def test_make_image(self): """test make hdf image file .........................""" imgfile = "test_make_image_1.h5" TestUtil.make_image_file(imgfile, IMAGE_HDF, EM_FLOAT) err = TestUtil.verify_image_file(imgfile, IMAGE_HDF, EM_FLOAT) self.assertEqual(err, 0) testlib.safe_unlink(imgfile)
def test_write_spider_stack(self):
"""test to write a spider stack image file ........."""
try:
if(os.path.isfile('test.spi')):
testlib.safe_unlink('test.spi')
e = EMData()
e.set_size(100,100)
e.process_inplace('testimage.squarecube', {'edge_length':20})
e.write_image('test.spi', 0)
e.process_inplace('testimage.circlesphere', {'radius':20})
e.write_image('test.spi', 1)
e.process_inplace('testimage.gaussian', {'sigma':20})
e.write_image('test.spi', 2)
e.process_inplace('testimage.sinewave', {'wavelength':20})
e.set_attr('SPIDER.title', 'The fourth image in the stack')
e.write_image('test.spi', 3)
f = EMData()
#read the overall herder
f.read_image('test.spi', -1, True)
d = f.get_attr_dict()
img_num = d['SPIDER.maxim']
#read the individual image from a stack
for i in range(img_num):
f.read_image('test.spi', i)
self.assertEqual(f.is_complex(), False)
self.assertEqual(f.get_xsize(), 100)
self.assertEqual(f.get_ysize(), 100)
self.assertEqual(f.get_zsize(), 1)
finally:
testlib.safe_unlink('test.spi')
def test_write_spider_stack(self):
"""test to write a spider stack image file ........."""
try:
if(os.path.isfile('test.spi')):
testlib.safe_unlink('test.spi')
e = EMData()
e.set_size(100,100)
e.process_inplace('testimage.squarecube', {'edge_length':20})
e.write_image('test.spi', 0)
e.process_inplace('testimage.circlesphere', {'radius':20})
e.write_image('test.spi', 1)
e.process_inplace('testimage.gaussian', {'sigma':20})
e.write_image('test.spi', 2)
e.process_inplace('testimage.sinewave', {'wavelength':20})
e.set_attr('SPIDER.title', 'The fourth image in the stack')
e.write_image('test.spi', 3)
f = EMData()
#read the overall herder
f.read_image('test.spi', -1, True)
d = f.get_attr_dict()
img_num = d['SPIDER.maxim']
#read the individual image from a stack
for i in range(img_num):
f.read_image('test.spi', i)
self.assertEqual(f.is_complex(), False)
self.assertEqual(f.get_xsize(), 100)
self.assertEqual(f.get_ysize(), 100)
self.assertEqual(f.get_zsize(), 1)
finally:
testlib.safe_unlink('test.spi')
def test_make_image(self): """test make hdf image file .........................""" imgfile = "test_make_image_1.h5" TestUtil.make_image_file(imgfile, IMAGE_HDF, EM_FLOAT) err = TestUtil.verify_image_file(imgfile, IMAGE_HDF, EM_FLOAT) self.assertEqual(err, 0) testlib.safe_unlink(imgfile)
def test_hdf_8bit_IO(self):
"""test read/write 8 bit HDF5........................"""
file = '8bit.hdf'
e = test_image()
e.write_image(file, -1, EMUtil.ImageType.IMAGE_HDF, False, None, EMUtil.EMDataType.EM_UCHAR)
e2 = EMData(file)
self.assertEqual(e2.get_attr('datatype'), EMUtil.EMDataType.EM_UCHAR)
testlib.safe_unlink(file)
def test_hdf_8bit_IO(self):
"""test read/write 8 bit HDF5........................"""
file = '8bit.hdf'
e = test_image()
e.write_image(file, -1, EMUtil.ImageType.IMAGE_HDF, False, None, EMUtil.EMDataType.EM_UCHAR)
e2 = EMData(file)
self.assertEqual(e2.get_attr('datatype'), EMUtil.EMDataType.EM_UCHAR)
testlib.safe_unlink(file)
def test_RotateTranslateFlipAligner(self):
"""test RotateTranslateFlip Aligner ................."""
e = EMData()
e.set_size(32, 32, 1)
e.process_inplace("testimage.noise.uniform.rand")
e2 = EMData()
e2.set_size(32, 32, 1)
e2.process_inplace("testimage.noise.uniform.rand")
e.align("rotate_translate_flip", e2, {"maxshift": 1})
for y in [64, 65]:
for x in [64, 65]:
size = (x, y)
ref = test_image(0, size)
ref.translate(4, 5, 0) # give it handedness
for i in range(0, 20):
mirror = Util.get_irand(0, 1)
e = ref.copy()
dx = Util.get_frand(-3, 3)
dy = Util.get_frand(-3, 3)
az = Util.get_frand(0, 360)
t = Transform({"type": "2d", "alpha": az})
t.set_trans(Vec2f(dx, dy))
t.set_mirror(mirror)
e.transform(t)
e.write_image("e.hdf", -1)
g = ref.align("rotate_translate_flip", e, {}, "phase")
g.write_image("e.hdf", -1)
t1 = g.get_attr("xform.align2d")
# params = t1.get_params("2d")
# params2 = t.get_params("2d")
# t.invert()
# print params2
# print params
# print fabs(params["tx"] - params2["tx"])
# print fabs(params["ty"] - params2["ty"])
#
# self.failIf(fabs(params["tx"] - params2["tx"]) > 1)
# self.failIf(fabs(params["ty"] - params2["ty"]) > 1)
# result = fabs(params["alpha"] - params2["alpha"])
# #print g.get_attr("align.az"), az
# if result > 180 and result < 360:
# result = 360-result
# if result > 360: result = result-360
# self.failIf( result > 3 ) # 3 seems accurate enough
#
#
# self.failIf( params2["mirror"] != params["mirror"] ) # 3 seems accurate enough
#
# we have to do it this way because of double to float conversions
f = ref.process("xform", {"transform": t1})
dif = f - g
dif.process_inplace("math.absvalue")
self.failIf(dif["mean"] > 0.01)
testlib.safe_unlink("e.hdf")
def test_RotateTranslateFlipAligner(self):
"""test RotateTranslateFlip Aligner ................."""
