def entry_print(ret_object):
""" 打印单条记录
通过读取全局变量（来自配置文件装载）
利用apply机制，执行每个打印配置项的gain元素方法进行打印控制
具体输出时，使用"string format".format(**dict)方法
其中"string format"内容，由两部分组成，组成方式与标题打印方法中实现的一致
"""
_entry = {}
_full_entry = {}
pf_fmt, pf_obj = apply(GainOption('patchset.files'), [ret_object])
for i in _fmt:
_entry[i[0]] = apply(GainOption(i[1]), [ret_object])
for pf in pf_obj:
_full_entry = dict(_entry, **pf)
fmtstr = sjoin(map(lambda x: sjoin(['"{', x[0], '}"'], ''), _fmt), ',')
fullfmtstr = fmtstr + ',' + sjoin(
map(lambda x: sjoin(['"{', x, '}"'], ''), pf_fmt), ',')
try:
_f = open(OUTFILE, 'a')
_f.write(fullfmtstr.format(**_full_entry))
_f.write('\r\n')
_f.flush()
except IOError as e:
logger.error('Output Entry Error')
logger.error(e)
finally:
_f.close()
def _reviewsMinus(ret):
_res = []
if not (ret.get('currentPatchSet', None)
and ret.get('currentPatchSet', None).get('approvals', None)):
return None
if not ret.get('comments', None):
return sjoin(_res, '\n')
_re = None
for c in ret.get('comments', None):
_re = re.compile('Code-Review\-2').search(c.get('message', None),
1)
if _re:
if c.get('reviewer', None).get('email', None):
if c.get('reviewer', None).get('email', None) in _ciowners:
continue
_res.append('' +
c.get('reviewer', None).get('email', None))
else:
if c.get('reviewer',
None).get('username',
None) in map(lambda x: x.split('@')[0],
_ciowners):
continue
_res.append('' +
c.get('reviewer', None).get('username', None))
return sjoin(_res, '\n')
def title_print(title):
""" 标题打印，标题由两部分组成
第一部分是配置文件装载的同时生成
第二部分是根据文件列表现实样式，动态生成
两部分合并后，生成新的标题。
"""
_pft = _config['patchset']\
['files']\
['title']\
[_config['patchset']['files']['using']]
_k_pft = _pft.keys()
_k_pft.sort()
fulltitle = dict(title, **_pft)
fmtstr = sjoin(map(lambda x: sjoin(['"{', x[0], '}"'], ''), _fmt), ',')
fullfmtstr = fmtstr + ',' + sjoin(
map(lambda x: sjoin(['"{', x, '}"'], ''), _k_pft), ',')
try:
_f = open(OUTFILE, 'w')
_f.write(fullfmtstr.format(**fulltitle))
_f.write('\r\n')
_f.flush()
except IOError:
logger.error('Output Title Error')
logger.error(e)
finally:
_f.close()
def dates_info(cf=CONF):
'''
Configuration start_date and end_date in the form yyyymmdd
'''
start_date, e = get_conf(cf, 'DATES', 'start_date', type=str)
end_date, e = get_conf(cf, 'DATES', 'end_date', type=str)
start_date = sjoin(start_date.split('-'), '')
end_date = sjoin(end_date.split('-'), '')
return dateu.parse_date(start_date), dateu.parse_date(end_date)
def dates_info(cf=CONF):
'''
Configuration start_date and end_date in the form yyyymmdd
'''
start_date,e = get_conf(cf,'DATES','start_date',type=str)
end_date,e = get_conf(cf,'DATES','end_date',type=str)
start_date = sjoin(start_date.split('-'),'')
end_date = sjoin(end_date.split('-'),'')
return dateu.parse_date(start_date),dateu.parse_date(end_date)
def check_line(templet, tlist, mlist, output, opts):
new_opts = copy.deepcopy(opts)
check_mlist_with_key = filter(
lambda x: x['msg'].find(templet['keywords']) >= 0, mlist)
check_mlist_real = mlist if templet.get('keywords',
'') == "" else check_mlist_with_key
check_mlist = filter(lambda x: x['line'] in templet['rel_scope'],
check_mlist_real)
new_opts.update({
"key_repeated":
len(check_mlist if templet.get('keywords', '') ==
"" else check_mlist_with_key)
})
if len(templet['rel_scope']) > 1 and len(check_mlist) == 0:
elog.error(
str("{msg} [{ctg}] [{confidence}]" if debug_mode else "{msg}").
