def _set_samples(self, re):
if not isinstance(re, RegexpDict):
raise TypeError("argument re must be of class " +
"{}".format(RegexpDict))
try:
self._samples = [re.parse(f)['SM'] for f in self._inputfiles]
except KeyError:
raise Exception("failed to parse sample name 'SM' from input list")
def function(index, r):
path = index[i]
try:
with tarfile.open(path, 'r:') as tar:
for tarinfo in tar:
if os.path.basename(tarinfo.name) != basename:
continue
with tar.extractfile(tarinfo.name) as f:
re = parse.compile(pattern)
for line in f.read().decode().split('\n'):
r = re.parse(line)
if r is not None:
return r.named['pattern']
break
except Exception as e:
print(traceback.format_exc())
pass
raise ColumnNotFoundException()
def getSignal(name,data=False):
from MDSplus.mdsscalar import Int8,Int16,Int32,Int64,Float32,Float64,String
if name=='TEXT':
return String('Wooppp!!')
from MDSplus._tdishr import TdiCompile
from MDSplus.mdsarray import Int8Array,Int16Array,Int32Array,Int64Array,Float32Array,Float64Array
from MDSplus import Dimension
if name=='IMAGE':
if data:
return TdiCompile('DATA:ARR1D32')
else:
name='ARR1D32'
if name=='IMAGES':
if data:
return TdiCompile('DATA:ARR2D32')
else:
name='ARR2D32'
from re import findall as parse
# time, dim1, dim2, ...
shapes=((10000,), (800,600), (64,64,64), (32,32,32,32), (16,16,16,16,16))
dtypes= {"8" : (Int8, Int8Array, 'BYTE' , 0x100, False),
"16" : (Int16, Int16Array, 'WORD' , 0x100, False),
"32" : (Int32, Int32Array, 'LONG' , 0x100, False),
"64" : (Int64, Int64Array, 'QUADWORD' , 0x10000, False),
"F" : (Float32, Float32Array, 'FLOAT' , 2., True),
"D" : (Float64, Float64Array, 'D_FLOAT' , 2., True)}
m = parse("(ARR|SEG|NUM)(?:([0-9]*)D|)([0-9FD]+)(?:_([0-9]+))?",name.upper())[0]
ntype = m[0]
ndims = int(m[1]) if not m[1]=='' else 1
dtype = m[2]
shape = shapes[ndims] if ndims<5 else (4,)*ndims
pysfun = dtypes[dtype][0]
pyafun = dtypes[dtype][1]
tdifun = dtypes[dtype][2]
factor = dtypes[dtype][3]
isfloat= dtypes[dtype][4]
from MDSplus.compound import Range,Signal
from numpy import pi,cos,array
if ntype=='NUM':
return pysfun(pi)
def tfun(x):
x = cos(2*pi*x)
if isfloat:
return x
return round(((x+1)/2.)*0x7F)
def dfun(x):
if isfloat:
return x
return round(x*0x7F)
def mrange(N):
return Range(0., 1., 1./(N-1))
def time(r):
return Dimension(None,r).setUnits("time")
def axis(r,idx):
return Dimension(None,r).setUnits("dim_of("+str(idx)+")")
data = TdiCompile(tdifun+'($VALUE)').setUnits('V')
dims = [[]]*(ndims+1)
dims[0] = mrange(shape[0])
raw = pysfun(0).data()
tfac = 1;
for i in range(ndims,0,-1):
dims[i] = X = mrange(shape[i])
raw = array([raw*factor+dfun(x) for x in X.data().tolist()])
tfac*= factor
dims[i] = axis(dims[i],i)
raw = array([raw+tfun(x)*tfac for x in dims[0].data().tolist()])
dims[0] = time(dims[0])
raw = pyafun(raw.tolist()).setUnits('data')
return Signal(data,raw,*dims).setHelp('this is the help text')
def getSignal(name, data=False):
from MDSplus.mdsscalar import Int8, Int16, Int32, Int64, Float32, Float64, String
if name == 'TEXT':
return String('Wooppp!!')
from MDSplus._tdishr import TdiCompile
from MDSplus.mdsarray import Int8Array, Int16Array, Int32Array, Int64Array, Float32Array, Float64Array
from MDSplus import Dimension
if name == 'IMAGE':
if data:
return TdiCompile('DATA:ARR1D32')
else:
name = 'ARR1D32'
if name == 'IMAGES':
if data:
return TdiCompile('DATA:ARR2D32')
else:
name = 'ARR2D32'
from re import findall as parse
# time, dim1, dim2, ...
shapes = ((10000, ), (800, 600), (64, 64, 64), (32, 32, 32, 32),
(16, 16, 16, 16, 16))
dtypes = {
"8": (Int8, Int8Array, 'BYTE', 0x100, False),
"16": (Int16, Int16Array, 'WORD', 0x100, False),
"32": (Int32, Int32Array, 'LONG', 0x100, False),
"64": (Int64, Int64Array, 'QUADWORD', 0x10000, False),
"F": (Float32, Float32Array, 'FLOAT', 2., True),
"D": (Float64, Float64Array, 'D_FLOAT', 2., True)
}
m = parse("(ARR|SEG|NUM)(?:([0-9]*)D|)([0-9FD]+)(?:_([0-9]+))?",
name.upper())[0]
ntype = m[0]
ndims = int(m[1]) if not m[1] == '' else 1
dtype = m[2]
shape = shapes[ndims] if ndims < 5 else (4, ) * ndims
pysfun = dtypes[dtype][0]
pyafun = dtypes[dtype][1]
tdifun = dtypes[dtype][2]
factor = dtypes[dtype][3]
isfloat = dtypes[dtype][4]
from MDSplus.compound import Range, Signal
from numpy import pi, cos, array
if ntype == 'NUM':
return pysfun(pi)
def tfun(x):
x = cos(2 * pi * x)
if isfloat:
return x
return round(((x + 1) / 2.) * 0x7F)
def dfun(x):
if isfloat:
return x
return round(x * 0x7F)
def mrange(N):
return Range(0., 1., 1. / (N - 1))
def time(r):
return Dimension(None, r).setUnits("time")
def axis(r, idx):
return Dimension(None, r).setUnits("dim_of(" + str(idx) + ")")
data = TdiCompile(tdifun + '($VALUE)').setUnits('V')
dims = [[]] * (ndims + 1)
dims[0] = mrange(shape[0])
raw = pysfun(0).data()
tfac = 1
for i in range(ndims, 0, -1):
dims[i] = X = mrange(shape[i])
raw = array([raw * factor + dfun(x) for x in X.data().tolist()])
tfac *= factor
dims[i] = axis(dims[i], i)
raw = array([raw + tfun(x) * tfac for x in dims[0].data().tolist()])
dims[0] = time(dims[0])
raw = pyafun(raw.tolist()).setUnits('data')
return Signal(data, raw, *dims).setHelp('this is the help text')