def test4(self):
""" fit 2 data concatenates with limited range of x and one model """
#load data
l = Loader()
data1 = l.load("testdata_line.txt")
data1.name = data1.filename
data2 = l.load("testdata_line1.txt")
data2.name = data2.filename
# Receives the type of model for the fitting
model1 = LineModel()
model1.name = "M1"
model1.setParam("A", 1.0)
model1.setParam("B", 1.0)
model = Model(model1, data1)
pars1 = ['A', 'B']
#Importing the Fit module
fitter = Fit('bumps')
fitter.set_data(data1, 1, qmin=0, qmax=7)
fitter.set_model(model, 1, pars1)
fitter.set_data(data2, 1, qmin=1, qmax=10)
fitter.select_problem_for_fit(id=1, value=1)
result2, = fitter.fit(handler=FitHandler())
self.assert_(result2)
self.assertTrue(
math.fabs(result2.pvec[0] - 4) / 3 <= result2.stderr[0])
self.assertTrue(
math.fabs(result2.pvec[1] - 2.5) / 3 <= result2.stderr[1])
self.assertTrue(result2.fitness / len(data1.x) < 2)
def test_double_trans_spectra(self):
xmlreader = XMLreader(self.isis_1_1_doubletrans, self.schema_1_1)
self.assertTrue(xmlreader.validate_xml())
reader = Loader()
data = reader.load(self.isis_1_1_doubletrans)
for item in data:
self._check_data(item)
def __init__(self):
PluginBase.__init__(self, name="Pr Inversion")
## Simulation window manager
self.simview = None
## State data
self.alpha = self.DEFAULT_ALPHA
self.nfunc = self.DEFAULT_NFUNC
self.max_length = self.DEFAULT_DMAX
self.q_min = None
self.q_max = None
self.has_bck = False
self.slit_height = 0
self.slit_width = 0
## Remember last plottable processed
self.last_data = ""
self._current_file_data = None
## Time elapsed for last computation [sec]
# Start with a good default
self.elapsed = 0.022
self.iq_data_shown = False
## Current invertor
self.invertor = None
self.pr = None
self.data_id = IQ_DATA_LABEL
# Copy of the last result in case we need to display it.
self._last_pr = None
self._last_out = None
self._last_cov = None
## Calculation thread
self.calc_thread = None
## Estimation thread
self.estimation_thread = None
## Result panel
self.control_panel = None
## Currently views plottable
self.current_plottable = None
## Number of P(r) points to display on the output plot
self._pr_npts = 51
self._normalize_output = False
self._scale_output_unity = False
## List of added P(r) plots
self._added_plots = {}
self._default_Iq = {}
self.list_plot_id = []
# Associate the inversion state reader with .prv files
from inversion_state import Reader
# Create a CanSAS/Pr reader
self.state_reader = Reader(self.set_state)
self._extensions = '.prv'
l = Loader()
l.associate_file_reader('.prv', self.state_reader)
#l.associate_file_reader(".svs", self.state_reader)
# Log startup
logging.info("Pr(r) plug-in started")
def get_panels(self, parent):
"""
Create and return the list of wx.Panels for your plug-in.
Define the plug-in perspective.
Panels should inherit from DefaultPanel defined below,
or should present the same interface. They must define
"window_caption" and "window_name".
:param parent: parent window
:return: list of panels
"""
# # Save a reference to the parent
self.parent = parent
self.frame = MDIFrame(self.parent, None, 'None', (100, 200))
self.invariant_panel = InvariantPanel(parent=self.frame)
self.frame.set_panel(self.invariant_panel)
self._frame_set_helper()
self.invariant_panel.set_manager(manager=self)
self.perspective.append(self.invariant_panel.window_name)
# Create reader when fitting panel are created
self.state_reader = reader(self.set_state)
# append that reader to list of available reader
loader = Loader()
loader.associate_file_reader(".inv", self.state_reader)
# loader.associate_file_reader(".svs", self.state_reader)
# Return the list of panels
return [self.invariant_panel]
def fit_single(self, isdream=False):
fitter = Fit()
data = Loader().load("testdata_line.txt")
data.name = data.filename
fitter.set_data(data,1)
# Receives the type of model for the fitting
model1 = LineModel()
model1.name = "M1"
model = Model(model1,data)
pars1= ['A','B']
fitter.set_model(model,1,pars1)
fitter.select_problem_for_fit(id=1,value=1)
result1, = fitter.fit(handler=FitHandler())
# The target values were generated from the following statements
p,s,fx = result1.pvec, result1.stderr, result1.fitness
#print "p0,p1,s0,s1,fx = %g, %g, %g, %g, %g"%(p[0],p[1],s[0],s[1],fx)
p0,p1,s0,s1,fx_ = 3.68353, 2.61004, 0.336186, 0.105244, 1.20189
if isdream:
# Dream is not a minimizer: just check that the fit is within
# uncertainty
self.assertTrue( abs(p[0]-p0) <= s0 )
self.assertTrue( abs(p[1]-p1) <= s1 )
else:
self.assertTrue( abs(p[0]-p0) <= 1e-5 )
self.assertTrue( abs(p[1]-p1) <= 1e-5 )
self.assertTrue( abs(fx-fx_) <= 1e-5 )
def test2(self):
""" fit 2 data and 2 model with no constrainst"""
#load data
l = Loader()
data1=l.load("testdata_line.txt")
data1.name = data1.filename
data2=l.load("testdata_line1.txt")
data2.name = data2.filename
#Importing the Fit module
fitter = Fit()
# Receives the type of model for the fitting
model11 = LineModel()
model11.name= "M1"
model22 = LineModel()
model11.name= "M2"
model1 = Model(model11,data1)
model2 = Model(model22,data2)
pars1= ['A','B']
fitter.set_data(data1,1)
fitter.set_model(model1,1,pars1)
fitter.select_problem_for_fit(id=1,value=0)
fitter.set_data(data2,2)
fitter.set_model(model2,2,pars1)
fitter.select_problem_for_fit(id=2,value=0)
try: result1, = fitter.fit(handler=FitHandler())
except RuntimeError,msg:
assert str(msg)=="Nothing to fit"
def setUp(self):
""" initialize data"""
self.data1=Loader().load("cyl_400_20.txt")
self.data2=Loader().load("cyl_400_40.txt")
# Receives the type of model for the fitting
from sas.models.CylinderModel import CylinderModel
cyl1 = CylinderModel()
cyl1.name = "C1"
self.model1 = Model(cyl1)
self.model1.set(scale= 1.0)
self.model1.set(radius=18)
self.model1.set(length=200)
self.model1.set(sldCyl=3e-006, sldSolv=0.0)
self.model1.set(background=0.0)