format(msg="'{}' not found at context.".format(
templet['keywords']),
ctg="scope/notfound",
confidence=7))
return False
pattern_check_result = filter(
lambda x: x is not None,
map(
lambda x: check_line_with_pattern(x, templet, mlist, output,
new_opts), check_mlist))
if len(pattern_check_result) != 0:
fields_output = list(
set(
reduce(
lambda x, y: x + y,
map(lambda x: x.get('field_output', ''),
pattern_check_result))))
if len(fields_output) > 0:
print sjoin(fields_output, ',')
empty_templet = copy.deepcopy(templet)
empty_templet.update({"message": {"line": -1}})
check_result_list = map(
lambda x: HandlerSetUp(x, output),
list([empty_templet])
if len(pattern_check_result) == 0 else pattern_check_result)
# 某个模板，可能对应多行msg，所以这里要根据范围、是否强制再判断一下
max_confidence = max(
map(lambda x: int(x["check_result"]["confidence"]), check_result_list))
error_result = filter(
lambda x: int(x["check_result"]["confidence"]) == max_confidence,
check_result_list)[0]
if max_confidence <= 6: return True
elog.error(
str("{msg} [{ctg}] [{confidence}]" if debug_mode else "{msg}").format(
**error_result["check_result"]))
return False
def _sumup(ret):
l = []
for i in ret.get('submitRecords', None)[0]['labels']:
if i.get('status', None) == 'NEED':
l.append(i.get('label', None))
if l:
return 'Wait For:' + sjoin(l)
d = []
if ret.get('dependsOn', None):
for i in ret.get('dependsOn', None):
if i.get('isCurrentPatchSet', None):
d.append(i.get('number', None))
if d:
return 'Wait For:' + sjoin(d)
return ret.get('status', None)
def parse_locations(files):
'''Reads locations file(s)
locations file first line must be:
#<label>, ex: #CITIES, #RIVERS
Then each line should include <name>, <country>, <lon> <lat>
'''
if isinstance(files,basestring): files=[files]
locs=[]
for c in files:
f=open(c).readlines()
for i in f:
if i.strip().startswith('#'): continue
tmp0=i.strip().split(',')
name=tmp0[0].strip()
tmp=tmp0[1].strip().split()
country=tmp[1]
for j in range(len(tmp)):
if tmp[j].isdigit(): break
country=sjoin(tmp[:j])
lat=float(tmp[j])+float(tmp[j+1])/60.
slat=tmp[j+2]
if slat=='S': lat=-lat
lon=float(tmp[j+3])+float(tmp[j+4])/60.
