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Closes #152. Test for omega rotation of sample.
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Janik Zikovsky committed Jun 7, 2010
1 parent caa8135 commit c0b61da
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Showing 3 changed files with 104 additions and 97 deletions.
69 changes: 1 addition & 68 deletions model/experiment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1777,7 +1777,7 @@ def compare_to_peaks_file(self, filename):
numbad += 1
else:
if ref.times_measured() <= 0:
out += "Peak was not measured: Det %d, hkl: %d, %d, %d\n" % (detnum, h, k, l)
out += "Measured peak was not calculated to be measured: Det %d, hkl: %d, %d, %d\n" % (detnum, h, k, l)
numbad += 1
else:
#Check that its on the right detector
Expand Down Expand Up @@ -1860,73 +1860,6 @@ def setUp(self):
e.crystal.make_ub_matrix()
e.crystal.calculate_reciprocal()

def do_test_compare_to_peaks_file(self, filebase, angles, measurement_file=None, measurement_angle=None,
expect_bad=0, expect_good=0):
if measurement_angle is None:
measurement_angle = angles
if measurement_file is None:
measurement_file = filebase
#@type e Experiment
instrument.inst = instrument.Instrument("../instruments/TOPAZ_detectors_2010.csv")
instrument.inst.goniometer = goniometer.Goniometer()
self.exp = Experiment(instrument.inst)
e = self.exp
e.inst.d_min = 0.5
e.inst.wl_min = 0.5
e.inst.wl_max = 4.0
e.crystal.read_ISAW_ubmatrix_file(filebase + ".mat", angles=angles)
e.range_automatic = True
e.range_limit_to_sphere = True
e.initialize_reflections()
#Position coverage object with 0 sample rotation
poscov = instrument.PositionCoverage( measurement_angle, None, e.crystal.u_matrix)
e.inst.positions.append(poscov)
pos_param = ParamPositions( {id(poscov):True} )
self.pos_param = pos_param
e.recalculate_reflections(pos_param)
#Now compare!
(numbad, numgood, out) = e.compare_to_peaks_file(measurement_file + ".peaks")
# print out, "\n\n%d were bad; %d were good" % (numbad, numgood)
print "%s: %d were bad; %d were good" % (filebase, numbad, numgood)
assert numbad==expect_bad, "%s: expected %d bad peaks, but got %d bad peaks.\n%s" % (filebase, expect_bad, numbad, out)
assert numgood==expect_good, "%s: expected %d good peaks, but got %d god peaks.\n%s" % (filebase, expect_good, numgood, out)


def test_compare_to_peaks_file1(self):
self.do_test_compare_to_peaks_file("data/natrolite_808_isaw", [0,0,0],
measurement_angle=[-np.pi/6,0,0], expect_good=63, expect_bad=11)

def test_compare_to_peaks_file2a(self):
self.do_test_compare_to_peaks_file("data/TOPAZ_1204", [0, 0, 0],
measurement_file="data/TOPAZ_1204", measurement_angle=[0, np.pi/4,0],
expect_good=34, expect_bad=2)

def test_compare_to_peaks_file2c(self):
self.do_test_compare_to_peaks_file("data/TOPAZ_1204_ev", [0,np.pi/4,0],
measurement_file="data/TOPAZ_1205_indexed_with_1204", measurement_angle=[np.pi/6, np.pi/4,0],
expect_good=33, expect_bad=4)

def test_compare_to_peaks_file2b(self):
self.do_test_compare_to_peaks_file("data/TOPAZ_1204", [0, 0, 0],
measurement_file="data/TOPAZ_1205_indexed_with_1204", measurement_angle=[np.pi/6, np.pi/4,0],
expect_good=33, expect_bad=4)

def test_compare_to_peaks_file3(self):
self.do_test_compare_to_peaks_file("data/natrolite_807_ev", [0,0,0],
"data/natrolite_808_indexed_with_807", [-np.pi/6,0,0],
expect_bad=17, expect_good=57)

def test_compare_to_peaks_file4(self):
self.do_test_compare_to_peaks_file("data/natrolite_807_ev", [0,0,0], expect_good=39)

def test_compare_to_peaks_file5(self):
self.do_test_compare_to_peaks_file("data/natrolite_808_ev", [-np.pi/6,0,0], expect_good=43)

