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base.py
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import os
import logging
import json
import genutil
import cdat_info
import cdutil
import MV2
import cdms2
import hashlib
import numpy
from collections import OrderedDict, Mapping
import pcmdi_metrics
import cdp.cdp_io
import subprocess
import sys
import shlex
import datetime
from pcmdi_metrics import LOG_LEVEL
import copy
import re
value = 0
cdms2.setNetcdfShuffleFlag(value) # where value is either 0 or 1
cdms2.setNetcdfDeflateFlag(value) # where value is either 0 or 1
# where value is a integer between 0 and 9 included
cdms2.setNetcdfDeflateLevelFlag(value)
logging.getLogger("pcmdi_metrics").setLevel(LOG_LEVEL)
try:
basestring # noqa
except Exception:
basestring = str
# Convert cdms MVs to json
def MV2Json(data, dic={}, struct=None):
if struct is None:
struct = []
if not isinstance(data, cdms2.tvariable.TransientVariable) and dic != {}:
raise RuntimeError("MV2Json needs a cdms2 transient variable as input")
if not isinstance(data, cdms2.tvariable.TransientVariable):
return data, struct # we reach the end
else:
axis = data.getAxis(0)
if axis.id not in struct:
struct.append(axis.id)
for i, name in enumerate(axis):
dic[name], _ = MV2Json(data[i], {}, struct)
return dic, struct
# Group merged axes
def groupAxes(axes, ids=None, separator="_"):
if ids is None:
ids = [ax.id for ax in axes]
if len(ids) != len(axes):
raise RuntimeError("You need to pass as many ids as axes")
final = []
while len(axes) > 0:
axis = axes.pop(-1)
if final == []:
final = [str(v) for v in axis]
else:
tmp = final
final = []
for v1 in axis:
for v2 in tmp:
final += ["{}{}{}".format(v1, separator, v2)]
return cdms2.createAxis(final, id=separator.join(ids))
# cdutil region object need a serializer
def update_dict(d, u):
for k, v in u.items():
if isinstance(v, Mapping):
r = update_dict(d.get(k, {}), v)
d[k] = r
else:
d[k] = u[k]
return d
# Platform
def populate_prov(prov, cmd, pairs, sep=None, index=1, fill_missing=False):
try:
p = subprocess.Popen(
shlex.split(cmd),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
except Exception:
return
out, stde = p.communicate()
if stde != '':
return
for strBit in out.splitlines():
for key, value in pairs.items():
if value in strBit:
prov[key] = strBit.split(sep)[index].strip()
if fill_missing is not False:
for k in pairs:
if k not in prov:
prov[k] = fill_missing
return
def generateProvenance():
prov = OrderedDict()
platform = os.uname()
platfrm = OrderedDict()
platfrm["OS"] = platform[0]
platfrm["Version"] = platform[2]
platfrm["Name"] = platform[1]
prov["platform"] = platfrm
try:
logname = os.getlogin()
except Exception:
try:
import pwd
logname = pwd.getpwuid(os.getuid())[0]
except Exception:
try:
logname = os.environ.get('LOGNAME', 'unknown')
except Exception:
logname = 'unknown-loginname'
prov["userId"] = logname
prov["osAccess"] = bool(os.access('/', os.W_OK) * os.access('/', os.R_OK))
prov["commandLine"] = " ".join(sys.argv)
prov["date"] = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
prov["conda"] = OrderedDict()
pairs = {
'Platform': 'platform ',
'Version': 'conda version ',
'IsPrivate': 'conda is private ',
'envVersion': 'conda-env version ',
'buildVersion': 'conda-build version ',
'PythonVersion': 'python version ',
'RootEnvironment': 'root environment ',
'DefaultEnvironment': 'default environment '
}
populate_prov(prov["conda"], "conda info", pairs, sep=":", index=-1)
pairs = {
'blas': 'blas',
'CDP': 'cdp ',
'cdms': 'cdms2 ',
'cdtime': 'cdtime ',
'cdutil': 'cdutil ',