slon=tmp[j+5]
if slon=='W': lon=-lon
locs+=[{'name': name,'country':country,'lon':lon,'lat':lat}]
return locs
def render_a2s(self, string):
p = Popen(['php', '/usr/share/asciitosvg/a2s'],
stdout=PIPE, stdin=PIPE)
# , stderr=STDOUT)
# r = '<svg width="237px" height="45px" version="1.1">'
r = sjoin(p.communicate(input=string)[0].split('\n')[4:], '\n')
return r
def gen_log(f, L):
i = open(f, 'w')
keys = L.keys()
keys.sort()
for d in keys:
scontents = sjoin(L[d], ' + ')
i.write('%s %s\n' % (d, scontents))
i.close()
def gen_log(f,L):
i=open(f,'w')
keys=L.keys()
keys.sort()
for d in keys:
scontents=sjoin(L[d],' + ')
i.write('%s %s\n' % (d,scontents))
i.close()
def query():
cmd = []
cmd.append("ssh {}".format("192.168.9.142"))
cmd.append("-p {}".format("29448"))
cmd.append("-l {}".format("lutx0528"))
cmd.append("gerrit query --current-patch-set")
cmd.append("--format={}".format("JSON"))
cmd.append('"{}"'.format('826'))
print sjoin(cmd)
changes = []
try:
p = Popen(sjoin(cmd),shell=True,stdout=PIPE,stderr=PIPE)
_out,_err = p.communicate()
_ret_objects = filter(lambda x:x.get('project',None)
,map(lambda x:encodeJson(json.loads(x,"UTF-8")),_out.splitlines()))
changes = map(lambda x:changeAttribute('change',x),_ret_objects)
except Exception as e:
print e
return changes
def do_query(querydict=None, limit=-1):
_limit = limit
if _limit == 0: return
current_ret_len = -1
current_sortkey = None
total_ret_len = 0
query_str = None
try:
_vcmd = ['ssh', '-p', _PORT, '-l', _USER, _HOST, 'gerrit', 'version']
p = Popen(sjoin(_vcmd), shell=True, stdout=PIPE, stderr=PIPE)
_out, _err = p.communicate()
_vstr = _out.replace('\n', '').split(' ')[2]
if _vstr not in _version:
raise Exception("version {} not have handler".format(_vstr))
except Exception as e:
logger.error("do_query[0]{}".format(e))
while (current_ret_len != 0 or total_ret_len == _limit):
vf = _version.get(_vstr, None)
query_str = sjoin(globals()[vf](querydict, total_ret_len,
current_sortkey))
try:
p = Popen(query_str, shell=True, stdout=PIPE, stderr=PIPE)
_out, _err = p.communicate()
query_ret_list = _out.splitlines()
query_ret_json = map(lambda x: json.loads(x, "UTF-8"),
query_ret_list)
ret_stat = filter(lambda x: x.get('rowCount', None),
query_ret_json)
if len(ret_stat) == 0: return
ret_objs = filter(lambda x: x.get('project', None), query_ret_json)
map(entry_handler, ret_objs)
current_ret_len = len(ret_objs)
tmp_objs = ret_objs
tmp_objs.reverse()
tmp_obj = tmp_objs.pop(0)
current_sortkey = tmp_obj.get('sortKey', None)
if total_ret_len is None: total_ret_len = 0
total_ret_len = total_ret_len + current_ret_len
except Exception as e:
logger.error("do_query[x]{}".format(e))
break
def query():
cmd = []
cmd.append("ssh {}".format("192.168.9.142"))
cmd.append("-p {}".format("29448"))
cmd.append("-l {}".format("?????"))
cmd.append("gerrit query --current-patch-set")
cmd.append("--format={}".format("JSON"))
cmd.append('"{}"'.format('826'))
print sjoin(cmd)
changes = []
try:
p = Popen(sjoin(cmd), shell=True, stdout=PIPE, stderr=PIPE)
_out, _err = p.communicate()
_ret_objects = filter(
lambda x: x.get('project', None),
map(lambda x: encodeJson(json.loads(x, "UTF-8")),
_out.splitlines()))
changes = map(lambda x: changeAttribute('change', x), _ret_objects)
except Exception as e:
print e
return changes
def get_version_info():
row={}
row['os'] = _get_os()
row['nvidia'] = _get_nvrm()
row['cuda_device'] = _get_cudadev()
row['cuda_toolkit'] = _get_cudatoolkit()
row['gcc'] = _get_gcc()
row['python'] = PYVERSION.split()[0]
row['numpy'] = numpy_version.version
row['pycuda'] = _get_pycuda()
row['pytables'] = getPyTablesVersion()
row['code_git'] = sjoin( _gitVersionDetector(), ':')
return row
def _test_genParams():
from string import join as sjoin
print ' -----------------------------------------------------------------------'
print ' | blk,thd:: | bestBlk | px_per_blk | bstThd | px_per_thd | '
print ' -----------------------------------------------------------------------'
for blocks in range(1,2049):
for threads in range(1,1025):
try:
ps = genParameters(blocks, threads, [2000,1000], silent=True, useOrigChk=False)
ps = (ps[0], ps[2], ps[1], ps[3])
psOut = [ '%4d x %4d'%(arr[0], arr[1]) for arr in ps ]
print ' |%4d, %4d:: | %s |'%(blocks, threads, sjoin(psOut, ' | '))
except ValueError:
pass
def CheckProgram(ctxt,progname,varname,moredirs=[],critical=1):
ctxt.Message("Checking for Program " + progname + "...")