cyl2 = CylinderModel()
cyl2.name = "C2"
self.model2 = Model(cyl2)
self.model2.set(scale= 1.0)
self.model2.set(radius=37)
self.model2.set(length=300)
self.model2.set(sldCyl=3e-006, sldSolv=0.0)
self.model2.set(background=0.0)
def on_click_save(self, event):
"""
Save change into a file
"""
if not self._data:
return
self.on_change_run(event=None)
self.on_change_title(event=None)
path = None
wildcard = "CanSAS 1D files(*.xml)|*.xml"
dlg = wx.FileDialog(self, "Choose a file",
self._default_save_location, "", wildcard , wx.SAVE)
for data in self._data:
if issubclass(data.__class__, Data2D):
msg = "No conventional writing format for \n\n"
msg += "Data2D at this time.\n"
dlg = wx.MessageDialog(None, msg, 'Error Loading File',
wx.OK | wx.ICON_EXCLAMATION)
dlg.ShowModal()
else:
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
mypath = os.path.basename(path)
loader = Loader()
format = ".xml"
if os.path.splitext(mypath)[1].lower() == format:
loader.save(path, data, format)
try:
self._default_save_location = os.path.dirname(path)
except:
pass
dlg.Destroy()
event.Skip()
def test4(self):
""" fit 2 data concatenates with limited range of x and one model """
#load data
l = Loader()
data1 = l.load("testdata_line.txt")
data1.name = data1.filename
data2 = l.load("testdata_line1.txt")
data2.name = data2.filename
# Receives the type of model for the fitting
model1 = LineModel()
model1.name= "M1"
model1.setParam("A", 1.0)
model1.setParam("B",1.0)
model = Model(model1,data1)
pars1= ['A','B']
#Importing the Fit module
fitter = Fit()
fitter.set_data(data1,1,qmin=0, qmax=7)
fitter.set_model(model,1,pars1)
fitter.set_data(data2,1,qmin=1,qmax=10)
fitter.select_problem_for_fit(id=1,value=1)
result2, = fitter.fit(handler=FitHandler())
self.assert_(result2)
self.assertTrue( math.fabs(result2.pvec[0]-4)/3 <= result2.stderr[0] )
self.assertTrue( math.fabs(result2.pvec[1]-2.5)/3 <= result2.stderr[1] )
self.assertTrue( result2.fitness/len(data1.x) < 2)
def test_double_trans_spectra(self):
xmlreader = XMLreader(self.isis_1_1_doubletrans, self.schema_1_1)
self.assertTrue(xmlreader.validate_xml())
reader = Loader()
data = reader.load(self.isis_1_1_doubletrans)
for item in data:
self._check_data(item)
def setUp(self):
"""
Set up the initial conditions before _each_ test
so that they all start from the same well-defined state.
"""
#Creating a loader
self.L=Loader()
def test2(self):
""" fit 2 data and 2 model with no constrainst"""
#load data
l = Loader()
data1 = l.load("testdata_line.txt")
data1.name = data1.filename
data2 = l.load("testdata_line1.txt")
data2.name = data2.filename
#Importing the Fit module
fitter = Fit('bumps')
# Receives the type of model for the fitting
model11 = LineModel()
model11.name = "M1"
model22 = LineModel()
model11.name = "M2"
model1 = Model(model11, data1)
model2 = Model(model22, data2)
pars1 = ['A', 'B']
fitter.set_data(data1, 1)
fitter.set_model(model1, 1, pars1)
fitter.select_problem_for_fit(id=1, value=0)
fitter.set_data(data2, 2)
fitter.set_model(model2, 2, pars1)
fitter.select_problem_for_fit(id=2, value=0)
try:
result1, = fitter.fit(handler=FitHandler())
except RuntimeError, msg:
assert str(msg) == "Nothing to fit"
def fit_single(self, fitter_name, isdream=False):
fitter = Fit(fitter_name)
data = Loader().load("testdata_line.txt")
data.name = data.filename
fitter.set_data(data, 1)
# Receives the type of model for the fitting
model1 = LineModel()
model1.name = "M1"
model = Model(model1, data)
pars1 = ['A', 'B']
fitter.set_model(model, 1, pars1)
fitter.select_problem_for_fit(id=1, value=1)
result1, = fitter.fit(handler=FitHandler())
# The target values were generated from the following statements
p, s, fx = result1.pvec, result1.stderr, result1.fitness
#print "p0,p1,s0,s1,fx = %g, %g, %g, %g, %g"%(p[0],p[1],s[0],s[1],fx)
p0, p1, s0, s1, fx_ = 3.68353, 2.61004, 0.336186, 0.105244, 1.20189
if isdream:
# Dream is not a minimizer: just check that the fit is within
# uncertainty
self.assertTrue(abs(p[0] - p0) <= s0)
self.assertTrue(abs(p[1] - p1) <= s1)
else:
self.assertTrue(abs(p[0] - p0) <= 1e-5)
self.assertTrue(abs(p[1] - p1) <= 1e-5)
self.assertTrue(abs(fx - fx_) <= 1e-5)
def test_singleton(self):
"""
Testing whether Loader is truly a singleton
"""
# Create a 'new' Loader
b = Loader()
self.assertEqual(self.loader._get_registry_creation_time(),
b._get_registry_creation_time())
def __init__(self,
path,
completefn=None,
updatefn=None,
yieldtime=0.01,
worktime=0.01):
CalcThread.__init__(self, completefn, updatefn, yieldtime, worktime)
self.path = path
#Instantiate a loader
self.loader = Loader()
self.starttime = 0
def test_old_cansas_files(self):
reader1 = XMLreader(self.cansas1d, self.schema_1_0)
self.assertTrue(reader1.validate_xml())
file_loader = Loader()
file1 = file_loader.load(self.cansas1d)
reader2 = XMLreader(self.cansas1d_units, self.schema_1_0)
self.assertTrue(reader2.validate_xml())
reader3 = XMLreader(self.cansas1d_badunits, self.schema_1_0)
self.assertTrue(reader3.validate_xml())
reader4 = XMLreader(self.cansas1d_slit, self.schema_1_0)
self.assertTrue(reader4.validate_xml())
def test_old_cansas_files(self):
reader1 = XMLreader(self.cansas1d, self.schema_1_0)
self.assertTrue(reader1.validate_xml())
file_loader = Loader()
file1 = file_loader.load(self.cansas1d)
reader2 = XMLreader(self.cansas1d_units, self.schema_1_0)
self.assertTrue(reader2.validate_xml())
reader3 = XMLreader(self.cansas1d_badunits, self.schema_1_0)
self.assertTrue(reader3.validate_xml())
reader4 = XMLreader(self.cansas1d_slit, self.schema_1_0)
self.assertTrue(reader4.validate_xml())
class testLoader(unittest.TestCase):
def setUp(self):
self.L = Loader()
self.L.find_plugins('../plugins')
def testplugin(self):
"""
test loading with a test reader only
found in the plugins directory
"""
output = self.L.load('test_data.test')
self.assertEqual(output.x[0], 1234.)
