "FIXED"
).sum()
outstandingCount = (k.datebcreation_ts <= iterDate).sum() - np.logical_and(
k.datemaxbabug_when <= iterDate, k.resolution <> ""
).sum()
fixRateList.append(fixRate)
incomingRateList.append(incomingRate)
resolvedFixedRateList.append(resolvedFixedRate)
outstandingList.append(outstandingCount)
width = 0.35
ind = np.arange(len(fixWeekList))
ax = plt.subplot(111)
rects1 = plt.bar(ind, incomingRateList, width, color="r")
rects2 = plt.bar(ind + width, fixRateList, width, color="y")
rects3 = plt.bar(ind + width, resolvedFixedRateList, width, color="b")
ax2 = ax.twinx()
rects5 = ax2.plot(ind + width, outstandingList, "b-", linewidth=3)
plt.ylabel("Defect Count")
ax.set_ylabel(r"Opened / Verified / Resolved")
ax2.set_ylabel(r"Outstanding Defect Count")
plt.title(title + " Defect Trend" + "-%s" % (datetime.date.today()))
plt.xticks(ind + width, fixWeekList)
# plt.legend((rects1[0], rects2[0] ,rects3[0],rects4[0],rects5[0],rects6[0],rects7[0],rects8[0]), ('incoming', 'resolved-other', 'resolved-fixed','regression','outstanding (right-axis)','SS_P1 (right-axis)','MustFix (right-axis)','Overall (right-axis)'),loc="upper left")
plt.legend(
(rects1[0], rects2[0], rects3[0], rects5[0]),
("Opend", "Verified", "Resolved", "outstanding (right-axis)"),
loc="upper left",
)
leg = plt.gca().get_legend()
ltext = leg.get_texts()
plt.setp(ltext, fontsize="xx-small")
autolabel(rects1, ax)
autolabel(rects2, ax)
plt.setp(ax.get_xticklabels(), rotation="90", fontsize=12)
F = plt.gcf()
F.set_size_inches(8, 6)
F.savefig(chartFileName, dpi=(100))
plt.clf()
from __future__ import print_function
import numpy as np
import matplotlib.mlab as mlab
import matplotlib.cbook as cbook
datafile = cbook.get_sample_data('aapl.csv', asfileobj=False)
print('loading', datafile)
r = mlab.csv2rec(datafile)
r.sort()
r1 = r[-10:]
# Create a new array
r2 = np.empty(12, dtype=[('date', '|O4'), ('high', np.float),
('marker', np.float)])
r2 = r2.view(np.recarray)
r2.date = r.date[-17:-5]
r2.high = r.high[-17:-5]
r2.marker = np.arange(12)
print("r1:")
print(mlab.rec2txt(r1))
print("r2:")
print(mlab.rec2txt(r2))
defaults = {'marker': -1, 'close': np.NaN, 'low': -4444.}
for s in ('inner', 'outer', 'leftouter'):
rec = mlab.rec_join(['date', 'high'], r1, r2,
jointype=s, defaults=defaults)
print("\n%sjoin :\n%s" % (s, mlab.rec2txt(rec)))
def run_diagnostic(self):
# Shortcut to the parameter parser
p = self.parameter_parser
# ID field
id_field = p.summary_level + 'ID'
# Root directory for Riemann files
root_dir = p.riemann_output_folder
# Read in hex input file
obs_data = utilities.csv2rec(self.hex_attribute_file)
# Get the hexagon levels and ensure that the fields exist in the
# hex_attribute file
hex_resolutions = p.riemann_hex_resolutions
hex_fields = [x[0] for x in hex_resolutions]
for field in hex_fields:
if field not in obs_data.dtype.names:
err_msg = 'Field ' + field + ' does not exist in the '
err_msg += 'hex_attribute file'
raise ValueError(err_msg)
# Create the directory structure based on the hex levels
hex_levels = ['hex_' + str(x[1]) for x in hex_resolutions]
all_levels = ['plot_pixel'] + hex_levels
for level in all_levels:
sub_dir = os.path.join(root_dir, level)
if not os.path.exists(sub_dir):
os.makedirs(sub_dir)
# Get the values of k
k_values = p.riemann_k_values
# Create a dictionary of plot ID to image year (or model_year for
# non-imagery models) for these plots
if p.model_type in p.imagery_model_types:
id_x_year = dict((x[id_field], x.IMAGE_YEAR) for x in obs_data)
else:
id_x_year = dict((x[id_field], p.model_year) for x in obs_data)
# Create a PredictionRun instance
pr = prediction_run.PredictionRun(p)
# Get the neighbors and distances for these IDs
pr.calculate_neighbors_at_ids(id_x_year, id_field=id_field)
# Create the lookup of id_field to LOC_ID for the hex plots
nsa_id_dict = dict((x[id_field], x.LOC_ID) for x in obs_data)
# Create a dictionary between id_field and no_self_assign_field
# for the model plots
env_file = p.environmental_matrix_file
