@pluto_class
class ToWorldNode(FlowNode):
pins = [
FlowPin('In', FlowPin.In),
FlowPin('Out', FlowPin.Out)
]
properties = [
IntProperty('order', 1)
]
def __init__(self):
super(ToWorldNode, self).__init__()
self.node_class = 'image.resample.ToWorldNode'
self.title = 'ToWorld'
self.category = 'Image/Resample'
self.ui_class = 'one_to_one_node'
def run(self, ctx):
img = ctx.read_pin('In')
if hasattr(img, 'spacing'):
out = Image(zoom(img, img.spacing[::-1], order=self.order), img.pixel_type)
out.spacing = [1]*len(img.spacing)
ctx.write_pin('Out', out)
else:
ctx.write_pin('Out', img)
install_node_template(ToWorldNode())
def run(self, ctx):
img = ctx.read_pin('In')
if img is None or not isinstance(img, np.ndarray):
raise ValueError('Expected an Image object')
ctx.write_pin('Out', img.shape)
@pluto_class
class DTypeNode(FlowNode):
pins = [FlowPin('In', FlowPin.In), FlowPin('Out', FlowPin.Out)]
def __init__(self):
super(DTypeNode, self).__init__()
self.node_class = 'image.info.DTypeNode'
self.title = 'DType'
self.category = 'Image/Info'
self.ui_class = 'one_to_one_node'
def run(self, ctx):
img = ctx.read_pin('In')
if img is None or not isinstance(img, np.ndarray):
raise ValueError('Expected an Image object')
ctx.write_pin('Out', str(img.dtype))
install_node_template(ImageInfoNode())
install_node_template(ShapeNode())
install_node_template(DTypeNode())
shape = eval(self.shape)
ctx.write_pin('Out', Image(np.ones(shape)))
@pluto_class
class ZerosNode(FlowNode):
pins = [FlowPin('Out', FlowPin.Out)]
properties = [
StringProperty('shape', '(0, 0)'),
]
def __init__(self):
super(ZerosNode, self).__init__()
self.node_class = 'image.new.ZerosNode'
self.title = 'Zeros'
self.category = 'Image/New'
self.ui_class = 'constant_node'
self.ui_node_title_var = 'shape'
def run(self, ctx):
if re.match('\((\s*\d+\s*,?\s*)*\)$', self.shape.strip()) is None:
raise ValueError('Invalid shape specifier: %s' % self.shape)
shape = eval(self.shape)
ctx.write_pin('Out', Image(np.zeros(shape)))
install_node_template(OnesNode())
install_node_template(ZerosNode())
def dec(fn):
flow.install_node_template(
ContextFunctionNode(fn=fn, title=title, category=category))
return fn
def register_node(fn, title, category):
flow.install_node_template(NumpyNode(fn, title, category))
fixed_mask = os.path.join(temp_dir, 'fmask.mhd')
if moving_mask == image.Image:
medkit.write(moving_mask, os.path.join(temp_dir, 'mmask.mhd'))
moving_mask = os.path.join(temp_dir, 'mmask.mhd')
t = ctx.read_pin('T')
if t:
t = list(t)
for i in range(0, len(t)):
if type(t[i]) == Parameters:
t[i].write(os.path.join(temp_dir, 't'+str(i)+'.txt'))
t[i] = os.path.join(temp_dir, 't'+str(i)+'.txt')
if self.param_file == '':
raise ValueError('Parameter file not set')
param_file = os.path.abspath(self.param_file)
run_elastix(param_file, fixed, moving, temp_dir, t=t, fixed_mask=fixed_mask, moving_mask=moving_mask, fp=fp, mp=mp)
if self.is_pin_linked('Out'):
ctx.write_pin('Out', medkit.read(os.path.join(temp_dir, 'result.0.mhd')))
if self.is_pin_linked('Transform'):
ctx.write_pin('Transform', Parameters(os.path.join(temp_dir, 'TransformParameters.0.txt')))
install_node_template(ElastixNode())
self.node_class = 'flow.constant.FloatNode'
self.title = 'Float'
self.category = 'Constants'
self.ui_class = 'constant_node'
def run(self, ctx):
ctx.write_pin('Out', self.value)
@pluto_class
class StringNode(FlowNode):
pins = [FlowPin('Out', FlowPin.Out)]
properties = [
StringProperty('value', ''),
]
def __init__(self):
super(StringNode, self).__init__()
self.node_class = 'flow.constant.StringNode'
self.title = 'String'
self.category = 'Constants'