e = EMData()
e.set_size(32, 32, 1)
e.process_inplace('testimage.noise.uniform.rand')
e2 = EMData()
e2.set_size(32, 32, 1)
e2.process_inplace('testimage.noise.uniform.rand')
e.align('rotate_translate_flip', e2, {'maxshift': 1})
for y in [64, 65]:
for x in [64, 65]:
size = (x, y)
ref = test_image(0, size)
ref.translate(4, 5, 0) # give it handedness
for i in range(0, 20):
mirror = Util.get_irand(0, 1)
e = ref.copy()
dx = Util.get_frand(-3, 3)
dy = Util.get_frand(-3, 3)
az = Util.get_frand(0, 360)
t = Transform({"type": "2d", "alpha": az})
t.set_trans(Vec2f(dx, dy))
t.set_mirror(mirror)
e.transform(t)
e.write_image("e.hdf", -1)
g = ref.align("rotate_translate_flip", e, {}, "phase")
g.write_image("e.hdf", -1)
t1 = g.get_attr("xform.align2d")
# params = t1.get_params("2d")
# params2 = t.get_params("2d")
# t.invert()
# print params2
# print params
# print fabs(params["tx"] - params2["tx"])
# print fabs(params["ty"] - params2["ty"])
#
# self.failIf(fabs(params["tx"] - params2["tx"]) > 1)
# self.failIf(fabs(params["ty"] - params2["ty"]) > 1)
# result = fabs(params["alpha"] - params2["alpha"])
# #print g.get_attr("align.az"), az
# if result > 180 and result < 360:
# result = 360-result
# if result > 360: result = result-360
# self.failIf( result > 3 ) # 3 seems accurate enough
#
#
# self.failIf( params2["mirror"] != params["mirror"] ) # 3 seems accurate enough
#
# we have to do it this way because of double to float conversions
f = ref.process("xform", {"transform": t1})
dif = f - g
dif.process_inplace("math.absvalue")
self.failIf(dif["mean"] > 0.01)
testlib.safe_unlink('e.hdf')
def test_overwrite_spider(self): """test overwrite spider image file .................""" try: file1 = "test_overwrite_spider.spi" nx1 = 24 ny1 = 32 TestUtil.make_image_file(file1, IMAGE_SINGLE_SPIDER, EM_FLOAT, nx1, ny1) TestUtil.make_image_file(file1, IMAGE_SINGLE_SPIDER, EM_FLOAT, nx1*2, ny1*2) finally: testlib.safe_unlink(file1)
def test_8bit_image(self):
"""test unsigned char df3 image I/O ................."""
e = test_image()
e.write_image(self.imgfile, -1, EMUtil.ImageType.IMAGE_DF3, False, None, EMUtil.EMDataType.EM_UCHAR)
f = EMData()
f.read_image(self.imgfile)
self.assertEqual(f.get_attr('nx'), 128)
self.assertEqual(f.get_attr('ny'), 128)
self.assertEqual(f.get_attr('nz'), 1)
testlib.safe_unlink(self.imgfile)
def test_8bit_image(self):
"""test unsigned char df3 image I/O ................."""
e = test_image()
e.write_image(self.imgfile, -1, EMUtil.ImageType.IMAGE_DF3, False, None, EMUtil.EMDataType.EM_UCHAR)
f = EMData()
f.read_image(self.imgfile)
self.assertEqual(f.get_attr('nx'), 128)
self.assertEqual(f.get_attr('ny'), 128)
self.assertEqual(f.get_attr('nz'), 1)
testlib.safe_unlink(self.imgfile)
def test_overwrite_spider(self): """test overwrite spider image file .................""" try: file1 = "test_overwrite_spider.spi" nx1 = 24 ny1 = 32 TestUtil.make_image_file(file1, IMAGE_SINGLE_SPIDER, EM_FLOAT, nx1, ny1) TestUtil.make_image_file(file1, IMAGE_SINGLE_SPIDER, EM_FLOAT, nx1*2, ny1*2) finally: testlib.safe_unlink(file1)
def no_test_write_transform_mrc(self):
"""test write mrc header info from Transform object ."""
filename = 'test_write_transform.'
img = EMData(32,32)
img.process_inplace('testimage.noise.uniform.rand')
t3d = Transform()
t3d.set_rotation({'type':'imagic', 'alpha':1.56, 'beta':2.56, 'gamma':3.56})
t3d.set_trans(10.78, 20.78, 30.78)
img.set_attr('xform.projection', t3d)
img.write_image(filename+'mrc')
del img
img2 = EMData(filename+'mrc')
self.assertAlmostEqual(img2.get_attr('MRC.alpha'), 1.56, 3)
self.assertAlmostEqual(img2.get_attr('MRC.beta'), 2.56, 3)
self.assertAlmostEqual(img2.get_attr('MRC.gamma'), 3.56, 3)
self.assertAlmostEqual(img2.get_attr('origin_x'), 10.78, 3)
self.assertAlmostEqual(img2.get_attr('origin_y'), 20.78, 3)
self.assertAlmostEqual(img2.get_attr('origin_z'), 30.78, 3)
trans = img2.get_attr('xform.projection')
d = trans.get_params('imagic')
self.assertAlmostEqual(d['alpha'], 0.0, 3)
self.assertAlmostEqual(d['beta'], 0.0, 3)
self.assertAlmostEqual(d['gamma'], 0.0, 3)
self.assertAlmostEqual(d['MRC.nxstart'], 10.78, 3)
self.assertAlmostEqual(d['MRC.nxstart'], 20.78, 3)
self.assertAlmostEqual(d['MRC.nxstart'], 30.78, 3)
del img2
testlib.safe_unlink(filename+'mrc')
filename2 = 'test_write_transform2.'
img = EMData(32,32,32)
img.process_inplace('testimage.noise.uniform.rand')
t3d = Transform()
t3d.set_rotation({'type':'imagic', 'alpha':1.56, 'beta':2.56, 'gamma':3.56})
t3d.set_trans(10.78, 20.78, 30.78)
img.set_attr('xform.align3d', t3d)
img.write_image(filename2+'mrc')
img2 = EMData(filename2+'mrc')
self.assertAlmostEqual(img2.get_attr('MRC.alpha'), 1.56, 3)
self.assertAlmostEqual(img2.get_attr('MRC.beta'), 2.56, 3)
self.assertAlmostEqual(img2.get_attr('MRC.gamma'), 3.56, 3)
self.assertAlmostEqual(img2.get_attr('origin_x'), 10.78, 3)
self.assertAlmostEqual(img2.get_attr('origin_y'), 20.78, 3)
self.assertAlmostEqual(img2.get_attr('origin_z'), 30.78, 3)
trans2 = img2.get_attr('xform.align3d')
d2 = trans2.get_params('imagic')
self.assertAlmostEqual(d2['alpha'], 1.56, 3)
self.assertAlmostEqual(d2['beta'], 2.56, 3)
self.assertAlmostEqual(d2['gamma'], 3.56, 3)
self.assertAlmostEqual(d2['tx'], 10.78, 3)
self.assertAlmostEqual(d2['ty'], 20.78, 3)
self.assertAlmostEqual(d2['tz'], 30.78, 3)
testlib.safe_unlink(filename2+'mrc')
def no_test_write_transform_mrc(self):
"""test write mrc header info from Transform object ."""
filename = 'test_write_transform.'
