def compute(self):
run_type = self.getInputFromPort("RunType")
run_count = self.getInputFromPort("Count")
output_file = self.interpreter.filePool.create_file()
os.chdir('/Users/blc/my_git/cybercom/mcmc')
copyline=['/usr/bin/matlab','-nodisplay','-r','MCMC '+run_type+' '+run_count+' '+output_file.name]
os.system(list2cmdline(copyline))
print list2cmdline(copyline)
self.setResult("Output_File", output_file)
def compute(self):
self.checkInputPort('input_file')
self.checkInputPort('iterations')
iters = self.getInputFromPort('iterations')
if iters < 1:
raise ModuleError(self, 'iterations must be >=1')
input_file = self.getInputFromPort('input_file')
if self.hasInputFromPort('output_format'):
output_suffix = self.getInputFromPort('output_format')
else:
output_suffix = self.guess_input_format(input_file.name)
if not output_suffix:
output_suffix = '.off'
output_file = self.interpreter.filePool.create_file(
suffix=output_suffix)
values = [
_mesh_filter_path, input_file.name, '-subdiv', output_file.name
]
cmdline = list2cmdline(values)
print cmdline
result = os.system(cmdline)
if result != 0:
raise ModuleError(self, 'Execution failed')
for i in xrange(iters - 1):
cmdline = '%s %s -subdiv %s' % (_mesh_filter_path,
output_file.name, output_file.name)
print cmdline
result = os.system(cmdline)
if result != 0:
raise ModuleError(self, 'Execution failed')
self.setResult('output_file', output_file)
def compute(self):
self.checkInputPort('input_file')
self.checkInputPort('iterations')
iters = self.getInputFromPort('iterations')
if iters < 1:
raise ModuleError(self, 'iterations must be >=1')
input_file = self.getInputFromPort('input_file')
if self.hasInputFromPort('output_format'):
output_suffix = self.getInputFromPort('output_format')
else:
output_suffix = self.guess_input_format(input_file.name)
if not output_suffix:
output_suffix = '.off'
output_file = self.interpreter.filePool.create_file(suffix=output_suffix)
values = [_mesh_filter_path,
input_file.name,
'-subdiv',
output_file.name]
cmdline = list2cmdline(values)
print cmdline
result = os.system(cmdline)
if result != 0:
raise ModuleError(self, 'Execution failed')
for i in xrange(iters-1):
cmdline = '%s %s -subdiv %s' % (_mesh_filter_path,
output_file.name,
output_file.name)
print cmdline
result = os.system(cmdline)
if result != 0:
raise ModuleError(self, 'Execution failed')
self.setResult('output_file', output_file)
def compute(self):
o = self.create_output_file()
r = self.getInputFromPort("r")
g = self.getInputFromPort("g")
b = self.getInputFromPort("b")
a = self.getInputFromPort("a")
path = None
if configuration.check('path'):
path = configuration.path
if path:
cmd = os.path.join(path, 'convert')
else:
cmd = 'convert'
cmd = [
cmd, '-channel', 'RGBA', '-combine', r.name, g.name, b.name,
a.name, o.name
]
if not configuration.quiet:
debug.log(cmd)
cmdline = list2cmdline(cmd)
result = os.system(cmdline)
if result != 0:
raise ModuleError(self, "system call failed: '%s'" % cmdline)
self.setResult("output", o)
def run(self):
cmd = [os.getenv("HOME") + "/bright/gui/bin/reprocess"]
cmdline = list2cmdline(cmd)
if self._debug:
print cmdline
result = os.system(cmdline)
if result != 0:
raise ModuleError(self, "Execution failed")
def compute(self):
cmd = ['pnmtojpeg']
i = self.getInputFromPort("input")
cmd.append(i.name)
o = self.interpreter.filePool.create_file(suffix='.jpg')
cmd.append(' >')
cmd.append(o.name)
self.run(list2cmdline(cmd))
self.setResult('output', o)
def compute(self):
cmd = ['pgmtoppm', 'white']
i = self.get_input("input")
cmd.append(i.name)
o = self.interpreter.filePool.create_file(suffix='.ppm')
cmd.append(' >')
cmd.append(o.name)
self.run(list2cmdline(cmd))
self.set_output('output', o)
def compute(self):
self.checkInputPort("input_file")
self.checkInputPort("iso_value")
input_file = self.getInputFromPort("input_file")
output_file = self.interpreter.filePool.create_file(suffix=".off")
iso_value = self.getInputFromPort("iso_value")
values = [get_path(), input_file.name, str(iso_value), output_file.name]
cmdline = list2cmdline(values)
print cmdline
result = os.system(cmdline)
if result != 0:
raise ModuleError(self, "Execution failed")
self.setResult("output_file", output_file)
def run(self, *args):
"""run(*args), runs ImageMagick's 'convert' on a shell, passing all
arguments to the program."""