if ctxt.env[varname] is not None and exists(ctxt.env[varname]):
ret = 1
else:
paths = sjoin(moredirs,':') + ':' + ctxt.env['ENV']['PATH']
fname = ctxt.env.WhereIs(progname,paths)
ret = fname != None
if ret:
ctxt.env[varname] = fname
else:
ctxt.env[varname] = None
ctxt.Result(ret)
if critical and not ret:
print "Required Program '" + progname + "' is missing."
ctxt.env.Exit(1)
return ret
def __config2cp(self):
config = ConfigParser.RawConfigParser(dict_type=OrderedDict)
keys = self.config.keys()
keys.sort()
print keys
for k in keys:
if k.find('.') > 0:
tmp = k.split('.')
section = tmp[0]
name = sjoin(tmp[1:], '')
else:
section = 'unknown'
name = k
if not config.has_section(section):
config.add_section(section)
print 'adding sec ', section
config.set(section, name, self.config[k])
self.cp = config
def __config2cp(self):
config=ConfigParser.RawConfigParser(dict_type=OrderedDict)
keys=self.config.keys()
keys.sort()
for k in keys:
if k.find('.')>0:
tmp=k.split('.')
section=tmp[0]
name=sjoin(tmp[1:],'')
else:
section='unknown'
name=k
if not config.has_section(section):
config.add_section(section)
#print 'adding sec ',section
config.set(section,name,self.config[k])
self.cp=config
def use(filename,varname,interface='auto',**kargs):
nc,close=__open(filename,interface)
if varname not in nc.varnames: return
v=nc.vars[varname]
shape=v.shape()
if not shape:
try: return v[:][0] # may be needed for dtype='|S1'
except: return v[:]
d=v.dims
dimStr=[':' for i in d.keys()]
for k in kargs.keys():
dval=kargs[k]
if k.isdigit(): k=d.keys()[int(k)] # allow use dim indice
elif k.startswith('SEARCH'): # allow *dimname or dimname*
kk=k[len('SEARCH'):]
for dn in nc.vars[varname].dimnames:
if dn.find(kk)>=0:
k=dn
break
elif k.endswith('SEARCH'):
kk=k[:-len('SEARCH')]
for dn in nc.vars[varname].dimnames:
if dn.find(kk)>=0:
k=dn
break
if k in d.keys():
i=d.index(k)
if isinstance(dval,basestring):
dimStr[i]=dval
elif isinstance(dval,int):
if dval<0: dval=shape[i]+dval
if dval>shape[i]-1:
print ':: max allowed '+k+' = '+str(shape[i]-1)
return
else:
dimStr[i]=str(dval)
elif calc.isiterable(dval):
exec(k+'_val=dval')
dimStr[i]=k+'_val'
else:
dimStr[i]=str(dval)
cmd='res=v['+sjoin(dimStr,',')+']'
exec(cmd)
if interface in ('pycdf','scientific'):
# about missing value:
miss=False
if '_FillValue' in v.attnames: miss = v.atts['_FillValue']['value']
elif 'missing_value' in v.attnames: miss = v.atts['missing_value']['value']
maskMissing=kargs.get('maskMissing',True)
if not miss is False and maskMissing and v.nctype()!='STRING':
res=np.ma.masked_where(res==miss,res)
## ensure strings have no mask:
#if v.nctype()=='STRING' and np.ma.isMA(res):