img = EMData(32,32)
img.process_inplace('testimage.noise.uniform.rand')
t3d = Transform()
t3d.set_rotation({'type':'imagic', 'alpha':1.56, 'beta':2.56, 'gamma':3.56})
t3d.set_trans(10.78, 20.78, 30.78)
img.set_attr('xform.projection', t3d)
img.write_image(filename+'mrc')
del img
img2 = EMData(filename+'mrc')
self.assertAlmostEqual(img2.get_attr('MRC.alpha'), 1.56, 3)
self.assertAlmostEqual(img2.get_attr('MRC.beta'), 2.56, 3)
self.assertAlmostEqual(img2.get_attr('MRC.gamma'), 3.56, 3)
self.assertAlmostEqual(img2.get_attr('origin_x'), 10.78, 3)
self.assertAlmostEqual(img2.get_attr('origin_y'), 20.78, 3)
self.assertAlmostEqual(img2.get_attr('origin_z'), 30.78, 3)
trans = img2.get_attr('xform.projection')
d = trans.get_params('imagic')
self.assertAlmostEqual(d['alpha'], 0.0, 3)
self.assertAlmostEqual(d['beta'], 0.0, 3)
self.assertAlmostEqual(d['gamma'], 0.0, 3)
self.assertAlmostEqual(d['MRC.nxstart'], 10.78, 3)
self.assertAlmostEqual(d['MRC.nxstart'], 20.78, 3)
self.assertAlmostEqual(d['MRC.nxstart'], 30.78, 3)
del img2
testlib.safe_unlink(filename+'mrc')
filename2 = 'test_write_transform2.'
img = EMData(32,32,32)
img.process_inplace('testimage.noise.uniform.rand')
t3d = Transform()
t3d.set_rotation({'type':'imagic', 'alpha':1.56, 'beta':2.56, 'gamma':3.56})
t3d.set_trans(10.78, 20.78, 30.78)
img.set_attr('xform.align3d', t3d)
img.write_image(filename2+'mrc')
img2 = EMData(filename2+'mrc')
self.assertAlmostEqual(img2.get_attr('MRC.alpha'), 1.56, 3)
self.assertAlmostEqual(img2.get_attr('MRC.beta'), 2.56, 3)
self.assertAlmostEqual(img2.get_attr('MRC.gamma'), 3.56, 3)
self.assertAlmostEqual(img2.get_attr('origin_x'), 10.78, 3)
self.assertAlmostEqual(img2.get_attr('origin_y'), 20.78, 3)
self.assertAlmostEqual(img2.get_attr('origin_z'), 30.78, 3)
trans2 = img2.get_attr('xform.align3d')
d2 = trans2.get_params('imagic')
self.assertAlmostEqual(d2['alpha'], 1.56, 3)
self.assertAlmostEqual(d2['beta'], 2.56, 3)
self.assertAlmostEqual(d2['gamma'], 3.56, 3)
self.assertAlmostEqual(d2['tx'], 10.78, 3)
self.assertAlmostEqual(d2['ty'], 20.78, 3)
self.assertAlmostEqual(d2['tz'], 30.78, 3)
testlib.safe_unlink(filename2+'mrc')
def test_variance(self):
"""test variance ...................................."""
imgfile1 = "test_variance_1.mrc"
TestUtil.make_image_file(imgfile1, IMAGE_MRC)
e1 = EMData()
e1.read_image(imgfile1)
e2 = e1.copy()
score = e2.cmp("sqeuclidean", e1)
self.assertEqual(score, 0)
testlib.safe_unlink(imgfile1)
def test_make_spider(self): """test make spider image file ......................""" try: file1 = "test_make_spider_1.spi" nx1 = 100 ny1 = 24 TestUtil.make_image_file(file1, IMAGE_SPIDER, EM_FLOAT, nx1, nx1) err = TestUtil.verify_image_file(file1, IMAGE_SPIDER, EM_FLOAT, nx1, nx1) self.assertEqual(err, 0) finally: testlib.safe_unlink(file1)
def test_variance(self):
"""test variance ...................................."""
imgfile1 = "test_variance_1.mrc"
TestUtil.make_image_file(imgfile1, IMAGE_MRC)
e1 = EMData()
e1.read_image(imgfile1)
e2 = e1.copy()
score = e2.cmp("sqeuclidean", e1)
self.assertEqual(score, 0)
testlib.safe_unlink(imgfile1)
def test_make_spider(self): """test make spider image file ......................""" try: file1 = "test_make_spider_1.spi" nx1 = 100 ny1 = 24 TestUtil.make_image_file(file1, IMAGE_SPIDER, EM_FLOAT, nx1, nx1) err = TestUtil.verify_image_file(file1, IMAGE_SPIDER, EM_FLOAT, nx1, nx1) self.assertEqual(err, 0) finally: testlib.safe_unlink(file1)
def test_hdf_overwrite(self): """test the overwriting of HDF5......................""" file = 'overwrite.hdf' e = EMData(2,2) e.to_zero() e.write_image(file) e.to_one() e.write_image(file) f = EMData(file) for i in range(2*2): self.assertEqual(1, f[i]) testlib.safe_unlink(file)
def test_hdf_overwrite(self): """test the overwriting of HDF5......................""" file = 'overwrite.hdf' e = EMData(2,2) e.to_zero() e.write_image(file) e.to_one() e.write_image(file) f = EMData(file) for i in range(2*2): self.assertEqual(1, f[i]) testlib.safe_unlink(file)
def no_test_pgm_region_io(self):
"""test pgm region io ..............................."""
try:
e = EMData()
e.set_size(1024,1024)
e.process_inplace('testimage.circlesphere', {'radius':300})
e.write_image('test_circle.pgm')
f = EMData()
#f.read_image('test_circle.pgm', 0, False, Region(300,300,200,200))
f.read_image('test_circle.pgm')
finally:
testlib.safe_unlink('test_circle.pgm')
def no_test_pgm_region_io(self):
"""test pgm region io ..............................."""
try:
e = EMData()
e.set_size(1024,1024)
e.process_inplace('testimage.circlesphere', {'radius':300})
e.write_image('test_circle.pgm')
f = EMData()
#f.read_image('test_circle.pgm', 0, False, Region(300,300,200,200))
f.read_image('test_circle.pgm')
finally:
testlib.safe_unlink('test_circle.pgm')
def test_FourierReconstructor(self):
"""test FourierReconstructor ........................"""