'clapack': 'clapack ',
'esmf': 'esmf ',
'esmpy': 'esmpy ',
'genutil': 'genutil ',
'lapack': 'lapack ',
'matplotlib': 'matplotlib ',
'mesalib': 'mesalib ',
'numpy': 'numpy ',
'python': 'python ',
'vcs': 'vcs ',
'vtk': 'vtk-cdat ',
}
prov["packages"] = OrderedDict()
populate_prov(prov["packages"], "conda list", pairs, fill_missing=None)
pairs = {
'vcs': 'vcs-nox ',
'vtk': 'vtk-cdat-nox ',
}
populate_prov(prov["packages"], "conda list", pairs, fill_missing=None)
pairs = {
'PMP': 'pcmdi_metrics',
'PMPObs': 'pcmdi_metrics_obs',
}
populate_prov(prov["packages"], "conda list", pairs, fill_missing=None)
# TRying to capture glxinfo
pairs = {
"vendor": "OpenGL vendor string",
"renderer": "OpenGL renderer string",
"version": "OpenGL version string",
"shading language version": "OpenGL shading language version string",
}
prov["openGL"] = OrderedDict()
populate_prov(prov["openGL"], "glxinfo", pairs, sep=":", index=-1)
prov["openGL"]["GLX"] = {
"server": OrderedDict(),
"client": OrderedDict()}
pairs = {
"version": "GLX version",
}
populate_prov(prov["openGL"]["GLX"], "glxinfo", pairs, sep=":", index=-1)
pairs = {
"vendor": "server glx vendor string",
"version": "server glx version string",
}
populate_prov(
prov["openGL"]["GLX"]["server"],
"glxinfo",
pairs,
sep=":",
index=-1)
pairs = {
"vendor": "client glx vendor string",
"version": "client glx version string",
}
populate_prov(
prov["openGL"]["GLX"]["client"],
"glxinfo",
pairs,
sep=":",
index=-1)
return prov
def sort_human(input_list):
lst = copy.copy(input_list)
def convert(text):
return int(text) if text.isdigit() else text
def alphanum(key):
return [convert(c) for c in re.split('([0-9]+)', key)]
lst.sort(key=alphanum)
return lst
def scrap(data, axis=0):
originalOrder = data.getOrder(ids=True)
if axis not in ['x', 'y', 'z', 't'] and not isinstance(axis, int):
order = "({})...".format(axis)
else:
order = "{}...".format(axis)
new = data(order=order)
axes = new.getAxisList() # Save for later
new = MV2.array(new.asma()) # lose dims
for i in range(new.shape[0] - 1, -1, -1):
tmp = new[i]
if not isinstance(tmp, (float, numpy.float)) and tmp.mask.all():
a = new[:i]
b = new[i + 1:]
if b.shape[0] == 0:
new = a
else:
new = MV2.concatenate((a, b))
newAxis = []
for v in new.getAxis(0):
newAxis.append(axes[0][int(v)])
ax = cdms2.createAxis(newAxis, id=axes[0].id)
axes[0] = ax
new.setAxisList(axes)
return new(order=originalOrder)
class CDMSDomainsEncoder(json.JSONEncoder):
def default(self, o):
components = o.components()[0].kargs
args = ','.join(
['%s=%s' % (key, val) for key, val in components.items()]
)
return {o.id: 'cdutil.region.domain(%s)' % args}
class Base(cdp.cdp_io.CDPIO, genutil.StringConstructor):
def __init__(self, root, file_template, file_mask_template=None):
genutil.StringConstructor.__init__(self, root + '/' + file_template)
self.target_grid = None
self.mask = None
self.target_mask = None
self.regrid_tool = 'esmf'
self.file_mask_template = file_mask_template
self.root = root
self.type = ''
self.setup_cdms2()
def __call__(self):
path = os.path.abspath(genutil.StringConstructor.__call__(self))
if self.type in path:
return path
else:
return path + '.' + self.type
def read(self):
pass
def write(self, data, type='json', *args, **kwargs):
self.type = type.lower()
file_name = self()
dir_path = os.path.split(file_name)[0]
if not os.path.exists(dir_path):
try:
os.makedirs(dir_path)
except Exception:
logging.getLogger("pcmdi_metrics").error(
'Could not create output directory: %s' % dir_path)
if self.type == 'json':
json_version = float(
kwargs.get(
"json_version",
data.get(