# res=np.array(res)
# about scale and offset:
if v.nctype()!='STRING':
scale=1
offset=0
if 'scale_factor' in v.attnames: scale=v.atts['scale_factor']['value']
if 'add_offset' in v.attnames: offset=v.atts['add_offset']['value']
if (scale,offset)!=(1,0): res = res*scale + offset
if close: nc.close()
if 1 in res.shape and res.ndim>1: res=np.squeeze(res)
# mask nan
maskNaN=kargs.get('maskNaN',True)
if maskNaN and not res.dtype.type==np.string_ and not np.ma.isMA(res) and np.any(np.isnan(res)):
res=np.ma.masked_where(np.isnan(res),res)
return res
def load(self):
if not self.logfile:
self.rout=False
return False
f=open(self.logfile)
L=f.readlines()
# tend and dt only written at the end of model run, so give some
# invalid values:
self.tend = -1
self.tend_str = 'not ended'
self.dt = -1
for i in range(len(L)-1):
k=L[i].strip()
val=L[i+1].strip()
if k.find('[job/process id]')==0: self.pid = val
elif k.find('[queue/local]')==0: self.job_type = val
# elif k.find('[date]')==0: self.date = val
# elif k.find('[FA]')==0: self.FA = val
elif k.find('[tstart]')==0: self.tstart,self.tstart_str = int(val.split()[0]),sjoin(val.split()[1:])
elif k.find('[tend]')==0: self.tend,self.tend_str = int(val.split()[0]),sjoin(val.split()[1:])
elif k.find('[dt (min)]')==0: self.dt=float(val)
self.rout=opt.nameof('out','rout',date=self.date,FA=self.FA,cf=self.conf)
return True
def event_design(event_spec, t, order=2, hrfs=[glover]):
"""
Create a design matrix for a GLM analysis based
on an event specification, evaluating
it a sequence of time values. Each column
in the design matrix will be convolved with each HRF in hrfs.
Parameters
----------
event_spec : np.recarray
A recarray having at least a field named 'time' signifying
the event time, and all other fields will be treated as factors
in an ANOVA-type model.
t : np.ndarray
An array of np.float values at which to evaluate
the design. Common examples would be the acquisition
times of an fMRI image.
order : int
The highest order interaction to be considered in
constructing the contrast matrices.
hrfs : seq
A sequence of (symbolic) HRF that will be convolved
with each event. If empty, glover is used.
Outputs
-------
X : np.ndarray
The design matrix with X.shape[0] == t.shape[0]. The number
of columns will depend on the other fields of event_spec.
contrasts : dict
Dictionary of contrasts that is expected to be of interest
from the event specification. For each interaction / effect
up to a given order will be returned. Also, a contrast
is generated for each interaction / effect for each HRF
specified in hrfs.