n = 32
e1 = EMData()
e1.set_size(n, n, 1)
e1.process_inplace('testimage.noise.uniform.rand')
#e1.do_fft_inplace()
e2 = EMData()
e2.set_size(n, n, 1)
e2.process_inplace('testimage.noise.uniform.rand')
#e2.do_fft_inplace()
e3 = EMData()
e3.set_size(n, n, 1)
e3.process_inplace('testimage.noise.uniform.rand')
#e3.do_fft_inplace()
r = Reconstructors.get('fourier', {
'size': (n, n, n),
'mode': 'gauss_2',
'sym': 'c1',
'quiet': True
})
r.setup()
r.insert_slice(
e1,
Transform({
'type': 'eman',
'alt': 1.56,
'az': 2.56,
'phi': 3.56
}))
r.insert_slice(
e2,
Transform({
'type': 'eman',
'alt': 2.56,
'az': 3.56,
'phi': 4.56
}))
r.insert_slice(
e3,
Transform({
'type': 'eman',
'alt': 3.56,
'az': 4.56,
'phi': 5.56
}))
result = r.finish(True)
testlib.safe_unlink('density.mrc')
def test_is_file_exist(self):
"""test is_file_exist() function ...................."""
imgfile1 = "test_is_file_exist.mrc"
TestUtil.make_image_file(imgfile1, IMAGE_MRC)
result1 = Util.is_file_exist(imgfile1)
self.assertEqual(result1, True)
result2 = Util.is_file_exist("__nosuchafile__.dm3")
self.assertEqual(result2, False)
result3 = Util.is_file_exist("")
self.assertEqual(result3, False)
testlib.safe_unlink(imgfile1)
def test_is_file_exist(self):
"""test is_file_exist() function ...................."""
imgfile1 = "test_is_file_exist.mrc"
TestUtil.make_image_file(imgfile1, IMAGE_MRC)
result1 = Util.is_file_exist(imgfile1)
self.assertEqual(result1, True)
result2 = Util.is_file_exist("__nosuchafile__.dm3")
self.assertEqual(result2, False)
result3 = Util.is_file_exist("")
self.assertEqual(result3, False)
testlib.safe_unlink(imgfile1)
def test_read_write_file(self):
"""test read/write file ............................."""
xy = XYData()
lx = range(10)
ly = (i + 100 for i in range(10))
xy.set_xy_list(lx, ly)
file = 'xydata.dat'
xy.write_file(file)
xy2 = XYData()
xy2.read_file(file)
self.assertAlmostEqual(5.0, xy2.get_x(5), 3)
self.assertAlmostEqual(105.0, xy2.get_y(5), 3)
self.assertAlmostEqual(106.0, xy2.get_yatx(6), 3)
testlib.safe_unlink(file)
def test_read_write_file(self):
"""test read/write file ............................."""
xy = XYData()
lx = range(10)
ly = (i+100 for i in range(10))
xy.set_xy_list(lx, ly)
file = 'xydata.dat'
xy.write_file(file)
xy2 = XYData()
xy2.read_file(file)
self.assertAlmostEqual(5.0, xy2.get_x(5), 3)
self.assertAlmostEqual(105.0, xy2.get_y(5), 3)
self.assertAlmostEqual(106.0, xy2.get_yatx(6), 3)
testlib.safe_unlink(file)
def test_OptVarianceCmp(self):
"""test OptVarianceCmp .............................."""
e = EMData()
e.set_size(64,64,1)
e.process_inplace('testimage.noise.uniform.rand')
e2 = EMData()
e2.set_size(64,64,1)
e2.process_inplace('testimage.noise.uniform.rand')
score = e.cmp('optvariance', e2, {}) #default argument
score2 = e.cmp('optvariance', e2, {'invert':1, 'keepzero':1, 'matchfilt':2, 'radweight':2, 'debug':1})
testlib.safe_unlink('a.hdf')
testlib.safe_unlink('dbug.optvar.txt')
def test_OptVarianceCmp(self):
"""test OptVarianceCmp .............................."""
e = EMData()
e.set_size(64,64,1)
e.process_inplace('testimage.noise.uniform.rand')
e2 = EMData()
e2.set_size(64,64,1)
e2.process_inplace('testimage.noise.uniform.rand')
score = e.cmp('optvariance', e2, {}) #default argument
score2 = e.cmp('optvariance', e2, {'invert':1, 'keepzero':1, 'matchfilt':2, 'radweight':2, 'debug':1})
testlib.safe_unlink('a.hdf')
testlib.safe_unlink('dbug.optvar.txt')
def test_eman2ctf_io(self):
"""test EMAN2Ctf object I/O ........................."""
filename = 'test_imagic_ctf2.hdf'
img = EMData(32,32)
img.process_inplace('testimage.noise.uniform.rand')
ctf1 = EMAN2Ctf()
ctf1.from_vector((1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0, 0, 0))
img.set_attr('ctf', ctf1)
img.write_image(filename)
img2 = EMData(filename)
ctf2 = img2.get_attr('ctf')
self.assertEqual(ctf1.to_string(), ctf2.to_string())
del ctf1, ctf2
testlib.safe_unlink(filename)
def test_read_write_pgm(self):
"""test pgm file read/write ........................."""
try:
e = EMData()
e.set_size(64,64)
e.process_inplace('testimage.noise.uniform.rand')
e.write_image('test_image.pgm')
f = EMData()
f.read_image('test_image.pgm')
#self.assertEqual(f==e,True)
finally:
testlib.safe_unlink('test_image.pgm')
def test_eman2ctf_io(self):
"""test EMAN2Ctf object I/O ........................."""
filename = 'test_imagic_ctf2.hdf'
img = EMData(32,32)
img.process_inplace('testimage.noise.uniform.rand')
ctf1 = EMAN2Ctf()
ctf1.from_vector((1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0, 0, 0))
img.set_attr('ctf', ctf1)
img.write_image(filename)
img2 = EMData(filename)
ctf2 = img2.get_attr('ctf')
self.assertEqual(ctf1.to_string(), ctf2.to_string())
del ctf1, ctf2
testlib.safe_unlink(filename)
def test_read_write_pgm(self):
"""test pgm file read/write ........................."""
try:
e = EMData()
e.set_size(64,64)
e.process_inplace('testimage.noise.uniform.rand')
e.write_image('test_image.pgm')
f = EMData()
f.read_image('test_image.pgm')
#self.assertEqual(f==e,True)
finally:
testlib.safe_unlink('test_image.pgm')
def test_get_all_attibutes(self):
"""test get_all_attributes function ................."""
e1 = test_image()
e1.set_attr('name', 'Tom')
e1.write_image('test.hdf', 0)
e2 = test_image()
e2.set_attr('name', 'Sam')
e2.write_image('test.hdf', 1)
e3 = test_image()
e3.write_image('test.hdf', 2)
l = EMUtil.get_all_attributes('test.hdf', 'name')
self.assertEqual(l, ['Tom', 'Sam', None])
testlib.safe_unlink('test.hdf')
def test_get_all_attibutes(self):
"""test get_all_attributes function ................."""