"json_version",
3.0)))
json_structure = kwargs.get(
"json_structure", data.get(
"json_structure", None))
if json_version >= 3.0 and json_structure is None:
raise Exception(
"json_version 3.0 of PMP requires json_structure to be passed" +
"to the write function or part of the dictionary dumped")
for k in ["json_structure", "json_version"]:
if k in kwargs:
del(kwargs[k])
data["json_version"] = json_version
data["json_structure"] = json_structure
f = open(file_name, 'w')
out_dict = OrderedDict({"provenance": generateProvenance()})
out_dict.update(data)
json.dump(out_dict, f, cls=CDMSDomainsEncoder, *args, **kwargs)
f.close()
elif self.type in ['asc', 'ascii', 'txt']:
f = open(file_name, 'w')
for key in list(data.keys()):
f.write('%s %s\n' % (key, data[key]))
f.close()
elif self.type == 'nc':
f = cdms2.open(file_name, 'w')
f.write(data, *args, **kwargs)
f.metrics_git_sha1 = pcmdi_metrics.__git_sha1__
f.uvcdat_version = cdat_info.get_version()
f.close()
else:
logging.getLogger("pcmdi_metrics").error('Unknown type: %s' % type)
raise RuntimeError('Unknown type: %s' % type)
logging.getLogger("pcmdi_metrics").info(
'Results saved to a %s file: %s' %
(type, file_name))
def get(self, var, var_in_file=None,
region={}, *args, **kwargs):
self.variable = var
self.var_from_file = self.extract_var_from_file(
var, var_in_file, *args, **kwargs)
self.region = region
if self.region is None:
self.region = {}
self.value = self.region.get('value', None)
if self.is_masking():
self.var_from_file = self.mask_var(self.var_from_file)
self.var_from_file = \
self.set_target_grid_and_mask_in_var(self.var_from_file)
self.var_from_file = \
self.set_domain_in_var(self.var_from_file, self.region)
return self.var_from_file
def extract_var_from_file(self, var, var_in_file, *args, **kwargs):
if var_in_file is None:
var_in_file = var
# self.extension = 'nc'
var_file = cdms2.open(self(), 'r')
for att in ["var_in_file,", "varInFile"]:
if att in kwargs:
del(kwargs[att])
extracted_var = var_file(var_in_file, *args, **kwargs)
var_file.close()
return extracted_var
def is_masking(self):
if self.value is not None:
return True
else:
return False
def mask_var(self, var):
if self.mask is None:
self.set_file_mask_template()
self.mask = self.get_mask_from_var(var)
if self.mask.shape != var.shape:
dummy, mask = genutil.grower(var, self.mask)
else:
mask = self.target_mask
mask = MV2.not_equal(mask, self.value)
return MV2.masked_where(mask, var)
def set_target_grid_and_mask_in_var(self, var):
if self.target_grid is not None:
var = var.regrid(self.target_grid, regridTool=self.regrid_tool,
regridMethod=self.regrid_method, coordSys='deg',
diag={}, periodicity=1
)
if self.target_mask is not None:
if self.target_mask.shape != var.shape:
dummy, mask = genutil.grower(var, self.target_mask)
else:
mask = self.target_mask
var = MV2.masked_where(mask, var)
return var
def set_domain_in_var(self, var, region):
domain = region.get('domain', None)
if domain is not None:
if isinstance(domain, dict):
var = var(**domain)
elif isinstance(domain, (list, tuple)):
var = var(*domain)
elif isinstance(domain, cdms2.selectors.Selector):
domain.id = region.get("id", "region")
var = var(*[domain])
return var
def set_file_mask_template(self):
if isinstance(self.file_mask_template, basestring):
self.file_mask_template = Base(self.root, self.file_mask_template,
{'domain': self.region.get('domain', None)})
def get_mask_from_var(self, var):
try:
o_mask = self.file_mask_template.get('sftlf')
except Exception:
o_mask = cdutil.generateLandSeaMask(
var, regridTool=self.regrid_tool).filled(1.) * 100.