def setUp(self):
# NIST sample data
self.data = Loader().load("CMSphere5.txt")
# NIST smeared sphere w/ param values below
self.answer = Loader().load("CMSphere5smearsphere.txt")
# call spheremodel
self.model = SphereModel()
# setparams consistent with Igor default
self.model.setParam('scale', 1.0)
self.model.setParam('background', 0.01)
self.model.setParam('radius', 60.0)
self.model.setParam('sldSolv', 6.3e-06)
self.model.setParam('sldSph', 1.0e-06)
class testLoader(unittest.TestCase):
def setUp(self):
self.L=Loader()
self.L.find_plugins('../plugins')
def testplugin(self):
"""
test loading with a test reader only
found in the plugins directory
"""
output = self.L.load('test_data.test')
self.assertEqual(output.x[0], 1234.)
def setUp(self):
loader = Loader()
## IGOR/NIST computation
self.output_gauss = loader.load('Gausssphere.txt')
self.output_shulz = loader.load('Schulzsphere.txt')
from sas.models.SphereModel import SphereModel
self.model = SphereModel()
self.model.setParam('scale', 0.01)
self.model.setParam('radius', 60.0)
self.model.setParam('sldSph', 1.e-6)
self.model.setParam('sldSolv', 3.e-6)
self.model.setParam('background', 0.001)
def setUp(self):
loader = Loader()
## IGOR/NIST computation
self.output_gauss=loader.load('Gausssphere.txt')
self.output_shulz=loader.load('Schulzsphere.txt')
from sas.models.SphereModel import SphereModel
self.model= SphereModel()
self.model.setParam('scale', 0.01)
self.model.setParam('radius', 60.0)
self.model.setParam('sldSph', 1.e-6)
self.model.setParam('sldSolv', 3.e-6)
self.model.setParam('background', 0.001)
def test_bad_pars(self):
fitter = Fit('bumps')
data = Loader().load("testdata_line.txt")
data.name = data.filename
fitter.set_data(data, 1)
model1 = LineModel()
model1.name = "M1"
model = Model(model1, data)
pars1 = ['param1', 'param2']
try:
fitter.set_model(model, 1, pars1)
except ValueError, exc:
#print "ValueError was correctly raised: "+str(msg)
assert str(exc).startswith('parameter param1')
def find_extension():
"""
Describe the extensions that can be read by the current application
"""
try:
list = []
EXCEPTION_LIST = ['*', '.', '']
from sas.dataloader.loader import Loader
wild_cards = Loader().get_wildcards()
for item in wild_cards:
#['All (*.*)|*.*']
file_type, ext = string.split(item, "|*.", 1)
if ext.strip() not in EXCEPTION_LIST and ext.strip() not in list:
list.append(ext)
except:
pass
try:
file_type, ext = string.split(local_config.APPLICATION_WLIST, "|*.", 1)
if ext.strip() not in EXCEPTION_LIST and ext.strip() not in list:
list.append(ext)
except:
pass
try:
for item in local_config.PLUGINS_WLIST:
file_type, ext = string.split(item, "|*.", 1)
if ext.strip() not in EXCEPTION_LIST and ext.strip() not in list:
list.append(ext)
except:
pass
return list
def test_slits(self):
"""
Check slit data
"""
filename = "cansas1d_slit.xml"
data = Loader().load(filename)
self.data = data[0]
self.assertEqual(self.data.filename, filename)
self.assertEqual(self.data.run[0], "1234")
# Data
self.assertEqual(len(self.data.x), 2)
self.assertEqual(self.data.x_unit, '1/A')
self.assertEqual(self.data.y_unit, '1/cm')
self.assertEqual(self.data.x[0], 0.02)
self.assertEqual(self.data.y[0], 1000)
self.assertEqual(self.data.dxl[0], 0.005)
self.assertEqual(self.data.dxw[0], 0.001)
self.assertEqual(self.data.dy[0], 3)
self.assertEqual(self.data.x[1], 0.03)
self.assertAlmostEquals(self.data.y[1], 1001.0)
self.assertEqual(self.data.dx, None)
self.assertEqual(self.data.dxl[1], 0.005)
self.assertEqual(self.data.dxw[1], 0.001)
self.assertEqual(self.data.dy[1], 4)
self.assertEqual(self.data.run_name['1234'], 'run name')
self.assertEqual(self.data.title, "Test title")
def test_cylinder_fit(self):
""" Simple cylinder model fit """
out = Loader().load("cyl_400_20.txt")
fitter = Fit('bumps')
# Receives the type of model for the fitting
from sas.models.CylinderModel import CylinderModel
model = CylinderModel()
model.setParam('sldCyl', 1)
model.setParam('sldSolv', 0)
model.setParam('scale', 1e-10)
pars1 = ['length', 'radius', 'scale']
fitter.set_data(out, 1)
fitter.set_model(model, 1, pars1, constraints=())
fitter.select_problem_for_fit(id=1, value=1)
result1, = fitter.fit()
#print result1
#print result1.__dict__
self.assert_(result1)
self.assertTrue(len(result1.pvec) > 0 or len(result1.pvec) == 0)
self.assertTrue(len(result1.stderr) > 0 or len(result1.stderr) == 0)
self.assertTrue(
math.fabs(result1.pvec[0] - 400.0) / 3.0 < result1.stderr[0])
self.assertTrue(
math.fabs(result1.pvec[1] - 20.0) / 3.0 < result1.stderr[1])
self.assertTrue(
math.fabs(result1.pvec[2] - 9.0e-12) / 3.0 < result1.stderr[2])
self.assertTrue(result1.fitness < 1.0)
def test_without_resolution(self):
""" Simple cylinder model fit """
out=Loader().load("cyl_400_20.txt")
# This data file has not error, add them
#out.dy = out.y
fitter = Fit()
fitter.set_data(out,1)
# Receives the type of model for the fitting
model1 = CylinderModel()
model1.setParam("scale", 1.0)
model1.setParam("radius",18)
model1.setParam("length", 397)
model1.setParam("sldCyl",3e-006 )
model1.setParam("sldSolv",0.0 )
model1.setParam("background", 0.0)
model = Model(model1)
pars1 =['length','radius','scale']
fitter.set_model(model,1,pars1)