e1 = test_image()
e1.set_attr('name', 'Tom')
e1.write_image('test.hdf', 0)
e2 = test_image()
e2.set_attr('name', 'Sam')
e2.write_image('test.hdf', 1)
e3 = test_image()
e3.write_image('test.hdf', 2)
l = EMUtil.get_all_attributes('test.hdf', 'name')
self.assertEqual(l, ['Tom', 'Sam', None])
testlib.safe_unlink('test.hdf')
def test_defaultargs(self):
"""test default arguments ..........................."""
imgfile1 = "test_defaultargs_1.mrc"
imgfile2 = "test_defaultargs_2.mrc"
TestUtil.make_image_file(imgfile1, IMAGE_MRC)
TestUtil.make_image_file(imgfile2, IMAGE_MRC)
image1 = EMData()
image1.read_image(imgfile1)
image2 = EMData()
image2.read_image(imgfile2)
image3 = image1.calc_ccf(image2)
testlib.check_emdata(image3, sys.argv[0])
testlib.safe_unlink(imgfile1)
testlib.safe_unlink(imgfile2)
def test_defaultargs(self):
"""test default arguments ..........................."""
imgfile1 = "test_defaultargs_1.mrc"
imgfile2 = "test_defaultargs_2.mrc"
TestUtil.make_image_file(imgfile1, IMAGE_MRC)
TestUtil.make_image_file(imgfile2, IMAGE_MRC)
image1 = EMData()
image1.read_image(imgfile1)
image2 = EMData()
image2.read_image(imgfile2)
image3 = image1.calc_ccf(image2)
testlib.check_emdata(image3, sys.argv[0])
testlib.safe_unlink(imgfile1)
testlib.safe_unlink(imgfile2)
def test_read_write_HDF_attribute(self):
"""test read/write single attribute from/to HDF5 file"""
file = 'test.hdf'
img = test_image()
img.write_image(file, -1)
img.write_image(file, -1)
EMUtil.write_hdf_attribute(file, 'count', 100)
EMUtil.write_hdf_attribute(file, 'count', 1000, 1)
c100 = EMUtil.read_hdf_attribute(file, 'count')
c1000 = EMUtil.read_hdf_attribute(file, 'count', 1)
self.assertEqual(EMUtil.read_hdf_attribute(file, 'count'), 100)
self.assertEqual(EMUtil.read_hdf_attribute(file, 'count', 1), 1000)
EMUtil.delete_hdf_attribute(file, 'count')
d = img.get_attr_dict()
self.assertEqual(d.has_key('count'), False)
testlib.safe_unlink(file)
def test_read_write_HDF_attribute(self):
"""test read/write single attribute from/to HDF5 file"""
file = 'test.hdf'
img = test_image()
img.write_image(file, -1)
img.write_image(file, -1)
EMUtil.write_hdf_attribute(file, 'count', 100)
EMUtil.write_hdf_attribute(file, 'count', 1000, 1)
c100 = EMUtil.read_hdf_attribute(file, 'count')
c1000 = EMUtil.read_hdf_attribute(file, 'count', 1)
self.assertEqual(EMUtil.read_hdf_attribute(file, 'count'), 100)
self.assertEqual(EMUtil.read_hdf_attribute(file, 'count', 1), 1000)
EMUtil.delete_hdf_attribute(file, 'count')
d = img.get_attr_dict()
self.assertEqual('count' in d, False)
testlib.safe_unlink(file)
def test_read_image(self): """test read hdf image file .........................""" nx = 20 ny = 30 nz = 2 imgfile = "test_read_image.h5" TestUtil.make_image_file(imgfile, IMAGE_HDF, EM_FLOAT, nx, ny, nz) e = EMData() e.read_image(imgfile) attrdict = e.get_attr_dict() self.assertEqual(attrdict["nx"], nx) self.assertEqual(attrdict["ny"], ny) self.assertEqual(attrdict["nz"], nz) self.assertEqual(attrdict["ImageEndian"], "big") self.assertEqual(attrdict["datatype"], EM_FLOAT) self.assertEqual(attrdict["is_complex"], 0) #self.assertEqual(attrdict["maximum"], 325.0) #self.assertEqual(attrdict["minimum"], 0.0) testlib.safe_unlink(imgfile)
def test_read_image(self): """test read hdf image file .........................""" nx = 20 ny = 30 nz = 2 imgfile = "test_read_image.h5" TestUtil.make_image_file(imgfile, IMAGE_HDF, EM_FLOAT, nx, ny, nz) e = EMData() e.read_image(imgfile) attrdict = e.get_attr_dict() self.assertEqual(attrdict["nx"], nx) self.assertEqual(attrdict["ny"], ny) self.assertEqual(attrdict["nz"], nz) self.assertEqual(attrdict["ImageEndian"], "big") self.assertEqual(attrdict["datatype"], EM_FLOAT) self.assertEqual(attrdict["is_complex"], 0) #self.assertEqual(attrdict["maximum"], 325.0) #self.assertEqual(attrdict["minimum"], 0.0) testlib.safe_unlink(imgfile)
def test_FourierReconstructor(self):
"""test FourierReconstructor ........................"""
n = 32
e1 = EMData()
e1.set_size(n,n,1)
e1.process_inplace('testimage.noise.uniform.rand')
#e1.do_fft_inplace()
e2 = EMData()
e2.set_size(n,n,1)
e2.process_inplace('testimage.noise.uniform.rand')
#e2.do_fft_inplace()
e3 = EMData()
e3.set_size(n,n,1)
e3.process_inplace('testimage.noise.uniform.rand')
#e3.do_fft_inplace()
r = Reconstructors.get('fourier', {'size':(n,n,n), 'mode':'gauss_2', 'sym':'c1', 'quiet':True})
r.setup()
r.insert_slice(e1, Transform({'type':'eman', 'alt':1.56, 'az':2.56, 'phi':3.56}))
r.insert_slice(e2, Transform({'type':'eman', 'alt':2.56, 'az':3.56, 'phi':4.56}))
r.insert_slice(e3, Transform({'type':'eman', 'alt':3.56, 'az':4.56, 'phi':5.56}))
result = r.finish(True)
testlib.safe_unlink('density.mrc')
def test_write_transform_to_euler(self):
"""test write Transform as euler angles ............."""
filename = 'test_write_transform.'
img = EMData(32,32)
img.process_inplace('testimage.noise.uniform.rand')
t3d = Transform()
t3d.set_rotation({'type':'imagic', 'alpha':1.56, 'beta':2.56, 'gamma':3.56})
img.set_attr('xform.projection', t3d)
img.write_image(filename+'img')
del img
img2 = EMData(filename+'img')
self.assertAlmostEqual(img2.get_attr('euler_alpha'), 1.56, 3)
self.assertAlmostEqual(img2.get_attr('euler_beta'), 2.56, 3)
self.assertAlmostEqual(img2.get_attr('euler_gamma'), 3.56, 3)
xform1 = img2.get_attr('xform.projection')
d = xform1.get_rotation('imagic')
self.assertAlmostEqual(d['alpha'], 1.56, 3)
self.assertAlmostEqual(d['beta'], 2.56, 3)
self.assertAlmostEqual(d['gamma'], 3.56, 3)
del img2
testlib.safe_unlink(filename+'img')
testlib.safe_unlink(filename+'hed')
filename2 = 'test_write_transform2.'