self.ui_class = 'constant_node'
def run(self, ctx):
ctx.write_pin('Out', self.value)
install_node_template(BoolNode())
install_node_template(IntNode())
install_node_template(FloatNode())
install_node_template(StringNode())
from flow import FlowNode, FlowPin, StringProperty, install_node_template
from pluto import pluto_class
@pluto_class
class VariableNode(FlowNode):
pins = [
FlowPin('Out', FlowPin.Out)
]
properties = [
StringProperty('name', ''),
StringProperty('default', '')
]
def __init__(self):
super(VariableNode, self).__init__()
self.node_class = 'flow.variable.VariableNode'
self.title = 'Variable'
self.category = 'Flow'
self.ui_class = 'variable_node'
def run(self, ctx):
if self.name in ctx.env:
ctx.write_pin('Out', ctx.env[self.name])
else:
ctx.write_pin('Out', self.default)
install_node_template(VariableNode())
self.ui_class = 'single_pin_node'
def run(self, ctx):
ctx.write_pin('Out', eval(self.code))
@pluto_class
class FileBrowse(FlowNode):
pins = [
FlowPin('Out', FlowPin.Out)
]
properties = [
FileProperty('file', ''),
]
def __init__(self):
super(FileBrowse, self).__init__()
self.node_class = 'flow.util.FileBrowse'
self.title = 'FileBrowse'
self.category = 'Flow/Util'
self.ui_class = 'single_pin_node'
def run(self, ctx):
ctx.write_pin('Out', self.file)
install_node_template(FileBrowse())
install_node_template(EvalNode())
]
def __init__(self):
super(JetNode, self).__init__()
self.node_class = 'image.colormap.JetNode'
self.title = 'Jet'
self.category = 'Image/Colormaps'
def run(self, ctx):
img = ctx.read_pin('In')
if self.is_pin_linked('Min'):
min = ctx.read_pin('Min')
else:
min = img.min()
if self.is_pin_linked('Max'):
max = ctx.read_pin('Max')
else:
max = img.max()
out = Image(colorize(img, min, max, 'jet'), PixelType_Vec4u8)
if hasattr(img, 'spacing'):
out.spacing = img.spacing
if hasattr(img, 'origin'):
out.origin = img.origin
ctx.write_pin('Out', out)
install_node_template(PerceptuallyUniformNode())
install_node_template(JetNode())
@pluto_class
class WriteNode(FlowNode):
pins = [FlowPin('Image', FlowPin.In), FlowPin('File', FlowPin.In)]
properties = [
FileProperty('file', '', FileProperty.File_Save, "Image (*.*)"),
]
def __init__(self):
super(WriteNode, self).__init__()
self.node_class = 'medkit.io.WriteNode'
self.title = 'Write'
self.category = 'Image/IO'
def run(self, ctx):
f = self.file
if self.is_pin_linked('File'):
f = ctx.read_pin('File')
im = ctx.read_pin('Image')
if im is not None:
if os.path.splitext(f)[1] == '.png':
write(im.astype(np.uint8), f)
else:
write(im, f)
install_node_template(ReadNode())
install_node_template(WriteNode())
settings = {
'step_size': 0.5,
'regularization_weight': 0.05,
'block_size': (12, 12, 12),
'pyramid_level_min': 0,
'pyramid_level_max': 6,
}
if self.param_file is not '':
settings.update(parse_settings_old(self.param_file))
eng = RegistrationEngine('blocked_graph_cut', image.PixelType_Float64,
settings)
if self.is_pin_linked('ConstraintValues') or self.is_pin_linked(
'ConstraintMask'):
eng.set_contraints(ctx.read_pin('ConstraintValues'),
ctx.read_pin('ConstraintMask'))
if self.is_pin_linked('StartingGuess'):
eng.set_starting_guess(ctx.read_pin('StartingGuess'))
fixed = ctx.read_pin('Fixed')
moving = ctx.read_pin('Moving')
df = eng.execute(fixed, moving)
ctx.write_pin('Deformation', df)
install_node_template(RegistrationNode())
IntProperty('time', 0),
]
def __init__(self):
super(SleepNode, self).__init__()
self.node_class = 'flow.debug.Sleep'
self.title = 'Sleep'
self.category = 'Debug'
self.value = ''
def run(self, ctx):
time.sleep(int(self.time))
ctx.write_pin('Out', ctx.read_pin('In'))
install_node_template(SleepNode())