# self.do_test_compare_to_peaks_file("data/TOPAZ_1204_ev", [0,0,0])
# self.do_test_compare_to_peaks_file("data/TOPAZ_1205", [0,0,0])
# self.do_test_compare_to_peaks_file("data/art_ox", [0,0,0])


def test_constructor(self):
"""Experiment.__init__()"""
e = self.exp
Expand Down
130 changes: 102 additions & 28 deletions model/system_tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -73,9 +73,65 @@ def test_reciprocal_matrix4(self):
#print c.reciprocal_lattice, "\n\n\n"
assert np.allclose(isaw_rec, c.reciprocal_lattice, atol=1e-5), "Reciprocal lattice of %s matches ISAW lattice." % c.name

# #----------------------------------------------------
# #----------------------------------------------------
# def do_get_hkls_measured(self, filebase, angles):
# #@type e Experiment
# instrument.inst = instrument.Instrument("../instruments/TOPAZ_detectors_2010.csv")
# instrument.inst.goniometer = goniometer.Goniometer()
# self.exp = Experiment(instrument.inst)
# e = self.exp
# e.inst.d_min = 0.5
# e.inst.wl_min = 0.5
# e.inst.wl_max = 4.0
# e.crystal.read_ISAW_ubmatrix_file(filebase + ".mat", angles=angles)
# e.range_automatic = True
# e.range_limit_to_sphere = True
# e.initialize_reflections()
# #Position coverage object with 0 sample rotation
# poscov = instrument.PositionCoverage( angles, None, e.crystal.u_matrix)
# e.inst.positions.append(poscov)
# pos_param = ParamPositions( {id(poscov):True} )
# self.pos_param = pos_param
# e.recalculate_reflections(pos_param)
# out = []
# for ref in e.reflections:
# if ref.times_measured() > 0:
# out.append( ref.hkl )
# return out
#
# def test_compare_to_peaks_file(self):
# original = self.do_get_hkls_measured("data/TOPAZ_1204", [.123, np.pi/4, -0.43])
# with_rotation = self.do_get_hkls_measured("data/TOPAZ_1204", [0, 0, 0])
# assert original==with_rotation, "Same HKLs are measured with/without rotation specified."


#----------------------------------------------------
#----------------------------------------------------
def do_get_hkls_measured(self, filebase, angles):
def dont_test_compare_ubs(self):
"""ISAWev does not take into account the goniometer angles when outputting the
UB matrix file. ISAW does. This compares the U and B matrices obtained from both.
"""
#0, np.pi/4, 0
c = Crystal("oxalic acid")
c.read_ISAW_ubmatrix_file("data/TOPAZ_1204.mat", angles=[0, np.pi/4, 0])
c2 = Crystal("oxalic acid from EV")
c2.read_ISAW_ubmatrix_file("data/TOPAZ_1204_ev.mat", angles=[0, 0, 0])
assert np.allclose(c.reciprocal_lattice, c2.reciprocal_lattice, atol=0.05), "B matrices match, roughly. %s vs %s" % (c.reciprocal_lattice, c2.reciprocal_lattice)
assert np.allclose(c.u_matrix, c2.u_matrix, atol=0.02), "U matrices match, roughly. %s vs %s" % (c.u_matrix, c2.u_matrix)
print "\n\n\n"
print c.u_matrix
print c2.u_matrix

#----------------------------------------------------
#----------------------------------------------------

def do_test_compare_to_peaks_file(self, filebase, angles, measurement_file=None, measurement_angle=None,
expect_bad=0, expect_good=0):
if measurement_angle is None:
measurement_angle = angles
if measurement_file is None:
measurement_file = filebase
#@type e Experiment
instrument.inst = instrument.Instrument("../instruments/TOPAZ_detectors_2010.csv")
instrument.inst.goniometer = goniometer.Goniometer()
Expand All @@ -89,40 +145,58 @@ def do_get_hkls_measured(self, filebase, angles):
e.range_limit_to_sphere = True
e.initialize_reflections()
#Position coverage object with 0 sample rotation
poscov = instrument.PositionCoverage( angles, None, e.crystal.u_matrix)
poscov = instrument.PositionCoverage( measurement_angle, None, e.crystal.u_matrix)
e.inst.positions.append(poscov)
pos_param = ParamPositions( {id(poscov):True} )
self.pos_param = pos_param
e.recalculate_reflections(pos_param)
out = []
for ref in e.reflections:
if ref.times_measured() > 0:
out.append( ref.hkl )
return out
#Now compare!
(numbad, numgood, out) = e.compare_to_peaks_file(measurement_file + ".peaks")
# print out, "\n\n%d were bad; %d were good" % (numbad, numgood)
print "%s: %d were bad; %d were good" % (filebase, numbad, numgood)
assert numbad==expect_bad, "%s: expected %d bad peaks, but got %d bad peaks.\n%s" % (filebase, expect_bad, numbad, out)
assert numgood==expect_good, "%s: expected %d good peaks, but got %d god peaks.\n%s" % (filebase, expect_good, numgood, out)