img = EMData(32,32,32)
img.process_inplace('testimage.noise.uniform.rand')
t3d = Transform()
t3d.set_rotation({'type':'imagic', 'alpha':1.56, 'beta':2.56, 'gamma':3.56})
img.set_attr('xform.align3d', t3d)
img.write_image(filename2+'img')
img2 = EMData(filename2+'img')
self.assertAlmostEqual(img2.get_attr('euler_alpha'), 1.56, 3)
self.assertAlmostEqual(img2.get_attr('euler_beta'), 2.56, 3)
self.assertAlmostEqual(img2.get_attr('euler_gamma'), 3.56, 3)
xform2 = img2.get_attr('xform.align3d')
d2 = xform2.get_rotation('imagic')
self.assertAlmostEqual(d2['alpha'], 1.56, 3)
self.assertAlmostEqual(d2['beta'], 2.56, 3)
self.assertAlmostEqual(d2['gamma'], 3.56, 3)
testlib.safe_unlink(filename2+'hed')
testlib.safe_unlink(filename2+'img')
def test_write_transform_to_euler(self):
"""test write Transform as euler angles ............."""
filename = 'test_write_transform.'
img = EMData(32,32)
img.process_inplace('testimage.noise.uniform.rand')
t3d = Transform()
t3d.set_rotation({'type':'imagic', 'alpha':1.56, 'beta':2.56, 'gamma':3.56})
img.set_attr('xform.projection', t3d)
img.write_image(filename+'img')
del img
img2 = EMData(filename+'img')
self.assertAlmostEqual(img2.get_attr('euler_alpha'), 1.56, 3)
self.assertAlmostEqual(img2.get_attr('euler_beta'), 2.56, 3)
self.assertAlmostEqual(img2.get_attr('euler_gamma'), 3.56, 3)
xform1 = img2.get_attr('xform.projection')
d = xform1.get_rotation('imagic')
self.assertAlmostEqual(d['alpha'], 1.56, 3)
self.assertAlmostEqual(d['beta'], 2.56, 3)
self.assertAlmostEqual(d['gamma'], 3.56, 3)
del img2
testlib.safe_unlink(filename+'img')
testlib.safe_unlink(filename+'hed')
filename2 = 'test_write_transform2.'
img = EMData(32,32,32)
img.process_inplace('testimage.noise.uniform.rand')
t3d = Transform()
t3d.set_rotation({'type':'imagic', 'alpha':1.56, 'beta':2.56, 'gamma':3.56})
img.set_attr('xform.align3d', t3d)
img.write_image(filename2+'img')
img2 = EMData(filename2+'img')
self.assertAlmostEqual(img2.get_attr('euler_alpha'), 1.56, 3)
self.assertAlmostEqual(img2.get_attr('euler_beta'), 2.56, 3)
self.assertAlmostEqual(img2.get_attr('euler_gamma'), 3.56, 3)
xform2 = img2.get_attr('xform.align3d')
d2 = xform2.get_rotation('imagic')
self.assertAlmostEqual(d2['alpha'], 1.56, 3)
self.assertAlmostEqual(d2['beta'], 2.56, 3)
self.assertAlmostEqual(d2['gamma'], 3.56, 3)
testlib.safe_unlink(filename2+'hed')
testlib.safe_unlink(filename2+'img')
def test_main():
p = OptionParser()
p.add_option("--t", action="store_true", help="test exception", default=False)
global IS_TEST_EXCEPTION
opt, args = p.parse_args()
if opt.t:
IS_TEST_EXCEPTION = True
Log.logger().set_level(-1) # perfect solution for quenching the Log error information, thank Liwei
suite = unittest.TestLoader().loadTestsFromTestCase(TestEMDataCuda)
unittest.TextTestRunner(verbosity=2).run(suite)
testlib.safe_unlink("mydb2")
testlib.safe_unlink("mydb1")
testlib.safe_unlink("mydb")
def test_main():
p = OptionParser()
p.add_option('--t', action='store_true', help='test exception', default=False )
global IS_TEST_EXCEPTION
opt, args = p.parse_args()
if opt.t:
IS_TEST_EXCEPTION = True
Log.logger().set_level(-1) #perfect solution for quenching the Log error information, thank Liwei
suite = unittest.TestLoader().loadTestsFromTestCase(TestEMDataCuda)
unittest.TextTestRunner(verbosity=2).run(suite)
testlib.safe_unlink('mydb2')
testlib.safe_unlink('mydb1')
testlib.safe_unlink('mydb')
def test_get_image_count(self):
"""test get_image_count function ...................."""
e = test_image()
e.write_image('test_image_count.mrc')
self.assertEqual(EMUtil.get_image_count('test_image_count.mrc'), 1)
testlib.safe_unlink('test_image_count.mrc')
f = test_image()
f.write_image('test_image_count.hdf', 0)
f.write_image('test_image_count.hdf', 1)
f.write_image('test_image_count.hdf', 2)
self.assertEqual(EMUtil.get_image_count('test_image_count.hdf'), 3)
testlib.safe_unlink('test_image_count.hdf')
g = test_image()
g.write_image('test_image_count.spi', 0, EMUtil.ImageType.IMAGE_SPIDER)
g.write_image('test_image_count.spi', 1, EMUtil.ImageType.IMAGE_SPIDER)
g.write_image('test_image_count.spi', 2, EMUtil.ImageType.IMAGE_SPIDER)
self.assertEqual(EMUtil.get_image_count('test_image_count.spi'), 3)
testlib.safe_unlink('test_image_count.spi')
def test_get_image_count(self):
"""test get_image_count function ...................."""
e = test_image()
e.write_image('test_image_count.mrc')
self.assertEqual(EMUtil.get_image_count('test_image_count.mrc'), 1)
testlib.safe_unlink('test_image_count.mrc')
f = test_image()
f.write_image('test_image_count.hdf', 0)
f.write_image('test_image_count.hdf', 1)
f.write_image('test_image_count.hdf', 2)
self.assertEqual(EMUtil.get_image_count('test_image_count.hdf'), 3)
testlib.safe_unlink('test_image_count.hdf')
g = test_image()
g.write_image('test_image_count.spi', 0, EMUtil.ImageType.IMAGE_SPIDER)
g.write_image('test_image_count.spi', 1, EMUtil.ImageType.IMAGE_SPIDER)
g.write_image('test_image_count.spi', 2, EMUtil.ImageType.IMAGE_SPIDER)
self.assertEqual(EMUtil.get_image_count('test_image_count.spi'), 3)
testlib.safe_unlink('test_image_count.spi')
def test_get_image_type(self):
"""test get_image_type function ....................."""