# What the hell is this line for?
fitter.select_problem_for_fit(id=1,value=1)
result1, = fitter.fit()
#print "result1",result1
self.assert_(result1)
self.assertTrue(len(result1.pvec) > 0)
self.assertTrue(len(result1.stderr) > 0)
self.assertTrue( math.fabs(result1.pvec[0]-400.0)/3.0 < result1.stderr[0] )
self.assertTrue( math.fabs(result1.pvec[1]-20.0)/3.0 < result1.stderr[1] )
self.assertTrue( math.fabs(result1.pvec[2]-1)/3.0 < result1.stderr[2] )
self.assertTrue( result1.fitness < 1.0 )
def test_sectorphi_full(self):
"""
Test sector averaging I(phi)
When considering the whole azimuthal range (2pi),
the answer should be the same as ring averaging.
The test data was not generated by IGOR.
"""
from sas.dataloader.manipulations import SectorPhi
import math
nbins = 19
phi_min = math.pi / (nbins + 1)
phi_max = math.pi * 2 - phi_min
r = SectorPhi(r_min=.005,
r_max=.01,
phi_min=phi_min,
phi_max=phi_max,
nbins=nbins)
o = r(self.data)
answer = Loader().load('ring_testdata.txt')
for i in range(len(o.x)):
self.assertAlmostEqual(o.x[i], answer.x[i], 4)
self.assertAlmostEqual(o.y[i], answer.y[i], 4)
self.assertAlmostEqual(o.dy[i], answer.dy[i], 4)
def test_bad_pars(self):
fitter = Fit()
data = Loader().load("testdata_line.txt")
data.name = data.filename
fitter.set_data(data,1)
model1 = LineModel()
model1.name = "M1"
model = Model(model1, data)
pars1= ['param1','param2']
try:
fitter.set_model(model,1,pars1)
except ValueError,exc:
#print "ValueError was correctly raised: "+str(msg)
assert str(exc).startswith('parameter param1')
def _reset_helper(self, path=None, npts=NPTS):
"""
Set value to fitter and prepare inputs for map function
"""
for i in range(npts):
data = Loader().load(path)
fitter = Fit()
#create model
model = CylinderModel()
model.setParam('scale', 1.0)
model.setParam('radius', 20.0)
model.setParam('length', 400.0)
model.setParam('sldCyl', 4e-006)
model.setParam('sldSolv', 1e-006)
model.setParam('background', 0.0)
for param in model.dispersion.keys():
model.set_dispersion(param, self.polydisp['gaussian']())
model.setParam('cyl_phi.width', 10)
model.setParam('cyl_phi.npts', 3)
model.setParam('cyl_theta.nsigmas', 10)
# for 2 data cyl_theta = 60.0 [deg] cyl_phi= 60.0 [deg]
fitter.set_model(model, i, self.param_to_fit,
self.list_of_constraints)
#smear data
current_smearer = smear_selection(data, model)
import cPickle
p = cPickle.dumps(current_smearer)
sm = cPickle.loads(p)
fitter.set_data(data=data, id=i,
smearer=current_smearer, qmin=self.qmin, qmax=self.qmax)
fitter.select_problem_for_fit(id=i, value=1)
self.list_of_fitter.append(copy.deepcopy(fitter))
self.list_of_function.append('fit')
self.list_of_mapper.append(classMapper)
def _dispersion(self, fitter):
# Load data
# This data is for a cylinder with
# length=400, radius=20, radius disp=5, scale=1e-10
out = Loader().load("cyl_400_20_disp5r.txt")
out.dy = numpy.zeros(len(out.y))
for i in range(len(out.y)):
out.dy[i] = math.sqrt(out.y[i])
# Receives the type of model for the fitting
model1 = CylinderModel()
model1.setParam("scale", 10.0)
model1.setParam("radius", 18)
model1.setParam("length", 397)
model1.setParam("sldCyl", 3e-006)
model1.setParam("sldSolv", 0.0)
model1.setParam("background", 0.0)
# Dispersion parameters
model1.dispersion['radius']['width'] = 0.25
model1.dispersion['radius']['npts'] = 50
model = Model(model1)
pars1 = ['length', 'radius', 'scale', 'radius.width']
fitter.set_data(out, 1)
fitter.set_model(model, 1, pars1)
fitter.select_problem_for_fit(id=1, value=1)
#import time; T0 = time.time()
result1, = fitter.fit()
#print "time",time.time()-T0,fitter._engine.__class__.__name__
self.assert_(result1)
self.assertTrue(len(result1.pvec) > 0)
self.assertTrue(len(result1.stderr) > 0)
#print [z for z in zip(result1.param_list,result1.pvec,result1.stderr)]
self.assertTrue(
math.fabs(result1.pvec[0] - 399.8) / 3.0 < result1.stderr[0])
self.assertTrue(
math.fabs(result1.pvec[1] - 17.5) / 3.0 < result1.stderr[1])
self.assertTrue(
math.fabs(result1.pvec[2] - 11.1) / 3.0 < result1.stderr[2])
self.assertTrue(
math.fabs(result1.pvec[3] - 0.276) / 3.0 < result1.stderr[3])
self.assertTrue(result1.fitness < 1.0)
def choose_data_file(self, location=None):
"""
Open a file dialog to allow loading a file
"""
path = None
if location == None:
location = os.getcwd()
l = Loader()
cards = l.get_wildcards()
wlist = '|'.join(cards)
dlg = wx.FileDialog(self, "Choose a file", location, "", wlist, wx.OPEN)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
mypath = os.path.basename(path)
dlg.Destroy()
return path
def test_units(self):
"""
Check units.