env_data = utilities.csv2rec(env_file)
model_nsa_id_dict = dict(
(getattr(x, id_field), x.LOC_ID) for x in env_data)
# Stitch the two dictionaries together
for id in sorted(model_nsa_id_dict.keys()):
if id not in nsa_id_dict:
nsa_id_dict[id] = model_nsa_id_dict[id]
# Get the stand attribute metadata and retrieve only the
# continuous accuracy attributes
stand_metadata_file = p.stand_metadata_file
mp = xsmp.XMLStandMetadataParser(stand_metadata_file)
attrs = [
x.field_name for x in mp.attributes
if x.field_type == 'CONTINUOUS' and x.accuracy_attr == 1
]
# Subset the attributes for fields that are in the
# hex_attribute file
attrs = [x for x in attrs if x in obs_data.dtype.names]
plot_pixel_obs = mlab.rec_keep_fields(obs_data, [id_field] + attrs)
# Write out the plot_pixel observed file
file_name = 'plot_pixel_observed.csv'
output_file = os.path.join(root_dir, 'plot_pixel', file_name)
utilities.rec2csv(plot_pixel_obs, output_file)
# Iterate over values of k
for k in k_values:
# Construct the output file name
file_name = '_'.join(('plot_pixel', 'predicted', 'k' + str(k)))
file_name += '.csv'
output_file = os.path.join(root_dir, 'plot_pixel', file_name)
out_fh = open(output_file, 'w')
# For the plot/pixel scale, retrieve the independent predicted
# data for this value of k. Even though attributes are being
# returned from this function, we want to use the attribute list
# that we've already found above.
prediction_generator = pr.calculate_predictions_at_k(
k=k,
id_field=id_field,
independent=True,
nsa_id_dict=nsa_id_dict)
# Write out the field names
out_fh.write(id_field + ',' + ','.join(attrs) + '\n')
# Write out the predictions for this k
for plot_prediction in prediction_generator:
# Write this record to the predicted attribute file
pr.write_predicted_record(plot_prediction, out_fh, attrs=attrs)
# Close this file
out_fh.close()
# Create the fields for which to extract statistics at the hexagon
# levels
mean_fields = [(id_field, len, 'PLOT_COUNT')]
mean_fields.extend([(x, np.mean, x) for x in attrs])
mean_fields = tuple(mean_fields)
sd_fields = [(id_field, len, 'PLOT_COUNT')]
sd_fields.extend([(x, np.std, x) for x in attrs])
sd_fields = tuple(sd_fields)
stat_sets = {
'mean': mean_fields,
'std': sd_fields,
}
# For each hexagon level, associate the plots with their hexagon ID
# and find observed and predicted statistics for each hexagon
for hex_resolution in hex_resolutions:
(hex_id_field, hex_distance) = hex_resolution[0:2]
min_plots_per_hex = hex_resolution[3]
prefix = 'hex_' + str(hex_distance)
# Create a crosswalk between the id_field and the hex_id_field
id_x_hex = mlab.rec_keep_fields(obs_data, [id_field, hex_id_field])
# Iterate over all sets of statistics and write a unique file
# for each set
for (stat_name, stat_fields) in stat_sets.iteritems():
# Get the output file name
obs_out_file = \
'_'.join((prefix, 'observed', stat_name)) + '.csv'
obs_out_file = os.path.join(root_dir, prefix, obs_out_file)
# Write out the observed file
self.write_hex_stats(obs_data, hex_id_field, stat_fields,
min_plots_per_hex, obs_out_file)
# Iterate over values of k for the predicted values
for k in k_values:
# Open the plot_pixel predicted file for this value of k
# and join the hex_id_field to the recarray
prd_file = 'plot_pixel_predicted_k' + str(k) + '.csv'
prd_file = os.path.join(root_dir, 'plot_pixel', prd_file)
prd_data = utilities.csv2rec(prd_file)
prd_data = mlab.rec_join(id_field, prd_data, id_x_hex)
# Iterate over all sets of statistics and write a unique file
# for each set
for (stat_name, stat_fields) in stat_sets.iteritems():
# Get the output file name
prd_out_file = '_'.join((prefix, 'predicted', 'k' + str(k),
stat_name)) + '.csv'
prd_out_file = os.path.join(root_dir, prefix, prd_out_file)
# Write out the predicted file
self.write_hex_stats(prd_data, hex_id_field, stat_fields,
min_plots_per_hex, prd_out_file)
