def loadImageAsGreyScale(self, subscriber=0):
im = PIL.Image.open(self.paramFilename.value)
if im.mode == "I;16":
im = im.convert("I")
data = scipy.misc.fromimage(im).astype("int16")
else:
data = scipy.misc.fromimage(im, flatten=True)
Ny, Nx = data.shape
xUnit = parseFCUnit(self.paramXScale.value)
xAxis = DataContainer.FieldContainer(
scipy.linspace(0.0, self._getScalar(xUnit), Nx, True),
xUnit / self._getScalar(xUnit),
longname="x-coordinate",
shortname="x",
)
if self.paramYScale.value == "link2X":
yUnit = xUnit * float(Ny) / Nx
else:
yUnit = parseFCUnit(self.paramYScale.value)
yAxis = DataContainer.FieldContainer(
scipy.linspace(0.0, self._getScalar(yUnit), Ny, True),
yUnit / self._getScalar(yUnit),
longname="y-coordinate",
shortname="y",
)
fieldUnit = parseFCUnit(self.paramFieldUnit.value)
result = DataContainer.FieldContainer(
data, fieldUnit, longname="Image", shortname="I", dimensions=[yAxis, xAxis]
)
result.seal()
return result
def loadImageAsGreyScale(self, subscriber=0):
im = PIL.Image.open(self.paramFilename.value)
if im.mode == "I;16":
im = im.convert("I")
data = scipy.misc.fromimage(im).astype("int16")
else:
data = scipy.misc.fromimage(im, flatten=True)
Ny, Nx = data.shape
xUnit = parseFCUnit(self.paramXScale.value)
xAxis = DataContainer.FieldContainer(
scipy.linspace(0.0, self._getScalar(xUnit), Nx, True),
xUnit / self._getScalar(xUnit),
longname='x-coordinate',
shortname='x'
)
if self.paramYScale.value == 'link2X':
yUnit = xUnit * float(Ny) / Nx
else:
yUnit = parseFCUnit(self.paramYScale.value)
yAxis = DataContainer.FieldContainer(
scipy.linspace(0.0, self._getScalar(yUnit), Ny, True),
yUnit / self._getScalar(yUnit),
longname='y-coordinate',
shortname='y'
)
fieldUnit = parseFCUnit(self.paramFieldUnit.value)
result = DataContainer.FieldContainer(
data,
fieldUnit,
longname="Image",
shortname="I",
dimensions=[yAxis, xAxis]
)
result.seal()
return result
def loadImageAsGreyScale(self, subscriber=0):
import os
import re
from scipy.misc import imread
import numpy
from pyphant.core.DataContainer import FieldContainer
path = os.path.realpath(self.paramPath.value)
if os.path.isfile(path):
path = os.path.dirname(path)
pattern = re.compile(self.paramRegex.value)
filenames = filter(lambda x: pattern.match(x) is not None,
os.listdir(path))
filenames.sort()
filenames = [os.path.join(path, fname) for fname in filenames]
print path
zClip = self.getClip(self.paramZClip.value)
filenames = filenames[zClip[0]:zClip[1]]
assert len(filenames) >= 1
yClip = self.getClip(self.paramYClip.value)
xClip = self.getClip(self.paramXClip.value)
dtype = self.paramDtype.value
data = []
for i, fn in enumerate(filenames):
subscriber %= 1 + 99 * i / len(filenames)
data.append(imread(fn, True)[yClip[0]:yClip[1], xClip[0]:xClip[1]])
data = numpy.array(data, dtype=dtype)
axes = ['z', 'y', 'x']
dimensions = [
self.getDimension(a, data.shape[i]) for i, a in enumerate(axes)
]
unit = parseFCUnit(self.paramFieldUnit.value)
longname = self.paramLongname.value
shortname = self.paramShortname.value
image = FieldContainer(data=data,
dimensions=dimensions,
unit=unit,
longname=longname,
shortname=shortname,
attributes={
'yFactor': parseFCUnit(self.paramDy.value),
'xFactor': parseFCUnit(self.paramDx.value)
})
image.seal()
subscriber %= 100
return image
def loadImageAsGreyScale(self, subscriber=0):
import os
import re
from scipy.misc import imread