Note that not all units are available.
"""
filename = "cansas1d_units.xml"
data = Loader().load(filename)
self.data = data[0]
self.assertEqual(self.data.filename, filename)
self._checkdata()
def setUp(self):
data = Loader().load("latex_smeared.xml")
self.data_res = data[0]
self.data_slit = data[1]
self.sphere = SphereModel()
self.sphere.setParam('background', 0)
self.sphere.setParam('radius', 5000.0)
self.sphere.setParam('scale', 0.4)
self.sphere.setParam('sldSolv',0)
self.sphere.setParam('sldSph',1e-6)
def test_save_cansas_v1_0(self):
filename = "isis_1_0_write_test.xml"
xmlreader = XMLreader(self.isis_1_0, self.schema_1_0)
valid = xmlreader.validate_xml()
self.assertTrue(valid)
reader_generic = Loader()
dataloader = reader_generic.load(self.isis_1_0)
reader_cansas = Reader()
cansasreader = reader_cansas.read(self.isis_1_0)
for i in range(len(dataloader)):
self._check_data(dataloader[i])
self._check_data(cansasreader[i])
reader_generic.save(filename, dataloader[i], None)
reader2 = Reader()
return_data = reader2.read(filename)
written_data = return_data[0]
xmlwrite = XMLreader(filename, self.schema_1_0)
valid = xmlreader.validate_xml()
self.assertTrue(valid)
self._check_data(written_data)
def test_save_cansas_v1_0(self):
filename = "isis_1_0_write_test.xml"
xmlreader = XMLreader(self.isis_1_0, self.schema_1_0)
valid = xmlreader.validate_xml()
self.assertTrue(valid)
reader_generic = Loader()
dataloader = reader_generic.load(self.isis_1_0)
reader_cansas = Reader()
cansasreader = reader_cansas.read(self.isis_1_0)
for i in range(len(dataloader)):
self._check_data(dataloader[i])
self._check_data(cansasreader[i])
reader_generic.save(filename, dataloader[i], None)
reader2 = Reader()
return_data = reader2.read(filename)
written_data = return_data[0]
xmlwrite = XMLreader(filename, self.schema_1_0)
valid = xmlreader.validate_xml()
self.assertTrue(valid)
self._check_data(written_data)
def test_constraints(self):
""" fit 2 data and 2 model with 1 constrainst"""
#load data
l = Loader()
data1 = l.load("testdata_line.txt")
data1.name = data1.filename
data2 = l.load("testdata_cst.txt")
data2.name = data2.filename
# Receives the type of model for the fitting
model11 = LineModel()
model11.name = "line"
model11.setParam("A", 1.0)
model11.setParam("B", 1.0)
model22 = Constant()
model22.name = "cst"
model22.setParam("value", 1.0)
model1 = Model(model11, data1)
model2 = Model(model22, data2)
model1.set(A=4)
model1.set(B=3)
# Constraint the constant value to be equal to parameter B (the real value is 2.5)
#model2.set(value='line.B')
pars1 = ['A', 'B']
pars2 = ['value']
#Importing the Fit module
fitter = Fit('bumps')
fitter.set_data(data1, 1)
fitter.set_model(model1, 1, pars1)
fitter.set_data(data2, 2, smearer=None)
fitter.set_model(model2, 2, pars2, constraints=[("value", "line.B")])
fitter.select_problem_for_fit(id=1, value=1)
fitter.select_problem_for_fit(id=2, value=1)
R1, R2 = fitter.fit(handler=FitHandler())
self.assertTrue(math.fabs(R1.pvec[0] - 4.0) / 3. <= R1.stderr[0])
self.assertTrue(math.fabs(R1.pvec[1] - 2.5) / 3. <= R1.stderr[1])
self.assertTrue(R1.fitness / (len(data1.x) + len(data2.x)) < 2)
def _dispersion(self, fitter):
# Load data
# This data is for a cylinder with
# length=400, radius=20, radius disp=5, scale=1e-10
out=Loader().load("cyl_400_20_disp5r.txt")
out.dy = numpy.zeros(len(out.y))
for i in range(len(out.y)):
out.dy[i] = math.sqrt(out.y[i])
# Receives the type of model for the fitting
model1 = CylinderModel()
model1.setParam("scale", 10.0)
model1.setParam("radius",18)
model1.setParam("length", 397)
model1.setParam("sldCyl",3e-006 )
model1.setParam("sldSolv",0.0 )
model1.setParam("background", 0.0)
# Dispersion parameters
model1.dispersion['radius']['width'] = 0.25
model1.dispersion['radius']['npts'] = 50
model = Model(model1)
pars1 =['length','radius','scale','radius.width']
fitter.set_data(out,1)
fitter.set_model(model,1,pars1)
fitter.select_problem_for_fit(id=1,value=1)
#import time; T0 = time.time()
result1, = fitter.fit()
self.assert_(result1)
self.assertTrue(len(result1.pvec)>0)
self.assertTrue(len(result1.stderr)>0)
#print [z for z in zip(result1.param_list,result1.pvec,result1.stderr)]
self.assertTrue( math.fabs(result1.pvec[0]-399.8)/3.0 < result1.stderr[0] )
self.assertTrue( math.fabs(result1.pvec[1]-17.5)/3.0 < result1.stderr[1] )