o_mask = MV2.array(o_mask)
o_mask.setAxis(-1, var.getLongitude())
o_mask.setAxis(-2, var.getLatitude())
return o_mask
def set_target_grid(self, target, regrid_tool='esmf',
regrid_method='linear'):
self.regrid_tool = regrid_tool
self.regrid_method = regrid_method
if target == '2.5x2.5':
self.target_grid = cdms2.createUniformGrid(
-88.875, 72, 2.5, 0, 144, 2.5
)
self.target_grid_name = target
elif cdms2.isGrid(target):
self.target_grid = target
self.target_grid_name = target
else:
logging.getLogger("pcmdi_metrics").error(
'Unknown grid: %s' % target)
raise RuntimeError('Unknown grid: %s' % target)
def setup_cdms2(self):
cdms2.setNetcdfShuffleFlag(0) # Argument is either 0 or 1
cdms2.setNetcdfDeflateFlag(0) # Argument is either 0 or 1
cdms2.setNetcdfDeflateLevelFlag(0) # Argument is int between 0 and 9
def hash(self, block_size=65536):
self_file = open(self(), 'rb')
buffer = self_file.read(block_size)
hasher = hashlib.md5()
while len(buffer) > 0:
hasher.update(buffer)
buffer = self_file.read(block_size)
self_file.close()
return hasher.hexdigest()
class JSONs(object):
def addDict2Self(self, json_dict, json_struct, json_version):
if float(json_version) == 1.0:
V = json_dict[list(json_dict.keys())[0]]
for model in list(V.keys()): # loop through models
m = V[model]
for ref in list(m.keys()):
aref = m[ref]
if not(isinstance(aref, dict) and
"source" in aref): # not an obs key
continue
reals = list(aref.keys())
src = reals.pop(reals.index("source"))
for real in reals:
areal = aref[real]
areal2 = {"source": src}
for region in list(areal.keys()):
reg = areal[region]
if region == "global":
region2 = ""
else:
region2 = region + "_"
areal2[region2 + "global"] = {}
areal2[region2 + "NHEX"] = {}
areal2[region2 + "SHEX"] = {}
areal2[region2 + "TROPICS"] = {}
key_stats = list(reg.keys())
for k in key_stats:
if k[:7] == "custom_":
continue
else:
sp = k.split("_")
new_key = "_".join(sp[:-1])
domain = sp[-1]
if domain == "GLB":
domain = "global"
sp = new_key.split("_")
stat = "_".join(sp[:-1])
stat_dict = areal2[region2 +
domain].get(stat, {})
season = sp[-1]
season_dict = stat_dict
stat_dict[season] = reg[k]
if stat in areal2[region2 + domain]:
areal2[region2 +
domain][stat].update(stat_dict)
else:
areal2[region2 +
domain][stat] = stat_dict
# Now we can replace the realization with the correctly
# formatted one
aref[real] = areal2
# restore ref into model
m[ref] = aref
elif float(json_version) == 2.0:
V = json_dict[list(json_dict.keys())[0]]
for model in list(V.keys()): # loop through models
m = V[model]
for ref in list(m.keys()):
aref = m[ref]
if not(isinstance(aref, dict) and
"source" in aref): # not an obs key
continue
reals = list(aref.keys())
src = reals.pop(reals.index("source"))
for real in reals:
areal = aref[real]
for region in list(areal.keys()):
reg = areal[region]
key_stats = list(reg.keys())
for k in key_stats:
if k[:7] == "custom_":
continue
sp = k.split("_")
season = sp[-1]
stat = "_".join(sp[:-1])
stat_dict = reg.get(stat, {})
season_dict = stat_dict.get(season, {})
season_dict[season] = reg[k]
# if stat_dict.has_key(stat):
# stat_dict[stat].update(season_dict)
# else:
# stat_dict[stat]=season_dict
del(reg[k])
if stat in reg:
reg[stat].update(season_dict)
else:
reg[stat] = season_dict
aref[real] = areal
# restore ref into model
m[ref] = aref
V[model] = m
json_dict[list(json_dict.keys())[0]] = V
update_dict(self.data, json_dict)
def get_axes_values_recursive(self, depth, max_depth, data, values):