path = None
if configuration.check('path'):
path = configuration.path
if path:
cmd = os.path.join(path,'convert')
else:
cmd = 'convert'
cmd = [cmd] + list(args)
cmdline = list2cmdline(cmd)
if not configuration.quiet:
debug.log(cmdline)
r = os.system(cmdline)
if r != 0:
raise ModuleError(self, "system call failed: '%s'" % cmdline)
def run(self, *args):
"""run(*args), runs ImageMagick's 'convert' on a shell, passing all
arguments to the program."""
path = None
if configuration.check('path'):
path = configuration.path
if path:
cmd = os.path.join(path, 'convert')
else:
cmd = 'convert'
cmd = [cmd] + list(args)
cmdline = list2cmdline(cmd)
if not configuration.quiet:
debug.log(cmdline)
r = os.system(cmdline)
if r != 0:
raise ModuleError(self, "system call failed: '%s'" % cmdline)
def compute(self):
self.check_input('input_file')
self.check_input('iso_value')
input_file = self.get_input('input_file')
output_file = self.interpreter.filePool.create_file(suffix='.off')
iso_value = self.get_input('iso_value')
values = [get_path(), input_file.name,
str(iso_value), output_file.name]
cmdline = list2cmdline(values)
print cmdline
result = os.system(cmdline)
if result != 0:
raise ModuleError(self, 'Execution failed')
self.set_output('output_file', output_file)
def compute(self):
self.checkInputPort('input_file')
input_file = self.getInputFromPort('input_file')
if self.hasInputFromPort('output_format'):
output_suffix = self.getInputFromPort('output_format')
else:
output_suffix = self.guess_input_format(input_file.name)
if not output_suffix:
output_suffix = '.off'
output_file = self.interpreter.filePool.create_file(
suffix=output_suffix)
values = [_mesh_filter_path, input_file.name, output_file.name]
cmdline = list2cmdline(values)
print cmdline
result = os.system(cmdline)
if result != 0:
raise ModuleError(self, 'Execution failed')
self.setResult('output_file', output_file)
def compute(self):
self.checkInputPort('input_file')
input_file = self.getInputFromPort('input_file')
if self.hasInputFromPort('output_format'):
output_suffix = self.getInputFromPort('output_format')
else:
output_suffix = self.guess_input_format(input_file.name)
if not output_suffix:
output_suffix = '.off'
output_file = self.interpreter.filePool.create_file(suffix=output_suffix)
values = [_mesh_filter_path,
input_file.name,
output_file.name]
cmdline = list2cmdline(values)
print cmdline
result = os.system(cmdline)
if result != 0:
raise ModuleError(self, 'Execution failed')
self.setResult('output_file', output_file)
def compute(self):
self.check_input('input_file')
self.check_input('iso_value')
input_file = self.get_input('input_file')
output_file = self.interpreter.filePool.create_file(suffix='.off')
iso_value = self.get_input('iso_value')
values = [
get_path(), input_file.name,
str(iso_value), output_file.name
]
cmdline = list2cmdline(values)
print cmdline
result = os.system(cmdline)
if result != 0:
raise ModuleError(self, 'Execution failed')
self.set_output('output_file', output_file)
def compute(self):
o = self.create_output_file()
r = self.getInputFromPort("r")
g = self.getInputFromPort("g")
b = self.getInputFromPort("b")
a = self.getInputFromPort("a")
path = None
if configuration.check('path'):
path = configuration.path
if path:
cmd = os.path.join(path,'convert')
else:
cmd = 'convert'
cmd = [cmd, '-channel', 'RGBA', '-combine',
r.name, g.name, b.name, a.name, o.name]
if not configuration.quiet:
debug.log(cmd)
cmdline = list2cmdline(cmd)
result = os.system(cmdline)
if result != 0:
raise ModuleError(self, "system call failed: '%s'" % cmdline)
self.setResult("output", o)
def compute(self):
self.checkInputPort('mesh1')
self.checkInputPort('mesh2')
f1 = self.getInputFromPort('mesh1')
f2 = self.getInputFromPort('mesh2')
make_file = self.interpreter.filePool.create_file
metro_output = make_file(suffix='.txt')
values = [get_path(), f1.name, f2.name, '-q']
need_error_meshes = False
if (self.outputPorts.has_key('error_mesh_1')