e = test_image()
e.write_image('mrcfile', 0, EMUtil.ImageType.IMAGE_MRC)
self.assertEqual(EMUtil.get_image_type('mrcfile'), EMUtil.ImageType.IMAGE_MRC)
testlib.safe_unlink('mrcfile')
e2 = test_image()
e2.write_image('hdffile', 0, EMUtil.ImageType.IMAGE_HDF)
self.assertEqual(EMUtil.get_image_type('hdffile'), EMUtil.ImageType.IMAGE_HDF)
testlib.safe_unlink('hdffile')
#e.write_image('lstfile', 0, EMUtil.ImageType.IMAGE_LST)
#self.assertEqual(EMUtil.get_image_type('lstfile'), EMUtil.ImageType.IMAGE_LST)
#testlib.safe_unlink('lstfile')
e3 = test_image()
e3.write_image('spiderfile', 0, EMUtil.ImageType.IMAGE_SPIDER)
self.assertEqual(EMUtil.get_image_type('spiderfile'), EMUtil.ImageType.IMAGE_SPIDER)
testlib.safe_unlink('spiderfile')
e3.write_image('sspiderfile', 0, EMUtil.ImageType.IMAGE_SINGLE_SPIDER)
self.assertEqual(EMUtil.get_image_type('sspiderfile'), EMUtil.ImageType.IMAGE_SINGLE_SPIDER)
testlib.safe_unlink('sspiderfile')
#e.write_image('piffile', 0, EMUtil.ImageType.IMAGE_PIF)
#self.assertEqual(EMUtil.get_image_type('piffile'), EMUtil.ImageType.IMAGE_PIF)
#testlib.safe_unlink('piffile')
platform = get_platform()
if platform!='Windows' and platform!='win32':
e4 = test_image()
e4.write_image('pngfile', 0, EMUtil.ImageType.IMAGE_PNG)
self.assertEqual(EMUtil.get_image_type('pngfile'), EMUtil.ImageType.IMAGE_PNG)
testlib.safe_unlink('pngfile')
e5 = test_image()
e5.write_image('vtkfile', 0, EMUtil.ImageType.IMAGE_VTK)
self.assertEqual(EMUtil.get_image_type('vtkfile'), EMUtil.ImageType.IMAGE_VTK)
testlib.safe_unlink('vtkfile')
e6 = test_image()
e6.write_image('pgmfile', 0, EMUtil.ImageType.IMAGE_PGM)
self.assertEqual(EMUtil.get_image_type('pgmfile'), EMUtil.ImageType.IMAGE_PGM)
testlib.safe_unlink('pgmfile')
e7 = test_image()
e7.write_image('icosfile', 0, EMUtil.ImageType.IMAGE_ICOS)
self.assertEqual(EMUtil.get_image_type('icosfile'), EMUtil.ImageType.IMAGE_ICOS)
testlib.safe_unlink('icosfile')
e8 = test_image()
e8.write_image('xplorfile', 0, EMUtil.ImageType.IMAGE_XPLOR)
self.assertEqual(EMUtil.get_image_type('xplorfile'), EMUtil.ImageType.IMAGE_XPLOR)
testlib.safe_unlink('xplorfile')
e9 = test_image()
e9.write_image('emfile', 0, EMUtil.ImageType.IMAGE_EM)
self.assertEqual(EMUtil.get_image_type('emfile'), EMUtil.ImageType.IMAGE_EM)
testlib.safe_unlink('emfile')
e10 = test_image()
e10.write_image('imagicfile', 0, EMUtil.ImageType.IMAGE_IMAGIC)
self.assertEqual(EMUtil.get_image_type('imagicfile.hed'), EMUtil.ImageType.IMAGE_IMAGIC)
testlib.safe_unlink('imagicfile.hed')
testlib.safe_unlink('imagicfile.img')
def test_write_transform_spider(self):
"""test write spi header info from Transform object ."""
filename = 'test_write_transform.'
img = EMData(32,32)
img.process_inplace('testimage.noise.uniform.rand')
t3d = Transform()
t3d.set_rotation({'type':'spider', 'phi':1.56, 'theta':2.56, 'psi':3.56})
t3d.set_trans(10.78, 20.78, 30.78)
t3d.set_scale(4.0)
img.set_attr('xform.projection', t3d)
img.write_image(filename+'spi')
del img
img2 = EMData(filename+'spi')
self.assertAlmostEqual(img2.get_attr('SPIDER.phi'), 1.56, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.theta'), 2.56, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.gamma'), 3.56, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.dx'), 10.78, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.dy'), 20.78, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.dz'), 30.78, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.scale'), 4.0, 3)
trans = img2.get_attr('xform.projection')
d = trans.get_params('spider')
self.assertAlmostEqual(d['phi'], 1.56, 3)
self.assertAlmostEqual(d['theta'], 2.56, 3)
self.assertAlmostEqual(d['psi'], 3.56, 3)
self.assertAlmostEqual(d['tx'], 10.78, 3)
self.assertAlmostEqual(d['ty'], 20.78, 3)
self.assertAlmostEqual(d['tz'], 30.78, 3)
self.assertAlmostEqual(d['scale'], 4.0, 3)
del img2
testlib.safe_unlink(filename+'spi')
filename2 = 'test_write_transform2.'
img = EMData(32,32,32)
img.process_inplace('testimage.noise.uniform.rand')
t3d = Transform()
t3d.set_rotation({'type':'spider', 'phi':1.56, 'theta':2.56, 'psi':3.56})
t3d.set_trans(10.78, 20.78, 30.78)
t3d.set_scale(4.0)
img.set_attr('xform.align3d', t3d)
img.write_image(filename2+'spi')
img2 = EMData(filename2+'spi')
self.assertAlmostEqual(img2.get_attr('SPIDER.phi'), 1.56, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.theta'), 2.56, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.gamma'), 3.56, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.dx'), 10.78, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.dy'), 20.78, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.dz'), 30.78, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.scale'), 4.0, 3)
trans2 = img2.get_attr('xform.align3d')
d2 = trans2.get_params('spider')
self.assertAlmostEqual(d2['phi'], 1.56, 3)
self.assertAlmostEqual(d2['theta'], 2.56, 3)
self.assertAlmostEqual(d2['psi'], 3.56, 3)
self.assertAlmostEqual(d2['tx'], 10.78, 3)
self.assertAlmostEqual(d2['ty'], 20.78, 3)
self.assertAlmostEqual(d2['tz'], 30.78, 3)
self.assertAlmostEqual(d2['scale'], 4.0, 3)
testlib.safe_unlink(filename2+'spi')
def test_get_image_type(self):
"""test get_image_type function ....................."""