for k in list(data.keys()):
if k not in self.ignored_keys and (
isinstance(data[k], dict) or depth == max_depth):
values[depth].add(k)
if depth != max_depth:
self.get_axes_values_recursive(
depth + 1, max_depth, data[k], values)
def get_array_values_from_dict_recursive(self, out, ids, nms, axval, axes):
if len(axes) > 0:
for i, val in enumerate(axes[0][:]):
self.get_array_values_from_dict_recursive(out, list(ids) +
[i, ], list(nms) +
[axes[0].id], list(axval) +
[val, ], axes[1:])
else:
vals = self.data
for k in axval:
try:
vals = vals[k]
except Exception:
vals = 9.99e20
try:
out[tuple(ids)] = float(vals)
except Exception:
out[tuple(ids)] = 9.99e20
def __init__(self, files=[], structure=[], ignored_keys=[],
oneVariablePerFile=True, sortHuman=True):
self.json_version = 3.0
self.json_struct = structure
self.data = {}
self.axes = None
self.ignored_keys = ignored_keys
self.oneVariablePerFile = oneVariablePerFile
self.sortHuman = sortHuman
if len(files) == 0:
raise Exception("You need to pass at least one file")
for fnm in files:
self.addJson(fnm)
def addJson(self, filename):
f = open(filename)
tmp_dict = json.load(f)
json_struct = tmp_dict.get("json_structure", list(self.json_struct))
json_version = tmp_dict.get("json_version", self.json_version)
if self.oneVariablePerFile and json_struct[0] == "variable":
json_struct = json_struct[1:]
if self.oneVariablePerFile and json_struct[0] != "variable":
json_struct.insert(0, "variable")
var = tmp_dict.get("Variable", None)
if var is None: # Not stored in json, need to get from file name
fnm = os.path.basename(filename)
varnm = fnm.split("_")[0]
else:
varnm = var["id"]
if "level" in var:
varnm += "-%i" % int(var["level"] / 100.)
tmp_dict = {varnm: tmp_dict["RESULTS"]}
else:
tmp_dict = tmp_dict["RESULTS"]
if json_struct != self.json_struct and self.json_struct == []:
self.json_struct = json_struct
self.addDict2Self(tmp_dict, json_struct, json_version)
def getAxis(self, axis):
axes = self.getAxisList()
for a in axes:
if a.id == axis:
return a
return None
def getAxisIds(self):
axes = self.getAxisList()
return [ax.id for ax in axes]
def getAxisList(self):
values = []
axes = []
for a in self.json_struct:
values.append(set())
self.get_axes_values_recursive(
0, len(self.json_struct) - 1, self.data, values)
autoBounds = cdms2.getAutoBounds()
cdms2.setAutoBounds("off")
if self.sortHuman:
sortFunc = sort_human
else:
sortFunc = sorted
for i, nm in enumerate(self.json_struct):
axes.append(cdms2.createAxis(sortFunc(list(values[i])), id=nm))
self.axes = axes
cdms2.setAutoBounds(autoBounds)
return self.axes
def __call__(self, merge=[], **kargs):
""" Returns the array of values"""
# First clean up kargs
if "merge" in kargs:
merge = kargs["merge"]
del(kargs["merge"])
order = None
axes_ids = self.getAxisIds()
if "order" in kargs:
# If it's an actual axis assume that it's what user wants
# Otherwise it's an out order keyword
if "order" not in axes_ids:
order = kargs["order"]
del(kargs["order"])
ab = cdms2.getAutoBounds()
cdms2.setAutoBounds("off")
axes = self.getAxisList()
if merge != []:
if isinstance(merge[0], str):
merge = [merge, ]
if merge != []:
for merger in merge:
for merge_axis_id in merger:
if merge_axis_id not in axes_ids:
raise RuntimeError(
"You requested to merge axis is '{}' which is not valid. Axes: {}".format(
merge_axis_id, axes_ids))
sh = []
ids = []
used_ids = []
for a in axes:
# Regular axis not a merged one
sh.append(len(a)) # store length to construct array shape