# Calculate the ECDF and AC statistics
# For ECDF and AC, it is a paired comparison between the observed
# and predicted data. We do this at each value of k and for each
# hex resolution level.
# Open the stats file
stats_file = p.hex_statistics_file
stats_fh = open(stats_file, 'w')
header_fields = ['LEVEL', 'K', 'VARIABLE', 'STATISTIC', 'VALUE']
stats_fh.write(','.join(header_fields) + '\n')
# Create a list of RiemannComparison instances which store the
# information needed to do comparisons between observed and predicted
# files for any level or value of k
compare_list = []
for hex_resolution in hex_resolutions:
(hex_id_field, hex_distance) = hex_resolution[0:2]
prefix = 'hex_' + str(hex_distance)
obs_file = '_'.join((prefix, 'observed', 'mean')) + '.csv'
obs_file = os.path.join(root_dir, prefix, obs_file)
for k in k_values:
prd_file = '_'.join(
(prefix, 'predicted', 'k' + str(k), 'mean')) + '.csv'
prd_file = os.path.join(root_dir, prefix, prd_file)
r = RiemannComparison(prefix, obs_file, prd_file, hex_id_field,
k)
compare_list.append(r)
# Add the plot_pixel comparisons to this list
prefix = 'plot_pixel'
obs_file = 'plot_pixel_observed.csv'
obs_file = os.path.join(root_dir, prefix, obs_file)
for k in k_values:
prd_file = 'plot_pixel_predicted_k' + str(k) + '.csv'
prd_file = os.path.join(root_dir, prefix, prd_file)
r = RiemannComparison(prefix, obs_file, prd_file, id_field, k)
compare_list.append(r)
# Do all the comparisons
for c in compare_list:
# Open the observed file
obs_data = utilities.csv2rec(c.obs_file)
# Open the predicted file
prd_data = utilities.csv2rec(c.prd_file)
# Ensure that the IDs between the observed and predicted
# data line up
ids1 = getattr(obs_data, c.id_field)
ids2 = getattr(prd_data, c.id_field)
if np.all(ids1 != ids2):
err_msg = 'IDs do not match between observed and '
err_msg += 'predicted data'
raise ValueError(err_msg)
for attr in attrs:
arr1 = getattr(obs_data, attr)
arr2 = getattr(prd_data, attr)
rv = RiemannVariable(arr1, arr2)
gmfr_stats = rv.gmfr_statistics()
for stat in ('gmfr_a', 'gmfr_b', 'ac', 'ac_sys', 'ac_uns'):
stat_line = '%s,%d,%s,%s,%.4f\n' % (c.prefix.upper(), c.k,
attr, stat.upper(),
gmfr_stats[stat])
stats_fh.write(stat_line)
ks_stats = rv.ks_statistics()
for stat in ('ks_max', 'ks_mean'):
stat_line = '%s,%d,%s,%s,%.4f\n' % (c.prefix.upper(), c.k,
attr, stat.upper(),
ks_stats[stat])
stats_fh.write(stat_line)
def run_diagnostic(self):
# Shortcut to the parameter parser
p = self.parameter_parser
# ID field
id_field = p.summary_level + 'ID'
# Root directory for Riemann files
root_dir = p.riemann_output_folder
# Read in hex input file
obs_data = utilities.csv2rec(self.hex_attribute_file)
# Get the hexagon levels and ensure that the fields exist in the
# hex_attribute file
hex_resolutions = p.riemann_hex_resolutions
hex_fields = [x[0] for x in hex_resolutions]
for field in hex_fields:
if field not in obs_data.dtype.names:
err_msg = 'Field ' + field + ' does not exist in the '
err_msg += 'hex_attribute file'
raise ValueError(err_msg)
# Create the directory structure based on the hex levels
hex_levels = ['hex_' + str(x[1]) for x in hex_resolutions]
all_levels = ['plot_pixel'] + hex_levels
for level in all_levels:
sub_dir = os.path.join(root_dir, level)
if not os.path.exists(sub_dir):
os.makedirs(sub_dir)
# Get the values of k
k_values = p.riemann_k_values
# Create a dictionary of plot ID to image year (or model_year for
# non-imagery models) for these plots
if p.model_type in p.imagery_model_types:
id_x_year = dict((x[id_field], x.IMAGE_YEAR) for x in obs_data)
else:
id_x_year = dict((x[id_field], p.model_year) for x in obs_data)
# Create a PredictionRun instance
pr = prediction_run.PredictionRun(p)
# Get the neighbors and distances for these IDs
pr.calculate_neighbors_at_ids(id_x_year, id_field=id_field)
# Create the lookup of id_field to LOC_ID for the hex plots
nsa_id_dict = dict((x[id_field], x.LOC_ID) for x in obs_data)
# Create a dictionary between id_field and no_self_assign_field
# for the model plots
env_file = p.environmental_matrix_file
env_data = utilities.csv2rec(env_file)
model_nsa_id_dict = dict((getattr(x, id_field), x.LOC_ID)
for x in env_data)
# Stitch the two dictionaries together
for id in sorted(model_nsa_id_dict.keys()):
if id not in nsa_id_dict:
nsa_id_dict[id] = model_nsa_id_dict[id]
# Get the stand attribute metadata and retrieve only the
# continuous accuracy attributes
stand_metadata_file = p.stand_metadata_file
mp = xsmp.XMLStandMetadataParser(stand_metadata_file)
attrs = [x.field_name for x in mp.attributes
if x.field_type == 'CONTINUOUS' and x.accuracy_attr == 1]
# Subset the attributes for fields that are in the
# hex_attribute file
attrs = [x for x in attrs if x in obs_data.dtype.names]
plot_pixel_obs = mlab.rec_keep_fields(obs_data, [id_field] + attrs)
# Write out the plot_pixel observed file
file_name = 'plot_pixel_observed.csv'
output_file = os.path.join(root_dir, 'plot_pixel', file_name)
utilities.rec2csv(plot_pixel_obs, output_file)
# Iterate over values of k
for k in k_values:
# Construct the output file name
file_name = '_'.join(('plot_pixel', 'predicted', 'k' + str(k)))
file_name += '.csv'
output_file = os.path.join(root_dir, 'plot_pixel', file_name)
out_fh = open(output_file, 'w')
# For the plot/pixel scale, retrieve the independent predicted
# data for this value of k. Even though attributes are being
# returned from this function, we want to use the attribute list
# that we've already found above.
prediction_generator = pr.calculate_predictions_at_k(
k=k, id_field=id_field, independent=True,
nsa_id_dict=nsa_id_dict)
# Write out the field names
out_fh.write(id_field + ',' + ','.join(attrs) + '\n')
# Write out the predictions for this k
for plot_prediction in prediction_generator:
# Write this record to the predicted attribute file
pr.write_predicted_record(plot_prediction, out_fh, attrs=attrs)
# Close this file
out_fh.close()
# Create the fields for which to extract statistics at the hexagon
# levels
mean_fields = [(id_field, len, 'PLOT_COUNT')]
mean_fields.extend([(x, np.mean, x) for x in attrs])
mean_fields = tuple(mean_fields)
sd_fields = [(id_field, len, 'PLOT_COUNT')]
sd_fields.extend([(x, np.std, x) for x in attrs])
sd_fields = tuple(sd_fields)
stat_sets = {
'mean': mean_fields,
'std': sd_fields,
}
# For each hexagon level, associate the plots with their hexagon ID
# and find observed and predicted statistics for each hexagon
for hex_resolution in hex_resolutions:
(hex_id_field, hex_distance) = hex_resolution[0:2]
min_plots_per_hex = hex_resolution[3]
prefix = 'hex_' + str(hex_distance)
# Create a crosswalk between the id_field and the hex_id_field
id_x_hex = mlab.rec_keep_fields(obs_data, [id_field, hex_id_field])
# Iterate over all sets of statistics and write a unique file
# for each set
for (stat_name, stat_fields) in stat_sets.iteritems():
# Get the output file name
obs_out_file = \