e = test_image()
e.write_image('mrcfile', 0, EMUtil.ImageType.IMAGE_MRC)
self.assertEqual(EMUtil.get_image_type('mrcfile'), EMUtil.ImageType.IMAGE_MRC)
testlib.safe_unlink('mrcfile')
e2 = test_image()
e2.write_image('hdffile', 0, EMUtil.ImageType.IMAGE_HDF)
self.assertEqual(EMUtil.get_image_type('hdffile'), EMUtil.ImageType.IMAGE_HDF)
testlib.safe_unlink('hdffile')
#e.write_image('lstfile', 0, EMUtil.ImageType.IMAGE_LST)
#self.assertEqual(EMUtil.get_image_type('lstfile'), EMUtil.ImageType.IMAGE_LST)
#testlib.safe_unlink('lstfile')
e3 = test_image()
e3.write_image('spiderfile', 0, EMUtil.ImageType.IMAGE_SPIDER)
self.assertEqual(EMUtil.get_image_type('spiderfile'), EMUtil.ImageType.IMAGE_SPIDER)
testlib.safe_unlink('spiderfile')
e3.write_image('sspiderfile', 0, EMUtil.ImageType.IMAGE_SINGLE_SPIDER)
self.assertEqual(EMUtil.get_image_type('sspiderfile'), EMUtil.ImageType.IMAGE_SINGLE_SPIDER)
testlib.safe_unlink('sspiderfile')
#e.write_image('piffile', 0, EMUtil.ImageType.IMAGE_PIF)
#self.assertEqual(EMUtil.get_image_type('piffile'), EMUtil.ImageType.IMAGE_PIF)
#testlib.safe_unlink('piffile')
platform = get_platform()
if platform!='Windows' and platform!='win32':
e4 = test_image()
e4.write_image('pngfile', 0, EMUtil.ImageType.IMAGE_PNG)
self.assertEqual(EMUtil.get_image_type('pngfile'), EMUtil.ImageType.IMAGE_PNG)
testlib.safe_unlink('pngfile')
e5 = test_image()
e5.write_image('vtkfile', 0, EMUtil.ImageType.IMAGE_VTK)
self.assertEqual(EMUtil.get_image_type('vtkfile'), EMUtil.ImageType.IMAGE_VTK)
testlib.safe_unlink('vtkfile')
e6 = test_image()
e6.write_image('pgmfile', 0, EMUtil.ImageType.IMAGE_PGM)
self.assertEqual(EMUtil.get_image_type('pgmfile'), EMUtil.ImageType.IMAGE_PGM)
testlib.safe_unlink('pgmfile')
e7 = test_image()
e7.write_image('icosfile', 0, EMUtil.ImageType.IMAGE_ICOS)
self.assertEqual(EMUtil.get_image_type('icosfile'), EMUtil.ImageType.IMAGE_ICOS)
testlib.safe_unlink('icosfile')
e8 = test_image()
e8.write_image('xplorfile', 0, EMUtil.ImageType.IMAGE_XPLOR)
self.assertEqual(EMUtil.get_image_type('xplorfile'), EMUtil.ImageType.IMAGE_XPLOR)
testlib.safe_unlink('xplorfile')
e9 = test_image()
e9.write_image('emfile', 0, EMUtil.ImageType.IMAGE_EM)
self.assertEqual(EMUtil.get_image_type('emfile'), EMUtil.ImageType.IMAGE_EM)
testlib.safe_unlink('emfile')
e10 = test_image()
e10.write_image('imagicfile', 0, EMUtil.ImageType.IMAGE_IMAGIC)
self.assertEqual(EMUtil.get_image_type('imagicfile.hed'), EMUtil.ImageType.IMAGE_IMAGIC)
testlib.safe_unlink('imagicfile.hed')
testlib.safe_unlink('imagicfile.img')
def test_write_transform_spider(self):
"""test write spi header info from Transform object ."""
filename = 'test_write_transform.'
img = EMData(32,32)
img.process_inplace('testimage.noise.uniform.rand')
t3d = Transform()
t3d.set_rotation({'type':'spider', 'phi':1.56, 'theta':2.56, 'psi':3.56})
t3d.set_trans(10.78, 20.78, 30.78)
t3d.set_scale(4.0)
img.set_attr('xform.projection', t3d)
img.write_image(filename+'spi')
del img
img2 = EMData(filename+'spi')
self.assertAlmostEqual(img2.get_attr('SPIDER.phi'), 1.56, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.theta'), 2.56, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.gamma'), 3.56, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.dx'), 10.78, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.dy'), 20.78, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.dz'), 30.78, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.scale'), 4.0, 3)
trans = img2.get_attr('xform.projection')
d = trans.get_params('spider')
self.assertAlmostEqual(d['phi'], 1.56, 3)
self.assertAlmostEqual(d['theta'], 2.56, 3)
self.assertAlmostEqual(d['psi'], 3.56, 3)
self.assertAlmostEqual(d['tx'], 10.78, 3)
self.assertAlmostEqual(d['ty'], 20.78, 3)
self.assertAlmostEqual(d['tz'], 30.78, 3)
self.assertAlmostEqual(d['scale'], 4.0, 3)
del img2
testlib.safe_unlink(filename+'spi')
filename2 = 'test_write_transform2.'
img = EMData(32,32,32)
img.process_inplace('testimage.noise.uniform.rand')
t3d = Transform()
t3d.set_rotation({'type':'spider', 'phi':1.56, 'theta':2.56, 'psi':3.56})
t3d.set_trans(10.78, 20.78, 30.78)
t3d.set_scale(4.0)
img.set_attr('xform.align3d', t3d)
img.write_image(filename2+'spi')
img2 = EMData(filename2+'spi')
self.assertAlmostEqual(img2.get_attr('SPIDER.phi'), 1.56, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.theta'), 2.56, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.gamma'), 3.56, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.dx'), 10.78, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.dy'), 20.78, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.dz'), 30.78, 3)
self.assertAlmostEqual(img2.get_attr('SPIDER.scale'), 4.0, 3)
trans2 = img2.get_attr('xform.align3d')
d2 = trans2.get_params('spider')
self.assertAlmostEqual(d2['phi'], 1.56, 3)
self.assertAlmostEqual(d2['theta'], 2.56, 3)
self.assertAlmostEqual(d2['psi'], 3.56, 3)
self.assertAlmostEqual(d2['tx'], 10.78, 3)
self.assertAlmostEqual(d2['ty'], 20.78, 3)
self.assertAlmostEqual(d2['tz'], 30.78, 3)
self.assertAlmostEqual(d2['scale'], 4.0, 3)
testlib.safe_unlink(filename2+'spi')