self.assertTrue( math.fabs(result1.pvec[2]-11.1)/3.0 < result1.stderr[2] )
self.assertTrue( math.fabs(result1.pvec[3]-0.276)/3.0 < result1.stderr[3] )
self.assertTrue( result1.fitness < 1.0 )
def test_constraints(self):
""" fit 2 data and 2 model with 1 constrainst"""
#load data
l = Loader()
data1= l.load("testdata_line.txt")
data1.name = data1.filename
data2= l.load("testdata_cst.txt")
data2.name = data2.filename
# Receives the type of model for the fitting
model11 = LineModel()
model11.name= "line"
model11.setParam("A", 1.0)
model11.setParam("B",1.0)
model22 = Constant()
model22.name= "cst"
model22.setParam("value", 1.0)
model1 = Model(model11,data1)
model2 = Model(model22,data2)
model1.set(A=4)
model1.set(B=3)
# Constraint the constant value to be equal to parameter B (the real value is 2.5)
#model2.set(value='line.B')
pars1= ['A','B']
pars2= ['value']
#Importing the Fit module
fitter = Fit()
fitter.set_data(data1,1)
fitter.set_model(model1,1,pars1)
fitter.set_data(data2,2,smearer=None)
fitter.set_model(model2,2,pars2,constraints=[("value","line.B")])
fitter.select_problem_for_fit(id=1,value=1)
fitter.select_problem_for_fit(id=2,value=1)
R1,R2 = fitter.fit(handler=FitHandler())
self.assertTrue( math.fabs(R1.pvec[0]-4.0)/3. <= R1.stderr[0])
self.assertTrue( math.fabs(R1.pvec[1]-2.5)/3. <= R1.stderr[1])
self.assertTrue( R1.fitness/(len(data1.x)+len(data2.x)) < 2)
def OnLoad(self, event):
path = None
dlg = wx.FileDialog(None, "Choose a file", os.getcwd(), "", "*", wx.OPEN)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
mypath = os.path.basename(path)
from sas.dataloader.loader import Loader
# Instantiate a loader
L = Loader()
# Recieves data
try:
output = L.load(path)
except:
raise
newplot = Data2D(image=output.data)
newplot.setValues(output)
self.plotpanel.add_image(newplot)
dlg.Destroy()
class designtest(unittest.TestCase):
def setUp(self):
self.loader = Loader()
def test_singleton(self):
"""
Testing whether Loader is truly a singleton
"""
# Create a 'new' Loader
b = Loader()
self.assertEqual(self.loader._get_registry_creation_time(),
b._get_registry_creation_time())
def test_writer(self):
from sas.dataloader.readers.cansas_reader import Reader
r = Reader()
x = numpy.ones(5)
y = numpy.ones(5)
dy = numpy.ones(5)
filename = "write_test.xml"
r.write(filename, self.data)
data = Loader().load(filename)
self.data = data[0]
self.assertEqual(self.data.filename, filename)
self._checkdata()
def __init__(self, path, completefn=None,
updatefn=None,
yieldtime=0.01,
worktime=0.01
):
CalcThread.__init__(self, completefn,
updatefn,
yieldtime,
worktime)
self.path = path
#Instantiate a loader
self.loader = Loader()
self.starttime = 0
def setUp(self):
""" initialize data"""
self.data = Loader().load("cyl_400_20.txt")
# Create model that fitting engine understands
from sas.models.CylinderModel import CylinderModel
self.model = CylinderModel()
self.model.setParam("scale", 1.0)
self.model.setParam("radius",18)
self.model.setParam("length", 397)
self.model.setParam("sldCyl",3e-006 )
self.model.setParam("sldSolv",0.0 )
self.model.setParam("background", 0.0)
#select parameters to fit
self.pars1 =['length','radius','scale']
class abs_reader(unittest.TestCase):
def setUp(self):
self.loader = Loader()
def test_checkdata(self):
"""
Test .DAT file loaded as IGOR/DAT 2D Q_map
"""
f = self.loader.load("exp18_14_igor_2dqxqy.dat")
# The length of the data is 10
self.assertEqual(len(f.qx_data), 36864)
self.assertEqual(f.qx_data[0],-0.03573497)
self.assertEqual(f.qx_data[36863],0.2908819)
self.assertEqual(f.Q_unit, '1/A')
self.assertEqual(f.I_unit, '1/cm')
self.assertEqual(f.meta_data['loader'],"IGOR/DAT 2D Q_map")
class DataReader(CalcThread):
"""
Load a data given a filename
"""
def __init__(self, path, completefn=None,
updatefn=None,
yieldtime=0.01,
worktime=0.01
):
CalcThread.__init__(self, completefn,
updatefn,
yieldtime,
worktime)
self.path = path
#Instantiate a loader
self.loader = Loader()
self.starttime = 0
def isquit(self):
"""
@raise KeyboardInterrupt: when the thread is interrupted
"""
try:
CalcThread.isquit(self)
except KeyboardInterrupt:
raise KeyboardInterrupt
def compute(self):
"""
read some data
"""
self.starttime = time.time()
try:
data = self.loader.load(self.path)
self.complete(data=data)
except KeyboardInterrupt:
# Thread was interrupted, just proceed and re-raise.
# Real code should not print, but this is an example...
raise
def test_cansas_xml(self):
filename = "isis_1_1_write_test.xml"
xmlreader = XMLreader(self.isis_1_1, self.schema_1_1)
valid = xmlreader.validate_xml()
xmlreader.set_processing_instructions()
self.assertTrue(valid)
fo = open(self.isis_1_1)
str = fo.read()
reader_generic = Loader()
dataloader = reader_generic.load(self.isis_1_1)
reader_cansas = Reader()
cansasreader = reader_cansas.read(self.isis_1_1)
for i in range(len(dataloader)):
self._check_data(dataloader[i])
self._check_data_1_1(dataloader[i])
self._check_data(cansasreader[i])
self._check_data_1_1(cansasreader[i])
reader_generic.save(filename, dataloader[i], None)
fo = open(filename)
str = fo.read()
reader2 = Loader()
return_data = reader2.load(filename)
written_data = return_data[0]
self._check_data(written_data)
def setUp(self):
self.L=Loader()
self.L.find_plugins('../plugins')
def __init__(self):
PluginBase.__init__(self, name="DataLoader")
# Default location
self._default_save_location = DEFAULT_OPEN_FOLDER
self.loader = Loader()
self._data_menu = None
class Plugin(PluginBase):
def __init__(self):
PluginBase.__init__(self, name="DataLoader")
# Default location
self._default_save_location = DEFAULT_OPEN_FOLDER
self.loader = Loader()
self._data_menu = None
def populate_file_menu(self):
"""
get a menu item and append it under file menu of the application
add load file menu item and load folder item
"""
# menu for data files
menu_list = []
data_file_hint = "load one or more data in the application"
menu_list = [('&Load Data File(s)', data_file_hint, self.load_data)]
gui_style = self.parent.get_style()
style = gui_style & GUIFRAME.MULTIPLE_APPLICATIONS
style1 = gui_style & GUIFRAME.DATALOADER_ON
if style == GUIFRAME.MULTIPLE_APPLICATIONS:
# menu for data from folder
data_folder_hint = "load multiple data in the application"
menu_list.append(('&Load Data Folder', data_folder_hint,
self._load_folder))
return menu_list
def load_data(self, event):
"""
Load data
"""
path = None
self._default_save_location = self.parent._default_save_location
if self._default_save_location == None:
self._default_save_location = os.getcwd()
cards = self.loader.get_wildcards()
temp = [APPLICATION_WLIST] + PLUGINS_WLIST
for item in temp:
if item in cards:
cards.remove(item)
wlist = '|'.join(cards)
style = wx.OPEN | wx.FD_MULTIPLE
dlg = wx.FileDialog(self.parent,
"Choose a file",
self._default_save_location, "",
wlist,
style=style)
if dlg.ShowModal() == wx.ID_OK:
file_list = dlg.GetPaths()
if len(file_list) >= 0 and not file_list[0] is None:
self._default_save_location = os.path.dirname(file_list[0])
path = self._default_save_location
dlg.Destroy()
if path is None or not file_list or file_list[0] is None:
return
self.parent._default_save_location = self._default_save_location
self.get_data(file_list)
def can_load_data(self):
"""
if return True, then call handler to laod data
"""
return True
def _load_folder(self, event):
"""
Load entire folder
"""
path = None
self._default_save_location = self.parent._default_save_location
if self._default_save_location == None:
self._default_save_location = os.getcwd()
dlg = wx.DirDialog(self.parent, "Choose a directory",
self._default_save_location,
style=wx.DD_DEFAULT_STYLE)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
self._default_save_location = path
dlg.Destroy()
if path is not None:
self._default_save_location = os.path.dirname(path)
else:
return
file_list = self.get_file_path(path)
self.get_data(file_list)
self.parent._default_save_location = self._default_save_location
def load_error(self, error=None):
"""
Pop up an error message.
:param error: details error message to be displayed
"""
if error is not None or str(error).strip() != "":
dial = wx.MessageDialog(self.parent, str(error), 'Error Loading File',
wx.OK | wx.ICON_EXCLAMATION)
dial.ShowModal()
def get_file_path(self, path):
"""
Receive a list containing folder then return a list of file
"""
if os.path.isdir(path):
return [os.path.join(os.path.abspath(path), filename) for filename in os.listdir(path)]
def _process_data_and_errors(self, item, p_file, output, message):
"""
Check to see if data set loaded with any errors. If so, append to
error message to be sure user knows the issue.
"""
data_error = False
for error_data in item.errors:
data_error = True
message += "\tError: {0}\n".format(error_data)
data = self.parent.create_gui_data(item, p_file)
output[data.id] = data
return output, message, data_error
def get_data(self, path, format=None):
"""
"""
message = ""
log_msg = ''
output = {}
any_error = False
data_error = False
error_message = ""
for p_file in path:
info = "info"
basename = os.path.basename(p_file)
_, extension = os.path.splitext(basename)
if extension.lower() in EXTENSIONS:
any_error = True
log_msg = "Data Loader cannot "
log_msg += "load: %s\n" % str(p_file)
log_msg += """Please try to open that file from "open project" """
log_msg += """or "open analysis" menu\n"""
error_message = log_msg + "\n"
logging.info(log_msg)
continue
try:
message = "Loading Data... " + str(p_file) + "\n"
self.load_update(output=output, message=message, info=info)
temp = self.loader.load(p_file, format)
if temp.__class__.__name__ == "list":
for item in temp:
output, error_message, data_error = \
self._process_data_and_errors(item,
p_file,
output,
error_message)
else:
output, error_message, data_error = \
self._process_data_and_errors(temp,
p_file,
output,
error_message)
except:
any_error = True
if any_error or error_message != "":
if error_message == "":
error = "Error: " + str(sys.exc_info()[1]) + "\n"
error += "while loading Data: \n%s\n" % str(basename)
error_message += "The data file you selected could not be loaded.\n"
error_message += "Make sure the content of your file"
error_message += " is properly formatted.\n\n"
error_message += "When contacting the SasView team, mention the"
error_message += " following:\n%s" % str(error)
elif data_error:
base_message = "Errors occurred while loading "
base_message += "{0}\n".format(basename)
base_message += "The data file loaded but with errors.\n"
error_message = base_message + error_message
else:
error_message += "%s\n" % str(p_file)
info = "error"
if any_error or error_message:
self.load_update(output=output, message=error_message, info=info)
else:
message = "Loading Data Complete! "
message += log_msg
self.load_complete(output=output, error_message=error_message,
message=message, path=path, info='info')
def load_update(self, output=None, message="", info="warning"):
"""
print update on the status bar
"""
if message != "":
wx.PostEvent(self.parent, StatusEvent(status=message, info=info,
type="progress"))
def load_complete(self, output, message="", error_message="", path=None,
info="warning"):
"""
post message to status bar and return list of data
"""
wx.PostEvent(self.parent, StatusEvent(status=message,
info=info,
type="stop"))
# if error_message != "":
# self.load_error(error_message)
self.parent.add_data(data_list=output)
class abs_reader(unittest.TestCase):
def setUp(self):
self.loader = Loader()
def test_checkdata(self):
"""
Test .ABS file loaded as ascii
"""
f = self.loader.load("ascii_test_1.txt")
# The length of the data is 10
self.assertEqual(len(f.x), 10)
self.assertEqual(f.x[0],0.002618)
self.assertEqual(f.x[9],0.0497)
self.assertEqual(f.x_unit, '1/A')
self.assertEqual(f.y_unit, '1/cm')
self.assertEqual(f.meta_data['loader'],"ASCII")
def test_truncated_1(self):
"""
Test an ascii file with header and a
comment line in the middle of the data section.