import numpy
from pyphant.core.DataContainer import FieldContainer
path = os.path.realpath(self.paramPath.value)
if os.path.isfile(path):
path = os.path.dirname(path)
pattern = re.compile(self.paramRegex.value)
filenames = filter(
lambda x: pattern.match(x) is not None, os.listdir(path)
)
filenames.sort()
filenames = [os.path.join(path, fname) for fname in filenames]
print path
zClip = self.getClip(self.paramZClip.value)
filenames = filenames[zClip[0]:zClip[1]]
assert len(filenames) >= 1
yClip = self.getClip(self.paramYClip.value)
xClip = self.getClip(self.paramXClip.value)
dtype = self.paramDtype.value
data = []
for i, fn in enumerate(filenames):
subscriber %= 1 + 99 * i / len(filenames)
data.append(imread(fn, True)[yClip[0]:yClip[1], xClip[0]:xClip[1]])
data = numpy.array(data, dtype=dtype)
axes = ['z', 'y', 'x']
dimensions = [
self.getDimension(a, data.shape[i]) for i, a in enumerate(axes)
]
unit = parseFCUnit(self.paramFieldUnit.value)
longname = self.paramLongname.value
shortname = self.paramShortname.value
image = FieldContainer(
data=data, dimensions=dimensions, unit=unit,
longname=longname, shortname=shortname,
attributes={'yFactor': parseFCUnit(self.paramDy.value),
'xFactor': parseFCUnit(self.paramDx.value)}
)
image.seal()
subscriber %= 100
return image
def getDimension(self, axis, length):
from pyphant.quantities import Quantity
from pyphant.core.DataContainer import FieldContainer
import numpy
delta = parseFCUnit(self.getParam('d' + axis).value)
start = parseFCUnit(self.getParam('start' + axis).value)
if isinstance(delta, Quantity):
unit = Quantity(1.0, delta.unit)
start = start.inUnitsOf(delta.unit).value
delta = delta.value
else:
unit = 1
data = start + numpy.arange(0, length, dtype=float) * delta
dim = FieldContainer(data,
unit=unit,
shortname=axis,
longname='%s-Axis' % (axis.upper(), ))
return dim
def getDimension(self, axis, length):
from pyphant.quantities import Quantity
from pyphant.core.DataContainer import FieldContainer
import numpy
delta = parseFCUnit(self.getParam('d' + axis).value)
start = parseFCUnit(self.getParam('start' + axis).value)
if isinstance(delta, Quantity):
unit = Quantity(1.0, delta.unit)
start = start.inUnitsOf(delta.unit).value
delta = delta.value
else:
unit = 1
data = start + numpy.arange(0, length, dtype=float) * delta
dim = FieldContainer(
data, unit=unit,
shortname=axis,
longname='%s-Axis' % (axis.upper(), )
)
return dim
def add_noise(self, input_fc, subscriber=0):
width = parseFCUnit(self.paramWidth.value)
scale = float(width / input_fc.unit)
noisy_data = input_fc.data + normal(
scale=scale, size=input_fc.data.shape
)
output_fc = FieldContainer(
data=noisy_data,
unit=deepcopy(input_fc.unit),
dimensions=deepcopy(input_fc.dimensions),
longname=input_fc.longname + u" with noise",
shortname=input_fc.shortname,
error=deepcopy(input_fc.error),
mask=deepcopy(input_fc.mask),
attributes=deepcopy(input_fc.attributes)
)
output_fc.seal()
return output_fc
def testQuantity(self):
self.assertEqual(parseFCUnit("120 mm"), Quantity("120 mm"))
def testInt(self):
self.assertEqual(parseFCUnit("42"), 42.0)
def testFloat(self):
self.assertEqual(parseFCUnit("2.3e-5"), 2.3e-5)
def testQuantity(self):
self.assertEqual(parseFCUnit("120 mm"), Quantity("120 mm"))
def testInt(self):
self.assertEqual(parseFCUnit("42"), 42.0)
def testFloat(self):
self.assertEqual(parseFCUnit("2.3e-5"), 2.3e-5)