"""
fields = list(event_spec.dtype.names)
if 'time' not in fields:
raise ValueError('expecting a field called "time"')
fields.pop(fields.index('time'))
e_factors = [formula.Factor(n, np.unique(event_spec[n])) for n in fields]
e_formula = np.product(e_factors)
e_contrasts = {}
if len(e_factors) > 1:
for i in range(1, order+1):
for comb in combinations(zip(fields, e_factors), i):
names = [c[0] for c in comb]
fs = [c[1].main_effect for c in comb]
e_contrasts[sjoin(names, ':')] = np.product(fs).design(event_spec)
e_contrasts['constant'] = formula.I.design(event_spec)
# Design and contrasts in event space
# TODO: make it so I don't have to call design twice here
# to get both the contrasts and the e_X matrix as a recarray
e_X = e_formula.design(event_spec)
e_dtype = e_formula.dtype
# Now construct the design in time space
t_terms = []
t_contrasts = {}
for l, h in enumerate(hrfs):
t_terms += [events(event_spec['time'], \
amplitudes=e_X[n], f=h) for i, n in enumerate(e_dtype.names)]
for n, c in e_contrasts.items():
t_contrasts["%s_%d" % (n, l)] = formula.Formula([ \
events(event_spec['time'], amplitudes=c[nn], f=h) for i, nn in enumerate(c.dtype.names)])
t_formula = formula.Formula(t_terms)
tval = formula.make_recarray(t, ['t'])
X_t, c_t = t_formula.design(tval, contrasts=t_contrasts)
return X_t, c_t
def _get_os():
_os = _doItLineNo('uname -a', 0).split()
_os = sjoin( _os[2:5], ':') + ":" + _os[11]
return _os
def _get_cudadev():
dev = _doItLineNo('cat /proc/driver/nvidia/gpus/0/information ', 0)
return sjoin( dev.split()[1:], ' ')
def use(filename, varname, interface="auto", **kargs):
nc, close = __open(filename, interface)
if varname not in nc.varnames:
return
v = nc.vars[varname]
shape = v.shape()
if not shape:
try:
return v[:][0] # may be needed for dtype='|S1'
except:
return v[:]
d = v.dims
dimStr = [":" for i in d.keys()]
for k in kargs.keys():
dval = kargs[k]
if k.isdigit():
k = d.keys()[int(k)] # allow use dim indice
elif k.startswith("SEARCH"): # allow *dimname or dimname*
kk = k[len("SEARCH") :]
for dn in nc.vars[varname].dimnames:
if dn.find(kk) >= 0:
k = dn
break
elif k.endswith("SEARCH"):
kk = k[: -len("SEARCH")]
for dn in nc.vars[varname].dimnames:
if dn.find(kk) >= 0:
k = dn
break
if k in d.keys():
i = d.index(k)
if isinstance(dval, basestring):
dimStr[i] = dval
elif isinstance(dval, int):
if dval < 0:
dval = shape[i] + dval
if dval > shape[i] - 1:
print ":: max allowed " + k + " = " + str(shape[i] - 1)
return
else:
dimStr[i] = str(dval)
elif calc.isiterable(dval):
exec (k + "_val=dval")
dimStr[i] = k + "_val"
else:
dimStr[i] = str(dval)
cmd = "res=v[" + sjoin(dimStr, ",") + "]"
exec (cmd)
if interface in ("pycdf", "scientific"):
# about missing value:
miss = False
if "_FillValue" in v.attnames:
miss = v.atts["_FillValue"]["value"]
elif "missing_value" in v.attnames:
miss = v.atts["missing_value"]["value"]
maskMissing = kargs.get("maskMissing", True)
if not miss is False and maskMissing and v.nctype() != "STRING":
res = np.ma.masked_where(res == miss, res)
## ensure strings have no mask:
# if v.nctype()=='STRING' and np.ma.isMA(res):
# res=np.array(res)
# about scale and offset:
if v.nctype() != "STRING":
scale = 1
offset = 0
if "scale_factor" in v.attnames:
scale = v.atts["scale_factor"]["value"]
if "add_offset" in v.attnames:
offset = v.atts["add_offset"]["value"]
if (scale, offset) != (1, 0):
res = res * scale + offset
if close:
nc.close()
if 1 in res.shape and res.ndim > 1:
res = np.squeeze(res)
# mask nan
maskNaN = kargs.get("maskNaN", True)
if maskNaN and not res.dtype.type == np.string_ and not np.ma.isMA(res) and np.any(np.isnan(res)):
res = np.ma.masked_where(np.isnan(res), res)
return res