'_'.join((prefix, 'observed', stat_name)) + '.csv'
obs_out_file = os.path.join(root_dir, prefix, obs_out_file)
# Write out the observed file
self.write_hex_stats(obs_data, hex_id_field, stat_fields,
min_plots_per_hex, obs_out_file)
# Iterate over values of k for the predicted values
for k in k_values:
# Open the plot_pixel predicted file for this value of k
# and join the hex_id_field to the recarray
prd_file = 'plot_pixel_predicted_k' + str(k) + '.csv'
prd_file = os.path.join(root_dir, 'plot_pixel', prd_file)
prd_data = utilities.csv2rec(prd_file)
prd_data = mlab.rec_join(id_field, prd_data, id_x_hex)
# Iterate over all sets of statistics and write a unique file
# for each set
for (stat_name, stat_fields) in stat_sets.iteritems():
# Get the output file name
prd_out_file = '_'.join((
prefix, 'predicted', 'k' + str(k), stat_name)) + '.csv'
prd_out_file = os.path.join(root_dir, prefix, prd_out_file)
# Write out the predicted file
self.write_hex_stats(prd_data, hex_id_field, stat_fields,
min_plots_per_hex, prd_out_file)
# Calculate the ECDF and AC statistics
# For ECDF and AC, it is a paired comparison between the observed
# and predicted data. We do this at each value of k and for each
# hex resolution level.
# Open the stats file
stats_file = p.hex_statistics_file
stats_fh = open(stats_file, 'w')
header_fields = ['LEVEL', 'K', 'VARIABLE', 'STATISTIC', 'VALUE']
stats_fh.write(','.join(header_fields) + '\n')
# Create a list of RiemannComparison instances which store the
# information needed to do comparisons between observed and predicted
# files for any level or value of k
compare_list = []
for hex_resolution in hex_resolutions:
(hex_id_field, hex_distance) = hex_resolution[0:2]
prefix = 'hex_' + str(hex_distance)
obs_file = '_'.join((prefix, 'observed', 'mean')) + '.csv'
obs_file = os.path.join(root_dir, prefix, obs_file)
for k in k_values:
prd_file = '_'.join((
prefix, 'predicted', 'k' + str(k), 'mean')) + '.csv'
prd_file = os.path.join(root_dir, prefix, prd_file)
r = RiemannComparison(
prefix, obs_file, prd_file, hex_id_field, k)
compare_list.append(r)
# Add the plot_pixel comparisons to this list
prefix = 'plot_pixel'
obs_file = 'plot_pixel_observed.csv'
obs_file = os.path.join(root_dir, prefix, obs_file)
for k in k_values:
prd_file = 'plot_pixel_predicted_k' + str(k) + '.csv'
prd_file = os.path.join(root_dir, prefix, prd_file)
r = RiemannComparison(prefix, obs_file, prd_file, id_field, k)
compare_list.append(r)
# Do all the comparisons
for c in compare_list:
# Open the observed file
obs_data = utilities.csv2rec(c.obs_file)
# Open the predicted file
prd_data = utilities.csv2rec(c.prd_file)
# Ensure that the IDs between the observed and predicted
# data line up
ids1 = getattr(obs_data, c.id_field)
ids2 = getattr(prd_data, c.id_field)
if np.all(ids1 != ids2):
err_msg = 'IDs do not match between observed and '
err_msg += 'predicted data'
raise ValueError(err_msg)
for attr in attrs:
arr1 = getattr(obs_data, attr)
arr2 = getattr(prd_data, attr)
rv = RiemannVariable(arr1, arr2)
gmfr_stats = rv.gmfr_statistics()
for stat in ('gmfr_a', 'gmfr_b', 'ac', 'ac_sys', 'ac_uns'):
stat_line = '%s,%d,%s,%s,%.4f\n' % (c.prefix.upper(), c.k,
attr, stat.upper(), gmfr_stats[stat])
stats_fh.write(stat_line)
ks_stats = rv.ks_statistics()
for stat in ('ks_max', 'ks_mean'):
stat_line = '%s,%d,%s,%s,%.4f\n' % (c.prefix.upper(), c.k,
attr, stat.upper(), ks_stats[stat])
stats_fh.write(stat_line)