or self.outputPorts.has_key('error_mesh_2')):
need_error_meshes = True
error_mesh_output = (make_file(suffix='.ply'),
make_file(suffix='.ply'))
values.append('-c')
values.append(error_mesh_output[0].name)
values.append(error_mesh_output[1].name)
need_histograms = False
if (self.outputPorts.has_key('error_hist_1')
or self.outputPorts.has_key('error_hist_2')):
need_histograms = True
error_hist_output = (make_file(suffix='.csv'),
make_file(suffix='.csv'))
values.append('-h')
values.append(error_hist_output[0].name)
values.append(error_hist_output[1].name)
values.append('>')
values.append(metro_output.name)
cmdline = list2cmdline(values)
# cmdline = ('%s ' * len(values)) % tuple(values)
# cmdline += '> '
# cmdline += metro_output.name
print cmdline
result = os.system(cmdline)
if result != 0:
raise ModuleError(self, "Execution failed")
l = [
x for x in file(metro_output.name).readlines()
if x.startswith('Hausdorff')
][0]
regexp = re.compile(
r'Hausdorff distance: ([0123456789.]+) \(([0123456789.]+) wrt bounding box diagonal\)'
)
results = regexp.match(l).groups()
if need_error_meshes:
self.setResult('error_mesh_1', error_mesh_output[0])
self.setResult('error_mesh_2', error_mesh_output[1])
if need_histograms:
self.setResult('error_hist_1', error_hist_output[0])
self.setResult('error_hist_2', error_hist_output[1])
self.need_error_meshes = need_error_meshes
self.need_histograms = need_histograms
self.setResult('hausdorff_error', float(results[0]))
self.setResult('normalized_hausdorff_error', float(results[1]))
def run(self, args):
cmd = ['afront', '-nogui'] + args
cmdline = list2cmdline(cmd)
print cmdline
os.system(cmdline)
def air_cmd_line(self, cmd, *params):
"""Runs a command-line command for the AIR tools."""
return list2cmdline([global_airpath + cmd] + list(params))
def fsl_cmd_line(self, cmd, *params):
"""Runs a command-line command for the FSL tools."""
return ('FSLOUTPUTTYPE=NIFTI_GZ ' +
list2cmdline([global_fslpath + cmd] + list(params)))
def run(self, args):
cmd = ['afront', '-nogui'] + args
cmdline = list2cmdline(cmd)
print cmdline
os.system(cmdline)
def compute(self):
self.check_input('mesh1')
self.check_input('mesh2')
f1 = self.get_input('mesh1')
f2 = self.get_input('mesh2')
make_file = self.interpreter.filePool.create_file
metro_output = make_file(suffix='.txt')
values = [get_path(), f1.name, f2.name, '-q']
need_error_meshes = False
if (self.outputPorts.has_key('error_mesh_1') or
self.outputPorts.has_key('error_mesh_2')):
need_error_meshes = True
error_mesh_output = (make_file(suffix='.ply'),
make_file(suffix='.ply'))
values.append('-c')
values.append(error_mesh_output[0].name)
values.append(error_mesh_output[1].name)
need_histograms = False
if (self.outputPorts.has_key('error_hist_1') or
self.outputPorts.has_key('error_hist_2')):
need_histograms = True
error_hist_output = (make_file(suffix='.csv'),
make_file(suffix='.csv'))
values.append('-h')
values.append(error_hist_output[0].name)
values.append(error_hist_output[1].name)
values.append('>')
values.append(metro_output.name)
cmdline = list2cmdline(values)
# cmdline = ('%s ' * len(values)) % tuple(values)
# cmdline += '> '
# cmdline += metro_output.name
print cmdline
result = os.system(cmdline)
if result != 0:
raise ModuleError(self, "Execution failed")
l = [x for x in file(metro_output.name).readlines()
if x.startswith('Hausdorff')][0]
regexp = re.compile(r'Hausdorff distance: ([0123456789.]+) \(([0123456789.]+) wrt bounding box diagonal\)')
results = regexp.match(l).groups()
if need_error_meshes:
self.set_output('error_mesh_1', error_mesh_output[0])
self.set_output('error_mesh_2', error_mesh_output[1])
if need_histograms:
self.set_output('error_hist_1', error_hist_output[0])
self.set_output('error_hist_2', error_hist_output[1])
self.need_error_meshes = need_error_meshes
self.need_histograms = need_histograms
self.set_output('hausdorff_error', float(results[0]))
self.set_output('normalized_hausdorff_error', float(results[1]))