The business rule says that we should stop
reading at the first comment once the data
section has started (and treat the comment
as though it were the start of a footer).
"""
# Test .ABS file loaded as ascii
f = self.loader.load("ascii_test_2.txt")
# The length of the data is 10
self.assertEqual(len(f.x), 5)
self.assertEqual(f.x[0],0.002618)
self.assertEqual(f.x[4],0.02356)
def test_truncated_2(self):
"""
Test a 6-col ascii file with header and a
line with only 2 columns in the middle of the data section.
The business rule says that we should stop
reading at the first inconsitent line.
"""
# Test .ABS file loaded as ascii
f = self.loader.load("ascii_test_3.txt")
# The length of the data is 5
self.assertEqual(len(f.x), 5)
self.assertEqual(f.x[0],0.002618)
self.assertEqual(f.x[4],0.02356)
def test_truncated_3(self):
"""
Test a 6-col ascii file with complex header and
many lines with 2 or 2 columns in the middle of the data section.
The business rule says that we should stop
reading at the last line of header.
"""
# Test .ABS file loaded as ascii
f = self.loader.load("ascii_test_4.abs")
# The length of the data is 5
self.assertEqual(len(f.x), 5)
self.assertEqual(f.x[0],0.012654)
self.assertEqual(f.x[4],0.02654)
def test_truncated_4(self):
"""
Test mix of 6-col and 2-col.
Only the last 5 2-col lines should be read.
"""
# Test .ABS file loaded as ascii
f = self.loader.load("ascii_test_5.txt")
# The length of the data is 5
self.assertEqual(len(f.x), 5)
self.assertEqual(f.x[0],0.02879)
self.assertEqual(f.x[4],0.0497)
def test_truncated_5(self):
"""
Test a 6-col ascii file with complex header where one of them has a letter and
many lines with 2 or 2 columns in the middle of the data section.
Only last four lines should be read.
"""
# Test .ABS file loaded as ascii
f = self.loader.load("ascii_test_6.txt")
# The length of the data is 5
self.assertEqual(len(f.x), 4)
self.assertEqual(f.x[0],0.013534)
self.assertEqual(f.x[3],0.022254)
class testLoader(unittest.TestCase):
logging.debug("Inside testLoad module")
""" test fitting """
def setUp(self):
"""
Set up the initial conditions before _each_ test
so that they all start from the same well-defined state.
"""
#Creating a loader
self.L=Loader()
def testLoad0(self):
"""test reading empty file"""
self.assertRaises(RuntimeError, self.L.load, 'empty.txt')
def testLoad1(self):
"""test reading 2 columns"""
#Testing loading a txt file of 2 columns, the only reader should be read1
output=self.L.load('test_2_columns.txt')
x=[2.83954,0.204082,0.408163,0.612245,0.816327,1.02041,1.22449,1.42857,1.63265]
y=[0.6,3.44938, 5.82026,5.27591,5.2781,5.22531,7.47487,7.85852,10.2278]
dx=[]
dy=[]
self.assertEqual(len(output.x),len(x))
self.assertEqual(len(output.y),len(y))
for i in range(len(x)):
self.assertEqual(output.x[i],x[i])
self.assertEqual(output.y[i],y[i])
def testLoad2(self):
"""Testing loading a txt file of 3 columns"""
output= self.L.load('test_3_columns.txt')
x=[0,0.204082,0.408163,0.612245,0.816327,1.02041,1.22449]
y=[2.83954,3.44938,5.82026,5.27591,5.2781,5.22531,7.47487]
dx=[]
dy=[0.6,0.676531,0.753061,0.829592,0.906122,0.982653,1.05918]
self.assertEqual(len(output.x),len(x))
self.assertEqual(len(output.y),len(y))
self.assertEqual(len(output.dy),len(dy))
for i in range(len(x)):
self.assertEqual(output.x[i],x[i])
self.assertEqual(output.y[i],y[i])
self.assertEqual(output.dy[i],dy[i])
def testLoad2_uppercase(self):
"""Testing loading a txt file of 3 columns"""
output= self.L.load('test_3_columns.TXT')
x=[0,0.204082,0.408163,0.612245,0.816327,1.02041,1.22449]
y=[2.83954,3.44938,5.82026,5.27591,5.2781,5.22531,7.47487]
dx=[]
dy=[0.6,0.676531,0.753061,0.829592,0.906122,0.982653,1.05918]
self.assertEqual(len(output.x),len(x))
self.assertEqual(len(output.y),len(y))
self.assertEqual(len(output.dy),len(dy))
for i in range(len(x)):
self.assertEqual(output.x[i],x[i])
self.assertEqual(output.y[i],y[i])
self.assertEqual(output.dy[i],dy[i])
def testload3(self):
""" Testing loading Igor data"""
#tested good file.asc
output= self.L.load('MAR07232_rest.ASC')
self.assertEqual(output.xmin,-0.018558945804750416)
self.assertEqual(output.xmax, 0.016234058202440633,)
self.assertEqual(output.ymin,-0.01684257151702391)
self.assertEqual(output.ymax,0.017950440578015116)
#tested corrupted file.asc
try:self.L.load('AR07232_rest.ASC')
except ValueError,msg:
#logging.log(10,str(msg))
logging.error(str(msg))
def setUp(self):
self.loader = Loader()
from bumps.names import *
from sasmodels import core, bumps_model
if True: # fix when data loader exists
# from sas.dataloader.readers\
from sas.dataloader.loader import Loader
loader = Loader()
filename = 'sphere.ses'
data = loader.load(filename)
if data is None: raise IOError("Could not load file %r"%(filename,))
data.x /= 10
# print data
# data = load_sesans('mydatfile.pz')
# sans_data = load_sans('mysansfile.xml')
else:
SElength = np.linspace(0, 2400, 61) # [A]
data = np.ones_like(SElength)
err_data = np.ones_like(SElength)*0.03
class Sample:
zacceptance = 0.1 # [A^-1]
thickness = 0.2 # [cm]
class SESANSData1D:
#q_zmax = 0.23 # [A^-1]
lam = 0.2 # [nm]
x = SElength
y = data
dy = err_data