@pluto_class
class FailNode(FlowNode):
pins = [
FlowPin('In', FlowPin.In),
]
properties = [
StringProperty('error', ''),
]
def __init__(self):
super(FailNode, self).__init__()
self.node_class = 'flow.debug.Fail'
self.title = 'Fail'
IntProperty('height', 0),
IntProperty('step', 1),
IntProperty('thickness', 1),
]
def __init__(self):
super(Grid2DNode, self).__init__()
self.node_class = 'image.grid.Grid2DNode'
self.title = 'Grid2D'
self.category = 'Image/New'
self.ui_class = 'single_pin_node'
def run(self, ctx):
h = self.height
w = self.width
img_data = np.zeros((h, w)).astype('uint8')
for y in range(0, int(h / self.step) + 1):
for x in range(0, w):
for t in range(0, min(self.thickness, h - y * self.step - 1)):
img_data[y * self.step + t, x] = 1
for x in range(0, int(w / self.step) + 1):
for y in range(0, h):
for t in range(0, min(self.thickness, w - x * self.step - 1)):
img_data[y, x * self.step + t] = 1
ctx.write_pin('Out', Image(img_data, PixelType_UInt8))
install_node_template(Grid2DNode())
import flow
from pluto import pluto_class
@pluto_class
class PrintNode(flow.Node):
pins = [
flow.Pin('In', flow.Pin.In)
]
def __init__(self):
super(PrintNode, self).__init__()
self.node_class = 'flow.Print'
self.title = 'Print'
self.category = 'Flow'
self.value = ''
self.ui_class = 'print_node'
def run(self, ctx):
self.value = str(ctx.read_pin('In'))
print(self.value)
flow.install_node_template(PrintNode())
@pluto_class
class IndexNode(FlowNode):
pins = [FlowPin('In', FlowPin.In), FlowPin('Out', FlowPin.Out)]
properties = [
StringProperty('index', '0'),
]
def __init__(self):
super(IndexNode, self).__init__()
self.node_class = 'flow.list.IndexNode'
self.title = 'Slice'
self.category = 'List'
self.ui_class = 'one_to_one_node'
self.ui_node_title_var = 'index'
def run(self, ctx):
lst = ctx.read_pin('In')
# Validate index
index = self.index.strip()
if not re.match('[\-0-9:]+$', index):
raise ValueError('Invalid index')
ctx.write_pin('Out', eval('lst[%s]' % index))
install_node_template(BuildNode())
install_node_template(ConcatenateNode())
install_node_template(IndexNode())
def run(self, ctx):
img = ctx.read_pin('In')
if img is None or not isinstance(img, np.ndarray):
raise ValueError('Expected an Image object')
value = ctx.read_pin('Value')
# Validate index
index = ''
tokens = self.slice.split(',')
for i in range(0, len(tokens)):
if i != len(tokens)-1 and tokens[i] == '': # Allow a trailing ','
index = index + ','
continue
if re.match('[\-0-9:]+$', tokens[i].strip()):
index = index + tokens[i].strip()
if i != len(tokens)-1:
index = index + ','
else:
raise SyntaxError('Invalid syntax: %s' % self.slice)
tmp = img
exec('tmp[%s] = value' % index)
ctx.write_pin('Out', tmp)
install_node_template(ImageSpacingNode())
install_node_template(ImageSetSpacingNode())
install_node_template(SliceImageNode())
install_node_template(SetSliceImageNode())
if self.is_pin_linked('Def'):
do_def = True
if self.is_pin_linked('Jac'):
do_jac = True
transform = ctx.read_pin('Transform')
if type(transform) == Parameters:
transform.write(os.path.join(temp_dir, 'tp.txt'))
transform = os.path.join(temp_dir, 'tp.txt')
if type(transform) != str:
raise ValueError('Unexpected type for pin \'Transform\'')
run_transformix(transform, temp_dir, img=img, df=do_def, jac=do_jac)
if self.is_pin_linked('Out') and img != None:
ctx.write_pin('Out',
medkit.read(os.path.join(temp_dir, 'result.nii')))
if do_def:
ctx.write_pin(
'Def',
medkit.read(os.path.join(temp_dir, 'deformationField.nii')))
if do_jac:
ctx.write_pin(
'Jac',
medkit.read(os.path.join(temp_dir, 'spatialJacobian.nii')))
install_node_template(TransformixNode())