ids.append(a.id) # store ids
used_ids.append(a.id)
# first let's see which vars are actually asked for
# for now assume all keys means restriction on dims
if not isinstance(merge, (list, tuple)):
raise RuntimeError(
"merge keyword must be a list of dimensions to merge together")
if len(merge) > 0 and not isinstance(merge[0], (list, tuple)):
merge = [merge, ]
for axis_id in kargs:
if axis_id not in ids:
raise ValueError("Invalid axis '%s'" % axis_id)
index = ids.index(axis_id)
value = kargs[axis_id]
if isinstance(value, basestring):
value = [value]
if not isinstance(value, (list, tuple, slice)):
raise TypeError(
"Invalid subsetting type for axis '%s', axes can only be subsetted by string,list or slice" %
axis_id)
if isinstance(value, slice):
axes[index] = axes[index].subAxis(
value.start, value.stop, value.step)
sh[index] = len(axes[index])
else: # ok it's a list
for v in value:
if v not in axes[index][:]:
raise ValueError(
"Unkwown value '%s' for axis '%s'" %
(v, axis_id))
axis = cdms2.createAxis(value, id=axes[index].id)
axes[index] = axis
sh[index] = len(axis)
array = numpy.ma.ones(sh, dtype=numpy.float)
# Now let's fill this array
self.get_array_values_from_dict_recursive(array, [], [], [], axes)
# Ok at this point we need to take care of merged axes
# First let's create the merged axes
axes_to_group = []
for merger in merge:
merged_axes = []
for axid in merger:
for ax in axes:
if ax.id == axid:
merged_axes.append(ax)
axes_to_group.append(merged_axes)
new_axes = [groupAxes(grp_axes) for grp_axes in axes_to_group]
sh2 = list(sh)
for merger in merge:
for merger in merge: # loop through all possible merging
merged_indices = []
for id in merger:
merged_indices.append(axes_ids.index(id))
for indx in merged_indices:
sh2[indx] = 1
smallest = min(merged_indices)
for indx in merged_indices:
sh2[smallest] *= sh[indx]
myorder = []
for index in range(len(sh)):
if index in myorder:
continue
for merger in merge:
merger = [axes_ids.index(x) for x in merger]
if index in merger and index not in myorder:
for indx in merger:
myorder.append(indx)
if index not in myorder: # ok did not find this one anywhere
myorder.append(index)
outData = numpy.transpose(array, myorder)
outData = numpy.reshape(outData, sh2)
yank = []
for merger in merge:
merger = [axes_ids.index(x) for x in merger]
mn = min(merger)
merger.remove(mn)
yank += merger
yank = sorted(yank, reverse=True)
for yk in yank:
extract = (slice(0, None),) * yk
extract += (0,)
outData = outData[extract]
# Ok now let's apply the newaxes
sub = 0
outData = MV2.array(outData)
merged_axis_done = []
for index in range(len(array.shape)):
foundInMerge = False
for imerge, merger in enumerate(merge):
merger = [axes_ids.index(x) for x in merger]
if index in merger:
foundInMerge = True
if imerge not in merged_axis_done:
merged_axis_done.append(imerge)
setMergedAxis = imerge
else:
setMergedAxis = -1
if not foundInMerge:
outData.setAxis(index - sub, axes[index])
else:
if setMergedAxis == -1:
sub += 1
else:
outData.setAxis(index - sub, new_axes[setMergedAxis])
outData = MV2.masked_greater(outData, 9.98e20)
outData.id = "pmp"
if order is not None:
myorder = "".join(["({})".format(nm) for nm in order])
outData = outData(order=myorder)
# Merge needs cleaning for extra dims crated
if merge != []:
for i in range(outData.ndim):
outData = scrap(outData, axis=i)
outData = MV2.masked_greater(outData, 9.9e19)
cdms2.setAutoBounds(ab)
return outData