def test_compare_to_peaks_file(self):
original = self.do_get_hkls_measured("data/TOPAZ_1204", [.123, np.pi/4, -0.43])
with_rotation = self.do_get_hkls_measured("data/TOPAZ_1204", [0, 0, 0])
assert original==with_rotation, "Same HKLs are measured with/without rotation specified."
def test_compare_to_peaks_file1(self):
self.do_test_compare_to_peaks_file("data/natrolite_808_isaw", [0,0,0],
measurement_angle=[-np.pi/6,0,0], expect_good=63, expect_bad=11)

def test_compare_to_peaks_file2a(self):
self.do_test_compare_to_peaks_file("data/TOPAZ_1204", [0, 0, 0],
measurement_file="data/TOPAZ_1204", measurement_angle=[0, np.pi/4,0],
expect_good=34, expect_bad=2)

def test_compare_to_peaks_file2c(self):
self.do_test_compare_to_peaks_file("data/TOPAZ_1204_ev", [0,np.pi/4,0],
measurement_file="data/TOPAZ_1205_indexed_with_1204", measurement_angle=[np.pi/6, np.pi/4,0],
expect_good=33, expect_bad=4)

def test_compare_to_peaks_file2b(self):
self.do_test_compare_to_peaks_file("data/TOPAZ_1204", [0, 0, 0],
measurement_file="data/TOPAZ_1205_indexed_with_1204", measurement_angle=[np.pi/6, np.pi/4,0],
expect_good=33, expect_bad=4)

def test_compare_to_peaks_file3(self):
self.do_test_compare_to_peaks_file("data/natrolite_807_ev", [0,0,0],
"data/natrolite_808_indexed_with_807", [-np.pi/6,0,0],
expect_bad=17, expect_good=57)

def test_compare_to_peaks_file4(self):
self.do_test_compare_to_peaks_file("data/natrolite_807_ev", [0,0,0], expect_good=39)

def test_compare_to_peaks_file5(self):
self.do_test_compare_to_peaks_file("data/natrolite_808_ev", [-np.pi/6,0,0], expect_good=43)

def test_compare_to_peaks_file_omega_rotation(self):
self.do_test_compare_to_peaks_file("data/natrolite_1223_isaw", [0,0,0],
measurement_file="data/natrolite_1224_with_1223_mat",
measurement_angle=np.deg2rad( [0.114, 45., 90] ), expect_good=114, expect_bad=10)


# self.do_test_compare_to_peaks_file("data/TOPAZ_1204_ev", [0,0,0])
# self.do_test_compare_to_peaks_file("data/TOPAZ_1205", [0,0,0])
# self.do_test_compare_to_peaks_file("data/art_ox", [0,0,0])

#----------------------------------------------------
#----------------------------------------------------
def dont_test_compare_ubs(self):
"""ISAWev does not take into account the goniometer angles when outputting the
UB matrix file. ISAW does. This compares the U and B matrices obtained from both.
"""
#0, np.pi/4, 0
c = Crystal("oxalic acid")
c.read_ISAW_ubmatrix_file("data/TOPAZ_1204.mat", angles=[0, np.pi/4, 0])
c2 = Crystal("oxalic acid from EV")
c2.read_ISAW_ubmatrix_file("data/TOPAZ_1204_ev.mat", angles=[0, 0, 0])
assert np.allclose(c.reciprocal_lattice, c2.reciprocal_lattice, atol=0.05), "B matrices match, roughly. %s vs %s" % (c.reciprocal_lattice, c2.reciprocal_lattice)
assert np.allclose(c.u_matrix, c2.u_matrix, atol=0.02), "U matrices match, roughly. %s vs %s" % (c.u_matrix, c2.u_matrix)
print "\n\n\n"
print c.u_matrix
print c2.u_matrix




Expand Down
2 changes: 1 addition & 1 deletion model/test_all.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@

module_list = ['config', 'crystal_calc', 'crystals', 'detectors', 'experiment', 'goniometer',
'instrument', 'messages', 'numpy_utils', 'optimize_coverage', 'reflections',
'ubmatrixreader']
'ubmatrixreader', 'system_tests', 'optimization']

import unittest
import string
Expand Down

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